segmentify/segmentify/_key_bindings.py at 2290a16c5d7d0f8482d5f57112ee07645d12c7a1 · transformify-plugins/segmentify · GitHub

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# from napari.layers.labels import Labels
# import math
# import os
# from skimage import morphology, measure
# from scipy import stats
# from .util import erode_img


# @Labels.bind_key('Shift-C')
# def closing(self, layer):
#     """Apply the closing operation (key-binding: SHIFT-C)

#     This function applies the closing operation by dilating the selected label
#     pixels, following by erosion

#     Parameters
#     ----------
#     layer : napari.layers.Labels
#     """
#     dilation(layer)
#     erosion(layer)


# @Labels.bind_key('Shift-O')
# def opening(self, layer):
#     """Apply the opening operation (key-binding: SHIFT-O)

#     This function applies the opening operation by eroding the selected label
#     pixels, following by dilation

#     Parameters
#     ----------
#     layer : napari.layers.Labels
#     """
#     erosion(layer)
#     dilation(layer)


# @Labels.bind_key('Shift-E')
# def erosion(self, layer):
#     """Apply the erosion operation (key-binding: SHIFT-E)

#     This function applies the erosion operation on selected label pixels

#     Parameters
#     ----------
#     layer : napari.layers.Labels
#     """
#     labeled = extract_label(layer.data, layer.selected_label)
#     selem = morphology.selem.square(3)
#     processed_img = erode_img(layer.data, target_label=layer.selected_label)
#     merged = merge_label(processed_img, layer.data, layer.selected_label)
#     layer.data = merged


# @Labels.bind_key('Shift-D')
# def dilation(self, layer):
#     """Apply the dilation operation (key-binding: SHIFT-D)

#     This function applies the dilation operation on selected label pixels

#     Parameters
#     ----------
#     layer : napari.layers.Labels
#     """
#     labeled = extract_label(layer.data, layer.selected_label)
#     selem = morphology.selem.square(3)
#     processed_img =  morphology.dilation(labeled, selem)
#     merged = merge_label(processed_img, layer.data, layer.selected_label)
#     layer.data = merged


# @Labels.bind_key('Shift-F')
# def fill_holes(self, layer):
#     """apply the fill holes operation (key-binding: SHIFT-D)

#     This function applies the fill holes operation on the selected label pixels

#     Parameters
#     ----------
#     viewer : Segmentify Viewer

#     Returns
#     -------
#     The procssed image
#     """
#     labeled = extract_label(layer.data, layer.selected_label)
#     if len(labeled.shape) > 2:
#         processed_imgs = []
#         for i in range(labeled.shape[0]):
#             processed_img = morphology.remove_small_holes(labeled[i].astype(bool)).astype(int)
#             processed_imgs.append(processed_img)
#         processed_img = np.stack(processed_imgs, 0)
#     else:
#         processed_img = morphology.remove_small_holes(labeled.astype(bool)).astype(int)
#     merged = merge_label(processed_img, layer.data, layer.selected_label)
#     layer.data = merged


# def extract_label(data, label):
#     """Extract data pixels with selected label"""
#     labeled = np.zeros_like(data)
#     labeled[data == label] = 1
#     return labeled


# def merge_label(processed, data, label):
#     """Extract data pixels with selected label"""
#     # merge processed image with original
#     stored_background_label = 1
#     all_labels = np.unique(data)
#     if len(all_labels) == 2:
#         background_label = all_labels[all_labels != label][0]
#         data[(processed == 0) & (data == label)] = background_label
#     else:
#         data[(processed == 0) & (original == curr_label)] = stored_background_label
#     data[processed == 1] = curr_label
#     return data