Standardize on rng over seed and fix miscellaneous deprecation wa…

…rnings (#621)

This PR fixes the following warnings observed when running the test suite:

```
src/cucim/core/operations/morphology/tests/test_distance_transform.py: 90 warnings
  /pyenv/versions/3.9.18/lib/python3.9/site-packages/cucim/core/operations/morphology/_distance_transform.py:160: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
    scalar_sampling = float(unique_sampling)
```

```
 src/cucim/skimage/feature/tests/test_corner.py::test_custom_eigvals_kernels_vs_linalg_eigvalsh[float64-shape2]
  /__w/cucim/cucim/python/cucim/src/cucim/skimage/feature/tests/test_corner.py:345: FutureWarning: use_gaussian_derivatives currently defaults to False, but will change to True in a future version. Please specify this argument explicitly to maintain the current behavior
    H = hessian_matrix(img)
```

```
 src/cucim/skimage/morphology/tests/test_binary.py: 148 warnings
  /__w/cucim/cucim/python/cucim/src/cucim/skimage/morphology/tests/test_binary.py:68: FutureWarning: `seed` is a deprecated argument name for `binary_blobs`. It will be removed in version 0.23. Please use `rng` instead.
    img = cp.asarray(data.binary_blobs(32, n_dim=ndim, seed=1))
```

Authors:
  - Gregory Lee (https://github.com/grlee77)

Approvers:
  - Gigon Bae (https://github.com/gigony)
  - https://github.com/jakirkham

URL: #621

benchmarks/skimage/cucim_metrics_bench.py

@@ -51,10 +51,10 @@ def __init__(
             run_cpu=run_cpu,
         )
 
-    def _generate_labels(self, dtype, seed=5):
+    def _generate_labels(self, dtype, rng=5):
         ndim = len(self.shape)
         blobs_kwargs = dict(
-            blob_size_fraction=0.05, volume_fraction=0.35, seed=seed
+            blob_size_fraction=0.05, volume_fraction=0.35, rng=rng
         )
         # binary blobs only creates square outputs
         labels = measure.label(
@@ -67,8 +67,8 @@ def _generate_labels(self, dtype, seed=5):
         return labels.astype(dtype, copy=False)
 
     def set_args(self, dtype):
-        labels1_d = self._generate_labels(dtype, seed=5)
-        labels2_d = self._generate_labels(dtype, seed=3)
+        labels1_d = self._generate_labels(dtype, rng=5)
+        labels2_d = self._generate_labels(dtype, rng=3)
         labels1 = cp.asnumpy(labels1_d)
         labels2 = cp.asnumpy(labels2_d)
         self.args_cpu = (labels1, labels2)

benchmarks/skimage/cucim_segmentation_bench.py

@@ -42,7 +42,7 @@ def __init__(
     def _generate_labels(self, dtype):
         ndim = len(self.shape)
         blobs_kwargs = dict(
-            blob_size_fraction=0.05, volume_fraction=0.35, seed=5
+            blob_size_fraction=0.05, volume_fraction=0.35, rng=5
         )
         # binary blobs only creates square outputs
         labels = measure.label(
@@ -107,7 +107,7 @@ def set_args(self, dtype):
         n_dim = len(self.shape)
         data = cucim.skimage.img_as_float(
             cucim.skimage.data.binary_blobs(
-                length=max(self.shape), n_dim=n_dim, seed=1
+                length=max(self.shape), n_dim=n_dim, rng=1
             )
         )
         data = data[tuple(slice(s) for s in self.shape)]

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

@@ -1,4 +1,4 @@
-import numpy as np
+import cupy as cp
 
 from ._pba_2d import _pba_2d
 from ._pba_3d import _pba_3d
@@ -153,7 +153,7 @@ def distance_transform_edt(
     """
     scalar_sampling = None
     if sampling is not None:
-        unique_sampling = np.unique(np.atleast_1d(sampling))
+        unique_sampling = cp.unique(cp.atleast_1d(sampling))
         if len(unique_sampling) == 1:
             # In the isotropic case, can use the kernels without sample scaling
             # and just adjust the final distance accordingly.

python/cucim/src/cucim/skimage/_shared/utils.py

@@ -638,8 +638,7 @@ def check_random_state(seed):
     if isinstance(seed, cp.random.RandomState):
         return seed
     raise ValueError(
-        "%r cannot be used to seed a numpy.random.RandomState"
-        " instance" % seed
+        f"{seed} cannot be used to seed a cupy.random.RandomState instance"
     )
 
