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{
lib,
buildPythonPackage,
fetchFromGitHub,
# build-system
setuptools,
# dependencies
gdcm,
nibabel,
numpy,
pydicom,
scipy,
# tests
pillow,
pylibjpeg,
pylibjpeg-libjpeg,
pytestCheckHook,
}:
buildPythonPackage rec {
pname = "dicom2nifti";
version = "2.6.2";
pyproject = true;
# no tests in PyPI dist
src = fetchFromGitHub {
owner = "icometrix";
repo = "dicom2nifti";
tag = version;
hash = "sha256-VS1ad7sAgVWkFkTPLxzloj0dvweW5wqBlQpFqD9uZLs=";
};
postPatch = ''
substituteInPlace tests/test_generic.py --replace-fail "from common" "from dicom2nifti.common"
substituteInPlace tests/test_ge.py --replace-fail "import convert_generic" "import dicom2nifti.convert_generic as convert_generic"
'';
build-system = [ setuptools ];
dependencies = [
gdcm
nibabel
numpy
pydicom
scipy
];
pythonImportsCheck = [ "dicom2nifti" ];
nativeCheckInputs = [
pillow
pylibjpeg
pylibjpeg-libjpeg
pytestCheckHook
];
disabledTests = [
# OverflowError: Python integer -1024 out of bounds for uint16
"test_not_a_volume"
"test_resampling"
"test_validate_orthogonal_disabled"
# RuntimeError: Unable to decompress 'JPEG 2000 Image Compression (Lossless O...
"test_anatomical"
"test_compressed_j2k"
"test_main_function"
"test_rgb"
# Missing script 'dicom2nifti_scrip'
"test_gantry_option"
"test_gantry_resampling"
];
meta = {
homepage = "https://github.com/icometrix/dicom2nifti";
description = "Library for converting dicom files to nifti";
mainProgram = "dicom2nifti";
license = lib.licenses.mit;
maintainers = with lib.maintainers; [ bcdarwin ];
};
}
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