histomicstk 1.4.1.dev20__tar.gz → 1.4.1.dev22__tar.gz

{histomicstk-1.4.1.dev20 → histomicstk-1.4.1.dev22}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: histomicstk
-Version: 1.4.1.dev20
+Version: 1.4.1.dev22
 Summary: A Python toolkit for Histopathology Image Analysis
 Keywords: histomicstk
 Author-Email: "Kitware, Inc." <developers@digitalslidearchive.net>

histomicstk-1.4.1.dev22/histomicstk/_version.py

@@ -0,0 +1 @@
+__version__ = '1.4.1.dev22'

{histomicstk-1.4.1.dev20 → histomicstk-1.4.1.dev22}/histomicstk/preprocessing/tests/test_normalization_and_augmentation.py

@@ -123,7 +123,7 @@ class TestColorNormalization():
             stain_unmixing_routine_params=stain_unmixing_routine_params)
         assert tuple(
             [int(tissue_rgb_normalized[..., i].mean()) for i in range(3)],
-        ) in {(188, 125, 175), (188, 124, 175), (191, 132, 179)}
+        ) in {(188, 125, 175), (188, 124, 175), (191, 132, 179), (191, 131, 179)}
 
         # Macenko - Masked, using W_target from good image
         tissue_rgb_normalized = deconvolution_based_normalization(
@@ -131,7 +131,7 @@ class TestColorNormalization():
             stain_unmixing_routine_params=stain_unmixing_routine_params)
         assert tuple(
             [int(tissue_rgb_normalized[..., i].mean()) for i in range(3)],
-        ) in {(188, 125, 175), (187, 125, 174), (192, 131, 179)}
+        ) in {(188, 125, 175), (187, 125, 174), (192, 131, 179), (191, 131, 179)}
 
 
 class TestColorAugmentation:

{histomicstk-1.4.1.dev20 → histomicstk-1.4.1.dev22}/pyproject.toml

@@ -3,7 +3,7 @@ requires = ["scikit-build-core>=0.7", "setuptools-scm", "cython>=0.29", "numpy"]
 build-backend = "scikit_build_core.build"
 
 [project]
-version = "1.4.1.dev20"
+version = "1.4.1.dev22"
 name = "histomicstk"
 description = "A Python toolkit for Histopathology Image Analysis"
 readme = "README.rst"

{histomicstk-1.4.1.dev20 → histomicstk-1.4.1.dev22}/ruff.toml

@@ -32,6 +32,7 @@ lint.ignore = [
     "PT011",
     "PT012",
     "PT017",
+    "PT031",
 ]
 line-length = 100
 lint.select = [

{histomicstk-1.4.1.dev20 → histomicstk-1.4.1.dev22}/tests/Dockerfile-gc-tests

@@ -5,7 +5,7 @@ LABEL HISTOMICSTK_GC_TEST=TRUE
 ENV PYTHONUNBUFFERED 1
 ENV PYTHONDONTWRITEBYTECODE 1
 
-RUN pip install --no-cache-dir -U pip
+RUN pip install --no-cache-dir -U pip 'setuptools<79'
 
 # Only sources needed in the test are added.
 RUN pip install --find-links https://girder.github.io/large_image_wheels \

{histomicstk-1.4.1.dev20 → histomicstk-1.4.1.dev22}/tests/datastore.py

@@ -36,6 +36,7 @@ registry = {
     # Source: TCGA-06-0129-01Z-00-DX3_fgnd_mask_lres.png
     'TCGA-06-0129-01Z-00-DX3_fgnd_mask_lres.png': 'sha512:58f04dd79ee5e14e68856321a9786e65b4e8b3075e84e13ff1dd20da820de933149b269bcb5f68184468d06b8956bf5426e4b11f4fa89a74c103946c1d974ec7',  # noqa
     'TCGA-06-0129-01Z-00-DX3_fgnd_mask_lres2.png': 'sha512:d3e62945013a239c2489bc0b6291951e741007509fca181bda079cd3c1464a28cd0514e2846db4a2cf7919c2d495e22d609d51b708481176e6574a3be5e6b0f3',  # noqa
+    'TCGA-06-0129-01Z-00-DX3_fgnd_mask_lres3.png': 'sha512:849f18d26d38f3a87d1c3126dbdf8df96cccff3481560ee9aa8cc8d1ed2567f0fadb25c7906d9e148683aeada74d09283f918f835e08f836367d798252d25fa3',  # noqa
     #
     # Source: TCGA-06-0129-01Z-00-DX3_roi_nuclei_bbox.anot
     'TCGA-06-0129-01Z-00-DX3_roi_nuclei_bbox.anot': 'sha512:d880fd29abf6e5c9afb624a93631697b4f8eb70ffad36a21689839783bcac206b6494352412ded0cb2129eb36b007ec67e0609c1862dd9ee3df2815c5f9e7c52',  # noqa

{histomicstk-1.4.1.dev20 → histomicstk-1.4.1.dev22}/tests/test_cli_common.py

@@ -72,6 +72,7 @@ class TestCliCommon:
         for gtruth in {
             'TCGA-06-0129-01Z-00-DX3_fgnd_mask_lres.png',
             'TCGA-06-0129-01Z-00-DX3_fgnd_mask_lres2.png',
+            'TCGA-06-0129-01Z-00-DX3_fgnd_mask_lres3.png',
         }:
             fgnd_mask_gtruth_file = os.path.join(datastore.fetch(gtruth))
 

{histomicstk-1.4.1.dev20 → histomicstk-1.4.1.dev22}/tests/test_color_normalization.py

@@ -40,8 +40,8 @@ class TestReinhardNormalization:
         # gt_stddev = [0.612143, 0.122667, 0.021361]
 
         # With icc correction
-        gt_mean = [8.977143, -0.082973, 0.021126]
-        gt_stddev = [0.561896, 0.124711, 0.025968]
+        gt_mean = [8.992413, -0.080213, 0.021194]
+        gt_stddev = [0.53575324, 0.12046163, 0.02542923]
 
         np.testing.assert_allclose(wsi_mean, gt_mean, atol=1e-2)
         np.testing.assert_allclose(wsi_stddev, gt_stddev, atol=1e-2)

histomicstk-1.4.1.dev20/histomicstk/_version.py

@@ -1 +0,0 @@
-__version__ = '1.4.1.dev20'