Finish vesicle pool widget

Author: constantinpape

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

synapse_net/tools/base_widget.py

@@ -1,4 +1,5 @@
 import os
+import sys
 from pathlib import Path
 
 import napari
@@ -16,6 +17,16 @@
     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):
     def __init__(self):
         super().__init__()
@@ -316,18 +327,17 @@ 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.update(table_data)
-        else:
-            layer.properties = table_data
+        layer.properties = table_data
 
         if add_table is not None:
             table = get_table(layer, self.viewer)
             if table is None:
-                add_table(layer, self.viewer)
+                with _SilencePrint():
+                    add_table(layer, self.viewer)
             else:
                 # FIXME updating the table does not yet work
-                table.update_content()
+                with _SilencePrint():
+                    table.update_content()
                 # table_dict = table_data.to_dict()
                 # table_dict["index"] = table_dict["label"]
                 # table.set_content(table_dict)

synapse_net/tools/vesicle_pool_widget.py

@@ -1,3 +1,5 @@
+from typing import Dict
+
 import napari
 import napari.layers
 import napari.viewer
@@ -13,59 +15,59 @@
 COLORMAP = ["red", "blue", "yellow", "cyan", "purple", "magenta", "orange", "green"]
 
 
+# TODO Make selection of the distance layers optional and add a second distance layer.
 class VesiclePoolWidget(BaseWidget):
     def __init__(self):
         super().__init__()
 
         self.viewer = napari.current_viewer()
         layout = QVBoxLayout()
 
-        self.image_selector_name = "Distances to Structure"
-        self.image_selector_name1 = "Vesicles Segmentation"
-        # Create the image selection dropdown.
-        self.image_selector_widget = self._create_layer_selector(self.image_selector_name, layer_type="Shapes")
-        self.segmentation1_selector_widget = self._create_layer_selector(self.image_selector_name1, layer_type="Labels")
-
-        # Create new layer name.
-        self.pool_layer_name_param, pool_layer_name_layout = self._add_string_param(
-            name="Output Layer Name", value="",
-        )
-
-        # Create pool name.
-        self.pool_name_param, pool_name_layout = self._add_string_param(
-            name="Vesicle Pool", value="",
-        )
-
-        # Create query string
+        # Create the selectors for the layers:
+        # 1. Selector for the labels layer with vesicles.
+        self.vesicle_selector_name = "Vesicle Segmentation"
+        self.vesicle_selector_widget = self._create_layer_selector(self.vesicle_selector_name, layer_type="Labels")
+        # 2. Selector for a distance layer.
+        self.dist_selector_name1 = "Distances to Structure"
+        self.dist_selector_widget1 = self._create_layer_selector(self.dist_selector_name1, layer_type="Shapes")
+
+        # Add the selector widgets to the layout.
+        layout.addWidget(self.vesicle_selector_widget)
+        layout.addWidget(self.dist_selector_widget1)
+
+        # Create the UI elements for defining the vesicle pools:
+        # The name of the output name, the name of the vesicle pool, and the criterion for the pool.
+        self.pool_layer_name_param, pool_layer_name_layout = self._add_string_param(name="Layer Name", value="")
+        self.pool_name_param, pool_name_layout = self._add_string_param(name="Vesicle Pool", value="")
         self.query_param, query_layout = self._add_string_param(
             name="Criterion", value="",
-            tooltip="Enter a comma separated query string (e.g., 'radius > 15, distance > 250') "
+            tooltip="Enter a comma separated criterion (e.g., 'radius > 15, distance > 250') "
             "Possible filters: radius, distance, area, intensity_max, intensity_mean, intensity_min, intensity_std"
         )
-
-        # Create advanced settings.
-        self.settings = self._create_settings_widget()
-
-        # Create and connect buttons.
-        self.measure_button1 = QPushButton("Create Vesicle Pool")
-        self.measure_button1.clicked.connect(self.on_pool_vesicles)
-
-        # Add the widgets to the layout.
-        layout.addWidget(self.image_selector_widget)
-        layout.addWidget(self.segmentation1_selector_widget)
-        layout.addLayout(query_layout)
         layout.addLayout(pool_layer_name_layout)
         layout.addLayout(pool_name_layout)
-        layout.addWidget(self.measure_button1)
+        layout.addLayout(query_layout)
+
+        # Create the UI elements for advanced settings and the run button.
+        self.settings = self._create_settings_widget()
+        self.measure_button = QPushButton("Create Vesicle Pool")
+        self.measure_button.clicked.connect(self.on_pool_vesicles)
+        layout.addWidget(self.settings)
+        layout.addWidget(self.measure_button)
 
         self.setLayout(layout)
 
