histomicstk 1.4.1.dev52__tar.gz → 1.4.1.dev54__tar.gz

{histomicstk-1.4.1.dev52 → histomicstk-1.4.1.dev54}/Dockerfile-wheels

@@ -1,9 +1,11 @@
 FROM dockcross/manylinux_2_28-x64
 
-# Don't build python < 3.9
+# Don't build python < 3.10
 RUN rm -rf /opt/python/cp36*
 RUN rm -rf /opt/python/cp37*
 RUN rm -rf /opt/python/cp38*
+RUN rm -rf /opt/python/cp39*
+RUN rm -rf /opt/python/cp*t
 RUN rm -rf /opt/python/pp*
 
 RUN for PYBIN in /opt/python/*/bin; do \
@@ -11,19 +13,19 @@ RUN for PYBIN in /opt/python/*/bin; do \
     done
 
 RUN for PYBIN in /opt/python/*/bin; do \
-      if [[ "${PYBIN}" =~ "312" ]]; then \
-        export VERSIONS="numpy==1.26.*"; \
+      if [[ "${PYBIN}" =~ "314" ]]; then \
+        export VERSIONS="numpy>=2"; \
+      elif [[ "${PYBIN}" =~ "313" ]]; then \
+        export VERSIONS="numpy>=2"; \
+      elif [[ "${PYBIN}" =~ "312" ]]; then \
+        export VERSIONS="numpy>=1.26"; \
       elif [[ "${PYBIN}" =~ "311" ]]; then \
-        export VERSIONS="numpy==1.23.*"; \
+        export VERSIONS="numpy>=1.24"; \
       elif [[ "${PYBIN}" =~ "310" ]]; then \
-        export VERSIONS="numpy==1.21.*"; \
-      elif [[ "${PYBIN}" =~ "39" ]]; then \
-        export VERSIONS="numpy==1.19.*"; \
-      elif [[ "${PYBIN}" =~ "38" ]]; then \
-        export VERSIONS="numpy==1.17.*"; \
+        export VERSIONS="numpy>=1.21"; \
       else \
-        # This could be numpy 1.11, but we specify 1.12.1 as our minimum \
-        export VERSIONS="numpy==1.12.*"; \
+        # Fallback for any remaining python versions (e.g. future releases) uses modern defaults \
+        export VERSIONS="numpy>=2"; \
       fi && \
       ${PYBIN}/pip install setuptools-scm 'Cython>=0.25.2' 'scikit-build>=0.8.1' 'cmake>=0.6.0' "${VERSIONS}"; \
     done
@@ -50,8 +52,7 @@ RUN cd $htk_path && \
     # Strip libraries before building any wheels \
     strip --strip-unneeded /usr/local/lib{,64}/*.{so,a} || true && \
     for PYBIN in /opt/python/*/bin; do \
-        # Anything newer requires manylinux2014 \
-        ${PYBIN}/pip install 'opencv-python-headless<4.3' && \
+        ${PYBIN}/pip install opencv-python-headless && \
         ${PYBIN}/pip install --no-cache-dir . && \
         # Remove any previous build artifacts && \
         git clean -fxd && \

{histomicstk-1.4.1.dev52 → histomicstk-1.4.1.dev54}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: histomicstk
-Version: 1.4.1.dev52
+Version: 1.4.1.dev54
 Summary: A Python toolkit for Histopathology Image Analysis
 Keywords: histomicstk
 Author-Email: "Kitware, Inc." <developers@digitalslidearchive.net>
@@ -8,15 +8,15 @@ License: Apache Software License 2.0
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Project-URL: Homepage, https://github.com/DigitalSlideArchive/HistomicsTK
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Requires-Dist: girder-client
 Requires-Dist: nimfa
 Requires-Dist: numpy
@@ -37,8 +37,7 @@ Requires-Dist: large-image[common]; sys_platform != "linux"
 Requires-Dist: large-image-converter; sys_platform == "linux"
 Requires-Dist: girder-slicer-cli-web
 Requires-Dist: ctk-cli
-Requires-Dist: opencv-python-headless<4.12; python_version < "3.10"
-Requires-Dist: opencv-python-headless; python_version >= "3.10"
+Requires-Dist: opencv-python-headless
 Description-Content-Type: text/x-rst
 
 ===========

histomicstk-1.4.1.dev54/histomicstk/_version.py

@@ -0,0 +1 @@
+__version__ = '1.4.1.dev54'

{histomicstk-1.4.1.dev52 → histomicstk-1.4.1.dev54}/histomicstk/cli/BackgroundIntensity/BackgroundIntensity.py

