Merge branch 'dev' into polydisperse_cylinders

.github/workflows/tests.yml

@@ -19,7 +19,7 @@ jobs:
       max-parallel: 9
       matrix:
         # Add '3.10' to the list once #611 is addressed
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.8', '3.9', '3.10', '3.11']
         os: [ubuntu-latest, macos-latest, windows-latest]
         include:
         - os: ubuntu-latest

porespy/__version__.py

@@ -1 +1 @@
-__version__ = '2.3.0.dev11'
+__version__ = '2.3.0.dev15'

porespy/filters/_funcs.py

@@ -403,9 +403,13 @@ def find_disconnected_voxels(im, conn=None, surface=False):
     if not surface:
         holes = clear_border(labels=labels) > 0
     else:
-        counts = np.bincount(labels.flatten())[1:]
-        keep = np.where(counts == counts.max())[0] + 1
-        holes = (labels != keep)*im
+        keep = set(np.unique(labels))
+        for ax in range(labels.ndim):
+            labels = np.swapaxes(labels, 0, ax)
+            keep.intersection_update(set(np.unique(labels[0, ...])))
+            keep.intersection_update(set(np.unique(labels[-1, ...])))
+            labels = np.swapaxes(labels, 0, ax)
+        holes = np.isin(labels, list(keep), invert=True)
     return holes
 
 

requirements/conda.txt

@@ -16,3 +16,4 @@ scikit-learn
 scipy
 tqdm
 trimesh
+PyWavelets

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.3.0.dev11
+current_version = 2.3.0.dev15
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)\.(?P<release>\D+)(?P<build>\d+)?
 serialize = {major}.{minor}.{patch}.{release}{build}
 

setup.py

@@ -83,6 +83,7 @@ def get_version(rel_path):
         'scikit-image',
         'scipy',
         'tqdm',
+        'PyWavelets',
     ],
     author='PoreSpy Team',
     author_email='jgostick@gmail.com',

test/unit/test_filters.py

@@ -223,6 +223,20 @@ def test_fill_blind_pores_w_surface(self):
         im3 = ps.filters.fill_blind_pores(im, surface=True)
         assert im3.sum() == 0
 
+    def test_fill_blind_pores_surface_blobs_2D(self):
+        im = ps.generators.blobs([100, 100], porosity=0.6, seed=0)
+        im2 = ps.filters.fill_blind_pores(im)
+        assert im.sum() == 6021
+        assert im2.sum() == 5981
+        im3 = ps.filters.fill_blind_pores(im, surface=True)
+        assert im3.sum() == 5699
+
+    def test_fill_blind_pores_surface_blobs_3D(self):
+        im = ps.generators.blobs([100, 100, 100], porosity=0.5)
+        im2 = ps.filters.fill_blind_pores(im, surface=True)
+        labels, N = spim.label(im2, ps.tools.ps_rect(3, ndim=3))
+        assert N == 1
+
     def test_trim_floating_solid(self):
         f = ps.filters.trim_floating_solid(~self.im)
         assert np.sum(f) > np.sum(~self.im)