Merge remote-tracking branch 'upstream/master' into correct-bug-Ortho…

…Slicer3D

.coveragerc

@@ -1,9 +1,18 @@
 [run]
 branch = True
 source = nibabel
-include = */nibabel/*
 omit =
     */externals/*
     */benchmarks/*
-    */tests/*
     nibabel/_version.py
+
+[report]
+exclude_also =
+    def __repr__
+    if (ty\.|typing\.)?TYPE_CHECKING:
+    class .*\((ty\.|typing\.)Protocol\):
+    @(ty\.|typing\.)overload
+    if 0:
+    if __name__ == .__main__.:
+    @(abc\.)?abstractmethod
+    raise NotImplementedError

.github/workflows/test.yml

@@ -125,9 +125,9 @@ jobs:
           - os: ubuntu-latest
             python-version: 3.8
             dependencies: 'min'
-          # NumPy 2.0
+          # NoGIL
           - os: ubuntu-latest
-            python-version: '3.12'
+            python-version: '3.13-dev'
             dependencies: 'dev'
         exclude:
           # x86 for Windows + Python<3.12
@@ -168,11 +168,18 @@ jobs:
           submodules: recursive
           fetch-depth: 0
       - name: Set up Python ${{ matrix.python-version }}
+        if: "!endsWith(matrix.python-version, '-dev')"
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           architecture: ${{ matrix.architecture }}
           allow-prereleases: true
+      - name: Set up Python ${{ matrix.python-version }}
+        if: endsWith(matrix.python-version, '-dev')
+        uses: deadsnakes/[email protected]
+        with:
+          python-version: ${{ matrix.python-version }}
+          nogil: true
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
       - name: Install tox
@@ -182,7 +189,7 @@ jobs:
       - name: Show tox config
         run: tox c
       - name: Run tox
-        run: tox -v --exit-and-dump-after 1200
+        run: tox -vv --exit-and-dump-after 1200
       - uses: codecov/codecov-action@v4
         if: ${{ always() }}
         with:

.pre-commit-config.yaml

@@ -16,7 +16,7 @@ repos:
     rev: v0.3.4
     hooks:
       - id: ruff
-        args: [--fix, --show-fix, --exit-non-zero-on-fix]
+        args: [--fix, --show-fixes, --exit-non-zero-on-fix]
         exclude: = ["doc", "tools"]
       - id: ruff-format
         exclude: = ["doc", "tools"]

Changelog

@@ -25,6 +25,33 @@ Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).
 
 References like "pr/298" refer to github pull request numbers.
 
+Upcoming release (To be determined)
+===================================
+
+New features
+------------
+
+Enhancements
+------------
+ * Ability to read data from many multiframe DICOM files that previously generated errors
+
+Bug fixes
+---------
+ * Fixed multiframe DICOM issue where data could be flipped along slice dimension relative to the
+   affine
+ * Fixed multiframe DICOM issue where ``image_position`` and the translation component in the
+   ``affine`` could be incorrect
+
+Documentation
+-------------
+
+Maintenance
+-----------
+
+API changes and deprecations
+----------------------------
+
+
 5.2.1 (Monday 26 February 2024)
 ===============================
 

doc/source/conf.py

@@ -28,6 +28,10 @@
     import tomli as tomllib
 
 # Check for external Sphinx extensions we depend on
+try:
+    import numpy as np
+except ImportError:
+    raise RuntimeError('Need to install "numpy" package for doc build')
 try:
     import numpydoc
 except ImportError:
@@ -45,6 +49,11 @@
         'Need nibabel on Python PATH; consider "make htmldoc" from nibabel root directory'
     )
 
+from packaging.version import Version
+
+if Version(np.__version__) >= Version('1.22'):
+    np.set_printoptions(legacy='1.21')
+
 # -- General configuration ----------------------------------------------------
 
 # We load the nibabel release info into a dict by explicit execution

doc/tools/build_modref_templates.py

@@ -9,7 +9,7 @@
 import sys
 
 # version comparison
-from distutils.version import LooseVersion as V
+from packaging.version import Version as V
 from os.path import join as pjoin
 
 # local imports
@@ -73,6 +73,8 @@ def abort(error):
                 if re.match('^_version_(major|minor|micro|extra)', v)
             ]
         )
+
+    source_version = V(source_version)
     print('***', source_version)
 
     if source_version != installed_version:

nibabel/_compression.py

@@ -17,7 +17,7 @@
 
 from .optpkg import optional_package
 
-if ty.TYPE_CHECKING:  # pragma: no cover
+if ty.TYPE_CHECKING:
     import indexed_gzip  # type: ignore[import]
     import pyzstd
 

nibabel/arrayproxy.py

@@ -57,7 +57,7 @@
 KEEP_FILE_OPEN_DEFAULT = False
 
 
-if ty.TYPE_CHECKING:  # pragma: no cover
+if ty.TYPE_CHECKING:
     import numpy.typing as npt
     from typing_extensions import Self  # PY310
 
@@ -75,19 +75,17 @@ class ArrayLike(ty.Protocol):
     shape: tuple[int, ...]
 
