From ada26a89c3402518b87d6d95a0ada7f6cc07fb98 Mon Sep 17 00:00:00 2001
From: Eugen Zdrincu <eugenzdrincu@gmail.com>
Date: Wed, 27 Mar 2024 20:39:21 +0100
Subject: [PATCH 001/100] added prototype for data source

---
 .../controller/TrackingDataController.java    | 21 ++++++++++++++++++
 src/main/java/inputOutput/AIDataSource.java   | 22 +++++++++++++++++++
 .../inputOutput/OIGTTrackingDataSource.java   |  1 +
 src/main/resources/view/TrackingDataView.fxml |  2 ++
 4 files changed, 46 insertions(+)
 create mode 100644 src/main/java/inputOutput/AIDataSource.java

diff --git a/src/main/java/controller/TrackingDataController.java b/src/main/java/controller/TrackingDataController.java
index 1960d63c..d8f4fe98 100644
--- a/src/main/java/controller/TrackingDataController.java
+++ b/src/main/java/controller/TrackingDataController.java
@@ -12,6 +12,7 @@
 import java.util.logging.Logger;
 
 import algorithm.*;
+import inputOutput.AIDataSource;
 import inputOutput.CSVFileReader;
 import inputOutput.OIGTTrackingDataSource;
 import javafx.animation.Animation;
@@ -122,6 +123,26 @@ public void loadCSVFile() {
         }
     }
 
+    @FXML
+    public void loadAIData() {
+        System.out.println("AI DATA LOADING");
+
+        AIDataSource newSource = new AIDataSource();
+
+        if (trackingService.getTrackingDataSource() != null) {
+            disconnectSource();
+        }
+
+        try {
+            trackingService.changeTrackingSource(newSource);
+            sourceConnected.setValue(true);
+            visualizationController.setSourceConnected(true);
+        } catch (Exception e) {
+            logger.log(Level.SEVERE, "Error loading AI DATA", e);
+            statusLabel.setText("Error loading AI DATA SOURCE");
+        }
+    }
+
     /**
      * Connect via OpenIGTLink.
      */
diff --git a/src/main/java/inputOutput/AIDataSource.java b/src/main/java/inputOutput/AIDataSource.java
new file mode 100644
index 00000000..699dad2a
--- /dev/null
+++ b/src/main/java/inputOutput/AIDataSource.java
@@ -0,0 +1,22 @@
+package inputOutput;
+
+import java.util.ArrayList;
+
+public class AIDataSource extends AbstractTrackingDataSource {
+
+    public AIDataSource() {
+        tempToolList = new ArrayList<>();
+    }
+    @Override
+    public ArrayList<TempTool> update() {
+        TempTool testTool1 = new TempTool();
+        testTool1.setData(1, 1, 1, 1, 1, 1, 1, 1, 1, "testTool");
+        tempToolList.add(testTool1);
+        return tempToolList;
+    }
+
+    @Override
+    public void closeConnection() {
+
+    }
+}
diff --git a/src/main/java/inputOutput/OIGTTrackingDataSource.java b/src/main/java/inputOutput/OIGTTrackingDataSource.java
index 3f2148a5..8fb44d5d 100644
--- a/src/main/java/inputOutput/OIGTTrackingDataSource.java
+++ b/src/main/java/inputOutput/OIGTTrackingDataSource.java
@@ -81,6 +81,7 @@ public void setValues(String n, TransformNR t) {
         newTempTool.setData(timestamp, valid, coordinate_x, coordinate_y,
                 coordinate_z, rotation_x, rotation_y, rotation_z, rotation_r,
                 name);
+
         this.tempToolList.add(newTempTool);
 
     }
diff --git a/src/main/resources/view/TrackingDataView.fxml b/src/main/resources/view/TrackingDataView.fxml
index 9ee47ab4..100d2386 100644
--- a/src/main/resources/view/TrackingDataView.fxml
+++ b/src/main/resources/view/TrackingDataView.fxml
@@ -100,6 +100,8 @@
 				</HBox>
 				<Button fx:id="loadCSVBtn" alignment="CENTER" mnemonicParsing="false" onAction="#loadCSVFile"
 						text="Load CSV" GridPane.columnIndex="1"/>
+				<Button fx:id="loadAIData" alignment="CENTER" mnemonicParsing="false" onAction="#loadAIData"
+						text="Load AI data" GridPane.columnIndex="2"/>
 				<Button fx:id="visualizeTrackingBtn" alignment="CENTER" mnemonicParsing="false"
 						onAction="#visualizeTracking" text="Start Tracking and Visualization" GridPane.rowIndex="1"/>
 				<ToggleButton fx:id="freezeTglBtn" mnemonicParsing="false" onAction="#freezeVisualization"

From 87d942be1ef7fe7e64e86c30900ccd8cb2b9142f Mon Sep 17 00:00:00 2001
From: Eugen Zdrincu <eugenzdrincu@gmail.com>
Date: Fri, 29 Mar 2024 06:31:56 +0100
Subject: [PATCH 002/100] added proof of concept of igt virtual device in
 python

---
 aitoigt/test.py | 51 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 aitoigt/test.py

diff --git a/aitoigt/test.py b/aitoigt/test.py
new file mode 100644
index 00000000..855db24e
--- /dev/null
+++ b/aitoigt/test.py
@@ -0,0 +1,51 @@
+"""
+============================
+Tracked image data server
+============================
+
+Simple application that starts a server that sends images, transforms, and strings
+
+"""
+
+import pyigtl  # pylint: disable=import-error
+from math import cos, sin, pi
+from time import sleep
+import numpy as np
+
+server = pyigtl.OpenIGTLinkServer(port=18944, local_server=True)
+
+image_size = [400, 200]
+
+timestep = 0
+
+while True:
+
+    if not server.is_connected():
+        # Wait for client to connect
+        sleep(0.1)
+        continue
+
+    timestep += 1
+
+    # Generate transform
+    matrix = np.eye(4)
+    matrix[0, 3] = sin(timestep * 0.01) * 20.0
+    rotation_angle_rad = timestep * 0.5 * pi / 180.0
+    matrix[1, 1] = cos(rotation_angle_rad)
+    matrix[2, 1] = -sin(rotation_angle_rad)
+    matrix[1, 2] = sin(rotation_angle_rad)
+    matrix[2, 2] = cos(rotation_angle_rad)
+    transform_message = pyigtl.TransformMessage(matrix, device_name="ImageToReference", timestamp=1)
+
+
+    # Send messages
+    server.send_message(transform_message)
+
+    # Print received messages
+    messages = server.get_latest_messages()
+    for message in messages:
+        print(message.device_name)
+
+    # Do not flood the message queue,
+    # but allow a little time for background network transfer
+    sleep(0.01)
\ No newline at end of file

From 9aef866142efb9ab391e8cbf38192dbf4f2ded4f Mon Sep 17 00:00:00 2001
From: Eugen Zdrincu <eugen.zdrincu@deutschepost.de>
Date: Tue, 9 Apr 2024 15:17:33 +0200
Subject: [PATCH 003/100] added igt server implementation in python yolov5

---
 aitoigt/detect.py | 334 ++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 334 insertions(+)
 create mode 100644 aitoigt/detect.py

diff --git a/aitoigt/detect.py b/aitoigt/detect.py
new file mode 100644
index 00000000..84d71d93
--- /dev/null
+++ b/aitoigt/detect.py
@@ -0,0 +1,334 @@
+# YOLOv5 🚀 by Ultralytics, AGPL-3.0 license
+"""
+Run YOLOv5 detection inference on images, videos, directories, globs, YouTube, webcam, streams, etc.
+ 
+Usage - sources:
+    $ python detect.py --weights yolov5s.pt --source 0                               # webcam
+                                                     img.jpg                         # image
+                                                     vid.mp4                         # video
+                                                     screen                          # screenshot
+                                                     path/                           # directory
+                                                     list.txt                        # list of images
+                                                     list.streams                    # list of streams
+                                                     'path/*.jpg'                    # glob
+                                                     'https://youtu.be/LNwODJXcvt4'  # YouTube
+                                                     'rtsp://example.com/media.mp4'  # RTSP, RTMP, HTTP stream
+ 
+Usage - formats:
+    $ python detect.py --weights yolov5s.pt                 # PyTorch
+                                 yolov5s.torchscript        # TorchScript
+                                 yolov5s.onnx               # ONNX Runtime or OpenCV DNN with --dnn
+                                 yolov5s_openvino_model     # OpenVINO
+                                 yolov5s.engine             # TensorRT
+                                 yolov5s.mlmodel            # CoreML (macOS-only)
+                                 yolov5s_saved_model        # TensorFlow SavedModel
+                                 yolov5s.pb                 # TensorFlow GraphDef
+                                 yolov5s.tflite             # TensorFlow Lite
+                                 yolov5s_edgetpu.tflite     # TensorFlow Edge TPU
+                                 yolov5s_paddle_model       # PaddlePaddle
+"""
+ 
+import argparse
+import csv
+import numpy as np
+import os
+import platform
+import sys
+import pyigtl as igtl
+from pathlib import Path
+ 
+import torch
+ 
+FILE = Path(__file__).resolve()
+ROOT = FILE.parents[0]  # YOLOv5 root directory
+if str(ROOT) not in sys.path:
+    sys.path.append(str(ROOT))  # add ROOT to PATH
+ROOT = Path(os.path.relpath(ROOT, Path.cwd()))  # relative
+ 
+from ultralytics.utils.plotting import Annotator, colors, save_one_box
+ 
+from models.common import DetectMultiBackend
+from utils.dataloaders import IMG_FORMATS, VID_FORMATS, LoadImages, LoadScreenshots, LoadStreams
+from utils.general import (
+    LOGGER,
+    Profile,
+    check_file,
+    check_img_size,
+    check_imshow,
+    check_requirements,
+    colorstr,
+    cv2,
+    increment_path,
+    non_max_suppression,
+    print_args,
+    scale_boxes,
+    strip_optimizer,
+    xyxy2xywh,
+)
+from utils.torch_utils import select_device, smart_inference_mode
+ 
+ 
+@smart_inference_mode()
+def run(
+    weights=ROOT / "yolov5s.pt",  # model path or triton URL
+    source=ROOT / "data/images",  # file/dir/URL/glob/screen/0(webcam)
+    data=ROOT / "data/coco128.yaml",  # dataset.yaml path
+    imgsz=(640, 640),  # inference size (height, width)
+    conf_thres=0.25,  # confidence threshold
+    iou_thres=0.45,  # NMS IOU threshold
+    max_det=1000,  # maximum detections per image
+    device="",  # cuda device, i.e. 0 or 0,1,2,3 or cpu
+    view_img=False,  # show results
+    open_igt=False, # stream data thru igtlink
+    save_txt=True,  # save results to *.txt
+    save_csv=False,  # save results in CSV format
+    save_conf=False,  # save confidences in --save-txt labels
+    save_crop=False,  # save cropped prediction boxes
+    nosave=False,  # do not save images/videos
+    classes=None,  # filter by class: --class 0, or --class 0 2 3
+    agnostic_nms=False,  # class-agnostic NMS
+    augment=False,  # augmented inference
+    visualize=False,  # visualize features
+    update=False,  # update all models
+    project=ROOT / "runs/detect",  # save results to project/name
+    name="exp",  # save results to project/name
+    exist_ok=False,  # existing project/name ok, do not increment
+    line_thickness=3,  # bounding box thickness (pixels)
+    hide_labels=False,  # hide labels
+    hide_conf=False,  # hide confidences
+    half=False,  # use FP16 half-precision inference
+    dnn=False,  # use OpenCV DNN for ONNX inference
+    vid_stride=1,  # video frame-rate stride
+):
+
+    if (open_igt):
+        # Create an OpenIGTLink object
+        server = igtl.OpenIGTLinkServer(port=18944)
+    
+        # Check if the server is running
+        if not server.is_connected():
+            print("Server started. Waiting for connections...")
+ 
+    source = str(source)
+    save_img = not nosave and not source.endswith(".txt")  # save inference images
+    is_file = Path(source).suffix[1:] in (IMG_FORMATS + VID_FORMATS)
+    is_url = source.lower().startswith(("rtsp://", "rtmp://", "http://", "https://"))
+    webcam = source.isnumeric() or source.endswith(".streams") or (is_url and not is_file)
+    screenshot = source.lower().startswith("screen")
+    if is_url and is_file:
+        source = check_file(source)  # download
+ 
+    # Directories
+    save_dir = increment_path(Path(project) / name, exist_ok=exist_ok)  # increment run
+    (save_dir / "labels" if save_txt else save_dir).mkdir(parents=True, exist_ok=True)  # make dir
+ 
+    # Load model
+    device = select_device(device)
+    model = DetectMultiBackend(weights, device=device, dnn=dnn, data=data, fp16=half)
+    stride, names, pt = model.stride, model.names, model.pt
+    imgsz = check_img_size(imgsz, s=stride)  # check image size
+ 
+    # Dataloader
+    bs = 1  # batch_size
+    if webcam:
+        view_img = check_imshow(warn=True)
+        dataset = LoadStreams(source, img_size=imgsz, stride=stride, auto=pt, vid_stride=vid_stride)
+        bs = len(dataset)
+    elif screenshot:
+        dataset = LoadScreenshots(source, img_size=imgsz, stride=stride, auto=pt)
+    else:
+        dataset = LoadImages(source, img_size=imgsz, stride=stride, auto=pt, vid_stride=vid_stride)
+    vid_path, vid_writer = [None] * bs, [None] * bs
+ 
+    # Run inference
+    model.warmup(imgsz=(1 if pt or model.triton else bs, 3, *imgsz))  # warmup
+    seen, windows, dt = 0, [], (Profile(device=device), Profile(device=device), Profile(device=device))
+    for path, im, im0s, vid_cap, s in dataset:
+        with dt[0]:
+            im = torch.from_numpy(im).to(model.device)
+            im = im.half() if model.fp16 else im.float()  # uint8 to fp16/32
+            im /= 255  # 0 - 255 to 0.0 - 1.0
+            if len(im.shape) == 3:
+                im = im[None]  # expand for batch dim
+            if model.xml and im.shape[0] > 1:
+                ims = torch.chunk(im, im.shape[0], 0)
+ 
+        # Inference
+        with dt[1]:
+            visualize = increment_path(save_dir / Path(path).stem, mkdir=True) if visualize else False
+            if model.xml and im.shape[0] > 1:
+                pred = None
+                for image in ims:
+                    if pred is None:
+                        pred = model(image, augment=augment, visualize=visualize).unsqueeze(0)
+                    else:
+                        pred = torch.cat((pred, model(image, augment=augment, visualize=visualize).unsqueeze(0)), dim=0)
+                pred = [pred, None]
+            else:
+                pred = model(im, augment=augment, visualize=visualize)
+        # NMS
+        with dt[2]:
+            pred = non_max_suppression(pred, conf_thres, iou_thres, classes, agnostic_nms, max_det=max_det)
+ 
+        # Second-stage classifier (optional)
+        # pred = utils.general.apply_classifier(pred, classifier_model, im, im0s)
+ 
+        # Define the path for the CSV file
+        csv_path = save_dir / "predictions.csv"
+ 
+        # Create or append to the CSV file
+        def write_to_csv(image_name, prediction, confidence):
+            """Writes prediction data for an image to a CSV file, appending if the file exists."""
+            data = {"Image Name": image_name, "Prediction": prediction, "Confidence": confidence}
+            with open(csv_path, mode="a", newline="") as f:
+                writer = csv.DictWriter(f, fieldnames=data.keys())
+                if not csv_path.is_file():
+                    writer.writeheader()
+                writer.writerow(data)
+ 
+        # Process predictions
+        for i, det in enumerate(pred):  # per image
+            seen += 1
+            if webcam:  # batch_size >= 1
+                p, im0, frame = path[i], im0s[i].copy(), dataset.count
+                s += f"{i}: "
+            else:
+                p, im0, frame = path, im0s.copy(), getattr(dataset, "frame", 0)
+ 
+            p = Path(p)  # to Path
+            save_path = str(save_dir / p.name)  # im.jpg
+            txt_path = str(save_dir / "labels" / p.stem) + ("" if dataset.mode == "image" else f"_{frame}")  # im.txt
+            s += "%gx%g " % im.shape[2:]  # print string
+            gn = torch.tensor(im0.shape)[[1, 0, 1, 0]]  # normalization gain whwh
+            imc = im0.copy() if save_crop else im0  # for save_crop
+            annotator = Annotator(im0, line_width=line_thickness, example=str(names))
+            if len(det):
+                # Rescale boxes from img_size to im0 size
+                det[:, :4] = scale_boxes(im.shape[2:], det[:, :4], im0.shape).round()
+ 
+                # Print results
+                for c in det[:, 5].unique():
+                    n = (det[:, 5] == c).sum()  # detections per class
+                    s += f"{n} {names[int(c)]}{'s' * (n > 1)}, "  # add to string
+ 
+                # Write results
+                for *xyxy, conf, cls in reversed(det):
+                    c = int(cls)  # integer class
+                    label = names[c] if hide_conf else f"{names[c]}"
+                    confidence = float(conf)
+                    confidence_str = f"{confidence:.2f}"
+ 
+                    if save_csv:
+                        write_to_csv(p.name, label, confidence_str)
+ 
+                    if save_txt:  # Write to file
+                        xywh = (xyxy2xywh(torch.tensor(xyxy).view(1, 4)) / gn).view(-1).tolist()  # normalized xywh
+                        line = (cls, *xywh, conf) if save_conf else (cls, *xywh)  # label format
+                        with open(f"{txt_path}.txt", "a") as f:
+                            f.write(("%g " * len(line)).rstrip() % line + "\n")
+ 
+                    if save_img or save_crop or view_img:  # Add bbox to image
+                        c = int(cls)  # integer class
+                        label = None if hide_labels else (names[c] if hide_conf else f"{names[c]} {conf:.2f}")
+                        annotator.box_label(xyxy, label, color=colors(c, True))
+                    if save_crop:
+                        save_one_box(xyxy, imc, file=save_dir / "crops" / names[c] / f"{p.stem}.jpg", BGR=True)
+ 
+                if open_igt:
+                    matrix = np.eye(4)
+    
+                    matrix[0, 3] = xyxy[0]
+                    matrix[1, 3] = xyxy[1]
+    
+                    transform_message = igtl.TransformMessage(matrix, device_name="ImageToReference", timestamp=1)
+    
+                    server.send_message(transform_message)
+ 
+            # Stream results
+            im0 = annotator.result()
+            if view_img:
+                if platform.system() == "Linux" and p not in windows:
+                    windows.append(p)
+                    cv2.namedWindow(str(p), cv2.WINDOW_NORMAL | cv2.WINDOW_KEEPRATIO)  # allow window resize (Linux)
+                    cv2.resizeWindow(str(p), im0.shape[1], im0.shape[0])
+                cv2.imshow(str(p), im0)
+                cv2.waitKey(1)  # 1 millisecond
+ 
+            # Save results (image with detections)
+            if save_img:
+                if dataset.mode == "image":
+                    cv2.imwrite(save_path, im0)
+                else:  # 'video' or 'stream'
+                    if vid_path[i] != save_path:  # new video
+                        vid_path[i] = save_path
+                        if isinstance(vid_writer[i], cv2.VideoWriter):
+                            vid_writer[i].release()  # release previous video writer
+                        if vid_cap:  # video
+                            fps = vid_cap.get(cv2.CAP_PROP_FPS)
+                            w = int(vid_cap.get(cv2.CAP_PROP_FRAME_WIDTH))
+                            h = int(vid_cap.get(cv2.CAP_PROP_FRAME_HEIGHT))
+                        else:  # stream
+                            fps, w, h = 30, im0.shape[1], im0.shape[0]
+                        save_path = str(Path(save_path).with_suffix(".mp4"))  # force *.mp4 suffix on results videos
+                        vid_writer[i] = cv2.VideoWriter(save_path, cv2.VideoWriter_fourcc(*"mp4v"), fps, (w, h))
+                    vid_writer[i].write(im0)
+ 
+        # Print time (inference-only)
+        LOGGER.info(f"{s}{'' if len(det) else '(no detections), '}{dt[1].dt * 1E3:.1f}ms")
+ 
+    # Print results
+    t = tuple(x.t / seen * 1e3 for x in dt)  # speeds per image
+    LOGGER.info(f"Speed: %.1fms pre-process, %.1fms inference, %.1fms NMS per image at shape {(1, 3, *imgsz)}" % t)
+    if save_txt or save_img:
+        s = f"\n{len(list(save_dir.glob('labels/*.txt')))} labels saved to {save_dir / 'labels'}" if save_txt else ""
+        LOGGER.info(f"Results saved to {colorstr('bold', save_dir)}{s}")
+    if update:
+        strip_optimizer(weights[0])  # update model (to fix SourceChangeWarning)
+ 
+ 
+def parse_opt():
+    """Parses command-line arguments for YOLOv5 detection, setting inference options and model configurations."""
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--weights", nargs="+", type=str, default=ROOT / "yolov5s.pt", help="model path or triton URL")
+    parser.add_argument("--source", type=str, default=ROOT / "data/images", help="file/dir/URL/glob/screen/0(webcam)")
+    parser.add_argument("--data", type=str, default=ROOT / "data/coco128.yaml", help="(optional) dataset.yaml path")
+    parser.add_argument("--imgsz", "--img", "--img-size", nargs="+", type=int, default=[640], help="inference size h,w")
+    parser.add_argument("--conf-thres", type=float, default=0.25, help="confidence threshold")
+    parser.add_argument("--iou-thres", type=float, default=0.45, help="NMS IoU threshold")
+    parser.add_argument("--max-det", type=int, default=1000, help="maximum detections per image")
+    parser.add_argument("--device", default="", help="cuda device, i.e. 0 or 0,1,2,3 or cpu")
+    parser.add_argument("--view-img", action="store_true", help="show results")
+    parser.add_argument("--open-igt", action="store_true", help="stream data thru igtlink")
+    parser.add_argument("--save-txt", action="store_true", help="save results to *.txt")
+    parser.add_argument("--save-csv", action="store_true", help="save results in CSV format")
+    parser.add_argument("--save-conf", action="store_true", help="save confidences in --save-txt labels")
+    parser.add_argument("--save-crop", action="store_true", help="save cropped prediction boxes")
+    parser.add_argument("--nosave", action="store_true", help="do not save images/videos")
+    parser.add_argument("--classes", nargs="+", type=int, help="filter by class: --classes 0, or --classes 0 2 3")
+    parser.add_argument("--agnostic-nms", action="store_true", help="class-agnostic NMS")
+    parser.add_argument("--augment", action="store_true", help="augmented inference")
+    parser.add_argument("--visualize", action="store_true", help="visualize features")
+    parser.add_argument("--update", action="store_true", help="update all models")
+    parser.add_argument("--project", default=ROOT / "runs/detect", help="save results to project/name")
+    parser.add_argument("--name", default="exp", help="save results to project/name")
+    parser.add_argument("--exist-ok", action="store_true", help="existing project/name ok, do not increment")
+    parser.add_argument("--line-thickness", default=3, type=int, help="bounding box thickness (pixels)")
+    parser.add_argument("--hide-labels", default=False, action="store_true", help="hide labels")
+    parser.add_argument("--hide-conf", default=False, action="store_true", help="hide confidences")
+    parser.add_argument("--half", action="store_true", help="use FP16 half-precision inference")
+    parser.add_argument("--dnn", action="store_true", help="use OpenCV DNN for ONNX inference")
+    parser.add_argument("--vid-stride", type=int, default=1, help="video frame-rate stride")
+    opt = parser.parse_args()
+    opt.imgsz *= 2 if len(opt.imgsz) == 1 else 1  # expand
+    print_args(vars(opt))
+    return opt
+ 
+def main(opt):
+    """Executes YOLOv5 model inference with given options, checking requirements before running the model."""
+    check_requirements(ROOT / "requirements.txt", exclude=("tensorboard", "thop"))
+    run(**vars(opt))
+ 
+ 
+if __name__ == "__main__":
+    opt = parse_opt()
+    main(opt)
\ No newline at end of file

From cd937509ef4f40b08c75c55ae4b29a78ecb659ef Mon Sep 17 00:00:00 2001
From: Eugen Zdrincu <eugenzdrincu@gmail.com>
Date: Tue, 9 Apr 2024 18:35:59 +0200
Subject: [PATCH 004/100] added virtual camera to detect py

---
 aitoigt/detect.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/aitoigt/detect.py b/aitoigt/detect.py
index 84d71d93..771dbbb7 100644
--- a/aitoigt/detect.py
+++ b/aitoigt/detect.py
@@ -36,7 +36,10 @@
 import sys
 import pyigtl as igtl
 from pathlib import Path
- 
+import pyvirtualcam
+
+CAM = pyvirtualcam.Camera(width=640, height=480, fps=20)
+
 import torch
  
 FILE = Path(__file__).resolve()
@@ -252,6 +255,10 @@ def write_to_csv(image_name, prediction, confidence):
                     cv2.namedWindow(str(p), cv2.WINDOW_NORMAL | cv2.WINDOW_KEEPRATIO)  # allow window resize (Linux)
                     cv2.resizeWindow(str(p), im0.shape[1], im0.shape[0])
                 cv2.imshow(str(p), im0)
+
+                # Send RGB image to virtual camera
+                im0VIRT = cv2.cvtColor(im0, cv2.COLOR_BGR2RGB)
+                CAM.send(im0VIRT)
                 cv2.waitKey(1)  # 1 millisecond
  
             # Save results (image with detections)

From c5de2f99faea7d6bd7a4b514b9546d9c39c96cf2 Mon Sep 17 00:00:00 2001
From: VincentStriegel <strivi01@thu.de>
Date: Wed, 10 Apr 2024 11:02:26 +0200
Subject: [PATCH 005/100] create annotation tab

---
 .../java/controller/AnnotationController.java | 19 +++++++++++++++++++
 src/main/resources/view/AnnotationView.fxml   | 11 +++++++++++
 src/main/resources/view/MainView.fxml         |  3 +++
 3 files changed, 33 insertions(+)
 create mode 100644 src/main/java/controller/AnnotationController.java
 create mode 100644 src/main/resources/view/AnnotationView.fxml

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
new file mode 100644
index 00000000..468b87e3
--- /dev/null
+++ b/src/main/java/controller/AnnotationController.java
@@ -0,0 +1,19 @@
+package controller;
+
+import javafx.fxml.FXML;
+import javafx.fxml.Initializable;
+import java.net.URL;
+import java.util.ResourceBundle;
+
+public class AnnotationController implements Controller {
+    @Override
+    public void initialize(URL location, ResourceBundle resources) {
+        // Initialization code goes here
+  }
+
+    @FXML
+    @Override
+    public void close() {
+        unregisterController();
+    }
+}
diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
new file mode 100644
index 00000000..a7dbed8d
--- /dev/null
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+        <?import javafx.geometry.*?>
+        <?import javafx.scene.chart.NumberAxis?>
+        <?import javafx.scene.control.*?>
+        <?import javafx.scene.layout.*?>
+        <?import userinterface.PlottableImage?>
+<ScrollPane fitToHeight="true" fitToWidth="true" maxHeight="Infinity" maxWidth="Infinity"
+            xmlns="http://javafx.com/javafx/17" xmlns:fx="http://javafx.com/fxml/1"
+            fx:controller="controller.AnnotationController">
+</ScrollPane>
diff --git a/src/main/resources/view/MainView.fxml b/src/main/resources/view/MainView.fxml
index 88ade970..d88b7bd6 100644
--- a/src/main/resources/view/MainView.fxml
+++ b/src/main/resources/view/MainView.fxml
@@ -44,6 +44,9 @@
             <Tab closable="false" fx:id="visualizationTab" text="Visualization" onSelectionChanged="#onChangeView">
                 <fx:include fx:id="visualization" source="VisualizationView.fxml"/>
             </Tab>
+                <Tab closable="false" fx:id="annotationTab" text="Annotation" onSelectionChanged="#onChangeView">
+                <fx:include fx:id="annotation" source="AnnotationView.fxml"/>
+            </Tab>
         </TabPane>
     </center>
     <bottom>

From 94cf3e500bcac346927c5639b927a46198ce9bb1 Mon Sep 17 00:00:00 2001
From: david <david.todorr@gmail.com>
Date: Thu, 11 Apr 2024 03:00:59 +0200
Subject: [PATCH 006/100] Basic GUI design added

---
 src/main/resources/view/AnnotationView.fxml | 59 ++++++++++++++++++---
 1 file changed, 51 insertions(+), 8 deletions(-)

diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index a7dbed8d..d14859b9 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -1,11 +1,54 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
-        <?import javafx.geometry.*?>
-        <?import javafx.scene.chart.NumberAxis?>
-        <?import javafx.scene.control.*?>
-        <?import javafx.scene.layout.*?>
-        <?import userinterface.PlottableImage?>
-<ScrollPane fitToHeight="true" fitToWidth="true" maxHeight="Infinity" maxWidth="Infinity"
-            xmlns="http://javafx.com/javafx/17" xmlns:fx="http://javafx.com/fxml/1"
-            fx:controller="controller.AnnotationController">
+<?import javafx.geometry.Insets?>
+<?import javafx.scene.control.Button?>
+<?import javafx.scene.control.ScrollPane?>
+<?import javafx.scene.control.TitledPane?>
+<?import javafx.scene.image.ImageView?>
+<?import javafx.scene.layout.BorderPane?>
+<?import javafx.scene.layout.HBox?>
+<?import javafx.scene.layout.VBox?>
+
+<ScrollPane fitToHeight="true" fitToWidth="true" maxHeight="Infinity" maxWidth="Infinity" xmlns="http://javafx.com/javafx/21" xmlns:fx="http://javafx.com/fxml/1" fx:controller="controller.AnnotationController">
+   <content>
+      <BorderPane>
+         <bottom>
+            <HBox alignment="CENTER" prefHeight="80.0" prefWidth="368.0" style="-fx-border-color: grey;" BorderPane.alignment="CENTER">
+               <BorderPane.margin>
+                  <Insets bottom="10.0" left="10.0" right="10.0" top="10.0" />
+               </BorderPane.margin>
+               <children>
+                  <Button mnemonicParsing="false" text="Example" />
+               </children></HBox>
+         </bottom>
+         <top>
+            <HBox alignment="CENTER" prefHeight="80.0" prefWidth="368.0" style="-fx-border-color: grey;" BorderPane.alignment="CENTER">
+               <BorderPane.margin>
+                  <Insets bottom="10.0" left="10.0" right="10.0" top="10.0" />
+               </BorderPane.margin>
+               <children>
+                  <Button mnemonicParsing="false" text="Example" />
+               </children></HBox>
+         </top>
+         <left>
+            <ScrollPane fitToHeight="true" fitToWidth="true" hbarPolicy="NEVER" prefHeight="202.0" prefWidth="188.0" vbarPolicy="ALWAYS" BorderPane.alignment="CENTER">
+               <content>
+                  <VBox id="uploadedImages" prefHeight="200.0" prefWidth="100.0" />
+               </content>
+               <BorderPane.margin>
+                  <Insets left="10.0" right="10.0" />
+               </BorderPane.margin>
+            </ScrollPane>
+         </left>
+         <center>
+            <TitledPane collapsible="false" text="Selected Image" textAlignment="CENTER" BorderPane.alignment="CENTER">
+               <content>
+                  <ImageView id="selectedImage" fitHeight="500.0" fitWidth="200.0" pickOnBounds="true" preserveRatio="true" />
+               </content>
+               <BorderPane.margin>
+                  <Insets right="10.0" />
+               </BorderPane.margin>
+            </TitledPane>
+         </center></BorderPane>
+   </content>
 </ScrollPane>

From a72a02c3c94aee87ae6565da3c59f821275fa073 Mon Sep 17 00:00:00 2001
From: nguyensl-rose <119351168+nguyensl-rose@users.noreply.github.com>
Date: Thu, 11 Apr 2024 10:28:49 +0200
Subject: [PATCH 007/100] the igtpt tracker points away from its last known
 position (essentially a velocity vector)

---
 aitoigt/test.py   |  28 ++++++--
 logging.log.1     | 176 ++++++++++++++++++++++++++++++++++++++++++++++
 logging.log.1.lck |   0
 3 files changed, 197 insertions(+), 7 deletions(-)
 create mode 100644 logging.log.1
 create mode 100644 logging.log.1.lck

diff --git a/aitoigt/test.py b/aitoigt/test.py
index 855db24e..1fe829e4 100644
--- a/aitoigt/test.py
+++ b/aitoigt/test.py
@@ -17,6 +17,7 @@
 image_size = [400, 200]
 
 timestep = 0
+last_matrix = np.eye(4)
 
 while True:
 
@@ -25,18 +26,31 @@
         sleep(0.1)
         continue
 
+    # Init vars
     timestep += 1
+    theta = timestep * 0.01
 
     # Generate transform
     matrix = np.eye(4)
-    matrix[0, 3] = sin(timestep * 0.01) * 20.0
-    rotation_angle_rad = timestep * 0.5 * pi / 180.0
-    matrix[1, 1] = cos(rotation_angle_rad)
-    matrix[2, 1] = -sin(rotation_angle_rad)
-    matrix[1, 2] = sin(rotation_angle_rad)
-    matrix[2, 2] = cos(rotation_angle_rad)
-    transform_message = pyigtl.TransformMessage(matrix, device_name="ImageToReference", timestamp=1)
 
+    # Set position
+    matrix[0, 3] = sin(theta) * 100.0
+    matrix[1, 3] = sin(theta) * cos(theta) * 100.0
+    
+    # Set orientation
+    direction = last_matrix[:3, 3] - matrix[:3, 3]
+    angle = (-np.pi) + np.arctan2(direction[1], direction[0])   # -90 degree offset because -X is the forward direction of the IGTP pointer model
+    nlah = np.array([[np.cos(angle), -np.sin(angle), 0], [np.sin(angle), np.cos(angle), 0], [0, 0, 1]])
+    matrix[:3, :3] = nlah
+    
+    # Debugging
+    print(f"Y Coord: {direction[1]}")
+    print(f"X Coord: {direction[0]}")
+    print(f"Angle: {angle}")
+
+    # Send transform message
+    last_matrix = matrix
+    transform_message = pyigtl.TransformMessage(matrix, device_name="ImageToReference", timestamp=1)
 
     # Send messages
     server.send_message(transform_message)
diff --git a/logging.log.1 b/logging.log.1
new file mode 100644
index 00000000..fae1c313
--- /dev/null
+++ b/logging.log.1
@@ -0,0 +1,176 @@
+Apr 11, 2024 2:04:20 AM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: true] focused=true
+Apr 11, 2024 2:04:20 AM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from null to TabPane[id=tabPane, styleClass=tab-pane]
+Apr 11, 2024 2:04:21 AM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: false] focused=false
+Apr 11, 2024 2:04:21 AM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ToggleButton@61665b10[styleClass=toggle-button green-toggle-button]'Connect via OpenIGTLink (localhost)', name: focused, value: true] focused=true
+Apr 11, 2024 2:04:21 AM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from TabPane[id=tabPane, styleClass=tab-pane] to ToggleButton@61665b10[styleClass=toggle-button green-toggle-button]'Connect via OpenIGTLink (localhost)'
+Apr 11, 2024 2:04:21 AM inputOutput.OpenIGTLinkConnection <init>
+INFO: Starting OIGTL client
+Apr 11, 2024 2:04:21 AM org.medcare.igtl.network.OpenIGTClient <init>
+SEVERE: OpenIGTClient Exception while creating socket
+java.net.ConnectException: Connection refused: connect
+	at java.base/sun.nio.ch.Net.connect0(Native Method)
+	at java.base/sun.nio.ch.Net.connect(Net.java:579)
+	at java.base/sun.nio.ch.Net.connect(Net.java:568)
+	at java.base/sun.nio.ch.NioSocketImpl.connect(NioSocketImpl.java:588)
+	at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:327)
+	at java.base/java.net.Socket.connect(Socket.java:633)
+	at java.base/java.net.Socket.connect(Socket.java:583)
+	at java.base/java.net.Socket.<init>(Socket.java:507)
+	at java.base/java.net.Socket.<init>(Socket.java:287)
+	at java.base/javax.net.DefaultSocketFactory.createSocket(SocketFactory.java:271)
+	at org.medcare.igtl.network.OpenIGTClient.<init>(OpenIGTClient.java:80)
+	at org.medcare.igtl.network.GenericIGTLinkClient.<init>(GenericIGTLinkClient.java:23)
+	at inputOutput.OpenIGTLinkConnection.<init>(OpenIGTLinkConnection.java:46)
+	at inputOutput.OIGTTrackingDataSource.connect(OIGTTrackingDataSource.java:31)
+	at controller.TrackingDataController.lambda$onConnectButtonClicked$1(TrackingDataController.java:157)
+	at java.base/java.lang.Thread.run(Thread.java:833)
+
+Apr 11, 2024 2:04:21 AM org.medcare.igtl.network.GenericIGTLinkClient <init>
+FINE: Starting GenericIGTLinkClient
+Apr 11, 2024 2:04:21 AM mainMethod.App lambda$start$0
+SEVERE: Uncaught exception in thread Thread-4
+java.lang.NullPointerException: Cannot invoke "java.net.Socket.isClosed()" because "this.socket" is null
+	at org.medcare.igtl.network.OpenIGTClient.isConnected(OpenIGTClient.java:246)
+	at org.medcare.igtl.network.GenericIGTLinkClient$Sender.run(GenericIGTLinkClient.java:246)
+
+Apr 11, 2024 2:04:22 AM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ToggleButton@61665b10[styleClass=toggle-button green-toggle-button]'Connect via OpenIGTLink (localhost)', name: focused, value: false] focused=false
+Apr 11, 2024 2:04:22 AM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=visualizeTrackingBtn, styleClass=button]'Start Tracking and Visualization', name: focused, value: true] focused=true
+Apr 11, 2024 2:04:22 AM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from ToggleButton@61665b10[styleClass=toggle-button green-toggle-button]'Connect via OpenIGTLink (localhost)' to Button[id=visualizeTrackingBtn, styleClass=button]'Start Tracking and Visualization'
+Apr 11, 2024 2:04:22 AM algorithm.TrackingDataManager getNextData
+WARNING: Toollist is empty.
+Apr 11, 2024 2:04:22 AM algorithm.TrackingDataManager getNextData
+WARNING: Toollist is empty.
+Apr 11, 2024 2:04:22 AM algorithm.VisualizationManager loadLastSTLModels
+INFO: STL file read from: C:\GitHub\IGTPrototypingTool\src\test\resources\Tool13_v2.stl
+Apr 11, 2024 2:04:22 AM algorithm.VisualizationManager loadLastSTLModels
+INFO: STL file read from: C:\GitHub\IGTPrototypingTool\src\test\resources\Phantom_final-decimated25000.stl
+Apr 11, 2024 2:04:22 AM algorithm.TrackingDataManager getNextData
+WARNING: Toollist is empty.
+Apr 11, 2024 2:04:22 AM algorithm.TrackingDataManager getNextData
+WARNING: Toollist is empty.
+Apr 11, 2024 2:04:22 AM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=visualizeTrackingBtn, styleClass=button]'Start Tracking and Visualization', name: focused, value: false] focused=false
+Apr 11, 2024 2:04:22 AM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from Button[id=visualizeTrackingBtn, styleClass=button]'Start Tracking and Visualization' to null
+Apr 11, 2024 2:04:22 AM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ToggleButton[id=freezeTglBtn, styleClass=toggle-button]'Freeze / Unfreeze', name: focused, value: true] focused=true
+Apr 11, 2024 2:04:22 AM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from null to ToggleButton[id=freezeTglBtn, styleClass=toggle-button]'Freeze / Unfreeze'
+Apr 11, 2024 2:04:22 AM algorithm.TrackingDataManager getNextData
+WARNING: Toollist is empty.
+Apr 11, 2024 2:04:23 AM algorithm.TrackingDataManager getNextData
+WARNING: Toollist is empty.
+Apr 11, 2024 2:04:23 AM algorithm.TrackingDataManager getNextData
+WARNING: Toollist is empty.
+Apr 11, 2024 2:04:23 AM algorithm.TrackingDataManager getNextData
+WARNING: Toollist is empty.
+Apr 11, 2024 2:04:23 AM algorithm.TrackingDataManager getNextData
+WARNING: Toollist is empty.
+Apr 11, 2024 2:04:23 AM algorithm.TrackingDataManager getNextData
+WARNING: Toollist is empty.
+Apr 11, 2024 2:04:23 AM algorithm.TrackingDataManager getNextData
+WARNING: Toollist is empty.
+Apr 11, 2024 2:04:23 AM algorithm.TrackingDataManager getNextData
+WARNING: Toollist is empty.
+Apr 11, 2024 2:04:23 AM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ToggleButton[id=freezeTglBtn, styleClass=toggle-button]'Freeze / Unfreeze', name: focused, value: false] focused=false
+Apr 11, 2024 2:04:23 AM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ToggleButton@61665b10[styleClass=toggle-button green-toggle-button]'Connect via OpenIGTLink (localhost)', name: focused, value: true] focused=true
+Apr 11, 2024 2:04:23 AM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from ToggleButton[id=freezeTglBtn, styleClass=toggle-button]'Freeze / Unfreeze' to ToggleButton@61665b10[styleClass=toggle-button green-toggle-button]'Connect via OpenIGTLink (localhost)'
+Apr 11, 2024 2:04:23 AM algorithm.TrackingDataManager getNextData
+WARNING: Toollist is empty.
+Apr 11, 2024 2:04:23 AM mainMethod.App lambda$start$0
+SEVERE: Uncaught exception in thread JavaFX Application Thread
+java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
+	at javafx.fxml/javafx.fxml.FXMLLoader$MethodHandler.invoke(FXMLLoader.java:1857)
+	at javafx.fxml/javafx.fxml.FXMLLoader$ControllerMethodEventHandler.handle(FXMLLoader.java:1724)
+	at javafx.base/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
+	at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234)
+	at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
+	at javafx.base/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
+	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
+	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
+	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
+	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
+	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
+	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
+	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
+	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
+	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
+	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
+	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
+	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
+	at javafx.base/com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
+	at javafx.base/com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
+	at javafx.base/javafx.event.Event.fireEvent(Event.java:198)
+	at javafx.graphics/javafx.scene.Node.fireEvent(Node.java:8792)
+	at javafx.controls/javafx.scene.control.ToggleButton.fire(ToggleButton.java:257)
+	at javafx.controls/com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208)
+	at javafx.controls/com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274)
+	at javafx.base/com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247)
+	at javafx.base/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
+	at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234)
+	at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
+	at javafx.base/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
+	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
+	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
+	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
+	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
+	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
+	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
+	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
+	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
+	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
+	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
+	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
+	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
+	at javafx.base/com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
+	at javafx.base/com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
+	at javafx.base/javafx.event.Event.fireEvent(Event.java:198)
+	at javafx.graphics/javafx.scene.Scene$MouseHandler.process(Scene.java:3897)
+	at javafx.graphics/javafx.scene.Scene.processMouseEvent(Scene.java:1878)
+	at javafx.graphics/javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2623)
+	at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:411)
+	at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:301)
+	at java.base/java.security.AccessController.doPrivileged(AccessController.java:399)
+	at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:450)
+	at javafx.graphics/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:424)
+	at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:449)
+	at javafx.graphics/com.sun.glass.ui.View.handleMouseEvent(View.java:557)
+	at javafx.graphics/com.sun.glass.ui.View.notifyMouse(View.java:943)
+	at javafx.graphics/com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
+	at javafx.graphics/com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:184)
+	at java.base/java.lang.Thread.run(Thread.java:833)
+Caused by: java.lang.reflect.InvocationTargetException
+	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
+	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
+	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
+	at com.sun.javafx.reflect.Trampoline.invoke(MethodUtil.java:77)
+	at jdk.internal.reflect.GeneratedMethodAccessor2.invoke(Unknown Source)
+	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
+	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
+	at javafx.base/com.sun.javafx.reflect.MethodUtil.invoke(MethodUtil.java:275)
+	at javafx.fxml/com.sun.javafx.fxml.MethodHelper.invoke(MethodHelper.java:84)
+	at javafx.fxml/javafx.fxml.FXMLLoader$MethodHandler.invoke(FXMLLoader.java:1854)
+	... 58 more
+Caused by: java.lang.NullPointerException: Cannot invoke "org.medcare.igtl.network.ResponseQueueManager.destroy()" because "this.responseQueue" is null
+	at org.medcare.igtl.network.OpenIGTClient.interrupt(OpenIGTClient.java:207)
+	at org.medcare.igtl.network.GenericIGTLinkClient.stopClient(GenericIGTLinkClient.java:160)
+	at inputOutput.OpenIGTLinkConnection.stop(OpenIGTLinkConnection.java:145)
+	at inputOutput.OIGTTrackingDataSource.closeConnection(OIGTTrackingDataSource.java:91)
+	at controller.TrackingDataController.disconnectSource(TrackingDataController.java:185)
+	at controller.TrackingDataController.onConnectButtonClicked(TrackingDataController.java:152)
+	... 69 more
+
+Apr 11, 2024 2:04:24 AM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ToggleButton@61665b10[styleClass=toggle-button green-toggle-button]'Connect via OpenIGTLink (localhost)', name: focused, value: false] focused=false
diff --git a/logging.log.1.lck b/logging.log.1.lck
new file mode 100644
index 00000000..e69de29b

From 635b590399c713d80659ab4db1e8253862e0aba1 Mon Sep 17 00:00:00 2001
From: nguyensl-rose <119351168+nguyensl-rose@users.noreply.github.com>
Date: Thu, 11 Apr 2024 11:08:34 +0200
Subject: [PATCH 008/100] orientation faces last position

---
 aitoigt/detect.py | 28 +++++++++++++++++-----------
 1 file changed, 17 insertions(+), 11 deletions(-)

diff --git a/aitoigt/detect.py b/aitoigt/detect.py
index 771dbbb7..9d7c2092 100644
--- a/aitoigt/detect.py
+++ b/aitoigt/detect.py
@@ -36,10 +36,7 @@
 import sys
 import pyigtl as igtl
 from pathlib import Path
-import pyvirtualcam
-
-CAM = pyvirtualcam.Camera(width=640, height=480, fps=20)
-
+ 
 import torch
  
 FILE = Path(__file__).resolve()
@@ -47,6 +44,8 @@
 if str(ROOT) not in sys.path:
     sys.path.append(str(ROOT))  # add ROOT to PATH
 ROOT = Path(os.path.relpath(ROOT, Path.cwd()))  # relative
+
+last_matrix = np.eye(4)
  
 from ultralytics.utils.plotting import Annotator, colors, save_one_box
  
@@ -238,15 +237,26 @@ def write_to_csv(image_name, prediction, confidence):
                         save_one_box(xyxy, imc, file=save_dir / "crops" / names[c] / f"{p.stem}.jpg", BGR=True)
  
                 if open_igt:
+
+                    # Generate matrix
+                    global last_matrix
                     matrix = np.eye(4)
     
+                    # Set position
                     matrix[0, 3] = xyxy[0]
                     matrix[1, 3] = xyxy[1]
-    
+
+                    # Set orientation
+                    direction = last_matrix[:3, 3] - matrix[:3, 3]
+                    angle = (-np.pi) + np.arctan2(direction[1], direction[0])   # -90 degree offset because -X is the forward direction of the IGTP pointer model
+                    rotation_matrix = np.array([[np.cos(angle), -np.sin(angle), 0], [np.sin(angle), np.cos(angle), 0], [0, 0, 1]])
+                    matrix[:3, :3] = rotation_matrix
+
+                    # Send transform message
+                    last_matrix = matrix
                     transform_message = igtl.TransformMessage(matrix, device_name="ImageToReference", timestamp=1)
-    
                     server.send_message(transform_message)
- 
+
             # Stream results
             im0 = annotator.result()
             if view_img:
@@ -255,10 +265,6 @@ def write_to_csv(image_name, prediction, confidence):
                     cv2.namedWindow(str(p), cv2.WINDOW_NORMAL | cv2.WINDOW_KEEPRATIO)  # allow window resize (Linux)
                     cv2.resizeWindow(str(p), im0.shape[1], im0.shape[0])
                 cv2.imshow(str(p), im0)
-
-                # Send RGB image to virtual camera
-                im0VIRT = cv2.cvtColor(im0, cv2.COLOR_BGR2RGB)
-                CAM.send(im0VIRT)
                 cv2.waitKey(1)  # 1 millisecond
  
             # Save results (image with detections)

From 04db0df4345b8983ae9b3f5c65dc1feb1166215d Mon Sep 17 00:00:00 2001
From: Muazzam Bin Aqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Fri, 12 Apr 2024 14:42:03 +0200
Subject: [PATCH 009/100] Multiple Functionalities (Upload Pictures + Import
 Button + Picture Selection + Picture View in the Big box)

---
 .../java/controller/AnnotationController.java | 65 +++++++++++++++++--
 src/main/resources/view/AnnotationView.fxml   | 22 +++++--
 2 files changed, 78 insertions(+), 9 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 468b87e3..c1549050 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -1,19 +1,76 @@
 package controller;
-
+import java.util.List;
+import javafx.event.ActionEvent;
 import javafx.fxml.FXML;
 import javafx.fxml.Initializable;
+import javafx.scene.image.Image;
+import javafx.scene.image.ImageView;
+import javafx.scene.input.MouseEvent;
+import javafx.scene.layout.VBox;
+import javafx.stage.FileChooser;
+import javafx.stage.Stage;
+import java.io.File;
 import java.net.URL;
 import java.util.ResourceBundle;
-
 public class AnnotationController implements Controller {
+    @FXML
+    public VBox uploadedImages;
+    @FXML
+    private ImageView selectedImageView;
+    private ImageView currentSelectedImageView;
+
     @Override
     public void initialize(URL location, ResourceBundle resources) {
         // Initialization code goes here
-  }
-
+    }
     @FXML
     @Override
     public void close() {
         unregisterController();
     }
+    @FXML
+    public void Handle_Upload_Functionality(ActionEvent actionEvent) {
+        try {
+            FileChooser fileChooser = new FileChooser();
+            fileChooser.setTitle("Select Images");
+            fileChooser.setInitialDirectory(new File(System.getProperty("user.home")));
+            fileChooser.getExtensionFilters().add(
+                    new FileChooser.ExtensionFilter("Image Files", "*.jpg", "*.png", "*.gif", "*.bmp")
+            );
+            Stage currentStage = (Stage) ((javafx.scene.Node) actionEvent.getSource()).getScene().getWindow();
+            List<File> files = fileChooser.showOpenMultipleDialog(currentStage);
+            if (files != null) {
+                for (File file : files) {
+                    displayImage(file);
+                }
+            }
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
+    }
+    private void displayImage(File file) {
+        Image image = new Image(file.toURI().toString());
+        ImageView imageView = new ImageView(image);
+        imageView.setFitHeight(100);
+        imageView.setFitWidth(100);
+        imageView.setPreserveRatio(true);
+
+        imageView.setOnMouseClicked(event -> {
+            if (currentSelectedImageView != null) {
+                currentSelectedImageView.setStyle("");
+            }
+            selectImage(image);
+            imageView.setStyle("-fx-effect: dropshadow(three-pass-box, rgba(0,0,0,0.8), 10, 0, 0, 0);");
+            currentSelectedImageView = imageView;
+        });
+
+        uploadedImages.getChildren().add(imageView);
+    }
+    private void selectImage(Image image) {
+        if (selectedImageView != null) {
+            selectedImageView.setImage(image);
+            selectedImageView.setFitWidth(selectedImageView.getScene().getWidth());
+            selectedImageView.setPreserveRatio(true);
+        }
+    }
 }
diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index d14859b9..37c27a78 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -22,18 +22,30 @@
                </children></HBox>
          </bottom>
          <top>
-            <HBox alignment="CENTER" prefHeight="80.0" prefWidth="368.0" style="-fx-border-color: grey;" BorderPane.alignment="CENTER">
+            <HBox alignment="CENTER_LEFT" prefHeight="100.0" prefWidth="368.0" style="-fx-border-color: grey;">
                <BorderPane.margin>
                   <Insets bottom="10.0" left="10.0" right="10.0" top="10.0" />
                </BorderPane.margin>
                <children>
-                  <Button mnemonicParsing="false" text="Example" />
-               </children></HBox>
+                  <HBox>
+                     <children>
+                        <Button fx:id="exampleButton" onAction="#Handle_Upload_Functionality" text="IMPORT"
+                                prefWidth="120.0" prefHeight="40.0"
+                                style="-fx-font-size: 16px;" />
+                     </children>
+                     <HBox.margin>
+                        <Insets left="195" top="30"/>
+                     </HBox.margin>
+                  </HBox>
+               </children>
+            </HBox>
          </top>
+
+
          <left>
             <ScrollPane fitToHeight="true" fitToWidth="true" hbarPolicy="NEVER" prefHeight="202.0" prefWidth="188.0" vbarPolicy="ALWAYS" BorderPane.alignment="CENTER">
                <content>
-                  <VBox id="uploadedImages" prefHeight="200.0" prefWidth="100.0" />
+                  <VBox fx:id="uploadedImages" prefHeight="200.0" prefWidth="100.0" />
                </content>
                <BorderPane.margin>
                   <Insets left="10.0" right="10.0" />
@@ -43,7 +55,7 @@
          <center>
             <TitledPane collapsible="false" text="Selected Image" textAlignment="CENTER" BorderPane.alignment="CENTER">
                <content>
-                  <ImageView id="selectedImage" fitHeight="500.0" fitWidth="200.0" pickOnBounds="true" preserveRatio="true" />
+                  <ImageView fx:id="selectedImageView" fitHeight="500.0" fitWidth="200.0" pickOnBounds="true" preserveRatio="true" />
                </content>
                <BorderPane.margin>
                   <Insets right="10.0" />

From f0d742ddb25d064419c976fcb863c8301bddd9d2 Mon Sep 17 00:00:00 2001
From: VincentStriegel <strivi01@thu.de>
Date: Sat, 13 Apr 2024 16:39:25 +0200
Subject: [PATCH 010/100] Update AnnotationView.fxml with new buttons and
 styles

---
 src/main/resources/view/AnnotationView.fxml | 52 +++++++++++++++------
 1 file changed, 37 insertions(+), 15 deletions(-)

diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index 37c27a78..b85de616 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -9,7 +9,9 @@
 <?import javafx.scene.layout.HBox?>
 <?import javafx.scene.layout.VBox?>
 
-<ScrollPane fitToHeight="true" fitToWidth="true" maxHeight="Infinity" maxWidth="Infinity" xmlns="http://javafx.com/javafx/21" xmlns:fx="http://javafx.com/fxml/1" fx:controller="controller.AnnotationController">
+<ScrollPane fitToHeight="true" fitToWidth="true" maxHeight="Infinity" maxWidth="Infinity"
+   xmlns="http://javafx.com/javafx/21"
+   xmlns:fx="http://javafx.com/fxml/1" fx:controller="controller.AnnotationController">
    <content>
       <BorderPane>
          <bottom>
@@ -18,30 +20,49 @@
                   <Insets bottom="10.0" left="10.0" right="10.0" top="10.0" />
                </BorderPane.margin>
                <children>
-                  <Button mnemonicParsing="false" text="Example" />
-               </children></HBox>
+                  <Button mnemonicParsing="false" text="No Tip" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;">
+                     <HBox.margin>
+                        <Insets left="55.0" right="55.0" />
+                     </HBox.margin>
+                  </Button>
+                  <Button mnemonicParsing="false" text="&lt;" prefHeight="40.0" style="-fx-font-weight: bold;-fx-font-size: 16px;">
+                     <HBox.margin>
+                        <Insets left="2.0" right="2.0" />
+                     </HBox.margin>
+                  </Button>
+                  <Button mnemonicParsing="false" text="&gt;" prefHeight="40.0" style="-fx-font-weight: bold;-fx-font-size: 16px;">
+                     <HBox.margin>
+                        <Insets left="2.0" right="2.0" />
+                     </HBox.margin>
+                  </Button>
+                  <Button mnemonicParsing="false" text="Done" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;">
+                     <HBox.margin>
+                        <Insets left="55.0" right="55.0" />
+                     </HBox.margin>
+                  </Button>
+               </children>
+            </HBox>
          </bottom>
          <top>
-            <HBox alignment="CENTER_LEFT" prefHeight="100.0" prefWidth="368.0" style="-fx-border-color: grey;">
+            <HBox alignment="CENTER" prefHeight="80.0" prefWidth="368.0" style="-fx-border-color: grey;" BorderPane.alignment="CENTER">
                <BorderPane.margin>
                   <Insets bottom="10.0" left="10.0" right="10.0" top="10.0" />
                </BorderPane.margin>
                <children>
-                  <HBox>
-                     <children>
-                        <Button fx:id="exampleButton" onAction="#Handle_Upload_Functionality" text="IMPORT"
-                                prefWidth="120.0" prefHeight="40.0"
-                                style="-fx-font-size: 16px;" />
-                     </children>
+                  <Button fx:id="exampleButton" onAction="#Handle_Upload_Functionality" text="Import" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;">
                      <HBox.margin>
-                        <Insets left="195" top="30"/>
+                        <Insets left="55.0" right="55.0" />
                      </HBox.margin>
-                  </HBox>
+                  </Button>
+                  <Button fx:id="exampleButton" text="Export" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;" />
+                  <Button fx:id="exampleButton" text="Clear Marks" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;">
+                     <HBox.margin>
+                        <Insets left="55.0" right="55.0" />
+                     </HBox.margin>
+                  </Button>
                </children>
             </HBox>
          </top>
-
-
          <left>
             <ScrollPane fitToHeight="true" fitToWidth="true" hbarPolicy="NEVER" prefHeight="202.0" prefWidth="188.0" vbarPolicy="ALWAYS" BorderPane.alignment="CENTER">
                <content>
@@ -61,6 +82,7 @@
                   <Insets right="10.0" />
                </BorderPane.margin>
             </TitledPane>
-         </center></BorderPane>
+         </center>
+      </BorderPane>
    </content>
 </ScrollPane>

From 41235acdfbdbbbc0fbcf5969d7c8feb0052165e5 Mon Sep 17 00:00:00 2001
From: david <david.todorr@gmail.com>
Date: Sun, 14 Apr 2024 20:01:30 +0200
Subject: [PATCH 011/100] Next and previous button functionality added

---
 .../java/controller/AnnotationController.java | 64 ++++++++++++++++---
 src/main/resources/view/AnnotationView.fxml   |  6 +-
 2 files changed, 57 insertions(+), 13 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index c1549050..304cbeae 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -1,8 +1,10 @@
 package controller;
+import java.util.ArrayList;
 import java.util.List;
 import javafx.event.ActionEvent;
 import javafx.fxml.FXML;
 import javafx.fxml.Initializable;
+import javafx.scene.control.Button;
 import javafx.scene.image.Image;
 import javafx.scene.image.ImageView;
 import javafx.scene.input.MouseEvent;
@@ -15,22 +17,28 @@
 public class AnnotationController implements Controller {
     @FXML
     public VBox uploadedImages;
+    public Button uploadImagesButton;
     @FXML
     private ImageView selectedImageView;
     private ImageView currentSelectedImageView;
 
+    private List<File> selectedImages;
+
     @Override
     public void initialize(URL location, ResourceBundle resources) {
         // Initialization code goes here
     }
+
     @FXML
     @Override
     public void close() {
         unregisterController();
     }
+
     @FXML
     public void Handle_Upload_Functionality(ActionEvent actionEvent) {
         try {
+
             FileChooser fileChooser = new FileChooser();
             fileChooser.setTitle("Select Images");
             fileChooser.setInitialDirectory(new File(System.getProperty("user.home")));
@@ -38,9 +46,11 @@ public void Handle_Upload_Functionality(ActionEvent actionEvent) {
                     new FileChooser.ExtensionFilter("Image Files", "*.jpg", "*.png", "*.gif", "*.bmp")
             );
             Stage currentStage = (Stage) ((javafx.scene.Node) actionEvent.getSource()).getScene().getWindow();
-            List<File> files = fileChooser.showOpenMultipleDialog(currentStage);
-            if (files != null) {
-                for (File file : files) {
+
+            this.selectedImages = fileChooser.showOpenMultipleDialog(currentStage);
+
+            if (selectedImages != null) {
+                for (File file : selectedImages) {
                     displayImage(file);
                 }
             }
@@ -48,6 +58,7 @@ public void Handle_Upload_Functionality(ActionEvent actionEvent) {
             e.printStackTrace();
         }
     }
+
     private void displayImage(File file) {
         Image image = new Image(file.toURI().toString());
         ImageView imageView = new ImageView(image);
@@ -56,21 +67,54 @@ private void displayImage(File file) {
         imageView.setPreserveRatio(true);
 
         imageView.setOnMouseClicked(event -> {
-            if (currentSelectedImageView != null) {
-                currentSelectedImageView.setStyle("");
-            }
-            selectImage(image);
-            imageView.setStyle("-fx-effect: dropshadow(three-pass-box, rgba(0,0,0,0.8), 10, 0, 0, 0);");
-            currentSelectedImageView = imageView;
+            selectImage(image, imageView);
         });
 
         uploadedImages.getChildren().add(imageView);
     }
-    private void selectImage(Image image) {
+
+    private void selectImage(Image image, ImageView imageView) {
+        if (currentSelectedImageView != null) {
+            currentSelectedImageView.setStyle("");
+        }
+
         if (selectedImageView != null) {
             selectedImageView.setImage(image);
             selectedImageView.setFitWidth(selectedImageView.getScene().getWidth());
             selectedImageView.setPreserveRatio(true);
         }
+        imageView.setStyle("-fx-effect: dropshadow(three-pass-box, rgba(0,0,0,0.8), 10, 0, 0, 0);");
+        currentSelectedImageView = imageView;
+    }
+
+    public void Select_Next_Image(ActionEvent actionEvent) {
+        try {
+            if (currentSelectedImageView != null) {
+                int currentIndex = uploadedImages.getChildren().indexOf(currentSelectedImageView);
+                if (currentIndex < uploadedImages.getChildren().size() - 1) {
+                    ImageView nextImageView = (ImageView) uploadedImages.getChildren().get(currentIndex + 1);
+                    Image image = nextImageView.getImage();
+                    selectImage(image, nextImageView);
+                }
+            }
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
+    }
+
+    public void Select_Previous_Image(ActionEvent actionEvent) {
+        try {
+            if (currentSelectedImageView != null) {
+                int currentIndex = uploadedImages.getChildren().indexOf(currentSelectedImageView);
+                if (currentIndex > 0) {
+                    ImageView previousImageView = (ImageView) uploadedImages.getChildren().get(currentIndex - 1);
+                    Image image = previousImageView.getImage();
+                    selectImage(image, previousImageView);
+                }
+            }
+        }
+        catch (Exception e) {
+            e.printStackTrace();
+        }
     }
 }
diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index b85de616..b9e8b57d 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -25,12 +25,12 @@
                         <Insets left="55.0" right="55.0" />
                      </HBox.margin>
                   </Button>
-                  <Button mnemonicParsing="false" text="&lt;" prefHeight="40.0" style="-fx-font-weight: bold;-fx-font-size: 16px;">
+                  <Button mnemonicParsing="false" text="&lt;" onAction="#Select_Previous_Image"  prefHeight="40.0" style="-fx-font-weight: bold;-fx-font-size: 16px;">
                      <HBox.margin>
                         <Insets left="2.0" right="2.0" />
                      </HBox.margin>
                   </Button>
-                  <Button mnemonicParsing="false" text="&gt;" prefHeight="40.0" style="-fx-font-weight: bold;-fx-font-size: 16px;">
+                  <Button mnemonicParsing="false" text="&gt;" onAction="#Select_Next_Image" prefHeight="40.0" style="-fx-font-weight: bold;-fx-font-size: 16px;">
                      <HBox.margin>
                         <Insets left="2.0" right="2.0" />
                      </HBox.margin>
@@ -49,7 +49,7 @@
                   <Insets bottom="10.0" left="10.0" right="10.0" top="10.0" />
                </BorderPane.margin>
                <children>
-                  <Button fx:id="exampleButton" onAction="#Handle_Upload_Functionality" text="Import" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;">
+                  <Button fx:id="uploadImagesButton" onAction="#Handle_Upload_Functionality" text="Import" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;">
                      <HBox.margin>
                         <Insets left="55.0" right="55.0" />
                      </HBox.margin>

