Merge pull request #46 from haesleinhuepf/dev2

fix skimage error

napari_skimage_regionprops/__init__.py

@@ -8,7 +8,7 @@
 try:
     from ._version import version as __version__
 except ImportError:
-    __version__ = "0.6.2"
+    __version__ = "0.7.0"
 
 
 @napari_hook_implementation

napari_skimage_regionprops/_regionprops.py

@@ -51,8 +51,13 @@ def regionprops_table(image : napari.types.ImageData, labels: napari.types.Label
     extra_properties = []
 
     if size:
-        properties = properties + ['area', 'bbox_area', 'convex_area', 'equivalent_diameter']
-
+        properties = properties + ['area', 'bbox_area', 'equivalent_diameter']
+        # Workaround to avoid existing scikit-image bug
+        # See https://github.com/scikit-image/scikit-image/issues/6432
+        if (len(labels.shape) == 3) and (_check_2D_labels_in_3D_images(labels)):
+            warnings.warn("2D labels are present in 3D label image, 'convex_area' not calculated")
+        else:
+            properties = properties + ['convex_area']
     if intensity:
         properties = properties + ['max_intensity', 'mean_intensity', 'min_intensity']
 
@@ -69,7 +74,13 @@ def standard_deviation_intensity(region, intensities):
             warnings.warn("Perimeter measurements are not supported in 3D")
 
     if shape:
-        properties = properties + ['solidity', 'extent', 'feret_diameter_max', 'local_centroid']
+        properties = properties + ['extent', 'local_centroid']
+        # Workaround to avoid existing scikit-image bug
+        # See https://github.com/scikit-image/scikit-image/issues/6432
+        if (len(labels.shape) == 3) and (_check_2D_labels_in_3D_images(labels)):
+            warnings.warn("2D labels are present in 3D label image, 'feret_diameter_max' and 'solidity' not calculated")
+        else:
+            properties = properties + ['solidity', 'feret_diameter_max']
         if len(labels.shape) == 2:
             properties = properties + ['major_axis_length', 'minor_axis_length', 'orientation', 'eccentricity']
             # we need these two to compute some shape descriptors
@@ -97,7 +108,7 @@ def standard_deviation_intensity(region, intensities):
     # weighted_moments_central
     # weighted_moments_hu
     # weighted_moments_normalized
-
+    print('PROPERTIES = ', properties)
     # quantitative analysis using scikit-image's regionprops
     from skimage.measure import regionprops_table as sk_regionprops_table
     table = sk_regionprops_table(np.asarray(labels).astype(int), intensity_image=np.asarray(image),
@@ -185,7 +196,18 @@ def ellipsoid_axis_lengths(table):
 regionprops_table_all_frames = analyze_all_frames(regionprops_table)
 register_function(regionprops_table_all_frames, menu="Measurement tables > Regionprops of all frames (nsr)")
 
-
+def _check_2D_labels_in_3D_images(label_image):
+    '''
+    Checks if there are 2D labels in a 3D label image
+    '''
+    from skimage.measure import regionprops as sk_regionprops
+
+    measurements = sk_regionprops(label_image)
+    for props in measurements:
+        label_shape = np.array(props.bbox[3:]) - np.array(props.bbox[:3])
+        if np.any(label_shape == 1):
+            return True
+    return False
 
 try:
     # morphometrics API

napari_skimage_regionprops/_tests/test_function.py

@@ -397,3 +397,21 @@ def test_measure_points():
     points = np.random.random((100, 2)) * 99
 
     nsr.measure_points(points, image)
+
+def test_2d_labels_in_3d_image():
+    import numpy as np
+    labels = np.zeros((6,6,6), dtype=np.uint8)
+    labels[1:4, 1:4, 1:4] = 1 # 3D label
+    labels[4, 1:4, 1:4] = 2 # 2D label
+
+    from napari_skimage_regionprops import regionprops_table
+    table = regionprops_table(labels, labels, size=True, intensity=True, perimeter=True, shape=True, position=True,
+                moments=True)
+
+    # check one measurement
+    assert np.array_equal(table['area'], [27, 9])
+
+    # check that measurements that depend on convex_area are absent in this case
+    assert "convex_area" not in table.keys()
+    assert "feret_max_diameter" not in table.keys()
+    assert "solidity" not in table.keys()

setup.py

@@ -36,7 +36,7 @@ def read(fname):
     packages=find_packages(),
     python_requires='>=3.8',
     install_requires=requirements,
-    version='0.6.2',
+    version='0.7.0',
     #use_scm_version=use_scm,
     setup_requires=['setuptools_scm'],
     classifiers=[