     @property
-    def ndim(self) -> int: ...  # pragma: no cover
+    def ndim(self) -> int: ...
 
     # If no dtype is passed, any dtype might be returned, depending on the array-like
     @ty.overload
-    def __array__(
-        self, dtype: None = ..., /
-    ) -> np.ndarray[ty.Any, np.dtype[ty.Any]]: ...  # pragma: no cover
+    def __array__(self, dtype: None = ..., /) -> np.ndarray[ty.Any, np.dtype[ty.Any]]: ...
 
     # Any dtype might be passed, and *that* dtype must be returned
     @ty.overload
-    def __array__(self, dtype: _DType, /) -> np.ndarray[ty.Any, _DType]: ...  # pragma: no cover
+    def __array__(self, dtype: _DType, /) -> np.ndarray[ty.Any, _DType]: ...
 
-    def __getitem__(self, key, /) -> npt.NDArray: ...  # pragma: no cover
+    def __getitem__(self, key, /) -> npt.NDArray: ...
 
 
 class ArrayProxy(ArrayLike):

nibabel/brikhead.py

@@ -391,7 +391,7 @@ def get_affine(self):
         # AFNI default is RAI- == LPS+ == DICOM order.  We need to flip RA sign
         # to align with nibabel RAS+ system
         affine = np.asarray(self.info['IJK_TO_DICOM_REAL']).reshape(3, 4)
-        affine = np.row_stack((affine * [[-1], [-1], [1]], [0, 0, 0, 1]))
+        affine = np.vstack((affine * [[-1], [-1], [1]], [0, 0, 0, 1]))
         return affine
 
     def get_data_scaling(self):

nibabel/cmdline/dicomfs.py

@@ -37,7 +37,7 @@ class dummy_fuse:
 import nibabel as nib
 import nibabel.dft as dft
 
-encoding = locale.getdefaultlocale()[1]
+encoding = locale.getlocale()[1]
 
 fuse.fuse_python_api = (0, 2)
 

nibabel/cmdline/nifti_dx.py

@@ -9,8 +9,7 @@
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Print nifti diagnostics for header files"""
 
-import sys
-from optparse import OptionParser
+from argparse import ArgumentParser
 
 import nibabel as nib
 
@@ -21,15 +20,27 @@
 
 def main(args=None):
     """Go go team"""
-    parser = OptionParser(
-        usage=f'{sys.argv[0]} [FILE ...]\n\n' + __doc__, version='%prog ' + nib.__version__
+    parser = ArgumentParser(description=__doc__)
+    parser.add_argument('--version', action='version', version=f'%(prog)s {nib.__version__}')
+    parser.add_argument(
+        '-1',
+        '--nifti1',
+        dest='header_class',
+        action='store_const',
+        const=nib.Nifti1Header,
+        default=nib.Nifti1Header,
     )
-    (opts, files) = parser.parse_args(args=args)
+    parser.add_argument(
+        '-2', '--nifti2', dest='header_class', action='store_const', const=nib.Nifti2Header
+    )
+    parser.add_argument('files', nargs='*', metavar='FILE', help='Nifti file names')
+
+    args = parser.parse_args(args=args)
 
-    for fname in files:
+    for fname in args.files:
         with nib.openers.ImageOpener(fname) as fobj:
-            hdr = fobj.read(nib.nifti1.header_dtype.itemsize)
-        result = nib.Nifti1Header.diagnose_binaryblock(hdr)
+            hdr = fobj.read(args.header_class.template_dtype.itemsize)
+        result = args.header_class.diagnose_binaryblock(hdr)
         if len(result):
             print(f'Picky header check output for "{fname}"\n')
             print(result + '\n')

nibabel/dataobj_images.py

@@ -19,7 +19,7 @@
 from .filebasedimages import FileBasedHeader, FileBasedImage
 from .fileholders import FileMap
 
-if ty.TYPE_CHECKING:  # pragma: no cover
+if ty.TYPE_CHECKING:
     import numpy.typing as npt
 
     from .filename_parser import FileSpec

nibabel/deprecated.py

@@ -8,7 +8,7 @@
 from .deprecator import Deprecator
 from .pkg_info import cmp_pkg_version
 
-if ty.TYPE_CHECKING:  # pragma: no cover
+if ty.TYPE_CHECKING:
     P = ty.ParamSpec('P')
 