From d96399b476ec41afd8ff4177800319c1e21dc1e4 Mon Sep 17 00:00:00 2001
From: david <david.todorr@gmail.com>
Date: Sun, 14 Apr 2024 23:35:48 +0200
Subject: [PATCH 012/100] Simple Zoom in and Zoom out functionality added

---
 .../java/controller/AnnotationController.java | 61 ++++++++++++++++---
 src/main/resources/view/AnnotationView.fxml   |  4 +-
 2 files changed, 55 insertions(+), 10 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 304cbeae..52d0b5dd 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -1,14 +1,16 @@
 package controller;
-import java.util.ArrayList;
 import java.util.List;
 import javafx.event.ActionEvent;
 import javafx.fxml.FXML;
-import javafx.fxml.Initializable;
+import javafx.geometry.Point2D;
+import javafx.scene.Group;
 import javafx.scene.control.Button;
+import javafx.scene.control.ScrollPane;
 import javafx.scene.image.Image;
 import javafx.scene.image.ImageView;
-import javafx.scene.input.MouseEvent;
+import javafx.scene.input.ScrollEvent;
 import javafx.scene.layout.VBox;
+import javafx.scene.transform.Scale;
 import javafx.stage.FileChooser;
 import javafx.stage.Stage;
 import java.io.File;
@@ -17,8 +19,11 @@
 public class AnnotationController implements Controller {
     @FXML
     public VBox uploadedImages;
+    @FXML
     public Button uploadImagesButton;
     @FXML
+    public ScrollPane selectedImagePane;
+    @FXML
     private ImageView selectedImageView;
     private ImageView currentSelectedImageView;
 
@@ -74,17 +79,57 @@ private void displayImage(File file) {
     }
 
     private void selectImage(Image image, ImageView imageView) {
-        if (currentSelectedImageView != null) {
-            currentSelectedImageView.setStyle("");
-        }
 
         if (selectedImageView != null) {
             selectedImageView.setImage(image);
             selectedImageView.setFitWidth(selectedImageView.getScene().getWidth());
             selectedImageView.setPreserveRatio(true);
+
+            // Create a new Scale transformation for the ImageView
+            Scale scale = new Scale();
+            selectedImageView.getTransforms().add(scale);
+
+            // Create a Group and add the ImageView to it
+            Group group = new Group(selectedImageView);
+
+            // Replace the content of the ScrollPane with the Group
+            this.selectedImagePane.setContent(group);
+
+            // Add a ScrollEvent handler to the ScrollPane
+            this.selectedImagePane.addEventFilter(ScrollEvent.ANY, event -> {
+                if (event.isControlDown()) {
+                    // Convert the mouse coordinates to the coordinate system of the Group
+                    double mouseX = event.getX() - group.getBoundsInParent().getMinX();
+                    double mouseY = event.getY() - group.getBoundsInParent().getMinY();
+
+                    // Adjust the pivot points to the mouse's current position
+                    scale.setPivotX(mouseX);
+                    scale.setPivotY(mouseY);
+
+                    double zoomFactor = 1.05;
+
+                    if (event.getDeltaY() > 0) {
+                        // Zoom in
+                        scale.setX(scale.getX() * zoomFactor);
+                        scale.setY(scale.getY() * zoomFactor);
+                    } else {
+                        // Zoom out, but do not go below a certain minimum value
+                        if (scale.getX() > 1.0 && scale.getY() > 1.0) {
+                            scale.setX(scale.getX() / zoomFactor);
+                            scale.setY(scale.getY() / zoomFactor);
+                        }
+                    }
+
+                    event.consume();
+                }
+            });
+
+            imageView.setStyle("-fx-effect: dropshadow(three-pass-box, rgba(0,0,0,0.8), 10, 0, 0, 0);");
+            currentSelectedImageView = imageView;
+
         }
-        imageView.setStyle("-fx-effect: dropshadow(three-pass-box, rgba(0,0,0,0.8), 10, 0, 0, 0);");
-        currentSelectedImageView = imageView;
+
+
     }
 
     public void Select_Next_Image(ActionEvent actionEvent) {
diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index b9e8b57d..689af8fb 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -74,14 +74,14 @@
             </ScrollPane>
          </left>
          <center>
-            <TitledPane collapsible="false" text="Selected Image" textAlignment="CENTER" BorderPane.alignment="CENTER">
+            <ScrollPane fx:id="selectedImagePane" hbarPolicy="AS_NEEDED" vbarPolicy="AS_NEEDED"  BorderPane.alignment="CENTER">
                <content>
                   <ImageView fx:id="selectedImageView" fitHeight="500.0" fitWidth="200.0" pickOnBounds="true" preserveRatio="true" />
                </content>
                <BorderPane.margin>
                   <Insets right="10.0" />
                </BorderPane.margin>
-            </TitledPane>
+            </ScrollPane>
          </center>
       </BorderPane>
    </content>

From ea1cb6bfa87288d14040b72d6473a7ac93777f8e Mon Sep 17 00:00:00 2001
From: Simon Engel <engesi02@thu.de>
Date: Mon, 15 Apr 2024 10:19:50 +0200
Subject: [PATCH 013/100] Create Rectangle Shape

---
 .../java/controller/AnnotationController.java | 29 ++++++++++++++++++-
 src/main/resources/view/AnnotationView.fxml   |  5 +++-
 2 files changed, 32 insertions(+), 2 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index c1549050..69628242 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -2,11 +2,13 @@
 import java.util.List;
 import javafx.event.ActionEvent;
 import javafx.fxml.FXML;
-import javafx.fxml.Initializable;
 import javafx.scene.image.Image;
 import javafx.scene.image.ImageView;
 import javafx.scene.input.MouseEvent;
+import javafx.scene.layout.Pane;
 import javafx.scene.layout.VBox;
+import javafx.scene.paint.Color;
+import javafx.scene.shape.Rectangle;
 import javafx.stage.FileChooser;
 import javafx.stage.Stage;
 import java.io.File;
@@ -18,6 +20,10 @@ public class AnnotationController implements Controller {
     @FXML
     private ImageView selectedImageView;
     private ImageView currentSelectedImageView;
+    @FXML
+    private Pane annotationPane;
+
+    private Rectangle annotatedRectangle;
 
     @Override
     public void initialize(URL location, ResourceBundle resources) {
@@ -71,6 +77,27 @@ private void selectImage(Image image) {
             selectedImageView.setImage(image);
             selectedImageView.setFitWidth(selectedImageView.getScene().getWidth());
             selectedImageView.setPreserveRatio(true);
+            selectedImageView.setOnMouseClicked(this::annotationEvent);
+
+        }
+    }
+
+    private void annotationEvent(MouseEvent event) {
+        //To not create Duplicates
+        if(annotatedRectangle == null) {
+            annotatedRectangle = new Rectangle(event.getX() - 10, event.getY() - 10, 20, 20);
+            annotatedRectangle.setFill(Color.TRANSPARENT);
+            annotatedRectangle.setStroke(Color.rgb(6, 207, 236));
+            annotatedRectangle.setStrokeWidth(2);
+            annotatedRectangle.setVisible(true);
+            annotationPane.getChildren().add(annotatedRectangle); // Add it to the Scene
+        }else{
+            annotatedRectangle.setX(event.getX() - 10);
+            annotatedRectangle.setY(event.getY() - 10);
+            annotatedRectangle.setWidth(20);
+            annotatedRectangle.setHeight(20);
         }
+
     }
+
 }
diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index b85de616..0aa32cbe 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -8,6 +8,7 @@
 <?import javafx.scene.layout.BorderPane?>
 <?import javafx.scene.layout.HBox?>
 <?import javafx.scene.layout.VBox?>
+<?import javafx.scene.layout.Pane?>
 
 <ScrollPane fitToHeight="true" fitToWidth="true" maxHeight="Infinity" maxWidth="Infinity"
    xmlns="http://javafx.com/javafx/21"
@@ -76,7 +77,9 @@
          <center>
             <TitledPane collapsible="false" text="Selected Image" textAlignment="CENTER" BorderPane.alignment="CENTER">
                <content>
-                  <ImageView fx:id="selectedImageView" fitHeight="500.0" fitWidth="200.0" pickOnBounds="true" preserveRatio="true" />
+                  <Pane fx:id="annotationPane">
+                     <ImageView fx:id="selectedImageView" fitHeight="500.0" fitWidth="200.0" pickOnBounds="true" preserveRatio="true" />
+                  </Pane>
                </content>
                <BorderPane.margin>
                   <Insets right="10.0" />

From 6d58abeceb59421c053026df1f8f6eebcf8bac45 Mon Sep 17 00:00:00 2001
From: Simon Engel <engesi02@thu.de>
Date: Mon, 15 Apr 2024 19:52:36 +0200
Subject: [PATCH 014/100] Create AnnotationData to save the Data

---
 .../java/controller/AnnotationController.java |  8 ++++
 src/main/java/util/AnnotationData.java        | 42 +++++++++++++++++++
 2 files changed, 50 insertions(+)
 create mode 100644 src/main/java/util/AnnotationData.java

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 69628242..139d32bd 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -11,6 +11,8 @@
 import javafx.scene.shape.Rectangle;
 import javafx.stage.FileChooser;
 import javafx.stage.Stage;
+import util.AnnotationData;
+
 import java.io.File;
 import java.net.URL;
 import java.util.ResourceBundle;
@@ -82,7 +84,12 @@ private void selectImage(Image image) {
         }
     }
 
+    /**
+     * Handle the Annotation Event
+     * @param event
+     */
     private void annotationEvent(MouseEvent event) {
+        System.out.println("MouseEvent: " + event);
         //To not create Duplicates
         if(annotatedRectangle == null) {
             annotatedRectangle = new Rectangle(event.getX() - 10, event.getY() - 10, 20, 20);
@@ -98,6 +105,7 @@ private void annotationEvent(MouseEvent event) {
             annotatedRectangle.setHeight(20);
         }
 
+        //AnnotationData.getInstance().addAnnotation(new AnnotationData.Annotation(event.getX() - 10, event.getY() - 10, ));
     }
 
 }
diff --git a/src/main/java/util/AnnotationData.java b/src/main/java/util/AnnotationData.java
new file mode 100644
index 00000000..2fbe1b96
--- /dev/null
+++ b/src/main/java/util/AnnotationData.java
@@ -0,0 +1,42 @@
+package util;
+
+import java.util.ArrayList;
+
+public class AnnotationData {
+
+    /**
+     * Private Class to save the Annotation Data
+     */
+    private static class Annotation{
+        private double middlePointX;
+        private double middlePointY;
+        private double boundingBoxWidth;
+        private double boundingBoxHeight;
+        private String imgName;
+
+        public Annotation(double middlePointX, double middlePointY, double boundingBoxWidth, double boundingBoxHeight, String imgName) {
+            this.middlePointX = middlePointX;
+            this.middlePointY = middlePointY;
+            this.boundingBoxWidth = boundingBoxWidth;
+            this.boundingBoxHeight = boundingBoxHeight;
+            this.imgName = imgName;
+        }
+        public double getMiddlePointX() {return middlePointX;}
+        public double getMiddlePointY() {return middlePointY;}
+        public double getBoundingBoxWidth() {return boundingBoxWidth;}
+        public double getBoundingBoxHeight() {return boundingBoxHeight;}
+    }
+
+    private static AnnotationData instance = new AnnotationData();
+
+    private ArrayList<Annotation> annotations;
+    private AnnotationData(){
+        annotations = new ArrayList<>();
+    }
+
+    public void addAnnotation(Annotation annotation){}
+
+    public static AnnotationData getInstance() {
+        return instance;
+    }
+}

From 018a01d9de54ea2fe431c4dcde9ac9b7a9f849de Mon Sep 17 00:00:00 2001
From: Simon Engel <engesi02@thu.de>
Date: Mon, 15 Apr 2024 21:25:46 +0200
Subject: [PATCH 015/100] Two-way Annotation Functionality

---
 .../java/controller/AnnotationController.java | 50 ++++++++++++++-----
 src/main/java/util/AnnotationData.java        | 18 ++++---
 2 files changed, 50 insertions(+), 18 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 139d32bd..4290d2d8 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -2,6 +2,7 @@
 import java.util.List;
 import javafx.event.ActionEvent;
 import javafx.fxml.FXML;
+import javafx.geometry.Point2D;
 import javafx.scene.image.Image;
 import javafx.scene.image.ImageView;
 import javafx.scene.input.MouseEvent;
@@ -26,6 +27,8 @@ public class AnnotationController implements Controller {
     private Pane annotationPane;
 
     private Rectangle annotatedRectangle;
+    private boolean dragged = false;
+    private double annotationPointX, annotationPointY;
 
     @Override
     public void initialize(URL location, ResourceBundle resources) {
@@ -79,33 +82,56 @@ private void selectImage(Image image) {
             selectedImageView.setImage(image);
             selectedImageView.setFitWidth(selectedImageView.getScene().getWidth());
             selectedImageView.setPreserveRatio(true);
-            selectedImageView.setOnMouseClicked(this::annotationEvent);
+            selectedImageView.setOnMousePressed(this::pressedAnnotationEvent);
+            selectedImageView.setOnMouseReleased(this::releasedAnnotationEvent);
+            selectedImageView.setOnMouseDragged(this::dragAnnotationEvent);
+        }
+    }
 
+    private void dragAnnotationEvent(MouseEvent event) {
+        if(event.isControlDown()){
+            double x2 = event.getX();
+            double y2 = event.getY();
+            annotatedRectangle.setX(annotationPointX);
+            annotatedRectangle.setY(annotationPointY);
+            annotatedRectangle.setWidth(Math.abs(x2 - annotationPointX));
+            annotatedRectangle.setHeight(Math.abs(y2 - annotationPointY));
+            dragged = true;
         }
     }
 
-    /**
-     * Handle the Annotation Event
-     * @param event
-     */
-    private void annotationEvent(MouseEvent event) {
-        System.out.println("MouseEvent: " + event);
+    private void pressedAnnotationEvent(MouseEvent event) {
         //To not create Duplicates
+        annotationPointX = event.getX();
+        annotationPointY = event.getY();
+
         if(annotatedRectangle == null) {
-            annotatedRectangle = new Rectangle(event.getX() - 10, event.getY() - 10, 20, 20);
+            annotatedRectangle = new Rectangle();
             annotatedRectangle.setFill(Color.TRANSPARENT);
             annotatedRectangle.setStroke(Color.rgb(6, 207, 236));
             annotatedRectangle.setStrokeWidth(2);
             annotatedRectangle.setVisible(true);
             annotationPane.getChildren().add(annotatedRectangle); // Add it to the Scene
-        }else{
-            annotatedRectangle.setX(event.getX() - 10);
-            annotatedRectangle.setY(event.getY() - 10);
+        }
+
+    }
+    /**
+     * Handle the Simple Annotation Event where the user clicks once without dragging.
+     * Here the size of the rectangle is fixed
+     * @param event
+     */
+    private void releasedAnnotationEvent(MouseEvent event) {
+        if(!dragged){
+            annotatedRectangle.setX(annotationPointX - 10);
+            annotatedRectangle.setY(annotationPointY - 10);
             annotatedRectangle.setWidth(20);
             annotatedRectangle.setHeight(20);
         }
+        dragged = false;
 
-        //AnnotationData.getInstance().addAnnotation(new AnnotationData.Annotation(event.getX() - 10, event.getY() - 10, ));
+        AnnotationData.getInstance().addAnnotation(
+                selectedImageView.getImage().getUrl(),
+                annotationPointX, annotationPointY, 20.0, 20.0);
     }
 
 }
diff --git a/src/main/java/util/AnnotationData.java b/src/main/java/util/AnnotationData.java
index 2fbe1b96..26088e75 100644
--- a/src/main/java/util/AnnotationData.java
+++ b/src/main/java/util/AnnotationData.java
@@ -1,6 +1,8 @@
 package util;
 
 import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Map;
 
 public class AnnotationData {
 
@@ -12,14 +14,12 @@ private static class Annotation{
         private double middlePointY;
         private double boundingBoxWidth;
         private double boundingBoxHeight;
-        private String imgName;
 
-        public Annotation(double middlePointX, double middlePointY, double boundingBoxWidth, double boundingBoxHeight, String imgName) {
+        public Annotation(double middlePointX, double middlePointY, double boundingBoxWidth, double boundingBoxHeight) {
             this.middlePointX = middlePointX;
             this.middlePointY = middlePointY;
             this.boundingBoxWidth = boundingBoxWidth;
             this.boundingBoxHeight = boundingBoxHeight;
-            this.imgName = imgName;
         }
         public double getMiddlePointX() {return middlePointX;}
         public double getMiddlePointY() {return middlePointY;}
@@ -29,12 +29,18 @@ public Annotation(double middlePointX, double middlePointY, double boundingBoxWi
 
     private static AnnotationData instance = new AnnotationData();
 
-    private ArrayList<Annotation> annotations;
+    private Map<String, Annotation> annotations;
     private AnnotationData(){
-        annotations = new ArrayList<>();
+        annotations = new HashMap();
     }
 
-    public void addAnnotation(Annotation annotation){}
+    public void addAnnotation(String path,
+                              double middlePointX,
+                              double middlePointY,
+                              double boundingBoxWidth,
+                              double boundingBoxHeight){
+
+    }
 
     public static AnnotationData getInstance() {
         return instance;

From 9777e667c73be6756a2f471f5eeff7ae50475a97 Mon Sep 17 00:00:00 2001
From: david <david.todorr@gmail.com>
Date: Tue, 16 Apr 2024 00:34:09 +0200
Subject: [PATCH 016/100] Focus of the image fixed, zooming functionality fixed
 when the image is changed during zooming with reseting the scale

---
 .../java/controller/AnnotationController.java | 21 +++++++------------
 src/main/resources/view/AnnotationView.fxml   | 16 +++++++-------
 2 files changed, 17 insertions(+), 20 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 52d0b5dd..fceb703e 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -80,31 +80,24 @@ private void displayImage(File file) {
 
     private void selectImage(Image image, ImageView imageView) {
 
-        if (selectedImageView != null) {
+        if (selectedImageView != null && currentSelectedImageView != imageView) {
             selectedImageView.setImage(image);
             selectedImageView.setFitWidth(selectedImageView.getScene().getWidth());
             selectedImageView.setPreserveRatio(true);
 
+            selectedImageView.getTransforms().clear();
             // Create a new Scale transformation for the ImageView
             Scale scale = new Scale();
             selectedImageView.getTransforms().add(scale);
 
-            // Create a Group and add the ImageView to it
-            Group group = new Group(selectedImageView);
-
-            // Replace the content of the ScrollPane with the Group
-            this.selectedImagePane.setContent(group);
-
             // Add a ScrollEvent handler to the ScrollPane
             this.selectedImagePane.addEventFilter(ScrollEvent.ANY, event -> {
                 if (event.isControlDown()) {
-                    // Convert the mouse coordinates to the coordinate system of the Group
-                    double mouseX = event.getX() - group.getBoundsInParent().getMinX();
-                    double mouseY = event.getY() - group.getBoundsInParent().getMinY();
+
 
                     // Adjust the pivot points to the mouse's current position
-                    scale.setPivotX(mouseX);
-                    scale.setPivotY(mouseY);
+                    scale.setPivotX(event.getX());
+                    scale.setPivotY(event.getY());
 
                     double zoomFactor = 1.05;
 
@@ -124,9 +117,11 @@ private void selectImage(Image image, ImageView imageView) {
                 }
             });
 
+            if (currentSelectedImageView != null){
+                currentSelectedImageView.setStyle("");
+            }
             imageView.setStyle("-fx-effect: dropshadow(three-pass-box, rgba(0,0,0,0.8), 10, 0, 0, 0);");
             currentSelectedImageView = imageView;
-
         }
 
 
diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index 689af8fb..5cb5f54d 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -9,9 +9,10 @@
 <?import javafx.scene.layout.HBox?>
 <?import javafx.scene.layout.VBox?>
 
+<?import javafx.scene.Group?>
 <ScrollPane fitToHeight="true" fitToWidth="true" maxHeight="Infinity" maxWidth="Infinity"
-   xmlns="http://javafx.com/javafx/21"
-   xmlns:fx="http://javafx.com/fxml/1" fx:controller="controller.AnnotationController">
+            xmlns="http://javafx.com/javafx/21"
+            xmlns:fx="http://javafx.com/fxml/1" fx:controller="controller.AnnotationController">
    <content>
       <BorderPane>
          <bottom>
@@ -74,13 +75,14 @@
             </ScrollPane>
          </left>
          <center>
-            <ScrollPane fx:id="selectedImagePane" hbarPolicy="AS_NEEDED" vbarPolicy="AS_NEEDED"  BorderPane.alignment="CENTER">
-               <content>
-                  <ImageView fx:id="selectedImageView" fitHeight="500.0" fitWidth="200.0" pickOnBounds="true" preserveRatio="true" />
-               </content>
+            <ScrollPane fx:id="selectedImagePane" BorderPane.alignment="CENTER">
                <BorderPane.margin>
-                  <Insets right="10.0" />
+                  <Insets right="10.0"/>
                </BorderPane.margin>
+               <Group>
+                  <ImageView fx:id="selectedImageView" fitHeight="500.0" fitWidth="200.0" pickOnBounds="true"
+                             preserveRatio="true"/>
+               </Group>
             </ScrollPane>
          </center>
       </BorderPane>

From 5c5a26d50c0e620770f31e3ded416f9d20019c7f Mon Sep 17 00:00:00 2001
From: Simon Engel <engesi02@thu.de>
Date: Wed, 17 Apr 2024 11:11:15 +0200
Subject: [PATCH 017/100] Finished Annotation Functionality

---
 .../java/controller/AnnotationController.java | 27 ++++++++---
 src/main/java/util/AnnotationData.java        | 45 +++++++++++++++----
 2 files changed, 59 insertions(+), 13 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 4290d2d8..585d46e8 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -2,7 +2,6 @@
 import java.util.List;
 import javafx.event.ActionEvent;
 import javafx.fxml.FXML;
-import javafx.geometry.Point2D;
 import javafx.scene.image.Image;
 import javafx.scene.image.ImageView;
 import javafx.scene.input.MouseEvent;
@@ -85,6 +84,17 @@ private void selectImage(Image image) {
             selectedImageView.setOnMousePressed(this::pressedAnnotationEvent);
             selectedImageView.setOnMouseReleased(this::releasedAnnotationEvent);
             selectedImageView.setOnMouseDragged(this::dragAnnotationEvent);
+
+            // Get Rectangle and 'unnormalize' the values
+            annotationPane.getChildren().remove(annotatedRectangle);
+            annotatedRectangle = AnnotationData.getInstance().getAnnotation(selectedImageView.getImage().getUrl());
+            if(annotatedRectangle != null) {
+                annotatedRectangle.setX(annotatedRectangle.getX()*selectedImageView.getImage().getWidth());
+                annotatedRectangle.setY(annotatedRectangle.getY()*selectedImageView.getImage().getHeight());
+                annotatedRectangle.setWidth(annotatedRectangle.getWidth()*selectedImageView.getImage().getWidth());
+                annotatedRectangle.setHeight(annotatedRectangle.getHeight()*selectedImageView.getImage().getHeight());
+                annotationPane.getChildren().add(annotatedRectangle);
+            }
         }
     }
 
@@ -118,7 +128,7 @@ private void pressedAnnotationEvent(MouseEvent event) {
     /**
      * Handle the Simple Annotation Event where the user clicks once without dragging.
      * Here the size of the rectangle is fixed
-     * @param event
+     * @param event The Mouse Event
      */
     private void releasedAnnotationEvent(MouseEvent event) {
         if(!dragged){
@@ -126,12 +136,19 @@ private void releasedAnnotationEvent(MouseEvent event) {
             annotatedRectangle.setY(annotationPointY - 10);
             annotatedRectangle.setWidth(20);
             annotatedRectangle.setHeight(20);
+        }else {
+            // Calculate the Middle point of the rectangle
+            annotationPointX += annotatedRectangle.getWidth()/2;
+            annotationPointY += annotatedRectangle.getHeight()/2;
         }
         dragged = false;
-
         AnnotationData.getInstance().addAnnotation(
                 selectedImageView.getImage().getUrl(),
-                annotationPointX, annotationPointY, 20.0, 20.0);
-    }
+                annotationPointX /selectedImageView.getImage().getWidth(),
+                annotationPointY /selectedImageView.getImage().getHeight(),
+                annotatedRectangle.getWidth()/selectedImageView.getImage().getWidth(),
+                annotatedRectangle.getHeight()/selectedImageView.getImage().getHeight()
+        );
 
+    }
 }
diff --git a/src/main/java/util/AnnotationData.java b/src/main/java/util/AnnotationData.java
index 26088e75..beb28897 100644
--- a/src/main/java/util/AnnotationData.java
+++ b/src/main/java/util/AnnotationData.java
@@ -1,19 +1,26 @@
 package util;
 
-import java.util.ArrayList;
+import javafx.scene.paint.Color;
+import javafx.scene.shape.Rectangle;
+
 import java.util.HashMap;
 import java.util.Map;
 
+/**
+ * Annotation Data handler responsible for collecting and saving the annotated data
+ * Singleton because we only want one instance of this, at a time.
+ *
+ */
 public class AnnotationData {
 
     /**
      * Private Class to save the Annotation Data
      */
     private static class Annotation{
-        private double middlePointX;
-        private double middlePointY;
-        private double boundingBoxWidth;
-        private double boundingBoxHeight;
+        private final double middlePointX;
+        private final double middlePointY;
+        private final double boundingBoxWidth;
+        private final double boundingBoxHeight;
 
         public Annotation(double middlePointX, double middlePointY, double boundingBoxWidth, double boundingBoxHeight) {
             this.middlePointX = middlePointX;
@@ -27,11 +34,11 @@ public Annotation(double middlePointX, double middlePointY, double boundingBoxWi
         public double getBoundingBoxHeight() {return boundingBoxHeight;}
     }
 
-    private static AnnotationData instance = new AnnotationData();
+    private static final AnnotationData instance = new AnnotationData();
 
-    private Map<String, Annotation> annotations;
+    private final Map<String, Annotation> annotations;
     private AnnotationData(){
-        annotations = new HashMap();
+        annotations = new HashMap<>();
     }
 
     public void addAnnotation(String path,
@@ -39,7 +46,29 @@ public void addAnnotation(String path,
                               double middlePointY,
                               double boundingBoxWidth,
                               double boundingBoxHeight){
+        if(!annotations.containsKey(path)){
+            annotations.put(path, new Annotation(middlePointX, middlePointY, boundingBoxWidth, boundingBoxHeight));
+        }else{
+            annotations.replace(path, new Annotation(middlePointX, middlePointY, boundingBoxWidth, boundingBoxHeight));
+        }
+    }
 
+    public Rectangle getAnnotation(String path){
+        if(annotations.containsKey(path)){
+            Annotation annotation = annotations.get(path);
+            // Calculate the Rectangle based on the annotated data
+            Rectangle rectangle = new Rectangle();
+            rectangle.setWidth(annotation.getBoundingBoxWidth());
+            rectangle.setHeight(annotation.getBoundingBoxHeight());
+            rectangle.setX(annotation.getMiddlePointX()-(annotation.getBoundingBoxWidth()/2));
+            rectangle.setY(annotation.getMiddlePointY()-(annotation.getBoundingBoxHeight()/2));
+            rectangle.setFill(Color.TRANSPARENT);
+            rectangle.setStroke(Color.rgb(6, 207, 236));
+            rectangle.setStrokeWidth(2);
+            rectangle.setVisible(true);
+          return rectangle;
+        }
+        return null;
     }
 
     public static AnnotationData getInstance() {

From 2232dd0c2f4a51343a2d512eb8a51d3743869bbe Mon Sep 17 00:00:00 2001
From: Eugen Zdrincu <eugenzdrincu@gmail.com>
Date: Wed, 17 Apr 2024 15:20:29 +0200
Subject: [PATCH 018/100] added reference point setting

---
 .../java/controller/AutoTrackController.java   | 18 +++++++++++++++++-
 src/main/resources/view/AutoTrackView.fxml     |  6 ++++++
 2 files changed, 23 insertions(+), 1 deletion(-)

diff --git a/src/main/java/controller/AutoTrackController.java b/src/main/java/controller/AutoTrackController.java
index 05789c4e..91d485e2 100644
--- a/src/main/java/controller/AutoTrackController.java
+++ b/src/main/java/controller/AutoTrackController.java
@@ -80,6 +80,8 @@ public class AutoTrackController implements Controller {
     public PlottableImage videoImagePlot;
     @FXML
     public CheckBox use3dTransformCheckBox;
+    @FXML
+    public CheckBox inSetReferenceMode;
 
     private TrackingDataController trackingDataController;
     private Label statusLabel;
@@ -102,6 +104,8 @@ public class AutoTrackController implements Controller {
     private final ObservableList<Point3> clicked_tracker_points = FXCollections.observableArrayList();
     private Mat cachedTransformMatrix = null;
 
+    private final XYChart.Series<Number, Number> referencePoint = new XYChart.Series<Number, Number>();
+
     @Override
     public void initialize(URL location, ResourceBundle resources) {
         registerController();
@@ -122,12 +126,23 @@ public void initialize(URL location, ResourceBundle resources) {
         generateMatrixButton.disableProperty().bind(Bindings.size(clicked_image_points).lessThan(4));
         generateMatrixButton.textProperty().bind(Bindings.concat("Generate (",Bindings.size(clicked_image_points),"/4)"));
 
+        referencePoint.setName("reference point");
+        referencePoint.getData().add(new XYChart.Data<>(100,100));
+        dataSeries.add(referencePoint);
+
         videoImagePlot.setData(dataSeries);
         videoImagePlot.registerImageClickedHandler(this::onImageClicked);
-
+        videoImagePlot.registerImageClickedHandler(this::onSRM);
         loadAvailableVideoDevicesAsync();
     }
 
+    private void onSRM(double v, double v1) {
+        if (inSetReferenceMode.isSelected()) {
+            System.out.println("Set reference point to "+v+" "+v1);
+            referencePoint.setData(FXCollections.observableArrayList(new XYChart.Data<>(v,v1)));
+        }
+    }
+
     @Override
     public void close() {
         unregisterController();
@@ -580,6 +595,7 @@ private double[] applyTrackingTransformation3d(double x, double y, double z){
      * @param y Y-Coordinate in the image
      */
     private void onImageClicked(double x, double y){
+        System.out.println("clicked on image");
         var trackingData = lastTrackingData;
         if(trackingData.size() > 0 && clicked_image_points.size() < 4) {
             // We also directly save the tracking-coordinates at this point.
diff --git a/src/main/resources/view/AutoTrackView.fxml b/src/main/resources/view/AutoTrackView.fxml
index f4b5ba69..aa189c70 100644
--- a/src/main/resources/view/AutoTrackView.fxml
+++ b/src/main/resources/view/AutoTrackView.fxml
@@ -82,6 +82,12 @@
                      <Insets left="10.0" right="10.0" top="5.0"/>
                   </padding>
                </CheckBox>
+               <CheckBox fx:id="inSetReferenceMode" mnemonicParsing="false"
+                         text="Set reference mode">
+                  <padding>
+                     <Insets left="10.0" right="10.0" top="5.0"/>
+                  </padding>
+               </CheckBox>
             </VBox>
          </TitledPane>
          <TitledPane animated="false" collapsible="false" graphicTextGap="10.0" layoutX="10.0" layoutY="10.0"

From 431894e2e4c71092c17842c2c89bfacfe4a85fce Mon Sep 17 00:00:00 2001
From: Simon Engel <engesi02@thu.de>
Date: Wed, 17 Apr 2024 16:32:25 +0200
Subject: [PATCH 019/100] Middle point for each Box

---
 .../java/controller/AnnotationController.java | 20 +++++++++++++++++++
 src/main/java/util/AnnotationData.java        |  8 ++++++++
 2 files changed, 28 insertions(+)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 585d46e8..0ea0865d 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -8,6 +8,7 @@
 import javafx.scene.layout.Pane;
 import javafx.scene.layout.VBox;
 import javafx.scene.paint.Color;
+import javafx.scene.shape.Circle;
 import javafx.scene.shape.Rectangle;
 import javafx.stage.FileChooser;
 import javafx.stage.Stage;
@@ -26,6 +27,7 @@ public class AnnotationController implements Controller {
     private Pane annotationPane;
 
     private Rectangle annotatedRectangle;
+    private Circle middlePoint;
     private boolean dragged = false;
     private double annotationPointX, annotationPointY;
 
@@ -87,13 +89,23 @@ private void selectImage(Image image) {
 
             // Get Rectangle and 'unnormalize' the values
             annotationPane.getChildren().remove(annotatedRectangle);
+            annotationPane.getChildren().remove(middlePoint);
             annotatedRectangle = AnnotationData.getInstance().getAnnotation(selectedImageView.getImage().getUrl());
+            if(middlePoint != null) {
+                middlePoint = null;
+            }
             if(annotatedRectangle != null) {
                 annotatedRectangle.setX(annotatedRectangle.getX()*selectedImageView.getImage().getWidth());
                 annotatedRectangle.setY(annotatedRectangle.getY()*selectedImageView.getImage().getHeight());
                 annotatedRectangle.setWidth(annotatedRectangle.getWidth()*selectedImageView.getImage().getWidth());
                 annotatedRectangle.setHeight(annotatedRectangle.getHeight()*selectedImageView.getImage().getHeight());
                 annotationPane.getChildren().add(annotatedRectangle);
+                middlePoint = new Circle(0,0,2);
+                middlePoint.setFill(Color.rgb(6, 207, 236));
+                middlePoint.setCenterX(annotatedRectangle.getX()+(annotatedRectangle.getWidth()/2));
+                middlePoint.setCenterY(annotatedRectangle.getY()+(annotatedRectangle.getHeight()/2));
+                annotationPane.getChildren().add(middlePoint);
+
             }
         }
     }
@@ -123,6 +135,11 @@ private void pressedAnnotationEvent(MouseEvent event) {
             annotatedRectangle.setVisible(true);
             annotationPane.getChildren().add(annotatedRectangle); // Add it to the Scene
         }
+        if(middlePoint == null) {
+            middlePoint = new Circle(0, 0, 2);
+            middlePoint.setFill(Color.rgb(6, 207, 236));
+            annotationPane.getChildren().add(middlePoint);
+        }
 
     }
     /**
@@ -141,7 +158,10 @@ private void releasedAnnotationEvent(MouseEvent event) {
             annotationPointX += annotatedRectangle.getWidth()/2;
             annotationPointY += annotatedRectangle.getHeight()/2;
         }
+        middlePoint.setCenterX(annotationPointX);
+        middlePoint.setCenterY(annotationPointY);
         dragged = false;
+
         AnnotationData.getInstance().addAnnotation(
                 selectedImageView.getImage().getUrl(),
                 annotationPointX /selectedImageView.getImage().getWidth(),
diff --git a/src/main/java/util/AnnotationData.java b/src/main/java/util/AnnotationData.java
index beb28897..99b6e564 100644
--- a/src/main/java/util/AnnotationData.java
+++ b/src/main/java/util/AnnotationData.java
@@ -71,6 +71,14 @@ public Rectangle getAnnotation(String path){
         return null;
     }
 
+    /**
+     * Function to delete the Annotation of one Image
+     * @param path Image path (Key for the Map)
+     */
+    public void deleteAnnotation(String path){
+        //Todo
+    }
+
     public static AnnotationData getInstance() {
         return instance;
     }

From a8f1187791aed88a42ab6f19f14f81334ab308ae Mon Sep 17 00:00:00 2001
From: Eugen Zdrincu <eugenzdrincu@gmail.com>
Date: Thu, 18 Apr 2024 18:22:08 +0200
Subject: [PATCH 020/100] added line plot overlay for showing distance

---
 .../java/controller/AutoTrackController.java  | 38 +++++++++++++++++++
 src/main/resources/view/AutoTrackView.fxml    | 38 ++++++++++++-------
 2 files changed, 63 insertions(+), 13 deletions(-)

diff --git a/src/main/java/controller/AutoTrackController.java b/src/main/java/controller/AutoTrackController.java
index 91d485e2..5bd6f067 100644
--- a/src/main/java/controller/AutoTrackController.java
+++ b/src/main/java/controller/AutoTrackController.java
@@ -14,6 +14,8 @@
 import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
 import javafx.fxml.FXML;
+import javafx.scene.chart.LineChart;
+import javafx.scene.chart.NumberAxis;
 import javafx.scene.chart.XYChart;
 import javafx.scene.control.Button;
 import javafx.scene.control.Label;
@@ -82,6 +84,8 @@ public class AutoTrackController implements Controller {
     public CheckBox use3dTransformCheckBox;
     @FXML
     public CheckBox inSetReferenceMode;
+    @FXML
+    public LineChart<Number, Number> lineChart;
 
     private TrackingDataController trackingDataController;
     private Label statusLabel;
@@ -106,6 +110,10 @@ public class AutoTrackController implements Controller {
 
     private final XYChart.Series<Number, Number> referencePoint = new XYChart.Series<Number, Number>();
 
+    NumberAxis xAxis = new NumberAxis(-500, 500, 100);
+    NumberAxis yAxis = new NumberAxis(-500, 500, 100);
+
+
     @Override
     public void initialize(URL location, ResourceBundle resources) {
         registerController();
@@ -134,6 +142,20 @@ public void initialize(URL location, ResourceBundle resources) {
         videoImagePlot.registerImageClickedHandler(this::onImageClicked);
         videoImagePlot.registerImageClickedHandler(this::onSRM);
         loadAvailableVideoDevicesAsync();
+
+        lineChart.getXAxis().setVisible(false);
+        lineChart.getYAxis().setVisible(false);
+        lineChart.setLegendVisible(false);
+        videoImagePlot.setLegendVisible(false);
+        lineChart.setMouseTransparent(true);
+        lineChart.setAnimated(false);
+        lineChart.setCreateSymbols(true);
+        lineChart.setAlternativeRowFillVisible(false);
+        lineChart.setAlternativeColumnFillVisible(false);
+        lineChart.setHorizontalGridLinesVisible(false);
+        lineChart.setVerticalGridLinesVisible(false);
+        lineChart.lookup(".chart-plot-background").setStyle("-fx-background-color: transparent;");
+
     }
 
     private void onSRM(double v, double v1) {
@@ -264,6 +286,22 @@ private void updateVideoImage() {
         }
         if(matrix != null && !matrix.empty()) {
             videoImagePlot.setImage(ImageDataProcessor.Mat2Image(matrix, ".png"));
+            System.out.println("setting new linechart axis");
+            ((NumberAxis) lineChart.getXAxis()).setAutoRanging(false);
+            ((NumberAxis) lineChart.getXAxis()).setLowerBound(((NumberAxis) videoImagePlot.getXAxis()).getLowerBound());
+            ((NumberAxis) lineChart.getXAxis()).setUpperBound(((NumberAxis) videoImagePlot.getXAxis()).getUpperBound());
+            ((NumberAxis) lineChart.getXAxis()).setTickUnit(((NumberAxis) videoImagePlot.getXAxis()).getTickUnit());
+            ((NumberAxis) lineChart.getYAxis()).setAutoRanging(false);
+            ((NumberAxis) lineChart.getYAxis()).setLowerBound(((NumberAxis) videoImagePlot.getYAxis()).getLowerBound());
+            ((NumberAxis) lineChart.getYAxis()).setUpperBound(((NumberAxis) videoImagePlot.getYAxis()).getUpperBound());
+            ((NumberAxis) lineChart.getYAxis()).setTickUnit(((NumberAxis) videoImagePlot.getYAxis()).getTickUnit());
+
+            lineChart.prefWidthProperty().bind(videoImagePlot.widthProperty());
+            lineChart.prefHeightProperty().bind(videoImagePlot.heightProperty());
+            lineChart.minWidthProperty().bind(videoImagePlot.widthProperty());
+            lineChart.minHeightProperty().bind(videoImagePlot.heightProperty());
+            lineChart.maxWidthProperty().bind(videoImagePlot.widthProperty());
+            lineChart.maxHeightProperty().bind(videoImagePlot.heightProperty());
         }
     }
 
diff --git a/src/main/resources/view/AutoTrackView.fxml b/src/main/resources/view/AutoTrackView.fxml
index aa189c70..36208846 100644
--- a/src/main/resources/view/AutoTrackView.fxml
+++ b/src/main/resources/view/AutoTrackView.fxml
@@ -5,22 +5,34 @@
 <?import javafx.scene.control.*?>
 <?import javafx.scene.layout.*?>
 <?import userinterface.PlottableImage?>
+<?import javafx.scene.chart.LineChart?>
 <ScrollPane fitToHeight="true" fitToWidth="true" maxHeight="Infinity" maxWidth="Infinity"
             xmlns="http://javafx.com/javafx/17" xmlns:fx="http://javafx.com/fxml/1"
             fx:controller="controller.AutoTrackController">
-   <VBox alignment="CENTER" maxHeight="Infinity" maxWidth="Infinity" spacing="20.0">
-      <padding>
-         <Insets bottom="20.0" left="20.0" right="20.0" top="20.0"/>
-      </padding>
-      <PlottableImage fx:id="videoImagePlot" horizontalGridLinesVisible="false" maxHeight="Infinity"
-                      maxWidth="Infinity" verticalGridLinesVisible="false">
-         <xAxis>
-            <NumberAxis autoRanging="false" lowerBound="-500.0" minorTickVisible="false" side="BOTTOM" upperBound="500.0"/>
-         </xAxis>
-         <yAxis>
-            <NumberAxis autoRanging="false" lowerBound="-500.0" minorTickVisible="false" side="LEFT" upperBound="500.0"/>
-         </yAxis>
-      </PlottableImage>
+   <VBox alignment="CENTER" maxHeight="Infinity" maxWidth="Infinity">
+      <StackPane>
+         <alignment>
+            <Pos fx:value="CENTER"/>
+         </alignment>
+         <PlottableImage fx:id="videoImagePlot" horizontalGridLinesVisible="false" maxHeight="Infinity"
+                         maxWidth="Infinity" verticalGridLinesVisible="false">
+            <xAxis>
+               <NumberAxis autoRanging="false" lowerBound="-500.0" minorTickVisible="false" side="BOTTOM" upperBound="500.0"/>
+            </xAxis>
+            <yAxis>
+               <NumberAxis autoRanging="false" lowerBound="-500.0" minorTickVisible="false" side="LEFT" upperBound="500.0"/>
+            </yAxis>
+         </PlottableImage>
+         <LineChart fx:id="lineChart">
+            <xAxis>
+               <NumberAxis autoRanging="false" lowerBound="-500.0" minorTickVisible="false" side="BOTTOM" upperBound="500.0"/>
+            </xAxis>
+            <yAxis>
+               <NumberAxis autoRanging="false" lowerBound="-500.0" minorTickVisible="false" side="LEFT" upperBound="500.0"/>
+            </yAxis>
+         </LineChart>
+      </StackPane>
+
       <HBox alignment="CENTER" spacing="20.0">
          <TitledPane animated="false" collapsible="false" graphicTextGap="10.0" text="Connections"
                      textAlignment="CENTER">

From bcd2324020dc2cc62ce639a3ef414a0f317a6b6f Mon Sep 17 00:00:00 2001
From: Eugen Zdrincu <eugenzdrincu@gmail.com>
Date: Thu, 18 Apr 2024 21:22:40 +0200
Subject: [PATCH 021/100] added line plot overlay for showing distance

---
 .../java/controller/AutoTrackController.java  | 37 +++++++++++++++----
 1 file changed, 29 insertions(+), 8 deletions(-)

diff --git a/src/main/java/controller/AutoTrackController.java b/src/main/java/controller/AutoTrackController.java
index 5bd6f067..39757e98 100644
--- a/src/main/java/controller/AutoTrackController.java
+++ b/src/main/java/controller/AutoTrackController.java
@@ -41,6 +41,7 @@
 import java.nio.file.Path;
 import java.util.List;
 import java.util.*;
+import java.util.logging.Level;
 import java.util.logging.Logger;
 import java.util.prefs.Preferences;
 
@@ -109,6 +110,7 @@ public class AutoTrackController implements Controller {
     private Mat cachedTransformMatrix = null;
 
     private final XYChart.Series<Number, Number> referencePoint = new XYChart.Series<Number, Number>();
+    private final ObservableList<XYChart.Series<Number,Number>> lineDataSeries = FXCollections.observableArrayList();
 
     NumberAxis xAxis = new NumberAxis(-500, 500, 100);
     NumberAxis yAxis = new NumberAxis(-500, 500, 100);
@@ -155,7 +157,7 @@ public void initialize(URL location, ResourceBundle resources) {
         lineChart.setHorizontalGridLinesVisible(false);
         lineChart.setVerticalGridLinesVisible(false);
         lineChart.lookup(".chart-plot-background").setStyle("-fx-background-color: transparent;");
-
+        lineChart.setData(lineDataSeries);
     }
 
     private void onSRM(double v, double v1) {
@@ -329,14 +331,27 @@ private void updateTrackingData(){
                 series.getData().remove(0);
                 // TODO: The sensor curve needs reworking (apply on transformed data and dont shrink)
 //                videoImagePlot.initSensorCurve(series);
+
+
+            }
+
+            if (lineDataSeries.size() <= i) {
+                // create series for line
+                // this series will include the reference point and current point
+                var lineSeries = new XYChart.Series<Number, Number>();
+                lineDataSeries.add(lineSeries);
+                lineSeries.getData().remove(0);
             }
 
             var series = dataSeries.get(i);
             var measurements = tool.getMeasurement();
             var point = measurements.get(measurements.size() - 1).getPos();
             var data = series.getData();
-            var max_num_points = 4; // 1
+            var max_num_points = 6; // 1
 
+            var lineSeries = lineDataSeries.get(i);
+            //var lineData = lineSeries.getData();
+            ObservableList<XYChart. Data<Number, Number>> lineData = FXCollections.observableArrayList();
             var shifted_points = use3dTransformCheckBox.isSelected() ? applyTrackingTransformation3d(point.getX(), point.getY(), point.getZ()) : applyTrackingTransformation2d(point.getX(), point.getY(), point.getZ());
             var x_normalized = shifted_points[0] / currentShowingImage.getWidth();
             var y_normalized = shifted_points[1] / currentShowingImage.getHeight();
@@ -344,8 +359,14 @@ private void updateTrackingData(){
 
             data.add(new XYChart.Data<>(shifted_points[0], shifted_points[1]));
 
+            lineData.add(new XYChart.Data<>(shifted_points[0], shifted_points[1]));
+            lineData.add(new XYChart.Data<>(referencePoint.getData().get(0).getXValue(), referencePoint.getData().get(0).getYValue()));
+
+            lineSeries.setData(lineData);
+
             if(data.size() > max_num_points){
                 data.remove(0);
+                //lineData.remove(0);
             }
         }
     }
@@ -375,7 +396,7 @@ private void saveCapturedData(BufferedImage image, List<ExportMeasurement> track
                 gson.toJson(trackingData, fw);
             }
         } catch (IOException e) {
-            logger.log(java.util.logging.Level.SEVERE, "Error saving captured data", e);
+            logger.log(Level.SEVERE, "Error saving captured data", e);
             e.printStackTrace();
         }
     }
@@ -407,7 +428,7 @@ public void on_openOutputDirectory() {
             try {
                 Desktop.getDesktop().open(new File(directory));
             } catch (IOException e) {
-                logger.log(java.util.logging.Level.SEVERE, "Error opening output directory", e);
+                logger.log(Level.SEVERE, "Error opening output directory", e);
                 e.printStackTrace();
             }
         }
@@ -468,7 +489,7 @@ public void on_importMatrix() {
             cachedTransformMatrix = null;
             userPreferences.put("matrixDirectory", inputFile.getAbsoluteFile().getParent());
         }catch (FileNotFoundException e) {
-            logger.log(java.util.logging.Level.SEVERE, "Error loading matrix", e);
+            logger.log(Level.SEVERE, "Error loading matrix", e);
             e.printStackTrace();
         }
     }
@@ -485,7 +506,7 @@ public void on_reloadMatrix(){
                 regMatrixStatusBox.setSelected(true);
                 cachedTransformMatrix = null;
             }catch (FileNotFoundException e) {
-                logger.log(java.util.logging.Level.SEVERE, "Error loading matrix", e);
+                logger.log(Level.SEVERE, "Error loading matrix", e);
                 e.printStackTrace();
             }
         }
@@ -515,7 +536,7 @@ public void on_generateMatrix(){
                 cachedTransformMatrix = null;
                 userPreferences.put("matrixDirectory", saveFile.getAbsoluteFile().getParent());
             } catch (IOException e) {
-                logger.log(java.util.logging.Level.SEVERE, "Error saving matrix", e);
+                logger.log(Level.SEVERE, "Error saving matrix", e);
                 e.printStackTrace();
             }
         }
@@ -525,7 +546,7 @@ private File getLastKnownFileLocation(String key, String defaultLocation){
         var lastLocation = userPreferences.get(key,defaultLocation);
         var lastLocationFile = new File(lastLocation);
         if(!lastLocationFile.exists()){
-            logger.log(java.util.logging.Level.WARNING, "Last directory does not exist, default directory instead");
+            logger.log(Level.WARNING, "Last directory does not exist, default directory instead");
             lastLocationFile = new File(defaultLocation);
         }
         return lastLocationFile;

From 33dfd7867b2ecf2ded1172f1e4a72a1d568dda4e Mon Sep 17 00:00:00 2001
From: Simon Engel <engesi02@thu.de>
Date: Thu, 18 Apr 2024 21:46:38 +0200
Subject: [PATCH 022/100] Merged Annotation with Zooming

---
 .../java/controller/AnnotationController.java | 108 +++++++++---------
 1 file changed, 53 insertions(+), 55 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index be3d7bfb..a8160ff2 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -1,28 +1,27 @@
 package controller;
-import java.util.List;
+
 import javafx.event.ActionEvent;
 import javafx.fxml.FXML;
-import javafx.geometry.Point2D;
-import javafx.scene.Group;
 import javafx.scene.control.Button;
 import javafx.scene.control.ScrollPane;
 import javafx.scene.image.Image;
 import javafx.scene.image.ImageView;
-import javafx.scene.input.ScrollEvent;
 import javafx.scene.input.MouseEvent;
 import javafx.scene.layout.Pane;
 import javafx.scene.layout.VBox;
-import javafx.scene.transform.Scale;
 import javafx.scene.paint.Color;
 import javafx.scene.shape.Circle;
 import javafx.scene.shape.Rectangle;
+import javafx.scene.transform.Scale;
 import javafx.stage.FileChooser;
 import javafx.stage.Stage;
 import util.AnnotationData;
 
 import java.io.File;
 import java.net.URL;
+import java.util.List;
 import java.util.ResourceBundle;
+
 public class AnnotationController implements Controller {
     @FXML
     public VBox uploadedImages;
@@ -47,11 +46,13 @@ public class AnnotationController implements Controller {
     public void initialize(URL location, ResourceBundle resources) {
         // Initialization code goes here
     }
+
     @FXML
     @Override
     public void close() {
         unregisterController();
     }
+
     @FXML
     public void Handle_Upload_Functionality(ActionEvent actionEvent) {
         try {
@@ -74,6 +75,7 @@ public void Handle_Upload_Functionality(ActionEvent actionEvent) {
             e.printStackTrace();
         }
     }
+
     private void displayImage(File file) {
         Image image = new Image(file.toURI().toString());
         ImageView imageView = new ImageView(image);
@@ -89,19 +91,18 @@ private void displayImage(File file) {
     }
 
     private void selectImage(Image image, ImageView imageView) {
-
         if (selectedImageView != null && currentSelectedImageView != imageView) {
             selectedImageView.setImage(image);
             selectedImageView.setFitWidth(selectedImageView.getScene().getWidth());
             selectedImageView.setPreserveRatio(true);
 
-            selectedImageView.getTransforms().clear();
+            annotationPane.getTransforms().clear();
             // Create a new Scale transformation for the ImageView
             Scale scale = new Scale();
-            selectedImageView.getTransforms().add(scale);
+            annotationPane.getTransforms().add(scale);
 
             // Add a ScrollEvent handler to the ScrollPane
-            this.selectedImagePane.addEventFilter(ScrollEvent.ANY, event -> {
+            annotationPane.setOnScroll(event -> {
                 if (event.isControlDown()) {
 
 
@@ -127,14 +128,16 @@ private void selectImage(Image image, ImageView imageView) {
                 }
             });
 
-            if (currentSelectedImageView != null){
+            if (currentSelectedImageView != null) {
                 currentSelectedImageView.setStyle("");
             }
             imageView.setStyle("-fx-effect: dropshadow(three-pass-box, rgba(0,0,0,0.8), 10, 0, 0, 0);");
             currentSelectedImageView = imageView;
+            checkForExistingAnnotationData();
+            selectedImageView.setOnMouseDragged(this::dragAnnotationEvent);
+            selectedImageView.setOnMousePressed(this::pressedAnnotationEvent);
+            selectedImageView.setOnMouseReleased(this::releasedAnnotationEvent);
         }
-
-
     }
 
     public void Select_Next_Image(ActionEvent actionEvent) {
@@ -162,61 +165,53 @@ public void Select_Previous_Image(ActionEvent actionEvent) {
                     selectImage(image, previousImageView);
                 }
             }
-        }
-        catch (Exception e) {
+        } catch (Exception e) {
             e.printStackTrace();
         }
     }
-    private void selectImage(Image image) {
-        if (selectedImageView != null) {
-            selectedImageView.setImage(image);
-            selectedImageView.setFitWidth(selectedImageView.getScene().getWidth());
-            selectedImageView.setPreserveRatio(true);
-            selectedImageView.setOnMousePressed(this::pressedAnnotationEvent);
-            selectedImageView.setOnMouseReleased(this::releasedAnnotationEvent);
-            selectedImageView.setOnMouseDragged(this::dragAnnotationEvent);
 
-            // Get Rectangle and 'unnormalize' the values
-            annotationPane.getChildren().remove(annotatedRectangle);
-            annotationPane.getChildren().remove(middlePoint);
-            annotatedRectangle = AnnotationData.getInstance().getAnnotation(selectedImageView.getImage().getUrl());
-            if(middlePoint != null) {
-                middlePoint = null;
-            }
-            if(annotatedRectangle != null) {
-                annotatedRectangle.setX(annotatedRectangle.getX()*selectedImageView.getImage().getWidth());
-                annotatedRectangle.setY(annotatedRectangle.getY()*selectedImageView.getImage().getHeight());
-                annotatedRectangle.setWidth(annotatedRectangle.getWidth()*selectedImageView.getImage().getWidth());
-                annotatedRectangle.setHeight(annotatedRectangle.getHeight()*selectedImageView.getImage().getHeight());
-                annotationPane.getChildren().add(annotatedRectangle);
-                middlePoint = new Circle(0,0,2);
-                middlePoint.setFill(Color.rgb(6, 207, 236));
-                middlePoint.setCenterX(annotatedRectangle.getX()+(annotatedRectangle.getWidth()/2));
-                middlePoint.setCenterY(annotatedRectangle.getY()+(annotatedRectangle.getHeight()/2));
-                annotationPane.getChildren().add(middlePoint);
+    private void checkForExistingAnnotationData() {
+        // Get Rectangle and 'unnormalize' the values
+        annotationPane.getChildren().remove(annotatedRectangle);
+        annotationPane.getChildren().remove(middlePoint);
+        annotatedRectangle = AnnotationData.getInstance().getAnnotation(selectedImageView.getImage().getUrl());
+        if (middlePoint != null) {
+            middlePoint = null;
+        }
+        if (annotatedRectangle != null) {
+            annotatedRectangle.setX(annotatedRectangle.getX() * selectedImageView.getImage().getWidth());
+            annotatedRectangle.setY(annotatedRectangle.getY() * selectedImageView.getImage().getHeight());
+            annotatedRectangle.setWidth(annotatedRectangle.getWidth() * selectedImageView.getImage().getWidth());
+            annotatedRectangle.setHeight(annotatedRectangle.getHeight() * selectedImageView.getImage().getHeight());
+            annotationPane.getChildren().add(annotatedRectangle);
+            middlePoint = new Circle(0, 0, 2);
+            middlePoint.setFill(Color.rgb(6, 207, 236));
+            middlePoint.setCenterX(annotatedRectangle.getX() + (annotatedRectangle.getWidth() / 2));
+            middlePoint.setCenterY(annotatedRectangle.getY() + (annotatedRectangle.getHeight() / 2));
+            annotationPane.getChildren().add(middlePoint);
 
-            }
         }
     }
 
     private void dragAnnotationEvent(MouseEvent event) {
-        if(event.isControlDown()){
+        if (event.isControlDown()) {
             double x2 = event.getX();
             double y2 = event.getY();
             annotatedRectangle.setX(annotationPointX);
             annotatedRectangle.setY(annotationPointY);
             annotatedRectangle.setWidth(Math.abs(x2 - annotationPointX));
             annotatedRectangle.setHeight(Math.abs(y2 - annotationPointY));
+            middlePoint.setCenterX(annotationPointX + annotatedRectangle.getWidth() / 2);
+            middlePoint.setCenterY(annotationPointY + annotatedRectangle.getHeight() / 2);
             dragged = true;
         }
     }
 
     private void pressedAnnotationEvent(MouseEvent event) {
-        //To not create Duplicates
         annotationPointX = event.getX();
         annotationPointY = event.getY();
 
-        if(annotatedRectangle == null) {
+        if (annotatedRectangle == null) {
             annotatedRectangle = new Rectangle();
             annotatedRectangle.setFill(Color.TRANSPARENT);
             annotatedRectangle.setStroke(Color.rgb(6, 207, 236));
@@ -224,39 +219,42 @@ private void pressedAnnotationEvent(MouseEvent event) {
             annotatedRectangle.setVisible(true);
             annotationPane.getChildren().add(annotatedRectangle); // Add it to the Scene
         }
-        if(middlePoint == null) {
+        if (middlePoint == null) {
             middlePoint = new Circle(0, 0, 2);
             middlePoint.setFill(Color.rgb(6, 207, 236));
             annotationPane.getChildren().add(middlePoint);
         }
 
     }
+
     /**
      * Handle the Simple Annotation Event where the user clicks once without dragging.
      * Here the size of the rectangle is fixed
+     *
      * @param event The Mouse Event
      */
     private void releasedAnnotationEvent(MouseEvent event) {
-        if(!dragged){
+        if (!dragged) {
             annotatedRectangle.setX(annotationPointX - 10);
             annotatedRectangle.setY(annotationPointY - 10);
             annotatedRectangle.setWidth(20);
             annotatedRectangle.setHeight(20);
-        }else {
+            middlePoint.setCenterX(annotationPointX);
+            middlePoint.setCenterY(annotationPointY);
+        } else {
             // Calculate the Middle point of the rectangle
-            annotationPointX += annotatedRectangle.getWidth()/2;
-            annotationPointY += annotatedRectangle.getHeight()/2;
+            annotationPointX += annotatedRectangle.getWidth() / 2;
+            annotationPointY += annotatedRectangle.getHeight() / 2;
         }
-        middlePoint.setCenterX(annotationPointX);
-        middlePoint.setCenterY(annotationPointY);
+
         dragged = false;
 
         AnnotationData.getInstance().addAnnotation(
                 selectedImageView.getImage().getUrl(),
-                annotationPointX /selectedImageView.getImage().getWidth(),
-                annotationPointY /selectedImageView.getImage().getHeight(),
-                annotatedRectangle.getWidth()/selectedImageView.getImage().getWidth(),
-                annotatedRectangle.getHeight()/selectedImageView.getImage().getHeight()
+                annotationPointX / selectedImageView.getImage().getWidth(),
+                annotationPointY / selectedImageView.getImage().getHeight(),
+                annotatedRectangle.getWidth() / selectedImageView.getImage().getWidth(),
+                annotatedRectangle.getHeight() / selectedImageView.getImage().getHeight()
         );
 
     }

From 6571f15a1f55b09be271bb8aefbdf7a92a823077 Mon Sep 17 00:00:00 2001
From: Eugen Zdrincu <eugenzdrincu@gmail.com>
Date: Fri, 19 Apr 2024 17:12:56 +0200
Subject: [PATCH 023/100] fixed bug in reference point lines

