fiexed morphology widgets

Author: lufre1

synaptic_reconstruction/napari.yaml

@@ -16,6 +16,9 @@ contributions:
     - id: synaptic_reconstruction.morphology
       python_name: synaptic_reconstruction.tools.morphology_widget:MorphologyWidget
       title: Morphology Analysis
+    - id: synaptic_reconstruction.vesicle_pooling
+      python_name: synaptic_reconstruction.tools.vesicle_pool_widget:VesiclePoolWidget
+      title: Vesicle Pooling
 
   readers:
     - command: synaptic_reconstruction.file_reader
@@ -32,3 +35,5 @@ contributions:
       display_name: Distance Measurement
     - command: synaptic_reconstruction.morphology
       display_name: Morphology Analysis
+    - command: synaptic_reconstruction.vesicle_pooling
+      display_name: Vesicle Pooling

synaptic_reconstruction/tools/base_widget.py

@@ -31,6 +31,8 @@ def _create_layer_selector(self, selector_name, layer_type="Image"):
             layer_filter = napari.layers.Image
         elif layer_type == "Labels":
             layer_filter = napari.layers.Labels
+        elif layer_type == "Shapes":
+            layer_filter = napari.layers.Shapes
         else:
             raise ValueError("layer_type must be either 'Image' or 'Labels'.")
 

synaptic_reconstruction/tools/distance_measure_widget.py

@@ -87,7 +87,10 @@ def _add_lines_and_table(self, lines, properties, table_data, name):
             blending="additive",
             properties=properties,
         )
-        line_layer.properties["distances"] = table_data
+        if line_layer.metadata is None:
+            line_layer.metadata = table_data
+        else:
+            line_layer.metadata["distances"] = table_data
 
         if add_table is not None:
             add_table(line_layer, self.viewer)

synaptic_reconstruction/tools/morphology_widget.py

@@ -157,13 +157,11 @@ def _add_table(self, coords, radii, props, name="Shapes Layer"):
 
         # Add the shapes layer
         layer = self._create_shapes_layer(table_data, name)
-        
+
         # Add properties to segmentation layer
         segmentation_layer = self._get_layer_selector_layer(self.image_selector_name1)
-        if not segmentation_layer.properties:
-            segmentation_layer.properties = table_data
-        else:
-            segmentation_layer.properties["morphology"] = table_data
+
+        segmentation_layer.metadata["morphology"] = table_data
 
         if add_table is not None:
             add_table(layer, self.viewer)
@@ -186,7 +184,7 @@ def on_measure_vesicle_morphology(self):
             return
 
         # get metadata from layer if available
-        metadata = self._get_layer_selector_data(self.image_selector_name1, return_metadata=True)
+        metadata = self._get_layer_selector_data(self.image_selector_name, return_metadata=True)
         resolution = metadata.get("voxel_size", None)
         if resolution is not None:
             resolution = [v for v in resolution.values()]
@@ -212,7 +210,7 @@ def on_measure_structure_morphology(self):
             show_info("INFO: Please choose a segmentation.")
             return
         # get metadata from layer if available
-        metadata = self._get_layer_selector_data(self.image_selector_name1, return_metadata=True)
+        metadata = self._get_layer_selector_data(self.image_selector_name, return_metadata=True)
         resolution = metadata.get("voxel_size", None)
         if resolution is not None:
             resolution = [v for v in resolution.values()]
@@ -226,10 +224,10 @@ def on_measure_structure_morphology(self):
     def _add_table_structure(self, morphology):
         segmentation_layer = self._get_layer_selector_layer(self.image_selector_name1)
         table_data = self._to_table_data_structure(morphology)
-        if not segmentation_layer.properties:
-            segmentation_layer.properties = table_data
-        else:
-            segmentation_layer.properties["morphology"] = table_data
+
+        segmentation_layer.metadata["morphology"] = table_data
+        segmentation_layer.properties = table_data
+        print("segmentation layer metadata:\n", segmentation_layer.metadata)
 
         # Add a table layer to the Napari viewer
         if add_table is not None:
@@ -244,11 +242,14 @@ def _add_table_structure(self, morphology):
 
     def _to_table_data_structure(self, morphology):
         # Create table data
-        table_data = {
-            "Name": morphology["perimeter [pixel]"],
-            "area [pixel^2]": morphology["area [pixel^2]"],
-            "perimeter [pixel]": morphology["perimeter [pixel]"],
-        }
+        return morphology
+        # for k, v in morphology.items():
+        #     table_data = {k: v}
+        # table_data = {
+        #     "Name": morphology["perimeter [pixel]"],
+        #     "area [pixel^2]": morphology["area [pixel^2]"],
+        #     "perimeter [pixel]": morphology["perimeter [pixel]"],
+        # }
         return pd.DataFrame(table_data)
 
     def _create_settings_widget(self):