@@ -37,7 +37,8 @@ def main(args):
     }
 
     with open(args.outputAnnotationFile, 'w') as annotation_file:
-        json.dump(annotation, annotation_file, separators=(',', ':'), sort_keys=False)
+        json.dump(annotation, annotation_file, separators=(',', ':'),
+                  sort_keys=False, default=utils.json_encoder)
 
 
 if __name__ == '__main__':

{histomicstk-1.4.1.dev52 → histomicstk-1.4.1.dev54}/histomicstk/cli/ColorDeconvolution/ColorDeconvolution.py

@@ -134,7 +134,8 @@ def main(args):
 
         if args.outputAnnotationFile:
             with open(args.outputAnnotationFile, 'w') as annotation_file:
-                json.dump(annotation, annotation_file, separators=(',', ':'), sort_keys=False)
+                json.dump(annotation, annotation_file, separators=(',', ':'),
+                          sort_keys=False, default=utils.json_encoder)
 
 
 if __name__ == '__main__':

{histomicstk-1.4.1.dev52 → histomicstk-1.4.1.dev54}/histomicstk/cli/ComputeNucleiFeatures/ComputeNucleiFeatures.py

@@ -92,7 +92,7 @@ def main(args):  # noqa
 
     ts_metadata = ts.getMetadata()
 
-    print(json.dumps(ts_metadata, indent=2))
+    print(json.dumps(ts_metadata, indent=2, default=cli_utils.json_encoder))
 
     is_wsi = ts_metadata['magnification'] is not None
 
@@ -281,7 +281,8 @@ def main(args):  # noqa
     }
 
     with open(args.outputNucleiAnnotationFile, 'w') as annotation_file:
-        json.dump(annotation, annotation_file, separators=(',', ':'), sort_keys=False)
+        json.dump(annotation, annotation_file, separators=(',', ':'),
+                  sort_keys=False, default=cli_utils.json_encoder)
 
     #
     # Create CSV Feature file

{histomicstk-1.4.1.dev52 → histomicstk-1.4.1.dev54}/histomicstk/cli/NucleiClassification/NucleiClassification.py

@@ -139,7 +139,7 @@ def process_feature_and_annotation(args):
 
     ts_metadata = ts.getMetadata()
 
-    print(json.dumps(ts_metadata, indent=2))
+    print(json.dumps(ts_metadata, indent=2, default=cli_utils.json_encoder))
 
     src_mu_lab = None
     src_sigma_lab = None
@@ -339,7 +339,8 @@ def main(args):
         },
     })
     with open(args.outputNucleiAnnotationFile, 'w') as annotation_file:
-        json.dump(annotation, annotation_file, separators=(',', ':'), sort_keys=False)
+        json.dump(annotation, annotation_file, separators=(',', ':'),
+                  sort_keys=False, default=cli_utils.json_encoder)
 
 
 if __name__ == '__main__':

{histomicstk-1.4.1.dev52 → histomicstk-1.4.1.dev54}/histomicstk/cli/NucleiDetection/NucleiDetection.py

@@ -27,7 +27,7 @@ def read_input_image(args, process_whole_image=False):
 
     ts_metadata = ts.getMetadata()
 
-    print(json.dumps(ts_metadata, indent=2))
+    print(json.dumps(ts_metadata, indent=2, default=cli_utils.json_encoder))
 
     is_wsi = ts_metadata['magnification'] is not None
 
@@ -379,7 +379,8 @@ def main(args):  # noqa
     }
 
     with open(args.outputNucleiAnnotationFile, 'w') as annotation_file:
-        json.dump(annotation, annotation_file, separators=(',', ':'), sort_keys=False)
+        json.dump(annotation, annotation_file, separators=(',', ':'),
+                  sort_keys=False, default=cli_utils.json_encoder)
 
     total_time_taken = time.time() - total_start_time
 

{histomicstk-1.4.1.dev52 → histomicstk-1.4.1.dev54}/histomicstk/cli/PositivePixelCount/PositivePixelCount.py

@@ -195,7 +195,8 @@ def main(opts):
     # Save the annotation dictionary to the output annotation file
     if opts.outputAnnotationFile:
         with open(opts.outputAnnotationFile, 'w') as annotation_file:
-            json.dump(annotation, annotation_file, separators=(',', ':'), sort_keys=False)
+            json.dump(annotation, annotation_file, separators=(',', ':'),
+                      sort_keys=False, default=utils.json_encoder)
         print('Finished time %s' % (utils.disp_time_hms(time.time() - start_time)))
 
 

{histomicstk-1.4.1.dev52 → histomicstk-1.4.1.dev54}/histomicstk/cli/SeparateStainsMacenkoPCA/SeparateStainsMacenkoPCA.py