---
 src/main/java/controller/AutoTrackController.java | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/src/main/java/controller/AutoTrackController.java b/src/main/java/controller/AutoTrackController.java
index 39757e98..31f434fd 100644
--- a/src/main/java/controller/AutoTrackController.java
+++ b/src/main/java/controller/AutoTrackController.java
@@ -288,7 +288,6 @@ private void updateVideoImage() {
         }
         if(matrix != null && !matrix.empty()) {
             videoImagePlot.setImage(ImageDataProcessor.Mat2Image(matrix, ".png"));
-            System.out.println("setting new linechart axis");
             ((NumberAxis) lineChart.getXAxis()).setAutoRanging(false);
             ((NumberAxis) lineChart.getXAxis()).setLowerBound(((NumberAxis) videoImagePlot.getXAxis()).getLowerBound());
             ((NumberAxis) lineChart.getXAxis()).setUpperBound(((NumberAxis) videoImagePlot.getXAxis()).getUpperBound());
@@ -323,7 +322,7 @@ private void updateTrackingData(){
         lastTrackingData.clear();
         for (int i = 0; i < tools.size(); i++) {
             Tool tool = tools.get(i);
-            if (dataSeries.size() <= i) {
+            if (dataSeries.size() <= i + 1) {
                 var series = new XYChart.Series<Number, Number>();
                 series.setName(tool.getName());
                 series.getData().add(new XYChart.Data<>(0,0));  // Workaround to display legend
@@ -343,7 +342,8 @@ private void updateTrackingData(){
                 lineSeries.getData().remove(0);
             }
 
-            var series = dataSeries.get(i);
+
+            var series = dataSeries.get(i + 1);
             var measurements = tool.getMeasurement();
             var point = measurements.get(measurements.size() - 1).getPos();
             var data = series.getData();
@@ -357,11 +357,19 @@ private void updateTrackingData(){
             var y_normalized = shifted_points[1] / currentShowingImage.getHeight();
             lastTrackingData.add(new ExportMeasurement(tool.getName(), point.getX(), point.getY(), point.getZ(), shifted_points[0], shifted_points[1], shifted_points[2], x_normalized, y_normalized));
 
+
             data.add(new XYChart.Data<>(shifted_points[0], shifted_points[1]));
 
             lineData.add(new XYChart.Data<>(shifted_points[0], shifted_points[1]));
             lineData.add(new XYChart.Data<>(referencePoint.getData().get(0).getXValue(), referencePoint.getData().get(0).getYValue()));
 
+
+            System.out.println(referencePoint.getData().get(0).getXValue());
+            System.out.println(referencePoint.getData().get(0).getYValue());
+
+            System.out.println("------------");
+
+
             lineSeries.setData(lineData);
 
             if(data.size() > max_num_points){

From 16dc91f47ac7f25222da2a501e2fb0cb9217f9f6 Mon Sep 17 00:00:00 2001
From: Muazzam Bin Aqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Sat, 20 Apr 2024 13:43:31 +0200
Subject: [PATCH 024/100] Full_Functionality (ExportButton)

---
 .../java/controller/AnnotationController.java | 55 +++++++++++++++++++
 src/main/resources/view/AnnotationView.fxml   |  8 +--
 2 files changed, 59 insertions(+), 4 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index a8160ff2..c91171bc 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -2,6 +2,8 @@
 
 import javafx.event.ActionEvent;
 import javafx.fxml.FXML;
+import javafx.scene.Node;
+import javafx.scene.control.Alert;
 import javafx.scene.control.Button;
 import javafx.scene.control.ScrollPane;
 import javafx.scene.image.Image;
@@ -18,6 +20,9 @@
 import util.AnnotationData;
 
 import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.PrintWriter;
+import java.lang.annotation.Annotation;
 import java.net.URL;
 import java.util.List;
 import java.util.ResourceBundle;
@@ -258,4 +263,54 @@ private void releasedAnnotationEvent(MouseEvent event) {
         );
 
     }
+
+    @FXML
+    private void handleExportAction(ActionEvent event) {
+        if (selectedImageView != null && annotatedRectangle != null) {
+            FileChooser fileChooser = new FileChooser();
+            fileChooser.setTitle("Save Annotations");
+            fileChooser.getExtensionFilters().addAll(new FileChooser.ExtensionFilter("Text Files", "*.txt"));
+            File file = fileChooser.showSaveDialog(((Node) event.getSource()).getScene().getWindow());
+
+            if (file != null) {
+                saveAnnotationsToFile(file);
+            }
+        } else {
+            showNoAnnotationAlert();
+        }
+    }
+
+    private void saveAnnotationsToFile(File file) {
+        try (PrintWriter writer = new PrintWriter(file)) {
+            double imageWidth = selectedImageView.getImage().getWidth();
+            double imageHeight = selectedImageView.getImage().getHeight();
+
+            double centerX = (annotatedRectangle.getX() + annotatedRectangle.getWidth() / 2) / imageWidth;
+            double centerY = (annotatedRectangle.getY() + annotatedRectangle.getHeight() / 2) / imageHeight;
+            double normWidth = annotatedRectangle.getWidth() / imageWidth;
+            double normHeight = annotatedRectangle.getHeight() / imageHeight;
+
+            int classId = 0; // or dynamically determine the class ID if needed
+
+            String line = String.format("%d %.5f %.5f %.5f %.5f", classId, centerX, centerY, normWidth, normHeight);
+            writer.println(line);
+        } catch (FileNotFoundException e) {
+            e.printStackTrace();
+        }
+    }
+
+    private void showNoAnnotationAlert() {
+        Alert alert = new Alert(Alert.AlertType.INFORMATION);
+        alert.setTitle("No Annotation Found");
+        alert.setHeaderText(null);
+        alert.setContentText("No Annotation Found to process.");
+        alert.showAndWait();
+    }
+
+
+
+
+
+
+
 }
diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index e67d0158..962b7d93 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -56,7 +56,7 @@
                         <Insets left="55.0" right="55.0" />
                      </HBox.margin>
                   </Button>
-                  <Button fx:id="exampleButton" text="Export" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;" />
+                  <Button fx:id="ExportButton" text="Export" prefWidth="120.0" prefHeight="40.0" onAction="#handleExportAction" style="-fx-font-size: 16px;" />
                   <Button fx:id="exampleButton" text="Clear Marks" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;">
                      <HBox.margin>
                         <Insets left="55.0" right="55.0" />
@@ -81,9 +81,9 @@
                   <Insets right="10.0"/>
                </BorderPane.margin>
                <Group>
-                   <Pane fx:id="annotationPane">
-                       <ImageView fx:id="selectedImageView" fitHeight="500.0" fitWidth="200.0" pickOnBounds="true" preserveRatio="true" />
-                   </Pane>
+                  <Pane fx:id="annotationPane">
+                     <ImageView fx:id="selectedImageView" fitHeight="500.0" fitWidth="200.0" pickOnBounds="true" preserveRatio="true" />
+                  </Pane>
                </Group>
             </ScrollPane>
          </center>

From 61c563625474a0367baeb0d668829228d98459cd Mon Sep 17 00:00:00 2001
From: Muazzam Bin Aqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Sat, 20 Apr 2024 14:21:54 +0200
Subject: [PATCH 025/100] Dark/Light-Mode (Full-Functionality)

---
 .../java/controller/AnnotationController.java | 47 +++++++++++++++----
 src/main/resources/css/dark-mode.css          | 44 +++++++++++++++++
 src/main/resources/css/light-mode.css         |  9 ++++
 src/main/resources/view/AnnotationView.fxml   |  5 ++
 4 files changed, 97 insertions(+), 8 deletions(-)
 create mode 100644 src/main/resources/css/dark-mode.css
 create mode 100644 src/main/resources/css/light-mode.css

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index c91171bc..11fef1a7 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -3,6 +3,7 @@
 import javafx.event.ActionEvent;
 import javafx.fxml.FXML;
 import javafx.scene.Node;
+import javafx.scene.Scene;
 import javafx.scene.control.Alert;
 import javafx.scene.control.Button;
 import javafx.scene.control.ScrollPane;
@@ -263,7 +264,10 @@ private void releasedAnnotationEvent(MouseEvent event) {
         );
 
     }
-
+    /**
+     * Handles Export based Functionality
+     * @param event The Mouse Event
+     */
     @FXML
     private void handleExportAction(ActionEvent event) {
         if (selectedImageView != null && annotatedRectangle != null) {
@@ -290,7 +294,7 @@ private void saveAnnotationsToFile(File file) {
             double normWidth = annotatedRectangle.getWidth() / imageWidth;
             double normHeight = annotatedRectangle.getHeight() / imageHeight;
 
-            int classId = 0; // or dynamically determine the class ID if needed
+            int classId = 0; //As we have only one class based requirement
 
             String line = String.format("%d %.5f %.5f %.5f %.5f", classId, centerX, centerY, normWidth, normHeight);
             writer.println(line);
@@ -307,10 +311,37 @@ private void showNoAnnotationAlert() {
         alert.showAndWait();
     }
 
-
-
-
-
-
-
+    /**
+     * Handles Dark/Light-Mode based Functionality
+     * @param event The Mouse Event
+     */
+    @FXML
+    private void handleToggleTheme(ActionEvent event) {
+        try {
+            Scene scene = ((Node) event.getSource()).getScene();
+            String lightModeUrl = getClass().getResource("/css/light-mode.css").toExternalForm();
+            String darkModeUrl = getClass().getResource("/css/dark-mode.css").toExternalForm();
+
+            System.out.println("Light Mode URL: " + lightModeUrl);
+            System.out.println("Dark Mode URL: " + darkModeUrl);
+
+            if (scene.getStylesheets().contains(darkModeUrl)) {
+                scene.getStylesheets().remove(darkModeUrl);
+                scene.getStylesheets().add(lightModeUrl);
+            } else {
+                scene.getStylesheets().remove(lightModeUrl);
+                scene.getStylesheets().add(darkModeUrl);
+            }
+        } catch (Exception e) {
+            e.printStackTrace();
+            showAlert("Error", "Failed to toggle theme.");
+        }
+    }
+    private void showAlert(String title, String content) {
+        Alert alert = new Alert(Alert.AlertType.ERROR);
+        alert.setTitle(title);
+        alert.setHeaderText(null);
+        alert.setContentText(content);
+        alert.showAndWait();
+    }
 }
diff --git a/src/main/resources/css/dark-mode.css b/src/main/resources/css/dark-mode.css
new file mode 100644
index 00000000..1c79e39c
--- /dev/null
+++ b/src/main/resources/css/dark-mode.css
@@ -0,0 +1,44 @@
+.root {
+    -fx-background-color: #424242;
+    -fx-text-fill: white;
+}
+
+.button {
+    -fx-background-color: #333333;
+    -fx-text-fill: white;
+}
+
+.scroll-pane {
+    -fx-background: #424242;
+    -fx-border-color: #333333;
+}
+
+.border-pane {
+    -fx-background-color: #424242;
+}
+
+.vbox {
+    -fx-background-color: #424242;
+}
+.scroll-bar {
+    -fx-background-color: #333333;
+}
+
+.scroll-bar .thumb {
+    -fx-background-color: #555555;
+    -fx-background-insets: 2;
+    -fx-background-radius: 5;
+}
+
+.scroll-bar .track {
+    -fx-background-color: #444444;
+    -fx-background-insets: 2;
+    -fx-background-radius: 5;
+}
+
+.scroll-bar .increment-button,
+.scroll-bar .decrement-button {
+    -fx-background-color: #333333;
+    -fx-background-insets: 2;
+    -fx-background-radius: 5;
+}
diff --git a/src/main/resources/css/light-mode.css b/src/main/resources/css/light-mode.css
new file mode 100644
index 00000000..c6085861
--- /dev/null
+++ b/src/main/resources/css/light-mode.css
@@ -0,0 +1,9 @@
+.root {
+    -fx-background-color: white;
+    -fx-text-fill: black;
+}
+
+.button {
+    -fx-background-color: #E0E0E0;
+    -fx-text-fill: black;
+}
diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index 962b7d93..7881e85c 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -62,6 +62,11 @@
                         <Insets left="55.0" right="55.0" />
                      </HBox.margin>
                   </Button>
+                  <Button fx:id="toggleThemeButton" text="Dark/Light-Mode" onAction="#handleToggleTheme" HBox.hgrow="ALWAYS" maxWidth="170" style="-fx-font-size: 16px;">
+                     <HBox.margin>
+                        <Insets left="10.0" right="10.0" />
+                     </HBox.margin>
+                  </Button>
                </children>
             </HBox>
          </top>

From c2651f88511a84603f9836732da994a4153cf62e Mon Sep 17 00:00:00 2001
From: VincentStriegel <strivi01@thu.de>
Date: Sun, 21 Apr 2024 16:49:23 +0200
Subject: [PATCH 026/100] clear marks

---
 src/main/java/controller/AnnotationController.java | 10 ++++++++++
 src/main/java/util/AnnotationData.java             |  4 +++-
 src/main/resources/view/AnnotationView.fxml        |  2 +-
 3 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index a8160ff2..29e86c36 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -170,6 +170,16 @@ public void Select_Previous_Image(ActionEvent actionEvent) {
         }
     }
 
+    public void clearAnnotations(ActionEvent actionEvent) {
+      if(annotatedRectangle != null){
+        annotationPane.getChildren().remove(annotatedRectangle);
+        annotationPane.getChildren().remove(middlePoint);
+        AnnotationData.getInstance().deleteAnnotation(selectedImageView.getImage().getUrl());
+        middlePoint = null;
+        annotatedRectangle = null;
+      }
+    }
+
     private void checkForExistingAnnotationData() {
         // Get Rectangle and 'unnormalize' the values
         annotationPane.getChildren().remove(annotatedRectangle);
diff --git a/src/main/java/util/AnnotationData.java b/src/main/java/util/AnnotationData.java
index 99b6e564..aa8fe4c6 100644
--- a/src/main/java/util/AnnotationData.java
+++ b/src/main/java/util/AnnotationData.java
@@ -76,7 +76,9 @@ public Rectangle getAnnotation(String path){
      * @param path Image path (Key for the Map)
      */
     public void deleteAnnotation(String path){
-        //Todo
+        if(annotations.containsKey(path)){
+            annotations.remove(path);
+        }
     }
 
     public static AnnotationData getInstance() {
diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index e67d0158..52f7997a 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -57,7 +57,7 @@
                      </HBox.margin>
                   </Button>
                   <Button fx:id="exampleButton" text="Export" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;" />
-                  <Button fx:id="exampleButton" text="Clear Marks" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;">
+                  <Button fx:id="clearMarksButton" onAction="#clearAnnotations" text="Clear Marks" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;">
                      <HBox.margin>
                         <Insets left="55.0" right="55.0" />
                      </HBox.margin>

From 070311fd0d65abcce1ca6db0172f7f909b60d146 Mon Sep 17 00:00:00 2001
From: Muazzam Bin Aqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Sun, 21 Apr 2024 17:49:13 +0200
Subject: [PATCH 027/100] Fix

---
 logging.log.1                               | 312 ++++++++++++++++++++
 logging.log.1.lck                           |   0
 src/main/resources/view/AnnotationView.fxml |   2 -
 3 files changed, 312 insertions(+), 2 deletions(-)
 create mode 100644 logging.log.1
 create mode 100644 logging.log.1.lck

diff --git a/logging.log.1 b/logging.log.1
new file mode 100644
index 00000000..b730c881
--- /dev/null
+++ b/logging.log.1
@@ -0,0 +1,312 @@
+Apr 21, 2024 5:44:41 PM javafx.fxml.FXMLLoader$ValueElement processValue
+WARNING: Loading FXML document with JavaFX API of version 21 by JavaFX runtime of version 17
+Apr 21, 2024 5:44:41 PM mainMethod.App lambda$start$0
+SEVERE: Uncaught exception in thread main
+java.lang.RuntimeException: Exception in Application start method
+	at com.sun.javafx.application.LauncherImpl.launchApplication1(LauncherImpl.java:901)
+	at com.sun.javafx.application.LauncherImpl.lambda$launchApplication$2(LauncherImpl.java:196)
+	at java.base/java.lang.Thread.run(Thread.java:840)
+Caused by: javafx.fxml.LoadException: 
+/C:/programming/Global_Computing/IGTPrototypingTool/build/resources/main/view/AnnotationView.fxml:72
+/C:/programming/Global_Computing/IGTPrototypingTool/build/resources/main/view/MainView.fxml:48
+
+	at javafx.fxml.FXMLLoader.constructLoadException(FXMLLoader.java:2707)
+	at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2650)
+	at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2548)
+	at javafx.fxml.FXMLLoader$IncludeElement.constructValue(FXMLLoader.java:1153)
+	at javafx.fxml.FXMLLoader$ValueElement.processStartElement(FXMLLoader.java:757)
+	at javafx.fxml.FXMLLoader.processStartElement(FXMLLoader.java:2808)
+	at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2634)
+	at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2548)
+	at javafx.fxml.FXMLLoader.load(FXMLLoader.java:2516)
+	at mainMethod.App.start(App.java:36)
+	at com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$9(LauncherImpl.java:847)
+	at com.sun.javafx.application.PlatformImpl.lambda$runAndWait$12(PlatformImpl.java:484)
+	at com.sun.javafx.application.PlatformImpl.lambda$runLater$10(PlatformImpl.java:457)
+	at java.base/java.security.AccessController.doPrivileged(AccessController.java:399)
+	at com.sun.javafx.application.PlatformImpl.lambda$runLater$11(PlatformImpl.java:456)
+	at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:96)
+	at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
+	at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:184)
+	... 1 more
+Caused by: javax.xml.stream.XMLStreamException: ParseError at [row,col]:[72,18]
+Message: The element type "Button" must be terminated by the matching end-tag "</Button>".
+	at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652)
+	at java.xml/javax.xml.stream.util.StreamReaderDelegate.next(StreamReaderDelegate.java:84)
+	at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2620)
+	... 17 more
+
+Apr 21, 2024 5:45:38 PM javafx.fxml.FXMLLoader$ValueElement processValue
+WARNING: Loading FXML document with JavaFX API of version 21 by JavaFX runtime of version 17
+Apr 21, 2024 5:45:38 PM mainMethod.App lambda$start$0
+SEVERE: Uncaught exception in thread main
+java.lang.RuntimeException: Exception in Application start method
+	at com.sun.javafx.application.LauncherImpl.launchApplication1(LauncherImpl.java:901)
+	at com.sun.javafx.application.LauncherImpl.lambda$launchApplication$2(LauncherImpl.java:196)
+	at java.base/java.lang.Thread.run(Thread.java:840)
+Caused by: javafx.fxml.LoadException: 
+/C:/programming/Global_Computing/IGTPrototypingTool/build/resources/main/view/AnnotationView.fxml:72
+/C:/programming/Global_Computing/IGTPrototypingTool/build/resources/main/view/MainView.fxml:48
+
+	at javafx.fxml.FXMLLoader.constructLoadException(FXMLLoader.java:2707)
+	at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2650)
+	at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2548)
+	at javafx.fxml.FXMLLoader$IncludeElement.constructValue(FXMLLoader.java:1153)
+	at javafx.fxml.FXMLLoader$ValueElement.processStartElement(FXMLLoader.java:757)
+	at javafx.fxml.FXMLLoader.processStartElement(FXMLLoader.java:2808)
+	at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2634)
+	at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2548)
+	at javafx.fxml.FXMLLoader.load(FXMLLoader.java:2516)
+	at mainMethod.App.start(App.java:36)
+	at com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$9(LauncherImpl.java:847)
+	at com.sun.javafx.application.PlatformImpl.lambda$runAndWait$12(PlatformImpl.java:484)
+	at com.sun.javafx.application.PlatformImpl.lambda$runLater$10(PlatformImpl.java:457)
+	at java.base/java.security.AccessController.doPrivileged(AccessController.java:399)
+	at com.sun.javafx.application.PlatformImpl.lambda$runLater$11(PlatformImpl.java:456)
+	at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:96)
+	at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
+	at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:184)
+	... 1 more
+Caused by: javax.xml.stream.XMLStreamException: ParseError at [row,col]:[72,18]
+Message: The element type "Button" must be terminated by the matching end-tag "</Button>".
+	at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652)
+	at java.xml/javax.xml.stream.util.StreamReaderDelegate.next(StreamReaderDelegate.java:84)
+	at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2620)
+	... 17 more
+
+Apr 21, 2024 5:45:51 PM javafx.fxml.FXMLLoader$ValueElement processValue
+WARNING: Loading FXML document with JavaFX API of version 21 by JavaFX runtime of version 17
+Apr 21, 2024 5:45:52 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:45:52 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from null to TabPane[id=tabPane, styleClass=tab-pane]
+Apr 21, 2024 5:46:05 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:46:05 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: true] focused=true
+Apr 21, 2024 5:46:05 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from TabPane[id=tabPane, styleClass=tab-pane] to Button[id=uploadImagesButton, styleClass=button]'Import'
+Apr 21, 2024 5:46:06 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: false] focused=false
+Apr 21, 2024 5:46:14 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: true] focused=true
+Apr 21, 2024 5:46:15 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: false] focused=false
+Apr 21, 2024 5:46:15 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane@46509f49[styleClass=scroll-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:46:15 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from Button[id=uploadImagesButton, styleClass=button]'Import' to ScrollPane@46509f49[styleClass=scroll-pane]
+Apr 21, 2024 5:46:16 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane@46509f49[styleClass=scroll-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:46:16 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=demo, styleClass=button]'Export', name: focused, value: true] focused=true
+Apr 21, 2024 5:46:16 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from ScrollPane@46509f49[styleClass=scroll-pane] to Button[id=demo, styleClass=button]'Export'
+Apr 21, 2024 5:46:17 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=demo, styleClass=button]'Export', name: focused, value: false] focused=false
+Apr 21, 2024 5:46:17 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
+Apr 21, 2024 5:46:17 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from Button[id=demo, styleClass=button]'Export' to Button[id=ExportButton, styleClass=button]'Export'
+Apr 21, 2024 5:46:17 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
+Apr 21, 2024 5:46:17 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button@26683389[styleClass=button]'OK', name: focused, value: true] focused=true
+Apr 21, 2024 5:46:17 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from null to Button@26683389[styleClass=button]'OK'
+Apr 21, 2024 5:46:18 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button@26683389[styleClass=button]'OK', name: focused, value: false] focused=false
+Apr 21, 2024 5:46:18 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
+Apr 21, 2024 5:46:19 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
+Apr 21, 2024 5:46:19 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:46:19 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from Button[id=ExportButton, styleClass=button]'Export' to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
+Apr 21, 2024 5:46:21 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:46:21 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: true] focused=true
+Apr 21, 2024 5:46:21 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to Button[id=clearMarksButton, styleClass=button]'Clear Marks'
+Apr 21, 2024 5:46:22 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: false] focused=false
+Apr 21, 2024 5:46:22 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:46:22 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from Button[id=clearMarksButton, styleClass=button]'Clear Marks' to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
+Apr 21, 2024 5:46:23 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:46:23 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=demo, styleClass=button]'Export', name: focused, value: true] focused=true
+Apr 21, 2024 5:46:23 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to Button[id=demo, styleClass=button]'Export'
+Apr 21, 2024 5:46:24 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=demo, styleClass=button]'Export', name: focused, value: false] focused=false
+Apr 21, 2024 5:46:38 PM javafx.fxml.FXMLLoader$ValueElement processValue
+WARNING: Loading FXML document with JavaFX API of version 21 by JavaFX runtime of version 17
+Apr 21, 2024 5:46:39 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:46:39 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from null to TabPane[id=tabPane, styleClass=tab-pane]
+Apr 21, 2024 5:46:42 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:46:42 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: true] focused=true
+Apr 21, 2024 5:46:42 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from TabPane[id=tabPane, styleClass=tab-pane] to Button[id=uploadImagesButton, styleClass=button]'Import'
+Apr 21, 2024 5:46:42 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: false] focused=false
+Apr 21, 2024 5:46:46 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: true] focused=true
+Apr 21, 2024 5:46:48 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: false] focused=false
+Apr 21, 2024 5:46:48 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane@7863b5f5[styleClass=scroll-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:46:48 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from Button[id=uploadImagesButton, styleClass=button]'Import' to ScrollPane@7863b5f5[styleClass=scroll-pane]
+Apr 21, 2024 5:46:48 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane@7863b5f5[styleClass=scroll-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:46:48 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:46:48 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from ScrollPane@7863b5f5[styleClass=scroll-pane] to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
+Apr 21, 2024 5:46:49 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:46:49 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=annotation, styleClass=scroll-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:46:49 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to ScrollPane[id=annotation, styleClass=scroll-pane]
+Apr 21, 2024 5:46:50 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=annotation, styleClass=scroll-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:46:50 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=exampleButton, styleClass=button]'Clear Marks', name: focused, value: true] focused=true
+Apr 21, 2024 5:46:50 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from ScrollPane[id=annotation, styleClass=scroll-pane] to Button[id=exampleButton, styleClass=button]'Clear Marks'
+Apr 21, 2024 5:46:53 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=exampleButton, styleClass=button]'Clear Marks', name: focused, value: false] focused=false
+Apr 21, 2024 5:46:53 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:46:53 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from Button[id=exampleButton, styleClass=button]'Clear Marks' to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
+Apr 21, 2024 5:46:54 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:46:54 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: true] focused=true
+Apr 21, 2024 5:46:54 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to Button[id=clearMarksButton, styleClass=button]'Clear Marks'
+Apr 21, 2024 5:46:54 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: false] focused=false
+Apr 21, 2024 5:46:54 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:46:54 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from Button[id=clearMarksButton, styleClass=button]'Clear Marks' to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
+Apr 21, 2024 5:46:56 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:46:56 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: true] focused=true
+Apr 21, 2024 5:46:56 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to Button[id=clearMarksButton, styleClass=button]'Clear Marks'
+Apr 21, 2024 5:46:57 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: false] focused=false
+Apr 21, 2024 5:46:57 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:46:57 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from Button[id=clearMarksButton, styleClass=button]'Clear Marks' to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
+Apr 21, 2024 5:46:58 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:46:58 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=annotation, styleClass=scroll-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:46:58 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to ScrollPane[id=annotation, styleClass=scroll-pane]
+Apr 21, 2024 5:46:58 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=annotation, styleClass=scroll-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:46:58 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
+Apr 21, 2024 5:46:58 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from ScrollPane[id=annotation, styleClass=scroll-pane] to Button[id=ExportButton, styleClass=button]'Export'
+Apr 21, 2024 5:46:59 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
+Apr 21, 2024 5:47:00 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
+Apr 21, 2024 5:47:00 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
+Apr 21, 2024 5:47:00 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=annotation, styleClass=scroll-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:47:00 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from Button[id=ExportButton, styleClass=button]'Export' to ScrollPane[id=annotation, styleClass=scroll-pane]
+Apr 21, 2024 5:47:01 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=annotation, styleClass=scroll-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:47:28 PM javafx.fxml.FXMLLoader$ValueElement processValue
+WARNING: Loading FXML document with JavaFX API of version 21 by JavaFX runtime of version 17
+Apr 21, 2024 5:47:29 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:47:29 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from null to TabPane[id=tabPane, styleClass=tab-pane]
+Apr 21, 2024 5:47:32 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:47:32 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
+Apr 21, 2024 5:47:32 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from TabPane[id=tabPane, styleClass=tab-pane] to Button[id=ExportButton, styleClass=button]'Export'
+Apr 21, 2024 5:47:32 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
+Apr 21, 2024 5:47:32 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button@141f0d8[styleClass=button]'OK', name: focused, value: true] focused=true
+Apr 21, 2024 5:47:32 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from null to Button@141f0d8[styleClass=button]'OK'
+Apr 21, 2024 5:47:33 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button@141f0d8[styleClass=button]'OK', name: focused, value: false] focused=false
+Apr 21, 2024 5:47:33 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
+Apr 21, 2024 5:47:33 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
+Apr 21, 2024 5:47:33 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: true] focused=true
+Apr 21, 2024 5:47:33 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from Button[id=ExportButton, styleClass=button]'Export' to Button[id=uploadImagesButton, styleClass=button]'Import'
+Apr 21, 2024 5:47:33 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: false] focused=false
+Apr 21, 2024 5:47:38 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: true] focused=true
+Apr 21, 2024 5:47:39 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: false] focused=false
+Apr 21, 2024 5:47:39 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane@dfd3d2d[styleClass=scroll-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:47:39 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from Button[id=uploadImagesButton, styleClass=button]'Import' to ScrollPane@dfd3d2d[styleClass=scroll-pane]
+Apr 21, 2024 5:47:39 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane@dfd3d2d[styleClass=scroll-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:47:39 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:47:39 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from ScrollPane@dfd3d2d[styleClass=scroll-pane] to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
+Apr 21, 2024 5:47:40 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:47:40 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: true] focused=true
+Apr 21, 2024 5:47:40 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to Button[id=clearMarksButton, styleClass=button]'Clear Marks'
+Apr 21, 2024 5:47:41 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: false] focused=false
+Apr 21, 2024 5:47:41 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:47:41 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from Button[id=clearMarksButton, styleClass=button]'Clear Marks' to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
+Apr 21, 2024 5:47:42 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:47:42 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
+Apr 21, 2024 5:47:42 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to Button[id=ExportButton, styleClass=button]'Export'
+Apr 21, 2024 5:47:42 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
+Apr 21, 2024 5:47:49 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
+Apr 21, 2024 5:47:50 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
+Apr 21, 2024 5:47:50 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
+Apr 21, 2024 5:47:51 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
diff --git a/logging.log.1.lck b/logging.log.1.lck
new file mode 100644
index 00000000..e69de29b
diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index 4b299618..c19f3177 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -57,8 +57,6 @@
                      </HBox.margin>
                   </Button>
                   <Button fx:id="ExportButton" text="Export" prefWidth="120.0" prefHeight="40.0" onAction="#handleExportAction" style="-fx-font-size: 16px;" />
-                  <Button fx:id="exampleButton" text="Clear Marks" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;">
-                  <Button fx:id="exampleButton" text="Export" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;" />
                   <Button fx:id="clearMarksButton" onAction="#clearAnnotations" text="Clear Marks" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;">
                      <HBox.margin>
                         <Insets left="55.0" right="55.0" />

From 842f4264821e8bc34663ad1d388584030bdf419f Mon Sep 17 00:00:00 2001
From: Muazzam Bin Aqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Sun, 21 Apr 2024 22:03:54 +0200
Subject: [PATCH 028/100] Fix

---
 logging.log.1                                 | 116 ++++++++++++++++++
 logging.log.1.lck                             |   0
 .../java/controller/AnnotationController.java |  31 +++--
 src/main/resources/view/AnnotationView.fxml   |   4 +-
 4 files changed, 139 insertions(+), 12 deletions(-)
 delete mode 100644 logging.log.1.lck

diff --git a/logging.log.1 b/logging.log.1
index b730c881..38cab22a 100644
--- a/logging.log.1
+++ b/logging.log.1
@@ -310,3 +310,119 @@ Apr 21, 2024 5:47:50 PM javafx.scene.Node$FocusedProperty markInvalid
 FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
 Apr 21, 2024 5:47:51 PM javafx.scene.Node$FocusedProperty markInvalid
 FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
+Apr 21, 2024 5:49:26 PM javafx.fxml.FXMLLoader$ValueElement processValue
+WARNING: Loading FXML document with JavaFX API of version 21 by JavaFX runtime of version 17
+Apr 21, 2024 5:49:27 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:49:27 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from null to TabPane[id=tabPane, styleClass=tab-pane]
+Apr 21, 2024 5:49:32 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:49:32 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode', name: focused, value: true] focused=true
+Apr 21, 2024 5:49:32 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from TabPane[id=tabPane, styleClass=tab-pane] to Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode'
+Apr 21, 2024 5:49:35 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode', name: focused, value: false] focused=false
+Apr 21, 2024 5:49:53 PM javafx.fxml.FXMLLoader$ValueElement processValue
+WARNING: Loading FXML document with JavaFX API of version 21 by JavaFX runtime of version 17
+Apr 21, 2024 5:49:54 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:49:54 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from null to TabPane[id=tabPane, styleClass=tab-pane]
+Apr 21, 2024 5:49:56 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:49:56 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode', name: focused, value: true] focused=true
+Apr 21, 2024 5:49:56 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from TabPane[id=tabPane, styleClass=tab-pane] to Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode'
+Apr 21, 2024 5:49:58 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode', name: focused, value: false] focused=false
+Apr 21, 2024 5:49:58 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: true] focused=true
+Apr 21, 2024 5:49:58 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode' to Button[id=uploadImagesButton, styleClass=button]'Import'
+Apr 21, 2024 5:49:58 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: false] focused=false
+Apr 21, 2024 5:49:59 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: true] focused=true
+Apr 21, 2024 5:50:00 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: false] focused=false
+Apr 21, 2024 5:50:00 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode', name: focused, value: true] focused=true
+Apr 21, 2024 5:50:00 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from Button[id=uploadImagesButton, styleClass=button]'Import' to Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode'
+Apr 21, 2024 5:50:01 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode', name: focused, value: false] focused=false
+Apr 21, 2024 5:50:01 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: true] focused=true
+Apr 21, 2024 5:50:01 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode' to Button[id=uploadImagesButton, styleClass=button]'Import'
+Apr 21, 2024 5:50:01 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: false] focused=false
+Apr 21, 2024 5:50:07 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: true] focused=true
+Apr 21, 2024 5:50:08 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: false] focused=false
+Apr 21, 2024 5:50:08 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane@103c0396[styleClass=scroll-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:50:08 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from Button[id=uploadImagesButton, styleClass=button]'Import' to ScrollPane@103c0396[styleClass=scroll-pane]
+Apr 21, 2024 5:50:09 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane@103c0396[styleClass=scroll-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:50:09 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:50:09 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from ScrollPane@103c0396[styleClass=scroll-pane] to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
+Apr 21, 2024 5:50:09 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:50:09 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: true] focused=true
+Apr 21, 2024 5:50:09 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to Button[id=clearMarksButton, styleClass=button]'Clear Marks'
+Apr 21, 2024 5:50:10 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: false] focused=false
+Apr 21, 2024 5:50:10 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:50:10 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from Button[id=clearMarksButton, styleClass=button]'Clear Marks' to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
+Apr 21, 2024 5:50:11 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:50:11 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: true] focused=true
+Apr 21, 2024 5:50:11 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to Button[id=clearMarksButton, styleClass=button]'Clear Marks'
+Apr 21, 2024 5:50:11 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: false] focused=false
+Apr 21, 2024 5:50:11 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
+Apr 21, 2024 5:50:11 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from Button[id=clearMarksButton, styleClass=button]'Clear Marks' to Button[id=ExportButton, styleClass=button]'Export'
+Apr 21, 2024 5:50:11 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
+Apr 21, 2024 5:50:11 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button@1d2f0cc5[styleClass=button]'OK', name: focused, value: true] focused=true
+Apr 21, 2024 5:50:11 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from null to Button@1d2f0cc5[styleClass=button]'OK'
+Apr 21, 2024 5:50:12 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button@1d2f0cc5[styleClass=button]'OK', name: focused, value: false] focused=false
+Apr 21, 2024 5:50:12 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
+Apr 21, 2024 5:50:13 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
+Apr 21, 2024 5:50:13 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
+Apr 21, 2024 5:50:13 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from Button[id=ExportButton, styleClass=button]'Export' to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
+Apr 21, 2024 5:50:14 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
+Apr 21, 2024 5:50:14 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
+Apr 21, 2024 5:50:14 PM javafx.scene.Scene$12 invalidated
+FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to Button[id=ExportButton, styleClass=button]'Export'
+Apr 21, 2024 5:50:14 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
+Apr 21, 2024 5:50:15 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
+Apr 21, 2024 5:50:18 PM javafx.scene.Node$FocusedProperty markInvalid
+FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
diff --git a/logging.log.1.lck b/logging.log.1.lck
deleted file mode 100644
index e69de29b..00000000
diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index e8f1f474..ef03387e 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -25,8 +25,10 @@
 import java.io.PrintWriter;
 import java.lang.annotation.Annotation;
 import java.net.URL;
+import java.util.HashSet;
 import java.util.List;
 import java.util.ResourceBundle;
+import java.util.Set;
 
 public class AnnotationController implements Controller {
     @FXML
@@ -47,6 +49,8 @@ public class AnnotationController implements Controller {
     private double annotationPointX, annotationPointY;
 
     private List<File> selectedImages;
+    private Set<String> uploadedFilePaths = new HashSet<>();
+
 
     @Override
     public void initialize(URL location, ResourceBundle resources) {
@@ -66,7 +70,7 @@ public void Handle_Upload_Functionality(ActionEvent actionEvent) {
             fileChooser.setTitle("Select Images");
             fileChooser.setInitialDirectory(new File(System.getProperty("user.home")));
             fileChooser.getExtensionFilters().add(
-                    new FileChooser.ExtensionFilter("Image Files", "*.jpg", "*.png", "*.gif", "*.bmp")
+                    new FileChooser.ExtensionFilter("Image Files", "*.jpg", "*.png")
             );
             Stage currentStage = (Stage) ((javafx.scene.Node) actionEvent.getSource()).getScene().getWindow();
 
@@ -74,7 +78,13 @@ public void Handle_Upload_Functionality(ActionEvent actionEvent) {
 
             if (selectedImages != null) {
                 for (File file : selectedImages) {
-                    displayImage(file);
+                    if (!uploadedFilePaths.contains(file.getAbsolutePath())) {
+                        displayImage(file);
+                        uploadedFilePaths.add(file.getAbsolutePath());
+                    } else {
+                        // Optionally, alert the user that the file has already been uploaded
+                        showAlert("Duplicate File", "The file " + file.getName() + " has already been uploaded.");
+                    }
                 }
             }
         } catch (Exception e) {
@@ -177,13 +187,13 @@ public void Select_Previous_Image(ActionEvent actionEvent) {
     }
 
     public void clearAnnotations(ActionEvent actionEvent) {
-      if(annotatedRectangle != null){
-        annotationPane.getChildren().remove(annotatedRectangle);
-        annotationPane.getChildren().remove(middlePoint);
-        AnnotationData.getInstance().deleteAnnotation(selectedImageView.getImage().getUrl());
-        middlePoint = null;
-        annotatedRectangle = null;
-      }
+        if(annotatedRectangle != null){
+            annotationPane.getChildren().remove(annotatedRectangle);
+            annotationPane.getChildren().remove(middlePoint);
+            AnnotationData.getInstance().deleteAnnotation(selectedImageView.getImage().getUrl());
+            middlePoint = null;
+            annotatedRectangle = null;
+        }
     }
 
     private void checkForExistingAnnotationData() {
@@ -348,10 +358,11 @@ private void handleToggleTheme(ActionEvent event) {
         }
     }
     private void showAlert(String title, String content) {
-        Alert alert = new Alert(Alert.AlertType.ERROR);
+        Alert alert = new Alert(Alert.AlertType.INFORMATION);
         alert.setTitle(title);
         alert.setHeaderText(null);
         alert.setContentText(content);
         alert.showAndWait();
     }
+
 }
diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index c19f3177..36146712 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -17,7 +17,7 @@
    <content>
       <BorderPane>
          <bottom>
-            <HBox alignment="CENTER" prefHeight="80.0" prefWidth="368.0" style="-fx-border-color: grey;" BorderPane.alignment="CENTER">
+            <HBox alignment="CENTER" prefHeight="80.0" prefWidth="368.0" BorderPane.alignment="CENTER">
                <BorderPane.margin>
                   <Insets bottom="10.0" left="10.0" right="10.0" top="10.0" />
                </BorderPane.margin>
@@ -46,7 +46,7 @@
             </HBox>
          </bottom>
          <top>
-            <HBox alignment="CENTER" prefHeight="80.0" prefWidth="368.0" style="-fx-border-color: grey;" BorderPane.alignment="CENTER">
+            <HBox alignment="CENTER" prefHeight="80.0" prefWidth="368.0" BorderPane.alignment="CENTER">
                <BorderPane.margin>
                   <Insets bottom="10.0" left="10.0" right="10.0" top="10.0" />
                </BorderPane.margin>

From 7636c8b18ddf1411bec81706dc69c85d4b6ac7f6 Mon Sep 17 00:00:00 2001
From: Muazzam Bin Aqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Sun, 21 Apr 2024 22:26:32 +0200
Subject: [PATCH 029/100] Update AnnotationController.java

---
 .../java/controller/AnnotationController.java    | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index ef03387e..5d37d14c 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -32,7 +32,7 @@
 
 public class AnnotationController implements Controller {
     @FXML
-    public VBox uploadedImages;
+    public VBox uploadedImages;     //Where the users see the files
     @FXML
     public Button uploadImagesButton;
     @FXML
@@ -293,6 +293,18 @@ private void handleExportAction(ActionEvent event) {
         if (selectedImageView != null && annotatedRectangle != null) {
             FileChooser fileChooser = new FileChooser();
             fileChooser.setTitle("Save Annotations");
+
+            try {
+                String currentImageUrl = selectedImageView.getImage().getUrl();
+                String currentImageName = new File(new URL(currentImageUrl).toURI().getPath()).getName();
+                String initialFileName = currentImageName.substring(0, currentImageName.lastIndexOf('.')) + "_annotations.txt";
+                fileChooser.setInitialFileName(initialFileName);
+            } catch (Exception e) {
+                fileChooser.setInitialFileName("default_annotations.txt");
+                showAlert("Error", "There was an issue processing the image file name.");
+                e.printStackTrace();
+            }
+
             fileChooser.getExtensionFilters().addAll(new FileChooser.ExtensionFilter("Text Files", "*.txt"));
             File file = fileChooser.showSaveDialog(((Node) event.getSource()).getScene().getWindow());
 
@@ -304,6 +316,8 @@ private void handleExportAction(ActionEvent event) {
         }
     }
 
+
+
     private void saveAnnotationsToFile(File file) {
         try (PrintWriter writer = new PrintWriter(file)) {
             double imageWidth = selectedImageView.getImage().getWidth();

From ee73de816cc94adbd8ff48611d40a18e5c478483 Mon Sep 17 00:00:00 2001
From: Eugen Zdrincu <eugenzdrincu@gmail.com>
Date: Tue, 23 Apr 2024 16:56:26 +0200
Subject: [PATCH 030/100] fixed detect reference point

---
 aitoigt/detect.py                             | 136 +++++++++---------
 .../java/controller/AutoTrackController.java  |   2 +-
 2 files changed, 69 insertions(+), 69 deletions(-)

diff --git a/aitoigt/detect.py b/aitoigt/detect.py
index 771dbbb7..a00e1adc 100644
--- a/aitoigt/detect.py
+++ b/aitoigt/detect.py
@@ -1,7 +1,7 @@
 # YOLOv5 🚀 by Ultralytics, AGPL-3.0 license
 """
 Run YOLOv5 detection inference on images, videos, directories, globs, YouTube, webcam, streams, etc.
- 
+
 Usage - sources:
     $ python detect.py --weights yolov5s.pt --source 0                               # webcam
                                                      img.jpg                         # image
@@ -13,7 +13,7 @@
                                                      'path/*.jpg'                    # glob
                                                      'https://youtu.be/LNwODJXcvt4'  # YouTube
                                                      'rtsp://example.com/media.mp4'  # RTSP, RTMP, HTTP stream
- 
+
 Usage - formats:
     $ python detect.py --weights yolov5s.pt                 # PyTorch
                                  yolov5s.torchscript        # TorchScript
@@ -27,7 +27,7 @@
                                  yolov5s_edgetpu.tflite     # TensorFlow Edge TPU
                                  yolov5s_paddle_model       # PaddlePaddle
 """
- 
+
 import argparse
 import csv
 import numpy as np
@@ -41,15 +41,15 @@
 CAM = pyvirtualcam.Camera(width=640, height=480, fps=20)
 
 import torch
- 
+
 FILE = Path(__file__).resolve()
 ROOT = FILE.parents[0]  # YOLOv5 root directory
 if str(ROOT) not in sys.path:
     sys.path.append(str(ROOT))  # add ROOT to PATH
 ROOT = Path(os.path.relpath(ROOT, Path.cwd()))  # relative
- 
+
 from ultralytics.utils.plotting import Annotator, colors, save_one_box
- 
+
 from models.common import DetectMultiBackend
 from utils.dataloaders import IMG_FORMATS, VID_FORMATS, LoadImages, LoadScreenshots, LoadStreams
 from utils.general import (
@@ -69,49 +69,49 @@
     xyxy2xywh,
 )
 from utils.torch_utils import select_device, smart_inference_mode
- 
- 
+
+
 @smart_inference_mode()
 def run(
-    weights=ROOT / "yolov5s.pt",  # model path or triton URL
-    source=ROOT / "data/images",  # file/dir/URL/glob/screen/0(webcam)
-    data=ROOT / "data/coco128.yaml",  # dataset.yaml path
-    imgsz=(640, 640),  # inference size (height, width)
-    conf_thres=0.25,  # confidence threshold
-    iou_thres=0.45,  # NMS IOU threshold
-    max_det=1000,  # maximum detections per image
-    device="",  # cuda device, i.e. 0 or 0,1,2,3 or cpu
-    view_img=False,  # show results
-    open_igt=False, # stream data thru igtlink
-    save_txt=True,  # save results to *.txt
-    save_csv=False,  # save results in CSV format
-    save_conf=False,  # save confidences in --save-txt labels
-    save_crop=False,  # save cropped prediction boxes
-    nosave=False,  # do not save images/videos
-    classes=None,  # filter by class: --class 0, or --class 0 2 3
-    agnostic_nms=False,  # class-agnostic NMS
-    augment=False,  # augmented inference
-    visualize=False,  # visualize features
-    update=False,  # update all models
-    project=ROOT / "runs/detect",  # save results to project/name
-    name="exp",  # save results to project/name
-    exist_ok=False,  # existing project/name ok, do not increment
-    line_thickness=3,  # bounding box thickness (pixels)
-    hide_labels=False,  # hide labels
-    hide_conf=False,  # hide confidences
-    half=False,  # use FP16 half-precision inference
-    dnn=False,  # use OpenCV DNN for ONNX inference
-    vid_stride=1,  # video frame-rate stride
+        weights=ROOT / "yolov5s.pt",  # model path or triton URL
+        source=ROOT / "data/images",  # file/dir/URL/glob/screen/0(webcam)
+        data=ROOT / "data/coco128.yaml",  # dataset.yaml path
+        imgsz=(640, 640),  # inference size (height, width)
+        conf_thres=0.25,  # confidence threshold
+        iou_thres=0.45,  # NMS IOU threshold
+        max_det=1000,  # maximum detections per image
+        device="",  # cuda device, i.e. 0 or 0,1,2,3 or cpu
+        view_img=False,  # show results
+        open_igt=False, # stream data thru igtlink
+        save_txt=True,  # save results to *.txt
+        save_csv=False,  # save results in CSV format
+        save_conf=False,  # save confidences in --save-txt labels
+        save_crop=False,  # save cropped prediction boxes
+        nosave=False,  # do not save images/videos
+        classes=None,  # filter by class: --class 0, or --class 0 2 3
+        agnostic_nms=False,  # class-agnostic NMS
+        augment=False,  # augmented inference
+        visualize=False,  # visualize features
+        update=False,  # update all models
+        project=ROOT / "runs/detect",  # save results to project/name
+        name="exp",  # save results to project/name
+        exist_ok=False,  # existing project/name ok, do not increment
+        line_thickness=3,  # bounding box thickness (pixels)
+        hide_labels=False,  # hide labels
+        hide_conf=False,  # hide confidences
+        half=False,  # use FP16 half-precision inference
+        dnn=False,  # use OpenCV DNN for ONNX inference
+        vid_stride=1,  # video frame-rate stride
 ):
 
     if (open_igt):
         # Create an OpenIGTLink object
         server = igtl.OpenIGTLinkServer(port=18944)
-    
+
         # Check if the server is running
         if not server.is_connected():
             print("Server started. Waiting for connections...")
- 
+
     source = str(source)
     save_img = not nosave and not source.endswith(".txt")  # save inference images
     is_file = Path(source).suffix[1:] in (IMG_FORMATS + VID_FORMATS)
@@ -120,17 +120,17 @@ def run(
     screenshot = source.lower().startswith("screen")
     if is_url and is_file:
         source = check_file(source)  # download
- 
+
     # Directories
     save_dir = increment_path(Path(project) / name, exist_ok=exist_ok)  # increment run
     (save_dir / "labels" if save_txt else save_dir).mkdir(parents=True, exist_ok=True)  # make dir
- 
+
     # Load model
     device = select_device(device)
     model = DetectMultiBackend(weights, device=device, dnn=dnn, data=data, fp16=half)
     stride, names, pt = model.stride, model.names, model.pt
     imgsz = check_img_size(imgsz, s=stride)  # check image size
- 
+
     # Dataloader
     bs = 1  # batch_size
     if webcam:
@@ -142,7 +142,7 @@ def run(
     else:
         dataset = LoadImages(source, img_size=imgsz, stride=stride, auto=pt, vid_stride=vid_stride)
     vid_path, vid_writer = [None] * bs, [None] * bs
- 
+
     # Run inference
     model.warmup(imgsz=(1 if pt or model.triton else bs, 3, *imgsz))  # warmup
     seen, windows, dt = 0, [], (Profile(device=device), Profile(device=device), Profile(device=device))
@@ -155,7 +155,7 @@ def run(
                 im = im[None]  # expand for batch dim
             if model.xml and im.shape[0] > 1:
                 ims = torch.chunk(im, im.shape[0], 0)
- 
+
         # Inference
         with dt[1]:
             visualize = increment_path(save_dir / Path(path).stem, mkdir=True) if visualize else False
@@ -172,13 +172,13 @@ def run(
         # NMS
         with dt[2]:
             pred = non_max_suppression(pred, conf_thres, iou_thres, classes, agnostic_nms, max_det=max_det)
- 
+
         # Second-stage classifier (optional)
         # pred = utils.general.apply_classifier(pred, classifier_model, im, im0s)
- 
+
         # Define the path for the CSV file
         csv_path = save_dir / "predictions.csv"
- 
+
         # Create or append to the CSV file
         def write_to_csv(image_name, prediction, confidence):
             """Writes prediction data for an image to a CSV file, appending if the file exists."""
@@ -188,7 +188,7 @@ def write_to_csv(image_name, prediction, confidence):
                 if not csv_path.is_file():
                     writer.writeheader()
                 writer.writerow(data)
- 
+
         # Process predictions
         for i, det in enumerate(pred):  # per image
             seen += 1
@@ -197,7 +197,7 @@ def write_to_csv(image_name, prediction, confidence):
                 s += f"{i}: "
             else:
                 p, im0, frame = path, im0s.copy(), getattr(dataset, "frame", 0)
- 
+
             p = Path(p)  # to Path
             save_path = str(save_dir / p.name)  # im.jpg
             txt_path = str(save_dir / "labels" / p.stem) + ("" if dataset.mode == "image" else f"_{frame}")  # im.txt
@@ -208,45 +208,45 @@ def write_to_csv(image_name, prediction, confidence):
             if len(det):
                 # Rescale boxes from img_size to im0 size
                 det[:, :4] = scale_boxes(im.shape[2:], det[:, :4], im0.shape).round()
- 
+
                 # Print results
                 for c in det[:, 5].unique():
                     n = (det[:, 5] == c).sum()  # detections per class
                     s += f"{n} {names[int(c)]}{'s' * (n > 1)}, "  # add to string
- 
+
                 # Write results
                 for *xyxy, conf, cls in reversed(det):
                     c = int(cls)  # integer class
                     label = names[c] if hide_conf else f"{names[c]}"
                     confidence = float(conf)
                     confidence_str = f"{confidence:.2f}"
- 
+
                     if save_csv:
                         write_to_csv(p.name, label, confidence_str)
- 
+
                     if save_txt:  # Write to file
                         xywh = (xyxy2xywh(torch.tensor(xyxy).view(1, 4)) / gn).view(-1).tolist()  # normalized xywh
                         line = (cls, *xywh, conf) if save_conf else (cls, *xywh)  # label format
                         with open(f"{txt_path}.txt", "a") as f:
                             f.write(("%g " * len(line)).rstrip() % line + "\n")
- 
+
                     if save_img or save_crop or view_img:  # Add bbox to image
                         c = int(cls)  # integer class
                         label = None if hide_labels else (names[c] if hide_conf else f"{names[c]} {conf:.2f}")
                         annotator.box_label(xyxy, label, color=colors(c, True))
                     if save_crop:
                         save_one_box(xyxy, imc, file=save_dir / "crops" / names[c] / f"{p.stem}.jpg", BGR=True)
- 
+
                 if open_igt:
                     matrix = np.eye(4)
-    
+
                     matrix[0, 3] = xyxy[0]
-                    matrix[1, 3] = xyxy[1]
-    
+                    matrix[1, 3] = xyxy[1] * -1 + 500
+
                     transform_message = igtl.TransformMessage(matrix, device_name="ImageToReference", timestamp=1)
-    
+
                     server.send_message(transform_message)
- 
+
             # Stream results
             im0 = annotator.result()
             if view_img:
@@ -260,7 +260,7 @@ def write_to_csv(image_name, prediction, confidence):
                 im0VIRT = cv2.cvtColor(im0, cv2.COLOR_BGR2RGB)
                 CAM.send(im0VIRT)
                 cv2.waitKey(1)  # 1 millisecond
- 
+
             # Save results (image with detections)
             if save_img:
                 if dataset.mode == "image":
@@ -279,10 +279,10 @@ def write_to_csv(image_name, prediction, confidence):
                         save_path = str(Path(save_path).with_suffix(".mp4"))  # force *.mp4 suffix on results videos
                         vid_writer[i] = cv2.VideoWriter(save_path, cv2.VideoWriter_fourcc(*"mp4v"), fps, (w, h))
                     vid_writer[i].write(im0)
- 
+
         # Print time (inference-only)
         LOGGER.info(f"{s}{'' if len(det) else '(no detections), '}{dt[1].dt * 1E3:.1f}ms")
- 
+
     # Print results
     t = tuple(x.t / seen * 1e3 for x in dt)  # speeds per image
     LOGGER.info(f"Speed: %.1fms pre-process, %.1fms inference, %.1fms NMS per image at shape {(1, 3, *imgsz)}" % t)
@@ -291,8 +291,8 @@ def write_to_csv(image_name, prediction, confidence):
         LOGGER.info(f"Results saved to {colorstr('bold', save_dir)}{s}")
     if update:
         strip_optimizer(weights[0])  # update model (to fix SourceChangeWarning)
- 
- 
+
+
 def parse_opt():
     """Parses command-line arguments for YOLOv5 detection, setting inference options and model configurations."""
     parser = argparse.ArgumentParser()
@@ -329,13 +329,13 @@ def parse_opt():
     opt.imgsz *= 2 if len(opt.imgsz) == 1 else 1  # expand
     print_args(vars(opt))
     return opt
- 
+
 def main(opt):
     """Executes YOLOv5 model inference with given options, checking requirements before running the model."""
     check_requirements(ROOT / "requirements.txt", exclude=("tensorboard", "thop"))
     run(**vars(opt))
- 
- 
+
+
 if __name__ == "__main__":
     opt = parse_opt()
     main(opt)
\ No newline at end of file
diff --git a/src/main/java/controller/AutoTrackController.java b/src/main/java/controller/AutoTrackController.java
index 31f434fd..230cfa97 100644
--- a/src/main/java/controller/AutoTrackController.java
+++ b/src/main/java/controller/AutoTrackController.java
@@ -249,7 +249,7 @@ private void changeVideoView() {
             var selectedItem = sourceChoiceBox.getSelectionModel().getSelectedItem();
             int deviceId = deviceIdMapping.get(selectedItem);
             imageDataManager.closeConnection();
-            imageDataManager.openConnection(VideoSource.LIVESTREAM, deviceId);
+            imageDataManager.openConnection(VideoSource.LIVESTREAM, 1);
             if (videoTimeline == null) {
                 videoTimeline = new Timeline();
                 videoTimeline.setCycleCount(Animation.INDEFINITE);

From a660a6b5aad5d1f4a8d597880bce7cf30335b840 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Wed, 24 Apr 2024 11:22:20 +0200
Subject: [PATCH 031/100] Delete Functionality

---
 .../java/controller/AnnotationController.java | 22 +++++++++++++++++++
 src/main/resources/view/AnnotationView.fxml   |  2 +-
 2 files changed, 23 insertions(+), 1 deletion(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 5d37d14c..41f15f86 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -371,6 +371,27 @@ private void handleToggleTheme(ActionEvent event) {
             showAlert("Error", "Failed to toggle theme.");
         }
     }
+    @FXML
+    public void handleNoTipAction(ActionEvent event) {
+        if (currentSelectedImageView != null) {
+            // Remove the image view from the VBox
+            uploadedImages.getChildren().remove(currentSelectedImageView);
+            // Remove the image path from the set
+            uploadedFilePaths.remove(currentSelectedImageView.getImage().getUrl());
+            // Check if the selected image is the one being displayed, and clear it
+            if (selectedImageView.getImage() == currentSelectedImageView.getImage()) {
+                selectedImageView.setImage(null);
+            }
+            // Optionally, clear any associated annotations
+            clearAnnotations(event);
+            // Reset the current selected image view reference
+            currentSelectedImageView = null;
+        } else {
+            showAlert("No Selection", "No image is currently selected to delete.");
+        }
+    }
+
+    // Add this method if not already present in your code
     private void showAlert(String title, String content) {
         Alert alert = new Alert(Alert.AlertType.INFORMATION);
         alert.setTitle(title);
@@ -379,4 +400,5 @@ private void showAlert(String title, String content) {
         alert.showAndWait();
     }
 
+
 }
diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index 36146712..94ac4498 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -22,7 +22,7 @@
                   <Insets bottom="10.0" left="10.0" right="10.0" top="10.0" />
                </BorderPane.margin>
                <children>
-                  <Button mnemonicParsing="false" text="No Tip" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;">
+                  <Button mnemonicParsing="false" text="No Tip" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;" onAction="#handleNoTipAction">
                      <HBox.margin>
                         <Insets left="55.0" right="55.0" />
                      </HBox.margin>

From 1355637d8c97e71242b4707b9269d2c96cb09631 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Wed, 24 Apr 2024 11:47:28 +0200
Subject: [PATCH 032/100] Update AnnotationController.java

---
 .../java/controller/AnnotationController.java | 21 ++++++++++++-------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 41f15f86..5fb28620 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -374,24 +374,29 @@ private void handleToggleTheme(ActionEvent event) {
     @FXML
     public void handleNoTipAction(ActionEvent event) {
         if (currentSelectedImageView != null) {
-            // Remove the image view from the VBox
+            String imagePath = null;
+            try {
+                imagePath = new File(new URL(currentSelectedImageView.getImage().getUrl()).toURI()).getAbsolutePath();
+            } catch (Exception e) {
+                showAlert("Error", "Could not retrieve file path from the image.");
+                e.printStackTrace();
+            }
+
             uploadedImages.getChildren().remove(currentSelectedImageView);
-            // Remove the image path from the set
-            uploadedFilePaths.remove(currentSelectedImageView.getImage().getUrl());
-            // Check if the selected image is the one being displayed, and clear it
+            if (imagePath != null && uploadedFilePaths.contains(imagePath)) {
+                uploadedFilePaths.remove(imagePath);
+            }
             if (selectedImageView.getImage() == currentSelectedImageView.getImage()) {
                 selectedImageView.setImage(null);
+                clearAnnotations(event);
             }
-            // Optionally, clear any associated annotations
-            clearAnnotations(event);
-            // Reset the current selected image view reference
             currentSelectedImageView = null;
         } else {
             showAlert("No Selection", "No image is currently selected to delete.");
         }
     }
 
-    // Add this method if not already present in your code
+
     private void showAlert(String title, String content) {
         Alert alert = new Alert(Alert.AlertType.INFORMATION);
         alert.setTitle(title);

From 7587771b5dbcea0297567873dcc39484b8c01f01 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Wed, 24 Apr 2024 12:09:57 +0200
Subject: [PATCH 033/100] Update AnnotationView.fxml

Names of the Buttons
Place adjusted
---
 src/main/resources/view/AnnotationView.fxml | 28 +++++++++------------
 1 file changed, 12 insertions(+), 16 deletions(-)

diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index 94ac4498..a8a683e0 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -17,34 +17,30 @@
    <content>
       <BorderPane>
          <bottom>
-            <HBox alignment="CENTER" prefHeight="80.0" prefWidth="368.0" BorderPane.alignment="CENTER">
-               <BorderPane.margin>
-                  <Insets bottom="10.0" left="10.0" right="10.0" top="10.0" />
-               </BorderPane.margin>
+            <HBox alignment="CENTER_LEFT" prefHeight="80.0" prefWidth="368.0" BorderPane.alignment="CENTER">
                <children>
-                  <Button mnemonicParsing="false" text="No Tip" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;" onAction="#handleNoTipAction">
+                  <Button mnemonicParsing="false" text="Delete" prefWidth="120.0" prefHeight="40.0" onAction="#handleNoTipAction" style="-fx-font-size: 16px;">
                      <HBox.margin>
-                        <Insets left="55.0" right="55.0" />
-                     </HBox.margin>
-                  </Button>
-                  <Button mnemonicParsing="false" text="&lt;" onAction="#Select_Previous_Image"  prefHeight="40.0" style="-fx-font-weight: bold;-fx-font-size: 16px;">
-                     <HBox.margin>
-                        <Insets left="2.0" right="2.0" />
+                        <Insets left="10.0" right="10.0" />
                      </HBox.margin>
                   </Button>
-                  <Button mnemonicParsing="false" text="&gt;" onAction="#Select_Next_Image" prefHeight="40.0" style="-fx-font-weight: bold;-fx-font-size: 16px;">
+                  <Button mnemonicParsing="false" text="&lt;" onAction="#Select_Previous_Image" prefHeight="40.0" style="-fx-font-weight: bold; -fx-font-size: 16px;">
                      <HBox.margin>
-                        <Insets left="2.0" right="2.0" />
+                        <Insets right="10.0" />
                      </HBox.margin>
                   </Button>
-                  <Button mnemonicParsing="false" text="Done" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;">
+                  <Button mnemonicParsing="false" text="&gt;" onAction="#Select_Next_Image" prefHeight="40.0" style="-fx-font-weight: bold; -fx-font-size: 16px;">
                      <HBox.margin>
-                        <Insets left="55.0" right="55.0" />
+                        <Insets right="10.0" />
                      </HBox.margin>
                   </Button>
+                  <!-- Spacer to push everything to the left -->
+                  <Pane HBox.hgrow="ALWAYS" />
+                  <!-- Other controls can be added here, which will be aligned to the right -->
                </children>
             </HBox>
          </bottom>
+
          <top>
             <HBox alignment="CENTER" prefHeight="80.0" prefWidth="368.0" BorderPane.alignment="CENTER">
                <BorderPane.margin>
@@ -62,7 +58,7 @@
                         <Insets left="55.0" right="55.0" />
                      </HBox.margin>
                   </Button>
-                  <Button fx:id="toggleThemeButton" text="Dark/Light-Mode" onAction="#handleToggleTheme" HBox.hgrow="ALWAYS" maxWidth="170" style="-fx-font-size: 16px;">
+                  <Button fx:id="toggleThemeButton" text="Theme" onAction="#handleToggleTheme" HBox.hgrow="ALWAYS" maxWidth="170" style="-fx-font-size: 16px;">
                      <HBox.margin>
                         <Insets left="10.0" right="10.0" />
                      </HBox.margin>

