python312Packages.pydicom: 2.4.4 -> 3.0.1; unbreak (#368584)

  lib,

  buildPythonPackage,

  fetchPypi,

  pythonAtLeast,

  pythonOlder,

  hatchling,

  hatch-vcs,

  numpy,

  packaging,

  importlib-resources,

  typing-extensions,

  pydicom,

  pillow,

  h5py,

buildPythonPackage rec {

  pname = "nibabel";

  version = "5.2.1";

  version = "5.3.2";

  pyproject = true;

  disabled = pythonOlder "3.8";

  disabled = pythonOlder "3.9";

  src = fetchPypi {

    inherit pname version;

    hash = "sha256-tsgLLnKOS8K2XxFC2bjSKHqRAqi/hHfhFe8NgzRVmXU=";

    hash = "sha256-C9ymUDsceEtEbHRaRUI2fed1bPug1yFDuR+f+3i+Vps=";

  };

  nativeBuildInputs = [

  build-system = [

    hatchling

    hatch-vcs

  ];

  propagatedBuildInputs = [

  dependencies =

    [

      numpy

      packaging

  ] ++ lib.optionals (pythonOlder "3.9") [ importlib-resources ];

    ]

    ++ lib.optionals (pythonOlder "3.12") [ importlib-resources ]

    ++ lib.optionals (pythonOlder "3.13") [ typing-extensions ];

  optional-dependencies = rec {

    all = dicom ++ dicomfs ++ minc2 ++ spm ++ zstd;

    export PATH=$out/bin:$PATH

  '';

  disabledTestPaths = lib.optionals (pythonAtLeast "3.12") [

    # uses distutils

    "nisext/tests/test_sexts.py"

  ];

  meta = with lib; {

    homepage = "https://nipy.org/nibabel";

    changelog = "https://github.com/nipy/nibabel/blob/${version}/Changelog";

  stdenv,

  buildPythonPackage,

  fetchFromGitHub,

  pythonOlder,

  flit-core,

  numpy,

  pillow,

  pytestCheckHook,

  pythonOlder,

  setuptools,

}:

  # optional/test dependencies

  gdcm,

  pillow,

  pylibjpeg,

  pylibjpeg-libjpeg,

}:

let

  pname = "pydicom";

  version = "2.4.4";

  src = fetchFromGitHub {

    owner = "pydicom";

    repo = "pydicom";

    rev = "refs/tags/v${version}";

    hash = "sha256-iJE1horEmdL7bKPn+NlZLgmtCbLZCZWQ8NjDBQPzXk8=";

  };

  # Pydicom needs pydicom-data to run some tests. If these files aren't downloaded

  # before the package creation, it'll try to download during the checkPhase.

  test_data = fetchFromGitHub {

    owner = "pydicom";

    repo = "pydicom-data";

    rev = "cbb9b2148bccf0f550e3758c07aca3d0e328e768";

    hash = "sha256-nF/j7pfcEpWHjjsqqTtIkW8hCEbuQ3J4IxpRk0qc1CQ=";

    rev = "8da482f208401d63cd63f3f4efc41b6856ef36c7";

    hash = "sha256-ji7SppKdiszaXs8yCSIPkJj4Ld++XWNw9FuxLoFLfFo=";

  };

in

buildPythonPackage {

  inherit pname version src;

buildPythonPackage rec {

  pname = "pydicom";

  version = "3.0.1";

  pyproject = true;

  disabled = pythonOlder "3.10";

  patches = [

    # backport of https://github.com/pydicom/pydicom/commit/2513a20cc41743a42bdb86f4cbb4873899b7823c

    ./pillow-10.1.0-compat.patch

  ];

  src = fetchFromGitHub {

    owner = "pydicom";

    repo = "pydicom";

    tag = "v${version}";

    hash = "sha256-SvRevQehRaSp+vCtJRQVEJiC5noIJS+bGG1/q4p7/XU=";

  };

  nativeBuildInputs = [ flit-core ];

  build-system = [ flit-core ];

  propagatedBuildInputs = [

  dependencies = [

    numpy

  ];

  optional-dependencies = {

    pixeldata = [

      pillow

    setuptools

      #pyjpegls # not in nixpkgs

      #pylibjpeg.optional-dependencies.openjpeg # infinite recursion

      #pylibjpeg.optional-dependencies.rle # not in nixpkgs

      pylibjpeg-libjpeg

      gdcm

    ];

  };

  nativeCheckInputs = [ pytestCheckHook ];

  nativeCheckInputs = [ pytestCheckHook ] ++ optional-dependencies.pixeldata;

  # Setting $HOME to prevent pytest to try to create a folder inside

  # /homeless-shelter which is read-only.

    [

      # tries to remove a dicom inside $HOME/.pydicom/data/ and download it again

      "test_fetch_data_files"

      # test_reference_expl{,_binary}[parametric_map_float.dcm] tries to download that file for some reason even though it's present in test-data

      "test_reference_expl"

      "test_reference_expl_binary"

      # slight error in regex matching

      "test_no_decoders_raises"

      "test_deepcopy_bufferedreader_raises"

    ]

    ++ lib.optionals stdenv.hostPlatform.isAarch64 [

      # https://github.com/pydicom/pydicom/issues/1386

diff --git a/pydicom/pixel_data_handlers/pillow_handler.py b/pydicom/pixel_data_handlers/pillow_handler.py

index ff781025d..a44eb9a41 100644

--- a/pydicom/pixel_data_handlers/pillow_handler.py

+++ b/pydicom/pixel_data_handlers/pillow_handler.py

@@ -119,18 +119,12 @@ def _decompress_single_frame(

     # space prior to compression, setting the value of "mode" to YCbCr

     # signals Pillow to not apply any color transformation upon

     # decompression.

-    if (transfer_syntax in PillowJPEGTransferSyntaxes and

-            photometric_interpretation == 'RGB'):

-        if 'adobe_transform' not in image.info:

-            color_mode = 'YCbCr'

-            image.tile = [(

-                'jpeg',

-                image.tile[0][1],

-                image.tile[0][2],

-                (color_mode, ''),

-            )]

-            image.mode = color_mode

-            image.rawmode = color_mode

+    if (

+        transfer_syntax in PillowJPEGTransferSyntaxes

+        and photometric_interpretation == 'RGB'

+        and "adobe_transform" not in image.info

+    ):

+        image.draft("YCbCr", image.size)

     return image

  pydicom,

  pylibjpeg-data,

  pylibjpeg-libjpeg,

  pylibjpeg-openjpeg,

}:

buildPythonPackage rec {

  dependencies = [ numpy ];

  optional-dependencies = {

    libjpeg = [ pylibjpeg-libjpeg ];

    openjpeg = [ pylibjpeg-openjpeg ];

    #rle = [ pylibjpeg-rle ]; # not in Nixpkgs

  };

  nativeCheckInputs = [

    pytestCheckHook

    pydicom