+        # The colormap for displaying the vesicle pools.
+        self.pool_colors = {}
+
     def on_pool_vesicles(self):
-        distances_layer = self._get_layer_selector_layer(self.image_selector_name)
-        distances = distances_layer.properties
-        segmentation = self._get_layer_selector_data(self.image_selector_name1)
-        morphology_layer = self._get_layer_selector_layer(self.image_selector_name1)
-        morphology = morphology_layer.properties
+        segmentation = self._get_layer_selector_data(self.vesicle_selector_name)
+        morphology = self._get_layer_selector_layer(self.vesicle_selector_name).properties
+        if not morphology:
+            morphology = None
+
+        distance_layer = self._get_layer_selector_layer(self.dist_selector_name1)
+        distances = None if distance_layer is None else distance_layer.properties
 
         if segmentation is None:
             show_info("INFO: Please choose a segmentation.")
@@ -76,61 +78,91 @@ def on_pool_vesicles(self):
         query = self.query_param.text()
 
         if self.pool_layer_name_param.text() == "":
-            show_info("INFO: Please enter a new layer name.")
+            show_info("INFO: Please enter a name for the pool layer.")
             return
         pool_layer_name = self.pool_layer_name_param.text()
         if self.pool_name_param.text() == "":
-            show_info("INFO: Please enter a pooled group name.")
+            show_info("INFO: Please enter a name for the vesicle pool.")
             return
         pool_name = self.pool_name_param.text()
 
-        if distances is None:
-            show_info("INFO: Distances layer could not be found or has no values.")
-            return
+        pool_color = self.pool_color_param.text()
+        self._compute_vesicle_pool(segmentation, distances, morphology, pool_layer_name, pool_name, query, pool_color)
 
-        self._compute_vesicle_pool(segmentation, distances, morphology, pool_layer_name, pool_name, query)
-
-    def _compute_vesicle_pool(self, segmentation, distances, morphology, pool_layer_name, pool_name, query):
-        """
-        Compute a vesicle pool based on the provided query parameters.
+    def _update_pool_colors(self, pool_name, pool_color):
+        if pool_color == "":
+            next_color_id = len(self.pool_colors)
+            next_color = COLORMAP[next_color_id]
+        else:
+            # We could check here that this is a valid color.
+            next_color = pool_color
+        self.pool_colors[pool_name] = next_color
+
+    def _compute_vesicle_pool(
+        self,
+        segmentation: np.ndarray,
+        distances: Dict,
+        morphology: Dict,
+        pool_layer_name: str,
+        pool_name: str,
+        query: str,
+        pool_color: str,
+    ):
+        """Compute a vesicle pool based on the provided query parameters.
 