From 46329499d1218b76e34d51622632130dda3abd9b Mon Sep 17 00:00:00 2001
From: muazzamaqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Wed, 24 Apr 2024 12:11:44 +0200
Subject: [PATCH 034/100] Variable Name Fix :)

---
 src/main/java/controller/AnnotationController.java | 3 +--
 src/main/resources/view/AnnotationView.fxml        | 2 +-
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 5fb28620..74e443ba 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -23,7 +23,6 @@
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.PrintWriter;
-import java.lang.annotation.Annotation;
 import java.net.URL;
 import java.util.HashSet;
 import java.util.List;
@@ -372,7 +371,7 @@ private void handleToggleTheme(ActionEvent event) {
         }
     }
     @FXML
-    public void handleNoTipAction(ActionEvent event) {
+    public void deletionfunctionality(ActionEvent event) {
         if (currentSelectedImageView != null) {
             String imagePath = null;
             try {
diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index a8a683e0..564350ec 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -19,7 +19,7 @@
          <bottom>
             <HBox alignment="CENTER_LEFT" prefHeight="80.0" prefWidth="368.0" BorderPane.alignment="CENTER">
                <children>
-                  <Button mnemonicParsing="false" text="Delete" prefWidth="120.0" prefHeight="40.0" onAction="#handleNoTipAction" style="-fx-font-size: 16px;">
+                  <Button mnemonicParsing="false" text="Delete" prefWidth="120.0" prefHeight="40.0" onAction="#deletionfunctionality" style="-fx-font-size: 16px;">
                      <HBox.margin>
                         <Insets left="10.0" right="10.0" />
                      </HBox.margin>

From d7b1430e59729480f9415004cfde4d6bb2677f6b Mon Sep 17 00:00:00 2001
From: Eugen Zdrincu <eugenzdrincu@gmail.com>
Date: Wed, 24 Apr 2024 13:16:30 +0200
Subject: [PATCH 035/100] removed unnecessary print statements

---
 src/main/java/controller/AutoTrackController.java | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/src/main/java/controller/AutoTrackController.java b/src/main/java/controller/AutoTrackController.java
index 230cfa97..7a884038 100644
--- a/src/main/java/controller/AutoTrackController.java
+++ b/src/main/java/controller/AutoTrackController.java
@@ -363,13 +363,6 @@ private void updateTrackingData(){
             lineData.add(new XYChart.Data<>(shifted_points[0], shifted_points[1]));
             lineData.add(new XYChart.Data<>(referencePoint.getData().get(0).getXValue(), referencePoint.getData().get(0).getYValue()));
 
-
-            System.out.println(referencePoint.getData().get(0).getXValue());
-            System.out.println(referencePoint.getData().get(0).getYValue());
-
-            System.out.println("------------");
-
-
             lineSeries.setData(lineData);
 
             if(data.size() > max_num_points){

From 98aca66deff9c17a09caac018bb685707746430f Mon Sep 17 00:00:00 2001
From: Simon Engel <engesi02@thu.de>
Date: Wed, 24 Apr 2024 13:47:48 +0200
Subject: [PATCH 036/100] Fixed Bug where Annotation wasn't deleted

---
 src/main/java/controller/AnnotationController.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 74e443ba..5f79ff18 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -386,8 +386,8 @@ public void deletionfunctionality(ActionEvent event) {
                 uploadedFilePaths.remove(imagePath);
             }
             if (selectedImageView.getImage() == currentSelectedImageView.getImage()) {
-                selectedImageView.setImage(null);
                 clearAnnotations(event);
+                selectedImageView.setImage(null);
             }
             currentSelectedImageView = null;
         } else {

From 81051cff73b194169f4f6a5376977c9943b1bc4d Mon Sep 17 00:00:00 2001
From: Eugen Zdrincu <eugenzdrincu@gmail.com>
Date: Wed, 24 Apr 2024 15:37:28 +0200
Subject: [PATCH 037/100] starting new tab work

---
 src/main/java/controller/AiController.java | 676 +++++++++++++++++++++
 src/main/resources/view/AiView.fxml        | 148 +++++
 src/main/resources/view/MainView.fxml      |   3 +
 3 files changed, 827 insertions(+)
 create mode 100644 src/main/java/controller/AiController.java
 create mode 100644 src/main/resources/view/AiView.fxml

diff --git a/src/main/java/controller/AiController.java b/src/main/java/controller/AiController.java
new file mode 100644
index 00000000..2e6ec787
--- /dev/null
+++ b/src/main/java/controller/AiController.java
@@ -0,0 +1,676 @@
+package controller;
+
+import algorithm.*;
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
+import inputOutput.ExportMeasurement;
+import inputOutput.TransformationMatrix;
+import inputOutput.VideoSource;
+import javafx.animation.Animation;
+import javafx.animation.KeyFrame;
+import javafx.animation.Timeline;
+import javafx.application.Platform;
+import javafx.beans.binding.Bindings;
+import javafx.collections.FXCollections;
+import javafx.collections.ObservableList;
+import javafx.fxml.FXML;
+import javafx.scene.chart.LineChart;
+import javafx.scene.chart.NumberAxis;
+import javafx.scene.chart.XYChart;
+import javafx.scene.control.*;
+import javafx.scene.control.Button;
+import javafx.scene.control.Label;
+import javafx.scene.control.TextField;
+import javafx.stage.DirectoryChooser;
+import javafx.stage.FileChooser;
+import javafx.util.Duration;
+import org.opencv.core.Core;
+import org.opencv.core.CvType;
+import org.opencv.core.Mat;
+import org.opencv.core.Point3;
+import userinterface.PlottableImage;
+
+import javax.imageio.ImageIO;
+import java.awt.*;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.net.URL;
+import java.nio.file.Path;
+import java.util.*;
+import java.util.List;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import java.util.prefs.Preferences;
+
+public class AiController implements Controller {
+
+    private final ImageDataManager imageDataManager = new ImageDataManager();
+    private final TrackingService trackingService = TrackingService.getInstance();
+    private final Map<String, Integer> deviceIdMapping = new LinkedHashMap<>();
+    private final Gson gson = new GsonBuilder().excludeFieldsWithoutExposeAnnotation().create();
+    private static final Preferences userPreferences = Preferences.userRoot().node("AutoTrack");
+    private static final Preferences userPreferencesGlobal = Preferences.userRoot().node("IGT_Settings");
+    private final Logger logger = Logger.getLogger(this.getClass().getName());
+
+    @FXML
+    public ChoiceBox<String> sourceChoiceBox;
+    @FXML
+    public CheckBox trackingConnectedStatusBox;
+    @FXML
+    public CheckBox regMatrixStatusBox;
+    @FXML
+    public Button regMatrixImportButton;
+    @FXML
+    public Button generateMatrixButton;
+    @FXML
+    public TextField outputPathField;
+    @FXML
+    public Button outputPathButton;
+    @FXML
+    public ComboBox<String> captureRateComboBox;
+    @FXML
+    public ToggleButton autoCaptureToggleButton;
+    @FXML
+    public Button singleCaptureButton;
+    @FXML
+    public ProgressIndicator captureProgressSpinner;
+    @FXML
+    public ProgressIndicator connectionProgressSpinner;
+    @FXML
+    public PlottableImage videoImagePlot;
+    @FXML
+    public CheckBox use3dTransformCheckBox;
+    @FXML
+    public CheckBox inSetReferenceMode;
+    @FXML
+    public LineChart<Number, Number> lineChart;
+
+    private TrackingDataController trackingDataController;
+    private Label statusLabel;
+    private Timeline videoTimeline;
+    private Timeline autoCaptureTimeline;
+    private BufferedImage currentShowingImage;
+    private boolean captureScheduled = false;
+    private String lastMatrixPath = "";
+    private List<ExportMeasurement> lastTrackingData = new ArrayList<>();
+
+    // Used to crop the image to the actual content. Dirty describes whether the roi cache needs to be updated on the next transform, it's set when a new matrix is loaded
+    private int[] matrixRoi = new int[4];
+    private boolean roiDirty = true;
+
+    private TransformationMatrix transformationMatrix = new TransformationMatrix();
+
+    private final ObservableList<XYChart.Series<Number, Number>> dataSeries = FXCollections.observableArrayList();
+
+    private final ObservableList<Point3> clicked_image_points = FXCollections.observableArrayList();
+    private final ObservableList<Point3> clicked_tracker_points = FXCollections.observableArrayList();
+    private Mat cachedTransformMatrix = null;
+
+    private final XYChart.Series<Number, Number> referencePoint = new XYChart.Series<Number, Number>();
+    private final ObservableList<XYChart.Series<Number,Number>> lineDataSeries = FXCollections.observableArrayList();
+
+    NumberAxis xAxis = new NumberAxis(-500, 500, 100);
+    NumberAxis yAxis = new NumberAxis(-500, 500, 100);
+
+
+    @Override
+    public void initialize(URL location, ResourceBundle resources) {
+        registerController();
+
+        trackingService.registerObserver((sourceChanged,dataServiceChanged,timelineChanged) -> updateTrackingInformation());
+
+        connectionProgressSpinner.setVisible(false);
+        captureProgressSpinner.setVisible(false);
+        sourceChoiceBox.getSelectionModel().selectedItemProperty().addListener(x -> changeVideoView());
+        sourceChoiceBox.setTooltip(new Tooltip("If you have multiple cameras connected, enable \"Search for more videos\" in the settings view to see all available devices"));
+        captureRateComboBox.getItems().addAll("1000", "2000", "5000", "10000", "30000");
+        captureRateComboBox.getSelectionModel().select(0);
+
+        var expression = trackingConnectedStatusBox.selectedProperty().and(regMatrixStatusBox.selectedProperty()).and(outputPathField.textProperty().isNotEmpty());
+        autoCaptureToggleButton.disableProperty().bind(expression.not());
+        singleCaptureButton.disableProperty().bind(expression.not());
+
+        generateMatrixButton.disableProperty().bind(Bindings.size(clicked_image_points).lessThan(4));
+        generateMatrixButton.textProperty().bind(Bindings.concat("Generate (",Bindings.size(clicked_image_points),"/4)"));
+
+        referencePoint.setName("reference point");
+        referencePoint.getData().add(new XYChart.Data<>(100,100));
+        dataSeries.add(referencePoint);
+
+        videoImagePlot.setData(dataSeries);
+        videoImagePlot.registerImageClickedHandler(this::onImageClicked);
+        videoImagePlot.registerImageClickedHandler(this::onSRM);
+        loadAvailableVideoDevicesAsync();
+
+        lineChart.getXAxis().setVisible(false);
+        lineChart.getYAxis().setVisible(false);
+        lineChart.setLegendVisible(false);
+        videoImagePlot.setLegendVisible(false);
+        lineChart.setMouseTransparent(true);
+        lineChart.setAnimated(false);
+        lineChart.setCreateSymbols(true);
+        lineChart.setAlternativeRowFillVisible(false);
+        lineChart.setAlternativeColumnFillVisible(false);
+        lineChart.setHorizontalGridLinesVisible(false);
+        lineChart.setVerticalGridLinesVisible(false);
+        lineChart.lookup(".chart-plot-background").setStyle("-fx-background-color: transparent;");
+        lineChart.setData(lineDataSeries);
+    }
+
+    private void onSRM(double v, double v1) {
+        if (inSetReferenceMode.isSelected()) {
+            System.out.println("Set reference point to "+v+" "+v1);
+            referencePoint.setData(FXCollections.observableArrayList(new XYChart.Data<>(v,v1)));
+        }
+    }
+
+    @Override
+    public void close() {
+        unregisterController();
+        if (videoTimeline != null) {
+            videoTimeline.stop();
+        }
+        if (autoCaptureTimeline != null) {
+            autoCaptureTimeline.stop();
+        }
+        imageDataManager.closeConnection();
+    }
+
+    /**
+     * Enables the Main View to inject the tracking data controller
+     *
+     */
+    public void updateTrackingInformation() {
+        var selected = trackingService.getTrackingDataSource() != null && trackingService.getTimeline() != null;
+        trackingConnectedStatusBox.setSelected(selected);
+    }
+
+    /**
+     * Enables the Main View to inject the status label at the bottom of the window
+     *
+     * @param statusLabel The injected label
+     */
+    public void setStatusLabel(Label statusLabel) {
+        this.statusLabel = statusLabel;
+        this.statusLabel.setText("");
+    }
+
+
+    /**
+     * Initializes the loading of available video devices. This is done asynchronously.
+     * While loading, the connection spinner shows.
+     */
+    private void loadAvailableVideoDevicesAsync() {
+        connectionProgressSpinner.setVisible(true);
+        new Thread(() -> {
+            createDeviceIdMapping(userPreferencesGlobal.getBoolean("searchForMoreVideos", false));
+            Platform.runLater(() -> {
+                sourceChoiceBox.getItems().addAll(deviceIdMapping.keySet());
+                if (!deviceIdMapping.isEmpty()) {
+                    sourceChoiceBox.getSelectionModel().select(0);
+                } else {
+                    statusLabel.setText("No video devices found!");
+                }
+                connectionProgressSpinner.setVisible(false);
+            });
+        }).start();
+    }
+
+    /**
+     * Tests out available video device ids. All devices that don't throw an error are added to the list.
+     * This is bad style, but openCV does not offer to list available devices.
+     * @param exhaustiveSearch Whether all available devices shall be enumerated. If set to false, there's a minimal performance gain.
+     */
+    private void createDeviceIdMapping(boolean exhaustiveSearch) {
+        if(!exhaustiveSearch){
+            deviceIdMapping.put("Default Camera",0);
+            return;
+        }
+
+        int currentDevice = 0;
+        boolean deviceExists = imageDataManager.openConnection(VideoSource.LIVESTREAM, currentDevice);
+        imageDataManager.closeConnection();
+        while (deviceExists) {
+            deviceIdMapping.put("Camera " + currentDevice, currentDevice);
+            currentDevice++;
+            deviceExists = imageDataManager.openConnection(VideoSource.LIVESTREAM, currentDevice);
+            imageDataManager.closeConnection();
+        }
+    }
+
+    /**
+     * Changes the input stream for the video view. Also starts the timeline to update the current image.
+     */
+    private void changeVideoView() {
+        if (!sourceChoiceBox.getSelectionModel().isEmpty()) {
+            var selectedItem = sourceChoiceBox.getSelectionModel().getSelectedItem();
+            int deviceId = deviceIdMapping.get(selectedItem);
+            imageDataManager.closeConnection();
+            imageDataManager.openConnection(VideoSource.LIVESTREAM, 1);
+            if (videoTimeline == null) {
+                videoTimeline = new Timeline();
+                videoTimeline.setCycleCount(Animation.INDEFINITE);
+                videoTimeline.getKeyFrames().add(
+                        new KeyFrame(Duration.millis(100),
+                                event -> this.updateVideoImage())
+                );
+                videoTimeline.play();
+            }
+        } else {
+            videoTimeline.stop();
+            videoTimeline = null;
+        }
+    }
+
+    /**
+     * Loads and displays the next image from the stream.
+     * If a measurement is scheduled, it queries the current tracking data and saves the data.
+     */
+    private void updateVideoImage() {
+        var matrix = imageDataManager.readMat();
+        if(matrix != null && !matrix.empty()) {
+            // Currently, we don't do image transformations, only tracking transformations
+            // matrix = applyImageTransformations(matrix);
+            currentShowingImage = ImageDataProcessor.Mat2BufferedImage(matrix);
+        }
+
+        // Show Tracking Data
+        if(trackingConnectedStatusBox.isSelected()){
+            updateTrackingData();
+        }
+
+        if (this.captureScheduled) {
+            this.captureScheduled = false;
+            saveCapturedData(currentShowingImage, lastTrackingData);
+        }
+        if(matrix != null && !matrix.empty()) {
+            videoImagePlot.setImage(ImageDataProcessor.Mat2Image(matrix, ".png"));
+            ((NumberAxis) lineChart.getXAxis()).setAutoRanging(false);
+            ((NumberAxis) lineChart.getXAxis()).setLowerBound(((NumberAxis) videoImagePlot.getXAxis()).getLowerBound());
+            ((NumberAxis) lineChart.getXAxis()).setUpperBound(((NumberAxis) videoImagePlot.getXAxis()).getUpperBound());
+            ((NumberAxis) lineChart.getXAxis()).setTickUnit(((NumberAxis) videoImagePlot.getXAxis()).getTickUnit());
+            ((NumberAxis) lineChart.getYAxis()).setAutoRanging(false);
+            ((NumberAxis) lineChart.getYAxis()).setLowerBound(((NumberAxis) videoImagePlot.getYAxis()).getLowerBound());
+            ((NumberAxis) lineChart.getYAxis()).setUpperBound(((NumberAxis) videoImagePlot.getYAxis()).getUpperBound());
+            ((NumberAxis) lineChart.getYAxis()).setTickUnit(((NumberAxis) videoImagePlot.getYAxis()).getTickUnit());
+
+            lineChart.prefWidthProperty().bind(videoImagePlot.widthProperty());
+            lineChart.prefHeightProperty().bind(videoImagePlot.heightProperty());
+            lineChart.minWidthProperty().bind(videoImagePlot.widthProperty());
+            lineChart.minHeightProperty().bind(videoImagePlot.heightProperty());
+            lineChart.maxWidthProperty().bind(videoImagePlot.widthProperty());
+            lineChart.maxHeightProperty().bind(videoImagePlot.heightProperty());
+        }
+    }
+
+    /**
+     * Loads the next tracking data point and displays it on the image-plot
+     */
+    private void updateTrackingData(){
+        var source = trackingService.getTrackingDataSource();
+        var service = trackingService.getDataService();
+        if(source == null || service == null){return;}
+
+        source.update();
+        List<Tool> tools = service.loadNextData(1);
+
+        if (tools.isEmpty()) return;
+
+        lastTrackingData.clear();
+        for (int i = 0; i < tools.size(); i++) {
+            Tool tool = tools.get(i);
+            if (dataSeries.size() <= i + 1) {
+                var series = new XYChart.Series<Number, Number>();
+                series.setName(tool.getName());
+                series.getData().add(new XYChart.Data<>(0,0));  // Workaround to display legend
+                dataSeries.add(series);
+                series.getData().remove(0);
+                // TODO: The sensor curve needs reworking (apply on transformed data and dont shrink)
+//                videoImagePlot.initSensorCurve(series);
+
+
+            }
+
+            if (lineDataSeries.size() <= i) {
+                // create series for line
+                // this series will include the reference point and current point
+                var lineSeries = new XYChart.Series<Number, Number>();
+                lineDataSeries.add(lineSeries);
+                lineSeries.getData().remove(0);
+            }
+
+
+            var series = dataSeries.get(i + 1);
+            var measurements = tool.getMeasurement();
+            var point = measurements.get(measurements.size() - 1).getPos();
+            var data = series.getData();
+            var max_num_points = 6; // 1
+
+            var lineSeries = lineDataSeries.get(i);
+            //var lineData = lineSeries.getData();
+            ObservableList<XYChart. Data<Number, Number>> lineData = FXCollections.observableArrayList();
+            var shifted_points = use3dTransformCheckBox.isSelected() ? applyTrackingTransformation3d(point.getX(), point.getY(), point.getZ()) : applyTrackingTransformation2d(point.getX(), point.getY(), point.getZ());
+            var x_normalized = shifted_points[0] / currentShowingImage.getWidth();
+            var y_normalized = shifted_points[1] / currentShowingImage.getHeight();
+            lastTrackingData.add(new ExportMeasurement(tool.getName(), point.getX(), point.getY(), point.getZ(), shifted_points[0], shifted_points[1], shifted_points[2], x_normalized, y_normalized));
+
+
+            data.add(new XYChart.Data<>(shifted_points[0], shifted_points[1]));
+
+            lineData.add(new XYChart.Data<>(shifted_points[0], shifted_points[1]));
+            lineData.add(new XYChart.Data<>(referencePoint.getData().get(0).getXValue(), referencePoint.getData().get(0).getYValue()));
+
+            lineSeries.setData(lineData);
+
+            if(data.size() > max_num_points){
+                data.remove(0);
+                //lineData.remove(0);
+            }
+        }
+    }
+
+    /**
+     * Request a capture in the next frame.
+     * We don't want to write out the current image and tracking position, as they might not match exactly (-> refresh rate of the video view)
+     * Therefore, we schedule to capture the next measurement once the video image is updated next.
+     */
+    private void doSingleCaptureOnNextFrame() {
+        this.captureScheduled = true;
+    }
+
+    /**
+     * Saves an image and tracking data to output files
+     *
+     * @param image        The current image to save
+     * @param trackingData The corresponding tracking data measurements
+     */
+    private void saveCapturedData(BufferedImage image, List<ExportMeasurement> trackingData) {
+        try {
+            File outputDirectory = new File(outputPathField.getText());
+            var files = outputDirectory.listFiles();
+            var nextIndex = ((files != null ? files.length : 0) / 2) + 1;
+            ImageIO.write(image, "png", Path.of(outputDirectory.getAbsolutePath(), "capture_" + nextIndex + ".png").toFile());
+            try (FileWriter fw = new FileWriter(Path.of(outputDirectory.getAbsolutePath(), "capture_" + nextIndex + ".json").toFile())) {
+                gson.toJson(trackingData, fw);
+            }
+        } catch (IOException e) {
+            logger.log(Level.SEVERE, "Error saving captured data", e);
+            e.printStackTrace();
+        }
+    }
+
+    /**
+     * Action that is called when the user wants to set an output directory
+     */
+    @FXML
+    public void on_browseOutputDirectory() {
+        DirectoryChooser directoryChooser = new DirectoryChooser();
+        directoryChooser.setTitle("Select Output Directory");
+        var lastLocationFile = getLastKnownFileLocation("outputDirectory",System.getProperty("user.home"));
+        directoryChooser.setInitialDirectory(lastLocationFile);
+        var directory = directoryChooser.showDialog(null);
+        if (directory != null) {
+            outputPathField.setText(directory.getAbsolutePath());
+            outputPathField.positionCaret(directory.getAbsolutePath().length());
+            userPreferences.put("outputDirectory", directory.getAbsolutePath());
+        }
+    }
+
+    /**
+     * Action that is called when the user wants to open the output directory
+     */
+    @FXML
+    public void on_openOutputDirectory() {
+        var directory = outputPathField.getText();
+        if (directory != null) {
+            try {
+                Desktop.getDesktop().open(new File(directory));
+            } catch (IOException e) {
+                logger.log(Level.SEVERE, "Error opening output directory", e);
+                e.printStackTrace();
+            }
+        }
+    }
+
+    /**
+     * Called when the "Single Capture" Button is pressed.
+     */
+    @FXML
+    public void on_doSingleCapture() {
+        doSingleCaptureOnNextFrame();
+    }
+
+    /**
+     * Called, when the "Auto Capture" Button is toggled (on or off)
+     */
+    @FXML
+    public void on_doAutoCapture() {
+        if (autoCaptureToggleButton.isSelected()) {
+            if (autoCaptureTimeline == null) {
+                captureProgressSpinner.setVisible(true);
+                autoCaptureTimeline = new Timeline();
+                autoCaptureTimeline.setCycleCount(Animation.INDEFINITE);
+                autoCaptureTimeline.getKeyFrames().add(
+                        new KeyFrame(Duration.millis(Integer.parseInt(captureRateComboBox.getSelectionModel().getSelectedItem())),
+                                event -> doSingleCaptureOnNextFrame())
+                );
+                autoCaptureTimeline.play();
+            }
+        } else {
+            if (autoCaptureTimeline != null) {
+                autoCaptureTimeline.stop();
+                autoCaptureTimeline = null;
+                captureProgressSpinner.setVisible(false);
+            }
+        }
+    }
+
+    /**
+     * Called, when "Import Matrix" Button is pressed.
+     */
+    @FXML
+    public void on_importMatrix() {
+        FileChooser fileChooser = new FileChooser();
+        fileChooser.setTitle("Select Matrix JSON");
+        var lastLocationFile = getLastKnownFileLocation("matrixDirectory",System.getProperty("user.home"));
+        fileChooser.setInitialDirectory(lastLocationFile);
+        var inputFile = fileChooser.showOpenDialog(null);
+        if(inputFile == null){
+            return;
+        }
+        try {
+            var path = inputFile.getAbsolutePath();
+            lastMatrixPath = path;
+            transformationMatrix = TransformationMatrix.loadFromJSON(path);
+            roiDirty = true;
+            regMatrixStatusBox.setSelected(true);
+            cachedTransformMatrix = null;
+            userPreferences.put("matrixDirectory", inputFile.getAbsoluteFile().getParent());
+        }catch (FileNotFoundException e) {
+            logger.log(Level.SEVERE, "Error loading matrix", e);
+            e.printStackTrace();
+        }
+    }
+
+    /**
+     * Reloads the matrix from the last given path (so it's easier to change from the outside)
+     */
+    @FXML
+    public void on_reloadMatrix(){
+        if (lastMatrixPath != null && !lastMatrixPath.isEmpty()) {
+            try {
+                transformationMatrix = TransformationMatrix.loadFromJSON(lastMatrixPath);
+                roiDirty = true;
+                regMatrixStatusBox.setSelected(true);
+                cachedTransformMatrix = null;
+            }catch (FileNotFoundException e) {
+                logger.log(Level.SEVERE, "Error loading matrix", e);
+                e.printStackTrace();
+            }
+        }
+    }
+
+    @FXML
+    public void on_generateMatrix(){
+        var transformationMatrix = new TransformationMatrix();
+        transformationMatrix.imagePoints = new float[4][];
+        transformationMatrix.trackingPoints = new float[4][];
+        for(int i = 0;i<clicked_image_points.size();i++){
+            transformationMatrix.imagePoints[i] = new float[]{(float) clicked_image_points.get(i).x, (float) clicked_image_points.get(i).y, (float) clicked_image_points.get(i).z};
+            transformationMatrix.trackingPoints[i] = new float[]{(float) clicked_tracker_points.get(i).x, (float) clicked_tracker_points.get(i).y, (float) clicked_tracker_points.get(i).z};
+        }
+
+        FileChooser fileChooser = new FileChooser();
+        fileChooser.setTitle("Set save location for matrix json");
+        var lastLocationFile = getLastKnownFileLocation("matrixDirectory",System.getProperty("user.home"));
+        fileChooser.setInitialDirectory(lastLocationFile);
+        fileChooser.setInitialFileName("transformationMatrix.json");
+        var saveFile = fileChooser.showSaveDialog(null);
+        if(saveFile != null){
+            try {
+                transformationMatrix.saveToJSON(saveFile);
+                this.transformationMatrix = transformationMatrix;
+                regMatrixStatusBox.setSelected(true);
+                cachedTransformMatrix = null;
+                userPreferences.put("matrixDirectory", saveFile.getAbsoluteFile().getParent());
+            } catch (IOException e) {
+                logger.log(Level.SEVERE, "Error saving matrix", e);
+                e.printStackTrace();
+            }
+        }
+    }
+
+    private File getLastKnownFileLocation(String key, String defaultLocation){
+        var lastLocation = userPreferences.get(key,defaultLocation);
+        var lastLocationFile = new File(lastLocation);
+        if(!lastLocationFile.exists()){
+            logger.log(Level.WARNING, "Last directory does not exist, default directory instead");
+            lastLocationFile = new File(defaultLocation);
+        }
+        return lastLocationFile;
+    }
+
+    /**
+     * Applies the transformation matrix to the image
+     * @param mat The image to be transformed
+     * @return The transformed image
+     */
+    private Mat applyImageTransformations(Mat mat){
+//        Imgproc.warpAffine(mat, mat, transformationMatrix.getTranslationMat(), mat.size());
+//        Imgproc.warpAffine(mat, mat, transformationMatrix.getRotationMat(), mat.size());
+//        Imgproc.warpAffine(mat, mat, transformationMatrix.getScaleMat(), mat.size());
+
+        /*
+        var imagePoints = transformationMatrix.getImagePoints();
+        var trackingPoints = transformationMatrix.getTrackingPoints();
+        var outMat = new Mat();
+        if(!imagePoints.empty() && !trackingPoints.empty()) {
+            //Mat srcPoints = Converters.vector_Point_to_Mat(imagePoints, CvType.CV_64F);
+            //Mat dstPoints = Converters.vector_Point_to_Mat(trackingPoints, CvType.CV_64F);
+
+            var matrix = Imgproc.getPerspectiveTransform(imagePoints, trackingPoints);
+            //var matrix = Calib3d.findHomography(imagePoints, trackingPoints, Calib3d.RANSAC);
+
+            Imgproc.warpPerspective(mat, outMat, matrix, new Size());
+            mat = outMat;
+            mat = outMat;
+            Imgproc.warpAffine(mat, outMat, transformationMatrix.getScaleMat(), mat.size());
+            mat = outMat;
+            Imgproc.warpAffine(mat, outMat, transformationMatrix.getTranslationMat(), mat.size());
+        }
+        */
+
+        if(roiDirty){
+            // Set noExecute to false if the Roi should be calculated (and thus, the image cropped)
+            matrixRoi = MatHelper.calculateRoi(mat, true);
+            roiDirty = false;
+        }
+        mat = mat.submat(matrixRoi[0],matrixRoi[1], matrixRoi[2],matrixRoi[3]);
+        return mat;
+    }
+
+    /**
+     * Applies the (2D) transformation on a tracking point
+     * @param x X-Coordinate of the point
+     * @param y Y-Coordinate of the point
+     * @param z Z-Coordinate of the point - Ignored in the 2d version
+     * @return The transformed point as array of length 3 (xyz)
+     */
+    private double[] applyTrackingTransformation2d(double x, double y, double z) {
+        // TODO: Cache matrix
+        if (cachedTransformMatrix == null){
+            cachedTransformMatrix = transformationMatrix.getTransformMatOpenCvEstimated2d();
+        }
+        var vector = new Mat(3,1, CvType.CV_64F);
+
+        if(userPreferencesGlobal.getBoolean("verticalFieldGenerator", false)){
+            vector.put(0,0,z);
+        }else{
+            vector.put(0,0,x);
+        }
+        vector.put(1,0,y);
+        vector.put(2,0,1);
+
+        var pos_star = new Mat(2,1,CvType.CV_64F);
+        Core.gemm(cachedTransformMatrix, vector,1, new Mat(),1,pos_star);
+        double[] out = new double[3];
+        out[0] = pos_star.get(0,0)[0];
+        out[1] = pos_star.get(1,0)[0];
+        out[2] = 0;
+        return out;
+    }
+
+    /**
+     * Applies the (3D) transformation on a tracking point
+     * @param x X-Coordinate of the point
+     * @param y Y-Coordinate of the point
+     * @param z Z-Coordinate of the point
+     * @return The transformed point as array of length 3 (xyz)
+     */
+    private double[] applyTrackingTransformation3d(double x, double y, double z){
+        var matrix = transformationMatrix.getTransformMatOpenCvEstimated3d();
+        var vector = new Mat(4,1, CvType.CV_64F);
+        vector.put(0,0,x);
+        vector.put(1,0,y);
+        vector.put(2,0,z);
+        vector.put(3,0,1);
+
+        var pos_star = new Mat();
+        Core.gemm(matrix, vector,1, new Mat(),1,pos_star);
+        //Core.perspectiveTransform();  // Maybe try this?
+        double[] out = new double[3];
+        out[0] = pos_star.get(0,0)[0];
+        out[1] = pos_star.get(1,0)[0];
+        out[2] = pos_star.get(2,0)[0];
+        return out;
+    }
+
+
+    /**
+     * Called, when the user clicks on the live image. Used to get landmarks for transformation. Uses 0 for the image plane as default
+     * @param x X-Coordinate in the image
+     * @param y Y-Coordinate in the image
+     */
+    private void onImageClicked(double x, double y){
+        System.out.println("clicked on image");
+        var trackingData = lastTrackingData;
+        if(trackingData.size() > 0 && clicked_image_points.size() < 4) {
+            // We also directly save the tracking-coordinates at this point.
+            System.out.println("Image: (" + String.format(Locale.ENGLISH, "%.2f", x) + "," + String.format(Locale.ENGLISH, "%.2f", y) + ",0)\nImage (Relative): (" + String.format(Locale.ENGLISH, "%.2f", x) + "," + String.format(Locale.ENGLISH, "%.2f", (currentShowingImage.getHeight() - y)) + ",0)");
+            for (var measurement : trackingData) {
+                System.out.println("Tracker " + measurement.toolName + ": (" + String.format(Locale.ENGLISH, "%.2f", measurement.x_raw) + "," + String.format(Locale.ENGLISH, "%.2f", measurement.y_raw) + "," + String.format(Locale.ENGLISH, "%.2f", measurement.z_raw) + ")\n");
+            }
+
+            clicked_image_points.add(new Point3(x, y, 0.0));
+            if(userPreferencesGlobal.getBoolean("verticalFieldGenerator", false)) {
+                clicked_tracker_points.add(new Point3(trackingData.get(0).z_raw, trackingData.get(0).y_raw, trackingData.get(0).x_raw));
+            }else {
+                clicked_tracker_points.add(new Point3(trackingData.get(0).x_raw, trackingData.get(0).y_raw, trackingData.get(0).z_raw));
+            }
+
+        }
+    }
+}
diff --git a/src/main/resources/view/AiView.fxml b/src/main/resources/view/AiView.fxml
new file mode 100644
index 00000000..28998e72
--- /dev/null
+++ b/src/main/resources/view/AiView.fxml
@@ -0,0 +1,148 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<?import javafx.geometry.*?>
+<?import javafx.scene.chart.NumberAxis?>
+<?import javafx.scene.control.*?>
+<?import javafx.scene.layout.*?>
+<?import userinterface.PlottableImage?>
+<?import javafx.scene.chart.LineChart?>
+<ScrollPane fitToHeight="true" fitToWidth="true" maxHeight="Infinity" maxWidth="Infinity"
+            xmlns="http://javafx.com/javafx/17" xmlns:fx="http://javafx.com/fxml/1"
+            fx:controller="controller.AiController">
+    <VBox alignment="CENTER" maxHeight="Infinity" maxWidth="Infinity">
+        <StackPane>
+            <alignment>
+                <Pos fx:value="CENTER"/>
+            </alignment>
+            <PlottableImage fx:id="videoImagePlot" horizontalGridLinesVisible="false" maxHeight="Infinity"
+                            maxWidth="Infinity" verticalGridLinesVisible="false">
+                <xAxis>
+                    <NumberAxis autoRanging="false" lowerBound="-500.0" minorTickVisible="false" side="BOTTOM" upperBound="500.0"/>
+                </xAxis>
+                <yAxis>
+                    <NumberAxis autoRanging="false" lowerBound="-500.0" minorTickVisible="false" side="LEFT" upperBound="500.0"/>
+                </yAxis>
+            </PlottableImage>
+            <LineChart fx:id="lineChart">
+                <xAxis>
+                    <NumberAxis autoRanging="false" lowerBound="-500.0" minorTickVisible="false" side="BOTTOM" upperBound="500.0"/>
+                </xAxis>
+                <yAxis>
+                    <NumberAxis autoRanging="false" lowerBound="-500.0" minorTickVisible="false" side="LEFT" upperBound="500.0"/>
+                </yAxis>
+            </LineChart>
+        </StackPane>
+
+        <HBox alignment="CENTER" spacing="20.0">
+            <TitledPane animated="false" collapsible="false" graphicTextGap="10.0" text="Connections"
+                        textAlignment="CENTER">
+                <graphic>
+                    <ProgressIndicator fx:id="connectionProgressSpinner" prefHeight="15.0" prefWidth="15.0"/>
+                </graphic>
+                <VBox>
+                    <HBox alignment="CENTER_LEFT" maxHeight="1.7976931348623157E308"
+                          maxWidth="1.7976931348623157E308" spacing="20.0">
+                        <padding>
+                            <Insets bottom="10.0" left="10.0" right="10.0" top="10.0"/>
+                        </padding>
+                        <Label text="Video Input" textAlignment="CENTER"/>
+                        <ChoiceBox fx:id="sourceChoiceBox"/>
+                    </HBox>
+                    <HBox>
+                        <CheckBox fx:id="trackingConnectedStatusBox" disable="true" mnemonicParsing="false"
+                                  styleClass="red-green-checkbox"/>
+                        <Label text="Trackingsource">
+                            <padding>
+                                <Insets left="5.0"/>
+                            </padding>
+                        </Label>
+                        <padding>
+                            <Insets bottom="10.0" left="10.0" right="10.0" top="10.0"/>
+                        </padding>
+                    </HBox>
+                    <BorderPane>
+                        <center>
+                            <Label text="Registration Matrix" textAlignment="CENTER">
+                                <BorderPane.margin>
+                                    <Insets left="5.0" right="10.0"/>
+                                </BorderPane.margin>
+                            </Label>
+                        </center>
+                        <left>
+                            <CheckBox fx:id="regMatrixStatusBox" disable="true" mnemonicParsing="false"
+                                      styleClass="red-green-checkbox" BorderPane.alignment="CENTER"/>
+                        </left>
+                        <right>
+                            <HBox alignment="CENTER_RIGHT">
+                                <Button fx:id="regMatrixImportButton"
+                                        mnemonicParsing="false" text="Import" BorderPane.alignment="CENTER"
+                                        onAction="#on_importMatrix"/>
+                                <Button alignment="CENTER" mnemonicParsing="false" text="Reload"
+                                        BorderPane.alignment="CENTER" onAction="#on_reloadMatrix"/>
+                                <Button fx:id="generateMatrixButton" alignment="CENTER_RIGHT"
+                                        mnemonicParsing="false" text="Generate (0/4)" BorderPane.alignment="CENTER"
+                                        onAction="#on_generateMatrix"/>
+                            </HBox>
+                        </right>
+                        <padding>
+                            <Insets bottom="10.0" left="10.0" right="10.0" top="10.0"/>
+                        </padding>
+                    </BorderPane>
+                    <CheckBox fx:id="use3dTransformCheckBox" mnemonicParsing="false"
+                              text="Use 3D transformation">
+                        <padding>
+                            <Insets left="10.0" right="10.0" top="5.0"/>
+                        </padding>
+                    </CheckBox>
+                    <CheckBox fx:id="inSetReferenceMode" mnemonicParsing="false"
+                              text="Set reference mode">
+                        <padding>
+                            <Insets left="10.0" right="10.0" top="5.0"/>
+                        </padding>
+                    </CheckBox>
+                </VBox>
+            </TitledPane>
+            <TitledPane animated="false" collapsible="false" graphicTextGap="10.0" layoutX="10.0" layoutY="10.0"
+                        text="Capture Studio" textAlignment="CENTER">
+                <graphic>
+                    <ProgressIndicator fx:id="captureProgressSpinner" prefHeight="15.0" prefWidth="15.0"/>
+                </graphic>
+                <VBox>
+                    <HBox alignment="CENTER_LEFT" maxHeight="1.7976931348623157E308"
+                          maxWidth="1.7976931348623157E308" spacing="20.0">
+                        <padding>
+                            <Insets bottom="10.0" left="10.0" right="10.0" top="10.0"/>
+                        </padding>
+                        <Label text="Output Path" textAlignment="CENTER"/>
+                        <TextField fx:id="outputPathField" editable="false" prefColumnCount="15"/>
+                        <Button fx:id="outputPathButton" mnemonicParsing="false"
+                                onAction="#on_browseOutputDirectory" text="Browse"/>
+                        <Button mnemonicParsing="false" onAction="#on_openOutputDirectory" text="Open Folder"/>
+                    </HBox>
+                    <HBox alignment="CENTER_LEFT" layoutX="20.0" layoutY="20.0"
+                          maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308" spacing="20.0">
+                        <padding>
+                            <Insets bottom="10.0" left="10.0" right="10.0" top="10.0"/>
+                        </padding>
+                        <Label text="Auto Capture Each" textAlignment="CENTER"/>
+                        <ComboBox fx:id="captureRateComboBox" editable="true" prefWidth="150.0"
+                                  visibleRowCount="5"/>
+                        <Label text="ms"/>
+                    </HBox>
+                    <HBox alignment="CENTER" layoutX="20.0" layoutY="20.0" maxHeight="1.7976931348623157E308"
+                          maxWidth="1.7976931348623157E308" spacing="50.0">
+                        <padding>
+                            <Insets bottom="10.0" left="10.0" right="10.0" top="10.0"/>
+                        </padding>
+                        <Button fx:id="singleCaptureButton" mnemonicParsing="false"
+                                onAction="#on_doSingleCapture" prefHeight="60.0" text="Capture Single Image"
+                                textAlignment="CENTER" wrapText="true"/>
+                        <ToggleButton fx:id="autoCaptureToggleButton" mnemonicParsing="false"
+                                      onAction="#on_doAutoCapture" prefHeight="60.0"
+                                      styleClass="green-toggle-button" text="Auto Capture"/>
+                    </HBox>
+                </VBox>
+            </TitledPane>
+        </HBox>
+    </VBox>
+</ScrollPane>
diff --git a/src/main/resources/view/MainView.fxml b/src/main/resources/view/MainView.fxml
index 88ade970..4251a882 100644
--- a/src/main/resources/view/MainView.fxml
+++ b/src/main/resources/view/MainView.fxml
@@ -44,6 +44,9 @@
             <Tab closable="false" fx:id="visualizationTab" text="Visualization" onSelectionChanged="#onChangeView">
                 <fx:include fx:id="visualization" source="VisualizationView.fxml"/>
             </Tab>
+            <Tab closable="false" fx:id="aiTab" text="AI" onSelectionChanged="#onChangeView">
+                <fx:include fx:id="ai" source="AiView.fxml"/>
+            </Tab>
         </TabPane>
     </center>
     <bottom>

From 044cca12132900ac88d3d42baad3f6b6e21ed1e4 Mon Sep 17 00:00:00 2001
From: nguyensl-rose <119351168+nguyensl-rose@users.noreply.github.com>
Date: Mon, 29 Apr 2024 15:40:21 -0400
Subject: [PATCH 038/100] cleaned up aicontroller and aiview

---
 src/main/java/controller/AiController.java | 268 +--------------------
 src/main/resources/view/AiView.fxml        |  77 +-----
 2 files changed, 2 insertions(+), 343 deletions(-)

diff --git a/src/main/java/controller/AiController.java b/src/main/java/controller/AiController.java
index 2e6ec787..08aeaa2b 100644
--- a/src/main/java/controller/AiController.java
+++ b/src/main/java/controller/AiController.java
@@ -10,7 +10,6 @@
 import javafx.animation.KeyFrame;
 import javafx.animation.Timeline;
 import javafx.application.Platform;
-import javafx.beans.binding.Bindings;
 import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
 import javafx.fxml.FXML;
@@ -18,11 +17,7 @@
 import javafx.scene.chart.NumberAxis;
 import javafx.scene.chart.XYChart;
 import javafx.scene.control.*;
-import javafx.scene.control.Button;
 import javafx.scene.control.Label;
-import javafx.scene.control.TextField;
-import javafx.stage.DirectoryChooser;
-import javafx.stage.FileChooser;
 import javafx.util.Duration;
 import org.opencv.core.Core;
 import org.opencv.core.CvType;
@@ -30,19 +25,10 @@
 import org.opencv.core.Point3;
 import userinterface.PlottableImage;
 
-import javax.imageio.ImageIO;
-import java.awt.*;
 import java.awt.image.BufferedImage;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileWriter;
-import java.io.IOException;
 import java.net.URL;
-import java.nio.file.Path;
 import java.util.*;
 import java.util.List;
-import java.util.logging.Level;
-import java.util.logging.Logger;
 import java.util.prefs.Preferences;
 
 public class AiController implements Controller {
@@ -50,51 +36,23 @@ public class AiController implements Controller {
     private final ImageDataManager imageDataManager = new ImageDataManager();
     private final TrackingService trackingService = TrackingService.getInstance();
     private final Map<String, Integer> deviceIdMapping = new LinkedHashMap<>();
-    private final Gson gson = new GsonBuilder().excludeFieldsWithoutExposeAnnotation().create();
-    private static final Preferences userPreferences = Preferences.userRoot().node("AutoTrack");
     private static final Preferences userPreferencesGlobal = Preferences.userRoot().node("IGT_Settings");
-    private final Logger logger = Logger.getLogger(this.getClass().getName());
 
     @FXML
     public ChoiceBox<String> sourceChoiceBox;
     @FXML
     public CheckBox trackingConnectedStatusBox;
-    @FXML
-    public CheckBox regMatrixStatusBox;
-    @FXML
-    public Button regMatrixImportButton;
-    @FXML
-    public Button generateMatrixButton;
-    @FXML
-    public TextField outputPathField;
-    @FXML
-    public Button outputPathButton;
-    @FXML
-    public ComboBox<String> captureRateComboBox;
-    @FXML
-    public ToggleButton autoCaptureToggleButton;
-    @FXML
-    public Button singleCaptureButton;
-    @FXML
-    public ProgressIndicator captureProgressSpinner;
-    @FXML
     public ProgressIndicator connectionProgressSpinner;
     @FXML
     public PlottableImage videoImagePlot;
     @FXML
-    public CheckBox use3dTransformCheckBox;
-    @FXML
     public CheckBox inSetReferenceMode;
     @FXML
     public LineChart<Number, Number> lineChart;
 
-    private TrackingDataController trackingDataController;
     private Label statusLabel;
     private Timeline videoTimeline;
-    private Timeline autoCaptureTimeline;
     private BufferedImage currentShowingImage;
-    private boolean captureScheduled = false;
-    private String lastMatrixPath = "";
     private List<ExportMeasurement> lastTrackingData = new ArrayList<>();
 
     // Used to crop the image to the actual content. Dirty describes whether the roi cache needs to be updated on the next transform, it's set when a new matrix is loaded
@@ -123,18 +81,8 @@ public void initialize(URL location, ResourceBundle resources) {
         trackingService.registerObserver((sourceChanged,dataServiceChanged,timelineChanged) -> updateTrackingInformation());
 
         connectionProgressSpinner.setVisible(false);
-        captureProgressSpinner.setVisible(false);
         sourceChoiceBox.getSelectionModel().selectedItemProperty().addListener(x -> changeVideoView());
         sourceChoiceBox.setTooltip(new Tooltip("If you have multiple cameras connected, enable \"Search for more videos\" in the settings view to see all available devices"));
-        captureRateComboBox.getItems().addAll("1000", "2000", "5000", "10000", "30000");
-        captureRateComboBox.getSelectionModel().select(0);
-
-        var expression = trackingConnectedStatusBox.selectedProperty().and(regMatrixStatusBox.selectedProperty()).and(outputPathField.textProperty().isNotEmpty());
-        autoCaptureToggleButton.disableProperty().bind(expression.not());
-        singleCaptureButton.disableProperty().bind(expression.not());
-
-        generateMatrixButton.disableProperty().bind(Bindings.size(clicked_image_points).lessThan(4));
-        generateMatrixButton.textProperty().bind(Bindings.concat("Generate (",Bindings.size(clicked_image_points),"/4)"));
 
         referencePoint.setName("reference point");
         referencePoint.getData().add(new XYChart.Data<>(100,100));
@@ -173,9 +121,6 @@ public void close() {
         if (videoTimeline != null) {
             videoTimeline.stop();
         }
-        if (autoCaptureTimeline != null) {
-            autoCaptureTimeline.stop();
-        }
         imageDataManager.closeConnection();
     }
 
@@ -282,10 +227,6 @@ private void updateVideoImage() {
             updateTrackingData();
         }
 
-        if (this.captureScheduled) {
-            this.captureScheduled = false;
-            saveCapturedData(currentShowingImage, lastTrackingData);
-        }
         if(matrix != null && !matrix.empty()) {
             videoImagePlot.setImage(ImageDataProcessor.Mat2Image(matrix, ".png"));
             ((NumberAxis) lineChart.getXAxis()).setAutoRanging(false);
@@ -352,7 +293,7 @@ private void updateTrackingData(){
             var lineSeries = lineDataSeries.get(i);
             //var lineData = lineSeries.getData();
             ObservableList<XYChart. Data<Number, Number>> lineData = FXCollections.observableArrayList();
-            var shifted_points = use3dTransformCheckBox.isSelected() ? applyTrackingTransformation3d(point.getX(), point.getY(), point.getZ()) : applyTrackingTransformation2d(point.getX(), point.getY(), point.getZ());
+            var shifted_points = applyTrackingTransformation2d(point.getX(), point.getY(), point.getZ());
             var x_normalized = shifted_points[0] / currentShowingImage.getWidth();
             var y_normalized = shifted_points[1] / currentShowingImage.getHeight();
             lastTrackingData.add(new ExportMeasurement(tool.getName(), point.getX(), point.getY(), point.getZ(), shifted_points[0], shifted_points[1], shifted_points[2], x_normalized, y_normalized));
@@ -372,187 +313,6 @@ private void updateTrackingData(){
         }
     }
 
-    /**
-     * Request a capture in the next frame.
-     * We don't want to write out the current image and tracking position, as they might not match exactly (-> refresh rate of the video view)
-     * Therefore, we schedule to capture the next measurement once the video image is updated next.
-     */
-    private void doSingleCaptureOnNextFrame() {
-        this.captureScheduled = true;
-    }
-
-    /**
-     * Saves an image and tracking data to output files
-     *
-     * @param image        The current image to save
-     * @param trackingData The corresponding tracking data measurements
-     */
-    private void saveCapturedData(BufferedImage image, List<ExportMeasurement> trackingData) {
-        try {
-            File outputDirectory = new File(outputPathField.getText());
-            var files = outputDirectory.listFiles();
-            var nextIndex = ((files != null ? files.length : 0) / 2) + 1;
-            ImageIO.write(image, "png", Path.of(outputDirectory.getAbsolutePath(), "capture_" + nextIndex + ".png").toFile());
-            try (FileWriter fw = new FileWriter(Path.of(outputDirectory.getAbsolutePath(), "capture_" + nextIndex + ".json").toFile())) {
-                gson.toJson(trackingData, fw);
-            }
-        } catch (IOException e) {
-            logger.log(Level.SEVERE, "Error saving captured data", e);
-            e.printStackTrace();
-        }
-    }
-
-    /**
-     * Action that is called when the user wants to set an output directory
-     */
-    @FXML
-    public void on_browseOutputDirectory() {
-        DirectoryChooser directoryChooser = new DirectoryChooser();
-        directoryChooser.setTitle("Select Output Directory");
-        var lastLocationFile = getLastKnownFileLocation("outputDirectory",System.getProperty("user.home"));
-        directoryChooser.setInitialDirectory(lastLocationFile);
-        var directory = directoryChooser.showDialog(null);
-        if (directory != null) {
-            outputPathField.setText(directory.getAbsolutePath());
-            outputPathField.positionCaret(directory.getAbsolutePath().length());
-            userPreferences.put("outputDirectory", directory.getAbsolutePath());
-        }
-    }
-
-    /**
-     * Action that is called when the user wants to open the output directory
-     */
-    @FXML
-    public void on_openOutputDirectory() {
-        var directory = outputPathField.getText();
-        if (directory != null) {
-            try {
-                Desktop.getDesktop().open(new File(directory));
-            } catch (IOException e) {
-                logger.log(Level.SEVERE, "Error opening output directory", e);
-                e.printStackTrace();
-            }
-        }
-    }
-
-    /**
-     * Called when the "Single Capture" Button is pressed.
-     */
-    @FXML
-    public void on_doSingleCapture() {
-        doSingleCaptureOnNextFrame();
-    }
-
-    /**
-     * Called, when the "Auto Capture" Button is toggled (on or off)
-     */
-    @FXML
-    public void on_doAutoCapture() {
-        if (autoCaptureToggleButton.isSelected()) {
-            if (autoCaptureTimeline == null) {
-                captureProgressSpinner.setVisible(true);
-                autoCaptureTimeline = new Timeline();
-                autoCaptureTimeline.setCycleCount(Animation.INDEFINITE);
-                autoCaptureTimeline.getKeyFrames().add(
-                        new KeyFrame(Duration.millis(Integer.parseInt(captureRateComboBox.getSelectionModel().getSelectedItem())),
-                                event -> doSingleCaptureOnNextFrame())
-                );
-                autoCaptureTimeline.play();
-            }
-        } else {
-            if (autoCaptureTimeline != null) {
-                autoCaptureTimeline.stop();
-                autoCaptureTimeline = null;
-                captureProgressSpinner.setVisible(false);
-            }
-        }
-    }
-
-    /**
-     * Called, when "Import Matrix" Button is pressed.
-     */
-    @FXML
-    public void on_importMatrix() {
-        FileChooser fileChooser = new FileChooser();
-        fileChooser.setTitle("Select Matrix JSON");
-        var lastLocationFile = getLastKnownFileLocation("matrixDirectory",System.getProperty("user.home"));
-        fileChooser.setInitialDirectory(lastLocationFile);
-        var inputFile = fileChooser.showOpenDialog(null);
-        if(inputFile == null){
-            return;
-        }
-        try {
-            var path = inputFile.getAbsolutePath();
-            lastMatrixPath = path;
-            transformationMatrix = TransformationMatrix.loadFromJSON(path);
-            roiDirty = true;
-            regMatrixStatusBox.setSelected(true);
-            cachedTransformMatrix = null;
-            userPreferences.put("matrixDirectory", inputFile.getAbsoluteFile().getParent());
-        }catch (FileNotFoundException e) {
-            logger.log(Level.SEVERE, "Error loading matrix", e);
-            e.printStackTrace();
-        }
-    }
-
-    /**
-     * Reloads the matrix from the last given path (so it's easier to change from the outside)
-     */
-    @FXML
-    public void on_reloadMatrix(){
-        if (lastMatrixPath != null && !lastMatrixPath.isEmpty()) {
-            try {
-                transformationMatrix = TransformationMatrix.loadFromJSON(lastMatrixPath);
-                roiDirty = true;
-                regMatrixStatusBox.setSelected(true);
-                cachedTransformMatrix = null;
-            }catch (FileNotFoundException e) {
-                logger.log(Level.SEVERE, "Error loading matrix", e);
-                e.printStackTrace();
-            }
-        }
-    }
-
-    @FXML
-    public void on_generateMatrix(){
-        var transformationMatrix = new TransformationMatrix();
-        transformationMatrix.imagePoints = new float[4][];
-        transformationMatrix.trackingPoints = new float[4][];
-        for(int i = 0;i<clicked_image_points.size();i++){
-            transformationMatrix.imagePoints[i] = new float[]{(float) clicked_image_points.get(i).x, (float) clicked_image_points.get(i).y, (float) clicked_image_points.get(i).z};
-            transformationMatrix.trackingPoints[i] = new float[]{(float) clicked_tracker_points.get(i).x, (float) clicked_tracker_points.get(i).y, (float) clicked_tracker_points.get(i).z};
-        }
-
-        FileChooser fileChooser = new FileChooser();
-        fileChooser.setTitle("Set save location for matrix json");
-        var lastLocationFile = getLastKnownFileLocation("matrixDirectory",System.getProperty("user.home"));
-        fileChooser.setInitialDirectory(lastLocationFile);
-        fileChooser.setInitialFileName("transformationMatrix.json");
-        var saveFile = fileChooser.showSaveDialog(null);
-        if(saveFile != null){
-            try {
-                transformationMatrix.saveToJSON(saveFile);
-                this.transformationMatrix = transformationMatrix;
-                regMatrixStatusBox.setSelected(true);
-                cachedTransformMatrix = null;
-                userPreferences.put("matrixDirectory", saveFile.getAbsoluteFile().getParent());
-            } catch (IOException e) {
-                logger.log(Level.SEVERE, "Error saving matrix", e);
-                e.printStackTrace();
-            }
-        }
-    }
-
-    private File getLastKnownFileLocation(String key, String defaultLocation){
-        var lastLocation = userPreferences.get(key,defaultLocation);
-        var lastLocationFile = new File(lastLocation);
-        if(!lastLocationFile.exists()){
-            logger.log(Level.WARNING, "Last directory does not exist, default directory instead");
-            lastLocationFile = new File(defaultLocation);
-        }
-        return lastLocationFile;
-    }
-
     /**
      * Applies the transformation matrix to the image
      * @param mat The image to be transformed
@@ -623,32 +383,6 @@ private double[] applyTrackingTransformation2d(double x, double y, double z) {
         return out;
     }
 
-    /**
-     * Applies the (3D) transformation on a tracking point
-     * @param x X-Coordinate of the point
-     * @param y Y-Coordinate of the point
-     * @param z Z-Coordinate of the point
-     * @return The transformed point as array of length 3 (xyz)
-     */
-    private double[] applyTrackingTransformation3d(double x, double y, double z){
-        var matrix = transformationMatrix.getTransformMatOpenCvEstimated3d();
-        var vector = new Mat(4,1, CvType.CV_64F);
-        vector.put(0,0,x);
-        vector.put(1,0,y);
-        vector.put(2,0,z);
-        vector.put(3,0,1);
-
-        var pos_star = new Mat();
-        Core.gemm(matrix, vector,1, new Mat(),1,pos_star);
-        //Core.perspectiveTransform();  // Maybe try this?
-        double[] out = new double[3];
-        out[0] = pos_star.get(0,0)[0];
-        out[1] = pos_star.get(1,0)[0];
-        out[2] = pos_star.get(2,0)[0];
-        return out;
-    }
-
-
     /**
      * Called, when the user clicks on the live image. Used to get landmarks for transformation. Uses 0 for the image plane as default
      * @param x X-Coordinate in the image
diff --git a/src/main/resources/view/AiView.fxml b/src/main/resources/view/AiView.fxml
index 28998e72..0a84b3b7 100644
--- a/src/main/resources/view/AiView.fxml
+++ b/src/main/resources/view/AiView.fxml
@@ -33,7 +33,7 @@
             </LineChart>
         </StackPane>
 
-        <HBox alignment="CENTER" spacing="20.0">
+        <HBox alignment="CENTER">
             <TitledPane animated="false" collapsible="false" graphicTextGap="10.0" text="Connections"
                         textAlignment="CENTER">
                 <graphic>
@@ -60,40 +60,6 @@
                             <Insets bottom="10.0" left="10.0" right="10.0" top="10.0"/>
                         </padding>
                     </HBox>
-                    <BorderPane>
-                        <center>
-                            <Label text="Registration Matrix" textAlignment="CENTER">
-                                <BorderPane.margin>
-                                    <Insets left="5.0" right="10.0"/>
-                                </BorderPane.margin>
-                            </Label>
-                        </center>
-                        <left>
-                            <CheckBox fx:id="regMatrixStatusBox" disable="true" mnemonicParsing="false"
-                                      styleClass="red-green-checkbox" BorderPane.alignment="CENTER"/>
-                        </left>
-                        <right>
-                            <HBox alignment="CENTER_RIGHT">
-                                <Button fx:id="regMatrixImportButton"
-                                        mnemonicParsing="false" text="Import" BorderPane.alignment="CENTER"
-                                        onAction="#on_importMatrix"/>
-                                <Button alignment="CENTER" mnemonicParsing="false" text="Reload"
-                                        BorderPane.alignment="CENTER" onAction="#on_reloadMatrix"/>
-                                <Button fx:id="generateMatrixButton" alignment="CENTER_RIGHT"
-                                        mnemonicParsing="false" text="Generate (0/4)" BorderPane.alignment="CENTER"
-                                        onAction="#on_generateMatrix"/>
-                            </HBox>
-                        </right>
-                        <padding>
-                            <Insets bottom="10.0" left="10.0" right="10.0" top="10.0"/>
-                        </padding>
-                    </BorderPane>
-                    <CheckBox fx:id="use3dTransformCheckBox" mnemonicParsing="false"
-                              text="Use 3D transformation">
-                        <padding>
-                            <Insets left="10.0" right="10.0" top="5.0"/>
-                        </padding>
-                    </CheckBox>
                     <CheckBox fx:id="inSetReferenceMode" mnemonicParsing="false"
                               text="Set reference mode">
                         <padding>
@@ -102,47 +68,6 @@
                     </CheckBox>
                 </VBox>
             </TitledPane>
-            <TitledPane animated="false" collapsible="false" graphicTextGap="10.0" layoutX="10.0" layoutY="10.0"
-                        text="Capture Studio" textAlignment="CENTER">
-                <graphic>
-                    <ProgressIndicator fx:id="captureProgressSpinner" prefHeight="15.0" prefWidth="15.0"/>
-                </graphic>
-                <VBox>
-                    <HBox alignment="CENTER_LEFT" maxHeight="1.7976931348623157E308"
-                          maxWidth="1.7976931348623157E308" spacing="20.0">
-                        <padding>
-                            <Insets bottom="10.0" left="10.0" right="10.0" top="10.0"/>
-                        </padding>
-                        <Label text="Output Path" textAlignment="CENTER"/>
-                        <TextField fx:id="outputPathField" editable="false" prefColumnCount="15"/>
-                        <Button fx:id="outputPathButton" mnemonicParsing="false"
-                                onAction="#on_browseOutputDirectory" text="Browse"/>
-                        <Button mnemonicParsing="false" onAction="#on_openOutputDirectory" text="Open Folder"/>
-                    </HBox>
-                    <HBox alignment="CENTER_LEFT" layoutX="20.0" layoutY="20.0"
-                          maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308" spacing="20.0">
-                        <padding>
-                            <Insets bottom="10.0" left="10.0" right="10.0" top="10.0"/>
-                        </padding>
-                        <Label text="Auto Capture Each" textAlignment="CENTER"/>
-                        <ComboBox fx:id="captureRateComboBox" editable="true" prefWidth="150.0"
-                                  visibleRowCount="5"/>
-                        <Label text="ms"/>
-                    </HBox>
-                    <HBox alignment="CENTER" layoutX="20.0" layoutY="20.0" maxHeight="1.7976931348623157E308"
-                          maxWidth="1.7976931348623157E308" spacing="50.0">
-                        <padding>
-                            <Insets bottom="10.0" left="10.0" right="10.0" top="10.0"/>
-                        </padding>
-                        <Button fx:id="singleCaptureButton" mnemonicParsing="false"
-                                onAction="#on_doSingleCapture" prefHeight="60.0" text="Capture Single Image"
-                                textAlignment="CENTER" wrapText="true"/>
-                        <ToggleButton fx:id="autoCaptureToggleButton" mnemonicParsing="false"
-                                      onAction="#on_doAutoCapture" prefHeight="60.0"
-                                      styleClass="green-toggle-button" text="Auto Capture"/>
-                    </HBox>
-                </VBox>
-            </TitledPane>
         </HBox>
     </VBox>
 </ScrollPane>

