Implement segmentation post-processing widget

Author: constantinpape

synapse_net/napari.yaml

@@ -22,6 +22,9 @@ contributions:
     - id: synapse_net.vesicle_pooling
       python_name: synapse_net.tools.vesicle_pool_widget:VesiclePoolWidget
       title: Pool Assignment
+    - id: synapse_net.postprocessing
+      python_name: synapse_net.tools.postprocessing_widget:PostprocessingWidget
+      title: Segmentation Postprocessing
 
     # Commands for sample data.
     - id: synapse_net.sample_data_tem_2d
@@ -48,6 +51,8 @@ contributions:
       display_name: Morphology Analysis
     - command: synapse_net.vesicle_pooling
       display_name: Pool Assignment
+    - command: synapse_net.postprocessing
+      display_name: Segmentation Postprocessing
 
   sample_data:
     - command: synapse_net.sample_data_tem_2d

synapse_net/tools/postprocessing_widget.py

@@ -0,0 +1,91 @@
+import napari
+import napari.layers
+import napari.viewer
+
+import numpy as np
+
+from napari.utils.notifications import show_info
+from qtpy.QtWidgets import QVBoxLayout, QPushButton
+from skimage.measure import regionprops
+from skimage.segmentation import find_boundaries
+
+from .base_widget import BaseWidget
+
+
+class PostprocessingWidget(BaseWidget):
+    def __init__(self):
+        super().__init__()
+
+        self.viewer = napari.current_viewer()
+        layout = QVBoxLayout()
+
+        # Create the dropdown to select the segmentation to post-process.
+        self.segmentation_selector_name = "Segmentation"
+        self.segmentation_selector_widget = self._create_layer_selector(
+            self.segmentation_selector_name, layer_type="Labels"
+        )
+        layout.addWidget(self.segmentation_selector_widget)
+
+        # Create dropdown to select the mask for filtering / intersection.
+        self.mask_selector_name = "Mask"
+        self.mask_selector_widget = self._create_layer_selector(self.mask_selector_name, layer_type="Labels")
+        layout.addWidget(self.mask_selector_widget)
+
+        # Create input for label id in the mask.
+        self.mask_id_param, _ = self._add_int_param(
+            "mask_id", 0, min_val=0, max_val=1000, layout=layout, title="Mask ID"
+        )
+
+        # Create text field to choose the name of the output layer.
+        self.output_layer_param, _ = self._add_string_param("output_layer", "", title="Output Layer", layout=layout)
+
+        # First postprocessing option: Filter with mask.
+        self.button1 = QPushButton("Filter")
+        self.button1.clicked.connect(self.on_filter)
+        layout.addWidget(self.button1)
+
+        # Second postprocessing option: intersect with boundary of the mask.
+        self.button2 = QPushButton("Intersect with Boundary")
+        self.button2.clicked.connect(self.on_intersect)
+        layout.addWidget(self.button2)
+
+        # Add the widgets to the layout.
+        self.setLayout(layout)
+
+    def _write_pp(self, segmentation):
+        layer_name = self.output_layer_param.text()
+        if layer_name in self.viewer.layers:
+            self.viewer.layers[layer_name].data = segmentation
+        else:
+            self.viewer.add_labels(segmentation, name=layer_name)
+
+    def _conditions_met(self):
+        if self.output_layer_param.text() == "":
+            show_info("Please choose an output layer.")
+            return False
+        return True
+
+    def _get_segmentation_and_mask(self):
+        segmentation = self._get_layer_selector_data(self.segmentation_selector_name).copy()
+        mask = self._get_layer_selector_data(self.mask_selector_name)
+        mask_id = self.mask_id_param.value()
+        if mask_id != 0:
+            mask = (mask == mask_id).astype(mask.dtype)
+        return segmentation, mask
+
+    def on_filter(self):
+        if not self._conditions_met():
+            return
+        segmentation, mask = self._get_segmentation_and_mask()
+        props = regionprops(segmentation, mask)
+        filter_ids = [prop.label for prop in props if prop.max_intensity == 0]
+        segmentation[np.isin(segmentation, filter_ids)] = 0
+        self._write_pp(segmentation)
+
+    def on_intersect(self):
+        if not self._conditions_met():
+            return
+        segmentation, mask = self._get_segmentation_and_mask()
+        boundary = find_boundaries(mask)
+        segmentation = np.logical_and(segmentation > 0, boundary).astype(segmentation.dtype)
+        self._write_pp(segmentation)

synapse_net/tools/vesicle_pool_widget.py

@@ -15,7 +15,6 @@
 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__()