 

nibabel/deprecator.py

@@ -9,7 +9,7 @@
 import warnings
 from textwrap import dedent
 
-if ty.TYPE_CHECKING:  # pragma: no cover
+if ty.TYPE_CHECKING:
     T = ty.TypeVar('T')
     P = ty.ParamSpec('P')
 

nibabel/ecat.py

@@ -390,7 +390,7 @@ def read_mlist(fileobj, endianness):
         mlist_index += n_rows
         if mlist_block_no <= 2:  # should block_no in (1, 2) be an error?
             break
-    return np.row_stack(mlists)
+    return np.vstack(mlists)
 
 
 def get_frame_order(mlist):

nibabel/filebasedimages.py

@@ -20,7 +20,7 @@
 from .filename_parser import TypesFilenamesError, _stringify_path, splitext_addext, types_filenames
 from .openers import ImageOpener
 
-if ty.TYPE_CHECKING:  # pragma: no cover
+if ty.TYPE_CHECKING:
     from .filename_parser import ExtensionSpec, FileSpec
 
 FileSniff = ty.Tuple[bytes, str]
@@ -54,13 +54,13 @@ def from_header(klass: type[HdrT], header: FileBasedHeader | ty.Mapping | None =
 
     @classmethod
     def from_fileobj(klass: type[HdrT], fileobj: io.IOBase) -> HdrT:
-        raise NotImplementedError  # pragma: no cover
+        raise NotImplementedError
 
     def write_to(self, fileobj: io.IOBase) -> None:
-        raise NotImplementedError  # pragma: no cover
+        raise NotImplementedError
 
     def __eq__(self, other: object) -> bool:
-        raise NotImplementedError  # pragma: no cover
+        raise NotImplementedError
 
     def __ne__(self, other: object) -> bool:
         return not self == other
@@ -251,7 +251,7 @@ def from_filename(klass: type[ImgT], filename: FileSpec) -> ImgT:
 
     @classmethod
     def from_file_map(klass: type[ImgT], file_map: FileMap) -> ImgT:
-        raise NotImplementedError  # pragma: no cover
+        raise NotImplementedError
 
     @classmethod
     def filespec_to_file_map(klass, filespec: FileSpec) -> FileMap:
@@ -308,7 +308,7 @@ def to_filename(self, filename: FileSpec, **kwargs) -> None:
         self.to_file_map(**kwargs)
 
     def to_file_map(self, file_map: FileMap | None = None, **kwargs) -> None:
-        raise NotImplementedError  # pragma: no cover
+        raise NotImplementedError
 
     @classmethod
     def make_file_map(klass, mapping: ty.Mapping[str, str | io.IOBase] | None = None) -> FileMap:
@@ -373,7 +373,7 @@ def from_image(klass: type[ImgT], img: FileBasedImage) -> ImgT:
         img : ``FileBasedImage`` instance
            Image, of our own class
         """
-        raise NotImplementedError  # pragma: no cover
+        raise NotImplementedError
 
     @classmethod
     def _sniff_meta_for(

nibabel/filename_parser.py

@@ -14,7 +14,7 @@
 import pathlib
 import typing as ty
 
-if ty.TYPE_CHECKING:  # pragma: no cover
+if ty.TYPE_CHECKING:
     FileSpec = str | os.PathLike[str]
     ExtensionSpec = tuple[str, str | None]
 

nibabel/loadsave.py

@@ -26,7 +26,7 @@
 _compressed_suffixes = ('.gz', '.bz2', '.zst')
 
 
-if ty.TYPE_CHECKING:  # pragma: no cover
+if ty.TYPE_CHECKING:
     from .filebasedimages import FileBasedImage
     from .filename_parser import FileSpec
 

nibabel/nicom/ascconv.py

@@ -91,7 +91,7 @@ def assign2atoms(assign_ast, default_class=int):
             prev_target_type = OrderedDict
         elif isinstance(target, ast.Subscript):
             if isinstance(target.slice, ast.Constant):  # PY39
-                index = target.slice.n
+                index = target.slice.value
             else:  # PY38
                 index = target.slice.value.n
             atoms.append(Atom(target, prev_target_type, index))
@@ -174,12 +174,10 @@ def obj_from_atoms(atoms, namespace):
 
 def _get_value(assign):
     value = assign.value
-    if isinstance(value, ast.Num):
-        return value.n
-    if isinstance(value, ast.Str):
-        return value.s
+    if isinstance(value, ast.Constant):
+        return value.value
     if isinstance(value, ast.UnaryOp) and isinstance(value.op, ast.USub):
-        return -value.operand.n
+        return -value.operand.value
     raise AscconvParseError(f'Unexpected RHS of assignment: {value}')