From 33c9dd5a053d75b69b9620ecd7d87bd1820a080e Mon Sep 17 00:00:00 2001
From: VincentStriegel <strivi01@thu.de>
Date: Thu, 2 May 2024 16:31:36 +0200
Subject: [PATCH 039/100] add export all button and functionality

---
 .../java/controller/AnnotationController.java | 50 +++++++++++++------
 src/main/java/util/AnnotationData.java        | 16 +++++-
 src/main/resources/view/AnnotationView.fxml   |  7 ++-
 3 files changed, 57 insertions(+), 16 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 5f79ff18..ce23fcc4 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -18,6 +18,7 @@
 import javafx.scene.transform.Scale;
 import javafx.stage.FileChooser;
 import javafx.stage.Stage;
+import javafx.stage.DirectoryChooser;
 import util.AnnotationData;
 
 import java.io.File;
@@ -308,29 +309,50 @@ private void handleExportAction(ActionEvent event) {
             File file = fileChooser.showSaveDialog(((Node) event.getSource()).getScene().getWindow());
 
             if (file != null) {
-                saveAnnotationsToFile(file);
+                saveAnnotationsToFile(file, AnnotationData.getInstance().getAnnotationEntry(selectedImageView.getImage().getUrl()));
             }
         } else {
             showNoAnnotationAlert();
         }
     }
 
+        /**
+     * Handles Export All based Functionality
+     * @param event The Mouse Event
+     */
+    @FXML
+    private void handleExportAllAction(ActionEvent event) {
+        if (selectedImageView != null && annotatedRectangle != null) {
+            DirectoryChooser directoryChooser = new DirectoryChooser();
+            directoryChooser.setTitle("Select Directory to Save Annotations");
+            File selectedDirectory = directoryChooser.showDialog(((Node) event.getSource()).getScene().getWindow());
+
+            if (selectedDirectory != null) {
+                AnnotationData.getInstance().getAnnotations().forEach((path, annotation) -> {
+                    try {
+                        File file = new File(new URL(path).toURI());
+                        String fileName = file.getName().substring(0, file.getName().lastIndexOf('.')) + "_annotations.txt";
+                        File annotationFile = new File(selectedDirectory, fileName);
+
+                        saveAnnotationsToFile(annotationFile, annotation);
+                    } catch (Exception e) {
+                        e.printStackTrace();
+                    }
+                });
+            }
+        }
+    }
 
+    /**
+     * Handles the Saving of Annotations to a File
+     * @param file The File to save the Annotations to
+     * @param annotation The Annotation Data to save
+     */
 
-    private void saveAnnotationsToFile(File file) {
+    private void saveAnnotationsToFile(File file, AnnotationData.PublicAnnotation annotation) {
         try (PrintWriter writer = new PrintWriter(file)) {
-            double imageWidth = selectedImageView.getImage().getWidth();
-            double imageHeight = selectedImageView.getImage().getHeight();
-
-            double centerX = (annotatedRectangle.getX() + annotatedRectangle.getWidth() / 2) / imageWidth;
-            double centerY = (annotatedRectangle.getY() + annotatedRectangle.getHeight() / 2) / imageHeight;
-            double normWidth = annotatedRectangle.getWidth() / imageWidth;
-            double normHeight = annotatedRectangle.getHeight() / imageHeight;
-
-            int classId = 0; //As we have only one class based requirement
-
-            String line = String.format("%d %.5f %.5f %.5f %.5f", classId, centerX, centerY, normWidth, normHeight);
-            writer.println(line);
+           String line = String.format("%d %.5f %.5f %.5f %.5f", 0, annotation.getMiddlePointX(), annotation.getMiddlePointY(), annotation.getBoundingBoxWidth(), annotation.getBoundingBoxHeight());
+                            writer.println(line);
         } catch (FileNotFoundException e) {
             e.printStackTrace();
         }
diff --git a/src/main/java/util/AnnotationData.java b/src/main/java/util/AnnotationData.java
index aa8fe4c6..01df86f5 100644
--- a/src/main/java/util/AnnotationData.java
+++ b/src/main/java/util/AnnotationData.java
@@ -13,10 +13,16 @@
  */
 public class AnnotationData {
 
+    public interface PublicAnnotation {
+        double getMiddlePointX();
+        double getMiddlePointY();
+        double getBoundingBoxWidth();
+        double getBoundingBoxHeight();
+    }
     /**
      * Private Class to save the Annotation Data
      */
-    private static class Annotation{
+    private static class Annotation implements PublicAnnotation{
         private final double middlePointX;
         private final double middlePointY;
         private final double boundingBoxWidth;
@@ -84,4 +90,12 @@ public void deleteAnnotation(String path){
     public static AnnotationData getInstance() {
         return instance;
     }
+
+    public Map<String, PublicAnnotation> getAnnotations() {
+        return new HashMap<>(annotations);
+    }
+
+    public PublicAnnotation getAnnotationEntry(String path){
+        return annotations.get(path);
+    }
 }
diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index 564350ec..a33e7063 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -53,9 +53,14 @@
                      </HBox.margin>
                   </Button>
                   <Button fx:id="ExportButton" text="Export" prefWidth="120.0" prefHeight="40.0" onAction="#handleExportAction" style="-fx-font-size: 16px;" />
+                  <Button fx:id="ExportButtonAll" text="Export All" prefWidth="120.0" prefHeight="40.0" onAction="#handleExportAllAction" style="-fx-font-size: 16px;">
+                    <HBox.margin>
+                        <Insets left="55.0" right="55.0" />
+                     </HBox.margin>
+                  </Button>
                   <Button fx:id="clearMarksButton" onAction="#clearAnnotations" text="Clear Marks" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;">
                      <HBox.margin>
-                        <Insets left="55.0" right="55.0" />
+                        <Insets left="10.0" right="55.0" />
                      </HBox.margin>
                   </Button>
                   <Button fx:id="toggleThemeButton" text="Theme" onAction="#handleToggleTheme" HBox.hgrow="ALWAYS" maxWidth="170" style="-fx-font-size: 16px;">

From 522c86392e37b036e999e336d9c1496b53c48df1 Mon Sep 17 00:00:00 2001
From: VincentStriegel <strivi01@thu.de>
Date: Thu, 2 May 2024 16:35:48 +0200
Subject: [PATCH 040/100] remove log and update gitignore

---
 .gitignore    |   2 +-
 logging.log.1 | 428 --------------------------------------------------
 2 files changed, 1 insertion(+), 429 deletions(-)
 delete mode 100644 logging.log.1

diff --git a/.gitignore b/.gitignore
index af39a2ec..4bed8c4c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,7 +2,7 @@
 *.class
 
 # Log file
-*.log
+*.log*
 *.log.lck
 
 # BlueJ files
diff --git a/logging.log.1 b/logging.log.1
deleted file mode 100644
index 38cab22a..00000000
--- a/logging.log.1
+++ /dev/null
@@ -1,428 +0,0 @@
-Apr 21, 2024 5:44:41 PM javafx.fxml.FXMLLoader$ValueElement processValue
-WARNING: Loading FXML document with JavaFX API of version 21 by JavaFX runtime of version 17
-Apr 21, 2024 5:44:41 PM mainMethod.App lambda$start$0
-SEVERE: Uncaught exception in thread main
-java.lang.RuntimeException: Exception in Application start method
-	at com.sun.javafx.application.LauncherImpl.launchApplication1(LauncherImpl.java:901)
-	at com.sun.javafx.application.LauncherImpl.lambda$launchApplication$2(LauncherImpl.java:196)
-	at java.base/java.lang.Thread.run(Thread.java:840)
-Caused by: javafx.fxml.LoadException: 
-/C:/programming/Global_Computing/IGTPrototypingTool/build/resources/main/view/AnnotationView.fxml:72
-/C:/programming/Global_Computing/IGTPrototypingTool/build/resources/main/view/MainView.fxml:48
-
-	at javafx.fxml.FXMLLoader.constructLoadException(FXMLLoader.java:2707)
-	at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2650)
-	at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2548)
-	at javafx.fxml.FXMLLoader$IncludeElement.constructValue(FXMLLoader.java:1153)
-	at javafx.fxml.FXMLLoader$ValueElement.processStartElement(FXMLLoader.java:757)
-	at javafx.fxml.FXMLLoader.processStartElement(FXMLLoader.java:2808)
-	at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2634)
-	at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2548)
-	at javafx.fxml.FXMLLoader.load(FXMLLoader.java:2516)
-	at mainMethod.App.start(App.java:36)
-	at com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$9(LauncherImpl.java:847)
-	at com.sun.javafx.application.PlatformImpl.lambda$runAndWait$12(PlatformImpl.java:484)
-	at com.sun.javafx.application.PlatformImpl.lambda$runLater$10(PlatformImpl.java:457)
-	at java.base/java.security.AccessController.doPrivileged(AccessController.java:399)
-	at com.sun.javafx.application.PlatformImpl.lambda$runLater$11(PlatformImpl.java:456)
-	at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:96)
-	at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
-	at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:184)
-	... 1 more
-Caused by: javax.xml.stream.XMLStreamException: ParseError at [row,col]:[72,18]
-Message: The element type "Button" must be terminated by the matching end-tag "</Button>".
-	at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652)
-	at java.xml/javax.xml.stream.util.StreamReaderDelegate.next(StreamReaderDelegate.java:84)
-	at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2620)
-	... 17 more
-
-Apr 21, 2024 5:45:38 PM javafx.fxml.FXMLLoader$ValueElement processValue
-WARNING: Loading FXML document with JavaFX API of version 21 by JavaFX runtime of version 17
-Apr 21, 2024 5:45:38 PM mainMethod.App lambda$start$0
-SEVERE: Uncaught exception in thread main
-java.lang.RuntimeException: Exception in Application start method
-	at com.sun.javafx.application.LauncherImpl.launchApplication1(LauncherImpl.java:901)
-	at com.sun.javafx.application.LauncherImpl.lambda$launchApplication$2(LauncherImpl.java:196)
-	at java.base/java.lang.Thread.run(Thread.java:840)
-Caused by: javafx.fxml.LoadException: 
-/C:/programming/Global_Computing/IGTPrototypingTool/build/resources/main/view/AnnotationView.fxml:72
-/C:/programming/Global_Computing/IGTPrototypingTool/build/resources/main/view/MainView.fxml:48
-
-	at javafx.fxml.FXMLLoader.constructLoadException(FXMLLoader.java:2707)
-	at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2650)
-	at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2548)
-	at javafx.fxml.FXMLLoader$IncludeElement.constructValue(FXMLLoader.java:1153)
-	at javafx.fxml.FXMLLoader$ValueElement.processStartElement(FXMLLoader.java:757)
-	at javafx.fxml.FXMLLoader.processStartElement(FXMLLoader.java:2808)
-	at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2634)
-	at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2548)
-	at javafx.fxml.FXMLLoader.load(FXMLLoader.java:2516)
-	at mainMethod.App.start(App.java:36)
-	at com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$9(LauncherImpl.java:847)
-	at com.sun.javafx.application.PlatformImpl.lambda$runAndWait$12(PlatformImpl.java:484)
-	at com.sun.javafx.application.PlatformImpl.lambda$runLater$10(PlatformImpl.java:457)
-	at java.base/java.security.AccessController.doPrivileged(AccessController.java:399)
-	at com.sun.javafx.application.PlatformImpl.lambda$runLater$11(PlatformImpl.java:456)
-	at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:96)
-	at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
-	at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:184)
-	... 1 more
-Caused by: javax.xml.stream.XMLStreamException: ParseError at [row,col]:[72,18]
-Message: The element type "Button" must be terminated by the matching end-tag "</Button>".
-	at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652)
-	at java.xml/javax.xml.stream.util.StreamReaderDelegate.next(StreamReaderDelegate.java:84)
-	at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2620)
-	... 17 more
-
-Apr 21, 2024 5:45:51 PM javafx.fxml.FXMLLoader$ValueElement processValue
-WARNING: Loading FXML document with JavaFX API of version 21 by JavaFX runtime of version 17
-Apr 21, 2024 5:45:52 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:45:52 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from null to TabPane[id=tabPane, styleClass=tab-pane]
-Apr 21, 2024 5:46:05 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:46:05 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: true] focused=true
-Apr 21, 2024 5:46:05 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from TabPane[id=tabPane, styleClass=tab-pane] to Button[id=uploadImagesButton, styleClass=button]'Import'
-Apr 21, 2024 5:46:06 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: false] focused=false
-Apr 21, 2024 5:46:14 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: true] focused=true
-Apr 21, 2024 5:46:15 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: false] focused=false
-Apr 21, 2024 5:46:15 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane@46509f49[styleClass=scroll-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:46:15 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from Button[id=uploadImagesButton, styleClass=button]'Import' to ScrollPane@46509f49[styleClass=scroll-pane]
-Apr 21, 2024 5:46:16 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane@46509f49[styleClass=scroll-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:46:16 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=demo, styleClass=button]'Export', name: focused, value: true] focused=true
-Apr 21, 2024 5:46:16 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from ScrollPane@46509f49[styleClass=scroll-pane] to Button[id=demo, styleClass=button]'Export'
-Apr 21, 2024 5:46:17 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=demo, styleClass=button]'Export', name: focused, value: false] focused=false
-Apr 21, 2024 5:46:17 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
-Apr 21, 2024 5:46:17 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from Button[id=demo, styleClass=button]'Export' to Button[id=ExportButton, styleClass=button]'Export'
-Apr 21, 2024 5:46:17 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
-Apr 21, 2024 5:46:17 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button@26683389[styleClass=button]'OK', name: focused, value: true] focused=true
-Apr 21, 2024 5:46:17 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from null to Button@26683389[styleClass=button]'OK'
-Apr 21, 2024 5:46:18 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button@26683389[styleClass=button]'OK', name: focused, value: false] focused=false
-Apr 21, 2024 5:46:18 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
-Apr 21, 2024 5:46:19 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
-Apr 21, 2024 5:46:19 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:46:19 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from Button[id=ExportButton, styleClass=button]'Export' to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
-Apr 21, 2024 5:46:21 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:46:21 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: true] focused=true
-Apr 21, 2024 5:46:21 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to Button[id=clearMarksButton, styleClass=button]'Clear Marks'
-Apr 21, 2024 5:46:22 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: false] focused=false
-Apr 21, 2024 5:46:22 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:46:22 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from Button[id=clearMarksButton, styleClass=button]'Clear Marks' to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
-Apr 21, 2024 5:46:23 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:46:23 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=demo, styleClass=button]'Export', name: focused, value: true] focused=true
-Apr 21, 2024 5:46:23 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to Button[id=demo, styleClass=button]'Export'
-Apr 21, 2024 5:46:24 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=demo, styleClass=button]'Export', name: focused, value: false] focused=false
-Apr 21, 2024 5:46:38 PM javafx.fxml.FXMLLoader$ValueElement processValue
-WARNING: Loading FXML document with JavaFX API of version 21 by JavaFX runtime of version 17
-Apr 21, 2024 5:46:39 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:46:39 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from null to TabPane[id=tabPane, styleClass=tab-pane]
-Apr 21, 2024 5:46:42 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:46:42 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: true] focused=true
-Apr 21, 2024 5:46:42 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from TabPane[id=tabPane, styleClass=tab-pane] to Button[id=uploadImagesButton, styleClass=button]'Import'
-Apr 21, 2024 5:46:42 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: false] focused=false
-Apr 21, 2024 5:46:46 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: true] focused=true
-Apr 21, 2024 5:46:48 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: false] focused=false
-Apr 21, 2024 5:46:48 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane@7863b5f5[styleClass=scroll-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:46:48 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from Button[id=uploadImagesButton, styleClass=button]'Import' to ScrollPane@7863b5f5[styleClass=scroll-pane]
-Apr 21, 2024 5:46:48 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane@7863b5f5[styleClass=scroll-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:46:48 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:46:48 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from ScrollPane@7863b5f5[styleClass=scroll-pane] to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
-Apr 21, 2024 5:46:49 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:46:49 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=annotation, styleClass=scroll-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:46:49 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to ScrollPane[id=annotation, styleClass=scroll-pane]
-Apr 21, 2024 5:46:50 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=annotation, styleClass=scroll-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:46:50 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=exampleButton, styleClass=button]'Clear Marks', name: focused, value: true] focused=true
-Apr 21, 2024 5:46:50 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from ScrollPane[id=annotation, styleClass=scroll-pane] to Button[id=exampleButton, styleClass=button]'Clear Marks'
-Apr 21, 2024 5:46:53 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=exampleButton, styleClass=button]'Clear Marks', name: focused, value: false] focused=false
-Apr 21, 2024 5:46:53 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:46:53 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from Button[id=exampleButton, styleClass=button]'Clear Marks' to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
-Apr 21, 2024 5:46:54 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:46:54 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: true] focused=true
-Apr 21, 2024 5:46:54 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to Button[id=clearMarksButton, styleClass=button]'Clear Marks'
-Apr 21, 2024 5:46:54 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: false] focused=false
-Apr 21, 2024 5:46:54 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:46:54 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from Button[id=clearMarksButton, styleClass=button]'Clear Marks' to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
-Apr 21, 2024 5:46:56 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:46:56 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: true] focused=true
-Apr 21, 2024 5:46:56 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to Button[id=clearMarksButton, styleClass=button]'Clear Marks'
-Apr 21, 2024 5:46:57 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: false] focused=false
-Apr 21, 2024 5:46:57 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:46:57 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from Button[id=clearMarksButton, styleClass=button]'Clear Marks' to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
-Apr 21, 2024 5:46:58 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:46:58 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=annotation, styleClass=scroll-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:46:58 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to ScrollPane[id=annotation, styleClass=scroll-pane]
-Apr 21, 2024 5:46:58 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=annotation, styleClass=scroll-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:46:58 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
-Apr 21, 2024 5:46:58 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from ScrollPane[id=annotation, styleClass=scroll-pane] to Button[id=ExportButton, styleClass=button]'Export'
-Apr 21, 2024 5:46:59 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
-Apr 21, 2024 5:47:00 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
-Apr 21, 2024 5:47:00 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
-Apr 21, 2024 5:47:00 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=annotation, styleClass=scroll-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:47:00 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from Button[id=ExportButton, styleClass=button]'Export' to ScrollPane[id=annotation, styleClass=scroll-pane]
-Apr 21, 2024 5:47:01 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=annotation, styleClass=scroll-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:47:28 PM javafx.fxml.FXMLLoader$ValueElement processValue
-WARNING: Loading FXML document with JavaFX API of version 21 by JavaFX runtime of version 17
-Apr 21, 2024 5:47:29 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:47:29 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from null to TabPane[id=tabPane, styleClass=tab-pane]
-Apr 21, 2024 5:47:32 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:47:32 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
-Apr 21, 2024 5:47:32 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from TabPane[id=tabPane, styleClass=tab-pane] to Button[id=ExportButton, styleClass=button]'Export'
-Apr 21, 2024 5:47:32 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
-Apr 21, 2024 5:47:32 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button@141f0d8[styleClass=button]'OK', name: focused, value: true] focused=true
-Apr 21, 2024 5:47:32 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from null to Button@141f0d8[styleClass=button]'OK'
-Apr 21, 2024 5:47:33 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button@141f0d8[styleClass=button]'OK', name: focused, value: false] focused=false
-Apr 21, 2024 5:47:33 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
-Apr 21, 2024 5:47:33 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
-Apr 21, 2024 5:47:33 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: true] focused=true
-Apr 21, 2024 5:47:33 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from Button[id=ExportButton, styleClass=button]'Export' to Button[id=uploadImagesButton, styleClass=button]'Import'
-Apr 21, 2024 5:47:33 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: false] focused=false
-Apr 21, 2024 5:47:38 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: true] focused=true
-Apr 21, 2024 5:47:39 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: false] focused=false
-Apr 21, 2024 5:47:39 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane@dfd3d2d[styleClass=scroll-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:47:39 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from Button[id=uploadImagesButton, styleClass=button]'Import' to ScrollPane@dfd3d2d[styleClass=scroll-pane]
-Apr 21, 2024 5:47:39 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane@dfd3d2d[styleClass=scroll-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:47:39 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:47:39 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from ScrollPane@dfd3d2d[styleClass=scroll-pane] to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
-Apr 21, 2024 5:47:40 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:47:40 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: true] focused=true
-Apr 21, 2024 5:47:40 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to Button[id=clearMarksButton, styleClass=button]'Clear Marks'
-Apr 21, 2024 5:47:41 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: false] focused=false
-Apr 21, 2024 5:47:41 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:47:41 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from Button[id=clearMarksButton, styleClass=button]'Clear Marks' to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
-Apr 21, 2024 5:47:42 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:47:42 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
-Apr 21, 2024 5:47:42 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to Button[id=ExportButton, styleClass=button]'Export'
-Apr 21, 2024 5:47:42 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
-Apr 21, 2024 5:47:49 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
-Apr 21, 2024 5:47:50 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
-Apr 21, 2024 5:47:50 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
-Apr 21, 2024 5:47:51 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
-Apr 21, 2024 5:49:26 PM javafx.fxml.FXMLLoader$ValueElement processValue
-WARNING: Loading FXML document with JavaFX API of version 21 by JavaFX runtime of version 17
-Apr 21, 2024 5:49:27 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:49:27 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from null to TabPane[id=tabPane, styleClass=tab-pane]
-Apr 21, 2024 5:49:32 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:49:32 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode', name: focused, value: true] focused=true
-Apr 21, 2024 5:49:32 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from TabPane[id=tabPane, styleClass=tab-pane] to Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode'
-Apr 21, 2024 5:49:35 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode', name: focused, value: false] focused=false
-Apr 21, 2024 5:49:53 PM javafx.fxml.FXMLLoader$ValueElement processValue
-WARNING: Loading FXML document with JavaFX API of version 21 by JavaFX runtime of version 17
-Apr 21, 2024 5:49:54 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:49:54 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from null to TabPane[id=tabPane, styleClass=tab-pane]
-Apr 21, 2024 5:49:56 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: TabPane[id=tabPane, styleClass=tab-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:49:56 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode', name: focused, value: true] focused=true
-Apr 21, 2024 5:49:56 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from TabPane[id=tabPane, styleClass=tab-pane] to Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode'
-Apr 21, 2024 5:49:58 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode', name: focused, value: false] focused=false
-Apr 21, 2024 5:49:58 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: true] focused=true
-Apr 21, 2024 5:49:58 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode' to Button[id=uploadImagesButton, styleClass=button]'Import'
-Apr 21, 2024 5:49:58 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: false] focused=false
-Apr 21, 2024 5:49:59 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: true] focused=true
-Apr 21, 2024 5:50:00 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: false] focused=false
-Apr 21, 2024 5:50:00 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode', name: focused, value: true] focused=true
-Apr 21, 2024 5:50:00 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from Button[id=uploadImagesButton, styleClass=button]'Import' to Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode'
-Apr 21, 2024 5:50:01 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode', name: focused, value: false] focused=false
-Apr 21, 2024 5:50:01 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: true] focused=true
-Apr 21, 2024 5:50:01 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from Button[id=toggleThemeButton, styleClass=button]'Dark/Light-Mode' to Button[id=uploadImagesButton, styleClass=button]'Import'
-Apr 21, 2024 5:50:01 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: false] focused=false
-Apr 21, 2024 5:50:07 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: true] focused=true
-Apr 21, 2024 5:50:08 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=uploadImagesButton, styleClass=button]'Import', name: focused, value: false] focused=false
-Apr 21, 2024 5:50:08 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane@103c0396[styleClass=scroll-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:50:08 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from Button[id=uploadImagesButton, styleClass=button]'Import' to ScrollPane@103c0396[styleClass=scroll-pane]
-Apr 21, 2024 5:50:09 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane@103c0396[styleClass=scroll-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:50:09 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:50:09 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from ScrollPane@103c0396[styleClass=scroll-pane] to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
-Apr 21, 2024 5:50:09 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:50:09 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: true] focused=true
-Apr 21, 2024 5:50:09 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to Button[id=clearMarksButton, styleClass=button]'Clear Marks'
-Apr 21, 2024 5:50:10 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: false] focused=false
-Apr 21, 2024 5:50:10 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:50:10 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from Button[id=clearMarksButton, styleClass=button]'Clear Marks' to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
-Apr 21, 2024 5:50:11 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:50:11 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: true] focused=true
-Apr 21, 2024 5:50:11 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to Button[id=clearMarksButton, styleClass=button]'Clear Marks'
-Apr 21, 2024 5:50:11 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=clearMarksButton, styleClass=button]'Clear Marks', name: focused, value: false] focused=false
-Apr 21, 2024 5:50:11 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
-Apr 21, 2024 5:50:11 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from Button[id=clearMarksButton, styleClass=button]'Clear Marks' to Button[id=ExportButton, styleClass=button]'Export'
-Apr 21, 2024 5:50:11 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
-Apr 21, 2024 5:50:11 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button@1d2f0cc5[styleClass=button]'OK', name: focused, value: true] focused=true
-Apr 21, 2024 5:50:11 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from null to Button@1d2f0cc5[styleClass=button]'OK'
-Apr 21, 2024 5:50:12 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button@1d2f0cc5[styleClass=button]'OK', name: focused, value: false] focused=false
-Apr 21, 2024 5:50:12 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
-Apr 21, 2024 5:50:13 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
-Apr 21, 2024 5:50:13 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: true] focused=true
-Apr 21, 2024 5:50:13 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from Button[id=ExportButton, styleClass=button]'Export' to ScrollPane[id=selectedImagePane, styleClass=scroll-pane]
-Apr 21, 2024 5:50:14 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: ScrollPane[id=selectedImagePane, styleClass=scroll-pane], name: focused, value: false] focused=false
-Apr 21, 2024 5:50:14 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
-Apr 21, 2024 5:50:14 PM javafx.scene.Scene$12 invalidated
-FINE: Changed focus from ScrollPane[id=selectedImagePane, styleClass=scroll-pane] to Button[id=ExportButton, styleClass=button]'Export'
-Apr 21, 2024 5:50:14 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false
-Apr 21, 2024 5:50:15 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: true] focused=true
-Apr 21, 2024 5:50:18 PM javafx.scene.Node$FocusedProperty markInvalid
-FINE: ReadOnlyBooleanProperty [bean: Button[id=ExportButton, styleClass=button]'Export', name: focused, value: false] focused=false

From 346e8fe356cddc8ac7e15ad0f494c0e3916a2799 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Thu, 2 May 2024 17:33:01 +0200
Subject: [PATCH 041/100] Update AnnotationController.java

Added a few conditions --- (Export All Check):

1. Handles now the case when there are no files in the directory
2. Handles now the case when there are some pictures that are not annotated
    a. Shows which pictures are not annotated
---
 .../java/controller/AnnotationController.java | 112 ++++++++++++------
 1 file changed, 76 insertions(+), 36 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index ce23fcc4..4204dc47 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -15,6 +15,7 @@
 import javafx.scene.paint.Color;
 import javafx.scene.shape.Circle;
 import javafx.scene.shape.Rectangle;
+import javafx.scene.text.Text;
 import javafx.scene.transform.Scale;
 import javafx.stage.FileChooser;
 import javafx.stage.Stage;
@@ -25,10 +26,7 @@
 import java.io.FileNotFoundException;
 import java.io.PrintWriter;
 import java.net.URL;
-import java.util.HashSet;
-import java.util.List;
-import java.util.ResourceBundle;
-import java.util.Set;
+import java.util.*;
 
 public class AnnotationController implements Controller {
     @FXML
@@ -316,33 +314,86 @@ private void handleExportAction(ActionEvent event) {
         }
     }
 
-        /**
-     * Handles Export All based Functionality
-     * @param event The Mouse Event
-     */
+
+
+    ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+    ///Export-All-Functionality----------START
+
     @FXML
     private void handleExportAllAction(ActionEvent event) {
-        if (selectedImageView != null && annotatedRectangle != null) {
-            DirectoryChooser directoryChooser = new DirectoryChooser();
-            directoryChooser.setTitle("Select Directory to Save Annotations");
-            File selectedDirectory = directoryChooser.showDialog(((Node) event.getSource()).getScene().getWindow());
-
-            if (selectedDirectory != null) {
-                AnnotationData.getInstance().getAnnotations().forEach((path, annotation) -> {
-                    try {
-                        File file = new File(new URL(path).toURI());
-                        String fileName = file.getName().substring(0, file.getName().lastIndexOf('.')) + "_annotations.txt";
-                        File annotationFile = new File(selectedDirectory, fileName);
-
-                        saveAnnotationsToFile(annotationFile, annotation);
-                    } catch (Exception e) {
-                        e.printStackTrace();
-                    }
-                });
+        // Checking if there are no images uploaded
+        if (uploadedImages.getChildren().isEmpty()) {
+            showAlert("Export Error", "There are no images to export.");
+            return;
+        }
+
+        List<String> unannotatedImages = new ArrayList<>();
+        for (Node node : uploadedImages.getChildren()) {
+            ImageView imageView = (ImageView) node;
+            if (AnnotationData.getInstance().getAnnotation(imageView.getImage().getUrl()) == null) {
+                unannotatedImages.add(new File(imageView.getImage().getUrl()).getName());
             }
         }
+
+        if (!unannotatedImages.isEmpty()) {
+            showUnannotatedImagesAlert(unannotatedImages);
+            return;
+        }
+
+        DirectoryChooser directoryChooser = new DirectoryChooser();
+        directoryChooser.setTitle("Select Directory to Save Annotations");
+        File selectedDirectory = directoryChooser.showDialog(((Node) event.getSource()).getScene().getWindow());
+
+        if (selectedDirectory != null) {
+            AnnotationData.getInstance().getAnnotations().forEach((path, annotation) -> {
+                File file = null;
+                try {
+                    file = new File(new URL(path).toURI());
+                    String fileName = file.getName().substring(0, file.getName().lastIndexOf('.')) + "_annotations.txt";
+                    File annotationFile = new File(selectedDirectory, fileName);
+                    saveAnnotationsToFile(annotationFile, annotation);
+                } catch (Exception e) {
+                    showAlert("Error", "Failed to save annotations for " + file.getName());
+                }
+            });
+        }
+    }
+
+    private void showAlert(String title, String content) {
+        Alert alert = new Alert(Alert.AlertType.INFORMATION);
+        alert.setTitle(title);
+        alert.setHeaderText(null);
+        alert.setContentText(content);
+        alert.showAndWait();
+    }
+
+    private void showUnannotatedImagesAlert(List<String> unannotatedImages) {
+        Alert alert = new Alert(Alert.AlertType.INFORMATION);
+        alert.setTitle("Unannotated Images");
+        alert.setHeaderText("The following images have no annotations:");
+
+        VBox vbox = new VBox(5);
+        for (String imageName : unannotatedImages) {
+            Text imageText = new Text(imageName);
+            vbox.getChildren().add(imageText);
+        }
+
+        ScrollPane scrollPane = new ScrollPane(vbox);
+        scrollPane.setPrefSize(300, 150);
+        scrollPane.setVbarPolicy(ScrollPane.ScrollBarPolicy.AS_NEEDED);
+        scrollPane.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER);
+
+        alert.getDialogPane().setContent(scrollPane);
+        alert.setResizable(true);
+        alert.showAndWait();
     }
 
+
+    ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+    ///Export-All-Functionality----------END
+
+
+
     /**
      * Handles the Saving of Annotations to a File
      * @param file The File to save the Annotations to
@@ -416,15 +467,4 @@ public void deletionfunctionality(ActionEvent event) {
             showAlert("No Selection", "No image is currently selected to delete.");
         }
     }
-
-
-    private void showAlert(String title, String content) {
-        Alert alert = new Alert(Alert.AlertType.INFORMATION);
-        alert.setTitle(title);
-        alert.setHeaderText(null);
-        alert.setContentText(content);
-        alert.showAndWait();
-    }
-
-
 }

From 17a56cf3dbcc08760afafd3b6f29a3fc304d97b5 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Thu, 2 May 2024 17:43:35 +0200
Subject: [PATCH 042/100] Update AnnotationController.java

File Names will be shown now in the sideview for a better user experience.
---
 .../java/controller/AnnotationController.java | 27 ++++++++++++++++---
 1 file changed, 23 insertions(+), 4 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 4204dc47..7343cda6 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -25,9 +25,16 @@
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.PrintWriter;
+import java.io.UnsupportedEncodingException;
 import java.net.URL;
 import java.util.*;
 
+import javafx.scene.control.Label;
+import javafx.scene.layout.VBox;
+import java.net.URLDecoder;
+import java.nio.charset.StandardCharsets;
+
+
 public class AnnotationController implements Controller {
     @FXML
     public VBox uploadedImages;     //Where the users see the files
@@ -90,20 +97,32 @@ public void Handle_Upload_Functionality(ActionEvent actionEvent) {
         }
     }
 
-    private void displayImage(File file) {
+    private void displayImage(File file) throws UnsupportedEncodingException {
         Image image = new Image(file.toURI().toString());
         ImageView imageView = new ImageView(image);
         imageView.setFitHeight(100);
         imageView.setFitWidth(100);
         imageView.setPreserveRatio(true);
 
+        // Decode the file name to handle URL-encoded spaces and other characters
+        String decodedFileName = URLDecoder.decode(file.getName(), StandardCharsets.UTF_8.toString());
+
+        // Create a label with the decoded file name
+        Label fileNameLabel = new Label(decodedFileName);
+        fileNameLabel.setStyle("-fx-text-fill: black; -fx-font-size: 12px;");
+
+        // Create a VBox to hold the label and the image view
+        VBox vbox = new VBox(5); // 5 is the spacing between the label and the image
+        vbox.getChildren().addAll(fileNameLabel, imageView);
+
         imageView.setOnMouseClicked(event -> {
             selectImage(image, imageView);
         });
 
-        uploadedImages.getChildren().add(imageView);
+        uploadedImages.getChildren().add(vbox);
     }
 
+
     private void selectImage(Image image, ImageView imageView) {
         if (selectedImageView != null && currentSelectedImageView != imageView) {
             selectedImageView.setImage(image);
@@ -402,8 +421,8 @@ private void showUnannotatedImagesAlert(List<String> unannotatedImages) {
 
     private void saveAnnotationsToFile(File file, AnnotationData.PublicAnnotation annotation) {
         try (PrintWriter writer = new PrintWriter(file)) {
-           String line = String.format("%d %.5f %.5f %.5f %.5f", 0, annotation.getMiddlePointX(), annotation.getMiddlePointY(), annotation.getBoundingBoxWidth(), annotation.getBoundingBoxHeight());
-                            writer.println(line);
+            String line = String.format("%d %.5f %.5f %.5f %.5f", 0, annotation.getMiddlePointX(), annotation.getMiddlePointY(), annotation.getBoundingBoxWidth(), annotation.getBoundingBoxHeight());
+            writer.println(line);
         } catch (FileNotFoundException e) {
             e.printStackTrace();
         }

From 0f1cf27d9ffdf8333be6e00dfb2b3330afea14a5 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Thu, 2 May 2024 17:44:12 +0200
Subject: [PATCH 043/100] Update AnnotationController.java

---
 src/main/java/controller/AnnotationController.java | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 7343cda6..31ae5c62 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -104,15 +104,12 @@ private void displayImage(File file) throws UnsupportedEncodingException {
         imageView.setFitWidth(100);
         imageView.setPreserveRatio(true);
 
-        // Decode the file name to handle URL-encoded spaces and other characters
         String decodedFileName = URLDecoder.decode(file.getName(), StandardCharsets.UTF_8.toString());
 
-        // Create a label with the decoded file name
         Label fileNameLabel = new Label(decodedFileName);
         fileNameLabel.setStyle("-fx-text-fill: black; -fx-font-size: 12px;");
 
-        // Create a VBox to hold the label and the image view
-        VBox vbox = new VBox(5); // 5 is the spacing between the label and the image
+        VBox vbox = new VBox(5);
         vbox.getChildren().addAll(fileNameLabel, imageView);
 
         imageView.setOnMouseClicked(event -> {

From 352e587a66b3ad0fa61f51082444928416bba24e Mon Sep 17 00:00:00 2001
From: muazzamaqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Thu, 2 May 2024 17:48:15 +0200
Subject: [PATCH 044/100] Revert "Merge pull request #28 from
 zegLine/group-e-FileNames-SideView"

This reverts commit 850ce1020708e32bca0e51e301cb6f1b1b8efcb0, reversing
changes made to 3f9f9e248f7446b7bb594f3232b1e09b80e7c2f3.
---
 .../java/controller/AnnotationController.java | 24 ++++---------------
 1 file changed, 4 insertions(+), 20 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 31ae5c62..4204dc47 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -25,16 +25,9 @@
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.PrintWriter;
-import java.io.UnsupportedEncodingException;
 import java.net.URL;
 import java.util.*;
 
-import javafx.scene.control.Label;
-import javafx.scene.layout.VBox;
-import java.net.URLDecoder;
-import java.nio.charset.StandardCharsets;
-
-
 public class AnnotationController implements Controller {
     @FXML
     public VBox uploadedImages;     //Where the users see the files
@@ -97,29 +90,20 @@ public void Handle_Upload_Functionality(ActionEvent actionEvent) {
         }
     }
 
-    private void displayImage(File file) throws UnsupportedEncodingException {
+    private void displayImage(File file) {
         Image image = new Image(file.toURI().toString());
         ImageView imageView = new ImageView(image);
         imageView.setFitHeight(100);
         imageView.setFitWidth(100);
         imageView.setPreserveRatio(true);
 
-        String decodedFileName = URLDecoder.decode(file.getName(), StandardCharsets.UTF_8.toString());
-
-        Label fileNameLabel = new Label(decodedFileName);
-        fileNameLabel.setStyle("-fx-text-fill: black; -fx-font-size: 12px;");
-
-        VBox vbox = new VBox(5);
-        vbox.getChildren().addAll(fileNameLabel, imageView);
-
         imageView.setOnMouseClicked(event -> {
             selectImage(image, imageView);
         });
 
-        uploadedImages.getChildren().add(vbox);
+        uploadedImages.getChildren().add(imageView);
     }
 
-
     private void selectImage(Image image, ImageView imageView) {
         if (selectedImageView != null && currentSelectedImageView != imageView) {
             selectedImageView.setImage(image);
@@ -418,8 +402,8 @@ private void showUnannotatedImagesAlert(List<String> unannotatedImages) {
 
     private void saveAnnotationsToFile(File file, AnnotationData.PublicAnnotation annotation) {
         try (PrintWriter writer = new PrintWriter(file)) {
-            String line = String.format("%d %.5f %.5f %.5f %.5f", 0, annotation.getMiddlePointX(), annotation.getMiddlePointY(), annotation.getBoundingBoxWidth(), annotation.getBoundingBoxHeight());
-            writer.println(line);
+           String line = String.format("%d %.5f %.5f %.5f %.5f", 0, annotation.getMiddlePointX(), annotation.getMiddlePointY(), annotation.getBoundingBoxWidth(), annotation.getBoundingBoxHeight());
+                            writer.println(line);
         } catch (FileNotFoundException e) {
             e.printStackTrace();
         }

From 4d3fdc0d66189c86fc2cc23632a9d026fbef92de Mon Sep 17 00:00:00 2001
From: muazzamaqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Thu, 2 May 2024 20:03:07 +0200
Subject: [PATCH 045/100] Theme Button (Placement Fix)

---
 .../java/controller/AnnotationController.java | 10 +++-
 src/main/java/controller/MainController.java  | 49 +++++++++++++++++++
 src/main/resources/view/AnnotationView.fxml   |  5 --
 src/main/resources/view/MainView.fxml         |  3 ++
 4 files changed, 61 insertions(+), 6 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 4204dc47..e66b53de 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -417,14 +417,18 @@ private void showNoAnnotationAlert() {
         alert.showAndWait();
     }
 
+
+
+    ///Below Code Now is part of the MainController Class, as it has been approved to be part of the main application
     /**
      * Handles Dark/Light-Mode based Functionality
      * @param event The Mouse Event
      */
+    /*
     @FXML
     private void handleToggleTheme(ActionEvent event) {
         try {
-            Scene scene = ((Node) event.getSource()).getScene();
+           Scene = ((Node) event.getSource()).getScene();
             String lightModeUrl = getClass().getResource("/css/light-mode.css").toExternalForm();
             String darkModeUrl = getClass().getResource("/css/dark-mode.css").toExternalForm();
 
@@ -443,6 +447,10 @@ private void handleToggleTheme(ActionEvent event) {
             showAlert("Error", "Failed to toggle theme.");
         }
     }
+    */
+
+
+
     @FXML
     public void deletionfunctionality(ActionEvent event) {
         if (currentSelectedImageView != null) {
diff --git a/src/main/java/controller/MainController.java b/src/main/java/controller/MainController.java
index f2445842..f16bb00e 100644
--- a/src/main/java/controller/MainController.java
+++ b/src/main/java/controller/MainController.java
@@ -2,14 +2,20 @@
 
 import java.io.IOException;
 import java.net.URL;
+import java.util.Objects;
 import java.util.ResourceBundle;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import algorithm.VisualizationManager;
 import javafx.application.Platform;
+import javafx.event.ActionEvent;
 import javafx.fxml.FXML;
 import javafx.fxml.FXMLLoader;
+import javafx.scene.Node;
 import javafx.scene.Scene;
+import javafx.scene.control.*;
+import javafx.stage.Modality;
+import javafx.stage.Stage;
 import javafx.scene.control.Alert;
 import javafx.scene.control.Label;
 import javafx.scene.control.Tab;
@@ -176,4 +182,47 @@ public void openAboutView() {
         a.setContentText("This application was and currently is developed by students of THU.\nIt is actively supervised by Prof. Dr. Alfred Franz.\nThe source code can be found at https://github.com/Alfred-Franz/IGTPrototypingTool");
         a.showAndWait();
     }
+
+
+
+    /*
+    This function has the implementation of dark and light mode for the whole application
+     */
+    @FXML
+    private void handleToggleTheme(ActionEvent event) {
+        try {
+            // Accessing the Scene from the MenuItem indirectly
+            MenuItem menuItem = (MenuItem) event.getSource();
+            Scene scene = menuItem.getParentPopup().getOwnerWindow().getScene();
+
+            String lightModeUrl = Objects.requireNonNull(getClass().getResource("/css/light-mode.css")).toExternalForm();
+            String darkModeUrl = Objects.requireNonNull(getClass().getResource("/css/dark-mode.css")).toExternalForm();
+
+            System.out.println("Light Mode URL: " + lightModeUrl);
+            System.out.println("Dark Mode URL: " + darkModeUrl);
+
+            if (lightModeUrl == null || darkModeUrl == null) {
+                throw new Exception("Theme CSS file(s) not found.");
+            }
+
+            if (scene.getStylesheets().contains(darkModeUrl)) {
+                scene.getStylesheets().remove(darkModeUrl);
+                scene.getStylesheets().add(lightModeUrl);
+            } else {
+                scene.getStylesheets().remove(lightModeUrl);
+                scene.getStylesheets().add(darkModeUrl);
+            }
+        } catch (Exception e) {
+            e.printStackTrace();
+            showAlert("Error", "Failed to toggle theme: " + e.getMessage());
+        }
+    }
+
+    private void showAlert(String title, String content) {
+        Alert alert = new Alert(Alert.AlertType.INFORMATION);
+        alert.setTitle(title);
+        alert.setHeaderText(null);
+        alert.setContentText(content);
+        alert.showAndWait();
+    }
 }
diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index a33e7063..c307c991 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -63,11 +63,6 @@
                         <Insets left="10.0" right="55.0" />
                      </HBox.margin>
                   </Button>
-                  <Button fx:id="toggleThemeButton" text="Theme" onAction="#handleToggleTheme" HBox.hgrow="ALWAYS" maxWidth="170" style="-fx-font-size: 16px;">
-                     <HBox.margin>
-                        <Insets left="10.0" right="10.0" />
-                     </HBox.margin>
-                  </Button>
                </children>
             </HBox>
          </top>
diff --git a/src/main/resources/view/MainView.fxml b/src/main/resources/view/MainView.fxml
index d88b7bd6..2539d725 100644
--- a/src/main/resources/view/MainView.fxml
+++ b/src/main/resources/view/MainView.fxml
@@ -31,6 +31,9 @@
             <Menu mnemonicParsing="false" text="Help">
                 <MenuItem mnemonicParsing="false" onAction="#openAboutView" text="About"/>
             </Menu>
+            <Menu mnemonicParsing="false" text="Theme">
+                <MenuItem mnemonicParsing="false" onAction="#handleToggleTheme" text="Toggle Dark/Light Mode"/>
+            </Menu>
         </MenuBar>
     </top>
     <center>

From cc8f9db0e5a08b7c924de13c3dcf7610d8ded04e Mon Sep 17 00:00:00 2001
From: Simon Engel <engesi02@thu.de>
Date: Thu, 2 May 2024 23:28:28 +0200
Subject: [PATCH 046/100] Select Multiple pictures in the Side View

---
 .../java/controller/AnnotationController.java | 27 ++++++++++++++++++-
 1 file changed, 26 insertions(+), 1 deletion(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 4204dc47..67f119e8 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -1,15 +1,19 @@
 package controller;
 
 import javafx.event.ActionEvent;
+import javafx.event.EventHandler;
 import javafx.fxml.FXML;
+import javafx.geometry.Insets;
 import javafx.scene.Node;
 import javafx.scene.Scene;
 import javafx.scene.control.Alert;
 import javafx.scene.control.Button;
+import javafx.scene.control.CheckBox;
 import javafx.scene.control.ScrollPane;
 import javafx.scene.image.Image;
 import javafx.scene.image.ImageView;
 import javafx.scene.input.MouseEvent;
+import javafx.scene.layout.HBox;
 import javafx.scene.layout.Pane;
 import javafx.scene.layout.VBox;
 import javafx.scene.paint.Color;
@@ -48,6 +52,8 @@ public class AnnotationController implements Controller {
 
     private List<File> selectedImages;
     private Set<String> uploadedFilePaths = new HashSet<>();
+    // store the paths of the selected Image, so you can Export the data based on these keys
+    private Set<String> selectedFilePaths = new HashSet<>();
 
 
     @Override
@@ -91,6 +97,15 @@ public void Handle_Upload_Functionality(ActionEvent actionEvent) {
     }
 
     private void displayImage(File file) {
+        HBox hbox = new HBox();
+        //Setting the space between the nodes of a HBox pane
+        hbox.setSpacing(10);
+
+        CheckBox checkBox = new CheckBox();
+        checkBox.setSelected(false);
+
+        hbox.setMargin(checkBox, new Insets(10, 30, 10, 10));
+
         Image image = new Image(file.toURI().toString());
         ImageView imageView = new ImageView(image);
         imageView.setFitHeight(100);
@@ -101,7 +116,17 @@ private void displayImage(File file) {
             selectImage(image, imageView);
         });
 
-        uploadedImages.getChildren().add(imageView);
+        checkBox.selectedProperty().addListener((observable, oldValue, newValue) -> {
+            if (newValue) { // Checkbox is now selected
+                selectedFilePaths.add(imageView.getImage().getUrl());
+            } else { // Checkbox is now unselected
+                selectedFilePaths.remove(imageView.getImage().getUrl());
+            }
+        });
+
+        hbox.getChildren().add(imageView);
+        hbox.getChildren().add(checkBox);
+        uploadedImages.getChildren().add(hbox);
     }
 
     private void selectImage(Image image, ImageView imageView) {

From 3b16e9233970e0bb8a9ee29efd04be94e470b91b Mon Sep 17 00:00:00 2001
From: Simon Engel <engesi02@thu.de>
Date: Fri, 3 May 2024 08:28:28 +0200
Subject: [PATCH 047/100] Removed few Warnings

---
 .../java/controller/AnnotationController.java | 25 +++++++++----------
 src/main/java/util/AnnotationData.java        |  4 +--
 2 files changed, 13 insertions(+), 16 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 67f119e8..1bf81da9 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -1,7 +1,6 @@
 package controller;
 
 import javafx.event.ActionEvent;
-import javafx.event.EventHandler;
 import javafx.fxml.FXML;
 import javafx.geometry.Insets;
 import javafx.scene.Node;
@@ -50,7 +49,6 @@ public class AnnotationController implements Controller {
     private boolean dragged = false;
     private double annotationPointX, annotationPointY;
 
-    private List<File> selectedImages;
     private Set<String> uploadedFilePaths = new HashSet<>();
     // store the paths of the selected Image, so you can Export the data based on these keys
     private Set<String> selectedFilePaths = new HashSet<>();
@@ -78,7 +76,7 @@ public void Handle_Upload_Functionality(ActionEvent actionEvent) {
             );
             Stage currentStage = (Stage) ((javafx.scene.Node) actionEvent.getSource()).getScene().getWindow();
 
-            this.selectedImages = fileChooser.showOpenMultipleDialog(currentStage);
+            List<File> selectedImages = fileChooser.showOpenMultipleDialog(currentStage);
 
             if (selectedImages != null) {
                 for (File file : selectedImages) {
@@ -92,7 +90,7 @@ public void Handle_Upload_Functionality(ActionEvent actionEvent) {
                 }
             }
         } catch (Exception e) {
-            e.printStackTrace();
+            System.err.println("Error while choosing File: " + e.getMessage()) ;
         }
     }
 
@@ -115,7 +113,7 @@ private void displayImage(File file) {
         imageView.setOnMouseClicked(event -> {
             selectImage(image, imageView);
         });
-
+        // Add or Remove the selected file paths to the HasSet
         checkBox.selectedProperty().addListener((observable, oldValue, newValue) -> {
             if (newValue) { // Checkbox is now selected
                 selectedFilePaths.add(imageView.getImage().getUrl());
@@ -190,7 +188,7 @@ public void Select_Next_Image(ActionEvent actionEvent) {
                 }
             }
         } catch (Exception e) {
-            e.printStackTrace();
+            System.err.println("Error while selecting next Image: " + e.getMessage()) ;
         }
     }
 
@@ -205,7 +203,7 @@ public void Select_Previous_Image(ActionEvent actionEvent) {
                 }
             }
         } catch (Exception e) {
-            e.printStackTrace();
+            System.err.println("Error while selecting previous Image: " + e.getMessage()) ;
         }
     }
 
@@ -325,7 +323,7 @@ private void handleExportAction(ActionEvent event) {
             } catch (Exception e) {
                 fileChooser.setInitialFileName("default_annotations.txt");
                 showAlert("Error", "There was an issue processing the image file name.");
-                e.printStackTrace();
+                System.err.println("Error while Exporting: " + e.getMessage()) ;
             }
 
             fileChooser.getExtensionFilters().addAll(new FileChooser.ExtensionFilter("Text Files", "*.txt"));
@@ -378,7 +376,7 @@ private void handleExportAllAction(ActionEvent event) {
                     File annotationFile = new File(selectedDirectory, fileName);
                     saveAnnotationsToFile(annotationFile, annotation);
                 } catch (Exception e) {
-                    showAlert("Error", "Failed to save annotations for " + file.getName());
+                    showAlert("Error", "Failed to save annotations for " + path);
                 }
             });
         }
@@ -430,7 +428,7 @@ private void saveAnnotationsToFile(File file, AnnotationData.PublicAnnotation an
            String line = String.format("%d %.5f %.5f %.5f %.5f", 0, annotation.getMiddlePointX(), annotation.getMiddlePointY(), annotation.getBoundingBoxWidth(), annotation.getBoundingBoxHeight());
                             writer.println(line);
         } catch (FileNotFoundException e) {
-            e.printStackTrace();
+            System.err.println("Error while saving Annotation to File: " + e.getMessage()) ;
         }
     }
 
@@ -464,7 +462,7 @@ private void handleToggleTheme(ActionEvent event) {
                 scene.getStylesheets().add(darkModeUrl);
             }
         } catch (Exception e) {
-            e.printStackTrace();
+            System.err.println("Error while changing Theme: " + e.getMessage()) ;
             showAlert("Error", "Failed to toggle theme.");
         }
     }
@@ -476,12 +474,13 @@ public void deletionfunctionality(ActionEvent event) {
                 imagePath = new File(new URL(currentSelectedImageView.getImage().getUrl()).toURI()).getAbsolutePath();
             } catch (Exception e) {
                 showAlert("Error", "Could not retrieve file path from the image.");
-                e.printStackTrace();
+                System.err.println("Error while retrieving filepath during deletion: " + e.getMessage()) ;
             }
 
             uploadedImages.getChildren().remove(currentSelectedImageView);
-            if (imagePath != null && uploadedFilePaths.contains(imagePath)) {
+            if (imagePath != null) {
                 uploadedFilePaths.remove(imagePath);
+                selectedFilePaths.remove(imagePath);
             }
             if (selectedImageView.getImage() == currentSelectedImageView.getImage()) {
                 clearAnnotations(event);
diff --git a/src/main/java/util/AnnotationData.java b/src/main/java/util/AnnotationData.java
index 01df86f5..172db61c 100644
--- a/src/main/java/util/AnnotationData.java
+++ b/src/main/java/util/AnnotationData.java
@@ -82,9 +82,7 @@ public Rectangle getAnnotation(String path){
      * @param path Image path (Key for the Map)
      */
     public void deleteAnnotation(String path){
-        if(annotations.containsKey(path)){
-            annotations.remove(path);
-        }
+        annotations.remove(path);
     }
 
     public static AnnotationData getInstance() {

From 704e38e079a02af344cd8264fe689e07e758f3ac Mon Sep 17 00:00:00 2001
From: muazzamaqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Sat, 4 May 2024 13:33:26 +0200
Subject: [PATCH 048/100] Default Color - Fix

---
 src/main/java/controller/MainController.java | 2 +-
 src/main/resources/css/light-mode.css        | 9 ---------
 2 files changed, 1 insertion(+), 10 deletions(-)
 delete mode 100644 src/main/resources/css/light-mode.css

diff --git a/src/main/java/controller/MainController.java b/src/main/java/controller/MainController.java
index f16bb00e..530f4d91 100644
--- a/src/main/java/controller/MainController.java
+++ b/src/main/java/controller/MainController.java
@@ -195,7 +195,7 @@ private void handleToggleTheme(ActionEvent event) {
             MenuItem menuItem = (MenuItem) event.getSource();
             Scene scene = menuItem.getParentPopup().getOwnerWindow().getScene();
 
-            String lightModeUrl = Objects.requireNonNull(getClass().getResource("/css/light-mode.css")).toExternalForm();
+            String lightModeUrl = Objects.requireNonNull(getClass().getResource("/css/customstyle.css")).toExternalForm();
             String darkModeUrl = Objects.requireNonNull(getClass().getResource("/css/dark-mode.css")).toExternalForm();
 
             System.out.println("Light Mode URL: " + lightModeUrl);
diff --git a/src/main/resources/css/light-mode.css b/src/main/resources/css/light-mode.css
deleted file mode 100644
index c6085861..00000000
--- a/src/main/resources/css/light-mode.css
+++ /dev/null
@@ -1,9 +0,0 @@
-.root {
-    -fx-background-color: white;
-    -fx-text-fill: black;
-}
-
-.button {
-    -fx-background-color: #E0E0E0;
-    -fx-text-fill: black;
-}

From 2b951cd3f4b78e6b311b9ade7db10f1c3284f7e1 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Sat, 4 May 2024 13:42:38 +0200
Subject: [PATCH 049/100] Update AnnotationController.java

---
 src/main/java/controller/AnnotationController.java | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index e3961d33..e30da4c9 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -352,12 +352,18 @@ private void handleExportAllAction(ActionEvent event) {
 
         List<String> unannotatedImages = new ArrayList<>();
         for (Node node : uploadedImages.getChildren()) {
-            ImageView imageView = (ImageView) node;
-            if (AnnotationData.getInstance().getAnnotation(imageView.getImage().getUrl()) == null) {
-                unannotatedImages.add(new File(imageView.getImage().getUrl()).getName());
+            if (node instanceof HBox) {
+                HBox hbox = (HBox) node;
+                for (Node child : hbox.getChildren()) {
+                    if (child instanceof ImageView) {
+                        ImageView imageView = (ImageView) child;
+                        if (AnnotationData.getInstance().getAnnotation(imageView.getImage().getUrl()) == null) {
+                            unannotatedImages.add(new File(imageView.getImage().getUrl()).getName());
+                        }
+                    }
+                }
             }
         }
-
         if (!unannotatedImages.isEmpty()) {
             showUnannotatedImagesAlert(unannotatedImages);
             return;

From 6ea68073deaeb46f472b1e8fe02e0243862aea58 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Sat, 4 May 2024 13:53:41 +0200
Subject: [PATCH 050/100] Update AnnotationController.java

---
 .../java/controller/AnnotationController.java | 84 ++++++++++++-------
 1 file changed, 52 insertions(+), 32 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index e30da4c9..eb9e82b6 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -90,7 +90,7 @@ public void Handle_Upload_Functionality(ActionEvent actionEvent) {
                 }
             }
         } catch (Exception e) {
-            System.err.println("Error while choosing File: " + e.getMessage()) ;
+            System.err.println("Error while choosing File: " + e.getMessage());
         }
     }
 
@@ -188,7 +188,7 @@ public void Select_Next_Image(ActionEvent actionEvent) {
                 }
             }
         } catch (Exception e) {
-            System.err.println("Error while selecting next Image: " + e.getMessage()) ;
+            System.err.println("Error while selecting next Image: " + e.getMessage());
         }
     }
 
@@ -203,12 +203,12 @@ public void Select_Previous_Image(ActionEvent actionEvent) {
                 }
             }
         } catch (Exception e) {
-            System.err.println("Error while selecting previous Image: " + e.getMessage()) ;
+            System.err.println("Error while selecting previous Image: " + e.getMessage());
         }
     }
 
     public void clearAnnotations(ActionEvent actionEvent) {
-        if(annotatedRectangle != null){
+        if (annotatedRectangle != null) {
             annotationPane.getChildren().remove(annotatedRectangle);
             annotationPane.getChildren().remove(middlePoint);
             AnnotationData.getInstance().deleteAnnotation(selectedImageView.getImage().getUrl());
@@ -305,8 +305,10 @@ private void releasedAnnotationEvent(MouseEvent event) {
         );
 
     }
+
     /**
      * Handles Export based Functionality
+     *
      * @param event The Mouse Event
      */
     @FXML
@@ -323,7 +325,7 @@ private void handleExportAction(ActionEvent event) {
             } catch (Exception e) {
                 fileChooser.setInitialFileName("default_annotations.txt");
                 showAlert("Error", "There was an issue processing the image file name.");
-                System.err.println("Error while Exporting: " + e.getMessage()) ;
+                System.err.println("Error while Exporting: " + e.getMessage());
             }
 
             fileChooser.getExtensionFilters().addAll(new FileChooser.ExtensionFilter("Text Files", "*.txt"));
@@ -338,7 +340,6 @@ private void handleExportAction(ActionEvent event) {
     }
 
 
-
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
     ///Export-All-Functionality----------START
 
@@ -422,19 +423,19 @@ private void showUnannotatedImagesAlert(List<String> unannotatedImages) {
     ///Export-All-Functionality----------END
 
 
-
     /**
      * Handles the Saving of Annotations to a File
-     * @param file The File to save the Annotations to
+     *
+     * @param file       The File to save the Annotations to
      * @param annotation The Annotation Data to save
      */
 
     private void saveAnnotationsToFile(File file, AnnotationData.PublicAnnotation annotation) {
         try (PrintWriter writer = new PrintWriter(file)) {
-           String line = String.format("%d %.5f %.5f %.5f %.5f", 0, annotation.getMiddlePointX(), annotation.getMiddlePointY(), annotation.getBoundingBoxWidth(), annotation.getBoundingBoxHeight());
-                            writer.println(line);
+            String line = String.format("%d %.5f %.5f %.5f %.5f", 0, annotation.getMiddlePointX(), annotation.getMiddlePointY(), annotation.getBoundingBoxWidth(), annotation.getBoundingBoxHeight());
+            writer.println(line);
         } catch (FileNotFoundException e) {
-            System.err.println("Error while saving Annotation to File: " + e.getMessage()) ;
+            System.err.println("Error while saving Annotation to File: " + e.getMessage());
         }
     }
 
@@ -447,10 +448,11 @@ private void showNoAnnotationAlert() {
     }
 
 
-
     ///Below Code Now is part of the MainController Class, as it has been approved to be part of the main application
+
     /**
      * Handles Dark/Light-Mode based Functionality
+     *
      * @param event The Mouse Event
      */
     /*
@@ -478,31 +480,49 @@ private void handleToggleTheme(ActionEvent event) {
     }
     */
 
