DEV: Update scikit-image Version

requirements.conda.yml

@@ -30,7 +30,7 @@ dependencies:
   - pytorch>=1.9.0
   - pyyaml>=5.1
   - requests
-  - scikit-image==0.18.3
+  - scikit-image>=0.19.1
   - scikit-learn>=0.23.2
   - shapely
   - sphinx_gallery

requirements.dev.conda.yml

@@ -36,7 +36,7 @@ dependencies:
   - pyyaml>=5.1
   - recommonmark
   - requests
-  - scikit-image==0.18.3
+  - scikit-image>=0.19.1
   - scikit-learn>=0.23.2
   - shapely
   - sphinx-gallery

requirements.txt

@@ -14,7 +14,7 @@ pillow
 pydicom # Used by wsidicom
 pyyaml>=5.1
 requests
-scikit-image==0.18.3
+scikit-image>=0.19.1
 scikit-learn>=0.23.2
 shapely
 sphinx>=4.1.2
@@ -24,4 +24,4 @@ torchvision>=0.10.1
 tqdm>=4.60.0
 umap-learn
 wsidicom
-zarr
+zarr

requirements.win64.conda.yml

@@ -31,7 +31,7 @@ dependencies:
   - pytorch>=1.9.0
   - pyyaml>=5.1
   - requests
-  - scikit-image==0.18.3
+  - scikit-image>=0.19.1
   - scikit-learn>=0.23.2
   - shapely
   - sphinx-gallery

requirements_dev.txt

@@ -24,7 +24,7 @@ pytest>=6.2.5
 pyyaml>=5.1
 recommonmark
 requests
-scikit-image==0.18.3
+scikit-image>=0.19.1
 scikit-learn>=0.23.2
 shapely
 sphinx>=4.1.2

setup.py

@@ -22,7 +22,7 @@
     "pandas",
     "glymur",
     "scikit-learn>=0.23.2",
-    "scikit-image==0.18.3",
+    "scikit-image>=0.19.1",
     "shapely",
     "torchvision>=0.10.1",
     "torch>=1.9.1",

tests/test_wsireader.py

@@ -194,7 +194,7 @@ def read_bounds_level_consistency(wsi, bounds):
     # Pair-wise check resolutions for mean squared error
     for i, a in enumerate(as_float):
         for b in as_float[i + 1 :]:
-            _, error, phase_diff = phase_cross_correlation(a, b)
+            _, error, phase_diff = phase_cross_correlation(a, b, normalization=None)
             assert phase_diff < 0.125
             assert error < 0.125
 
@@ -1186,7 +1186,7 @@ def test_virtual_wsi_reader_read_bounds_virtual_levels(source_image):
     target = cv2.resize(
         img_array[:50, :25, :], target_size, interpolation=cv2.INTER_CUBIC
     )
-    offset, error, _ = phase_cross_correlation(target, region)
+    offset, error, _ = phase_cross_correlation(target, region, normalization=None)
     assert all(offset == 0)
     assert error < 0.1
     psnr = peak_signal_noise_ratio(target, region)
@@ -1221,7 +1221,7 @@ def test_virtual_wsi_reader_read_rect_virtual_levels_mpp(source_image):
     target = cv2.resize(
         img_array[:200, :100, :], (50, 100), interpolation=cv2.INTER_CUBIC
     )
-    offset, error, _ = phase_cross_correlation(target, region)
+    offset, error, _ = phase_cross_correlation(target, region, normalization=None)
     assert all(offset == 0)
     assert error < 0.1
     psnr = peak_signal_noise_ratio(target, region)
@@ -1261,7 +1261,7 @@ def test_virtual_wsi_reader_read_bounds_virtual_levels_mpp(source_image):
     target = cv2.resize(
         img_array[:50, :25, :], target_size, interpolation=cv2.INTER_CUBIC
     )
-    offset, error, _ = phase_cross_correlation(target, region)
+    offset, error, _ = phase_cross_correlation(target, region, normalization=None)
     assert all(offset == 0)
     assert error < 0.1
     psnr = peak_signal_noise_ratio(target, region)
@@ -1892,7 +1892,7 @@ def test_read_rect_level_consistency(sample_key, reader_class):
         # Pair-wise check resolutions for mean squared error
         for i, a in enumerate(as_float):
             for b in as_float[i + 1 :]:
-                _, error, phase_diff = phase_cross_correlation(a, b)
+                _, error, phase_diff = phase_cross_correlation(a, b, normalization=None)
                 assert phase_diff < 0.125
                 assert error < 0.125