morphology: add h_maxima, h_minima, local_maxima, local_minima. improve reconstruct

.pre-commit-config.yaml

@@ -201,12 +201,14 @@ repos:
             ^python/cucim/src/cucim/skimage/morphology/_medial_axis_lookup[.]py$|
             ^python/cucim/src/cucim/skimage/morphology/binary[.]py$|
             ^python/cucim/src/cucim/skimage/morphology/convex_hull[.]py$|
+            ^python/cucim/src/cucim/skimage/morphology/extrema[.]py$|
             ^python/cucim/src/cucim/skimage/morphology/footprints[.]py$|
             ^python/cucim/src/cucim/skimage/morphology/gray[.]py$|
             ^python/cucim/src/cucim/skimage/morphology/isotropic[.]py$|
             ^python/cucim/src/cucim/skimage/morphology/misc[.]py$|
             ^python/cucim/src/cucim/skimage/morphology/tests/test_binary[.]py$|
             ^python/cucim/src/cucim/skimage/morphology/tests/test_convex_hull[.]py$|
+            ^python/cucim/src/cucim/skimage/morphology/tests/test_extrema[.]py$|
             ^python/cucim/src/cucim/skimage/morphology/tests/test_footprints[.]py$|
             ^python/cucim/src/cucim/skimage/morphology/tests/test_gray[.]py$|
             ^python/cucim/src/cucim/skimage/morphology/tests/test_isotropic[.]py$|
@@ -483,12 +485,14 @@ repos:
             python/cucim/src/cucim/skimage/morphology/_medial_axis_lookup[.]py$|
             python/cucim/src/cucim/skimage/morphology/binary[.]py$|
             python/cucim/src/cucim/skimage/morphology/convex_hull[.]py$|
+            python/cucim/src/cucim/skimage/morphology/extrema[.]py$|
             python/cucim/src/cucim/skimage/morphology/footprints[.]py$|
             python/cucim/src/cucim/skimage/morphology/gray[.]py$|
             python/cucim/src/cucim/skimage/morphology/isotropic[.]py$|
             python/cucim/src/cucim/skimage/morphology/misc[.]py$|
             python/cucim/src/cucim/skimage/morphology/tests/test_binary[.]py$|
             python/cucim/src/cucim/skimage/morphology/tests/test_convex_hull[.]py$|
+            python/cucim/src/cucim/skimage/morphology/tests/test_extrema[.]py$|
             python/cucim/src/cucim/skimage/morphology/tests/test_footprints[.]py$|
             python/cucim/src/cucim/skimage/morphology/tests/test_gray[.]py$|
             python/cucim/src/cucim/skimage/morphology/tests/test_isotropic[.]py$|

benchmarks/skimage/cucim_morphology_bench.py

@@ -16,10 +16,15 @@
 import skimage.data
 import skimage.morphology
 from _image_bench import ImageBench
+from packaging.version import Version
 
 import cucim.skimage
 import cucim.skimage.morphology
 
+# scikit-image >= 0.26 renamed min_size -> max_size in remove_small_objects
+# and area_threshold -> max_size in remove_small_holes
+_skimage_has_max_size = Version(skimage.__version__) >= Version("0.26")
+
 
 class BinaryMorphologyBench(ImageBench):
     def __init__(
@@ -107,15 +112,26 @@ def _init_test_data(self, dtype):
 
     def set_args(self, dtype):
         a = self._init_test_data(dtype)
-        self.args_cpu = (cp.asnumpy(a), 6)
-        self.args_gpu = (a, 6)
+        self.args_cpu = (cp.asnumpy(a),)
+        self.args_gpu = (a,)
+        # scikit-image < 0.26 uses min_size, >= 0.26 uses max_size
+        if _skimage_has_max_size:
+            self.fixed_kwargs_cpu["max_size"] = 6
+        else:
+            self.fixed_kwargs_cpu["min_size"] = 6
+        self.fixed_kwargs_gpu["max_size"] = 6
 
 
 class RemoveSmallHolesBench(RemoveSmallObjectsBench):
     def set_args(self, dtype):
         a = ~self._init_test_data(dtype)
-        self.args_cpu = (cp.asnumpy(a), 5)
-        self.args_gpu = (a, 5)
+        self.args_cpu = (cp.asnumpy(a),)
+        self.args_gpu = (a,)
+        if _skimage_has_max_size:
+            self.fixed_kwargs_cpu["max_size"] = 5
+        else:
+            self.fixed_kwargs_cpu["area_threshold"] = 5
+        self.fixed_kwargs_gpu["max_size"] = 5
 
