saenopySheroid and saenopy2D show empy image when image is not found

Author: rgerum

saenopy/gui/common/PipelineModule.py

@@ -180,7 +180,7 @@ def setResult(self, result: Result):
             #    self.t_slider.setRange(0, len(result.images) - 1)
             #else:
             #    self.t_slider.setRange(0, len(result.stacks) - 2)
-            self.t_slider.setRange(0, data["time_point_count"])
+            self.t_slider.setRange(0, data["time_point_count"] - 1)
 
         self.state_changed(result)
         if self.tab is not None:

saenopy/gui/spheroid/modules/DeformationDetector.py

@@ -182,7 +182,8 @@ def update_display(self, *, plotter=None):
 
         import imageio
         t = self.t_slider.value()
-        im = imageio.v2.imread(self.result.images[t]).astype(float)
+        im = self.result.get_image_data(t).astype(float)
+        #im = imageio.v2.imread(self.result.images[t]).astype(float)
         im0 = im.copy()
         im = im - im.min()
         im = (im / im.max() * 255).astype(np.uint8)

saenopy/gui/spheroid/modules/path_editor.py

@@ -11,8 +11,10 @@ def start_path_change(parent, result):
     if not path_editor.exec():
         return
 
-    path_changer = PathChanger(result.template.replace("*", "{t}"), path_editor.input_folder.value())
+    path_changer = PathChanger(result.template.replace("*", "{t}"), path_editor.input_folder.value().replace("*", "{t}"))
+    print(result.images)
     result.images = [path_changer.change_path(path) for path in result.images]
+    print(result.images)
     result.template = path_changer.change_path(result.template.replace("*", "{t}")).replace("{t}", "*")
 
     #if path_editor.input_folder2 is not None:

saenopy/gui/spheroid/modules/result.py

@@ -1,14 +1,16 @@
+import numpy as np
 import io
 from typing import List
+import traceback
+from natsort import natsorted
+import re
 
+from tifffile import imread
 import matplotlib.pyplot as plt
 
 from saenopy.saveable import Saveable
-import numpy as np
-from tifffile import imread
 from saenopy.result_file import make_path_absolute
-from natsort import natsorted
-import re
+
 
 
 class Mesh2D:
@@ -18,7 +20,7 @@ class Mesh2D:
 class ResultSpheroid(Saveable):
     __save_parameters__ = ['template', 'images', 'output', 'pixel_size', 'time_delta',
                            'thresh_segmentation', 'continuous_segmentation',
-                           'custom_mask', 'n_min', 'n_max',
+                           'custom_mask', 'n_min', 'n_max', 'shape',
 
                            'piv_parameters', 'force_parameters',
 
@@ -56,6 +58,8 @@ def __init__(self, template, images, output, **kwargs):
         self.template = template
         self.images = images
         self.output = str(output)
+        if "shape" not in kwargs:
+            kwargs["shape"] = None
         if "res_data" not in kwargs:
             kwargs["res_data"] = {}
         self.res_data = {}
@@ -97,7 +101,17 @@ def get_data_structure(self):
         }
 
     def get_image_data(self, time_point, channel="default", use_reference=False):
-        im = imread(self.images[time_point])
+        try:
+            im = imread(self.images[time_point])
+        except FileNotFoundError as err:
+            traceback.print_exception(err)
+            h = 255
+            w = 255
+            if self.shape is not None:
+                h, w = self.shape[:2]
+            im = np.zeros([h, w, 3], dtype=np.uint8)
+            im[:, :, 0] = 255
+            im[:, :, 2] = 255
         if len(im.shape) == 2:
             return im[:, :, None, None]
         return im[:, :, :, None]

saenopy/gui/tfm2d/modules/path_editor.py

@@ -15,6 +15,13 @@ def start_path_change(parent, result):
     result.reference_stack = path_editor.input_folder2.value()
     result.input = path_editor.input_folder3.value()
 
+    path_b = Path(result.input)
+    path_a = Path(result.reference_stack)
+    path_b = path_b.parent / (path_b.stem + "_corrected" + path_b.suffix)
+    path_a = path_a.parent / (path_a.stem + "_corrected" + path_a.suffix)
+    result.input_corrected = str(path_b)
+    result.reference_stack_corrected = str(path_a)
+
     #if path_editor.input_pack.value():
     #    for stack in result.stacks:
     #        stack.pack_files()

saenopy/gui/tfm2d/modules/result.py

@@ -5,6 +5,7 @@
 import numpy as np
 from tifffile import imread
 import matplotlib.pyplot as plt
+import traceback
 
 from saenopy.saveable import Saveable
 from saenopy.result_file import make_path_absolute
@@ -85,24 +86,34 @@ def __init__(self, output, bf, input, reference_stack, pixel_size, **kwargs):
         super().__init__(**kwargs)
 
     def get_image(self, index, corrected=True):
-        if index == 0:
-            if corrected:
-                try:
-                    im = imread(self.input_corrected)
-                except FileNotFoundError:
+        try:
+            if index == 0:
+                if corrected:
+                    try:
+                        im = imread(self.input_corrected)
+                    except FileNotFoundError:
+                        im = imread(self.input)
+                else:
                     im = imread(self.input)
+            elif index == -1:
+                im = imread(self.bf)
             else:
-                im = imread(self.input)
-        elif index == -1:
-            im = imread(self.bf)
-        else:
-            if corrected:
-                try:
-                    im = imread(self.reference_stack_corrected)
-                except FileNotFoundError:
+                if corrected:
+                    try:
+                        im = imread(self.reference_stack_corrected)
+                    except FileNotFoundError:
+                        im = imread(self.reference_stack)
+                else:
                     im = imread(self.reference_stack)
-            else:
-                im = imread(self.reference_stack)
+        except FileNotFoundError as err:
+            traceback.print_exception(err)
+            h = 255
+            w = 255
+            if self.shape is not None:
+                h, w = self.shape[:2]
+            im = np.zeros([h, w, 3], dtype=np.uint8)
+            im[:, :, 0] = 255
+            im[:, :, 2] = 255
         if self.shape is None:
             self.shape = im.shape
         return im