Forward-merge branch-22.08 to branch-22.10 [skip gpuci]

CHANGELOG.md

@@ -2,9 +2,53 @@
 
 Please see https://github.com/rapidsai/cucim/releases/tag/v22.10.00a for the latest changes to this development branch.
 
-# cuCIM 22.08.00 (Date TBD)
+# cuCIM 22.08.00 (17 Aug 2022)
 
-Please see https://github.com/rapidsai/cucim/releases/tag/v22.08.00a for the latest changes to this development branch.
+## 🚨 Breaking Changes
+
+- Stain extraction: use a less strict condition across channels when thresholding ([#316](https://github.com/rapidsai/cucim/pull/316)) [@grlee77](https://github.com/grlee77)
+
+## 🐛 Bug Fixes
+
+- create SimilarityTransform using CuPy 9.x-compatible indexing ([#365](https://github.com/rapidsai/cucim/pull/365)) [@grlee77](https://github.com/grlee77)
+- Add `__init__.py` in `cucim.core` ([#359](https://github.com/rapidsai/cucim/pull/359)) [@jakirkham](https://github.com/jakirkham)
+- Stain extraction: use a less strict condition across channels when thresholding ([#316](https://github.com/rapidsai/cucim/pull/316)) [@grlee77](https://github.com/grlee77)
+- Incorporate bug fixes from skimage 0.19.3 ([#312](https://github.com/rapidsai/cucim/pull/312)) [@grlee77](https://github.com/grlee77)
+- fix RawKernel bug for canny filter when quantiles are used ([#310](https://github.com/rapidsai/cucim/pull/310)) [@grlee77](https://github.com/grlee77)
+
+## 📖 Documentation
+
+- Defer loading of `custom.js` ([#383](https://github.com/rapidsai/cucim/pull/383)) [@galipremsagar](https://github.com/galipremsagar)
+- add cucim.core.morphology to API docs + other docstring fixes ([#367](https://github.com/rapidsai/cucim/pull/367)) [@grlee77](https://github.com/grlee77)
+- Update README.md ([#361](https://github.com/rapidsai/cucim/pull/361)) [@HesAnEasyCoder](https://github.com/HesAnEasyCoder)
+- remove unimplemented functions from See Also and fix version numbers in deprecation warnings ([#356](https://github.com/rapidsai/cucim/pull/356)) [@grlee77](https://github.com/grlee77)
+- Forward-merge branch-22.06 to branch-22.08 ([#344](https://github.com/rapidsai/cucim/pull/344)) [@grlee77](https://github.com/grlee77)
+- Update README.md ([#315](https://github.com/rapidsai/cucim/pull/315)) [@HesAnEasyCoder](https://github.com/HesAnEasyCoder)
+- Update index.rst ([#314](https://github.com/rapidsai/cucim/pull/314)) [@HesAnEasyCoder](https://github.com/HesAnEasyCoder)
+- Update PyPI package documentation for v22.06.00 ([#311](https://github.com/rapidsai/cucim/pull/311)) [@gigony](https://github.com/gigony)
+
+## 🚀 New Features
+
+- Add segmentation with the Chan-Vese active contours method ([#343](https://github.com/rapidsai/cucim/pull/343)) [@grlee77](https://github.com/grlee77)
+- Add cucim.skimage.morphology.medial_axis ([#342](https://github.com/rapidsai/cucim/pull/342)) [@grlee77](https://github.com/grlee77)
+- Add cucim.skimage.segmentation.expand_labels ([#341](https://github.com/rapidsai/cucim/pull/341)) [@grlee77](https://github.com/grlee77)
+- Add Euclidean distance transform for images/volumes ([#318](https://github.com/rapidsai/cucim/pull/318)) [@grlee77](https://github.com/grlee77)
+
+## 🛠️ Improvements
+
+- Revert "Allow CuPy 11" ([#362](https://github.com/rapidsai/cucim/pull/362)) [@galipremsagar](https://github.com/galipremsagar)
+- Fix issues with day & night modes in python docs ([#360](https://github.com/rapidsai/cucim/pull/360)) [@galipremsagar](https://github.com/galipremsagar)
+- Allow CuPy 11 ([#357](https://github.com/rapidsai/cucim/pull/357)) [@jakirkham](https://github.com/jakirkham)
+- more efficient separable convolution ([#355](https://github.com/rapidsai/cucim/pull/355)) [@grlee77](https://github.com/grlee77)
+- Support resolution and spacing metadata ([#349](https://github.com/rapidsai/cucim/pull/349)) [@gigony](https://github.com/gigony)
+- Performance optimizations to morphological segmentation functions ([#340](https://github.com/rapidsai/cucim/pull/340)) [@grlee77](https://github.com/grlee77)
+- benchmarks: avoid use of deprecated pandas API ([#339](https://github.com/rapidsai/cucim/pull/339)) [@grlee77](https://github.com/grlee77)
+- Reduce memory overhead and improve performance of normalize_colors_pca ([#328](https://github.com/rapidsai/cucim/pull/328)) [@grlee77](https://github.com/grlee77)
+- Protect against obscure divide by zero error in edge case of `normalize_colors_pca` ([#327](https://github.com/rapidsai/cucim/pull/327)) [@grlee77](https://github.com/grlee77)
+- complete parametrization of cucim.skimage benchmarks ([#324](https://github.com/rapidsai/cucim/pull/324)) [@grlee77](https://github.com/grlee77)
+- parameterization of `filters` and `features` benchmarks (v2) ([#322](https://github.com/rapidsai/cucim/pull/322)) [@grlee77](https://github.com/grlee77)
+- Add a fast histogram-based median filter ([#317](https://github.com/rapidsai/cucim/pull/317)) [@grlee77](https://github.com/grlee77)
+- Remove custom compiler environment variables ([#307](https://github.com/rapidsai/cucim/pull/307)) [@ajschmidt8](https://github.com/ajschmidt8)
 
