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Accepting request 1198702 from devel:languages:python

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OBS-URL: https://build.opensuse.org/request/show/1198702
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-pydicom?expand=0&rev=16
This commit is contained in:
Ana Guerrero 2024-09-05 13:46:50 +00:00 committed by Git OBS Bridge
commit cd93bd7c06
3 changed files with 109 additions and 1 deletions
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101
pydicom-pr2076-np2.patch Normal file
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@ -0,0 +1,101 @@
Index: pydicom-2.4.4/pydicom/pixel_data_handlers/pillow_handler.py
===================================================================
--- pydicom-2.4.4.orig/pydicom/pixel_data_handlers/pillow_handler.py
+++ pydicom-2.4.4/pydicom/pixel_data_handlers/pillow_handler.py
@@ -255,14 +255,14 @@ def get_pixeldata(ds: "Dataset") -> "num
if ds.PixelRepresentation == 1:
# Pillow converts signed data to unsigned
# so we need to undo this conversion
- arr -= 2**(bits_allocated - 1)
+ arr -= numpy.uint32(2**(bits_allocated - 1))
if shift:
arr = numpy.right_shift(arr, shift)
else:
# Corrections based on dataset elements
if ds.PixelRepresentation == 1:
- arr -= 2**(bits_allocated - 1)
+ arr -= numpy.uint32(2**(bits_allocated - 1))
if shift:
arr = numpy.right_shift(arr, shift)
Index: pydicom-2.4.4/pydicom/pixel_data_handlers/pylibjpeg_handler.py
===================================================================
--- pydicom-2.4.4.orig/pydicom/pixel_data_handlers/pylibjpeg_handler.py
+++ pydicom-2.4.4/pydicom/pixel_data_handlers/pylibjpeg_handler.py
@@ -66,11 +66,7 @@ except ImportError:
HAVE_PYLIBJPEG = False
if HAVE_PYLIBJPEG:
- try:
- from pylibjpeg.utils import get_pixel_data_decoders
- except ImportError:
- # Old import, deprecated in 1.2, removal in 2.0
- from pylibjpeg.pydicom.utils import get_pixel_data_decoders
+ from pylibjpeg.utils import get_pixel_data_decoders, Decoder
try:
import openjpeg
@@ -249,7 +245,7 @@ def generate_frames(
"elements are missing from the dataset: " + ", ".join(missing)
)
- decoder = _DECODERS[tsyntax]
+ decoder = cast(Decoder, _DECODERS[tsyntax])
LOGGER.debug(f"Decoding {tsyntax.name} encoded Pixel Data using {decoder}")
nr_frames = getattr(ds, "NumberOfFrames", 1)
@@ -260,7 +256,7 @@ def generate_frames(
bits_allocated = cast(int, ds.BitsAllocated)
for frame in generate_pixel_data_frame(ds.PixelData, nr_frames):
- arr = decoder(frame, pixel_module)
+ arr = decoder(frame, ds=pixel_module)
if (
tsyntax in [JPEG2000, JPEG2000Lossless]
Index: pydicom-2.4.4/pydicom/tests/test_encoders_pydicom.py
===================================================================
--- pydicom-2.4.4.orig/pydicom/tests/test_encoders_pydicom.py
+++ pydicom-2.4.4/pydicom/tests/test_encoders_pydicom.py
@@ -444,7 +444,7 @@ class TestRLEEncodeFrame:
assert ds.SamplesPerPixel == 3
assert ds.PixelRepresentation == 0
- arr = ref.newbyteorder('>')
+ arr = ref.view(ref.dtype.newbyteorder('>'))
assert id(arr) != id(ref)
assert arr.dtype == '>u2'
encoded = rle_encode_frame(arr)
Index: pydicom-2.4.4/pydicom/pixel_data_handlers/util.py
===================================================================
--- pydicom-2.4.4.orig/pydicom/pixel_data_handlers/util.py
+++ pydicom-2.4.4/pydicom/pixel_data_handlers/util.py
@@ -200,7 +200,7 @@ def apply_color_lut(
# IVs >= `first_map` are mapped by the Palette Color LUTs
# `first_map` may be negative, positive or 0
mapped_pixels = arr >= first_map
- clipped_iv[mapped_pixels] = arr[mapped_pixels] - first_map
+ clipped_iv[mapped_pixels] = arr[mapped_pixels] - np.int32(first_map)
# IVs > number of entries get set to last entry
np.clip(clipped_iv, 0, nr_entries - 1, out=clipped_iv)
@@ -276,7 +276,7 @@ def apply_modality_lut(arr: "np.ndarray"
# IVs >= `first_map` are mapped by the Modality LUT
# `first_map` may be negative, positive or 0
mapped_pixels = arr >= first_map
- clipped_iv[mapped_pixels] = arr[mapped_pixels] - first_map
+ clipped_iv[mapped_pixels] = arr[mapped_pixels] - np.int32(first_map)
# IVs > number of entries get set to last entry
np.clip(clipped_iv, 0, nr_entries - 1, out=clipped_iv)
@@ -458,7 +458,7 @@ def apply_voi(
# IVs >= `first_map` are mapped by the VOI LUT
# `first_map` may be negative, positive or 0
mapped_pixels = arr >= first_map
- clipped_iv[mapped_pixels] = arr[mapped_pixels] - first_map
+ clipped_iv[mapped_pixels] = arr[mapped_pixels] - np.int32(first_map)
# IVs > number of entries get set to last entry
np.clip(clipped_iv, 0, nr_entries - 1, out=clipped_iv)

5
python-pydicom.changes
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@ -1,3 +1,8 @@
-------------------------------------------------------------------
Wed Sep 4 07:18:47 UTC 2024 - Ben Greiner <code@bnavigator.de>
- Add pydicom-pr2076-np2.patch backport of gh#pydicom/pydicom#2076
-------------------------------------------------------------------
Mon Feb 19 10:16:16 UTC 2024 - Andreas Schwab <schwab@suse.de>

4
python-pydicom.spec
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@ -26,6 +26,8 @@ URL: https://github.com/darcymason/pydicom
Source: https://github.com/pydicom/pydicom/archive/refs/tags/v%{version}.tar.gz#/pydicom-%{version}-gh.tar.gz
# PATCH-FIX-UPSTREAM pydicom-pr1908-fixpillow.patch gh#pydicom/pydicom#1908 fixes gh#pydicom/pydicom#1907
Patch0: pydicom-pr1908-fixpillow.patch
# PATCH-FIX-UPSTREAM pydicom-pr2076-np2.patch gh#pydicom/pydicom#2076
Patch1: pydicom-pr2076-np2.patch
BuildRequires: %{python_module base >= 3.7}
BuildRequires: %{python_module flit-core >= 3.2}
BuildRequires: %{python_module pip}
@ -44,7 +46,7 @@ BuildRequires: python3-gdcm
# /SECTION
BuildArch: noarch
Requires(post): update-alternatives
Requires(postun):update-alternatives
Requires(postun): update-alternatives
%python_subpackages
%description