Update vesicle pool widget WIP

Author: constantinpape

synapse_net/tools/base_widget.py

@@ -11,9 +11,9 @@
 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 BaseWidget(QWidget):
@@ -317,11 +317,21 @@ def _save_table(self, save_path, data):
 
     def _add_properties_and_table(self, layer, table_data, save_path=""):
         if layer.properties:
-            layer.properties = layer.properties.update(table_data)
+            layer.properties.update(table_data)
         else:
             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:
+                add_table(layer, self.viewer)
+            else:
+                # FIXME updating the table does not yet work
+                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)

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)})

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],

synapse_net/tools/vesicle_pool_widget.py

@@ -9,11 +9,6 @@
 
 from .base_widget import BaseWidget
 
-try:
-    from napari_skimage_regionprops import add_table
-except ImportError:
-    add_table = None
-
 # This will fail if we have more than 8 pools.
 COLORMAP = ["red", "blue", "yellow", "cyan", "purple", "magenta", "orange", "green"]
 
@@ -107,9 +102,8 @@ def _compute_vesicle_pool(self, segmentation, distances, morphology, pool_layer_
             pool_name (str): Name for the pooled group to be assigned.
             query (dict): Query parameters.
         """
-
-        distance_ids = distances.get("label_id", [])
-        morphology_ids = morphology.get("label_id", [])
+        distance_ids = distances.get("label", [])
+        morphology_ids = morphology.get("label", [])
 
         # Ensure that IDs are identical.
         if set(distance_ids) != set(morphology_ids):
@@ -120,11 +114,11 @@ def _compute_vesicle_pool(self, segmentation, distances, morphology, pool_layer_
         # TODO: select the dataframes more dynamically depending on the criterion defined by the user.
         distances = pd.DataFrame(distances)
         morphology = pd.DataFrame(morphology)
-        merged_df = morphology.merge(distances, left_on="label_id", right_on="label_id", suffixes=("_morph", "_dist"))
+        merged_df = morphology.merge(distances, left_on="label", right_on="label", suffixes=("_morph", "_dist"))
 
         # Assign the vesicles to the current pool by filtering the mergeddataframe based on the query.
         filtered_df = self._parse_query(query, merged_df)
-        pool_vesicle_ids = filtered_df.label_id.values.tolist()
+        pool_vesicle_ids = filtered_df.label.values.tolist()
 
         # Check if this layer was already created in a previous pool assignment.
         if pool_layer_name in self.viewer.layers:
@@ -140,7 +134,7 @@ def _compute_vesicle_pool(self, segmentation, distances, morphology, pool_layer_
 
             # Combine the vesicle ids corresponding to the previous assignment with the
             # assignment for the new / current pool.
-            old_pool_ids = pool_properties.label_id.values.tolist()
+            old_pool_ids = pool_properties.label.values.tolist()
             pool_assignments = sorted(pool_vesicle_ids + old_pool_ids)
 
             # Get a map for each vesicle id to its pool.
@@ -161,7 +155,14 @@ def _compute_vesicle_pool(self, segmentation, distances, morphology, pool_layer_
         vesicle_pools[~np.isin(vesicle_pools, pool_assignments)] = 0
 
         # Create the pool properties.
-        pool_properties = merged_df[merged_df.label_id.isin(pool_assignments)]
+        pool_properties = merged_df[merged_df.label.isin(pool_assignments)]
+        # Remove columns that are not relevant for measurements.
+        keep_columns = [
+            col for col in pool_properties.columns
+            if col not in ("x", "y", "z", "begin-x", "begin-y", "begin-z", "end-x", "end-y", "end-z")
+        ]
+        pool_properties = pool_properties[keep_columns].reset_index()
+        # Add a colun for the pool.
         pool_properties.insert(1, "pool", pool_values)
 
         # Create the colormap to group the pools in the layer rendering.
@@ -170,26 +171,25 @@ def _compute_vesicle_pool(self, segmentation, distances, morphology, pool_layer_
         # To avoid this the user has to specify the pool color (not yet implemented, see next todo).
         pool_names = np.unique(pool_values).tolist()
         # TODO: add setting so that users can over-ride the color for a pool.
-        # TODO: provide a default color (how?) to avoid the warning
         pool_colors = {pname: COLORMAP[pool_names.index(pname)] for pname in pool_names}
         vesicle_colors = {
             label_id: pool_colors[pname] for label_id, pname
-            in zip(pool_properties.label_id.values, pool_properties.pool.values)
+            in zip(pool_properties.label.values, pool_properties.pool.values)
         }
+        vesicle_colors[None] = "gray"
 
         # TODO print some messages
         # Add or replace the pool layer and properties.
         if pool_layer_name in self.viewer.layers:
             # message about added or over-ridden pool, including number of vesicles in pool
             pool_layer = self.viewer.layers[pool_layer_name]
             pool_layer.data = vesicle_pools
-            pool_layer.color_map = vesicle_colors
+            pool_layer.colormap = vesicle_colors
         else:
             # message about new pool, including number of vesicles in pool
             pool_layer = self.viewer.add_labels(vesicle_pools, name=pool_layer_name, colormap=vesicle_colors)
 
-        # TODO add the save path
-        self._add_properties_and_table(pool_layer, pool_properties, save_path="")
+        self._add_properties_and_table(pool_layer, pool_properties, save_path=self.save_path.text())
         pool_layer.refresh()
 
     def _parse_query(self, query: str, data: pd.DataFrame) -> pd.DataFrame:
@@ -220,8 +220,5 @@ def _create_settings_widget(self):
         self.save_path, layout = self._add_path_param(name="Save Table", select_type="file", value="")
         setting_values.layout().addLayout(layout)
 
-        self.voxel_size_param, layout = self._add_float_param("voxel_size", 0.0, min_val=0.0, max_val=100.0)
-        setting_values.layout().addLayout(layout)
-
         settings = self._make_collapsible(widget=setting_values, title="Advanced Settings")
         return settings