         Args:
-            segmentation (array): Segmentation data (e.g., labeled regions).
-            distances (dict): Properties from the distances layer.
-            morphology (dict): Properties from the morphology layer.
-            pool_layer_name (str): Name for the new layer to be created.
-            pool_name (str): Name for the pooled group to be assigned.
-            query (dict): Query parameters.
+            segmentation: Segmentation data (e.g., labeled regions).
+            distances: Properties from the distances layer.
+            morphology: Properties from the morphology layer.
+            pool_layer_name: Name for the new layer to be created.
+            pool_name: Name for the pooled group to be assigned.
+            query: Query parameters.
+            pool_color: Optional color for the vesicle pool.
         """
-        distance_ids = distances.get("label", [])
-        morphology_ids = morphology.get("label", [])
-
-        # Ensure that IDs are identical.
-        if set(distance_ids) != set(morphology_ids):
-            show_info("ERROR: The IDs in distances and morphology are not identical.")
+        # Check which of the properties are present and construct the combined properties based on this.
+        if distances is None and morphology is None:  # No properties were given -> we can't do anything.
+            show_info("ERROR: Neither distances nor vesicle morphology were found.")
             return
-
-        # Create a merged dataframe from the dataframes which are relevant for the criterion.
-        # 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", right_on="label", suffixes=("_morph", "_dist"))
+        elif distances is None and morphology is not None:  # Only morphology props were found.
+            merged_df = pd.DataFrame(morphology).drop(columns=["index"])
+        elif distances is not None and morphology is None:  # Only distances were found.
+            merged_df = pd.DataFrame(distances).drop(columns=["index"])
+        else:  # Both were found.
+            distance_ids = distances.get("label", [])
+            morphology_ids = morphology.get("label", [])
+
+            # Ensure that IDs are identical.
+            if set(distance_ids) != set(morphology_ids):
+                show_info("ERROR: The IDs in distances and morphology are not identical.")
+                return
+
+            # Create a merged dataframe from the dataframes which are relevant for the criterion.
+            distances = pd.DataFrame(distances).drop(columns=["index"])
+            morphology = pd.DataFrame(morphology).drop(columns=["index"])
+            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)
+        if len(filtered_df) == 0:
+            show_info("No vesicles were found matching the condition.")
+            return
         pool_vesicle_ids = filtered_df.label.values.tolist()
+        vesicles_in_pool = len(pool_vesicle_ids)
 
         # Check if this layer was already created in a previous pool assignment.
         if pool_layer_name in self.viewer.layers:
             # If yes then load the previous pool assignments and merge them with the new pool assignments
             pool_layer = self.viewer.layers[pool_layer_name]
             pool_properties = pd.DataFrame.from_dict(pool_layer.properties)
 
-            pool_names = pd.unique(pool_properties.pool).tolist()
+            pool_names = pd.unique(pool_properties.pool)
             if pool_name in pool_names:
+                show_info(f"Updating pool '{pool_name}' with {vesicles_in_pool} vesicles.")
                 # This pool has already been assigned and we changed the criterion.
                 # Its old assignment has to be over-written, remove the rows for this pool.
                 pool_properties = pool_properties[pool_properties.pool != pool_name]
+            else:
+                show_info(f"Creating pool '{pool_name}' with {vesicles_in_pool} vesicles.")
 
             # Combine the vesicle ids corresponding to the previous assignment with the
             # assignment for the new / current pool.
@@ -146,6 +178,7 @@ def _compute_vesicle_pool(self, segmentation, distances, morphology, pool_layer_
             pool_values = [id_to_pool_name[ves_id] for ves_id in pool_assignments]
 
         else:
+            show_info(f"Creating pool '{pool_name}' with {vesicles_in_pool} vesicles.")
             # Otherwise, this is the first pool assignment.
             pool_assignments = pool_vesicle_ids
             pool_values = [pool_name] * len(pool_assignments)
@@ -161,32 +194,27 @@ def _compute_vesicle_pool(self, segmentation, distances, morphology, pool_layer_
             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()
+        pool_properties = pool_properties[keep_columns]
         # Add a colun for the pool.
         pool_properties.insert(1, "pool", pool_values)
 
-        # Create the colormap to group the pools in the layer rendering.
-        # This can lead to color switches: if a new pool gets added which starts with
-        # a letter that's earlier in the alphabet the color will switch.
-        # 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.
-        pool_colors = {pname: COLORMAP[pool_names.index(pname)] for pname in pool_names}
+        # Update the colormap to display the pools.
+        self._update_pool_colors(pool_name, pool_color)
+
+        # Assign the vesicle ids to their pool color.
         vesicle_colors = {
-            label_id: pool_colors[pname] for label_id, pname
-            in zip(pool_properties.label.values, pool_properties.pool.values)
+            label_id: self.pool_colors[pname] for label_id, pname 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.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)
 
         self._add_properties_and_table(pool_layer, pool_properties, save_path=self.save_path.text())
@@ -220,5 +248,8 @@ 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.pool_color_param, layout = self._add_string_param(name="Pool Color", value="")
+        setting_values.layout().addLayout(layout)
+
         settings = self._make_collapsible(widget=setting_values, title="Advanced Settings")
         return settings