Add gui hookimpls

examples/launch.py

@@ -1,6 +1,5 @@
 import os
 import napari
-from segmentify import segmentation
 import numpy as np
 
 
@@ -11,17 +10,6 @@
 with napari.gui_qt():
     viewer = napari.Viewer()
 
-    # instantiate the widget
-    gui = segmentation.Gui()
-
-    # add our new widget to the napari viewer
-    viewer.window.add_dock_widget(gui)
-
-    # keep the dropdown menus in the gui in sync with the layer model
-    viewer.layers.events.changed.connect(lambda x: gui.refresh_choices())
-
-    gui.refresh_choices()
-
     # load data
     viewer.open(example_image)
     viewer.open(example_labels, layer_type='labels')

segmentify/__init__.py

@@ -1,9 +1,9 @@
-__version__ = '0.1.0'
+from .segmentify import segmentation
+from ._hookimpl import napari_experimental_provide_function_widget
 
-from .gui import segmentation
-from . import _key_bindings
+# from . import _key_bindings
 
-# Note that importing _key_bindings is needed as the Labels layer gets
-# decorated with keybindings during that process, but it is not directly needed
-# by our users and so is deleted below
-del _key_bindings
+# # Note that importing _key_bindings is needed as the Labels layer gets
+# # decorated with keybindings during that process, but it is not directly needed
+# # by our users and so is deleted below
+# del _key_bindings

segmentify/_hookimpl.py

@@ -0,0 +1,7 @@
+from napari_plugin_engine import napari_hook_implementation
+from .segmentify import segmentation
+
+
+@napari_hook_implementation
+def napari_experimental_provide_function_widget():
+    return (segmentation, {'call_button': "execute"})

segmentify/_key_bindings.py

@@ -1,118 +1,118 @@
-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
+# 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

segmentify/gui.py → segmentify/segmentify.py

@@ -2,16 +2,13 @@
 """
 
 import numpy as np
-from magicgui import magicgui
-from napari import layers
 from .semantic import fit, predict
 from .util import Featurizers, norm_entropy
 
 
-@magicgui(call_button="execute")
-def segmentation(base_image: layers.Image,
-                       initial_labels: layers.Labels,
-                       featurizer:Featurizers) -> layers.Labels:
+def segmentation(base_image: 'napari.layers.Image',
+                 initial_labels: 'napari.layers.Labels',
+                 featurizer:Featurizers) -> 'napari.layers.Labels':
     """Segment an image based on an initial labeling."""
 
     print("Segmenting...")
@@ -35,6 +32,6 @@ def segmentation(base_image: layers.Image,
     entropy = (entropy - np.min(entropy)) / np.ptp(entropy)
     entropy = np.squeeze(entropy)
 
-    print("... Completed")  
+    print("... Completed")
 
     return np.squeeze(segmentation)

setup.py

@@ -15,7 +15,7 @@ def parse_requirements_file(filename):
 setup(
     name='segmentify',
     packages=find_packages(),
-    version='0.1.1',
+    version='0.2.0',
     description='Python image segmentation plugin.',
     maintainer='Nicholas Sofroniew',
     maintainer_email='[email protected]',
@@ -44,5 +44,9 @@ def parse_requirements_file(filename):
     ],
     install_requires=INSTALL_REQUIRES,
     include_package_data=True,
-    entry_points={},
+    entry_points={
+        'napari.plugin': [
+            'segmentify = segmentify',
+        ],
+    },
 )