-
-
+    /**
+     * Handles Deleting Functionality - Multiple Deletion Functionality has been also implemented
+     *
+     * @param event The Mouse Event
+     */
     @FXML
     public void deletionfunctionality(ActionEvent event) {
-        if (currentSelectedImageView != null) {
-            String imagePath = null;
-            try {
-                imagePath = new File(new URL(currentSelectedImageView.getImage().getUrl()).toURI()).getAbsolutePath();
-            } catch (Exception e) {
-                showAlert("Error", "Could not retrieve file path from the image.");
-                System.err.println("Error while retrieving filepath during deletion: " + e.getMessage()) ;
-            }
+        List<Node> toRemove = new ArrayList<>();
+        boolean currentDisplayedRemoved = false;
 
-            uploadedImages.getChildren().remove(currentSelectedImageView);
-            if (imagePath != null) {
-                uploadedFilePaths.remove(imagePath);
-                selectedFilePaths.remove(imagePath);
-            }
-            if (selectedImageView.getImage() == currentSelectedImageView.getImage()) {
-                clearAnnotations(event);
-                selectedImageView.setImage(null);
+        for (Node node : uploadedImages.getChildren()) {
+            if (node instanceof HBox) {
+                HBox hbox = (HBox) node;
+                ImageView imageView = (ImageView) hbox.getChildren().get(0);
+                CheckBox checkBox = (CheckBox) hbox.getChildren().get(1);
+                if (checkBox.isSelected()) {
+                    String imagePath = null;
+                    try {
+                        imagePath = new File(new URL(imageView.getImage().getUrl()).toURI()).getAbsolutePath();
+                        toRemove.add(node); // Mark for removal
+                        uploadedFilePaths.remove(imagePath);
+                        selectedFilePaths.remove(imagePath);
+                        AnnotationData.getInstance().deleteAnnotation(imageView.getImage().getUrl());
+                        if (imageView.equals(currentSelectedImageView)) {
+                            currentDisplayedRemoved = true;
+                        }
+                    } catch (Exception e) {
+                        showAlert("Error", "Could not retrieve file path from the image.");
+                        System.err.println("Error while retrieving filepath during deletion: " + e.getMessage());
+                    }
+                }
             }
+        }
+
+        uploadedImages.getChildren().removeAll(toRemove); // Removing from the UI
+
+        if (currentDisplayedRemoved) {
+            selectedImageView.setImage(null);
             currentSelectedImageView = null;
-        } else {
-            showAlert("No Selection", "No image is currently selected to delete.");
+        }
+
+        if (uploadedImages.getChildren().isEmpty()) {
+            showAlert("Notice", "All images have been deleted.");
         }
     }
 }

From 8337e690bc8f7f58c48a10184ded23978d3fcfe5 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Sun, 5 May 2024 17:25:29 +0200
Subject: [PATCH 051/100] Deleting Annotation Data

Annotation Data Gets Deleted Now
---
 .../java/controller/AnnotationController.java | 32 +++++++++++++------
 src/main/java/util/AnnotationData.java        |  5 ++-
 2 files changed, 26 insertions(+), 11 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index eb9e82b6..a2dc0e49 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -489,40 +489,52 @@ private void handleToggleTheme(ActionEvent event) {
     public void deletionfunctionality(ActionEvent event) {
         List<Node> toRemove = new ArrayList<>();
         boolean currentDisplayedRemoved = false;
-
+        boolean atLeastOneSelected = false;
+        // Iterate over each node in the uploadedImages VBox
         for (Node node : uploadedImages.getChildren()) {
             if (node instanceof HBox) {
                 HBox hbox = (HBox) node;
                 ImageView imageView = (ImageView) hbox.getChildren().get(0);
                 CheckBox checkBox = (CheckBox) hbox.getChildren().get(1);
+                // Check if the CheckBox is selected for deletion
                 if (checkBox.isSelected()) {
+                    atLeastOneSelected = true;
                     String imagePath = null;
                     try {
                         imagePath = new File(new URL(imageView.getImage().getUrl()).toURI()).getAbsolutePath();
-                        toRemove.add(node); // Mark for removal
+                        // Delete annotation from AnnotationData
+                        if (AnnotationData.getInstance().deleteAnnotation(imageView.getImage().getUrl())) {
+                            System.out.println("Annotation deleted for image: " + imagePath);
+                        } else {
+                            System.out.println("No annotation found or error deleting annotation for image: " + imagePath);
+                        }
+                        toRemove.add(node);
                         uploadedFilePaths.remove(imagePath);
                         selectedFilePaths.remove(imagePath);
-                        AnnotationData.getInstance().deleteAnnotation(imageView.getImage().getUrl());
                         if (imageView.equals(currentSelectedImageView)) {
                             currentDisplayedRemoved = true;
                         }
                     } catch (Exception e) {
-                        showAlert("Error", "Could not retrieve file path from the image.");
+                        showAlert("Error", "Could not retrieve file path from the image: " + e.getMessage());
                         System.err.println("Error while retrieving filepath during deletion: " + e.getMessage());
                     }
                 }
             }
         }
-
-        uploadedImages.getChildren().removeAll(toRemove); // Removing from the UI
-
-        if (currentDisplayedRemoved) {
-            selectedImageView.setImage(null);
-            currentSelectedImageView = null;
+        if (atLeastOneSelected) {
+            uploadedImages.getChildren().removeAll(toRemove);
+            if (currentDisplayedRemoved) {
+                selectedImageView.setImage(null);
+                currentSelectedImageView = null;
+            }
+        } else {
+            showAlert("Notice", "No images selected for deletion.");
         }
 
+        // Notify if all images have been deleted
         if (uploadedImages.getChildren().isEmpty()) {
             showAlert("Notice", "All images have been deleted.");
         }
     }
+
 }
diff --git a/src/main/java/util/AnnotationData.java b/src/main/java/util/AnnotationData.java
index 172db61c..980107ec 100644
--- a/src/main/java/util/AnnotationData.java
+++ b/src/main/java/util/AnnotationData.java
@@ -79,10 +79,13 @@ public Rectangle getAnnotation(String path){
 
     /**
      * Function to delete the Annotation of one Image
+     *
      * @param path Image path (Key for the Map)
+     * @return
      */
-    public void deleteAnnotation(String path){
+    public boolean deleteAnnotation(String path){
         annotations.remove(path);
+        return false;
     }
 
     public static AnnotationData getInstance() {

From 134e5e4c5309499577e4a97a40c32e6a149b1aa4 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Sun, 5 May 2024 17:39:40 +0200
Subject: [PATCH 052/100] Update AnnotationController.java

Requirements from Group A and C
---
 src/main/java/controller/AnnotationController.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index a2dc0e49..332b2d35 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -320,7 +320,7 @@ private void handleExportAction(ActionEvent event) {
             try {
                 String currentImageUrl = selectedImageView.getImage().getUrl();
                 String currentImageName = new File(new URL(currentImageUrl).toURI().getPath()).getName();
-                String initialFileName = currentImageName.substring(0, currentImageName.lastIndexOf('.')) + "_annotations.txt";
+                String initialFileName = currentImageName.substring(0, currentImageName.lastIndexOf('.')) + ".txt";
                 fileChooser.setInitialFileName(initialFileName);
             } catch (Exception e) {
                 fileChooser.setInitialFileName("default_annotations.txt");
@@ -379,7 +379,7 @@ private void handleExportAllAction(ActionEvent event) {
                 File file = null;
                 try {
                     file = new File(new URL(path).toURI());
-                    String fileName = file.getName().substring(0, file.getName().lastIndexOf('.')) + "_annotations.txt";
+                    String fileName = file.getName().substring(0, file.getName().lastIndexOf('.')) + ".txt";
                     File annotationFile = new File(selectedDirectory, fileName);
                     saveAnnotationsToFile(annotationFile, annotation);
                 } catch (Exception e) {

From 2951d6ef8366f656f85cc375f4fb53e9fb65098f Mon Sep 17 00:00:00 2001
From: muazzamaqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Sun, 5 May 2024 17:55:13 +0200
Subject: [PATCH 053/100] Update AnnotationController.java

Code Optimization
---
 .../java/controller/AnnotationController.java | 55 ++++---------------
 1 file changed, 10 insertions(+), 45 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 332b2d35..7dfbe6af 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -4,7 +4,6 @@
 import javafx.fxml.FXML;
 import javafx.geometry.Insets;
 import javafx.scene.Node;
-import javafx.scene.Scene;
 import javafx.scene.control.Alert;
 import javafx.scene.control.Button;
 import javafx.scene.control.CheckBox;
@@ -49,9 +48,9 @@ public class AnnotationController implements Controller {
     private boolean dragged = false;
     private double annotationPointX, annotationPointY;
 
-    private Set<String> uploadedFilePaths = new HashSet<>();
+    private final Set<String> uploadedFilePaths = new HashSet<>();
     // store the paths of the selected Image, so you can Export the data based on these keys
-    private Set<String> selectedFilePaths = new HashSet<>();
+    private final Set<String> selectedFilePaths = new HashSet<>();
 
 
     @Override
@@ -102,7 +101,7 @@ private void displayImage(File file) {
         CheckBox checkBox = new CheckBox();
         checkBox.setSelected(false);
 
-        hbox.setMargin(checkBox, new Insets(10, 30, 10, 10));
+        HBox.setMargin(checkBox, new Insets(10, 30, 10, 10));
 
         Image image = new Image(file.toURI().toString());
         ImageView imageView = new ImageView(image);
@@ -177,7 +176,7 @@ private void selectImage(Image image, ImageView imageView) {
         }
     }
 
-    public void Select_Next_Image(ActionEvent actionEvent) {
+    public void Select_Next_Image() {
         try {
             if (currentSelectedImageView != null) {
                 int currentIndex = uploadedImages.getChildren().indexOf(currentSelectedImageView);
@@ -192,7 +191,7 @@ public void Select_Next_Image(ActionEvent actionEvent) {
         }
     }
 
-    public void Select_Previous_Image(ActionEvent actionEvent) {
+    public void Select_Previous_Image() {
         try {
             if (currentSelectedImageView != null) {
                 int currentIndex = uploadedImages.getChildren().indexOf(currentSelectedImageView);
@@ -207,7 +206,7 @@ public void Select_Previous_Image(ActionEvent actionEvent) {
         }
     }
 
-    public void clearAnnotations(ActionEvent actionEvent) {
+    public void clearAnnotations() {
         if (annotatedRectangle != null) {
             annotationPane.getChildren().remove(annotatedRectangle);
             annotationPane.getChildren().remove(middlePoint);
@@ -353,11 +352,9 @@ private void handleExportAllAction(ActionEvent event) {
 
         List<String> unannotatedImages = new ArrayList<>();
         for (Node node : uploadedImages.getChildren()) {
-            if (node instanceof HBox) {
-                HBox hbox = (HBox) node;
+            if (node instanceof HBox hbox) {
                 for (Node child : hbox.getChildren()) {
-                    if (child instanceof ImageView) {
-                        ImageView imageView = (ImageView) child;
+                    if (child instanceof ImageView imageView) {
                         if (AnnotationData.getInstance().getAnnotation(imageView.getImage().getUrl()) == null) {
                             unannotatedImages.add(new File(imageView.getImage().getUrl()).getName());
                         }
@@ -450,50 +447,18 @@ private void showNoAnnotationAlert() {
 
     ///Below Code Now is part of the MainController Class, as it has been approved to be part of the main application
 
-    /**
-     * Handles Dark/Light-Mode based Functionality
-     *
-     * @param event The Mouse Event
-     */
-    /*
-    @FXML
-    private void handleToggleTheme(ActionEvent event) {
-        try {
-           Scene = ((Node) event.getSource()).getScene();
-            String lightModeUrl = getClass().getResource("/css/light-mode.css").toExternalForm();
-            String darkModeUrl = getClass().getResource("/css/dark-mode.css").toExternalForm();
-
-            System.out.println("Light Mode URL: " + lightModeUrl);
-            System.out.println("Dark Mode URL: " + darkModeUrl);
-
-            if (scene.getStylesheets().contains(darkModeUrl)) {
-                scene.getStylesheets().remove(darkModeUrl);
-                scene.getStylesheets().add(lightModeUrl);
-            } else {
-                scene.getStylesheets().remove(lightModeUrl);
-                scene.getStylesheets().add(darkModeUrl);
-            }
-        } catch (Exception e) {
-            System.err.println("Error while changing Theme: " + e.getMessage()) ;
-            showAlert("Error", "Failed to toggle theme.");
-        }
-    }
-    */
-
     /**
      * Handles Deleting Functionality - Multiple Deletion Functionality has been also implemented
      *
-     * @param event The Mouse Event
      */
     @FXML
-    public void deletionfunctionality(ActionEvent event) {
+    public void deletionfunctionality() {
         List<Node> toRemove = new ArrayList<>();
         boolean currentDisplayedRemoved = false;
         boolean atLeastOneSelected = false;
         // Iterate over each node in the uploadedImages VBox
         for (Node node : uploadedImages.getChildren()) {
-            if (node instanceof HBox) {
-                HBox hbox = (HBox) node;
+            if (node instanceof HBox hbox) {
                 ImageView imageView = (ImageView) hbox.getChildren().get(0);
                 CheckBox checkBox = (CheckBox) hbox.getChildren().get(1);
                 // Check if the CheckBox is selected for deletion

From 2383c5b64f14ba907bde6f60c75daa18a405a84d Mon Sep 17 00:00:00 2001
From: muazzamaqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Sun, 5 May 2024 18:26:41 +0200
Subject: [PATCH 054/100] Update AnnotationController.java

---
 src/main/java/controller/AnnotationController.java | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 7dfbe6af..373f4b47 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -83,7 +83,6 @@ public void Handle_Upload_Functionality(ActionEvent actionEvent) {
                         displayImage(file);
                         uploadedFilePaths.add(file.getAbsolutePath());
                     } else {
-                        // Optionally, alert the user that the file has already been uploaded
                         showAlert("Duplicate File", "The file " + file.getName() + " has already been uploaded.");
                     }
                 }
@@ -95,7 +94,6 @@ public void Handle_Upload_Functionality(ActionEvent actionEvent) {
 
     private void displayImage(File file) {
         HBox hbox = new HBox();
-        //Setting the space between the nodes of a HBox pane
         hbox.setSpacing(10);
 
         CheckBox checkBox = new CheckBox();
@@ -445,7 +443,6 @@ private void showNoAnnotationAlert() {
     }
 
 
-    ///Below Code Now is part of the MainController Class, as it has been approved to be part of the main application
 
     /**
      * Handles Deleting Functionality - Multiple Deletion Functionality has been also implemented

From d1e17a4dbc517ba02e195c2acfb5be921be01d2b Mon Sep 17 00:00:00 2001
From: muazzamaqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Sun, 5 May 2024 18:36:50 +0200
Subject: [PATCH 055/100] Update AnnotationController.java

---
 .../java/controller/AnnotationController.java | 21 ++++++++-----------
 1 file changed, 9 insertions(+), 12 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 373f4b47..909d743d 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -47,17 +47,13 @@ public class AnnotationController implements Controller {
     private Circle middlePoint;
     private boolean dragged = false;
     private double annotationPointX, annotationPointY;
-
     private final Set<String> uploadedFilePaths = new HashSet<>();
     // store the paths of the selected Image, so you can Export the data based on these keys
     private final Set<String> selectedFilePaths = new HashSet<>();
-
-
     @Override
     public void initialize(URL location, ResourceBundle resources) {
         // Initialization code goes here
     }
-
     @FXML
     @Override
     public void close() {
@@ -215,7 +211,7 @@ public void clearAnnotations() {
     }
 
     private void checkForExistingAnnotationData() {
-        // Get Rectangle and 'unnormalize' the values
+        // Get Rectangle and 'normalize' the values
         annotationPane.getChildren().remove(annotatedRectangle);
         annotationPane.getChildren().remove(middlePoint);
         annotatedRectangle = AnnotationData.getInstance().getAnnotation(selectedImageView.getImage().getUrl());
@@ -277,6 +273,7 @@ private void pressedAnnotationEvent(MouseEvent event) {
      *
      * @param event The Mouse Event
      */
+
     private void releasedAnnotationEvent(MouseEvent event) {
         if (!dragged) {
             annotatedRectangle.setX(annotationPointX - 10);
@@ -308,6 +305,7 @@ private void releasedAnnotationEvent(MouseEvent event) {
      *
      * @param event The Mouse Event
      */
+
     @FXML
     private void handleExportAction(ActionEvent event) {
         if (selectedImageView != null && annotatedRectangle != null) {
@@ -336,7 +334,6 @@ private void handleExportAction(ActionEvent event) {
         }
     }
 
-
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
     ///Export-All-Functionality----------START
 
@@ -347,7 +344,6 @@ private void handleExportAllAction(ActionEvent event) {
             showAlert("Export Error", "There are no images to export.");
             return;
         }
-
         List<String> unannotatedImages = new ArrayList<>();
         for (Node node : uploadedImages.getChildren()) {
             if (node instanceof HBox hbox) {
@@ -364,11 +360,9 @@ private void handleExportAllAction(ActionEvent event) {
             showUnannotatedImagesAlert(unannotatedImages);
             return;
         }
-
         DirectoryChooser directoryChooser = new DirectoryChooser();
         directoryChooser.setTitle("Select Directory to Save Annotations");
         File selectedDirectory = directoryChooser.showDialog(((Node) event.getSource()).getScene().getWindow());
-
         if (selectedDirectory != null) {
             AnnotationData.getInstance().getAnnotations().forEach((path, annotation) -> {
                 File file = null;
@@ -413,7 +407,6 @@ private void showUnannotatedImagesAlert(List<String> unannotatedImages) {
         alert.showAndWait();
     }
 
-
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
     ///Export-All-Functionality----------END
 
@@ -442,12 +435,11 @@ private void showNoAnnotationAlert() {
         alert.showAndWait();
     }
 
-
-
     /**
      * Handles Deleting Functionality - Multiple Deletion Functionality has been also implemented
      *
      */
+
     @FXML
     public void deletionfunctionality() {
         List<Node> toRemove = new ArrayList<>();
@@ -499,4 +491,9 @@ public void deletionfunctionality() {
         }
     }
 
+
+
+
+
+    
 }

From 7e3e08bd2a6476007b517426ddffa513bd6b440f Mon Sep 17 00:00:00 2001
From: muazzamaqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Sun, 5 May 2024 18:39:10 +0200
Subject: [PATCH 056/100] Update AnnotationController.java

---
 src/main/java/controller/AnnotationController.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 909d743d..d30a08f7 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -460,7 +460,7 @@ public void deletionfunctionality() {
                         if (AnnotationData.getInstance().deleteAnnotation(imageView.getImage().getUrl())) {
                             System.out.println("Annotation deleted for image: " + imagePath);
                         } else {
-                            System.out.println("No annotation found or error deleting annotation for image: " + imagePath);
+                            //System.out.println("No annotation found or error deleting annotation for image: " + imagePath);
                         }
                         toRemove.add(node);
                         uploadedFilePaths.remove(imagePath);
@@ -495,5 +495,5 @@ public void deletionfunctionality() {
 
 
 
-    
+
 }

From b6a2d2d1070753f98107bc0262f2830e0995ee9a Mon Sep 17 00:00:00 2001
From: muazzamaqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Sun, 5 May 2024 20:27:10 +0200
Subject: [PATCH 057/100] Fix-ClearBox-After all of the pictures get deleted

---
 src/main/java/controller/AnnotationController.java | 1 +
 src/main/resources/css/dark-mode.css               | 4 ++++
 2 files changed, 5 insertions(+)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index d30a08f7..04629e5b 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -489,6 +489,7 @@ public void deletionfunctionality() {
         if (uploadedImages.getChildren().isEmpty()) {
             showAlert("Notice", "All images have been deleted.");
         }
+        clearAnnotations();
     }
 
 
diff --git a/src/main/resources/css/dark-mode.css b/src/main/resources/css/dark-mode.css
index 1c79e39c..93bad55f 100644
--- a/src/main/resources/css/dark-mode.css
+++ b/src/main/resources/css/dark-mode.css
@@ -42,3 +42,7 @@
     -fx-background-insets: 2;
     -fx-background-radius: 5;
 }
+
+.red-green-checkbox{
+    -fx-border-color: red;
+}
\ No newline at end of file

From e362f0f790249f1af36aa6a875a743e38856916c Mon Sep 17 00:00:00 2001
From: osama <os.os20.osama@gmail.com>
Date: Tue, 7 May 2024 15:33:17 +0200
Subject: [PATCH 058/100] Removed refrence point checkbox (eugense work) and
 added choice box (our work(me and friends(yassine and c(ceasar)))))

---
 src/main/resources/view/AiView.fxml | 24 ++++++++++++++++--------
 1 file changed, 16 insertions(+), 8 deletions(-)

diff --git a/src/main/resources/view/AiView.fxml b/src/main/resources/view/AiView.fxml
index 0a84b3b7..90f7e306 100644
--- a/src/main/resources/view/AiView.fxml
+++ b/src/main/resources/view/AiView.fxml
@@ -1,11 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
+<?import javafx.collections.FXCollections?>
 <?import javafx.geometry.*?>
-<?import javafx.scene.chart.NumberAxis?>
+<?import javafx.scene.chart.*?>
 <?import javafx.scene.control.*?>
 <?import javafx.scene.layout.*?>
 <?import userinterface.PlottableImage?>
-<?import javafx.scene.chart.LineChart?>
+<?import java.lang.String?>
 <ScrollPane fitToHeight="true" fitToWidth="true" maxHeight="Infinity" maxWidth="Infinity"
             xmlns="http://javafx.com/javafx/17" xmlns:fx="http://javafx.com/fxml/1"
             fx:controller="controller.AiController">
@@ -60,12 +61,19 @@
                             <Insets bottom="10.0" left="10.0" right="10.0" top="10.0"/>
                         </padding>
                     </HBox>
-                    <CheckBox fx:id="inSetReferenceMode" mnemonicParsing="false"
-                              text="Set reference mode">
-                        <padding>
-                            <Insets left="10.0" right="10.0" top="5.0"/>
-                        </padding>
-                    </CheckBox>
+                    <HBox alignment="CENTER_LEFT" maxHeight="1.7976931348623157E308"
+                          maxWidth="1.7976931348623157E308" spacing="20.0">
+                    <Label text="Refrence mode" textAlignment="CENTER"/>
+                    <ChoiceBox fx:id="ModeSelection">
+                        <items>
+                            <FXCollections fx:factory="observableArrayList">
+                                <String fx:value="Single Point Mode" />
+                                <String fx:value="Path Mode" />
+                            </FXCollections>
+                        </items>
+
+                    </ChoiceBox>
+                    </HBox>
                 </VBox>
             </TitledPane>
         </HBox>

From 084ab895aa53a6fcb4ac9661e4a10483d05a1c93 Mon Sep 17 00:00:00 2001
From: osama <os.os20.osama@gmail.com>
Date: Tue, 7 May 2024 16:24:31 +0200
Subject: [PATCH 059/100] added functionlity to choicebox to allows single
 point mode

---
 src/main/java/controller/AiController.java | 36 ++++++++++++++--------
 src/main/resources/view/AiView.fxml        |  2 +-
 2 files changed, 24 insertions(+), 14 deletions(-)

diff --git a/src/main/java/controller/AiController.java b/src/main/java/controller/AiController.java
index 08aeaa2b..9fc83ad8 100644
--- a/src/main/java/controller/AiController.java
+++ b/src/main/java/controller/AiController.java
@@ -1,8 +1,6 @@
 package controller;
 
 import algorithm.*;
-import com.google.gson.Gson;
-import com.google.gson.GsonBuilder;
 import inputOutput.ExportMeasurement;
 import inputOutput.TransformationMatrix;
 import inputOutput.VideoSource;
@@ -17,7 +15,6 @@
 import javafx.scene.chart.NumberAxis;
 import javafx.scene.chart.XYChart;
 import javafx.scene.control.*;
-import javafx.scene.control.Label;
 import javafx.util.Duration;
 import org.opencv.core.Core;
 import org.opencv.core.CvType;
@@ -28,7 +25,6 @@
 import java.awt.image.BufferedImage;
 import java.net.URL;
 import java.util.*;
-import java.util.List;
 import java.util.prefs.Preferences;
 
 public class AiController implements Controller {
@@ -46,9 +42,9 @@ public class AiController implements Controller {
     @FXML
     public PlottableImage videoImagePlot;
     @FXML
-    public CheckBox inSetReferenceMode;
-    @FXML
     public LineChart<Number, Number> lineChart;
+    @FXML
+    public ChoiceBox<String> ModeSelection;
 
     private Label statusLabel;
     private Timeline videoTimeline;
@@ -68,6 +64,7 @@ public class AiController implements Controller {
     private Mat cachedTransformMatrix = null;
 
     private final XYChart.Series<Number, Number> referencePoint = new XYChart.Series<Number, Number>();
+    private final XYChart.Series<Number, Number> referencePoint2 = new XYChart.Series<Number, Number>();
     private final ObservableList<XYChart.Series<Number,Number>> lineDataSeries = FXCollections.observableArrayList();
 
     NumberAxis xAxis = new NumberAxis(-500, 500, 100);
@@ -84,10 +81,6 @@ public void initialize(URL location, ResourceBundle resources) {
         sourceChoiceBox.getSelectionModel().selectedItemProperty().addListener(x -> changeVideoView());
         sourceChoiceBox.setTooltip(new Tooltip("If you have multiple cameras connected, enable \"Search for more videos\" in the settings view to see all available devices"));
 
-        referencePoint.setName("reference point");
-        referencePoint.getData().add(new XYChart.Data<>(100,100));
-        dataSeries.add(referencePoint);
-
         videoImagePlot.setData(dataSeries);
         videoImagePlot.registerImageClickedHandler(this::onImageClicked);
         videoImagePlot.registerImageClickedHandler(this::onSRM);
@@ -106,13 +99,30 @@ public void initialize(URL location, ResourceBundle resources) {
         lineChart.setVerticalGridLinesVisible(false);
         lineChart.lookup(".chart-plot-background").setStyle("-fx-background-color: transparent;");
         lineChart.setData(lineDataSeries);
+
+        ModeSelection.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> {
+            dataSeries.clear();
+            if (Objects.equals(newValue, "Single Point Mode")) {
+                dataSeries.add(referencePoint);
+            }
+            System.out.println("Selected item: " + newValue );
+            // Add your custom code here...
+        });
     }
 
     private void onSRM(double v, double v1) {
-        if (inSetReferenceMode.isSelected()) {
-            System.out.println("Set reference point to "+v+" "+v1);
-            referencePoint.setData(FXCollections.observableArrayList(new XYChart.Data<>(v,v1)));
+        switch (ModeSelection.getValue()){
+            case "Single Point Mode":
+                System.out.println("Set reference point to "+v+" "+v1);
+                referencePoint.setData(FXCollections.observableArrayList(new XYChart.Data<>(v,v1)));
+                break;
+            case "Path Mode":
+                System.out.println("Pathmmode wow");
+                referencePoint.setData(null);
+                //Add the section here chatgpt
+                break;
         }
+
     }
 
     @Override
diff --git a/src/main/resources/view/AiView.fxml b/src/main/resources/view/AiView.fxml
index 90f7e306..f560be5e 100644
--- a/src/main/resources/view/AiView.fxml
+++ b/src/main/resources/view/AiView.fxml
@@ -63,7 +63,7 @@
                     </HBox>
                     <HBox alignment="CENTER_LEFT" maxHeight="1.7976931348623157E308"
                           maxWidth="1.7976931348623157E308" spacing="20.0">
-                    <Label text="Refrence mode" textAlignment="CENTER"/>
+                    <Label text="Reference mode" textAlignment="CENTER"/>
                     <ChoiceBox fx:id="ModeSelection">
                         <items>
                             <FXCollections fx:factory="observableArrayList">

From 460c20e81f440d45ada5227acd6ee1a3e0509382 Mon Sep 17 00:00:00 2001
From: osama <os.os20.osama@gmail.com>
Date: Tue, 7 May 2024 16:53:38 +0200
Subject: [PATCH 060/100] Added multipoint functinality, no path yet

---
 src/main/java/controller/AiController.java | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/src/main/java/controller/AiController.java b/src/main/java/controller/AiController.java
index 9fc83ad8..1d94b0de 100644
--- a/src/main/java/controller/AiController.java
+++ b/src/main/java/controller/AiController.java
@@ -65,6 +65,7 @@ public class AiController implements Controller {
 
     private final XYChart.Series<Number, Number> referencePoint = new XYChart.Series<Number, Number>();
     private final XYChart.Series<Number, Number> referencePoint2 = new XYChart.Series<Number, Number>();
+    private final ArrayList<XYChart.Series<Number, Number>> referencePointsListPath = new ArrayList<XYChart.Series<Number, Number>>();
     private final ObservableList<XYChart.Series<Number,Number>> lineDataSeries = FXCollections.observableArrayList();
 
     NumberAxis xAxis = new NumberAxis(-500, 500, 100);
@@ -105,6 +106,9 @@ public void initialize(URL location, ResourceBundle resources) {
             if (Objects.equals(newValue, "Single Point Mode")) {
                 dataSeries.add(referencePoint);
             }
+            if (Objects.equals(newValue, "Path Mode")) {
+                dataSeries.addAll(referencePointsListPath);
+            }
             System.out.println("Selected item: " + newValue );
             // Add your custom code here...
         });
@@ -117,9 +121,9 @@ private void onSRM(double v, double v1) {
                 referencePoint.setData(FXCollections.observableArrayList(new XYChart.Data<>(v,v1)));
                 break;
             case "Path Mode":
-                System.out.println("Pathmmode wow");
-                referencePoint.setData(null);
-                //Add the section here chatgpt
+                referencePointsListPath.add(new XYChart.Series<>("Reference Funny",FXCollections.observableArrayList(new XYChart.Data<>(v,v1))));
+                dataSeries.add(referencePointsListPath.get(referencePointsListPath.size()-1));
+                //dataSeries.add(new XYChart.Series<>("Reference Funny",FXCollections.observableArrayList(new XYChart.Data<>(v,v1))));
                 break;
         }
 

From a058120a927d88f6ffe56f647e5d83d3bd55848c Mon Sep 17 00:00:00 2001
From: osama <os.os20.osama@gmail.com>
Date: Tue, 7 May 2024 17:15:09 +0200
Subject: [PATCH 061/100] Added clear all boints

---
 src/main/java/controller/AiController.java | 14 +++++++++++++-
 src/main/resources/view/AiView.fxml        |  9 +++++++++
 2 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/src/main/java/controller/AiController.java b/src/main/java/controller/AiController.java
index 1d94b0de..42cd79d3 100644
--- a/src/main/java/controller/AiController.java
+++ b/src/main/java/controller/AiController.java
@@ -45,6 +45,10 @@ public class AiController implements Controller {
     public LineChart<Number, Number> lineChart;
     @FXML
     public ChoiceBox<String> ModeSelection;
+    @FXML
+    public TitledPane PathControlPanel;
+    @FXML
+    public Button clearAll;
 
     private Label statusLabel;
     private Timeline videoTimeline;
@@ -64,7 +68,6 @@ public class AiController implements Controller {
     private Mat cachedTransformMatrix = null;
 
     private final XYChart.Series<Number, Number> referencePoint = new XYChart.Series<Number, Number>();
-    private final XYChart.Series<Number, Number> referencePoint2 = new XYChart.Series<Number, Number>();
     private final ArrayList<XYChart.Series<Number, Number>> referencePointsListPath = new ArrayList<XYChart.Series<Number, Number>>();
     private final ObservableList<XYChart.Series<Number,Number>> lineDataSeries = FXCollections.observableArrayList();
 
@@ -101,17 +104,26 @@ public void initialize(URL location, ResourceBundle resources) {
         lineChart.lookup(".chart-plot-background").setStyle("-fx-background-color: transparent;");
         lineChart.setData(lineDataSeries);
 
+
+        //State machine for the choice box for point mode selection
         ModeSelection.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> {
             dataSeries.clear();
             if (Objects.equals(newValue, "Single Point Mode")) {
                 dataSeries.add(referencePoint);
+                PathControlPanel.setVisible(false);
             }
             if (Objects.equals(newValue, "Path Mode")) {
                 dataSeries.addAll(referencePointsListPath);
+                PathControlPanel.setVisible(true);
             }
             System.out.println("Selected item: " + newValue );
             // Add your custom code here...
         });
+
+        clearAll.setOnAction((event) -> {
+            dataSeries.clear();
+            referencePointsListPath.clear();
+        });
     }
 
     private void onSRM(double v, double v1) {
diff --git a/src/main/resources/view/AiView.fxml b/src/main/resources/view/AiView.fxml
index f560be5e..678f06e7 100644
--- a/src/main/resources/view/AiView.fxml
+++ b/src/main/resources/view/AiView.fxml
@@ -76,6 +76,15 @@
                     </HBox>
                 </VBox>
             </TitledPane>
+            <padding>
+                <Insets bottom="0.0" left="80.0" right="0.0" top="0.0"/>
+            </padding>
+            <TitledPane fx:id="PathControlPanel" animated="false" collapsible="false" graphicTextGap="10.0" text="Path Control Panel"
+            textAlignment="CENTER" minHeight="100" minWidth="100" visible="false">
+                <Button fx:id="clearAll" text="Clear All">
+
+                </Button>
+            </TitledPane>
         </HBox>
     </VBox>
 </ScrollPane>

From d75def3a958116ce5a60a38a786fc2571bf7aafa Mon Sep 17 00:00:00 2001
From: muazzamaqeel <128594910+muazzamaqeel@users.noreply.github.com>
Date: Fri, 10 May 2024 00:23:29 +0200
Subject: [PATCH 062/100] Update AnnotationController.java

---
 .../java/controller/AnnotationController.java | 132 ++++++++++--------
 1 file changed, 71 insertions(+), 61 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 04629e5b..a5be9a6e 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -23,7 +23,6 @@
 import javafx.stage.Stage;
 import javafx.stage.DirectoryChooser;
 import util.AnnotationData;
-
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.PrintWriter;
@@ -50,9 +49,18 @@ public class AnnotationController implements Controller {
     private final Set<String> uploadedFilePaths = new HashSet<>();
     // store the paths of the selected Image, so you can Export the data based on these keys
     private final Set<String> selectedFilePaths = new HashSet<>();
+    private int currentImageIndex = 0; // Default to the first image
+    private final List<Image> imageList = new ArrayList<>(); // Store all loaded images
+
     @Override
     public void initialize(URL location, ResourceBundle resources) {
-        // Initialization code goes here
+        System.out.println("Initializing Controller");
+        if (selectedImageView == null) {
+            System.out.println("Error: selectedImageView is null");
+        }
+        if (uploadedImages == null) {
+            System.out.println("Error: uploadedImages is null");
+        }
     }
     @FXML
     @Override
@@ -98,6 +106,7 @@ private void displayImage(File file) {
         HBox.setMargin(checkBox, new Insets(10, 30, 10, 10));
 
         Image image = new Image(file.toURI().toString());
+        imageList.add(image); // Adding the image to the list
         ImageView imageView = new ImageView(image);
         imageView.setFitHeight(100);
         imageView.setFitWidth(100);
@@ -121,85 +130,86 @@ private void displayImage(File file) {
     }
 
     private void selectImage(Image image, ImageView imageView) {
-        if (selectedImageView != null && currentSelectedImageView != imageView) {
+        try {
+            // Check if the necessary UI components are available
+            if (selectedImageView == null) {
+                System.out.println("Error: selectedImageView is not initialized.");
+                return;
+            }
+
+            // Update the display image
             selectedImageView.setImage(image);
             selectedImageView.setFitWidth(selectedImageView.getScene().getWidth());
             selectedImageView.setPreserveRatio(true);
 
-            annotationPane.getTransforms().clear();
-            // Create a new Scale transformation for the ImageView
-            Scale scale = new Scale();
-            annotationPane.getTransforms().add(scale);
-
-            // Add a ScrollEvent handler to the ScrollPane
-            annotationPane.setOnScroll(event -> {
-                if (event.isControlDown()) {
-
-
-                    // Adjust the pivot points to the mouse's current position
-                    scale.setPivotX(event.getX());
-                    scale.setPivotY(event.getY());
+            // Reset style of previously selected image if it exists
+            if (currentSelectedImageView != null && currentSelectedImageView != imageView) {
+                currentSelectedImageView.setStyle("");  // Remove any special styling
+            }
 
-                    double zoomFactor = 1.05;
+            // Highlight the new selected image view if it's not null
+            if (imageView != null) {
+                currentSelectedImageView = imageView;
+                imageView.setStyle("-fx-effect: dropshadow(three-pass-box, deepskyblue, 10, 0, 0, 0); -fx-border-color: blue; -fx-border-width: 2;");
+            }
 
-                    if (event.getDeltaY() > 0) {
-                        // Zoom in
-                        scale.setX(scale.getX() * zoomFactor);
-                        scale.setY(scale.getY() * zoomFactor);
-                    } else {
-                        // Zoom out, but do not go below a certain minimum value
-                        if (scale.getX() > 1.0 && scale.getY() > 1.0) {
+            // Scroll to the selected image
+            scrollToSelectedImage();
+
+            // Update annotation pane if necessary
+            if (annotationPane != null) {
+                annotationPane.getTransforms().clear();
+                Scale scale = new Scale();
+                annotationPane.getTransforms().add(scale);
+
+                // Handle scroll events for zooming
+                annotationPane.setOnScroll(event -> {
+                    if (event.isControlDown()) {
+                        double zoomFactor = 1.05;
+                        scale.setPivotX(event.getX());
+                        scale.setPivotY(event.getY());
+
+                        if (event.getDeltaY() > 0) {
+                            scale.setX(scale.getX() * zoomFactor);
+                            scale.setY(scale.getY() * zoomFactor);
+                        } else if (scale.getX() > 1.0 && scale.getY() > 1.0) {
                             scale.setX(scale.getX() / zoomFactor);
                             scale.setY(scale.getY() / zoomFactor);
                         }
+                        event.consume();
                     }
-
-                    event.consume();
-                }
-            });
-
-            if (currentSelectedImageView != null) {
-                currentSelectedImageView.setStyle("");
+                });
             }
-            imageView.setStyle("-fx-effect: dropshadow(three-pass-box, rgba(0,0,0,0.8), 10, 0, 0, 0);");
-            currentSelectedImageView = imageView;
+
+            // Check and load existing annotation data
             checkForExistingAnnotationData();
-            selectedImageView.setOnMouseDragged(this::dragAnnotationEvent);
-            selectedImageView.setOnMousePressed(this::pressedAnnotationEvent);
-            selectedImageView.setOnMouseReleased(this::releasedAnnotationEvent);
+
+        } catch (Exception e) {
+            System.out.println("Exception in selectImage: " + e.getMessage());
+            e.printStackTrace();
+        }
+    }
+    private void scrollToSelectedImage() {
+        if (currentSelectedImageView != null && selectedImagePane != null) {
+            double viewportHeight = selectedImagePane.getHeight();
+            double imageY = currentSelectedImageView.localToScene(currentSelectedImageView.getBoundsInLocal()).getMinY();
+            double offsetY = imageY - selectedImagePane.getScene().getY() - viewportHeight / 2 + currentSelectedImageView.getBoundsInLocal().getHeight() / 2;
+            double vValue = offsetY / (uploadedImages.getHeight() - viewportHeight);
+            selectedImagePane.setVvalue(Math.max(0, Math.min(vValue, 1)));  // Clamp vValue to be between 0 and 1
         }
     }
-
     public void Select_Next_Image() {
-        try {
-            if (currentSelectedImageView != null) {
-                int currentIndex = uploadedImages.getChildren().indexOf(currentSelectedImageView);
-                if (currentIndex < uploadedImages.getChildren().size() - 1) {
-                    ImageView nextImageView = (ImageView) uploadedImages.getChildren().get(currentIndex + 1);
-                    Image image = nextImageView.getImage();
-                    selectImage(image, nextImageView);
-                }
-            }
-        } catch (Exception e) {
-            System.err.println("Error while selecting next Image: " + e.getMessage());
+        if (currentImageIndex < imageList.size() - 1) {
+            currentImageIndex++;
+            selectImage(imageList.get(currentImageIndex), null); // Update the image display
         }
     }
-
     public void Select_Previous_Image() {
-        try {
-            if (currentSelectedImageView != null) {
-                int currentIndex = uploadedImages.getChildren().indexOf(currentSelectedImageView);
-                if (currentIndex > 0) {
-                    ImageView previousImageView = (ImageView) uploadedImages.getChildren().get(currentIndex - 1);
-                    Image image = previousImageView.getImage();
-                    selectImage(image, previousImageView);
-                }
-            }
-        } catch (Exception e) {
-            System.err.println("Error while selecting previous Image: " + e.getMessage());
+        if (currentImageIndex > 0) {
+            currentImageIndex--;
+            selectImage(imageList.get(currentImageIndex), null); // Update the image display
         }
     }
-
     public void clearAnnotations() {
         if (annotatedRectangle != null) {
             annotationPane.getChildren().remove(annotatedRectangle);

From 84c1df98f9df04c21805228857033bb5956c7ca5 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 13 May 2024 00:11:06 +0200
Subject: [PATCH 063/100] Left-Right Button Fix + Annotation Code adjustment

a lot of refracting had to be done, because there is a lot of dependency problems generally with the code but now most of the bugs have been fixed for example:
1. Export All functionality
2. Undeleted Pictures (With respect to the arrow key buttons)
---
 .../java/controller/AnnotationController.java | 230 ++++++++++++------
 src/main/resources/view/AnnotationView.fxml   |   4 +-
 2 files changed, 162 insertions(+), 72 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index a5be9a6e..f5f0b929 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -28,6 +28,7 @@
 import java.io.PrintWriter;
 import java.net.URL;
 import java.util.*;
+import java.util.stream.Collectors;
 
 public class AnnotationController implements Controller {
     @FXML
@@ -51,16 +52,66 @@ public class AnnotationController implements Controller {
     private final Set<String> selectedFilePaths = new HashSet<>();
     private int currentImageIndex = 0; // Default to the first image
     private final List<Image> imageList = new ArrayList<>(); // Store all loaded images
-
     @Override
     public void initialize(URL location, ResourceBundle resources) {
         System.out.println("Initializing Controller");
-        if (selectedImageView == null) {
-            System.out.println("Error: selectedImageView is null");
+        if (annotationPane != null) {
+            setupAnnotationHandlers();
+        }
+
+        uploadedImages.setFocusTraversable(true);
+        uploadedImages.setOnKeyPressed(event -> {
+            switch (event.getCode()) {
+                case RIGHT:
+                    selectNextImage();
+                    break;
+                case LEFT:
+                    selectPreviousImage();
+                    break;
+                default:
+                    break;
+            }
+        });
+    }
+    private void setupAnnotationHandlers() {
+        annotationPane.setOnMousePressed(this::pressedAnnotationEvent);
+        annotationPane.setOnMouseDragged(this::dragAnnotationEvent);
+        annotationPane.setOnMouseReleased(this::releasedAnnotationEvent);
+    }
+    public void selectNextImage() {
+        // Check if there's a next image in the list
+        if (currentImageIndex < imageList.size() - 1) {
+            currentImageIndex++;
+            Image nextImage = imageList.get(currentImageIndex);
+            ImageView nextImageView = findImageViewForImage(nextImage);
+            selectImage(nextImage, nextImageView);
+        } else {
+            System.out.println("No next image available.");
+        }
+    }
+
+    public void selectPreviousImage() {
+        // Check if there's a previous image in the list
+        if (currentImageIndex > 0) {
+            currentImageIndex--;
+            Image prevImage = imageList.get(currentImageIndex);
+            ImageView prevImageView = findImageViewForImage(prevImage);
+            selectImage(prevImage, prevImageView);
+        } else {
+            System.out.println("No previous image available.");
         }
-        if (uploadedImages == null) {
-            System.out.println("Error: uploadedImages is null");
+    }
+
+    private ImageView findImageViewForImage(Image image) {
+        for (Node node : uploadedImages.getChildren()) {
+            if (node instanceof HBox) {
+                ImageView imageView = (ImageView) ((HBox) node).getChildren().get(0);
+                if (imageView.getImage().equals(image)) {
+                    return imageView;
+                }
+            }
         }
+        return null; // Not found
     }
     @FXML
     @Override
@@ -68,6 +119,16 @@ public void close() {
         unregisterController();
     }
 
+
+
+
+
+
+
+
+
+
+
     @FXML
     public void Handle_Upload_Functionality(ActionEvent actionEvent) {
         try {
@@ -95,7 +156,6 @@ public void Handle_Upload_Functionality(ActionEvent actionEvent) {
             System.err.println("Error while choosing File: " + e.getMessage());
         }
     }
-
     private void displayImage(File file) {
         HBox hbox = new HBox();
         hbox.setSpacing(10);
@@ -131,6 +191,20 @@ private void displayImage(File file) {
 
     private void selectImage(Image image, ImageView imageView) {
         try {
+            // Ensure there are images in the list before attempting to select one
+            if (imageList.isEmpty()) {
+                selectedImageView.setImage(null);
+                System.out.println("No images to display.");
+                return;
+            }
+
+            // Update the current image index to the selected image's index in the list
+            currentImageIndex = imageList.indexOf(image);
+            if (currentImageIndex == -1) { // If the image is not found in the list, log an error
+                System.out.println("Selected image is not in the image list.");
+                return;
+            }
+
             // Check if the necessary UI components are available
             if (selectedImageView == null) {
                 System.out.println("Error: selectedImageView is not initialized.");
@@ -142,7 +216,7 @@ private void selectImage(Image image, ImageView imageView) {
             selectedImageView.setFitWidth(selectedImageView.getScene().getWidth());
             selectedImageView.setPreserveRatio(true);
 
-            // Reset style of previously selected image if it exists
+            // Reset style of previously selected image view, if it exists
             if (currentSelectedImageView != null && currentSelectedImageView != imageView) {
                 currentSelectedImageView.setStyle("");  // Remove any special styling
             }
@@ -153,7 +227,7 @@ private void selectImage(Image image, ImageView imageView) {
                 imageView.setStyle("-fx-effect: dropshadow(three-pass-box, deepskyblue, 10, 0, 0, 0); -fx-border-color: blue; -fx-border-width: 2;");
             }
 
-            // Scroll to the selected image
+            // Scroll to the selected image in the scroll pane
             scrollToSelectedImage();
 
             // Update annotation pane if necessary
@@ -181,7 +255,7 @@ private void selectImage(Image image, ImageView imageView) {
                 });
             }
 
-            // Check and load existing annotation data
+            // Check and load existing annotation data if available
             checkForExistingAnnotationData();
 
         } catch (Exception e) {
@@ -198,18 +272,6 @@ private void scrollToSelectedImage() {
             selectedImagePane.setVvalue(Math.max(0, Math.min(vValue, 1)));  // Clamp vValue to be between 0 and 1
         }
     }
-    public void Select_Next_Image() {
-        if (currentImageIndex < imageList.size() - 1) {
-            currentImageIndex++;
-            selectImage(imageList.get(currentImageIndex), null); // Update the image display
-        }
-    }
-    public void Select_Previous_Image() {
-        if (currentImageIndex > 0) {
-            currentImageIndex--;
-            selectImage(imageList.get(currentImageIndex), null); // Update the image display
-        }
-    }
     public void clearAnnotations() {
         if (annotatedRectangle != null) {
             annotationPane.getChildren().remove(annotatedRectangle);
@@ -221,25 +283,32 @@ public void clearAnnotations() {
     }
 
     private void checkForExistingAnnotationData() {
-        // Get Rectangle and 'normalize' the values
-        annotationPane.getChildren().remove(annotatedRectangle);
-        annotationPane.getChildren().remove(middlePoint);
-        annotatedRectangle = AnnotationData.getInstance().getAnnotation(selectedImageView.getImage().getUrl());
+        // Clear existing annotations if any
+        if (annotatedRectangle != null) {
+            annotationPane.getChildren().remove(annotatedRectangle);
+            annotatedRectangle = null;
+        }
         if (middlePoint != null) {
+            annotationPane.getChildren().remove(middlePoint);
             middlePoint = null;
         }
+
+        // Reload annotation if it exists
+        annotatedRectangle = AnnotationData.getInstance().getAnnotation(selectedImageView.getImage().getUrl());
         if (annotatedRectangle != null) {
+            // Apply the transformations to the rectangle to match the image dimensions
             annotatedRectangle.setX(annotatedRectangle.getX() * selectedImageView.getImage().getWidth());
             annotatedRectangle.setY(annotatedRectangle.getY() * selectedImageView.getImage().getHeight());
             annotatedRectangle.setWidth(annotatedRectangle.getWidth() * selectedImageView.getImage().getWidth());
             annotatedRectangle.setHeight(annotatedRectangle.getHeight() * selectedImageView.getImage().getHeight());
+
             annotationPane.getChildren().add(annotatedRectangle);
+
             middlePoint = new Circle(0, 0, 2);
             middlePoint.setFill(Color.rgb(6, 207, 236));
             middlePoint.setCenterX(annotatedRectangle.getX() + (annotatedRectangle.getWidth() / 2));
             middlePoint.setCenterY(annotatedRectangle.getY() + (annotatedRectangle.getHeight() / 2));
             annotationPane.getChildren().add(middlePoint);
-
         }
     }
 
@@ -283,7 +352,6 @@ private void pressedAnnotationEvent(MouseEvent event) {
      *
      * @param event The Mouse Event
      */
-
     private void releasedAnnotationEvent(MouseEvent event) {
         if (!dragged) {
             annotatedRectangle.setX(annotationPointX - 10);
@@ -315,7 +383,6 @@ private void releasedAnnotationEvent(MouseEvent event) {
      *
      * @param event The Mouse Event
      */
-
     @FXML
     private void handleExportAction(ActionEvent event) {
         if (selectedImageView != null && annotatedRectangle != null) {
@@ -344,47 +411,60 @@ private void handleExportAction(ActionEvent event) {
         }
     }
 
+
+
+
+
+
+
+
+
+
+
+
+
+
+
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
     ///Export-All-Functionality----------START
 
     @FXML
     private void handleExportAllAction(ActionEvent event) {
-        // Checking if there are no images uploaded
+        // Check if there are no images uploaded
         if (uploadedImages.getChildren().isEmpty()) {
             showAlert("Export Error", "There are no images to export.");
             return;
         }
-        List<String> unannotatedImages = new ArrayList<>();
-        for (Node node : uploadedImages.getChildren()) {
-            if (node instanceof HBox hbox) {
-                for (Node child : hbox.getChildren()) {
-                    if (child instanceof ImageView imageView) {
-                        if (AnnotationData.getInstance().getAnnotation(imageView.getImage().getUrl()) == null) {
-                            unannotatedImages.add(new File(imageView.getImage().getUrl()).getName());
-                        }
-                    }
-                }
-            }
-        }
-        if (!unannotatedImages.isEmpty()) {
-            showUnannotatedImagesAlert(unannotatedImages);
-            return;
-        }
+
+        // Collect currently displayed images' URLs
+        Set<String> displayedImagesUrls = uploadedImages.getChildren().stream()
+                .filter(node -> node instanceof HBox)
+                .map(node -> (HBox) node)
+                .map(hbox -> (ImageView) hbox.getChildren().get(0))
+                .map(ImageView::getImage)
+                .map(Image::getUrl)
+                .collect(Collectors.toSet());
+
+        // Directory chooser for user to select where to save annotations
         DirectoryChooser directoryChooser = new DirectoryChooser();
         directoryChooser.setTitle("Select Directory to Save Annotations");
         File selectedDirectory = directoryChooser.showDialog(((Node) event.getSource()).getScene().getWindow());
+
         if (selectedDirectory != null) {
-            AnnotationData.getInstance().getAnnotations().forEach((path, annotation) -> {
-                File file = null;
-                try {
-                    file = new File(new URL(path).toURI());
-                    String fileName = file.getName().substring(0, file.getName().lastIndexOf('.')) + ".txt";
-                    File annotationFile = new File(selectedDirectory, fileName);
-                    saveAnnotationsToFile(annotationFile, annotation);
-                } catch (Exception e) {
-                    showAlert("Error", "Failed to save annotations for " + path);
-                }
-            });
+            // Iterate over each annotation and save only those that match the displayed images
+            AnnotationData.getInstance().getAnnotations().entrySet().stream()
+                    .filter(entry -> displayedImagesUrls.contains(entry.getKey()))
+                    .forEach(entry -> {
+                        try {
+                            String path = entry.getKey();
+                            File file = new File(new URL(path).toURI());
+                            String fileName = file.getName().substring(0, file.getName().lastIndexOf('.')) + ".txt";
+                            File annotationFile = new File(selectedDirectory, fileName);
+                            saveAnnotationsToFile(annotationFile, entry.getValue());
+                        } catch (Exception e) {
+                            showAlert("Error", "Failed to save annotations for " + entry.getKey());
+                        }
+                    });
         }
     }
 
@@ -421,6 +501,23 @@ private void showUnannotatedImagesAlert(List<String> unannotatedImages) {
     ///Export-All-Functionality----------END
 
 
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
     /**
      * Handles the Saving of Annotations to a File
      *
@@ -430,7 +527,9 @@ private void showUnannotatedImagesAlert(List<String> unannotatedImages) {
 
     private void saveAnnotationsToFile(File file, AnnotationData.PublicAnnotation annotation) {
         try (PrintWriter writer = new PrintWriter(file)) {
-            String line = String.format("%d %.5f %.5f %.5f %.5f", 0, annotation.getMiddlePointX(), annotation.getMiddlePointY(), annotation.getBoundingBoxWidth(), annotation.getBoundingBoxHeight());
+            String line = String.format("%d %.5f %.5f %.5f %.5f",
+                    0, annotation.getMiddlePointX(), annotation.getMiddlePointY(),
+                    annotation.getBoundingBoxWidth(), annotation.getBoundingBoxHeight());
             writer.println(line);
         } catch (FileNotFoundException e) {
             System.err.println("Error while saving Annotation to File: " + e.getMessage());
@@ -453,25 +552,19 @@ private void showNoAnnotationAlert() {
     @FXML
     public void deletionfunctionality() {
         List<Node> toRemove = new ArrayList<>();
+        List<Image> imagesToRemove = new ArrayList<>();
         boolean currentDisplayedRemoved = false;
         boolean atLeastOneSelected = false;
-        // Iterate over each node in the uploadedImages VBox
         for (Node node : uploadedImages.getChildren()) {
             if (node instanceof HBox hbox) {
                 ImageView imageView = (ImageView) hbox.getChildren().get(0);
                 CheckBox checkBox = (CheckBox) hbox.getChildren().get(1);
-                // Check if the CheckBox is selected for deletion
                 if (checkBox.isSelected()) {
                     atLeastOneSelected = true;
                     String imagePath = null;
                     try {
                         imagePath = new File(new URL(imageView.getImage().getUrl()).toURI()).getAbsolutePath();
-                        // Delete annotation from AnnotationData
-                        if (AnnotationData.getInstance().deleteAnnotation(imageView.getImage().getUrl())) {
-                            System.out.println("Annotation deleted for image: " + imagePath);
-                        } else {
-                            //System.out.println("No annotation found or error deleting annotation for image: " + imagePath);
-                        }
+                        imagesToRemove.add(imageView.getImage());
                         toRemove.add(node);
                         uploadedFilePaths.remove(imagePath);
                         selectedFilePaths.remove(imagePath);
@@ -487,9 +580,11 @@ public void deletionfunctionality() {
         }
         if (atLeastOneSelected) {
             uploadedImages.getChildren().removeAll(toRemove);
+            imageList.removeAll(imagesToRemove);
             if (currentDisplayedRemoved) {
                 selectedImageView.setImage(null);
                 currentSelectedImageView = null;
+                currentImageIndex = Math.min(currentImageIndex, imageList.size() - 1);
             }
         } else {
             showAlert("Notice", "No images selected for deletion.");
@@ -502,9 +597,4 @@ public void deletionfunctionality() {
         clearAnnotations();
     }
 
-
-
-
-
-
 }
diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index c307c991..e9608517 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -24,12 +24,12 @@
                         <Insets left="10.0" right="10.0" />
                      </HBox.margin>
                   </Button>
-                  <Button mnemonicParsing="false" text="&lt;" onAction="#Select_Previous_Image" prefHeight="40.0" style="-fx-font-weight: bold; -fx-font-size: 16px;">
+                  <Button mnemonicParsing="false" text="&lt;" onAction="#selectPreviousImage" prefHeight="40.0" style="-fx-font-weight: bold; -fx-font-size: 16px;">
                      <HBox.margin>
                         <Insets right="10.0" />
                      </HBox.margin>
                   </Button>
-                  <Button mnemonicParsing="false" text="&gt;" onAction="#Select_Next_Image" prefHeight="40.0" style="-fx-font-weight: bold; -fx-font-size: 16px;">
+                  <Button mnemonicParsing="false" text="&gt;" onAction="#selectNextImage" prefHeight="40.0" style="-fx-font-weight: bold; -fx-font-size: 16px;">
                      <HBox.margin>
                         <Insets right="10.0" />
                      </HBox.margin>

From a17edc896c4cdc30330f98463273e241e27aaa13 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 13 May 2024 00:14:39 +0200
Subject: [PATCH 064/100] Update AnnotationController.java

---
 .../java/controller/AnnotationController.java | 23 ++-----------------
 1 file changed, 2 insertions(+), 21 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index f5f0b929..015c621c 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -191,52 +191,36 @@ private void displayImage(File file) {
 
     private void selectImage(Image image, ImageView imageView) {
         try {
-            // Ensure there are images in the list before attempting to select one
             if (imageList.isEmpty()) {
                 selectedImageView.setImage(null);
                 System.out.println("No images to display.");
                 return;
             }
-
-            // Update the current image index to the selected image's index in the list
             currentImageIndex = imageList.indexOf(image);
-            if (currentImageIndex == -1) { // If the image is not found in the list, log an error
+            if (currentImageIndex == -1) {
                 System.out.println("Selected image is not in the image list.");
                 return;
             }
-
-            // Check if the necessary UI components are available
             if (selectedImageView == null) {
                 System.out.println("Error: selectedImageView is not initialized.");
                 return;
             }
-
-            // Update the display image
             selectedImageView.setImage(image);
             selectedImageView.setFitWidth(selectedImageView.getScene().getWidth());
             selectedImageView.setPreserveRatio(true);
-
-            // Reset style of previously selected image view, if it exists
             if (currentSelectedImageView != null && currentSelectedImageView != imageView) {
-                currentSelectedImageView.setStyle("");  // Remove any special styling
+                currentSelectedImageView.setStyle("");
             }
 
-            // Highlight the new selected image view if it's not null
             if (imageView != null) {
                 currentSelectedImageView = imageView;
                 imageView.setStyle("-fx-effect: dropshadow(three-pass-box, deepskyblue, 10, 0, 0, 0); -fx-border-color: blue; -fx-border-width: 2;");
             }
-
-            // Scroll to the selected image in the scroll pane
             scrollToSelectedImage();
-
-            // Update annotation pane if necessary
             if (annotationPane != null) {
                 annotationPane.getTransforms().clear();
                 Scale scale = new Scale();
                 annotationPane.getTransforms().add(scale);
-
-                // Handle scroll events for zooming
                 annotationPane.setOnScroll(event -> {
                     if (event.isControlDown()) {
                         double zoomFactor = 1.05;
@@ -254,10 +238,7 @@ private void selectImage(Image image, ImageView imageView) {
                     }
                 });
             }
-
-            // Check and load existing annotation data if available
             checkForExistingAnnotationData();
-
         } catch (Exception e) {
             System.out.println("Exception in selectImage: " + e.getMessage());
             e.printStackTrace();

From 415257ed2dbf7d0fc95e60e5a035cacd165e9b41 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 13 May 2024 00:33:46 +0200
Subject: [PATCH 065/100] Update AnnotationController.java

---
 .../java/controller/AnnotationController.java | 61 +------------------
 1 file changed, 1 insertion(+), 60 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 015c621c..9c242a14 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -118,17 +118,6 @@ private ImageView findImageViewForImage(Image image) {
     public void close() {
         unregisterController();
     }
-
-
-
-
-
-
-
-
-
-
-
     @FXML
     public void Handle_Upload_Functionality(ActionEvent actionEvent) {
         try {
@@ -188,7 +177,6 @@ private void displayImage(File file) {
         hbox.getChildren().add(checkBox);
         uploadedImages.getChildren().add(hbox);
     }
-
     private void selectImage(Image image, ImageView imageView) {
         try {
             if (imageList.isEmpty()) {
@@ -262,7 +250,6 @@ public void clearAnnotations() {
             annotatedRectangle = null;
         }
     }
-
     private void checkForExistingAnnotationData() {
         // Clear existing annotations if any
         if (annotatedRectangle != null) {
@@ -292,7 +279,6 @@ private void checkForExistingAnnotationData() {
             annotationPane.getChildren().add(middlePoint);
         }
     }
-
     private void dragAnnotationEvent(MouseEvent event) {
         if (event.isControlDown()) {
             double x2 = event.getX();
@@ -306,7 +292,6 @@ private void dragAnnotationEvent(MouseEvent event) {
             dragged = true;
         }
     }
-
     private void pressedAnnotationEvent(MouseEvent event) {
         annotationPointX = event.getX();
         annotationPointY = event.getY();
@@ -326,7 +311,6 @@ private void pressedAnnotationEvent(MouseEvent event) {
         }
 
     }
-
     /**
      * Handle the Simple Annotation Event where the user clicks once without dragging.
      * Here the size of the rectangle is fixed
@@ -358,7 +342,6 @@ private void releasedAnnotationEvent(MouseEvent event) {
         );
 
