Merge pull request #688 from rapidsai/branch-24.02

Forward-merge branch-24.02 to branch-24.04
rapidsai · Jan 29, 2024 · baabda6 · baabda6
2 parents 2654a7a + caade43
commit baabda6
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Showing 40 changed files with 444 additions and 369 deletions.
diff --git a/conda/environments/all_cuda-118_arch-x86_64.yaml b/conda/environments/all_cuda-118_arch-x86_64.yaml
@@ -28,7 +28,7 @@ dependencies:
 - nbsphinx
 - ninja
 - numpy>=1.21.3
-- numpydoc
+- numpydoc>=1.5
 - nvcc_linux-64=11.8
 - openslide-python>=1.3.0
 - pip
@@ -41,8 +41,9 @@ dependencies:
 - pytest-xdist
 - pytest>=6.2.4
 - python>=3.8,<3.11
+- pywavelets>=1.0
 - recommonmark
-- scikit-image>=0.19.0,<0.22.0a0
+- scikit-image>=0.19.0,<0.23.0a0
 - scipy
 - sphinx<6
 - sysroot_linux-64==2.17

diff --git a/conda/environments/all_cuda-120_arch-x86_64.yaml b/conda/environments/all_cuda-120_arch-x86_64.yaml
@@ -28,7 +28,7 @@ dependencies:
 - nbsphinx
 - ninja
 - numpy>=1.21.3
-- numpydoc
+- numpydoc>=1.5
 - openslide-python>=1.3.0
 - pip
 - pooch>=1.6.0
@@ -40,8 +40,9 @@ dependencies:
 - pytest-xdist
 - pytest>=6.2.4
 - python>=3.8,<3.11
+- pywavelets>=1.0
 - recommonmark
-- scikit-image>=0.19.0,<0.22.0a0
+- scikit-image>=0.19.0,<0.23.0a0
 - scipy
 - sphinx<6
 - sysroot_linux-64==2.17

diff --git a/conda/recipes/cucim/meta.yaml b/conda/recipes/cucim/meta.yaml
@@ -59,7 +59,7 @@ requirements:
     - libcucim ={{ version }}
     - numpy 1.21
     - python
-    - scikit-image >=0.19.0,<0.22.0a0
+    - scikit-image >=0.19.0,<0.23.0a0
     - scipy
   run:
     - {{ pin_compatible('cuda-version', max_pin='x', min_pin='x') }}
@@ -69,7 +69,7 @@ requirements:
     - lazy_loader >=0.1
     - libcucim ={{ version }}
     - python
-    - scikit-image >=0.19.0,<0.22.0a0
+    - scikit-image >=0.19.0,<0.23.0a0
     - scipy
   run_constrained:
     - openslide-python >=1.3.0

