remove unimplemented functions from See Also and fix version numbers in deprecation warnings

python/cucim/src/cucim/skimage/_shared/tests/test_utils.py

@@ -66,13 +66,13 @@ def bar(arg0, arg1=0, arg2=1):
 
 def test_deprecate_kwarg():
 
-    @deprecate_kwarg({'old_arg1': 'new_arg1'}, '0.19')
+    @deprecate_kwarg({'old_arg1': 'new_arg1'}, '22.02.00')
     def foo(arg0, new_arg1=1, arg2=None):
         """Expected docstring"""
         return arg0, new_arg1, arg2
 
     @deprecate_kwarg({'old_arg1': 'new_arg1'},
-                     deprecated_version='0.19',
+                     deprecated_version='22.02.00',
                      warning_msg="Custom warning message")
     def bar(arg0, new_arg1=1, arg2=None):
         """Expected docstring"""
@@ -116,7 +116,7 @@ def bar(arg0, new_arg1=1, arg2=None):
     old_arg1 : DEPRECATED
         Deprecated in favor of `new_arg1`.
 
-        .. deprecated:: 0.19
+        .. deprecated:: 22.02.00
 """
 
     assert len(recorded) == 0

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

@@ -95,10 +95,11 @@ def __call__(self, func):
         parameters = inspect.signature(func).parameters
         arg_idx = list(parameters.keys()).index(self.arg_name)
         warning_msg = (
-            f"{self.arg_name} argument is deprecated and will be removed "
-            f"in version {self.changed_version}. To avoid this warning, "
-            f"please do not use the {self.arg_name} argument. Please "
-            f"see {func.__name__} documentation for more details.")
+            f"{self.arg_name} argument is deprecated in upstream scikit-image "
+            f"and will be removed in cuCIM {self.changed_version}. To avoid "
+            f"this warning, please do not use the {self.arg_name} argument. "
+            f"Please see {func.__name__} documentation for more details."
+        )
 
         if self.help_msg is not None:
             warning_msg += f" {self.help_msg}"
@@ -206,7 +207,7 @@ def __init__(self, kwarg_mapping, deprecated_version, warning_msg=None,
             self.warning_msg = ("`{old_arg}` is a deprecated argument name "
                                 "for `{func_name}`. ")
             if removed_version is not None:
-                self.warning_msg += (f'It will be removed in '
+                self.warning_msg += (f'It will be removed in cuCIM '
                                      f'version {removed_version}.')
             self.warning_msg += "Please use `{new_arg}` instead."
         else:
@@ -248,10 +249,11 @@ class deprecate_multichannel_kwarg(deprecate_kwarg):
 
     """
 
-    def __init__(self, removed_version='1.0', multichannel_position=None):
+    def __init__(self, removed_version='2023.02.00',
+                 multichannel_position=None):
         super().__init__(
             kwarg_mapping={'multichannel': 'channel_axis'},
-            deprecated_version='0.19',
+            deprecated_version='22.02.00',
             warning_msg=None,
             removed_version=removed_version)
         self.position = multichannel_position
@@ -293,7 +295,7 @@ def fixed_func(*args, **kwargs):
 
         if func.__doc__ is not None:
             newdoc = docstring_add_deprecated(
-                func, {'multichannel': 'channel_axis'}, '0.19')
+                func, {'multichannel': 'channel_axis'}, '22.02.00')
             fixed_func.__doc__ = newdoc
         return fixed_func
 

python/cucim/src/cucim/skimage/_vendored/signaltools.py

@@ -424,7 +424,7 @@ def choose_conv_method(in1, in2, mode="full", measure=False):
     returns `direct` (e.g., to protect against floating point integer
     precision).
 
-    .. versionadded:: 0.19
+    .. versionadded:: 22.02.00
 
     Examples
     --------

python/cucim/src/cucim/skimage/exposure/tests/test_exposure.py

@@ -297,11 +297,7 @@ def test_rescale_in_range_clip():
 def test_rescale_out_range(dtype):
     """Check that output range is correct.
 
