Unet integration

src/client/dcp_client/config.cfg

@@ -1,9 +1,9 @@
 {
     "server":{
-        "user": "ubuntu",
-        "host": "jusuf-vm2", 
-        "data-path": "/home/ubuntu/dcp-data",
-        "ip": "134.94.88.74", 
+        "user": "local",
+        "host": "local", 
+        "data-path": "None",
+        "ip": "localhost", 
         "port": 7010
     }
 }

src/client/dcp_client/gui/main_window.py

@@ -15,7 +15,7 @@
 class MainWindow(QWidget):
     '''Main Window Widget object.
     Opens the main window of the app where selected images in both directories are listed. 
-    User can view the images, train the mdoel to get the labels, and visualise the result.
+    User can view the images, train the model to get the labels, and visualise the result.
     :param eval_data_path: Chosen path to images without labeles, selected by the user in the WelcomeWindow
     :type eval_data_path: string
     :param train_data_path: Chosen path to images with labeles, selected by the user in the WelcomeWindow

src/client/dcp_client/gui/napari_window.py

@@ -1,14 +1,19 @@
 from __future__ import annotations
 from typing import List, TYPE_CHECKING
 
-from PyQt5.QtWidgets import QWidget, QPushButton, QVBoxLayout, QHBoxLayout
+import numpy as np
+
+from PyQt5.QtWidgets import QWidget, QPushButton, QVBoxLayout, QHBoxLayout, QComboBox, QLabel, QGridLayout
+from PyQt5.QtCore import Qt
 import napari
+from napari.qt import thread_worker
 
 if TYPE_CHECKING:
     from dcp_client.app import Application
 
 from dcp_client.utils import utils
 
+
 class NapariWindow(QWidget):
     '''Napari Window Widget object.
     Opens the napari image viewer to view and fix the labeles.
@@ -26,29 +31,106 @@ def __init__(self, app: Application):
         self.app.search_segs()
 
         # Set the viewer
+
+        # with thread_worker():
         self.viewer = napari.Viewer(show=False)
+
         self.viewer.add_image(img, name=utils.get_path_stem(self.app.cur_selected_img))
+
         for seg_file in self.app.seg_filepaths:
             self.viewer.add_labels(self.app.load_image(seg_file), name=utils.get_path_stem(seg_file))
 
+        layer = self.viewer.layers[utils.get_path_stem(self.app.seg_filepaths[0])]
+
+        self.changed = False
+
         main_window = self.viewer.window._qt_window
-        layout = QVBoxLayout()
-        layout.addWidget(main_window)
+
+        layout = QGridLayout()
+        layout.addWidget(main_window, 0, 0, 1, 4)
+
+        # set first mask as active by default
+        self.active_mask_index = 0
+
+        if layer.data.shape[0] >= 2:
+            # User hint
+            message_label = QLabel('Choose an active mask')
+            message_label.setAlignment(Qt.AlignRight)
+            layout.addWidget(message_label, 1, 0)
+
+        # Drop list to choose which is an active mask
+
+            self.mask_choice_dropdown = QComboBox()
+            self.mask_choice_dropdown.addItem('Instance Segmentation Mask', userData=0)
+            self.mask_choice_dropdown.addItem('Labels Mask', userData=1)
+            layout.addWidget(self.mask_choice_dropdown, 1, 1)
+
+
+
+            # when user has chosen the mask, we don't want to change it anymore to avoid errors
+            lock_button = QPushButton("Confirm Final Choice")
+            lock_button.clicked.connect(self.set_active_mask)
+
+            layout.addWidget(lock_button, 1, 2)
+            layer.mouse_drag_callbacks.append(self.copy_mask_callback)
+            layer.events.set_data.connect(lambda event: self.copy_mask_callback(layer, event))
 