     }
-
     /**
      * Handles Export based Functionality
      *
@@ -391,24 +374,8 @@ private void handleExportAction(ActionEvent event) {
             showNoAnnotationAlert();
         }
     }
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
     ///Export-All-Functionality----------START
-
     @FXML
     private void handleExportAllAction(ActionEvent event) {
         // Check if there are no images uploaded
@@ -448,7 +415,6 @@ private void handleExportAllAction(ActionEvent event) {
                     });
         }
     }
-
     private void showAlert(String title, String content) {
         Alert alert = new Alert(Alert.AlertType.INFORMATION);
         alert.setTitle(title);
@@ -456,7 +422,6 @@ private void showAlert(String title, String content) {
         alert.setContentText(content);
         alert.showAndWait();
     }
-
     private void showUnannotatedImagesAlert(List<String> unannotatedImages) {
         Alert alert = new Alert(Alert.AlertType.INFORMATION);
         alert.setTitle("Unannotated Images");
@@ -477,35 +442,14 @@ private void showUnannotatedImagesAlert(List<String> unannotatedImages) {
         alert.setResizable(true);
         alert.showAndWait();
     }
-
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
     ///Export-All-Functionality----------END
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
     /**
      * Handles the Saving of Annotations to a File
      *
      * @param file       The File to save the Annotations to
      * @param annotation The Annotation Data to save
      */
-
     private void saveAnnotationsToFile(File file, AnnotationData.PublicAnnotation annotation) {
         try (PrintWriter writer = new PrintWriter(file)) {
             String line = String.format("%d %.5f %.5f %.5f %.5f",
@@ -516,7 +460,6 @@ private void saveAnnotationsToFile(File file, AnnotationData.PublicAnnotation an
             System.err.println("Error while saving Annotation to File: " + e.getMessage());
         }
     }
-
     private void showNoAnnotationAlert() {
         Alert alert = new Alert(Alert.AlertType.INFORMATION);
         alert.setTitle("No Annotation Found");
@@ -524,12 +467,10 @@ private void showNoAnnotationAlert() {
         alert.setContentText("No Annotation Found to process.");
         alert.showAndWait();
     }
-
     /**
      * Handles Deleting Functionality - Multiple Deletion Functionality has been also implemented
      *
      */
-
     @FXML
     public void deletionfunctionality() {
         List<Node> toRemove = new ArrayList<>();
@@ -578,4 +519,4 @@ public void deletionfunctionality() {
         clearAnnotations();
     }
 
-}
+}
\ No newline at end of file

From 5bcd7d1aa432784672b3b6f42d456469bab19278 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 13 May 2024 12:05:30 +0200
Subject: [PATCH 066/100] Update AnnotationController.java

Bug fix - Export all button
---
 .../java/controller/AnnotationController.java | 31 +++++++++----------
 1 file changed, 15 insertions(+), 16 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 9c242a14..f258c26f 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -378,13 +378,10 @@ private void handleExportAction(ActionEvent event) {
     ///Export-All-Functionality----------START
     @FXML
     private void handleExportAllAction(ActionEvent event) {
-        // Check if there are no images uploaded
         if (uploadedImages.getChildren().isEmpty()) {
             showAlert("Export Error", "There are no images to export.");
             return;
         }
-
-        // Collect currently displayed images' URLs
         Set<String> displayedImagesUrls = uploadedImages.getChildren().stream()
                 .filter(node -> node instanceof HBox)
                 .map(node -> (HBox) node)
@@ -392,14 +389,19 @@ private void handleExportAllAction(ActionEvent event) {
                 .map(ImageView::getImage)
                 .map(Image::getUrl)
                 .collect(Collectors.toSet());
+        List<String> unannotatedImages = displayedImagesUrls.stream()
+                .filter(url -> AnnotationData.getInstance().getAnnotation(url) == null)
+                .map(url -> new File(url).getName())
+                .collect(Collectors.toList());
 
-        // Directory chooser for user to select where to save annotations
+        if (!unannotatedImages.isEmpty()) {
+            showUnannotatedImagesAlert(unannotatedImages);
+            return;
+        }
         DirectoryChooser directoryChooser = new DirectoryChooser();
         directoryChooser.setTitle("Select Directory to Save Annotations");
         File selectedDirectory = directoryChooser.showDialog(((Node) event.getSource()).getScene().getWindow());
-
         if (selectedDirectory != null) {
-            // Iterate over each annotation and save only those that match the displayed images
             AnnotationData.getInstance().getAnnotations().entrySet().stream()
                     .filter(entry -> displayedImagesUrls.contains(entry.getKey()))
                     .forEach(entry -> {
@@ -415,33 +417,30 @@ private void handleExportAllAction(ActionEvent event) {
                     });
         }
     }
-    private void showAlert(String title, String content) {
-        Alert alert = new Alert(Alert.AlertType.INFORMATION);
-        alert.setTitle(title);
-        alert.setHeaderText(null);
-        alert.setContentText(content);
-        alert.showAndWait();
-    }
     private void showUnannotatedImagesAlert(List<String> unannotatedImages) {
         Alert alert = new Alert(Alert.AlertType.INFORMATION);
         alert.setTitle("Unannotated Images");
         alert.setHeaderText("The following images have no annotations:");
-
         VBox vbox = new VBox(5);
         for (String imageName : unannotatedImages) {
             Text imageText = new Text(imageName);
             vbox.getChildren().add(imageText);
         }
-
         ScrollPane scrollPane = new ScrollPane(vbox);
         scrollPane.setPrefSize(300, 150);
         scrollPane.setVbarPolicy(ScrollPane.ScrollBarPolicy.AS_NEEDED);
         scrollPane.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER);
-
         alert.getDialogPane().setContent(scrollPane);
         alert.setResizable(true);
         alert.showAndWait();
     }
+    private void showAlert(String title, String content) {
+        Alert alert = new Alert(Alert.AlertType.INFORMATION);
+        alert.setTitle(title);
+        alert.setHeaderText(null);
+        alert.setContentText(content);
+        alert.showAndWait();
+    }
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
     ///Export-All-Functionality----------END
     /**

From 4fcbb2ca3728b2114f56b9c0c6533320e6aeefe6 Mon Sep 17 00:00:00 2001
From: osama <os.os20.osama@gmail.com>
Date: Mon, 13 May 2024 13:31:57 +0200
Subject: [PATCH 067/100] added path in bath mode )wow)

---
 src/main/java/controller/AiController.java | 27 ++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/src/main/java/controller/AiController.java b/src/main/java/controller/AiController.java
index 42cd79d3..805b4503 100644
--- a/src/main/java/controller/AiController.java
+++ b/src/main/java/controller/AiController.java
@@ -104,6 +104,8 @@ public void initialize(URL location, ResourceBundle resources) {
         lineChart.lookup(".chart-plot-background").setStyle("-fx-background-color: transparent;");
         lineChart.setData(lineDataSeries);
 
+        ModeSelection.setValue("Single Point Mode");
+        dataSeries.add(referencePoint);
 
         //State machine for the choice box for point mode selection
         ModeSelection.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> {
@@ -111,10 +113,12 @@ public void initialize(URL location, ResourceBundle resources) {
             if (Objects.equals(newValue, "Single Point Mode")) {
                 dataSeries.add(referencePoint);
                 PathControlPanel.setVisible(false);
+                lineDataSeries.clear();
             }
             if (Objects.equals(newValue, "Path Mode")) {
                 dataSeries.addAll(referencePointsListPath);
                 PathControlPanel.setVisible(true);
+                connectPointsPathMode();
             }
             System.out.println("Selected item: " + newValue );
             // Add your custom code here...
@@ -123,6 +127,7 @@ public void initialize(URL location, ResourceBundle resources) {
         clearAll.setOnAction((event) -> {
             dataSeries.clear();
             referencePointsListPath.clear();
+            lineDataSeries.clear();
         });
     }
 
@@ -136,11 +141,33 @@ private void onSRM(double v, double v1) {
                 referencePointsListPath.add(new XYChart.Series<>("Reference Funny",FXCollections.observableArrayList(new XYChart.Data<>(v,v1))));
                 dataSeries.add(referencePointsListPath.get(referencePointsListPath.size()-1));
                 //dataSeries.add(new XYChart.Series<>("Reference Funny",FXCollections.observableArrayList(new XYChart.Data<>(v,v1))));
+                connectPointsPathMode();
+
+                lineDataSeries.get(lineDataSeries.size() - 1).setName("Line");
                 break;
         }
 
     }
 
+    private void connectPointsPathMode(){
+        for (int i = 0; i < referencePointsListPath.size() - 1; i++) {
+            XYChart.Series<Number, Number> series = referencePointsListPath.get(i);
+            XYChart.Series<Number, Number> nextSeries = referencePointsListPath.get(i + 1);
+
+            // Get the last point of the current series and the first point of the next series
+            XYChart.Data<Number, Number> lastPoint = series.getData().get(series.getData().size() - 1);
+            XYChart.Data<Number, Number> firstPointNext = nextSeries.getData().get(0);
+
+            // Create a new series to represent the line between the two points
+            XYChart.Series<Number, Number> lineSeries = new XYChart.Series<>();
+            lineSeries.getData().add(new XYChart.Data<>(lastPoint.getXValue(), lastPoint.getYValue()));
+            lineSeries.getData().add(new XYChart.Data<>(firstPointNext.getXValue(), firstPointNext.getYValue()));
+
+            // Add the line series to the line chart
+            lineDataSeries.add(lineSeries);
+        }
+    }
+
     @Override
     public void close() {
         unregisterController();

From 8114cab21f10a6273fcdd18abf0eb0cc26abd163 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 13 May 2024 14:47:06 +0200
Subject: [PATCH 068/100] Revert "Update AnnotationController.java"

This reverts commit 5bcd7d1aa432784672b3b6f42d456469bab19278.
---
 .../java/controller/AnnotationController.java | 31 ++++++++++---------
 1 file changed, 16 insertions(+), 15 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index f258c26f..9c242a14 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -378,10 +378,13 @@ private void handleExportAction(ActionEvent event) {
     ///Export-All-Functionality----------START
     @FXML
     private void handleExportAllAction(ActionEvent event) {
+        // Check if there are no images uploaded
         if (uploadedImages.getChildren().isEmpty()) {
             showAlert("Export Error", "There are no images to export.");
             return;
         }
+
+        // Collect currently displayed images' URLs
         Set<String> displayedImagesUrls = uploadedImages.getChildren().stream()
                 .filter(node -> node instanceof HBox)
                 .map(node -> (HBox) node)
@@ -389,19 +392,14 @@ private void handleExportAllAction(ActionEvent event) {
                 .map(ImageView::getImage)
                 .map(Image::getUrl)
                 .collect(Collectors.toSet());
-        List<String> unannotatedImages = displayedImagesUrls.stream()
-                .filter(url -> AnnotationData.getInstance().getAnnotation(url) == null)
-                .map(url -> new File(url).getName())
-                .collect(Collectors.toList());
 
-        if (!unannotatedImages.isEmpty()) {
-            showUnannotatedImagesAlert(unannotatedImages);
-            return;
-        }
+        // Directory chooser for user to select where to save annotations
         DirectoryChooser directoryChooser = new DirectoryChooser();
         directoryChooser.setTitle("Select Directory to Save Annotations");
         File selectedDirectory = directoryChooser.showDialog(((Node) event.getSource()).getScene().getWindow());
+
         if (selectedDirectory != null) {
+            // Iterate over each annotation and save only those that match the displayed images
             AnnotationData.getInstance().getAnnotations().entrySet().stream()
                     .filter(entry -> displayedImagesUrls.contains(entry.getKey()))
                     .forEach(entry -> {
@@ -417,30 +415,33 @@ private void handleExportAllAction(ActionEvent event) {
                     });
         }
     }
+    private void showAlert(String title, String content) {
+        Alert alert = new Alert(Alert.AlertType.INFORMATION);
+        alert.setTitle(title);
+        alert.setHeaderText(null);
+        alert.setContentText(content);
+        alert.showAndWait();
+    }
     private void showUnannotatedImagesAlert(List<String> unannotatedImages) {
         Alert alert = new Alert(Alert.AlertType.INFORMATION);
         alert.setTitle("Unannotated Images");
         alert.setHeaderText("The following images have no annotations:");
+
         VBox vbox = new VBox(5);
         for (String imageName : unannotatedImages) {
             Text imageText = new Text(imageName);
             vbox.getChildren().add(imageText);
         }
+
         ScrollPane scrollPane = new ScrollPane(vbox);
         scrollPane.setPrefSize(300, 150);
         scrollPane.setVbarPolicy(ScrollPane.ScrollBarPolicy.AS_NEEDED);
         scrollPane.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER);
+
         alert.getDialogPane().setContent(scrollPane);
         alert.setResizable(true);
         alert.showAndWait();
     }
-    private void showAlert(String title, String content) {
-        Alert alert = new Alert(Alert.AlertType.INFORMATION);
-        alert.setTitle(title);
-        alert.setHeaderText(null);
-        alert.setContentText(content);
-        alert.showAndWait();
-    }
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
     ///Export-All-Functionality----------END
     /**

From 6a3131d9d054d69eb60ced4f881b27d5d418e9f8 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 13 May 2024 14:47:25 +0200
Subject: [PATCH 069/100] Revert "Update AnnotationController.java"

This reverts commit 415257ed2dbf7d0fc95e60e5a035cacd165e9b41.
---
 .../java/controller/AnnotationController.java | 61 ++++++++++++++++++-
 1 file changed, 60 insertions(+), 1 deletion(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 9c242a14..015c621c 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -118,6 +118,17 @@ private ImageView findImageViewForImage(Image image) {
     public void close() {
         unregisterController();
     }
+
+
+
+
+
+
+
+
+
+
+
     @FXML
     public void Handle_Upload_Functionality(ActionEvent actionEvent) {
         try {
@@ -177,6 +188,7 @@ private void displayImage(File file) {
         hbox.getChildren().add(checkBox);
         uploadedImages.getChildren().add(hbox);
     }
+
     private void selectImage(Image image, ImageView imageView) {
         try {
             if (imageList.isEmpty()) {
@@ -250,6 +262,7 @@ public void clearAnnotations() {
             annotatedRectangle = null;
         }
     }
+
     private void checkForExistingAnnotationData() {
         // Clear existing annotations if any
         if (annotatedRectangle != null) {
@@ -279,6 +292,7 @@ private void checkForExistingAnnotationData() {
             annotationPane.getChildren().add(middlePoint);
         }
     }
+
     private void dragAnnotationEvent(MouseEvent event) {
         if (event.isControlDown()) {
             double x2 = event.getX();
@@ -292,6 +306,7 @@ private void dragAnnotationEvent(MouseEvent event) {
             dragged = true;
         }
     }
+
     private void pressedAnnotationEvent(MouseEvent event) {
         annotationPointX = event.getX();
         annotationPointY = event.getY();
@@ -311,6 +326,7 @@ private void pressedAnnotationEvent(MouseEvent event) {
         }
 
     }
+
     /**
      * Handle the Simple Annotation Event where the user clicks once without dragging.
      * Here the size of the rectangle is fixed
@@ -342,6 +358,7 @@ private void releasedAnnotationEvent(MouseEvent event) {
         );
 
     }
+
     /**
      * Handles Export based Functionality
      *
@@ -374,8 +391,24 @@ private void handleExportAction(ActionEvent event) {
             showNoAnnotationAlert();
         }
     }
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
     ///Export-All-Functionality----------START
+
     @FXML
     private void handleExportAllAction(ActionEvent event) {
         // Check if there are no images uploaded
@@ -415,6 +448,7 @@ private void handleExportAllAction(ActionEvent event) {
                     });
         }
     }
+
     private void showAlert(String title, String content) {
         Alert alert = new Alert(Alert.AlertType.INFORMATION);
         alert.setTitle(title);
@@ -422,6 +456,7 @@ private void showAlert(String title, String content) {
         alert.setContentText(content);
         alert.showAndWait();
     }
+
     private void showUnannotatedImagesAlert(List<String> unannotatedImages) {
         Alert alert = new Alert(Alert.AlertType.INFORMATION);
         alert.setTitle("Unannotated Images");
@@ -442,14 +477,35 @@ private void showUnannotatedImagesAlert(List<String> unannotatedImages) {
         alert.setResizable(true);
         alert.showAndWait();
     }
+
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
     ///Export-All-Functionality----------END
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
     /**
      * Handles the Saving of Annotations to a File
      *
      * @param file       The File to save the Annotations to
      * @param annotation The Annotation Data to save
      */
+
     private void saveAnnotationsToFile(File file, AnnotationData.PublicAnnotation annotation) {
         try (PrintWriter writer = new PrintWriter(file)) {
             String line = String.format("%d %.5f %.5f %.5f %.5f",
@@ -460,6 +516,7 @@ private void saveAnnotationsToFile(File file, AnnotationData.PublicAnnotation an
             System.err.println("Error while saving Annotation to File: " + e.getMessage());
         }
     }
+
     private void showNoAnnotationAlert() {
         Alert alert = new Alert(Alert.AlertType.INFORMATION);
         alert.setTitle("No Annotation Found");
@@ -467,10 +524,12 @@ private void showNoAnnotationAlert() {
         alert.setContentText("No Annotation Found to process.");
         alert.showAndWait();
     }
+
     /**
      * Handles Deleting Functionality - Multiple Deletion Functionality has been also implemented
      *
      */
+
     @FXML
     public void deletionfunctionality() {
         List<Node> toRemove = new ArrayList<>();
@@ -519,4 +578,4 @@ public void deletionfunctionality() {
         clearAnnotations();
     }
 
-}
\ No newline at end of file
+}

From 8eca647233753408878c90e8b05efd49fdf35ad9 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 13 May 2024 14:51:42 +0200
Subject: [PATCH 070/100] Revert "Update AnnotationController.java"

This reverts commit 5bcd7d1aa432784672b3b6f42d456469bab19278.

# Conflicts:
#	src/main/java/controller/AnnotationController.java
---
 .../java/controller/AnnotationController.java | 92 ++++---------------
 1 file changed, 16 insertions(+), 76 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 015c621c..f258c26f 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -118,17 +118,6 @@ private ImageView findImageViewForImage(Image image) {
     public void close() {
         unregisterController();
     }
-
-
-
-
-
-
-
-
-
-
-
     @FXML
     public void Handle_Upload_Functionality(ActionEvent actionEvent) {
         try {
@@ -188,7 +177,6 @@ private void displayImage(File file) {
         hbox.getChildren().add(checkBox);
         uploadedImages.getChildren().add(hbox);
     }
-
     private void selectImage(Image image, ImageView imageView) {
         try {
             if (imageList.isEmpty()) {
@@ -262,7 +250,6 @@ public void clearAnnotations() {
             annotatedRectangle = null;
         }
     }
-
     private void checkForExistingAnnotationData() {
         // Clear existing annotations if any
         if (annotatedRectangle != null) {
@@ -292,7 +279,6 @@ private void checkForExistingAnnotationData() {
             annotationPane.getChildren().add(middlePoint);
         }
     }
-
     private void dragAnnotationEvent(MouseEvent event) {
         if (event.isControlDown()) {
             double x2 = event.getX();
@@ -306,7 +292,6 @@ private void dragAnnotationEvent(MouseEvent event) {
             dragged = true;
         }
     }
-
     private void pressedAnnotationEvent(MouseEvent event) {
         annotationPointX = event.getX();
         annotationPointY = event.getY();
@@ -326,7 +311,6 @@ private void pressedAnnotationEvent(MouseEvent event) {
         }
 
     }
-
     /**
      * Handle the Simple Annotation Event where the user clicks once without dragging.
      * Here the size of the rectangle is fixed
@@ -358,7 +342,6 @@ private void releasedAnnotationEvent(MouseEvent event) {
         );
 
     }
-
     /**
      * Handles Export based Functionality
      *
@@ -391,33 +374,14 @@ private void handleExportAction(ActionEvent event) {
             showNoAnnotationAlert();
         }
     }
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
     ///Export-All-Functionality----------START
-
     @FXML
     private void handleExportAllAction(ActionEvent event) {
-        // Check if there are no images uploaded
         if (uploadedImages.getChildren().isEmpty()) {
             showAlert("Export Error", "There are no images to export.");
             return;
         }
-
-        // Collect currently displayed images' URLs
         Set<String> displayedImagesUrls = uploadedImages.getChildren().stream()
                 .filter(node -> node instanceof HBox)
                 .map(node -> (HBox) node)
@@ -425,14 +389,19 @@ private void handleExportAllAction(ActionEvent event) {
                 .map(ImageView::getImage)
                 .map(Image::getUrl)
                 .collect(Collectors.toSet());
+        List<String> unannotatedImages = displayedImagesUrls.stream()
+                .filter(url -> AnnotationData.getInstance().getAnnotation(url) == null)
+                .map(url -> new File(url).getName())
+                .collect(Collectors.toList());
 
-        // Directory chooser for user to select where to save annotations
+        if (!unannotatedImages.isEmpty()) {
+            showUnannotatedImagesAlert(unannotatedImages);
+            return;
+        }
         DirectoryChooser directoryChooser = new DirectoryChooser();
         directoryChooser.setTitle("Select Directory to Save Annotations");
         File selectedDirectory = directoryChooser.showDialog(((Node) event.getSource()).getScene().getWindow());
-
         if (selectedDirectory != null) {
-            // Iterate over each annotation and save only those that match the displayed images
             AnnotationData.getInstance().getAnnotations().entrySet().stream()
                     .filter(entry -> displayedImagesUrls.contains(entry.getKey()))
                     .forEach(entry -> {
@@ -448,64 +417,38 @@ private void handleExportAllAction(ActionEvent event) {
                     });
         }
     }
-
-    private void showAlert(String title, String content) {
-        Alert alert = new Alert(Alert.AlertType.INFORMATION);
-        alert.setTitle(title);
-        alert.setHeaderText(null);
-        alert.setContentText(content);
-        alert.showAndWait();
-    }
-
     private void showUnannotatedImagesAlert(List<String> unannotatedImages) {
         Alert alert = new Alert(Alert.AlertType.INFORMATION);
         alert.setTitle("Unannotated Images");
         alert.setHeaderText("The following images have no annotations:");
-
         VBox vbox = new VBox(5);
         for (String imageName : unannotatedImages) {
             Text imageText = new Text(imageName);
             vbox.getChildren().add(imageText);
         }
-
         ScrollPane scrollPane = new ScrollPane(vbox);
         scrollPane.setPrefSize(300, 150);
         scrollPane.setVbarPolicy(ScrollPane.ScrollBarPolicy.AS_NEEDED);
         scrollPane.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER);
-
         alert.getDialogPane().setContent(scrollPane);
         alert.setResizable(true);
         alert.showAndWait();
     }
-
+    private void showAlert(String title, String content) {
+        Alert alert = new Alert(Alert.AlertType.INFORMATION);
+        alert.setTitle(title);
+        alert.setHeaderText(null);
+        alert.setContentText(content);
+        alert.showAndWait();
+    }
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
     ///Export-All-Functionality----------END
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
     /**
      * Handles the Saving of Annotations to a File
      *
      * @param file       The File to save the Annotations to
      * @param annotation The Annotation Data to save
      */
-
     private void saveAnnotationsToFile(File file, AnnotationData.PublicAnnotation annotation) {
         try (PrintWriter writer = new PrintWriter(file)) {
             String line = String.format("%d %.5f %.5f %.5f %.5f",
@@ -516,7 +459,6 @@ private void saveAnnotationsToFile(File file, AnnotationData.PublicAnnotation an
             System.err.println("Error while saving Annotation to File: " + e.getMessage());
         }
     }
-
     private void showNoAnnotationAlert() {
         Alert alert = new Alert(Alert.AlertType.INFORMATION);
         alert.setTitle("No Annotation Found");
@@ -524,12 +466,10 @@ private void showNoAnnotationAlert() {
         alert.setContentText("No Annotation Found to process.");
         alert.showAndWait();
     }
-
     /**
      * Handles Deleting Functionality - Multiple Deletion Functionality has been also implemented
      *
      */
-
     @FXML
     public void deletionfunctionality() {
         List<Node> toRemove = new ArrayList<>();
@@ -578,4 +518,4 @@ public void deletionfunctionality() {
         clearAnnotations();
     }
 
-}
+}
\ No newline at end of file

From 14b0280ce5911db731fd1425d69ffc649ce49606 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 13 May 2024 20:13:57 +0200
Subject: [PATCH 071/100] Major Changes --- Export Functionality to now
 (Specific Export)

1. Now we are able to export pictures that have checkboxes ticked in front of them
2. Cleaned the Structure of the code, removed unused Function
---
 .../java/controller/AnnotationController.java | 91 +++++++++----------
 src/main/resources/view/AnnotationView.fxml   |  2 +-
 2 files changed, 46 insertions(+), 47 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index f258c26f..4fe5a405 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -1,5 +1,4 @@
 package controller;
-
 import javafx.event.ActionEvent;
 import javafx.fxml.FXML;
 import javafx.geometry.Insets;
@@ -29,7 +28,6 @@
 import java.net.URL;
 import java.util.*;
 import java.util.stream.Collectors;
-
 public class AnnotationController implements Controller {
     @FXML
     public VBox uploadedImages;     //Where the users see the files
@@ -342,40 +340,54 @@ private void releasedAnnotationEvent(MouseEvent event) {
         );
 
     }
-    /**
-     * Handles Export based Functionality
-     *
-     * @param event The Mouse Event
-     */
+    ///Export-Functionality---------- START
     @FXML
     private void handleExportAction(ActionEvent event) {
-        if (selectedImageView != null && annotatedRectangle != null) {
-            FileChooser fileChooser = new FileChooser();
-            fileChooser.setTitle("Save Annotations");
-
-            try {
-                String currentImageUrl = selectedImageView.getImage().getUrl();
-                String currentImageName = new File(new URL(currentImageUrl).toURI().getPath()).getName();
-                String initialFileName = currentImageName.substring(0, currentImageName.lastIndexOf('.')) + ".txt";
-                fileChooser.setInitialFileName(initialFileName);
-            } catch (Exception e) {
-                fileChooser.setInitialFileName("default_annotations.txt");
-                showAlert("Error", "There was an issue processing the image file name.");
-                System.err.println("Error while Exporting: " + e.getMessage());
-            }
-
-            fileChooser.getExtensionFilters().addAll(new FileChooser.ExtensionFilter("Text Files", "*.txt"));
-            File file = fileChooser.showSaveDialog(((Node) event.getSource()).getScene().getWindow());
+        if (uploadedImages.getChildren().isEmpty()) {
+            showAlert("Export Error", "There are no images to export.");
+            return;
+        }
+        Set<String> selectedImagesUrls = uploadedImages.getChildren().stream()
+                .filter(node -> node instanceof HBox)
+                .map(node -> (HBox) node)
+                .filter(hbox -> ((CheckBox) hbox.getChildren().get(1)).isSelected())
+                .map(hbox -> (ImageView) hbox.getChildren().get(0))
+                .map(ImageView::getImage)
+                .map(Image::getUrl)
+                .collect(Collectors.toSet());
 
-            if (file != null) {
-                saveAnnotationsToFile(file, AnnotationData.getInstance().getAnnotationEntry(selectedImageView.getImage().getUrl()));
-            }
-        } else {
-            showNoAnnotationAlert();
+        if (selectedImagesUrls.isEmpty()) {
+            showAlert("No Selection", "No images have been check-marked for export.");
+            return;
+        }
+        Map<String, AnnotationData.PublicAnnotation> annotations = AnnotationData.getInstance().getAnnotations();
+        Set<String> annotatedAndSelectedUrls = selectedImagesUrls.stream()
+                .filter(annotations::containsKey)
+                .collect(Collectors.toSet());
+        List<String> unannotatedSelectedImages = selectedImagesUrls.stream()
+                .filter(url -> !annotations.containsKey(url))
+                .map(url -> new File(url).getName())
+                .collect(Collectors.toList());
+        if (!unannotatedSelectedImages.isEmpty()) {
+            showUnannotatedImagesAlert(unannotatedSelectedImages);
+            return;
+        }
+        DirectoryChooser directoryChooser = new DirectoryChooser();
+        directoryChooser.setTitle("Select Directory to Save Annotations");
+        File selectedDirectory = directoryChooser.showDialog(((Node) event.getSource()).getScene().getWindow());
+        if (selectedDirectory != null) {
+            annotatedAndSelectedUrls.forEach(url -> {
+                try {
+                    File file = new File(new URL(url).toURI());
+                    String fileName = file.getName().substring(0, file.getName().lastIndexOf('.')) + ".txt";
+                    File annotationFile = new File(selectedDirectory, fileName);
+                    saveAnnotationsToFile(annotationFile, annotations.get(url));
+                } catch (Exception e) {
+                    showAlert("Error", "Failed to save annotations for " + url);
+                }
+            });
         }
     }
-    ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-    ///Export-All-Functionality----------START
     @FXML
     private void handleExportAllAction(ActionEvent event) {
         if (uploadedImages.getChildren().isEmpty()) {
@@ -442,7 +454,7 @@ private void showAlert(String title, String content) {
         alert.showAndWait();
     }
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-    ///Export-All-Functionality----------END
+    ///Export-Functionality----------END
     /**
      * Handles the Saving of Annotations to a File
      *
@@ -459,17 +471,6 @@ private void saveAnnotationsToFile(File file, AnnotationData.PublicAnnotation an
             System.err.println("Error while saving Annotation to File: " + e.getMessage());
         }
     }
-    private void showNoAnnotationAlert() {
-        Alert alert = new Alert(Alert.AlertType.INFORMATION);
-        alert.setTitle("No Annotation Found");
-        alert.setHeaderText(null);
-        alert.setContentText("No Annotation Found to process.");
-        alert.showAndWait();
-    }
-    /**
-     * Handles Deleting Functionality - Multiple Deletion Functionality has been also implemented
-     *
-     */
     @FXML
     public void deletionfunctionality() {
         List<Node> toRemove = new ArrayList<>();
@@ -510,12 +511,10 @@ public void deletionfunctionality() {
         } else {
             showAlert("Notice", "No images selected for deletion.");
         }
-
         // Notify if all images have been deleted
         if (uploadedImages.getChildren().isEmpty()) {
             showAlert("Notice", "All images have been deleted.");
         }
         clearAnnotations();
     }
-
-}
\ No newline at end of file
+}
diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index e9608517..40ab96bb 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -52,7 +52,7 @@
                         <Insets left="55.0" right="55.0" />
                      </HBox.margin>
                   </Button>
-                  <Button fx:id="ExportButton" text="Export" prefWidth="120.0" prefHeight="40.0" onAction="#handleExportAction" style="-fx-font-size: 16px;" />
+                  <Button fx:id="ExportButton" text="Specific Export" prefWidth="150.0" prefHeight="40.0" onAction="#handleExportAction" style="-fx-font-size: 16px;" />
                   <Button fx:id="ExportButtonAll" text="Export All" prefWidth="120.0" prefHeight="40.0" onAction="#handleExportAllAction" style="-fx-font-size: 16px;">
                     <HBox.margin>
                         <Insets left="55.0" right="55.0" />

From e7c4afa52abda6eed908f13266e45722098ab6c0 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 13 May 2024 20:26:45 +0200
Subject: [PATCH 072/100] Update AnnotationController.java

---
 src/main/java/controller/AnnotationController.java | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 4fe5a405..8ff44af5 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -227,7 +227,6 @@ private void selectImage(Image image, ImageView imageView) {
             checkForExistingAnnotationData();
         } catch (Exception e) {
             System.out.println("Exception in selectImage: " + e.getMessage());
-            e.printStackTrace();
         }
     }
     private void scrollToSelectedImage() {

From 7018c82dbfe8b05c5686b460697e21570903eea4 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 13 May 2024 20:54:42 +0200
Subject: [PATCH 073/100] Fix Button Placements

---
 .../java/controller/AnnotationController.java |   3 +
 src/main/resources/view/AnnotationView.fxml   | 155 +++++++++---------
 2 files changed, 81 insertions(+), 77 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 8ff44af5..9ddbabf8 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -35,6 +35,9 @@ public class AnnotationController implements Controller {
     public Button uploadImagesButton;
     @FXML
     public ScrollPane selectedImagePane;
+    public Button ExportButtonAll;
+    public Button ExportButton;
+    public Button clearMarksButton;
     @FXML
     private ImageView selectedImageView;
     private ImageView currentSelectedImageView;
diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index 40ab96bb..858f3d94 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -1,9 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-
 <?import javafx.geometry.Insets?>
 <?import javafx.scene.control.Button?>
 <?import javafx.scene.control.ScrollPane?>
-<?import javafx.scene.control.TitledPane?>
 <?import javafx.scene.image.ImageView?>
 <?import javafx.scene.layout.BorderPane?>
 <?import javafx.scene.layout.HBox?>
@@ -14,80 +12,83 @@
 <ScrollPane fitToHeight="true" fitToWidth="true" maxHeight="Infinity" maxWidth="Infinity"
             xmlns="http://javafx.com/javafx/21"
             xmlns:fx="http://javafx.com/fxml/1" fx:controller="controller.AnnotationController">
-   <content>
-      <BorderPane>
-         <bottom>
-            <HBox alignment="CENTER_LEFT" prefHeight="80.0" prefWidth="368.0" BorderPane.alignment="CENTER">
-               <children>
-                  <Button mnemonicParsing="false" text="Delete" prefWidth="120.0" prefHeight="40.0" onAction="#deletionfunctionality" style="-fx-font-size: 16px;">
-                     <HBox.margin>
-                        <Insets left="10.0" right="10.0" />
-                     </HBox.margin>
-                  </Button>
-                  <Button mnemonicParsing="false" text="&lt;" onAction="#selectPreviousImage" prefHeight="40.0" style="-fx-font-weight: bold; -fx-font-size: 16px;">
-                     <HBox.margin>
-                        <Insets right="10.0" />
-                     </HBox.margin>
-                  </Button>
-                  <Button mnemonicParsing="false" text="&gt;" onAction="#selectNextImage" prefHeight="40.0" style="-fx-font-weight: bold; -fx-font-size: 16px;">
-                     <HBox.margin>
-                        <Insets right="10.0" />
-                     </HBox.margin>
-                  </Button>
-                  <!-- Spacer to push everything to the left -->
-                  <Pane HBox.hgrow="ALWAYS" />
-                  <!-- Other controls can be added here, which will be aligned to the right -->
-               </children>
-            </HBox>
-         </bottom>
-
-         <top>
-            <HBox alignment="CENTER" prefHeight="80.0" prefWidth="368.0" BorderPane.alignment="CENTER">
-               <BorderPane.margin>
-                  <Insets bottom="10.0" left="10.0" right="10.0" top="10.0" />
-               </BorderPane.margin>
-               <children>
-                  <Button fx:id="uploadImagesButton" onAction="#Handle_Upload_Functionality" text="Import" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;">
-                     <HBox.margin>
-                        <Insets left="55.0" right="55.0" />
-                     </HBox.margin>
-                  </Button>
-                  <Button fx:id="ExportButton" text="Specific Export" prefWidth="150.0" prefHeight="40.0" onAction="#handleExportAction" style="-fx-font-size: 16px;" />
-                  <Button fx:id="ExportButtonAll" text="Export All" prefWidth="120.0" prefHeight="40.0" onAction="#handleExportAllAction" style="-fx-font-size: 16px;">
-                    <HBox.margin>
-                        <Insets left="55.0" right="55.0" />
-                     </HBox.margin>
-                  </Button>
-                  <Button fx:id="clearMarksButton" onAction="#clearAnnotations" text="Clear Marks" prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;">
-                     <HBox.margin>
-                        <Insets left="10.0" right="55.0" />
-                     </HBox.margin>
-                  </Button>
-               </children>
-            </HBox>
-         </top>
-         <left>
-            <ScrollPane fitToHeight="true" fitToWidth="true" hbarPolicy="NEVER" prefHeight="202.0" prefWidth="188.0" vbarPolicy="ALWAYS" BorderPane.alignment="CENTER">
-               <content>
-                  <VBox fx:id="uploadedImages" prefHeight="200.0" prefWidth="100.0" />
-               </content>
-               <BorderPane.margin>
-                  <Insets left="10.0" right="10.0" />
-               </BorderPane.margin>
-            </ScrollPane>
-         </left>
-         <center>
-            <ScrollPane fx:id="selectedImagePane" BorderPane.alignment="CENTER">
-               <BorderPane.margin>
+   <BorderPane>
+      <bottom>
+         <HBox alignment="CENTER_LEFT" prefHeight="80.0" prefWidth="368.0" BorderPane.alignment="CENTER">
+            <Button mnemonicParsing="false" text="Delete" prefWidth="120.0" prefHeight="40.0"
+                    onAction="#deletionfunctionality" style="-fx-font-size: 16px;">
+               <HBox.margin>
+                  <Insets left="10.0" right="10.0"/>
+               </HBox.margin>
+            </Button>
+            <Button mnemonicParsing="false" text="&lt;" onAction="#selectPreviousImage" prefHeight="40.0"
+                    style="-fx-font-weight: bold; -fx-font-size: 16px;">
+               <HBox.margin>
+                  <Insets right="10.0"/>
+               </HBox.margin>
+            </Button>
+            <Button mnemonicParsing="false" text="&gt;" onAction="#selectNextImage" prefHeight="40.0"
+                    style="-fx-font-weight: bold; -fx-font-size: 16px;">
+               <HBox.margin>
+                  <Insets right="10.0"/>
+               </HBox.margin>
+            </Button>
+            <Pane HBox.hgrow="ALWAYS"/> <!-- Spacer to push everything to the right -->
+            <Button fx:id="ExportButton" text="Specific Export" prefWidth="150.0" prefHeight="40.0"
+                    onAction="#handleExportAction" style="-fx-font-size: 16px;">
+               <HBox.margin>
+                  <Insets left="10.0" right="10.0"/>
+               </HBox.margin>
+            </Button>
+            <Button fx:id="ExportButtonAll" text="Export All" prefWidth="120.0" prefHeight="40.0"
+                    onAction="#handleExportAllAction" style="-fx-font-size: 16px;">
+               <HBox.margin>
+                  <Insets right="10.0"/>
+               </HBox.margin>
+            </Button>
+         </HBox>
+      </bottom>
+      <top>
+         <HBox alignment="CENTER" prefHeight="80.0" prefWidth="368.0" BorderPane.alignment="CENTER">
+            <BorderPane.margin>
+               <Insets bottom="10.0" left="10.0" right="10.0" top="10.0"/>
+            </BorderPane.margin>
+            <Pane HBox.hgrow="ALWAYS"/> <!-- Spacer to push the buttons to the right -->
+            <Button fx:id="uploadImagesButton" onAction="#Handle_Upload_Functionality" text="Import"
+                    prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;">
+               <HBox.margin>
+                  <Insets left="10.0" right="10.0"/>
+               </HBox.margin>
+            </Button>
+            <Button fx:id="clearMarksButton" onAction="#clearAnnotations" text="Clear Marks" prefWidth="120.0"
+                    prefHeight="40.0" style="-fx-font-size: 16px;">
+               <HBox.margin>
                   <Insets right="10.0"/>
-               </BorderPane.margin>
-               <Group>
-                  <Pane fx:id="annotationPane">
-                     <ImageView fx:id="selectedImageView" fitHeight="500.0" fitWidth="200.0" pickOnBounds="true" preserveRatio="true" />
-                  </Pane>
-               </Group>
-            </ScrollPane>
-         </center>
-      </BorderPane>
-   </content>
+               </HBox.margin>
+            </Button>
+         </HBox>
+      </top>
+      <left>
+         <ScrollPane fitToHeight="true" fitToWidth="true" hbarPolicy="NEVER" prefHeight="202.0" prefWidth="188.0"
+                     vbarPolicy="ALWAYS" BorderPane.alignment="CENTER">
+            <BorderPane.margin>
+               <Insets left="10.0" right="10.0"/>
+            </BorderPane.margin>
+            <VBox fx:id="uploadedImages" prefHeight="200.0" prefWidth="100.0"/>
+         </ScrollPane>
+      </left>
+      <center>
+         <ScrollPane fx:id="selectedImagePane" BorderPane.alignment="CENTER">
+            <BorderPane.margin>
+               <Insets right="10.0"/>
+            </BorderPane.margin>
+            <Group>
+               <Pane fx:id="annotationPane">
+                  <ImageView fx:id="selectedImageView" fitHeight="500.0" fitWidth="200.0" pickOnBounds="true"
+                             preserveRatio="true"/>
+               </Pane>
+            </Group>
+         </ScrollPane>
+      </center>
+   </BorderPane>
 </ScrollPane>

From 68105fdee1af11ca6b1a07871ee5828f0d95ad20 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Tue, 14 May 2024 00:15:46 +0200
Subject: [PATCH 074/100] Update AnnotationController.java

---
 src/main/java/controller/AnnotationController.java | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 9ddbabf8..9b55fd39 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -342,7 +342,6 @@ private void releasedAnnotationEvent(MouseEvent event) {
         );
 
     }
-    ///Export-Functionality---------- START
     @FXML
     private void handleExportAction(ActionEvent event) {
         if (uploadedImages.getChildren().isEmpty()) {
@@ -455,8 +454,6 @@ private void showAlert(String title, String content) {
         alert.setContentText(content);
         alert.showAndWait();
     }
-    ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-    ///Export-Functionality----------END
     /**
      * Handles the Saving of Annotations to a File
      *

From 0dbeb97622642b5682804e0817a730fc7f3fa6c4 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Tue, 14 May 2024 11:37:58 +0200
Subject: [PATCH 075/100] Help Section - Full Functionality

---
 .../java/controller/AnnotationController.java | 68 ++++++++++++++++++-
 src/main/resources/view/AnnotationView.fxml   | 10 ++-
 2 files changed, 75 insertions(+), 3 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 9b55fd39..e11ce33e 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -1,8 +1,12 @@
 package controller;
+
+import javafx.animation.FadeTransition;
 import javafx.event.ActionEvent;
 import javafx.fxml.FXML;
+import javafx.geometry.HPos;
 import javafx.geometry.Insets;
 import javafx.scene.Node;
+import javafx.scene.Scene;
 import javafx.scene.control.Alert;
 import javafx.scene.control.Button;
 import javafx.scene.control.CheckBox;
@@ -10,17 +14,22 @@
 import javafx.scene.image.Image;
 import javafx.scene.image.ImageView;
 import javafx.scene.input.MouseEvent;
+import javafx.scene.layout.GridPane;
 import javafx.scene.layout.HBox;
 import javafx.scene.layout.Pane;
 import javafx.scene.layout.VBox;
 import javafx.scene.paint.Color;
 import javafx.scene.shape.Circle;
 import javafx.scene.shape.Rectangle;
+import javafx.scene.text.Font;
+import javafx.scene.text.FontWeight;
 import javafx.scene.text.Text;
 import javafx.scene.transform.Scale;
+import javafx.stage.DirectoryChooser;
 import javafx.stage.FileChooser;
+import javafx.stage.Modality;
 import javafx.stage.Stage;
-import javafx.stage.DirectoryChooser;
+import javafx.util.Duration;
 import util.AnnotationData;
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -38,6 +47,7 @@ public class AnnotationController implements Controller {
     public Button ExportButtonAll;
     public Button ExportButton;
     public Button clearMarksButton;
+    public Button helpButton;
     @FXML
     private ImageView selectedImageView;
     private ImageView currentSelectedImageView;
@@ -516,4 +526,60 @@ public void deletionfunctionality() {
         }
         clearAnnotations();
     }
+    @FXML
+    public void handleHelpButtonAction() {
+        try {
+            Stage helpStage = new Stage();
+            helpStage.initModality(Modality.APPLICATION_MODAL);
+            helpStage.setTitle("Help");
+            VBox helpContent = new VBox();
+            helpContent.setPadding(new Insets(10));
+            helpContent.setSpacing(10);
+            helpContent.setStyle("-fx-background-color: #f0f0f0; -fx-border-radius: 10; -fx-background-radius: 10;");
+            GridPane helpGrid = getHelpGrid();
+            helpGrid.setPadding(new Insets(10));
+            helpGrid.setVgap(10);
+            helpGrid.setHgap(10);
+            helpGrid.setStyle("-fx-background-color: #ffffff; -fx-border-radius: 10; -fx-background-radius: 10; -fx-border-color: #cccccc; -fx-border-width: 1;");
+            helpContent.getChildren().add(helpGrid);
+            Scene helpScene = new Scene(helpContent);
+            FadeTransition fadeIn = new FadeTransition(Duration.millis(500), helpContent);
+            fadeIn.setFromValue(0.0);
+            fadeIn.setToValue(1.0);
+            fadeIn.play();
+            helpStage.setScene(helpScene);
+            helpStage.sizeToScene();
+            helpStage.showAndWait();
+        } catch (Exception e) {
+            System.err.println("Error while opening Help window: " + e.getMessage());
+        }
+    }
+    private static GridPane getHelpGrid() {
+        String[][] helpTextArray = {
+                {"Import", "Click this button to import images into the tool."},
+                {"Clear Marks", "Click this button to clear all annotation marks from the currently displayed image."},
+                {"Delete", "Click this button to delete the selected images from the tool."},
+                {"Specific Export", "Click this button to export annotations for the selected images."},
+                {"Export All", "Click this button to export annotations for all images."},
+                {"Next", "Click this button to navigate to the next image."},
+                {"Previous", "Click this button to navigate to the previous image."},
+                {"", "To annotate an image, click and drag to create a bounding box. Hold down the Ctrl key to resize the bounding box."}
+        };
+        GridPane gridPane = new GridPane();
+        gridPane.setPadding(new Insets(10));
+        gridPane.setVgap(10);
+        gridPane.setHgap(10);
+        for (int i = 0; i < helpTextArray.length; i++) {
+            String[] helpEntry = helpTextArray[i];
+            Text buttonName = new Text(helpEntry[0]);
+            buttonName.setFont(Font.font("Arial", FontWeight.BOLD, 16));
+            GridPane.setHalignment(buttonName, HPos.LEFT);
+            Text description = new Text(helpEntry[1]);
+            description.setFont(Font.font("Arial", 16));
+            GridPane.setHalignment(description, HPos.LEFT);
+            gridPane.add(buttonName, 0, i);
+            gridPane.add(description, 1, i);
+        }
+        return gridPane;
+    }
 }
diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index 858f3d94..e44ccd05 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -7,8 +7,8 @@
 <?import javafx.scene.layout.HBox?>
 <?import javafx.scene.layout.VBox?>
 <?import javafx.scene.layout.Pane?>
-
 <?import javafx.scene.Group?>
+
 <ScrollPane fitToHeight="true" fitToWidth="true" maxHeight="Infinity" maxWidth="Infinity"
             xmlns="http://javafx.com/javafx/21"
             xmlns:fx="http://javafx.com/fxml/1" fx:controller="controller.AnnotationController">
@@ -33,7 +33,7 @@
                   <Insets right="10.0"/>
                </HBox.margin>
             </Button>
-            <Pane HBox.hgrow="ALWAYS"/> <!-- Spacer to push everything to the right -->
+            <Pane HBox.hgrow="ALWAYS"/>
             <Button fx:id="ExportButton" text="Specific Export" prefWidth="150.0" prefHeight="40.0"
                     onAction="#handleExportAction" style="-fx-font-size: 16px;">
                <HBox.margin>
@@ -53,6 +53,12 @@
             <BorderPane.margin>
                <Insets bottom="10.0" left="10.0" right="10.0" top="10.0"/>
             </BorderPane.margin>
+            <Button fx:id="helpButton" onAction="#handleHelpButtonAction" text="Help"
+                    prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px; -fx-background-color: lightblue; -fx-text-fill: Black;">
+               <HBox.margin>
+                  <Insets left="10.0" right="10.0"/>
+               </HBox.margin>
+            </Button>
             <Pane HBox.hgrow="ALWAYS"/> <!-- Spacer to push the buttons to the right -->
             <Button fx:id="uploadImagesButton" onAction="#Handle_Upload_Functionality" text="Import"
                     prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;">

From 690a10844b6ae8486b3a2c10cdd838b27d7b4389 Mon Sep 17 00:00:00 2001
From: osama <os.os20.osama@gmail.com>
Date: Tue, 14 May 2024 14:58:03 +0200
Subject: [PATCH 076/100] Fixed colour change issue

---
 src/main/java/controller/AiController.java | 22 ++++++++++++++++++++--
 1 file changed, 20 insertions(+), 2 deletions(-)

diff --git a/src/main/java/controller/AiController.java b/src/main/java/controller/AiController.java
index 805b4503..3419c111 100644
--- a/src/main/java/controller/AiController.java
+++ b/src/main/java/controller/AiController.java
@@ -118,7 +118,7 @@ public void initialize(URL location, ResourceBundle resources) {
             if (Objects.equals(newValue, "Path Mode")) {
                 dataSeries.addAll(referencePointsListPath);
                 PathControlPanel.setVisible(true);
-                connectPointsPathMode();
+                redrawPointsPathMode();
             }
             System.out.println("Selected item: " + newValue );
             // Add your custom code here...
@@ -150,6 +150,24 @@ private void onSRM(double v, double v1) {
     }
 
     private void connectPointsPathMode(){
+        for (int i = referencePointsListPath.size() - 2; i < referencePointsListPath.size() - 1; i++) {
+            XYChart.Series<Number, Number> series = referencePointsListPath.get(i);
+            XYChart.Series<Number, Number> nextSeries = referencePointsListPath.get(i + 1);
+
+            // Get the last point of the current series and the first point of the next series
+            XYChart.Data<Number, Number> lastPoint = series.getData().get(series.getData().size() - 1);
+            XYChart.Data<Number, Number> firstPointNext = nextSeries.getData().get(0);
+
+            // Create a new series to represent the line between the two points
+            XYChart.Series<Number, Number> lineSeries = new XYChart.Series<>();
+            lineSeries.getData().add(new XYChart.Data<>(lastPoint.getXValue(), lastPoint.getYValue()));
+            lineSeries.getData().add(new XYChart.Data<>(firstPointNext.getXValue(), firstPointNext.getYValue()));
+
+            // Add the line series to the line chart
+            lineDataSeries.add(lineSeries);
+        }
+    }
+    private void redrawPointsPathMode(){
         for (int i = 0; i < referencePointsListPath.size() - 1; i++) {
             XYChart.Series<Number, Number> series = referencePointsListPath.get(i);
             XYChart.Series<Number, Number> nextSeries = referencePointsListPath.get(i + 1);
@@ -247,7 +265,7 @@ private void changeVideoView() {
             var selectedItem = sourceChoiceBox.getSelectionModel().getSelectedItem();
             int deviceId = deviceIdMapping.get(selectedItem);
             imageDataManager.closeConnection();
-            imageDataManager.openConnection(VideoSource.LIVESTREAM, 1);
+            imageDataManager.openConnection(VideoSource.LIVESTREAM, 2);
             if (videoTimeline == null) {
                 videoTimeline = new Timeline();
                 videoTimeline.setCycleCount(Animation.INDEFINITE);

From 00b2a9f8e46aecf96c401f4afce3803263532296 Mon Sep 17 00:00:00 2001
From: osama <os.os20.osama@gmail.com>
Date: Tue, 14 May 2024 14:58:52 +0200
Subject: [PATCH 077/100] Removed AI tab from start up and moved the "window"
 tab

---
 src/main/java/controller/MainController.java | 35 +++++++++++++++++---
 src/main/resources/view/MainView.fxml        |  5 ++-
 2 files changed, 32 insertions(+), 8 deletions(-)

diff --git a/src/main/java/controller/MainController.java b/src/main/java/controller/MainController.java
index f2445842..80459606 100644
--- a/src/main/java/controller/MainController.java
+++ b/src/main/java/controller/MainController.java
@@ -1,10 +1,5 @@
 package controller;
 
-import java.io.IOException;
-import java.net.URL;
-import java.util.ResourceBundle;
-import java.util.logging.Level;
-import java.util.logging.Logger;
 import algorithm.VisualizationManager;
 import javafx.application.Platform;
 import javafx.fxml.FXML;
@@ -17,6 +12,12 @@
 import javafx.stage.Modality;
 import javafx.stage.Stage;
 
+import java.io.IOException;
+import java.net.URL;
+import java.util.ResourceBundle;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
 public class MainController implements Controller {
 
     @FXML
@@ -38,6 +39,8 @@ public class MainController implements Controller {
     private MeasurementController measurementController;
     private ThrombectomyController thrombectomyController;
     private AutoTrackController autoTrackController;
+
+    private AiController AiController;
     private SettingsController settingsController;
     private final VisualizationManager visualizationManager = new VisualizationManager();
     private final Logger logger = Logger.getLogger(this.getClass().getName());
@@ -113,6 +116,28 @@ private void openAutoTrackView(){
         }
     }
 
+    @FXML
+    private void openAIView(){
+        if (this.AiController != null) return;
+
+        try {
+            setupFXMLLoader("AiView");
+            Tab t = new Tab("AiView", this.loader.load());
+
+            this.AiController = this.loader.getController();
+            this.AiController.setStatusLabel(this.status);
+
+            this.tabPane.getTabs().add(t);
+            this.tabPane.getSelectionModel().select(t);
+            t.setOnCloseRequest(e -> {
+                this.AiController.close();
+                this.AiController = null;
+            });
+        } catch(IOException e) {
+            logger.log(Level.SEVERE, "Error loading AutoTrack View", e);
+        }
+    }
+
     @FXML
     private void openSettings() {
         try {
diff --git a/src/main/resources/view/MainView.fxml b/src/main/resources/view/MainView.fxml
index 4251a882..98b1ef30 100644
--- a/src/main/resources/view/MainView.fxml
+++ b/src/main/resources/view/MainView.fxml
@@ -26,6 +26,7 @@
                     <MenuItem mnemonicParsing="false" onAction="#openMeasurementView" text="Measurement"/>
                     <MenuItem mnemonicParsing="false" onAction="#openThrombectomyView" text="Thrombectomy"/>
                     <MenuItem mnemonicParsing="false" onAction="#openAutoTrackView" text="AutoTrack"/>
+                    <MenuItem mnemonicParsing="false" onAction="#openAIView" text="AI View"/>
                 </Menu>
             </Menu>
             <Menu mnemonicParsing="false" text="Help">
@@ -44,9 +45,7 @@
             <Tab closable="false" fx:id="visualizationTab" text="Visualization" onSelectionChanged="#onChangeView">
                 <fx:include fx:id="visualization" source="VisualizationView.fxml"/>
             </Tab>
-            <Tab closable="false" fx:id="aiTab" text="AI" onSelectionChanged="#onChangeView">
-                <fx:include fx:id="ai" source="AiView.fxml"/>
-            </Tab>
+
         </TabPane>
     </center>
     <bottom>

From 09bc8613c7ddbc70adc4b6f2b231f6d5656380c4 Mon Sep 17 00:00:00 2001
From: Simon Engel <engesi02@thu.de>
Date: Wed, 15 May 2024 10:39:01 +0200
Subject: [PATCH 078/100] Added Keybinding toHelp Window

---
 src/main/java/controller/AnnotationController.java | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index e11ce33e..00767e6c 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -563,7 +563,12 @@ private static GridPane getHelpGrid() {
                 {"Export All", "Click this button to export annotations for all images."},
                 {"Next", "Click this button to navigate to the next image."},
                 {"Previous", "Click this button to navigate to the previous image."},
-                {"", "To annotate an image, click and drag to create a bounding box. Hold down the Ctrl key to resize the bounding box."}
+                {"", "To annotate an image, click and drag to create a bounding box. Hold down the Ctrl key to resize the bounding box."},
+                {"Special Keybindnings:", ""},
+                {"Ctrl + Mousewheel (on an image): ", "Zoom"},
+                {"Ctrl + Mouse drag (on an image): ", "Custom sized annotation box"},
+                {"Arrows: ", "Move zoomed images"}
+
         };
         GridPane gridPane = new GridPane();
         gridPane.setPadding(new Insets(10));

From e66fcc262730acea1f29cca10623f45f014a8d5c Mon Sep 17 00:00:00 2001
From: Simon Engel <engesi02@thu.de>
Date: Wed, 15 May 2024 10:39:56 +0200
Subject: [PATCH 079/100] Added Keybinding toHelp Window

---
 src/main/java/controller/AnnotationController.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 00767e6c..ece8ce47 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -564,7 +564,7 @@ private static GridPane getHelpGrid() {
                 {"Next", "Click this button to navigate to the next image."},
                 {"Previous", "Click this button to navigate to the previous image."},
                 {"", "To annotate an image, click and drag to create a bounding box. Hold down the Ctrl key to resize the bounding box."},
-                {"Special Keybindnings:", ""},
+                {"Special Keybindings:", ""},
                 {"Ctrl + Mousewheel (on an image): ", "Zoom"},
                 {"Ctrl + Mouse drag (on an image): ", "Custom sized annotation box"},
                 {"Arrows: ", "Move zoomed images"}

From cc511e544ddb9bd44876cf179d27230aee32a1f3 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Wed, 15 May 2024 11:12:57 +0200
Subject: [PATCH 080/100] Update AnnotationView.fxml

---
 src/main/resources/view/AnnotationView.fxml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index e44ccd05..a4033b79 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -53,7 +53,7 @@
             <BorderPane.margin>
                <Insets bottom="10.0" left="10.0" right="10.0" top="10.0"/>
             </BorderPane.margin>
-            <Button fx:id="helpButton" onAction="#handleHelpButtonAction" text="Help"
+            <Button fx:id="helpButton" onAction="#handleHelpButtonAction" text="Guide"
                     prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px; -fx-background-color: lightblue; -fx-text-fill: Black;">
                <HBox.margin>
                   <Insets left="10.0" right="10.0"/>

From 8d71936660afa0f890c9aacd8e27ef89533a4b17 Mon Sep 17 00:00:00 2001
From: Eugen Zdrincu <eugenzdrincu@gmail.com>
Date: Wed, 15 May 2024 13:45:17 +0200
Subject: [PATCH 081/100] reversed shanes changes

---
 aitoigt/detect.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/aitoigt/detect.py b/aitoigt/detect.py
index 500cf19d..83d31523 100644
--- a/aitoigt/detect.py
+++ b/aitoigt/detect.py
@@ -36,7 +36,11 @@
 import sys
 import pyigtl as igtl
 from pathlib import Path
- 
+
+import pyvirtualcam
+
+CAM = pyvirtualcam.Camera(width=640, height=480, fps=20)
+
 import torch
 
 FILE = Path(__file__).resolve()
@@ -244,7 +248,7 @@ def write_to_csv(image_name, prediction, confidence):
     
                     # Set position
                     matrix[0, 3] = xyxy[0]
-                    matrix[1, 3] = xyxy[1]
+                    matrix[1, 3] = xyxy[1] * -1 + 500
 
                     # Set orientation
                     direction = last_matrix[:3, 3] - matrix[:3, 3]
@@ -266,7 +270,9 @@ def write_to_csv(image_name, prediction, confidence):
                     cv2.resizeWindow(str(p), im0.shape[1], im0.shape[0])
                 cv2.imshow(str(p), im0)
                 cv2.waitKey(1)  # 1 millisecond
-
+                # Send RGB image to virtual camera
+                im0VIRT = cv2.cvtColor(im0, cv2.COLOR_BGR2RGB)
+                CAM.send(im0VIRT)
             # Save results (image with detections)
             if save_img:
                 if dataset.mode == "image":

From bb90a4d9a057be91dc9faa507528a85ef6a8dcd7 Mon Sep 17 00:00:00 2001
From: osama <os.os20.osama@gmail.com>
Date: Wed, 15 May 2024 14:09:44 +0200
Subject: [PATCH 082/100] fixed ppoint tracking

---
 src/main/java/controller/AiController.java | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/src/main/java/controller/AiController.java b/src/main/java/controller/AiController.java
index 3419c111..b34fd807 100644
--- a/src/main/java/controller/AiController.java
+++ b/src/main/java/controller/AiController.java
@@ -68,6 +68,7 @@ public class AiController implements Controller {
     private Mat cachedTransformMatrix = null;
 
     private final XYChart.Series<Number, Number> referencePoint = new XYChart.Series<Number, Number>();
+    private XYChart.Series<Number, Number> trackingPoint = new XYChart.Series<Number, Number>();
     private final ArrayList<XYChart.Series<Number, Number>> referencePointsListPath = new ArrayList<XYChart.Series<Number, Number>>();
     private final ObservableList<XYChart.Series<Number,Number>> lineDataSeries = FXCollections.observableArrayList();
 
@@ -114,11 +115,13 @@ public void initialize(URL location, ResourceBundle resources) {
                 dataSeries.add(referencePoint);
                 PathControlPanel.setVisible(false);
                 lineDataSeries.clear();
+                trackingPoint.setData(referencePoint.getData());
             }
             if (Objects.equals(newValue, "Path Mode")) {
                 dataSeries.addAll(referencePointsListPath);
                 PathControlPanel.setVisible(true);
                 redrawPointsPathMode();
+                trackingPoint = referencePointsListPath.get(0);
             }
             System.out.println("Selected item: " + newValue );
             // Add your custom code here...
@@ -138,7 +141,7 @@ private void onSRM(double v, double v1) {
                 referencePoint.setData(FXCollections.observableArrayList(new XYChart.Data<>(v,v1)));
                 break;
             case "Path Mode":
-                referencePointsListPath.add(new XYChart.Series<>("Reference Funny",FXCollections.observableArrayList(new XYChart.Data<>(v,v1))));
+                referencePointsListPath.add(new XYChart.Series<>("point",FXCollections.observableArrayList(new XYChart.Data<>(v,v1))));
                 dataSeries.add(referencePointsListPath.get(referencePointsListPath.size()-1));
                 //dataSeries.add(new XYChart.Series<>("Reference Funny",FXCollections.observableArrayList(new XYChart.Data<>(v,v1))));
                 connectPointsPathMode();
@@ -150,7 +153,11 @@ private void onSRM(double v, double v1) {
     }
 
     private void connectPointsPathMode(){
-        for (int i = referencePointsListPath.size() - 2; i < referencePointsListPath.size() - 1; i++) {
+        if(referencePointsListPath.size() == 1) {
+            return;
+        }
+        int i = referencePointsListPath.size() - 2;
+
             XYChart.Series<Number, Number> series = referencePointsListPath.get(i);
             XYChart.Series<Number, Number> nextSeries = referencePointsListPath.get(i + 1);
 
@@ -165,7 +172,7 @@ private void connectPointsPathMode(){
 
             // Add the line series to the line chart
             lineDataSeries.add(lineSeries);
-        }
+
     }
     private void redrawPointsPathMode(){
         for (int i = 0; i < referencePointsListPath.size() - 1; i++) {

From c967ec200b267ea668887637123682e4f45203f6 Mon Sep 17 00:00:00 2001
From: osama <os.os20.osama@gmail.com>
Date: Wed, 15 May 2024 14:14:01 +0200
Subject: [PATCH 083/100] fixed ppoint tracking