-    .. versionchanged:: 0.17
-        This function used to return dtype matching the input dtype. It now
-        matches the output.
-
-    .. versionchanged:: 0.19
+    .. versionchanged:: 22.02.00
         float16 and float32 inputs now result in float32 output. Formerly they
         would give float64 outputs.
     """

python/cucim/src/cucim/skimage/filters/_median.py

@@ -6,8 +6,9 @@
 from .._shared.utils import deprecate_kwarg
 
 
-@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'}, removed_version="1.0",
-                 deprecated_version="0.19")
+@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'},
+                 removed_version="23.02.00",
+                 deprecated_version="22.02.00")
 def median(image, footprint=None, out=None, mode='nearest', cval=0.0,
            behavior='ndimage'):
     """Return local median of an image.

python/cucim/src/cucim/skimage/filters/thresholding.py

@@ -735,8 +735,8 @@ def threshold_li(image, *, tolerance=None, initial_guess=None,
     return threshold
 
 
-@deprecate_kwarg({'max_iter': 'max_num_iter'}, removed_version="1.0",
-                 deprecated_version="0.19")
+@deprecate_kwarg({'max_iter': 'max_num_iter'}, removed_version="23.02.00",
+                 deprecated_version="22.02.00")
 def threshold_minimum(image=None, nbins=256, max_num_iter=10000, *, hist=None):
     """Return threshold value based on minimum method.
 

python/cucim/src/cucim/skimage/measure/_label.py

@@ -16,8 +16,8 @@ def _get_structure(ndim, connectivity):
 
 # TODO: currently uses int32 for the labels. should add int64 option as well
 @deprecate_kwarg({'input': 'label_image'},
-                 deprecated_version='0.19',
-                 removed_version='1.0')
+                 deprecated_version='22.02.00',
+                 removed_version='23.02.00')
 def label(label_image, background=None, return_num=False, connectivity=None):
     r"""Label connected regions of an integer array.
 

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

@@ -39,8 +39,8 @@
                        0, 0, 0, 0, 0, 0, 0, 0, 0], dtype=bool)
 
 
-@deprecate_kwarg({'max_iter': 'max_num_iter'}, removed_version="1.0",
-                 deprecated_version="0.19")
+@deprecate_kwarg({'max_iter': 'max_num_iter'}, removed_version="23.02.00",
+                 deprecated_version="22.02.00")
 def thin(image, max_num_iter=None):
     """
     Perform morphological thinning of a binary image.
@@ -62,7 +62,7 @@ def thin(image, max_num_iter=None):
 
     See Also
     --------
-    skeletonize, medial_axis
+    medial_axis
 
     Notes
     -----

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

@@ -37,8 +37,9 @@ def _iterate_binary_func(binary_func, image, footprint, out):
 # default with the same dimension as the input image and size 3 along each
 # axis.
 @default_footprint
-@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'}, removed_version="1.0",
-                 deprecated_version="0.19")
+@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'},
+                 removed_version="23.02.00",
+                 deprecated_version="22.02.00")
 def binary_erosion(image, footprint=None, out=None):
     """Return fast binary morphological erosion of an image.
 
@@ -94,8 +95,9 @@ def binary_erosion(image, footprint=None, out=None):
 
 
 @default_footprint
-@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'}, removed_version="1.0",
-                 deprecated_version="0.19")
+@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'},
+                 removed_version="23.02.00",
+                 deprecated_version="22.02.00")
 def binary_dilation(image, footprint=None, out=None):
     """Return fast binary morphological dilation of an image.
 
@@ -149,8 +151,9 @@ def binary_dilation(image, footprint=None, out=None):
 
 
 @default_footprint
-@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'}, removed_version="1.0",
-                 deprecated_version="0.19")
+@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'},
+                 removed_version="23.02.00",
+                 deprecated_version="22.02.00")
 def binary_opening(image, footprint=None, out=None):
     """Return fast binary morphological opening of an image.
 
@@ -199,8 +202,9 @@ def binary_opening(image, footprint=None, out=None):
 
 
 @default_footprint
-@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'}, removed_version="1.0",
-                 deprecated_version="0.19")
+@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'},
+                 removed_version="23.02.00",
+                 deprecated_version="22.02.00")
 def binary_closing(image, footprint=None, out=None):
     """Return fast binary morphological closing of an image.
 

