Merge pull request soft-matter#457 from tacaswell/mnt/np2_compat

MNT: numpy2 compatibility

.github/workflows/tests.yaml

@@ -12,7 +12,7 @@ jobs:
  runs-on: ubuntu-latest
  strategy:
  matrix:
- python-version: ['3.7', '3.8', '3.9', '3.10']
+ python-version: ['3.9', '3.10', "3.11", "3.12"]
  optional-deps: ['no-extras', 'extras']
  fail-fast: false
  steps:

pims/frame.py

@@ -47,12 +47,12 @@ def __array_finalize__(self, obj):
  self.frame_no = getattr(obj, 'frame_no', None)
  self.metadata = getattr(obj, 'metadata', None)
 
- def __array_wrap__(self, out_arr, context=None):
+ def __array_wrap__(self, out_arr, context=None, return_scalar=False):
  # Handle scalars so as not to break ndimage.
  # See http://stackoverflow.com/a/794812/1221924
  if out_arr.ndim == 0:
  return out_arr[()]
- return ndarray.__array_wrap__(self, out_arr, context)
+ return ndarray.__array_wrap__(self, out_arr, context, return_scalar)
 
  def __reduce__(self):
  """Necessary for making this object picklable"""

pims/process.py

@@ -25,11 +25,111 @@ def as_grey(frame):
 # Source of this patch: https://github.com/scikit-image/scikit-image/pull/3556
 # See also: https://github.com/numpy/numpy/pull/11966
 
-from numpy.lib.arraypad import _as_pairs
+
+# Vendored from numpy @7649fe2e
+# This function is
+#
+# Copyright (c) 2005-2024, NumPy Developers.
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+#
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# * Redistributions in binary form must reproduce the above
+# copyright notice, this list of conditions and the following
+# disclaimer in the documentation and/or other materials provided
+# with the distribution.
+#
+# * Neither the name of the NumPy Developers nor the names of any
+# contributors may be used to endorse or promote products derived
+# from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+def _as_pairs(x, ndim, as_index=False):
+ """
+ Broadcast `x` to an array with the shape (`ndim`, 2).
+
+ A helper function for `pad` that prepares and validates arguments like
+ `pad_width` for iteration in pairs.
+
+ Parameters
+ ----------
+ x : {None, scalar, array-like}
+ The object to broadcast to the shape (`ndim`, 2).
+ ndim : int
+ Number of pairs the broadcasted `x` will have.
+ as_index : bool, optional
+ If `x` is not None, try to round each element of `x` to an integer
+ (dtype `np.intp`) and ensure every element is positive.
+
+ Returns
+ -------
+ pairs : nested iterables, shape (`ndim`, 2)
+ The broadcasted version of `x`.
+
+ Raises
+ ------
+ ValueError
+ If `as_index` is True and `x` contains negative elements.
+ Or if `x` is not broadcastable to the shape (`ndim`, 2).
+ """
+ if x is None:
+ # Pass through None as a special case, otherwise np.round(x) fails
+ # with an AttributeError
+ return ((None, None),) * ndim
+
+ x = np.array(x)
+ if as_index:
+ x = np.round(x).astype(np.intp, copy=False)
+
+ if x.ndim < 3:
+ # Optimization: Possibly use faster paths for cases where `x` has
+ # only 1 or 2 elements. `np.broadcast_to` could handle these as well
+ # but is currently slower
+
+ if x.size == 1:
+ # x was supplied as a single value
+ x = x.ravel() # Ensure x[0] works for x.ndim == 0, 1, 2
+ if as_index and x < 0:
+ raise ValueError("index can't contain negative values")
+ return ((x[0], x[0]),) * ndim
+
+ if x.size == 2 and x.shape != (2, 1):
+ # x was supplied with a single value for each side
+ # but except case when each dimension has a single value
+ # which should be broadcasted to a pair,
+ # e.g. [[1], [2]] -> [[1, 1], [2, 2]] not [[1, 2], [1, 2]]
+ x = x.ravel() # Ensure x[0], x[1] works
+ if as_index and (x[0] < 0 or x[1] < 0):
+ raise ValueError("index can't contain negative values")
+ return ((x[0], x[1]),) * ndim
+
+ if as_index and x.min() < 0:
+ raise ValueError("index can't contain negative values")
+
+ # Converting the array with `tolist` seems to improve performance
+ # when iterating and indexing the result (see usage in `pad`)
+ return np.broadcast_to(x, (ndim, 2)).tolist()
+
 
 def validate_lengths(ar, crop_width):
  return _as_pairs(crop_width, ar.ndim, as_index=True)
 
+
 def _crop(frame, bbox):
  return frame[bbox[0]:bbox[2], bbox[1]:bbox[3]]
 

pims/tests/test_common.py

@@ -242,7 +242,7 @@ def test_slice_with_generator(self):
 
 
 def _rescale(img):
- return (img - img.min()) / img.ptp()
+ return (img - img.min()) / np.ptp(img)
 
 
 def _color_channel(img, channel):