diff --git a/dependencies.yaml b/dependencies.yaml
@@ -193,7 +193,7 @@ dependencies:
         packages:
           - ipython
           - nbsphinx
-          - numpydoc
+          - numpydoc>=1.5
           - pydata-sphinx-theme
           - recommonmark
           # TODO: sphinx upper version limit can likely be removed after pydata 0.13
@@ -223,7 +223,7 @@ dependencies:
       - output_types: [conda, requirements, pyproject]
         packages:
           - lazy_loader>=0.1
-          - scikit-image>=0.19.0,<0.22.0a0
+          - scikit-image>=0.19.0,<0.23.0a0
           - scipy
       - output_types: conda
         packages:
@@ -260,6 +260,7 @@ dependencies:
           - pytest-xdist
           - tifffile>=2022.7.28
           - pooch>=1.6.0  # needed to download scikit-image sample data
+          - pywavelets>=1.0
       - output_types: [conda]
         packages:
           - imagecodecs>=2021.6.8
@@ -276,3 +277,7 @@ dependencies:
           - matplotlib
           - opencv-python-headless>=4.6
           - click
+      - output_types: [pyproject]
+        packages:
+          # Already added to requirements via docs. This is for tests.
+          - numpydoc>=1.5
diff --git a/python/cucim/pyproject.toml b/python/cucim/pyproject.toml
@@ -27,7 +27,7 @@ dependencies = [
     "cupy-cuda11x>=12.0.0",
     "lazy_loader>=0.1",
     "numpy",
-    "scikit-image>=0.19.0,<0.22.0a0",
+    "scikit-image>=0.19.0,<0.23.0a0",
     "scipy",
 ] # This list was generated by `rapids-dependency-file-generator`. To make changes, edit ../../dependencies.yaml and run `rapids-dependency-file-generator`.
 classifiers = [
@@ -64,6 +64,7 @@ test = [
     "click",
     "imagecodecs>=2021.6.8; platform_machine=='x86_64'",
     "matplotlib",
+    "numpydoc>=1.5",
     "opencv-python-headless>=4.6",
     "openslide-python>=1.3.0; platform_machine=='x86_64'",
     "pooch>=1.6.0",
@@ -72,6 +73,7 @@ test = [
     "pytest-lazy-fixture>=0.6.3",
     "pytest-xdist",
     "pytest>=6.2.4",
+    "pywavelets>=1.0",
     "tifffile>=2022.7.28",
 ] # This list was generated by `rapids-dependency-file-generator`. To make changes, edit ../../dependencies.yaml and run `rapids-dependency-file-generator`.
 developer = [
@@ -83,7 +85,7 @@ developer = [
 docs = [
     "ipython",
     "nbsphinx",
-    "numpydoc",
+    "numpydoc>=1.5",
     "pydata-sphinx-theme",
     "recommonmark",
     "sphinx<6",

diff --git a/python/cucim/src/cucim/py.typed b/python/cucim/src/cucim/py.typed
diff --git a/python/cucim/src/cucim/skimage/_shared/filters.py b/python/cucim/src/cucim/skimage/_shared/filters.py
@@ -10,26 +10,7 @@
 
 import cucim.skimage._vendored.ndimage as ndi
 
-from .._shared.utils import _supported_float_type, convert_to_float, warn
-
-
-class _PatchClassRepr(type):
-    """Control class representations in rendered signatures."""
-
-    def __repr__(cls):
-        return f"<{cls.__name__}>"
-
-
-class ChannelAxisNotSet(metaclass=_PatchClassRepr):
-    """Signal that the `channel_axis` parameter is not set.
-    This is a proxy object, used to signal to `skimage.filters.gaussian` that
-    the `channel_axis` parameter has not been set, in which case the function
-    will determine whether a color channel is present. We cannot use ``None``
-    for this purpose as it has its own meaning which indicates that the given
-    image is grayscale.
-    This automatic behavior was broken in v0.19, recovered but deprecated in
-    v0.20 and will be removed in v0.21.
-    """
+from .._shared.utils import _supported_float_type, convert_to_float
 
 
 def gaussian(
@@ -41,7 +22,7 @@ def gaussian(
     preserve_range=False,
     truncate=4.0,
     *,
-    channel_axis=ChannelAxisNotSet,
+    channel_axis=None,
 ):
     """Multi-dimensional Gaussian filter.
 
@@ -77,12 +58,10 @@ def gaussian(
         to channels.
 
         .. warning::
-            Automatic detection of the color channel based on the old deprecated
-            ``multichannel=None`` was broken in version 0.19. In 0.20 this
-            behavior is recovered. The last axis of an `image` with dimensions
-            (M, N, 3) is interpreted as a color channel if `channel_axis` is
-            not set. Starting with release 23.04.02, ``channel_axis=None`` will
-            be used as the new default value.
+            In versions prior to 24.02, the last axis of an `image` with
+            dimensions (M, N, 3) was interpreted as a color channel if
+            `channel_axis` was not set. Starting with release 24.02,
+            ``channel_axis=None`` will be used as the new default value.
 