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

@@ -175,8 +175,8 @@ def _decompose_size(size, kernel_size=3):
 
 
 @deprecate_kwarg({'height': 'ncols', 'width': 'nrows'},
-                 deprecated_version='0.18.0',
-                 removed_version='0.20.0')
+                 deprecated_version='21.06.00',
+                 removed_version='22.02.00')
 def rectangle(nrows, ncols, dtype=cp.uint8, *, decomposition=None):
     """Generates a flat, rectangular-shaped footprint.
 

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

@@ -157,8 +157,8 @@ def func_out(image, footprint, out=None, *args, **kwargs):
 
 
 @default_footprint
-@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'}, removed_version="1.0",
-                 deprecated_version="0.19")
+@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'},
+                 removed_version="23.02.00", deprecated_version="22.02.00")
 def erosion(image, footprint=None, out=None, shift_x=False, shift_y=False):
     """Return grayscale morphological erosion of an image.
 
@@ -236,8 +236,8 @@ def erosion(image, footprint=None, out=None, shift_x=False, shift_y=False):
 
 
 @default_footprint
-@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'}, removed_version="1.0",
-                 deprecated_version="0.19")
+@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'},
+                 removed_version="23.02.00", deprecated_version="22.02.00")
 def dilation(image, footprint=None, out=None, shift_x=False, shift_y=False):
     """Return grayscale morphological dilation of an image.
 
@@ -324,8 +324,8 @@ def dilation(image, footprint=None, out=None, shift_x=False, shift_y=False):
     return out
 
 
-@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'}, removed_version="1.0",
-                 deprecated_version="0.19")
+@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'},
+                 removed_version="23.02.00", deprecated_version="22.02.00")
 @default_footprint
 @pad_for_eccentric_footprints
 def opening(image, footprint=None, out=None):
@@ -390,8 +390,8 @@ def opening(image, footprint=None, out=None):
     return out
 
 
-@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'}, removed_version="1.0",
-                 deprecated_version="0.19")
+@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'},
+                 removed_version="23.02.00", deprecated_version="22.02.00")
 @default_footprint
 @pad_for_eccentric_footprints
 def closing(image, footprint=None, out=None):
@@ -474,8 +474,8 @@ def _white_tophat_seqence(image, footprints, out):
 
 
 @default_footprint
-@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'}, removed_version="1.0",
-                 deprecated_version="0.19")
+@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'},
+                 removed_version="23.02.00", deprecated_version="22.02.00")
 def white_tophat(image, footprint=None, out=None):
     """Return white top hat of an image.
 
@@ -565,8 +565,8 @@ def white_tophat(image, footprint=None, out=None):
 
 
 @default_footprint
-@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'}, removed_version="1.0",
-                 deprecated_version="0.19")
+@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'},
+                 removed_version="23.02.00", deprecated_version="22.02.00")
 def black_tophat(image, footprint=None, out=None):
     """Return black top hat of an image.
 

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

@@ -15,8 +15,8 @@
 from .._shared.utils import deprecate_kwarg
 
 
-@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'}, removed_version="1.0",
-                 deprecated_version="0.19")
+@deprecate_kwarg(kwarg_mapping={'selem': 'footprint'},
+                 removed_version="23.02.00", deprecated_version="22.02.00")
 def reconstruction(seed, mask, method='dilation', footprint=None, offset=None):
     """Perform a morphological reconstruction of an image.
 

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

@@ -73,7 +73,7 @@ def remove_small_objects(ar, min_size=64, connectivity=1, in_place=False,
         labelling if `ar` is bool.
     in_place : bool, optional (default: False)
         If ``True``, remove the objects in the input array itself.
-        Otherwise, make a copy. Deprecated since version 0.19. Please
+        Otherwise, make a copy. Deprecated since version 22.02.00. Please
         use `out` instead.
     out : ndarray
         Array of the same shape as `ar`, into which the output is
@@ -172,7 +172,7 @@ def remove_small_holes(ar, area_threshold=64, connectivity=1, in_place=False,
         The connectivity defining the neighborhood of a pixel.
     in_place : bool, optional (default: False)
         If `True`, remove the connected components in the input array
-        itself. Otherwise, make a copy. Deprecated since version 0.19.
+        itself. Otherwise, make a copy. Deprecated since version 22.02.00.
         Please use `out` instead.
     out : ndarray
         Array of the same shape as `ar` and bool dtype, into which the

