Implement size filtering widget

Author: constantinpape

synapse_net/napari.yaml

@@ -25,6 +25,9 @@ contributions:
     - id: synapse_net.postprocessing
       python_name: synapse_net.tools.postprocessing_widget:PostprocessingWidget
       title: Segmentation Postprocessing
+    - id: synapse_net.size_filter
+      python_name: synapse_net.tools.size_filter_widget:SizeFilterWidget
+      title: Size Filter
 
     # Commands for sample data.
     - id: synapse_net.sample_data_tem_2d
@@ -59,6 +62,8 @@ contributions:
       display_name: Pool Assignment
     - command: synapse_net.postprocessing
       display_name: Segmentation Postprocessing
+    - command: synapse_net.size_filter
+      display_name: Size Filter
 
   sample_data:
     - command: synapse_net.sample_data_tem_2d

synapse_net/tools/size_filter_widget.py

@@ -0,0 +1,72 @@
+import napari
+import napari.layers
+import napari.viewer
+
+import numpy as np
+
+from qtpy.QtWidgets import QHBoxLayout, QVBoxLayout, QPushButton, QSpinBox, QLabel
+from skimage.measure import regionprops, label
+
+from .base_widget import BaseWidget
+
+
+class SizeFilterWidget(BaseWidget):
+    def __init__(self):
+        super().__init__()
+
+        self.viewer = napari.current_viewer()
+        layout = QVBoxLayout()
+
+        # Create the dropdown to select the segmentation to filter.
+        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)
+
+        # Add a field for entering the minimal size.
+        self.size_threshold_widget = QSpinBox()
+        self.size_threshold_widget.setRange(int(-1e9), int(1e9))
+        self.size_threshold_widget.setSingleStep(1)
+
+        threshold_layout = QHBoxLayout()
+        threshold_layout.addWidget(QLabel("Minimal Size"))
+        threshold_layout.addWidget(self.size_threshold_widget)
+        layout.addLayout(threshold_layout)
+
+        # Add a boolean field for processing binary masks.
+        self.is_mask = False
+        layout.addWidget(self._add_boolean_param("is_mask", self.is_mask, title="Binary Mask"))
+
+        # Add an optional output layer name. If not given the segmentation will be over-written.
+        self.output_layer_param, _ = self._add_string_param("output_layer", "", title="Output Layer", layout=layout)
+
+        self.button = QPushButton("Apply Size Filter")
+        self.button.clicked.connect(self.on_size_filter)
+        layout.addWidget(self.button)
+
+        # Add the widgets to the layout.
+        self.setLayout(layout)
+
+    def on_size_filter(self):
+        size_threshold = self.size_threshold_widget.value()
+        seg_layer = self._get_layer_selector_layer(self.segmentation_selector_name)
+        segmentation = seg_layer.data.copy()
+
+        if self.is_mask:
+            segmentation = label(segmentation).astype(segmentation.dtype)
+
+        props = regionprops(segmentation)
+        filter_ids = [prop.label for prop in props if prop.area < size_threshold]
+        segmentation[np.isin(segmentation, filter_ids)] = 0
+        if self.is_mask:
+            segmentation = (segmentation > 0).astype(segmentation.dtype)
+
+        # Write or overwrite segmentation layer.
+        layer_name = self.output_layer_param.text()
+        if layer_name is None or layer_name == "":
+            seg_layer.data = segmentation
+        elif layer_name in self.viewer.layers:
+            self.viewer.layers[layer_name].data = segmentation
+        else:
+            self.viewer.add_labels(segmentation, name=layer_name)