@@ -31,7 +31,7 @@ def main(origargs):
         annotation['attributes'][f'stainColor_{i + 1}'] = stain.tolist()
 
     with open(args.outputAnnotationFile, 'w') as annotation_file:
-        json.dump(annotation, annotation_file, sort_keys=False)
+        json.dump(annotation, annotation_file, sort_keys=False, default=utils.json_encoder)
 
 
 if __name__ == '__main__':

{histomicstk-1.4.1.dev52 → histomicstk-1.4.1.dev54}/histomicstk/cli/SeparateStainsXuSnmf/SeparateStainsXuSnmf.py

@@ -41,7 +41,7 @@ def main(origargs):
     for i, stain in enumerate(w_est.T):
         annotation['attributes'][f'stainColor_{i + 1}'] = stain.tolist()
     with open(args.outputAnnotationFile, 'w') as annotation_file:
-        json.dump(annotation, annotation_file, sort_keys=False)
+        json.dump(annotation, annotation_file, sort_keys=False, default=utils.json_encoder)
 
 
 if __name__ == '__main__':

{histomicstk-1.4.1.dev52 → histomicstk-1.4.1.dev54}/histomicstk/cli/SuperpixelSegmentation/SuperpixelSegmentation.py

@@ -201,7 +201,8 @@ def createSuperPixels(opts):  # noqa
     img.set_type(
         pyvips.GValue.gstr_type, 'image-description',
         json.dumps(dict(
-            {k: v for k, v in vars(opts).items() if k != 'callback'}, indexCount=found)))
+            {k: v for k, v in vars(opts).items() if k != 'callback'}, indexCount=found),
+            default=utils.json_encoder))
     img.write_to_file(
         opts.outputImageFile, tile=True, tile_width=256, tile_height=256, pyramid=True,
         region_shrink=pyvips.RegionShrink.NEAREST,
@@ -268,7 +269,8 @@ def createSuperPixels(opts):  # noqa
             annotation = [annotation, bboxannotation]
         with open(opts.outputAnnotationFile, 'w') as annotation_file:
             try:
-                json.dump(annotation, annotation_file, separators=(',', ':'), sort_keys=False)
+                json.dump(annotation, annotation_file, separators=(',', ':'),
+                          sort_keys=False, default=utils.json_encoder)
             except Exception:
                 print('Failed to serialize annotation')
                 print(repr(annotation))

{histomicstk-1.4.1.dev52 → histomicstk-1.4.1.dev54}/histomicstk/cli/utils.py

@@ -476,7 +476,6 @@ def splitArgs(args, split='_'):
 def sample_pixels(args):
     """Version of histomicstk.utils.sample_pixels that takes a Namespace
     and handles the special default values.
-
     """
     args = (args._asdict() if hasattr(args, '_asdict') else vars(args)).copy()
     for k in 'magnification', 'sample_fraction', 'sample_approximate_total':
@@ -485,6 +484,18 @@ def sample_pixels(args):
     return htk_utils.sample_pixels(**args)
 
 
+def json_encoder(obj):
+    """
+    Default encoder for `json.dump`/`json.dumps` to handle NumPy scalars that
+    fail native serialization (e.g., int64, float64).
+    """
+    if isinstance(obj, np.integer):
+        return int(obj)
+    elif isinstance(obj, np.floating):
+        return float(obj)
+    raise TypeError
+
+
 __all__ = (
     'CLIArgumentParser',
     'create_dask_client',
@@ -495,6 +506,7 @@ __all__ = (
     'get_region_dict',
     'get_stain_matrix',
     'get_stain_vector',
+    'json_encoder',
     'sample_pixels',
     'segment_wsi_foreground_at_low_res',
     'splitArgs',

{histomicstk-1.4.1.dev52 → histomicstk-1.4.1.dev54}/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.dev52"
+version = "1.4.1.dev54"
 name = "histomicstk"
 description = "A Python toolkit for Histopathology Image Analysis"
 readme = "README.rst"
@@ -16,16 +16,16 @@ classifiers = [
     "Development Status :: 5 - Production/Stable",
     "License :: OSI Approved :: Apache Software License",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Topic :: Scientific/Engineering :: Artificial Intelligence",
     "Topic :: Software Development :: Libraries :: Python Modules",
 ]
 keywords = ["histomicstk"]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
     "girder-client",
     "nimfa",
@@ -47,8 +47,7 @@ dependencies = [
     "large-image-converter;sys.platform=='linux'",
     "girder-slicer-cli-web",
     "ctk-cli",
-    "opencv-python-headless<4.12; python_version < '3.10'",
-    "opencv-python-headless; python_version >= '3.10'",
+    "opencv-python-headless",
 ]
 
 [project.scripts]