 

python/cucim/src/cucim/skimage/data/_binary_blobs.py

@@ -1,8 +1,14 @@
 import cupy as cp
 
+from .._shared.filters import gaussian
+from .._shared.utils import deprecate_kwarg
 
+
+@deprecate_kwarg(
+    {"seed": "rng"}, deprecated_version="23.12.00", removed_version="24.12.00"
+)
 def binary_blobs(
-    length=512, blob_size_fraction=0.1, n_dim=2, volume_fraction=0.5, seed=None
+    length=512, blob_size_fraction=0.1, n_dim=2, volume_fraction=0.5, rng=None
 ):
     """
     Generate synthetic binary image with several rounded blob-like objects.
@@ -19,12 +25,10 @@ def binary_blobs(
     volume_fraction : float, default 0.5
         Fraction of image pixels covered by the blobs (where the output is 1).
         Should be in [0, 1].
-    seed : {None, int, `cupy.random.Generator`}, optional
-        If `seed` is None the `cupy.random.Generator` singleton is used.
-        If `seed` is an int, a new ``Generator`` instance is used,
-        seeded with `seed`.
-        If `seed` is already a ``Generator`` instance then that instance is
-        used.
+    rng : {`cupy.random.Generator`, int}, optional
+        Pseudo-random number generator.
+        By default, a PCG64 generator is used (see :func:`cupy.random.default_rng`).
+        If `rng` is an int, it is used to seed the generator.
 
     Returns
     -------
@@ -34,7 +38,7 @@ def binary_blobs(
     Notes
     -----
     Warning: CuPy does not give identical randomly generated numbers as NumPy,
-    so using a specific seed here will not give an identical pattern to the
+    so using a specific `rng` here will not give an identical pattern to the
     scikit-image implementation.
 
     The behavior for a given random seed may also change across CuPy major
@@ -45,19 +49,16 @@ def binary_blobs(
     --------
     >>> from cucim.skimage import data
     >>> # tiny size (5, 5)
-    >>> blobs = data.binary_blobs(length=5, blob_size_fraction=0.2, seed=1)
+    >>> blobs = data.binary_blobs(length=5, blob_size_fraction=0.2)
     >>> # larger size
     >>> blobs = data.binary_blobs(length=256, blob_size_fraction=0.1)
     >>> # Finer structures
     >>> blobs = data.binary_blobs(length=256, blob_size_fraction=0.05)
     >>> # Blobs cover a smaller volume fraction of the image
     >>> blobs = data.binary_blobs(length=256, volume_fraction=0.3)
-    """
-    # filters is quite an expensive import since it imports all of scipy.signal
-    # We lazy import here
-    from .._shared.filters import gaussian
+    """  # noqa: E501
 
-    rs = cp.random.default_rng(seed)
+    rs = cp.random.default_rng(rng)
     shape = tuple([length] * n_dim)
     mask = cp.zeros(shape)
     n_pts = max(int(1.0 / blob_size_fraction) ** n_dim, 1)

python/cucim/src/cucim/skimage/data/tests/test_data.py

@@ -1,4 +1,5 @@
 import cupy as cp
+import pytest
 from numpy.testing import assert_almost_equal
 
 from cucim.skimage import data
@@ -15,3 +16,8 @@ def test_binary_blobs():
         length=32, volume_fraction=0.25, n_dim=3
     )
     assert not cp.all(blobs == other_realization)
+
+
+def test_binary_blobs_futurewarning():
+    with pytest.warns(FutureWarning):
+        data.binary_blobs(length=128, seed=5)

python/cucim/src/cucim/skimage/feature/tests/test_corner.py

@@ -342,7 +342,7 @@ def _reference_eigvals_computation(S_elems):
 def test_custom_eigvals_kernels_vs_linalg_eigvalsh(shape, dtype):
     rng = cp.random.default_rng(seed=5)
     img = rng.integers(0, 256, shape)
-    H = hessian_matrix(img)
+    H = hessian_matrix(img, use_gaussian_derivatives=False)
     H = tuple(h.astype(dtype, copy=False) for h in H)
     evs1 = _reference_eigvals_computation(H)
     evs2 = hessian_matrix_eigvals(H)
@@ -492,8 +492,8 @@ def test_corner_foerstner_dtype(dtype):
 def test_noisy_square_image():
     im = cp.zeros((50, 50)).astype(float)
     im[:25, :25] = 1.0
-    np.random.seed(seed=1234)  # result is specific to this NumPy seed
-    im = im + cp.asarray(np.random.uniform(size=im.shape)) * 0.2
+    rng = np.random.default_rng(1234)  # result is specific to this NumPy seed
+    im = im + cp.asarray(rng.uniform(size=im.shape)) * 0.2
 