---
 src/main/java/controller/AiController.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/controller/AiController.java b/src/main/java/controller/AiController.java
index b34fd807..24ec93c7 100644
--- a/src/main/java/controller/AiController.java
+++ b/src/main/java/controller/AiController.java
@@ -380,7 +380,7 @@ private void updateTrackingData(){
             data.add(new XYChart.Data<>(shifted_points[0], shifted_points[1]));
 
             lineData.add(new XYChart.Data<>(shifted_points[0], shifted_points[1]));
-            lineData.add(new XYChart.Data<>(referencePoint.getData().get(0).getXValue(), referencePoint.getData().get(0).getYValue()));
+            lineData.add(new XYChart.Data<>(trackingPoint.getData().get(0).getXValue(), trackingPoint.getData().get(0).getYValue()));
 
             lineSeries.setData(lineData);
 

From f6038a2534f02941fc8b0c1d8e6af57f0d9498a1 Mon Sep 17 00:00:00 2001
From: osama <os.os20.osama@gmail.com>
Date: Wed, 15 May 2024 14:16:46 +0200
Subject: [PATCH 084/100] fixed ppoint tracking

---
 src/main/java/controller/AiController.java | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/main/java/controller/AiController.java b/src/main/java/controller/AiController.java
index 24ec93c7..aaecf03e 100644
--- a/src/main/java/controller/AiController.java
+++ b/src/main/java/controller/AiController.java
@@ -139,14 +139,15 @@ private void onSRM(double v, double v1) {
             case "Single Point Mode":
                 System.out.println("Set reference point to "+v+" "+v1);
                 referencePoint.setData(FXCollections.observableArrayList(new XYChart.Data<>(v,v1)));
+                trackingPoint.setData(referencePoint.getData());
                 break;
             case "Path Mode":
                 referencePointsListPath.add(new XYChart.Series<>("point",FXCollections.observableArrayList(new XYChart.Data<>(v,v1))));
                 dataSeries.add(referencePointsListPath.get(referencePointsListPath.size()-1));
                 //dataSeries.add(new XYChart.Series<>("Reference Funny",FXCollections.observableArrayList(new XYChart.Data<>(v,v1))));
                 connectPointsPathMode();
+                trackingPoint = referencePointsListPath.get(0);
 
-                lineDataSeries.get(lineDataSeries.size() - 1).setName("Line");
                 break;
         }
 

From ba4e71f12c766d620c6a6a54b5a7d11039f873a8 Mon Sep 17 00:00:00 2001
From: osama <os.os20.osama@gmail.com>
Date: Wed, 15 May 2024 14:21:58 +0200
Subject: [PATCH 085/100] fixed ppoint tracking

---
 src/main/java/controller/AiController.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/controller/AiController.java b/src/main/java/controller/AiController.java
index aaecf03e..6240f8e0 100644
--- a/src/main/java/controller/AiController.java
+++ b/src/main/java/controller/AiController.java
@@ -146,7 +146,7 @@ private void onSRM(double v, double v1) {
                 dataSeries.add(referencePointsListPath.get(referencePointsListPath.size()-1));
                 //dataSeries.add(new XYChart.Series<>("Reference Funny",FXCollections.observableArrayList(new XYChart.Data<>(v,v1))));
                 connectPointsPathMode();
-                trackingPoint = referencePointsListPath.get(0);
+                trackingPoint = new XYChart.Series<>("hi",FXCollections.observableArrayList(new XYChart.Data<>(referencePointsListPath.get(0).getData().get(0).getXValue(),referencePointsListPath.get(0).getData().get(0).getXValue())));
 
                 break;
         }

From a9ba4a6c0cec3d6976dd85ff71808476662f87be Mon Sep 17 00:00:00 2001
From: Muazzam Bin Aqeel <muazzamaqeel14@gmail.com>
Date: Fri, 17 May 2024 13:33:39 +0200
Subject: [PATCH 086/100] No Tip Functionality + More extension

---
 .../java/controller/AnnotationController.java | 78 ++++++++++++++++++-
 src/main/resources/view/AnnotationView.fxml   |  7 ++
 2 files changed, 83 insertions(+), 2 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index ece8ce47..44cb5475 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -54,6 +54,9 @@ public class AnnotationController implements Controller {
     @FXML
     private Pane annotationPane;
 
+    @FXML
+    private Button noTipButton;
+
     private Rectangle annotatedRectangle;
     private Circle middlePoint;
     private boolean dragged = false;
@@ -136,7 +139,7 @@ public void Handle_Upload_Functionality(ActionEvent actionEvent) {
             fileChooser.setTitle("Select Images");
             fileChooser.setInitialDirectory(new File(System.getProperty("user.home")));
             fileChooser.getExtensionFilters().add(
-                    new FileChooser.ExtensionFilter("Image Files", "*.jpg", "*.png")
+                    new FileChooser.ExtensionFilter("Image Files", "*.jpg", "*.png", "*.bmp", "*.gif", "*.jpeg", "*.tiff", "*.tif")
             );
             Stage currentStage = (Stage) ((javafx.scene.Node) actionEvent.getSource()).getScene().getWindow();
 
@@ -561,6 +564,7 @@ private static GridPane getHelpGrid() {
                 {"Delete", "Click this button to delete the selected images from the tool."},
                 {"Specific Export", "Click this button to export annotations for the selected images."},
                 {"Export All", "Click this button to export annotations for all images."},
+                {"No Tip", "Click this button to rename selected images to 'NoTipFound_<original name>' and remove them from the application."},
                 {"Next", "Click this button to navigate to the next image."},
                 {"Previous", "Click this button to navigate to the previous image."},
                 {"", "To annotate an image, click and drag to create a bounding box. Hold down the Ctrl key to resize the bounding box."},
@@ -568,12 +572,13 @@ private static GridPane getHelpGrid() {
                 {"Ctrl + Mousewheel (on an image): ", "Zoom"},
                 {"Ctrl + Mouse drag (on an image): ", "Custom sized annotation box"},
                 {"Arrows: ", "Move zoomed images"}
-
         };
+
         GridPane gridPane = new GridPane();
         gridPane.setPadding(new Insets(10));
         gridPane.setVgap(10);
         gridPane.setHgap(10);
+
         for (int i = 0; i < helpTextArray.length; i++) {
             String[] helpEntry = helpTextArray[i];
             Text buttonName = new Text(helpEntry[0]);
@@ -585,6 +590,75 @@ private static GridPane getHelpGrid() {
             gridPane.add(buttonName, 0, i);
             gridPane.add(description, 1, i);
         }
+
         return gridPane;
     }
+
+
+    @FXML
+    private void handleNoTipAction(ActionEvent event) {
+        List<Node> nodesToRemove = new ArrayList<>();
+        List<String> selectedImageUrls = new ArrayList<>();
+
+        for (Node node : uploadedImages.getChildren()) {
+            if (node instanceof HBox hbox) {
+                CheckBox checkBox = (CheckBox) hbox.getChildren().get(1);
+                if (checkBox.isSelected()) {
+                    ImageView imageView = (ImageView) hbox.getChildren().get(0);
+                    selectedImageUrls.add(imageView.getImage().getUrl());
+                    nodesToRemove.add(node);
+                }
+            }
+        }
+        if (selectedImageUrls.isEmpty()) {
+            showAlert("No Selection", "No images have been check-marked for No Tip processing.");
+            return;
+        }
+        boolean allRenamed = true;
+        StringBuilder successMessage = new StringBuilder("The following files have been renamed to NoTipFound_<original name>:\n");
+        for (String imageUrl : selectedImageUrls) {
+            try {
+                File selectedFile = new File(new URL(imageUrl).toURI());
+                String fileName = selectedFile.getName();
+                String newFileName = "NoTipFound_" + fileName;
+                File renamedFile = new File(selectedFile.getParent(), newFileName);
+
+                if (selectedFile.renameTo(renamedFile)) {
+                    successMessage.append(newFileName).append("\n");
+                    removeImageFromApplication(imageUrl, nodesToRemove);
+                } else {
+                    allRenamed = false;
+                    showAlert("Error", "Failed to rename file: " + fileName);
+                }
+            } catch (Exception e) {
+                allRenamed = false;
+                showAlert("Error", "An error occurred: " + e.getMessage());
+            }
+        }
+        if (allRenamed) {
+            showAlert("Success", successMessage.toString());
+        }
+    }
+    private void removeImageFromApplication(String imageUrl, List<Node> nodesToRemove) {
+        imageList.removeIf(image -> image.getUrl().equals(imageUrl));
+        uploadedFilePaths.remove(imageUrl);
+        selectedFilePaths.remove(imageUrl);
+
+        // Remove the image from the uploadedImages VBox
+        for (Node node : nodesToRemove) {
+            if (node instanceof HBox) {
+                ImageView imageView = (ImageView) ((HBox) node).getChildren().get(0);
+                if (imageView.getImage().getUrl().equals(imageUrl)) {
+                    uploadedImages.getChildren().remove(node);
+                    break;
+                }
+            }
+        }
+        if (currentSelectedImageView != null && currentSelectedImageView.getImage().getUrl().equals(imageUrl)) {
+            selectedImageView.setImage(null);
+            currentSelectedImageView = null;
+            currentImageIndex = Math.min(currentImageIndex, imageList.size() - 1);
+        }
+        clearAnnotations();
+    }
 }
diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index a4033b79..96654516 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -60,6 +60,13 @@
                </HBox.margin>
             </Button>
             <Pane HBox.hgrow="ALWAYS"/> <!-- Spacer to push the buttons to the right -->
+            <Button fx:id="noTipButton" text="No Tip" prefWidth="120.0" prefHeight="40.0"
+                    onAction="#handleNoTipAction" style="-fx-font-size: 16px;">
+               <HBox.margin>
+                  <Insets right="10.0"/>
+               </HBox.margin>
+            </Button>
+
             <Button fx:id="uploadImagesButton" onAction="#Handle_Upload_Functionality" text="Import"
                     prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;">
                <HBox.margin>

From afad6dfe0e106ac33acd0ad1ce33a90ada72bc0f Mon Sep 17 00:00:00 2001
From: Muazzam Bin Aqeel <muazzamaqeel14@gmail.com>
Date: Fri, 17 May 2024 13:39:06 +0200
Subject: [PATCH 087/100] Update AnnotationController.java

New Functionalities
Ctrl A functionality
---
 .../java/controller/AnnotationController.java | 32 ++++++++++++++++---
 1 file changed, 28 insertions(+), 4 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 44cb5475..0f5551d6 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -7,10 +7,7 @@
 import javafx.geometry.Insets;
 import javafx.scene.Node;
 import javafx.scene.Scene;
-import javafx.scene.control.Alert;
-import javafx.scene.control.Button;
-import javafx.scene.control.CheckBox;
-import javafx.scene.control.ScrollPane;
+import javafx.scene.control.*;
 import javafx.scene.image.Image;
 import javafx.scene.image.ImageView;
 import javafx.scene.input.MouseEvent;
@@ -82,11 +79,26 @@ public void initialize(URL location, ResourceBundle resources) {
                 case LEFT:
                     selectPreviousImage();
                     break;
+                case A:
+                    if (event.isControlDown()) {
+                        selectAllCheckboxes();
+                    }
+                    break;
                 default:
                     break;
             }
         });
     }
+
+    private void selectAllCheckboxes() {
+        for (Node node : uploadedImages.getChildren()) {
+            if (node instanceof HBox) {
+                CheckBox checkBox = (CheckBox) ((HBox) node).getChildren().get(1);
+                checkBox.setSelected(true);
+            }
+        }
+    }
+
     private void setupAnnotationHandlers() {
         annotationPane.setOnMousePressed(this::pressedAnnotationEvent);
         annotationPane.setOnMouseDragged(this::dragAnnotationEvent);
@@ -614,6 +626,17 @@ private void handleNoTipAction(ActionEvent event) {
             showAlert("No Selection", "No images have been check-marked for No Tip processing.");
             return;
         }
+
+        // Confirmation dialog
+        Alert confirmationAlert = new Alert(Alert.AlertType.CONFIRMATION);
+        confirmationAlert.setTitle("Confirmation");
+        confirmationAlert.setHeaderText("Mark as No Tip");
+        confirmationAlert.setContentText("Are you sure you want to mark these pictures as No Tip Found?");
+        Optional<ButtonType> result = confirmationAlert.showAndWait();
+        if (result.isPresent() && result.get() != ButtonType.OK) {
+            return; // If not confirmed, exit the method
+        }
+
         boolean allRenamed = true;
         StringBuilder successMessage = new StringBuilder("The following files have been renamed to NoTipFound_<original name>:\n");
         for (String imageUrl : selectedImageUrls) {
@@ -639,6 +662,7 @@ private void handleNoTipAction(ActionEvent event) {
             showAlert("Success", successMessage.toString());
         }
     }
+
     private void removeImageFromApplication(String imageUrl, List<Node> nodesToRemove) {
         imageList.removeIf(image -> image.getUrl().equals(imageUrl));
         uploadedFilePaths.remove(imageUrl);

From c0c0bbb38b05fd575e7cd6e384db4816462720e4 Mon Sep 17 00:00:00 2001
From: Muazzam Bin Aqeel <muazzamaqeel14@gmail.com>
Date: Fri, 17 May 2024 13:46:41 +0200
Subject: [PATCH 088/100] Update AnnotationController.java

---
 src/main/java/controller/AnnotationController.java | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 0f5551d6..284ef89c 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -583,6 +583,7 @@ private static GridPane getHelpGrid() {
                 {"Special Keybindings:", ""},
                 {"Ctrl + Mousewheel (on an image): ", "Zoom"},
                 {"Ctrl + Mouse drag (on an image): ", "Custom sized annotation box"},
+                {"Ctrl + A (After Selecting one image Checkbox): ", "All pictures will be check marked"},
                 {"Arrows: ", "Move zoomed images"}
         };
 

From 5832ec0b2ae729a74d6b8bb5cc7d5f3b86a91e53 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 20 May 2024 16:22:55 +0200
Subject: [PATCH 089/100] Update AnnotationController.java

---
 .../java/controller/AnnotationController.java | 127 +++++++++++++-----
 1 file changed, 92 insertions(+), 35 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 284ef89c..cc2107fe 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -63,6 +63,8 @@ public class AnnotationController implements Controller {
     private final Set<String> selectedFilePaths = new HashSet<>();
     private int currentImageIndex = 0; // Default to the first image
     private final List<Image> imageList = new ArrayList<>(); // Store all loaded images
+    private final Set<String> noTipImageUrls = new HashSet<>();
+
     @Override
     public void initialize(URL location, ResourceBundle resources) {
         System.out.println("Initializing Controller");
@@ -100,9 +102,21 @@ private void selectAllCheckboxes() {
     }
 
     private void setupAnnotationHandlers() {
-        annotationPane.setOnMousePressed(this::pressedAnnotationEvent);
-        annotationPane.setOnMouseDragged(this::dragAnnotationEvent);
-        annotationPane.setOnMouseReleased(this::releasedAnnotationEvent);
+        annotationPane.setOnMousePressed(event -> {
+            if (currentSelectedImageView != null && !noTipImageUrls.contains(currentSelectedImageView.getImage().getUrl())) {
+                pressedAnnotationEvent(event);
+            }
+        });
+        annotationPane.setOnMouseDragged(event -> {
+            if (currentSelectedImageView != null && !noTipImageUrls.contains(currentSelectedImageView.getImage().getUrl())) {
+                dragAnnotationEvent(event);
+            }
+        });
+        annotationPane.setOnMouseReleased(event -> {
+            if (currentSelectedImageView != null && !noTipImageUrls.contains(currentSelectedImageView.getImage().getUrl())) {
+                releasedAnnotationEvent(event);
+            }
+        });
     }
     public void selectNextImage() {
         // Check if there's a next image in the list
@@ -257,6 +271,7 @@ private void selectImage(Image image, ImageView imageView) {
             System.out.println("Exception in selectImage: " + e.getMessage());
         }
     }
+
     private void scrollToSelectedImage() {
         if (currentSelectedImageView != null && selectedImagePane != null) {
             double viewportHeight = selectedImagePane.getHeight();
@@ -286,8 +301,14 @@ private void checkForExistingAnnotationData() {
             middlePoint = null;
         }
 
+        String imageUrl = selectedImageView.getImage().getUrl();
+        if (noTipImageUrls.contains(imageUrl)) {
+            showAlert("Info", "This image is marked as 'No Tip' and cannot be annotated.");
+            return;
+        }
+
         // Reload annotation if it exists
-        annotatedRectangle = AnnotationData.getInstance().getAnnotation(selectedImageView.getImage().getUrl());
+        annotatedRectangle = AnnotationData.getInstance().getAnnotation(imageUrl);
         if (annotatedRectangle != null) {
             // Apply the transformations to the rectangle to match the image dimensions
             annotatedRectangle.setX(annotatedRectangle.getX() * selectedImageView.getImage().getWidth());
@@ -387,33 +408,27 @@ private void handleExportAction(ActionEvent event) {
             return;
         }
         Map<String, AnnotationData.PublicAnnotation> annotations = AnnotationData.getInstance().getAnnotations();
-        Set<String> annotatedAndSelectedUrls = selectedImagesUrls.stream()
-                .filter(annotations::containsKey)
-                .collect(Collectors.toSet());
-        List<String> unannotatedSelectedImages = selectedImagesUrls.stream()
-                .filter(url -> !annotations.containsKey(url))
-                .map(url -> new File(url).getName())
-                .collect(Collectors.toList());
-        if (!unannotatedSelectedImages.isEmpty()) {
-            showUnannotatedImagesAlert(unannotatedSelectedImages);
-            return;
-        }
         DirectoryChooser directoryChooser = new DirectoryChooser();
         directoryChooser.setTitle("Select Directory to Save Annotations");
         File selectedDirectory = directoryChooser.showDialog(((Node) event.getSource()).getScene().getWindow());
         if (selectedDirectory != null) {
-            annotatedAndSelectedUrls.forEach(url -> {
+            selectedImagesUrls.forEach(url -> {
                 try {
                     File file = new File(new URL(url).toURI());
                     String fileName = file.getName().substring(0, file.getName().lastIndexOf('.')) + ".txt";
                     File annotationFile = new File(selectedDirectory, fileName);
-                    saveAnnotationsToFile(annotationFile, annotations.get(url));
+                    if (annotations.containsKey(url)) {
+                        saveAnnotationsToFile(annotationFile, annotations.get(url));
+                    } else {
+                        saveNoTipAnnotationToFile(annotationFile);
+                    }
                 } catch (Exception e) {
                     showAlert("Error", "Failed to save annotations for " + url);
                 }
             });
         }
     }
+
     @FXML
     private void handleExportAllAction(ActionEvent event) {
         if (uploadedImages.getChildren().isEmpty()) {
@@ -427,15 +442,6 @@ private void handleExportAllAction(ActionEvent event) {
                 .map(ImageView::getImage)
                 .map(Image::getUrl)
                 .collect(Collectors.toSet());
-        List<String> unannotatedImages = displayedImagesUrls.stream()
-                .filter(url -> AnnotationData.getInstance().getAnnotation(url) == null)
-                .map(url -> new File(url).getName())
-                .collect(Collectors.toList());
-
-        if (!unannotatedImages.isEmpty()) {
-            showUnannotatedImagesAlert(unannotatedImages);
-            return;
-        }
         DirectoryChooser directoryChooser = new DirectoryChooser();
         directoryChooser.setTitle("Select Directory to Save Annotations");
         File selectedDirectory = directoryChooser.showDialog(((Node) event.getSource()).getScene().getWindow());
@@ -453,8 +459,30 @@ private void handleExportAllAction(ActionEvent event) {
                             showAlert("Error", "Failed to save annotations for " + entry.getKey());
                         }
                     });
+            // Export "No Tip" annotations
+            displayedImagesUrls.stream()
+                    .filter(url -> !AnnotationData.getInstance().getAnnotations().containsKey(url))
+                    .forEach(url -> {
+                        try {
+                            File file = new File(new URL(url).toURI());
+                            String fileName = file.getName().substring(0, file.getName().lastIndexOf('.')) + ".txt";
+                            File annotationFile = new File(selectedDirectory, fileName);
+                            saveNoTipAnnotationToFile(annotationFile);
+                        } catch (Exception e) {
+                            showAlert("Error", "Failed to save annotations for " + url);
+                        }
+                    });
+        }
+    }
+
+    private void saveNoTipAnnotationToFile(File file) {
+        try (PrintWriter writer = new PrintWriter(file)) {
+            writer.println("0 0 0 0 0");
+        } catch (FileNotFoundException e) {
+            System.err.println("Error while saving No Tip Annotation to File: " + e.getMessage());
         }
     }
+
     private void showUnannotatedImagesAlert(List<String> unannotatedImages) {
         Alert alert = new Alert(Alert.AlertType.INFORMATION);
         alert.setTitle("Unannotated Images");
@@ -638,32 +666,61 @@ private void handleNoTipAction(ActionEvent event) {
             return; // If not confirmed, exit the method
         }
 
-        boolean allRenamed = true;
-        StringBuilder successMessage = new StringBuilder("The following files have been renamed to NoTipFound_<original name>:\n");
+        boolean allMarked = true;
+        StringBuilder successMessage = new StringBuilder("The following files have been marked as NoTipFound_<original name>:\n");
         for (String imageUrl : selectedImageUrls) {
             try {
                 File selectedFile = new File(new URL(imageUrl).toURI());
                 String fileName = selectedFile.getName();
                 String newFileName = "NoTipFound_" + fileName;
-                File renamedFile = new File(selectedFile.getParent(), newFileName);
+                File markedFile = new File(selectedFile.getParent(), newFileName);
 
-                if (selectedFile.renameTo(renamedFile)) {
+                if (selectedFile.renameTo(markedFile)) {
                     successMessage.append(newFileName).append("\n");
-                    removeImageFromApplication(imageUrl, nodesToRemove);
+                    markImageAsNoTip(imageUrl);  // Only passing imageUrl now
                 } else {
-                    allRenamed = false;
-                    showAlert("Error", "Failed to rename file: " + fileName);
+                    allMarked = false;
+                    showAlert("Error", "Failed to mark file: " + fileName);
                 }
             } catch (Exception e) {
-                allRenamed = false;
+                allMarked = false;
                 showAlert("Error", "An error occurred: " + e.getMessage());
             }
         }
-        if (allRenamed) {
+        if (allMarked) {
             showAlert("Success", successMessage.toString());
         }
     }
 
+
+    private void markImageAsNoTip(String imageUrl) {
+        // Add "No Tip" annotation
+        AnnotationData.getInstance().addAnnotation(
+                imageUrl, 0, 0, 0, 0);
+
+        // Add to No Tip set
+        noTipImageUrls.add(imageUrl);
+
+        // Update the UI
+        for (Node node : uploadedImages.getChildren()) {
+            if (node instanceof HBox) {
+                ImageView imageView = (ImageView) ((HBox) node).getChildren().get(0);
+                if (imageView.getImage().getUrl().equals(imageUrl)) {
+                    ((CheckBox) ((HBox) node).getChildren().get(1)).setText("No Tip");
+                    break;
+                }
+            }
+        }
+
+        if (currentSelectedImageView != null && currentSelectedImageView.getImage().getUrl().equals(imageUrl)) {
+            selectedImageView.setImage(null);
+            currentSelectedImageView = null;
+            currentImageIndex = Math.min(currentImageIndex, imageList.size() - 1);
+        }
+        clearAnnotations();
+    }
+
+
     private void removeImageFromApplication(String imageUrl, List<Node> nodesToRemove) {
         imageList.removeIf(image -> image.getUrl().equals(imageUrl));
         uploadedFilePaths.remove(imageUrl);

From 24227d53fceaf1b50e53ff8d673a48b84596d243 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 20 May 2024 16:29:30 +0200
Subject: [PATCH 090/100] Update AnnotationController.java

---
 .../java/controller/AnnotationController.java | 20 ++++---------------
 1 file changed, 4 insertions(+), 16 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index cc2107fe..962a3585 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -638,7 +638,6 @@ private static GridPane getHelpGrid() {
 
     @FXML
     private void handleNoTipAction(ActionEvent event) {
-        List<Node> nodesToRemove = new ArrayList<>();
         List<String> selectedImageUrls = new ArrayList<>();
 
         for (Node node : uploadedImages.getChildren()) {
@@ -647,7 +646,6 @@ private void handleNoTipAction(ActionEvent event) {
                 if (checkBox.isSelected()) {
                     ImageView imageView = (ImageView) hbox.getChildren().get(0);
                     selectedImageUrls.add(imageView.getImage().getUrl());
-                    nodesToRemove.add(node);
                 }
             }
         }
@@ -667,21 +665,11 @@ private void handleNoTipAction(ActionEvent event) {
         }
 
         boolean allMarked = true;
-        StringBuilder successMessage = new StringBuilder("The following files have been marked as NoTipFound_<original name>:\n");
+        StringBuilder successMessage = new StringBuilder("The following files have been marked as No Tip Found in the application:\n");
         for (String imageUrl : selectedImageUrls) {
             try {
-                File selectedFile = new File(new URL(imageUrl).toURI());
-                String fileName = selectedFile.getName();
-                String newFileName = "NoTipFound_" + fileName;
-                File markedFile = new File(selectedFile.getParent(), newFileName);
-
-                if (selectedFile.renameTo(markedFile)) {
-                    successMessage.append(newFileName).append("\n");
-                    markImageAsNoTip(imageUrl);  // Only passing imageUrl now
-                } else {
-                    allMarked = false;
-                    showAlert("Error", "Failed to mark file: " + fileName);
-                }
+                markImageAsNoTip(imageUrl);
+                successMessage.append(imageUrl).append("\n");
             } catch (Exception e) {
                 allMarked = false;
                 showAlert("Error", "An error occurred: " + e.getMessage());
@@ -692,7 +680,6 @@ private void handleNoTipAction(ActionEvent event) {
         }
     }
 
-
     private void markImageAsNoTip(String imageUrl) {
         // Add "No Tip" annotation
         AnnotationData.getInstance().addAnnotation(
@@ -721,6 +708,7 @@ private void markImageAsNoTip(String imageUrl) {
     }
 
 
+
     private void removeImageFromApplication(String imageUrl, List<Node> nodesToRemove) {
         imageList.removeIf(image -> image.getUrl().equals(imageUrl));
         uploadedFilePaths.remove(imageUrl);

From 2f9d56590aad64653213ac58d8b3d69f464185d7 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 20 May 2024 16:46:01 +0200
Subject: [PATCH 091/100] Update AnnotationController.java

---
 .../java/controller/AnnotationController.java | 37 ++++++++++++-------
 1 file changed, 24 insertions(+), 13 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 962a3585..256020fd 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -407,6 +407,18 @@ private void handleExportAction(ActionEvent event) {
             showAlert("No Selection", "No images have been check-marked for export.");
             return;
         }
+
+        // Check if all selected images have annotations
+        List<String> unannotatedSelectedImages = selectedImagesUrls.stream()
+                .filter(url -> !AnnotationData.getInstance().getAnnotations().containsKey(url))
+                .map(url -> new File(url).getName())
+                .collect(Collectors.toList());
+
+        if (!unannotatedSelectedImages.isEmpty()) {
+            showUnannotatedImagesAlert(unannotatedSelectedImages);
+            return;
+        }
+
         Map<String, AnnotationData.PublicAnnotation> annotations = AnnotationData.getInstance().getAnnotations();
         DirectoryChooser directoryChooser = new DirectoryChooser();
         directoryChooser.setTitle("Select Directory to Save Annotations");
@@ -442,6 +454,18 @@ private void handleExportAllAction(ActionEvent event) {
                 .map(ImageView::getImage)
                 .map(Image::getUrl)
                 .collect(Collectors.toSet());
+
+        // Check if all displayed images have annotations
+        List<String> unannotatedDisplayedImages = displayedImagesUrls.stream()
+                .filter(url -> !AnnotationData.getInstance().getAnnotations().containsKey(url))
+                .map(url -> new File(url).getName())
+                .collect(Collectors.toList());
+
+        if (!unannotatedDisplayedImages.isEmpty()) {
+            showUnannotatedImagesAlert(unannotatedDisplayedImages);
+            return;
+        }
+
         DirectoryChooser directoryChooser = new DirectoryChooser();
         directoryChooser.setTitle("Select Directory to Save Annotations");
         File selectedDirectory = directoryChooser.showDialog(((Node) event.getSource()).getScene().getWindow());
@@ -459,19 +483,6 @@ private void handleExportAllAction(ActionEvent event) {
                             showAlert("Error", "Failed to save annotations for " + entry.getKey());
                         }
                     });
-            // Export "No Tip" annotations
-            displayedImagesUrls.stream()
-                    .filter(url -> !AnnotationData.getInstance().getAnnotations().containsKey(url))
-                    .forEach(url -> {
-                        try {
-                            File file = new File(new URL(url).toURI());
-                            String fileName = file.getName().substring(0, file.getName().lastIndexOf('.')) + ".txt";
-                            File annotationFile = new File(selectedDirectory, fileName);
-                            saveNoTipAnnotationToFile(annotationFile);
-                        } catch (Exception e) {
-                            showAlert("Error", "Failed to save annotations for " + url);
-                        }
-                    });
         }
     }
 

From b13c8abf4e32853bfcca8b83a33a3b9f0a161493 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 20 May 2024 16:59:31 +0200
Subject: [PATCH 092/100] Update AnnotationController.java

---
 .../java/controller/AnnotationController.java | 25 ++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 256020fd..7aaa8079 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -172,19 +172,42 @@ public void Handle_Upload_Functionality(ActionEvent actionEvent) {
             List<File> selectedImages = fileChooser.showOpenMultipleDialog(currentStage);
 
             if (selectedImages != null) {
+                List<String> duplicateFiles = new ArrayList<>();
                 for (File file : selectedImages) {
                     if (!uploadedFilePaths.contains(file.getAbsolutePath())) {
                         displayImage(file);
                         uploadedFilePaths.add(file.getAbsolutePath());
                     } else {
-                        showAlert("Duplicate File", "The file " + file.getName() + " has already been uploaded.");
+                        duplicateFiles.add(file.getName());
                     }
                 }
+                if (!duplicateFiles.isEmpty()) {
+                    showDuplicateFilesAlert(duplicateFiles);
+                }
             }
         } catch (Exception e) {
             System.err.println("Error while choosing File: " + e.getMessage());
         }
     }
+
+    private void showDuplicateFilesAlert(List<String> duplicateFiles) {
+        Alert alert = new Alert(Alert.AlertType.INFORMATION);
+        alert.setTitle("Duplicate Files");
+        alert.setHeaderText("The following files have already been uploaded:");
+        VBox vbox = new VBox(5);
+        for (String fileName : duplicateFiles) {
+            Text fileText = new Text(fileName);
+            vbox.getChildren().add(fileText);
+        }
+        ScrollPane scrollPane = new ScrollPane(vbox);
+        scrollPane.setPrefSize(300, 150);
+        scrollPane.setVbarPolicy(ScrollPane.ScrollBarPolicy.AS_NEEDED);
+        scrollPane.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER);
+        alert.getDialogPane().setContent(scrollPane);
+        alert.setResizable(true);
+        alert.showAndWait();
+    }
+
     private void displayImage(File file) {
         HBox hbox = new HBox();
         hbox.setSpacing(10);

From 7b7b9ee30813b6e197f4a76914182bb153265632 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 20 May 2024 17:52:43 +0200
Subject: [PATCH 093/100] Bugs+Count_Functionality

---
 .../java/controller/AnnotationController.java | 73 +++++++------------
 src/main/resources/view/AnnotationView.fxml   | 42 ++++++-----
 2 files changed, 51 insertions(+), 64 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 7aaa8079..7f829fe1 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -1,5 +1,5 @@
 package controller;
-
+import javafx.scene.control.Label;
 import javafx.animation.FadeTransition;
 import javafx.event.ActionEvent;
 import javafx.fxml.FXML;
@@ -45,14 +45,15 @@ public class AnnotationController implements Controller {
     public Button ExportButton;
     public Button clearMarksButton;
     public Button helpButton;
+    public Button noTipButton;
     @FXML
     private ImageView selectedImageView;
     private ImageView currentSelectedImageView;
     @FXML
     private Pane annotationPane;
-
     @FXML
-    private Button noTipButton;
+    private Label uploadedImagesCountLabel;
+
 
     private Rectangle annotatedRectangle;
     private Circle middlePoint;
@@ -114,7 +115,7 @@ private void setupAnnotationHandlers() {
         });
         annotationPane.setOnMouseReleased(event -> {
             if (currentSelectedImageView != null && !noTipImageUrls.contains(currentSelectedImageView.getImage().getUrl())) {
-                releasedAnnotationEvent(event);
+                releasedAnnotationEvent();
             }
         });
     }
@@ -227,7 +228,7 @@ private void displayImage(File file) {
         imageView.setOnMouseClicked(event -> {
             selectImage(image, imageView);
         });
-        // Add or Remove the selected file paths to the HasSet
+        // Add or Remove the selected file paths to the HashSet
         checkBox.selectedProperty().addListener((observable, oldValue, newValue) -> {
             if (newValue) { // Checkbox is now selected
                 selectedFilePaths.add(imageView.getImage().getUrl());
@@ -239,7 +240,9 @@ private void displayImage(File file) {
         hbox.getChildren().add(imageView);
         hbox.getChildren().add(checkBox);
         uploadedImages.getChildren().add(hbox);
+        updateUploadedImagesCount();
     }
+
     private void selectImage(Image image, ImageView imageView) {
         try {
             if (imageList.isEmpty()) {
@@ -384,9 +387,8 @@ private void pressedAnnotationEvent(MouseEvent event) {
      * Handle the Simple Annotation Event where the user clicks once without dragging.
      * Here the size of the rectangle is fixed
      *
-     * @param event The Mouse Event
      */
-    private void releasedAnnotationEvent(MouseEvent event) {
+    private void releasedAnnotationEvent() {
         if (!dragged) {
             annotatedRectangle.setX(annotationPointX - 10);
             annotatedRectangle.setY(annotationPointY - 10);
@@ -452,11 +454,7 @@ private void handleExportAction(ActionEvent event) {
                     File file = new File(new URL(url).toURI());
                     String fileName = file.getName().substring(0, file.getName().lastIndexOf('.')) + ".txt";
                     File annotationFile = new File(selectedDirectory, fileName);
-                    if (annotations.containsKey(url)) {
-                        saveAnnotationsToFile(annotationFile, annotations.get(url));
-                    } else {
-                        saveNoTipAnnotationToFile(annotationFile);
-                    }
+                    saveAnnotationsToFile(annotationFile, annotations.get(url));
                 } catch (Exception e) {
                     showAlert("Error", "Failed to save annotations for " + url);
                 }
@@ -464,13 +462,14 @@ private void handleExportAction(ActionEvent event) {
         }
     }
 
+
     @FXML
     private void handleExportAllAction(ActionEvent event) {
         if (uploadedImages.getChildren().isEmpty()) {
             showAlert("Export Error", "There are no images to export.");
             return;
         }
-        Set<String> displayedImagesUrls = uploadedImages.getChildren().stream()
+        Set<String> allImagesUrls = uploadedImages.getChildren().stream()
                 .filter(node -> node instanceof HBox)
                 .map(node -> (HBox) node)
                 .map(hbox -> (ImageView) hbox.getChildren().get(0))
@@ -478,14 +477,14 @@ private void handleExportAllAction(ActionEvent event) {
                 .map(Image::getUrl)
                 .collect(Collectors.toSet());
 
-        // Check if all displayed images have annotations
-        List<String> unannotatedDisplayedImages = displayedImagesUrls.stream()
+        // Check if all uploaded images have annotations
+        List<String> unannotatedImages = allImagesUrls.stream()
                 .filter(url -> !AnnotationData.getInstance().getAnnotations().containsKey(url))
                 .map(url -> new File(url).getName())
                 .collect(Collectors.toList());
 
-        if (!unannotatedDisplayedImages.isEmpty()) {
-            showUnannotatedImagesAlert(unannotatedDisplayedImages);
+        if (!unannotatedImages.isEmpty()) {
+            showUnannotatedImagesAlert(unannotatedImages);
             return;
         }
 
@@ -494,7 +493,7 @@ private void handleExportAllAction(ActionEvent event) {
         File selectedDirectory = directoryChooser.showDialog(((Node) event.getSource()).getScene().getWindow());
         if (selectedDirectory != null) {
             AnnotationData.getInstance().getAnnotations().entrySet().stream()
-                    .filter(entry -> displayedImagesUrls.contains(entry.getKey()))
+                    .filter(entry -> allImagesUrls.contains(entry.getKey()))
                     .forEach(entry -> {
                         try {
                             String path = entry.getKey();
@@ -509,6 +508,7 @@ private void handleExportAllAction(ActionEvent event) {
         }
     }
 
+
     private void saveNoTipAnnotationToFile(File file) {
         try (PrintWriter writer = new PrintWriter(file)) {
             writer.println("0 0 0 0 0");
@@ -594,6 +594,7 @@ public void deletionfunctionality() {
                 currentSelectedImageView = null;
                 currentImageIndex = Math.min(currentImageIndex, imageList.size() - 1);
             }
+            updateUploadedImagesCount();
         } else {
             showAlert("Notice", "No images selected for deletion.");
         }
@@ -603,6 +604,13 @@ public void deletionfunctionality() {
         }
         clearAnnotations();
     }
+
+    private void updateUploadedImagesCount() {
+        int count = uploadedImages.getChildren().size();
+        uploadedImagesCountLabel.setText("Images: " + count);
+    }
+
+
     @FXML
     public void handleHelpButtonAction() {
         try {
@@ -671,7 +679,7 @@ private static GridPane getHelpGrid() {
 
 
     @FXML
-    private void handleNoTipAction(ActionEvent event) {
+    private void handleNoTipAction() {
         List<String> selectedImageUrls = new ArrayList<>();
 
         for (Node node : uploadedImages.getChildren()) {
@@ -706,7 +714,7 @@ private void handleNoTipAction(ActionEvent event) {
                 successMessage.append(imageUrl).append("\n");
             } catch (Exception e) {
                 allMarked = false;
-                showAlert("Error", "An error occurred: " + e.getMessage());
+               // showAlert("Error", "An error occurred: " + e.getMessage());
             }
         }
         if (allMarked) {
@@ -740,29 +748,4 @@ private void markImageAsNoTip(String imageUrl) {
         }
         clearAnnotations();
     }
-
-
-
-    private void removeImageFromApplication(String imageUrl, List<Node> nodesToRemove) {
-        imageList.removeIf(image -> image.getUrl().equals(imageUrl));
-        uploadedFilePaths.remove(imageUrl);
-        selectedFilePaths.remove(imageUrl);
-
-        // Remove the image from the uploadedImages VBox
-        for (Node node : nodesToRemove) {
-            if (node instanceof HBox) {
-                ImageView imageView = (ImageView) ((HBox) node).getChildren().get(0);
-                if (imageView.getImage().getUrl().equals(imageUrl)) {
-                    uploadedImages.getChildren().remove(node);
-                    break;
-                }
-            }
-        }
-        if (currentSelectedImageView != null && currentSelectedImageView.getImage().getUrl().equals(imageUrl)) {
-            selectedImageView.setImage(null);
-            currentSelectedImageView = null;
-            currentImageIndex = Math.min(currentImageIndex, imageList.size() - 1);
-        }
-        clearAnnotations();
-    }
 }
diff --git a/src/main/resources/view/AnnotationView.fxml b/src/main/resources/view/AnnotationView.fxml
index 96654516..aa0862aa 100644
--- a/src/main/resources/view/AnnotationView.fxml
+++ b/src/main/resources/view/AnnotationView.fxml
@@ -1,6 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <?import javafx.geometry.Insets?>
 <?import javafx.scene.control.Button?>
+<?import javafx.scene.control.Label?>
 <?import javafx.scene.control.ScrollPane?>
 <?import javafx.scene.image.ImageView?>
 <?import javafx.scene.layout.BorderPane?>
@@ -60,25 +61,28 @@
                </HBox.margin>
             </Button>
             <Pane HBox.hgrow="ALWAYS"/> <!-- Spacer to push the buttons to the right -->
-            <Button fx:id="noTipButton" text="No Tip" prefWidth="120.0" prefHeight="40.0"
-                    onAction="#handleNoTipAction" style="-fx-font-size: 16px;">
-               <HBox.margin>
-                  <Insets right="10.0"/>
-               </HBox.margin>
-            </Button>
-
-            <Button fx:id="uploadImagesButton" onAction="#Handle_Upload_Functionality" text="Import"
-                    prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;">
-               <HBox.margin>
-                  <Insets left="10.0" right="10.0"/>
-               </HBox.margin>
-            </Button>
-            <Button fx:id="clearMarksButton" onAction="#clearAnnotations" text="Clear Marks" prefWidth="120.0"
-                    prefHeight="40.0" style="-fx-font-size: 16px;">
-               <HBox.margin>
-                  <Insets right="10.0"/>
-               </HBox.margin>
-            </Button>
+            <Label fx:id="uploadedImagesCountLabel" prefWidth="425 " text="Total Images: 0" style="-fx-font-size: 16px;"/>
+            <HBox spacing="10.0" alignment="CENTER">
+               <Pane HBox.hgrow="ALWAYS"/>
+               <Button fx:id="noTipButton" text="No Tip" prefWidth="120.0" prefHeight="40.0"
+                       onAction="#handleNoTipAction" style="-fx-font-size: 16px;">
+                  <HBox.margin>
+                     <Insets right="10.0"/>
+                  </HBox.margin>
+               </Button>
+               <Button fx:id="uploadImagesButton" onAction="#Handle_Upload_Functionality" text="Import"
+                       prefWidth="120.0" prefHeight="40.0" style="-fx-font-size: 16px;">
+                  <HBox.margin>
+                     <Insets left="10.0" right="10.0"/>
+                  </HBox.margin>
+               </Button>
+               <Button fx:id="clearMarksButton" onAction="#clearAnnotations" text="Clear Marks" prefWidth="120.0"
+                       prefHeight="40.0" style="-fx-font-size: 16px;">
+                  <HBox.margin>
+                     <Insets right="10.0"/>
+                  </HBox.margin>
+               </Button>
+            </HBox>
          </HBox>
       </top>
       <left>

From 80b7cb5a6b1efa17c3c8edac4a45f8902e286ec0 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 20 May 2024 17:59:53 +0200
Subject: [PATCH 094/100] Update AnnotationController.java

---
 src/main/java/controller/AnnotationController.java | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 7f829fe1..5fbdc85d 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -508,15 +508,6 @@ private void handleExportAllAction(ActionEvent event) {
         }
     }
 
-
-    private void saveNoTipAnnotationToFile(File file) {
-        try (PrintWriter writer = new PrintWriter(file)) {
-            writer.println("0 0 0 0 0");
-        } catch (FileNotFoundException e) {
-            System.err.println("Error while saving No Tip Annotation to File: " + e.getMessage());
-        }
-    }
-
     private void showUnannotatedImagesAlert(List<String> unannotatedImages) {
         Alert alert = new Alert(Alert.AlertType.INFORMATION);
         alert.setTitle("Unannotated Images");

From b7d56a3af30f0fe995f85fdcc384478124f0357a Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 20 May 2024 19:33:36 +0200
Subject: [PATCH 095/100] Update AnnotationController.java

---
 src/main/java/controller/AnnotationController.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 5fbdc85d..b590882c 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -637,7 +637,7 @@ private static GridPane getHelpGrid() {
                 {"Delete", "Click this button to delete the selected images from the tool."},
                 {"Specific Export", "Click this button to export annotations for the selected images."},
                 {"Export All", "Click this button to export annotations for all images."},
-                {"No Tip", "Click this button to rename selected images to 'NoTipFound_<original name>' and remove them from the application."},
+                {"No Tip", "Click this button to rename selected images to be marked as NoTip found, now the picture won't be allowed to be annotated, unless you reload in the application again."},
                 {"Next", "Click this button to navigate to the next image."},
                 {"Previous", "Click this button to navigate to the previous image."},
                 {"", "To annotate an image, click and drag to create a bounding box. Hold down the Ctrl key to resize the bounding box."},

From 93f3ebddf0a1243676ca39a6ab03783ef088ce50 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 20 May 2024 19:47:05 +0200
Subject: [PATCH 096/100] Update AnnotationController.java

---
 src/main/java/controller/AnnotationController.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index b590882c..b3aa3f0a 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -637,7 +637,8 @@ private static GridPane getHelpGrid() {
                 {"Delete", "Click this button to delete the selected images from the tool."},
                 {"Specific Export", "Click this button to export annotations for the selected images."},
                 {"Export All", "Click this button to export annotations for all images."},
-                {"No Tip", "Click this button to rename selected images to be marked as NoTip found, now the picture won't be allowed to be annotated, unless you reload in the application again."},
+                {"No Tip", "Click this button to rename selected images to be marked as NoTip found. Now the picture "},
+                { "", "won't be allowed to be annotated, unless you reload in the application again."},
                 {"Next", "Click this button to navigate to the next image."},
                 {"Previous", "Click this button to navigate to the previous image."},
                 {"", "To annotate an image, click and drag to create a bounding box. Hold down the Ctrl key to resize the bounding box."},
@@ -647,7 +648,6 @@ private static GridPane getHelpGrid() {
                 {"Ctrl + A (After Selecting one image Checkbox): ", "All pictures will be check marked"},
                 {"Arrows: ", "Move zoomed images"}
         };
-
         GridPane gridPane = new GridPane();
         gridPane.setPadding(new Insets(10));
         gridPane.setVgap(10);

From db59a140a1d89c670b830bfed5941440772ae697 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 20 May 2024 19:54:40 +0200
Subject: [PATCH 097/100] Update AnnotationController.java

---
 src/main/java/controller/AnnotationController.java | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index b3aa3f0a..a6b18083 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -554,6 +554,7 @@ public void deletionfunctionality() {
         List<Image> imagesToRemove = new ArrayList<>();
         boolean currentDisplayedRemoved = false;
         boolean atLeastOneSelected = false;
+
         for (Node node : uploadedImages.getChildren()) {
             if (node instanceof HBox hbox) {
                 ImageView imageView = (ImageView) hbox.getChildren().get(0);
@@ -567,6 +568,8 @@ public void deletionfunctionality() {
                         toRemove.add(node);
                         uploadedFilePaths.remove(imagePath);
                         selectedFilePaths.remove(imagePath);
+                        noTipImageUrls.remove(imageView.getImage().getUrl()); // Remove from noTipImageUrls set
+
                         if (imageView.equals(currentSelectedImageView)) {
                             currentDisplayedRemoved = true;
                         }
@@ -577,6 +580,7 @@ public void deletionfunctionality() {
                 }
             }
         }
+
         if (atLeastOneSelected) {
             uploadedImages.getChildren().removeAll(toRemove);
             imageList.removeAll(imagesToRemove);
@@ -589,13 +593,16 @@ public void deletionfunctionality() {
         } else {
             showAlert("Notice", "No images selected for deletion.");
         }
+
         // Notify if all images have been deleted
         if (uploadedImages.getChildren().isEmpty()) {
             showAlert("Notice", "All images have been deleted.");
         }
+
         clearAnnotations();
     }
 
+
     private void updateUploadedImagesCount() {
         int count = uploadedImages.getChildren().size();
         uploadedImagesCountLabel.setText("Images: " + count);

From 16a45f7d00054c5aa61677e05baadc8f388fb6d3 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 20 May 2024 19:58:17 +0200
Subject: [PATCH 098/100] Update AnnotationController.java

---
 src/main/java/controller/AnnotationController.java | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index a6b18083..d61f46a9 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -569,6 +569,7 @@ public void deletionfunctionality() {
                         uploadedFilePaths.remove(imagePath);
                         selectedFilePaths.remove(imagePath);
                         noTipImageUrls.remove(imageView.getImage().getUrl()); // Remove from noTipImageUrls set
+                        AnnotationData.getInstance().deleteAnnotation(imageView.getImage().getUrl()); // Remove annotation
 
                         if (imageView.equals(currentSelectedImageView)) {
                             currentDisplayedRemoved = true;
@@ -603,6 +604,7 @@ public void deletionfunctionality() {
     }
 
 
+
     private void updateUploadedImagesCount() {
         int count = uploadedImages.getChildren().size();
         uploadedImagesCountLabel.setText("Images: " + count);

From aadaf52b0d600ea1221b91a34090313f387a9692 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 20 May 2024 19:58:55 +0200
Subject: [PATCH 099/100] Update AnnotationController.java

---
 src/main/java/controller/AnnotationController.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index d61f46a9..754f8bfa 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -647,7 +647,7 @@ private static GridPane getHelpGrid() {
                 {"Specific Export", "Click this button to export annotations for the selected images."},
                 {"Export All", "Click this button to export annotations for all images."},
                 {"No Tip", "Click this button to rename selected images to be marked as NoTip found. Now the picture "},
-                { "", "won't be allowed to be annotated, unless you reload in the application again."},
+                { "", "won't be allowed to be annotated, unless you reload it in the application again."},
                 {"Next", "Click this button to navigate to the next image."},
                 {"Previous", "Click this button to navigate to the previous image."},
                 {"", "To annotate an image, click and drag to create a bounding box. Hold down the Ctrl key to resize the bounding box."},

From 465d1285681329b10bb3be7fe8c896c876b24857 Mon Sep 17 00:00:00 2001
From: muazzamaqeel <aqeemu01@thu.de>
Date: Mon, 20 May 2024 20:44:38 +0200
Subject: [PATCH 100/100] Comments

---
 .../java/controller/AnnotationController.java | 165 ++++++++++++++++--
 1 file changed, 148 insertions(+), 17 deletions(-)

diff --git a/src/main/java/controller/AnnotationController.java b/src/main/java/controller/AnnotationController.java
index 754f8bfa..b1de7a2d 100644
--- a/src/main/java/controller/AnnotationController.java
+++ b/src/main/java/controller/AnnotationController.java
@@ -1,4 +1,5 @@
 package controller;
+
 import javafx.scene.control.Label;
 import javafx.animation.FadeTransition;
 import javafx.event.ActionEvent;
@@ -34,9 +35,14 @@
 import java.net.URL;
 import java.util.*;
 import java.util.stream.Collectors;
+
+/**
+ * The AnnotationController class manages the user interface for
+ * uploading, viewing, and annotating images in the application.
+ */
 public class AnnotationController implements Controller {
     @FXML
-    public VBox uploadedImages;     //Where the users see the files
+    public VBox uploadedImages;     // Where the users see the files
     @FXML
     public Button uploadImagesButton;
     @FXML
@@ -54,18 +60,23 @@ public class AnnotationController implements Controller {
     @FXML
     private Label uploadedImagesCountLabel;
 
-
     private Rectangle annotatedRectangle;
     private Circle middlePoint;
     private boolean dragged = false;
     private double annotationPointX, annotationPointY;
     private final Set<String> uploadedFilePaths = new HashSet<>();
-    // store the paths of the selected Image, so you can Export the data based on these keys
+    // Store the paths of the selected Image, so you can Export the data based on these keys
     private final Set<String> selectedFilePaths = new HashSet<>();
     private int currentImageIndex = 0; // Default to the first image
     private final List<Image> imageList = new ArrayList<>(); // Store all loaded images
     private final Set<String> noTipImageUrls = new HashSet<>();
 
+    /**
+     * Initializes the controller then sets up event handlers and initial states.
+     *
+     * @param location  The location used to resolve relative paths for the root object.
+     * @param resources The resources used to localize the root object.
+     */
     @Override
     public void initialize(URL location, ResourceBundle resources) {
         System.out.println("Initializing Controller");
@@ -93,6 +104,9 @@ public void initialize(URL location, ResourceBundle resources) {
         });
     }
 
+    /**
+     * Selects all checkboxes for uploaded images.
+     */
     private void selectAllCheckboxes() {
         for (Node node : uploadedImages.getChildren()) {
             if (node instanceof HBox) {
@@ -102,6 +116,9 @@ private void selectAllCheckboxes() {
         }
     }
 
+    /**
+     * Sets up mouse event handlers for annotation actions.
+     */
     private void setupAnnotationHandlers() {
         annotationPane.setOnMousePressed(event -> {
             if (currentSelectedImageView != null && !noTipImageUrls.contains(currentSelectedImageView.getImage().getUrl())) {
@@ -119,6 +136,11 @@ private void setupAnnotationHandlers() {
             }
         });
     }
+
+    /**
+     * Selects the next image in the list.
+     * If no next image is available, it prints a message.
+     */
     public void selectNextImage() {
         // Check if there's a next image in the list
         if (currentImageIndex < imageList.size() - 1) {
@@ -131,6 +153,10 @@ public void selectNextImage() {
         }
     }
 
+    /**
+     * Selects the previous image in the list.
+     * If no previous image is available, it prints a message.
+     */
     public void selectPreviousImage() {
         // Check if there's a previous image in the list
         if (currentImageIndex > 0) {
@@ -143,6 +169,12 @@ public void selectPreviousImage() {
         }
     }
 
+    /**
+     * Finds the ImageView of a given image.
+     *
+     * @param image The image to find the ImageView for.
+     * @return The ImageView of the image.
+     */
     private ImageView findImageViewForImage(Image image) {
         for (Node node : uploadedImages.getChildren()) {
             if (node instanceof HBox) {
@@ -154,11 +186,21 @@ private ImageView findImageViewForImage(Image image) {
         }
         return null; // Not found
     }
+
+    /**
+     * Closes the controller and cleans up.
+     */
     @FXML
     @Override
     public void close() {
         unregisterController();
     }
+
+    /**
+     * Handles the upload functionality for selecting and displaying images.
+     *
+     * @param actionEvent The event triggered by the upload button.
+     */
     @FXML
     public void Handle_Upload_Functionality(ActionEvent actionEvent) {
         try {
@@ -191,6 +233,11 @@ public void Handle_Upload_Functionality(ActionEvent actionEvent) {
         }
     }
 
+    /**
+     * Displays an alert for duplicate files.
+     *
+     * @param duplicateFiles List of duplicate files.
+     */
     private void showDuplicateFilesAlert(List<String> duplicateFiles) {
         Alert alert = new Alert(Alert.AlertType.INFORMATION);
         alert.setTitle("Duplicate Files");
@@ -209,6 +256,11 @@ private void showDuplicateFilesAlert(List<String> duplicateFiles) {
         alert.showAndWait();
     }
 
+    /**
+     * Displays an image file in the application.
+     *
+     * @param file The image file to be displayed.
+     */
     private void displayImage(File file) {
         HBox hbox = new HBox();
         hbox.setSpacing(10);
@@ -243,6 +295,13 @@ private void displayImage(File file) {
         updateUploadedImagesCount();
     }
 
+    /**
+     * Selects an image for display and annotation.
+     * Updates image view, also handles scrolling and zooming functionalities.
+     *
+     * @param image     The image to be selected.
+     * @param imageView The ImageView of the selected image.
+     */
     private void selectImage(Image image, ImageView imageView) {
         try {
             if (imageList.isEmpty()) {
@@ -298,6 +357,10 @@ private void selectImage(Image image, ImageView imageView) {
         }
     }
 
+    /**
+     * Scrolls the selected image into view within the selectedImagePane.
+     * Also adjusts the scrollbar.
+     */
     private void scrollToSelectedImage() {
         if (currentSelectedImageView != null && selectedImagePane != null) {
             double viewportHeight = selectedImagePane.getHeight();
@@ -307,6 +370,11 @@ private void scrollToSelectedImage() {
             selectedImagePane.setVvalue(Math.max(0, Math.min(vValue, 1)));  // Clamp vValue to be between 0 and 1
         }
     }
+
+    /**
+     * Removes any existing annotations from pane.
+     * Also deletes the annotation data of the selected image.
+     */
     public void clearAnnotations() {
         if (annotatedRectangle != null) {
             annotationPane.getChildren().remove(annotatedRectangle);
@@ -316,6 +384,11 @@ public void clearAnnotations() {
             annotatedRectangle = null;
         }
     }
+
+    /**
+     * Clears any existing annotations, then retrieves and displays annotation data.
+     * Also creates and displays the middle point of the annotation.
+     */
     private void checkForExistingAnnotationData() {
         // Clear existing annotations if any
         if (annotatedRectangle != null) {
@@ -351,6 +424,11 @@ private void checkForExistingAnnotationData() {
             annotationPane.getChildren().add(middlePoint);
         }
     }
+
+    /**
+     * Allows for a variable annotation rectangle to be displayed at the cursor position.
+     * Only works when control is held down.
+     */
     private void dragAnnotationEvent(MouseEvent event) {
         if (event.isControlDown()) {
             double x2 = event.getX();
@@ -364,6 +442,11 @@ private void dragAnnotationEvent(MouseEvent event) {
             dragged = true;
         }
     }
+
+    /**
+     * Allows for a square annotation rectangle to be displayed at the cursor position.
+     * Default size for annotations.
+     */
     private void pressedAnnotationEvent(MouseEvent event) {
         annotationPointX = event.getX();
         annotationPointY = event.getY();
@@ -381,12 +464,11 @@ private void pressedAnnotationEvent(MouseEvent event) {
             middlePoint.setFill(Color.rgb(6, 207, 236));
             annotationPane.getChildren().add(middlePoint);
         }
-
     }
+
     /**
-     * Handle the Simple Annotation Event where the user clicks once without dragging.
-     * Here the size of the rectangle is fixed
-     *
+     * Handles the released annotation event.
+     * Finalizes the dragged annotation and stores annotation data.
      */
     private void releasedAnnotationEvent() {
         if (!dragged) {
@@ -411,8 +493,15 @@ private void releasedAnnotationEvent() {
                 annotatedRectangle.getWidth() / selectedImageView.getImage().getWidth(),
                 annotatedRectangle.getHeight() / selectedImageView.getImage().getHeight()
         );
-
     }
+
+    /**
+     * Handles the export action for saving annotations of selected images to files.
+     * Allows for annotation data to be saved as text files in the desired directory.
+     * Does not allow for unannotated images to be exported.
+     *
+     * @param event The ActionEvent representing the export action.
+     */
     @FXML
     private void handleExportAction(ActionEvent event) {
         if (uploadedImages.getChildren().isEmpty()) {
@@ -462,7 +551,13 @@ private void handleExportAction(ActionEvent event) {
         }
     }
 
-
+    /**
+     * Handles the export action for saving annotations of all displayed images to files.
+     * Allows for annotation data to be saved as text files in the desired directory.
+     * Does not allow for unannotated images to be exported.
+     *
+     * @param event The ActionEvent representing the export all action.
+     */
     @FXML
     private void handleExportAllAction(ActionEvent event) {
         if (uploadedImages.getChildren().isEmpty()) {
@@ -508,6 +603,11 @@ private void handleExportAllAction(ActionEvent event) {
         }
     }
 
+    /**
+     * Handles the alert that unannotated images cannot be exported.
+     *
+     * @param unannotatedImages A list of the names of unannotated images.
+     */
     private void showUnannotatedImagesAlert(List<String> unannotatedImages) {
         Alert alert = new Alert(Alert.AlertType.INFORMATION);
         alert.setTitle("Unannotated Images");
@@ -525,6 +625,13 @@ private void showUnannotatedImagesAlert(List<String> unannotatedImages) {
         alert.setResizable(true);
         alert.showAndWait();
     }
+
+    /**
+     * Displays a generic information alert.
+     *
+     * @param title   The title of the alert.
+     * @param content The content of the alert.
+     */
     private void showAlert(String title, String content) {
         Alert alert = new Alert(Alert.AlertType.INFORMATION);
         alert.setTitle(title);
@@ -532,11 +639,12 @@ private void showAlert(String title, String content) {
         alert.setContentText(content);
         alert.showAndWait();
     }
+
     /**
-     * Handles the Saving of Annotations to a File
+     * Handles the Saving of Annotations to a File.
      *
-     * @param file       The File to save the Annotations to
-     * @param annotation The Annotation Data to save
+     * @param file       The file to save the annotations to.
+     * @param annotation The annotation data to save.
      */
     private void saveAnnotationsToFile(File file, AnnotationData.PublicAnnotation annotation) {
         try (PrintWriter writer = new PrintWriter(file)) {
@@ -548,6 +656,12 @@ private void saveAnnotationsToFile(File file, AnnotationData.PublicAnnotation an
             System.err.println("Error while saving Annotation to File: " + e.getMessage());
         }
     }
+
+    /**
+     * Handles the deletion functionality for selected images.
+     * Removes related image data and annotation data from all locations.
+     * Updates currently displayed image and image status.
+     */
     @FXML
     public void deletionfunctionality() {
         List<Node> toRemove = new ArrayList<>();
@@ -603,14 +717,18 @@ public void deletionfunctionality() {
         clearAnnotations();
     }
 
-
-
+    /**
+     * Updates the count of uploaded images.
+     */
     private void updateUploadedImagesCount() {
         int count = uploadedImages.getChildren().size();
         uploadedImagesCountLabel.setText("Images: " + count);
     }
 
-
+    /**
+     * Handles the action when the help button is clicked.
+     * Creates window with information on how to use this application.
+     */
     @FXML
     public void handleHelpButtonAction() {
         try {
@@ -639,6 +757,12 @@ public void handleHelpButtonAction() {
             System.err.println("Error while opening Help window: " + e.getMessage());
         }
     }
+
+    /**
+     * Generates a grid containing helpful information.
+     *
+     * @return A GridPane containing helpful information.
+     */
     private static GridPane getHelpGrid() {
         String[][] helpTextArray = {
                 {"Import", "Click this button to import images into the tool."},
@@ -677,7 +801,9 @@ private static GridPane getHelpGrid() {
         return gridPane;
     }
 
-
+    /**
+     * Handles the action to mark images as No Tip.
+     */
     @FXML
     private void handleNoTipAction() {
         List<String> selectedImageUrls = new ArrayList<>();
@@ -714,7 +840,7 @@ private void handleNoTipAction() {
                 successMessage.append(imageUrl).append("\n");
             } catch (Exception e) {
                 allMarked = false;
-               // showAlert("Error", "An error occurred: " + e.getMessage());
+                // showAlert("Error", "An error occurred: " + e.getMessage());
             }
         }
         if (allMarked) {
@@ -722,6 +848,11 @@ private void handleNoTipAction() {
         }
     }
 
+    /**
+     * Marks an image as No Tip.
+     *
+     * @param imageUrl The URL of the image to be marked as No Tip.
+     */
     private void markImageAsNoTip(String imageUrl) {
         // Add "No Tip" annotation
         AnnotationData.getInstance().addAnnotation(