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python-scikit-image
skimage-pr7414-np2.patch
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File skimage-pr7414-np2.patch of Package python-scikit-image
From 24e84822508a886c0433875889608f7aa31848ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lars=20Gr=C3=BCter?= <lagru@mailbox.org> Date: Tue, 7 May 2024 20:07:48 +0200 Subject: [PATCH 1/5] Fix NumPy2 dtype promotion issues in pywt dependent code --- skimage/metrics/simple_metrics.py | 1 + skimage/restoration/_denoise.py | 4 +++- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/skimage/metrics/simple_metrics.py b/skimage/metrics/simple_metrics.py index 37cd69ee1c9..7bb13acf189 100644 --- a/skimage/metrics/simple_metrics.py +++ b/skimage/metrics/simple_metrics.py @@ -164,6 +164,7 @@ def peak_signal_noise_ratio(image_true, image_test, *, data_range=None): image_true, image_test = _as_floats(image_true, image_test) err = mean_squared_error(image_true, image_test) + data_range = float(data_range) # prevent overflow for small integer types return 10 * np.log10((data_range**2) / err) diff --git a/skimage/restoration/_denoise.py b/skimage/restoration/_denoise.py index 791a8c9f25b..4f4a235ac40 100644 --- a/skimage/restoration/_denoise.py +++ b/skimage/restoration/_denoise.py @@ -788,7 +788,9 @@ def _wavelet_threshold( for thresh, level in zip(threshold, dcoeffs) ] denoised_coeffs = [coeffs[0]] + denoised_detail - return pywt.waverecn(denoised_coeffs, wavelet)[original_extent] + out = pywt.waverecn(denoised_coeffs, wavelet)[original_extent] + out = out.astype(image.dtype) + return out def _scale_sigma_and_image_consistently(image, sigma, multichannel, rescale_sigma): From bfbf88aad4fbd04b3657c682266d43aa0fe01ec4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lars=20Gr=C3=BCter?= <lagru+github@mailbox.org> Date: Wed, 8 May 2024 00:17:00 +0200 Subject: [PATCH 2/5] Update skimage/metrics/simple_metrics.py Co-authored-by: Mark Harfouche <mark.harfouche@gmail.com> --- skimage/metrics/simple_metrics.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/skimage/metrics/simple_metrics.py b/skimage/metrics/simple_metrics.py index 7bb13acf189..6a255ed4211 100644 --- a/skimage/metrics/simple_metrics.py +++ b/skimage/metrics/simple_metrics.py @@ -164,8 +164,7 @@ def peak_signal_noise_ratio(image_true, image_test, *, data_range=None): image_true, image_test = _as_floats(image_true, image_test) err = mean_squared_error(image_true, image_test) - data_range = float(data_range) # prevent overflow for small integer types - return 10 * np.log10((data_range**2) / err) + return 20 * np.log10(data_range / err) def _pad_to(arr, shape): From b90376cbfbbfdf7d3a8f910b4fec03621b3cc2a5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lars=20Gr=C3=BCter?= <lagru@mailbox.org> Date: Wed, 8 May 2024 00:41:34 +0200 Subject: [PATCH 3/5] Catch and warn about pyamg not supporting NumPy 2 yet --- TODO.txt | 4 ++++ pyproject.toml | 1 + skimage/segmentation/random_walker_segmentation.py | 10 ++++++++++ 3 files changed, 15 insertions(+) diff --git a/TODO.txt b/TODO.txt index f8b35a6ea39..476f160dcd2 100644 --- a/TODO.txt +++ b/TODO.txt @@ -27,6 +27,10 @@ Other skimage/exposure/tests/test_exposure.py::test_rescale_nan_warning * Finalize ``skimage.future.manual_segmentation`` API, see https://github.com/scikit-image/scikit-image/issues/2624 +* Remove ``except AttributeError`` block in + ``skimage/segmentation/random_walker_segmentation.py`` as well as the warning filter + in ``pyproject.toml``, once pyamg supports NumPy 2 + (see https://github.com/pyamg/pyamg/issues/406). Post numpy 2 ------------ diff --git a/pyproject.toml b/pyproject.toml index 9e839b4b098..0ff6f176e9e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -195,6 +195,7 @@ python_classes = ["Test*", "*Suite"] python_functions = ["time_*", "test_*", "peakmem_*"] filterwarnings = [ "error", + 'default:.*pyamg, which cannot \(yet\) be imported with NumPy >=2:RuntimeWarning' ] [tool.coverage.run] diff --git a/skimage/segmentation/random_walker_segmentation.py b/skimage/segmentation/random_walker_segmentation.py index c4dd2fe314b..d5c2cabcff7 100644 --- a/skimage/segmentation/random_walker_segmentation.py +++ b/skimage/segmentation/random_walker_segmentation.py @@ -43,6 +43,16 @@ def new_del(self): amg_loaded = True except ImportError: amg_loaded = False +except AttributeError as e: + if "`np.deprecate` was removed" not in e.args[0]: + raise e + warn( + "found optional dependency pyamg, which cannot (yet) be imported with " + "NumPy >=2 and will be treated as if not available", + RuntimeWarning, + ) + amg_loaded = False + from ..util import img_as_float From ad081e184464f74be2057060812d5ba745317b1d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lars=20Gr=C3=BCter?= <lagru@mailbox.org> Date: Wed, 8 May 2024 00:50:28 +0200 Subject: [PATCH 4/5] Revert "Update skimage/metrics/simple_metrics.py" This reverts commit bfbf88aad4fbd04b3657c682266d43aa0fe01ec4. --- skimage/metrics/simple_metrics.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/skimage/metrics/simple_metrics.py b/skimage/metrics/simple_metrics.py index 6a255ed4211..7bb13acf189 100644 --- a/skimage/metrics/simple_metrics.py +++ b/skimage/metrics/simple_metrics.py @@ -164,7 +164,8 @@ def peak_signal_noise_ratio(image_true, image_test, *, data_range=None): image_true, image_test = _as_floats(image_true, image_test) err = mean_squared_error(image_true, image_test) - return 20 * np.log10(data_range / err) + data_range = float(data_range) # prevent overflow for small integer types + return 10 * np.log10((data_range**2) / err) def _pad_to(arr, shape): From 05d585cff4ccdef84db024fc1c99841b9fb57a38 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lars=20Gr=C3=BCter?= <lagru@mailbox.org> Date: Wed, 8 May 2024 10:14:40 +0200 Subject: [PATCH 5/5] Simplify except block a little bit --- .../random_walker_segmentation.py | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/skimage/segmentation/random_walker_segmentation.py b/skimage/segmentation/random_walker_segmentation.py index d5c2cabcff7..68d7c46cd1d 100644 --- a/skimage/segmentation/random_walker_segmentation.py +++ b/skimage/segmentation/random_walker_segmentation.py @@ -43,15 +43,16 @@ def new_del(self): amg_loaded = True except ImportError: amg_loaded = False -except AttributeError as e: - if "`np.deprecate` was removed" not in e.args[0]: - raise e - warn( - "found optional dependency pyamg, which cannot (yet) be imported with " - "NumPy >=2 and will be treated as if not available", - RuntimeWarning, - ) - amg_loaded = False +except AttributeError as error: + if "`np.deprecate` was removed" in error.args[0]: + warn( + "found optional dependency pyamg, which cannot (yet) be imported with " + "NumPy >=2 and will be treated as if not available", + RuntimeWarning, + ) + amg_loaded = False + else: + raise error from ..util import img_as_float
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