 # cuCIM 22.06.00 (7 Jun 2022)
 

python/cucim/src/cucim/core/operations/morphology/_pba_2d.py

@@ -1,8 +1,40 @@
+import functools
 import math
+import numbers
 import os
 
+
 import cupy
 
+try:
+    # math.lcm was introduced in Python 3.9
+    from math import lcm
+except ImportError:
+
+    """Fallback implementation of least common multiple (lcm)
+
+    TODO: remove once minimum Python requirement is >= 3.9
+    """
+
+    def _lcm(a, b):
+        return abs(b * (a // math.gcd(a, b)))
+
+    @functools.lru_cache()
+    def lcm(*args):
+        nargs = len(args)
+        if not all(isinstance(a, numbers.Integral) for a in args):
+            raise TypeError("all arguments must be integers")
+        if nargs == 0:
+            return 1
+        res = int(args[0])
+        if nargs == 1:
+            return abs(res)
+        for i in range(1, nargs):
+            x = int(args[i])
+            res = _lcm(res, x)
+        return res
+
+
 pba2d_defines_template = """
 
 // MARKER is used to mark blank pixels in the texture.
@@ -119,27 +151,39 @@ def _pba_2d(arr, sampling=None, return_distances=True, return_indices=False,
         # if len(sampling) != 2:
         #     raise ValueError("sampling must be a sequence of two values.")
 
-    padded_size = math.ceil(max(arr.shape) / block_size) * block_size
     if block_params is None:
-        # should be <= size / 64. sy must be a multiple of m1
-        m1 = max(1, min(padded_size // block_size, 32))
+        padded_size = math.ceil(max(arr.shape) / block_size) * block_size
 
+        # should be <= size / block_size. sy must be a multiple of m1
+        m1 = padded_size // block_size
         # size must be a multiple of m2
-        m2 = max(1, min(padded_size // block_size, 32))
+        m2 = max(1, min(padded_size // block_size, block_size))
         # m2 must also be a power of two
         m2 = 2**math.floor(math.log2(m2))
         if padded_size % m2 != 0:
             raise RuntimeError("error in setting default m2")
-
-        # should be <= 64. texture size must be a multiple of m3
         m3 = min(min(m1, m2), 2)
     else:
+        if any(p < 1 for p in block_params):
+            raise ValueError("(m1, m2, m3) in blockparams must be >= 1")
         m1, m2, m3 = block_params
+        if math.log2(m2) % 1 > 1e-5:
+            raise ValueError("m2 must be a power of 2")
+        multiple = lcm(block_size, m1, m2, m3)
+        padded_size = math.ceil(max(arr.shape) / multiple) * multiple
 
     if m1 > padded_size // block_size:
-        raise ValueError("m1 too large. must be <= arr.shape[0] // 32")
+        raise ValueError(
+            f"m1 too large. must be <= padded arr.shape[0] // {block_size}"
+        )
     if m2 > padded_size // block_size:
-        raise ValueError("m2 too large. must be <= arr.shape[1] // 32")
+        raise ValueError(
+            f"m2 too large. must be <= padded arr.shape[1] // {block_size}"
+        )
+    if m3 > padded_size // block_size:
+        raise ValueError(
+            f"m3 too large. must be <= padded arr.shape[1] // {block_size}"
+        )
     for m in (m1, m2, m3):
         if padded_size % m != 0:
             raise ValueError(