{histomicstk-1.4.1.dev52 → histomicstk-1.4.1.dev54}/pyproject.toml.bak

@@ -15,16 +15,16 @@ classifiers = [
     "Development Status :: 5 - Production/Stable",
     "License :: OSI Approved :: Apache Software License",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Topic :: Scientific/Engineering :: Artificial Intelligence",
     "Topic :: Software Development :: Libraries :: Python Modules",
 ]
 keywords = ["histomicstk"]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
     "girder-client",
     "nimfa",
@@ -46,8 +46,7 @@ dependencies = [
     "large-image-converter;sys.platform=='linux'",
     "girder-slicer-cli-web",
     "ctk-cli",
-    "opencv-python-headless<4.12; python_version < '3.10'",
-    "opencv-python-headless; python_version >= '3.10'",
+    "opencv-python-headless",
 ]
 dynamic = ["version"]
 

{histomicstk-1.4.1.dev52 → histomicstk-1.4.1.dev54}/test_wheels.py

@@ -19,11 +19,11 @@ python "$CLIPATH/NucleiDetection/NucleiDetection.py" tcga.svs sample.anot \\
 true"""
 
 containers = [
-    'python:3.9',
     'python:3.10',
     'python:3.11',
     'python:3.12',
-    'centos/python-38-centos7',
+    'python:3.13',
+    'python:3.14',
 ]
 
 for container in containers:

{histomicstk-1.4.1.dev52 → histomicstk-1.4.1.dev54}/tests/test_cli_results.py

@@ -112,3 +112,73 @@ class TestColorDeconvolution:
             '479066d2016122b2b60575f4e9abe201b4f79d8a894ce76191419e21c7539186',
             'd06317130f4a4aabd155c97f32cec4708ec3eec24d09d16daa2181f18b2051bb',
         }
+
+
+class TestPositivePixelCount:
+    POSITIVE_PIXEL_COUNT_DEFAULTS = [
+        '0.83',      # hue_value
+        '0.15',      # hue_width
+        '0.05',      # saturation_minimum
+        '0.95',      # intensity_upper_limit
+        '0.65',      # intensity_weak_threshold
+        '0.35',      # intensity_strong_threshold
+        '0.05',       # intensity_lower_limit
+    ]
+
+    def _runTest(self, image_file, extra_args=None):
+        """
+        Run PositivePixelCount CLI and return the annotation file contents.
+
+        Plus optional named flags like --image_annotation for output files.
+        """
+        with tempfile.TemporaryDirectory() as tmpdirname:
+            outpath = os.path.join(tmpdirname, 'result.anot')
+            args = [image_file] + self.POSITIVE_PIXEL_COUNT_DEFAULTS
+            args.append('--image_annotation')
+            args.append(outpath)
+            if extra_args:
+                args += extra_args
+            _runCLITest('PositivePixelCount', args)
+            with open(outpath) as f:
+                return json.load(f)
+
+    def test_positive_pixel_count_with_annotation(self):
+        """
+        Test that PositivePixelCount completes and writes valid JSON
+        annotation.
+        """
+        src = datastore.fetch('Easy1.png')
+        annot = self._runTest(src, ['--scheduler=multithreading'])
+
+        assert 'name' in annot
+        assert 'elements' in annot
+        assert 'attributes' in annot
+        assert 'stats' in annot['attributes']
+
+    def test_positive_pixel_count_json_serialization(self):
+        """
+        Directly test that annotation JSON can be parsed.
+        """
+        from histomicstk.cli.PositivePixelCount import PositivePixelCount
+        from histomicstk.cli.utils import CLIArgumentParser
+
+        src = datastore.fetch('Easy1.png')
+
+        with tempfile.TemporaryDirectory() as tmpdirname:
+            outpath = os.path.join(tmpdirname, 'result.anot')
+            args = [src] + self.POSITIVE_PIXEL_COUNT_DEFAULTS  #
+            args.append('--image_annotation')
+            args.append(outpath)
+            parser = CLIArgumentParser(
+                os.path.join(os.path.dirname(PositivePixelCount.__file__),
+                             'PositivePixelCount.xml'),
+            )
+            parsed_args = parser.parse_args(args)
+            PositivePixelCount.main(parsed_args)
+            with open(outpath) as f:
+                annot = json.load(f)
+            stats = annot['attributes']['stats']
+            assert 'NumberWeakPositive' in stats
+            assert 'NumberPositive' in stats
+            assert 'NumberStrongPositive' in stats
+            assert 'NumberTotalPixels' in stats

histomicstk-1.4.1.dev52/histomicstk/_version.py

@@ -1 +0,0 @@
-__version__ = '1.4.1.dev52'