Update vesicle pool widget (#77)

* Update vesicle pool widget WIP * Finish vesicle pool widget
computational-cell-analytics · Dec 7, 2024 · 8a4d26d · 8a4d26d
1 parent 9b94807
commit 8a4d26d
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Showing 5 changed files with 152 additions and 104 deletions.
diff --git a/synapse_net/napari.yaml b/synapse_net/napari.yaml
@@ -9,7 +9,7 @@ contributions:
     # Commands for widgets.
     - id: synapse_net.segment
       python_name: synapse_net.tools.segmentation_widget:SegmentationWidget
-      title: Segment
+      title: Segmentation
     - id: synapse_net.distance_measure
       python_name: synapse_net.tools.distance_measure_widget:DistanceMeasureWidget
       title: Distance Measurement
@@ -21,7 +21,7 @@ contributions:
       title: Morphology Analysis
     - id: synapse_net.vesicle_pooling
       python_name: synapse_net.tools.vesicle_pool_widget:VesiclePoolWidget
-      title: Vesicle Pooling
+      title: Pool Assignment
 
     # Commands for sample data.
     - id: synapse_net.sample_data_tem_2d
@@ -47,7 +47,7 @@ contributions:
     - command: synapse_net.morphology
       display_name: Morphology Analysis
     - command: synapse_net.vesicle_pooling
-      display_name: Vesicle Pooling
+      display_name: Pool Assignment
 
   sample_data:
     - command: synapse_net.sample_data_tem_2d

diff --git a/synapse_net/tools/base_widget.py b/synapse_net/tools/base_widget.py
@@ -1,4 +1,5 @@
 import os
+import sys
 from pathlib import Path
 
 import napari
@@ -11,9 +12,19 @@
 from superqt import QCollapsible
 
 try:
-    from napari_skimage_regionprops import add_table
+    from napari_skimage_regionprops import add_table, get_table
 except ImportError:
-    add_table = None
+    add_table, get_table = None, None
+
+
+class _SilencePrint:
+    def __enter__(self):
+        self._original_stdout = sys.stdout
+        sys.stdout = open(os.devnull, "w")
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        sys.stdout.close()
+        sys.stdout = self._original_stdout
 
 
 class BaseWidget(QWidget):
@@ -316,12 +327,21 @@ def _save_table(self, save_path, data):
         return file_path
 
     def _add_properties_and_table(self, layer, table_data, save_path=""):
-        if layer.properties:
-            layer.properties = layer.properties.update(table_data)
-        else:
-            layer.properties = table_data
+        layer.properties = table_data
+
         if add_table is not None:
-            add_table(layer, self.viewer)
+            table = get_table(layer, self.viewer)
+            if table is None:
+                with _SilencePrint():
+                    add_table(layer, self.viewer)
+            else:
+                # FIXME updating the table does not yet work
+                with _SilencePrint():
+                    table.update_content()
+                # table_dict = table_data.to_dict()
+                # table_dict["index"] = table_dict["label"]
+                # table.set_content(table_dict)
+
         # Save table to file if save path is provided.
         if save_path != "":
             file_path = self._save_table(self.save_path.text(), table_data)

diff --git a/synapse_net/tools/distance_measure_widget.py b/synapse_net/tools/distance_measure_widget.py
@@ -45,9 +45,9 @@ def __init__(self):
     def _to_table_data(self, distances, seg_ids, endpoints1=None, endpoints2=None):
         assert len(distances) == len(seg_ids), f"{distances.shape}, {seg_ids.shape}"
         if seg_ids.ndim == 2:
-            table_data = {"label_id1": seg_ids[:, 0], "label_id2": seg_ids[:, 1], "distance": distances}
+            table_data = {"label1": seg_ids[:, 0], "label2": seg_ids[:, 1], "distance": distances}
         else:
-            table_data = {"label_id": seg_ids, "distance": distances}
+            table_data = {"label": seg_ids, "distance": distances}
         if endpoints1 is not None:
             axis_names = "zyx" if endpoints1.shape[1] == 3 else "yx"
             table_data.update({f"begin-{ax}": endpoints1[:, i] for i, ax in enumerate(axis_names)})

diff --git a/synapse_net/tools/morphology_widget.py b/synapse_net/tools/morphology_widget.py
@@ -121,7 +121,7 @@ def _to_table_data(self, coords, radii, props):
         # Define columns based on dimension (2D or 3D)
         col_names = ["x", "y"] if coords.shape[1] == 2 else ["x", "y", "z"]
         table_data = {
-            "label_id": [prop.label for prop in props],
+            "label": [prop.label for prop in props],
             **{col: coords[:, i] for i, col in enumerate(col_names)},
             "radius": radii,
             "intensity_max": [prop.intensity_max for prop in props],