     Returns
     -------
@@ -133,21 +112,7 @@ def gaussian(
     >>> from skimage.data import astronaut
     >>> image = cp.array(astronaut())
     >>> filtered_img = gaussian(image, sigma=1, channel_axis=-1)
-
     """
-    if channel_axis is ChannelAxisNotSet:
-        if image.ndim == 3 and image.shape[-1] == 3:
-            warn(
-                "Automatic detection of the color channel was deprecated in "
-                "v0.19, and `channel_axis=None` will be the new default in "
-                "v0.21. Set `channel_axis=-1` explicitly to silence this "
-                "warning.",
-                FutureWarning,
-                stacklevel=2,
-            )
-            channel_axis = -1
-        else:
-            channel_axis = None
 
     # CuPy Backend: refactor to avoid overhead of cp.any(cp.asarray(sigma))
     sigma_msg = "Sigma values less than zero are not valid"

diff --git a/python/cucim/src/cucim/skimage/_vendored/_internal.py b/python/cucim/src/cucim/skimage/_vendored/_internal.py
@@ -3,7 +3,14 @@
 from operator import mul
 
 import cupy
-import numpy
+
+# TODO: when minimum numpy dependency is 1.25 use:
+# np.exceptions.AxisError instead of AxisError
+# and remove this try-except
+try:
+    from numpy import AxisError
+except ImportError:
+    from numpy.exceptions import AxisError
 
 try:
     # try importing Cython-based private axis handling functions from CuPy
@@ -37,7 +44,7 @@ def _normalize_axis_index(axis, ndim):  # NOQA
         if axis < 0:
             axis += ndim
         if not (0 <= axis < ndim):
-            raise numpy.AxisError("axis out of bounds")
+            raise AxisError("axis out of bounds")
         return axis
 
     def _normalize_axis_indices(axes, ndim):  # NOQA

diff --git a/python/cucim/src/cucim/skimage/color/colorconv.py b/python/cucim/src/cucim/skimage/color/colorconv.py
@@ -63,6 +63,14 @@
 )
 from ..util import dtype, dtype_limits
 
+# TODO: when minimum numpy dependency is 1.25 use:
+# np.exceptions.AxisError instead of AxisError
+# and remove this try-except
+try:
+    from numpy import AxisError
+except ImportError:
+    from numpy.exceptions import AxisError
+
 
 def convert_colorspace(arr, fromspace, tospace, *, channel_axis=-1):
     """Convert an image array to a new color space.
@@ -173,7 +181,7 @@ def _validate_channel_axis(channel_axis, ndim):
     if not isinstance(channel_axis, int):
         raise TypeError("channel_axis must be an integer")
     if channel_axis < -ndim or channel_axis >= ndim:
-        raise np.AxisError("channel_axis exceeds array dimensions")
+        raise AxisError("channel_axis exceeds array dimensions")
 
 
 @cp.memoize(for_each_device=True)

diff --git a/python/cucim/src/cucim/skimage/color/tests/test_colorconv.py b/python/cucim/src/cucim/skimage/color/tests/test_colorconv.py
@@ -63,6 +63,14 @@
 )
 from cucim.skimage.util import img_as_float, img_as_float32, img_as_ubyte
 
+# TODO: when minimum numpy dependency is 1.25 use:
+# np.exceptions.AxisError instead of AxisError
+# and remove this try-except
+try:
+    from numpy import AxisError
+except ImportError:
+    from numpy.exceptions import AxisError
+
 data_dir = os.path.join(os.path.dirname(__file__), "data")
 
 
@@ -133,7 +141,7 @@ def test_rgba2rgb_error_channel_axis_invalid(self, channel_axis):
 