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

@@ -91,8 +91,9 @@ def _denoise_tv_chambolle_nd(image, weight=0.1, eps=2.0e-4, max_num_iter=200):
     return out
 
 
-@utils.deprecate_kwarg({'n_iter_max': 'max_num_iter'}, removed_version="1.0",
-                       deprecated_version="0.19.2")
+@utils.deprecate_kwarg({'n_iter_max': 'max_num_iter'},
+                       removed_version="23.02.00",
+                       deprecated_version="22.06.00")
 @utils.deprecate_multichannel_kwarg(multichannel_position=4)
 def denoise_tv_chambolle(image, weight=0.1, eps=2.0e-4, max_num_iter=200,
                          multichannel=False, *, channel_axis=None):

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

@@ -383,8 +383,8 @@ def unsupervised_wiener(image, psf, reg=None, user_params=None, is_real=True,
     return (x_postmean, {'noise': gn_chain, 'prior': gx_chain})
 
 
-@deprecate_kwarg({'iterations': 'num_iter'}, removed_version="1.0",
-                 deprecated_version="0.19")
+@deprecate_kwarg({'iterations': 'num_iter'}, removed_version="23.02.00",
+                 deprecated_version="22.02.00")
 def richardson_lucy(image, psf, num_iter=50, clip=True, filter_epsilon=None):
     """Richardson-Lucy deconvolution.
 

python/cucim/src/cucim/skimage/restoration/tests/test_j_invariant.py

@@ -25,7 +25,7 @@
 # TODO: replace with CuPy version once completed
 def _denoise_wavelet(image, rescale_sigma=True, **kwargs):
 
-    if 'channel_axis' in kwargs and skimage.__version__ < '0.19':
+    if 'channel_axis' in kwargs and skimage.__version__ < '22.02.00':
         # convert channel_axis to older multichannel kwarg for skimage 0.18.x
         channel_axis = kwargs.pop('channel_axis')
         kwargs['multichannel'] = False if channel_axis is None else True
@@ -62,7 +62,7 @@ def test_invariant_denoise_color(dtype):
 
 def test_invariant_denoise_color_deprecated():
 
-    # can remove \A\Z here if only testing with scikit-image 0.19
+    # can remove \A\Z here if only testing with cuCIM 22.02.00
     with expected_warnings([r"`multichannel` is a deprecated argument|\A\Z"]):
         denoised_img_color = _invariant_denoise(
             noisy_img_color, _denoise_wavelet,

python/cucim/src/cucim/skimage/segmentation/morphsnakes.py

@@ -219,8 +219,9 @@ def inverse_gaussian_gradient(image, alpha=100.0, sigma=5.0):
     return 1.0 / cp.sqrt(1.0 + alpha * gradnorm)
 
 
-@deprecate_kwarg({'iterations': 'num_iter'}, removed_version="1.0",
-                 deprecated_version="0.19")
+@deprecate_kwarg({'iterations': 'num_iter'},
+                 removed_version="23.02.00",
+                 deprecated_version="22.02.00")
 def morphological_chan_vese(image, num_iter, init_level_set='checkerboard',
                             smoothing=1, lambda1=1, lambda2=1,
                             iter_callback=lambda x: None):
@@ -326,8 +327,9 @@ def morphological_chan_vese(image, num_iter, init_level_set='checkerboard',
     return u
 
 
-@deprecate_kwarg({'iterations': 'num_iter'}, removed_version="1.0",
-                 deprecated_version="0.19")
+@deprecate_kwarg({'iterations': 'num_iter'},
+                 removed_version="23.02.00",
+                 deprecated_version="22.02.00")
 def morphological_geodesic_active_contour(gimage, num_iter,
                                           init_level_set='disk', smoothing=1,
                                           threshold='auto', balloon=0,

python/cucim/src/cucim/skimage/segmentation/random_walker_segmentation.py

@@ -343,12 +343,6 @@ def random_walker(data, labels, beta=130, mode='cg_j', tol=1.e-3, copy=True,
           probability that label `label_nb` reaches the pixel `(i, j)`
           first.
 
-    See Also
-    --------
-    skimage.morphology.watershed : watershed segmentation
-        A segmentation algorithm based on mathematical morphology
-        and "flooding" of regions from markers.
-
     Notes
     -----
     Multichannel inputs are scaled with all channel data combined. Ensure all