python/cucim/src/cucim/core/operations/morphology/_pba_3d.py

@@ -1,40 +1,10 @@
-import functools
 import math
-import numbers
 import os
 
 import cupy
 import numpy as np
 
-from ._pba_2d import _get_block_size
-
-try:
-    # math.lcm was introduced in Python 3.9
-    from math import lcm
-except ImportError:
-
-    """Fallback implementation of least common multiple (lcm)
-
-    TODO: remove once minimum Python requirement is >= 3.9
-    """
-
-    def _lcm(a, b):
-        return abs(b * (a // math.gcd(a, b)))
-
-    @functools.lru_cache()
-    def lcm(*args):
-        nargs = len(args)
-        if not all(isinstance(a, numbers.Integral) for a in args):
-            raise TypeError("all arguments must be integers")
-        if nargs == 0:
-            return 1
-        res = int(args[0])
-        if nargs == 1:
-            return abs(res)
-        for i in range(1, nargs):
-            x = int(args[i])
-            res = _lcm(res, x)
-        return res
+from ._pba_2d import _get_block_size, lcm
 
 
 pba3d_defines_template = """

python/cucim/src/cucim/core/operations/morphology/tests/test_distance_transform.py

@@ -32,7 +32,7 @@ def assert_percentile_equal(arr1, arr2, pct=95):
         ((384, 256), (1.5, 1.5)),
         ((14, 32, 50), None),
         ((50, 32, 24), (2, 2, 2)),
-    ]
+    ],
 )
 @pytest.mark.parametrize('density', [5, 50, 95])
 @pytest.mark.parametrize('block_params', [None, (1, 1, 1)])
@@ -65,6 +65,60 @@ def test_distance_transform_edt(
         assert_percentile_equal(out, expected, pct=95)
 
 
+@pytest.mark.parametrize(
+    'shape',
+    (
+        [(s,) * 2 for s in range(512, 512 + 32)]
+        + [(s,) * 2 for s in range(1024, 1024 + 16)]
+        + [(s,) * 2 for s in range(2050, 2050)]
+        + [(s,) * 2 for s in range(4100, 4100)]
+    ),
+)
+@pytest.mark.parametrize('density', [2, 98])
+def test_distance_transform_edt_additional_shapes(shape, density):
+
+    kwargs_scipy = dict(return_distances=True, return_indices=False)
+    kwargs_cucim = copy(kwargs_scipy)
+    img = binary_image(shape, pct_true=density)
+    distances = distance_transform_edt(img, **kwargs_cucim)
+    expected = ndi_cpu.distance_transform_edt(cp.asnumpy(img), **kwargs_scipy)
+    cp.testing.assert_allclose(distances, expected)
+
+
+@pytest.mark.parametrize(
+    'shape',
+    [(s,) * 2 for s in range(1024, 1024 + 4)],
+)
+@pytest.mark.parametrize(
+    'block_params',
+    [(1, 1, 1), (5, 4, 2), (3, 8, 4), (7, 16, 1), (11, 32, 3), (1, 1, 16)]
+)
+def test_distance_transform_edt_block_params(shape, block_params):
+
+    kwargs_scipy = dict(return_distances=True, return_indices=False)
+    kwargs_cucim = copy(kwargs_scipy)
+    kwargs_cucim['block_params'] = block_params
+    img = binary_image(shape, pct_true=4)
+    distances = distance_transform_edt(img, **kwargs_cucim)
+    expected = ndi_cpu.distance_transform_edt(cp.asnumpy(img), **kwargs_scipy)
+    cp.testing.assert_allclose(distances, expected)
+
+
+@pytest.mark.parametrize(
+    'block_params', [
+        (0, 1, 1), (1, 0, 1), (1, 1, 0),  # no elements can be < 1
+        (1, 3, 1), (1, 5, 1), (1, 7, 1),  # 2nd element must be a power of 2
+        (128, 1, 1),  # m1 too large for the array size
+        (1, 128, 1),  # m2 too large for the array size
+        (1, 1, 128),  # m3 too large for the array size
+    ]
+)
+def test_distance_transform_edt_block_params_invalid(block_params):
+    img = binary_image((512, 512), pct_true=4)
+    with pytest.raises(ValueError):
+        distance_transform_edt(img, block_params=block_params)
+
+
 @pytest.mark.parametrize('return_indices', [False, True])
 @pytest.mark.parametrize('return_distances', [False, True])
 @pytest.mark.parametrize(