     # # Moravec
     # results = peak_local_max(corner_moravec(im),

python/cucim/src/cucim/skimage/filters/tests/test_edges.py

@@ -640,7 +640,7 @@ def test_vertical_mask_line(grad_func):
     ],
 )
 def test_3d_edge_filters(func, max_edge):
-    blobs = binary_blobs(length=128, n_dim=3, seed=5)
+    blobs = binary_blobs(length=128, n_dim=3, rng=5)
     edges = func(blobs)
     center = max_edge.shape[0] // 2
     if center == 2:
@@ -663,7 +663,7 @@ def test_3d_edge_filters(func, max_edge):
     ],
 )
 def test_3d_edge_filters_single_axis(func, max_edge):
-    blobs = binary_blobs(length=128, n_dim=3, seed=5)
+    blobs = binary_blobs(length=128, n_dim=3, rng=5)
     edges0 = func(blobs, axis=0)
     center = max_edge.shape[0] // 2
     if center == 2:

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

@@ -171,11 +171,14 @@ def _get_tiebreaker(n, seed):
 
 
 @deprecate_kwarg(
-    {"random_state": "seed"},
+    {"random_state": "rng"},
     deprecated_version="23.08",
     removed_version="24.06",
 )
-def medial_axis(image, mask=None, return_distance=False, *, seed=None):
+@deprecate_kwarg(
+    {"seed": "rng"}, deprecated_version="23.12", removed_version="24.12"
+)
+def medial_axis(image, mask=None, return_distance=False, *, rng=None):
     """Compute the medial axis transform of a binary image.
 
     Parameters
@@ -187,14 +190,17 @@ def medial_axis(image, mask=None, return_distance=False, *, seed=None):
         value in `mask` are used for computing the medial axis.
     return_distance : bool, optional
         If true, the distance transform is returned as well as the skeleton.
-    seed : {None, int, `numpy.random.Generator`}, optional
-        If `seed` is None, the `numpy.random.Generator` singleton is used.
-        If `seed` is an int, a new ``Generator`` instance is used, seeded with
-        `seed`.
-        If `seed` is already a ``Generator`` instance, then that instance is
-        used.
+    rng : {`numpy.random.Generator`, int}, optional
+        Pseudo-random number generator.
+        By default, a PCG64 generator is used
+        (see :func:`numpy.random.default_rng`).
+        If `rng` is an int, it is used to seed the generator.
+
+        The PRNG determines the order in which pixels are processed for
+        tiebreaking.
 
-        .. versionadded:: 0.19
+        Note: Due to a missing `permute` method on CuPy's random Generator
+        class, only a `numpy.random.Generator` is currently supported.
 
     Returns
     -------
@@ -304,7 +310,16 @@ def medial_axis(image, mask=None, return_distance=False, *, seed=None):
     # We use a random # for tiebreaking. Assign each pixel in the image a
     # predictable, random # so that masking doesn't affect arbitrary choices
     # of skeletons
-    tiebreaker = _get_tiebreaker(n=distance.size, seed=seed)
+
+    if rng is None or isinstance(rng, int):
+        tiebreaker = _get_tiebreaker(n=distance.size, seed=rng)
+    elif isinstance(rng, np.random.Generator):
+        generator = np.random.default_rng(rng)
+        tiebreaker = cp.asarray(generator.permutation(np.arange(distance.size)))
+    else:
+        raise ValueError(
+            f"{type(rng)} class not yet supported for use in " "`medial_axis`."
+        )
     order = cp.lexsort(
         cp.stack((tiebreaker, corner_score[masked_image], distance), axis=0)
     )

python/cucim/src/cucim/skimage/morphology/tests/test_binary.py

@@ -65,7 +65,7 @@ def _get_decomp_test_data(function, ndim=2):
         img = cp.zeros((17,) * ndim, dtype=cp.uint8)
         img[(8,) * ndim] = 1
     else:
-        img = cp.asarray(data.binary_blobs(32, n_dim=ndim, seed=1))
+        img = cp.asarray(data.binary_blobs(32, n_dim=ndim, rng=1))
     return img
 
