synapse_net.tools.postprocessing_widget

  1import napari
  2import napari.layers
  3import napari.viewer
  4
  5import numpy as np
  6
  7from napari.utils.notifications import show_info
  8from qtpy.QtWidgets import QVBoxLayout, QPushButton
  9from skimage.measure import regionprops
 10from skimage.segmentation import find_boundaries
 11
 12from .base_widget import BaseWidget
 13
 14
 15class PostprocessingWidget(BaseWidget):
 16    def __init__(self):
 17        super().__init__()
 18
 19        self.viewer = napari.current_viewer()
 20        layout = QVBoxLayout()
 21
 22        # Create the dropdown to select the segmentation to post-process.
 23        self.segmentation_selector_name = "Segmentation"
 24        self.segmentation_selector_widget = self._create_layer_selector(
 25            self.segmentation_selector_name, layer_type="Labels"
 26        )
 27        layout.addWidget(self.segmentation_selector_widget)
 28
 29        # Create dropdown to select the mask for filtering / intersection.
 30        self.mask_selector_name = "Mask"
 31        self.mask_selector_widget = self._create_layer_selector(self.mask_selector_name, layer_type="Labels")
 32        layout.addWidget(self.mask_selector_widget)
 33
 34        # Create input for label id in the mask.
 35        self.mask_id_param, _ = self._add_int_param(
 36            "mask_id", 0, min_val=0, max_val=1000, layout=layout, title="Mask ID"
 37        )
 38
 39        # Create text field to choose the name of the output layer.
 40        self.output_layer_param, _ = self._add_string_param("output_layer", "", title="Output Layer", layout=layout)
 41
 42        # First postprocessing option: Filter with mask.
 43        self.button1 = QPushButton("Filter")
 44        self.button1.clicked.connect(self.on_filter)
 45        layout.addWidget(self.button1)
 46
 47        # Second postprocessing option: intersect with boundary of the mask.
 48        self.button2 = QPushButton("Intersect with Boundary")
 49        self.button2.clicked.connect(self.on_intersect_boundary)
 50        layout.addWidget(self.button2)
 51
 52        # Third postprocessing option: intersect with the mask.
 53        self.button3 = QPushButton("Intersect")
 54        self.button3.clicked.connect(self.on_intersect)
 55        layout.addWidget(self.button3)
 56
 57        # Add the widgets to the layout.
 58        self.setLayout(layout)
 59
 60    def _write_pp(self, segmentation):
 61        layer_name = self.output_layer_param.text()
 62        self.add_or_update_labels(layer_name, segmentation)
 63
 64    def _conditions_met(self):
 65        if self.output_layer_param.text() == "":
 66            show_info("Please choose an output layer.")
 67            return False
 68        return True
 69
 70    def _get_segmentation_and_mask(self):
 71        segmentation = self._get_layer_selector_data(self.segmentation_selector_name).copy()
 72        mask = self._get_layer_selector_data(self.mask_selector_name)
 73        mask_id = self.mask_id_param.value()
 74        if mask_id != 0:
 75            mask = (mask == mask_id).astype(mask.dtype)
 76        return segmentation, mask
 77
 78    def on_filter(self):
 79        if not self._conditions_met():
 80            return
 81        segmentation, mask = self._get_segmentation_and_mask()
 82        props = regionprops(segmentation, mask)
 83        filter_ids = [prop.label for prop in props if prop.max_intensity == 0]
 84        segmentation[np.isin(segmentation, filter_ids)] = 0
 85        self._write_pp(segmentation)
 86
 87    def on_intersect_boundary(self):
 88        if not self._conditions_met():
 89            return
 90        segmentation, mask = self._get_segmentation_and_mask()
 91        boundary = find_boundaries(mask)
 92        segmentation = np.logical_and(segmentation > 0, boundary).astype(segmentation.dtype)
 93        self._write_pp(segmentation)
 94
 95    def on_intersect(self):
 96        if not self._conditions_met():
 97            return
 98        segmentation, mask = self._get_segmentation_and_mask()
 99        segmentation = np.logical_and(segmentation > 0, mask > 0).astype(segmentation.dtype)
100        self._write_pp(segmentation)