     @pytest.mark.parametrize("channel_axis", [-4, 3])
     def test_rgba2rgb_error_channel_axis_out_of_range(self, channel_axis):
-        with pytest.raises(np.AxisError):
+        with pytest.raises(AxisError):
             rgba2rgb(self.img_rgba, channel_axis=channel_axis)
 
     def test_rgba2rgb_error_rgb(self):

diff --git a/python/cucim/src/cucim/skimage/feature/__init__.py b/python/cucim/src/cucim/skimage/feature/__init__.py
@@ -1,48 +1,3 @@
-from ._basic_features import multiscale_basic_features
-from ._canny import canny
-from ._daisy import daisy
-from .blob import blob_dog, blob_doh, blob_log
-from .corner import (
-    corner_foerstner,
-    corner_harris,
-    corner_kitchen_rosenfeld,
-    corner_peaks,
-    corner_shi_tomasi,
-    hessian_matrix,
-    hessian_matrix_det,
-    hessian_matrix_eigvals,
-    shape_index,
-    structure_tensor,
-    structure_tensor_eigenvalues,
-)
-from .match import match_descriptors
-from .peak import peak_local_max
-from .template import match_template
+import lazy_loader as lazy
 
-__all__ = [
-    "canny",
-    "daisy",
-    "multiscale_basic_features",
-    "peak_local_max",
-    "structure_tensor",
-    "structure_tensor_eigenvalues",
-    "structure_tensor_eigvals",
-    "hessian_matrix",
-    "hessian_matrix_det",
-    "hessian_matrix_eigvals",
-    "shape_index",
-    "corner_kitchen_rosenfeld",
-    "corner_harris",
-    "corner_shi_tomasi",
-    "corner_foerstner",
-    # 'corner_subpix',
-    "corner_peaks",
-    # 'corner_moravec',
-    # 'corner_fast',
-    # 'corner_orientations',
-    "match_template",
-    "match_descriptors",
-    "blob_dog",
-    "blob_log",
-    "blob_doh",
-]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)
diff --git a/python/cucim/src/cucim/skimage/feature/__init__.pyi b/python/cucim/src/cucim/skimage/feature/__init__.pyi
@@ -0,0 +1,47 @@
+# Explicitly setting `__all__` is necessary for type inference engines
+# to know which symbols are exported. See
+# https://peps.python.org/pep-0484/#stub-files
+
+__all__ = [
+    "canny",
+    "daisy",
+    "peak_local_max",
+    "structure_tensor",
+    "structure_tensor_eigenvalues",
+    "hessian_matrix",
+    "hessian_matrix_det",
+    "hessian_matrix_eigvals",
+    "shape_index",
+    "corner_kitchen_rosenfeld",
+    "corner_harris",
+    "corner_shi_tomasi",
+    "corner_foerstner",
+    "corner_peaks",
+    "match_template",
+    "match_descriptors",
+    "blob_dog",
+    "blob_doh",
+    "blob_log",
+    "multiscale_basic_features",
+]
+
+from ._basic_features import multiscale_basic_features
+from ._canny import canny
+from ._daisy import daisy
+from .blob import blob_dog, blob_doh, blob_log
+from .corner import (
+    corner_foerstner,
+    corner_harris,
+    corner_kitchen_rosenfeld,
+    corner_peaks,
+    corner_shi_tomasi,
+    hessian_matrix,
+    hessian_matrix_det,
+    hessian_matrix_eigvals,
+    shape_index,
+    structure_tensor,
+    structure_tensor_eigenvalues,
+)
+from .match import match_descriptors
+from .peak import peak_local_max
+from .template import match_template
diff --git a/python/cucim/src/cucim/skimage/feature/peak.py b/python/cucim/src/cucim/skimage/feature/peak.py
@@ -23,7 +23,7 @@ def _get_high_intensity_peaks(image, mask, num_peaks, min_distance, p_norm):
     coord = cp.nonzero(mask)
     intensities = image[coord]
     # Highest peak first
-    idx_maxsort = cp.argsort(-intensities)
+    idx_maxsort = cp.argsort(-intensities, kind="stable")
     coord = cp.column_stack(coord)[idx_maxsort]
 
     if np.isfinite(num_peaks):