 

python/cucim/src/cucim/skimage/morphology/tests/test_skeletonize.py

@@ -1,4 +1,5 @@
 import cupy as cp
+import numpy as np
 import pytest
 from cupy.testing import assert_array_equal
 from skimage import data
@@ -93,7 +94,7 @@ def test_00_01_zeros_masked(self):
         result = medial_axis(cp.zeros((10, 10), bool), cp.zeros((10, 10), bool))
         assert not cp.any(result)
 
-    def test_vertical_line(self):
+    def _test_vertical_line(self, **kwargs):
         """Test a thick vertical line, issue #3861"""
         img = cp.zeros((9, 9))
         img[:, 2] = 1
@@ -103,9 +104,35 @@ def test_vertical_line(self):
         expected = cp.full(img.shape, False)
         expected[:, 3] = True
 
-        result = medial_axis(img)
+        result = medial_axis(img, **kwargs)
         assert_array_equal(result, expected)
 
+    def test_vertical_line(self):
+        """Test a thick vertical line, issue #3861"""
+        self._test_vertical_line()
+
+    def test_rng_numpy(self):
+        # NumPy Generator allowed
+        self._test_vertical_line(rng=np.random.default_rng())
+
+    def test_rng_cupy(self):
+        # CuPy Generator not currently supported
+        with pytest.raises(ValueError):
+            self._test_vertical_line(rng=cp.random.default_rng())
+
+    def test_rng_int(self):
+        self._test_vertical_line(rng=15)
+
+    def test_vertical_line_seed(self):
+        """seed was deprecated (now use rng)"""
+        with pytest.warns(FutureWarning):
+            self._test_vertical_line(seed=15)
+
+    def test_vertical_line_random_state(self):
+        """random_state was deprecated (now use rng)"""
+        with pytest.warns(FutureWarning):
+            self._test_vertical_line(random_state=15)
+
     def test_01_01_rectangle(self):
         """Test skeletonize on a rectangle"""
         image = cp.zeros((9, 15), bool)

python/cucim/src/cucim/skimage/restoration/deconvolution.py

@@ -148,10 +148,15 @@ def wiener(image, psf, balance, reg=None, is_real=True, clip=True):
 
 
 @deprecate_kwarg(
-    {"random_state": "seed"},
+    {"random_state": "rng"},
     removed_version="23.08.00",
     deprecated_version="24.06.00",
 )
+@deprecate_kwarg(
+    {"seed": "rng"},
+    removed_version="23.08.00",
+    deprecated_version="24.12.00",
+)
 def unsupervised_wiener(
     image,
     psf,
@@ -160,7 +165,7 @@ def unsupervised_wiener(
     is_real=True,
     clip=True,
     *,
-    seed=None,
+    rng=None,
 ):
     """Unsupervised Wiener-Hunt deconvolution.
 
@@ -186,12 +191,11 @@ def unsupervised_wiener(
     clip : boolean, optional
        True by default. If true, pixel values of the result above 1 or
        under -1 are thresholded for skimage pipeline compatibility.
-    seed : {None, int, `numpy.random.Generator`}, optional
-        If `seed` is None, the `numpy.random.Generator` singleton is used.
-        If `seed` is an int, a new ``Generator`` instance is used, seeded with
-        `seed`.
-        If `seed` is already a ``Generator`` instance, then that instance is
-        used.
+    rng : {`cupy.random.Generator`, int}, optional
+        Pseudo-random number generator.
+        By default, a PCG64 generator is used
+        (see :func:`cupy.random.default_rng`).
+        If `rng` is an int, it is used to seed the generator.
 
     Returns
     -------
@@ -233,7 +237,8 @@ def unsupervised_wiener(
     >>> img = color.rgb2gray(cp.array(data.astronaut()))
     >>> psf = cp.ones((5, 5)) / 25
     >>> img = ndi.uniform_filter(img, size=psf.shape)
-    >>> img += 0.1 * img.std() * cp.random.standard_normal(img.shape)
+    >>> rng = cp.random.default_rng()
+    >>> img += 0.1 * img.std() * rng.standard_normal(img.shape)
     >>> deconvolved_img = restoration.unsupervised_wiener(img, psf)
 
     Notes
@@ -321,11 +326,7 @@ def unsupervised_wiener(
     else:
         data_spectrum = uft.ufft2(image)
 
-    try:
-        rng = cp.random.default_rng(seed)
-    except AttributeError:
-        # older CuPy without default_rng
-        rng = cp.random.RandomState(seed)
+    rng = cp.random.default_rng(rng)
 
     # Gibbs sampling
     for iteration in range(params["max_num_iter"]):