-        buttons_layout = QHBoxLayout()
 
         add_to_inprogress_button = QPushButton('Move to \'Curatation in progress\' folder')
-        buttons_layout.addWidget(add_to_inprogress_button)
+        layout.addWidget(add_to_inprogress_button, 2, 0, 1, 2)
         add_to_inprogress_button.clicked.connect(self.on_add_to_inprogress_button_clicked)
 
         add_to_curated_button = QPushButton('Move to \'Curated dataset\' folder')
-        buttons_layout.addWidget(add_to_curated_button)
+        layout.addWidget(add_to_curated_button, 2, 2, 1, 2)
         add_to_curated_button.clicked.connect(self.on_add_to_curated_button_clicked)
 
-        layout.addLayout(buttons_layout)
-
         self.setLayout(layout)
-        self.show()
+
+    def set_active_mask(self):
+        self.mask_choice_dropdown.setDisabled(True)
+        self.active_mask_index = self.mask_choice_dropdown.currentData()
+
+    def on_mask_choice_changed(self, index):
+        self.active_mask_index = self.mask_choice_dropdown.itemData(index)
+
+    def copy_mask_callback(self, layer, event):
+
+        source_mask = layer.data
+
+        if event.type == "mouse_press":
+
+            c, event_x, event_y = event.position
+            c, event_x, event_y = int(c), int(np.round(event_x)), int(np.round(event_y))
+
+            self.event_coords = (c, event_x, event_y)
+
+
+        elif event.type == "set_data":
+
+
+            if self.event_coords is not None:
+                c, event_x, event_y = self.event_coords
+
+                if c == self.active_mask_index:
+
+                    labels, counts = np.unique(source_mask[c, event_x - 1: event_x + 2, event_y - 1: event_y + 2], return_counts=True)
+
+                    if labels.size > 0:
+
+                        idx = np.argmax(counts)
+                        label = labels[idx]
+
+                        mask_fill = source_mask[c] == label
+                        source_mask[abs(c - 1)][mask_fill] = label
+
+                        self.changed = True
+
+                else:
+
+                    mask_fill = source_mask[abs(c - 1)] == 0
+                    source_mask[c][mask_fill] = 0
+
+
 
     def on_add_to_curated_button_clicked(self):
         '''
@@ -66,6 +148,7 @@ def on_add_to_curated_button_clicked(self):
             message_text = "Please select the segmenation you wish to save from the layer list"
             utils.create_warning_box(message_text, message_title="Warning")
             return
+
         seg = self.viewer.layers[cur_seg_selected].data
 
         # Move original image
@@ -78,6 +161,7 @@ def on_add_to_curated_button_clicked(self):
         self.app.delete_images(self.app.seg_filepaths)
         # TODO Create the Archive folder for the rest? Or move them as well? 
 
+        self.viewer.close()
         self.close()
 
     def on_add_to_inprogress_button_clicked(self):
@@ -105,4 +189,5 @@ def on_add_to_inprogress_button_clicked(self):
         seg = self.viewer.layers[cur_seg_selected].data
         self.app.save_image(self.app.inprogr_data_path, cur_seg_selected+'.tiff', seg)
 
+        self.viewer.close()
         self.close()

src/server/dcp_server/config.cfg

@@ -22,6 +22,11 @@
             "num_classes": 3,
             "black_bg": "False",
             "include_mask": "False"
+        },
+        "unet":{
+            "in_channels":1,
+            "out_channels":4,
+            "features":[64,128,256,512]
         }
     },
 
@@ -45,6 +50,12 @@
             "lr": 0.001,
             "batch_size": 1,
             "optimizer": "Adam"
+        },
+        "unet":{
+            "n_epochs": 2,
+            "lr": 0.001,
+            "batch_size": 1,
+            "optimizer": "Adam"
         }
     },
 
@@ -60,6 +71,9 @@
                 "patch_size": 64,
                 "noise_intensity": 5
             }
+        },
+        "unet": {
+
         },
         "mask_channel_axis": 0
     }