WIP added metrics utils + fixes + new utils.py

Author: C-Achard

src/napari_cellseg_annotator/_tests/test_utils.py

@@ -8,7 +8,42 @@
 from napari_cellseg_annotator import utils
 
 
-def test_get_padding_dim(make_napari_viewer):
+def test_align_array_sizes():
+
+    im = np.zeros((128, 512, 256))
+    print(im.shape)
+
+    dim_1 = (64, 64, 512)
+    ground = np.array((512, 64, 64))
+    pred = np.array(dim_1)
+
+    ori, targ = utils.align_array_sizes(ground, pred)
+
+    im_1 = np.moveaxis(im, ori, targ)
+    print(im_1.shape)
+    assert im_1.shape == (512, 256, 128)
+
+    dim_2 = (512, 256, 128)
+    ground = np.array((128, 512, 256))
+    pred = np.array(dim_2)
+
+    ori, targ = utils.align_array_sizes(ground, pred)
+
+    im_2 = np.moveaxis(im, ori, targ)
+    print(im_2.shape)
+    assert im_2.shape == dim_2
+
+    dim_3 = (128, 128, 128)
+    ground = np.array(dim_3)
+    pred = np.array(dim_3)
+
+    ori, targ = utils.align_array_sizes(ground, pred)
+    im_3 = np.moveaxis(im, ori, targ)
+    print(im_3.shape)
+    assert im_3.shape == im.shape
+
+
+def test_get_padding_dim():
 
     tensor = torch.randn(100, 30, 40)
     size = tensor.size()

src/napari_cellseg_annotator/model_instance_seg.py

@@ -91,7 +91,7 @@ def binary_watershed(
     return np.array(segm)
 
 
-def to_instance(image, is_file_path=True):
+def to_instance(image, is_file_path=False):
     """Converts a **ground-truth** label to instance (unique id per object) labels. Does not remove small objects.
 
     Args:
@@ -112,7 +112,7 @@ def to_instance(image, is_file_path=True):
     return result
 
 
-def to_semantic(image, is_file_path=True):
+def to_semantic(image, is_file_path=False):
     """Converts a **ground-truth** label to semantic (binary 0/1) labels.
 
     Args:

src/napari_cellseg_annotator/plugin_base.py

@@ -239,7 +239,7 @@ def load_image_dataset(self):
         filenames = self.load_dataset_paths()
         # print(filenames)
         if filenames != "" and filenames != [""] and filenames != []:
-            self.images_filepaths = filenames
+            self.images_filepaths = sorted(filenames)
             # print(filenames)
             path = os.path.dirname(filenames[0])
             self.lbl_image_files.setText(path)
@@ -250,7 +250,7 @@ def load_label_dataset(self):
         """Show file dialog to set :py:attr:`~labels_filepaths`"""
         filenames = self.load_dataset_paths()
         if filenames != "" and filenames != [""] and filenames != []:
-            self.labels_filepaths = filenames
+            self.labels_filepaths = sorted(filenames)
             path = os.path.dirname(filenames[0])
             self.lbl_label_files.setText(path)
             self.update_default()

src/napari_cellseg_annotator/plugin_convert.py

@@ -139,7 +139,7 @@ def folder_to_semantic(self):
 
         for file in self.labels_filepaths:
 
-            image = to_semantic(file)
+            image = to_semantic(file, is_file_path=True)
 
             imwrite(
                 results_folder + "/" + os.path.basename(file),
@@ -151,7 +151,7 @@ def layer_to_semantic(self):
 
         im = self._viewer.layers.selection.active.data
         name = self._viewer.layers.selection.active.name
-        semantic_labels = to_semantic(im, is_file_path=False)
+        semantic_labels = to_semantic(im)
 
         if self.results_path != "":
             imwrite(
@@ -175,7 +175,7 @@ def folder_to_instance(self):
 
         for file in self.labels_filepaths:
 
-            image = to_instance(file)
+            image = to_instance(file, is_file_path=True)
 
             imwrite(
                 results_folder + "/" + os.path.basename(file),
@@ -187,7 +187,7 @@ def layer_to_instance(self):
 
         im = [self._viewer.layers.selection.active.data]
         name = self._viewer.layers.selection.active.name
-        instance_labels = to_instance(im, is_file_path=False)
+        instance_labels = to_instance(im)
 
         if self.results_path != "":
             imwrite(

src/napari_cellseg_annotator/plugin_crop.py

@@ -6,7 +6,6 @@
 from magicgui import magicgui
 from magicgui.widgets import Container
 from magicgui.widgets import Slider
-
 # Qt
 from qtpy.QtWidgets import QLabel
 from qtpy.QtWidgets import QSizePolicy
@@ -73,6 +72,20 @@ def __init__(self, viewer: "napari.viewer.Viewer", parent):
 
         self.build()
 
+        ###########################################
+        if utils.ENABLE_TEST_MODE():
+            # TODO : remove/disable once done
+            if self.as_folder:
+                self.image_path = "C:/Users/Cyril/Desktop/Proj_bachelor/data/visual_png/sample"
+                if self.crop_label_choice.isChecked():
+                    self.label_path = "C:/Users/Cyril/Desktop/Proj_bachelor/data/visual_png/sample_labels"
+            else:
+                self.image_path = "C:/Users/Cyril/Desktop/Proj_bachelor/data/visual_tif/volumes/images.tif"
+                if self.crop_label_choice.isChecked():
+                    self.label_path = "C:/Users/Cyril/Desktop/Proj_bachelor/data/visual_tif/labels/testing_im.tif"
+
+        ###########################################
+
     def toggle_label_path(self):
         if self.crop_label_choice.isChecked():
             self.lbl_label.setVisible(True)
@@ -141,16 +154,20 @@ def quicksave(self):
         if not self.as_folder:
             if self.image is not None:
                 im_filename = os.path.basename(self.image_path).split(".")[0]
+                print(im_filename)
                 im_dir = os.path.split(self.image_path)[0] + "/cropped"
+                print(im_dir)
                 os.makedirs(im_dir, exist_ok=True)
                 viewer.layers["cropped"].save(
                     im_dir + "/" + im_filename + "_cropped_" + time + ".tif"
                 )
 
-            print(self.label)
+            # print(self.label)
             if self.label is not None:
                 im_filename = os.path.basename(self.label_path).split(".")[0]
+                print(im_filename)
                 im_dir = os.path.split(self.label_path)[0] + "/cropped"
+                print(im_dir)
                 name = (
                     im_dir
                     + "/"
@@ -202,20 +219,6 @@ def start(self):
         self.filetype = self.filetype_choice.currentText()
         self.crop_labels = self.crop_label_choice.isChecked()
 
-        ###########################################
-        if utils.ENABLE_TEST_MODE():
-            # TODO : remove/disable once done
-            if self.as_folder:
-                self.image_path = "C:/Users/Cyril/Desktop/Proj_bachelor/data/visual_png/sample"
-                if self.crop_labels:
-                    self.label_path = "C:/Users/Cyril/Desktop/Proj_bachelor/data/visual_png/sample_labels"
-            else:
-                self.image_path = "C:/Users/Cyril/Desktop/Proj_bachelor/data/visual_tif/volumes/images.tif"
-                if self.crop_labels:
-                    self.label_path = "C:/Users/Cyril/Desktop/Proj_bachelor/data/visual_tif/labels/testing_im.tif"
-
-        ###########################################
-
         if not self.check_ready():
             return