 
 def main(args):
@@ -161,6 +177,37 @@ def main(args):
         ("thin", dict(), dict(), False, True),
         # grayreconstruct.py
         ("reconstruction", dict(), dict(), False, True),
+        # extrema.py
+        (
+            "local_maxima",
+            dict(),
+            dict(connectivity=list(range(1, len(shape) + 1))),
+            False,
+            True,
+        ),
+        (
+            "local_minima",
+            dict(),
+            dict(connectivity=list(range(1, len(shape) + 1))),
+            False,
+            True,
+        ),
+        # h values scaled to image range: integers use camera (0-255),
+        # floats use camera/255 (0-1)
+        (
+            "h_maxima",
+            dict(),
+            dict(h=[10, 40] if np.issubdtype(dtypes[0], np.integer) else [0.04, 0.16]),
+            False,
+            True,
+        ),
+        (
+            "h_minima",
+            dict(),
+            dict(h=[10, 40] if np.issubdtype(dtypes[0], np.integer) else [0.04, 0.16]),
+            False,
+            True,
+        ),
         # footprints.py
         # OMIT the functions from this file (each creates a structuring element)
     ]:
@@ -298,7 +345,8 @@ def main(args):
         'binary_closing', 'isotropic_erosion', 'isotropic_dilation',
         'isotropic_opening', 'isotropic_closing','remove_small_objects',
         'remove_small_holes', 'erosion', 'dilation', 'opening', 'closing',
-        'white_tophat', 'black_tophat', 'thin', 'medial_axis', 'reconstruction'
+        'white_tophat', 'black_tophat', 'thin', 'medial_axis', 'reconstruction',
+        'local_maxima', 'local_minima', 'h_maxima', 'h_minima',
     ]
     # fmt: on
     dtype_choices = [

benchmarks/skimage/run-nv-bench-morphology.sh

@@ -6,7 +6,7 @@
 MAX_DURATION="${CUCIM_BENCHMARK_MAX_DURATION:-10}"
 
 param_shape=("512,512" "3840,2160" "3840,2160,3" "192,192,192")
-param_filt=(binary_erosion binary_dilation binary_opening binary_closing isotropic_erosion isotropic_dilation isotropic_opening isotropic_closing remove_small_objects remove_small_holes erosion dilation opening closing white_tophat black_tophat medial_axis thin reconstruction)
+param_filt=(binary_erosion binary_dilation binary_opening binary_closing isotropic_erosion isotropic_dilation isotropic_opening isotropic_closing remove_small_objects remove_small_holes erosion dilation opening closing white_tophat black_tophat medial_axis thin reconstruction h_maxima h_minima local_maxima local_minima)
 param_dt=(uint8)
 for shape in "${param_shape[@]}"; do
     for filt in "${param_filt[@]}"; do
@@ -18,7 +18,7 @@ done
 
 # Note: Omit binary_*, medial_axis and thin from floating point benchmarks.
 #       (these functions only take binary input).
-param_filt_float=(remove_small_objects remove_small_holes erosion dilation opening closing white_tophat black_tophat reconstruction)
+param_filt_float=(remove_small_objects remove_small_holes erosion dilation opening closing white_tophat black_tophat reconstruction h_maxima h_minima local_maxima local_minima)
 param_dt=(float32)
 for shape in "${param_shape[@]}"; do
     for filt in "${param_filt_float[@]}"; do

python/cucim/src/cucim/skimage/morphology/__init__.py

@@ -1,10 +1,11 @@
 # SPDX-FileCopyrightText: 2009-2022 the scikit-image team
-# SPDX-FileCopyrightText: Copyright (c) 2021-2025, NVIDIA CORPORATION. All rights reserved.
+# SPDX-FileCopyrightText: Copyright (c) 2021-2026, NVIDIA CORPORATION. All rights reserved.
 # SPDX-License-Identifier: Apache-2.0 AND BSD-3-Clause
 
 """Morphological algorithms, e.g., closing, opening, skeletonization."""
 
 from ._skeletonize import medial_axis, thin
+from .extrema import h_maxima, h_minima, local_maxima, local_minima
 from .binary import (
     binary_closing,
     binary_dilation,
@@ -50,6 +51,10 @@
     "binary_dilation",
     "binary_opening",
     "binary_closing",
+    "h_maxima",
+    "h_minima",
+    "local_maxima",
+    "local_minima",
     "isotropic_dilation",
     "isotropic_erosion",
     "isotropic_opening",