Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from https://github.com/nipy/NiBabel/releases below:

Website Navigation

• Releases
• Tags

Releases · nipy/nibabel · GitHub

Bug-fix release in the 5.3.x series.

• Restore access to private attribute Nifti1Extension._content to unbreak subclasses that did not use public accessor methods. (#1378) (CM, reviewed by Basile Pinsard)
• Remove test order dependency in test_api_validators (#1377) (CM)

This release primarily adds support for Python 3.13 and Numpy 2.0.

NiBabel 6.0 will drop support for Numpy 1.x.

• Update NIfTI extension protocol to include .content : bytes, .text : str and .json : dict properties for accessing extension contents. Exceptions will be raised on .text and .json if conversion fails. (#1336) (CM)

• Ability to read data from many multiframe DICOM files that previously generated errors (#1340) (Brendan Moloney, reviewed by CM)
• nib-nifti-dx now supports NIfTI-2 files with a --nifti2 flag (#1323) (CM)
• Update nibabel.streamlines.tractogram to support ragged arrays. (#1291) (Serge Koudoro, reviewed by CM)
• Filter numpy UserWarning on np.finfo(np.longdouble). This can occur on Windows systems, but it's done in the context of checking for the problem that is being warned against, so there's no need to be noisy. (#1310) (Joshua Newton, reviewed by CM)
• Improve error message for for dicomwrapper errors in shape calculation (#1302) (YOH, reviewed by CM)
• Support "flat" ASCII-encoded GIFTI DataArrays (#1298) (PM, reviewed by CM)

• Fix location initialization/update in OrthoSlicer3D for permuted axes (#1319, #1350) (Guillaume Becq, reviewed by CM)
• Fix DICOM scaling, making frame filtering explicit (#1342) (Brendan Moloney, reviewed by CM)
• Fixed multiframe DICOM issue where data could be flipped along slice dimension relative to the affine (#1340) (Brendan Moloney, reviewed by CM)
• Fixed multiframe DICOM issue where image_position and the translation component in the affine could be incorrect (#1340) (Brendan Moloney, reviewed by CM)

• Numpy 2.0 compatibility and addressing deprecations in numpy API (#1304, #1330, #1331, #1334, #1337) (Jon Haitz Legarreta Gorroño, CM)
• Python 3.13 compatibility (#1315) (Sandro from the Fedora Project, reviewed by CM)
• Testing on Python 3.13 with free-threading (#1339) (CM)
• Testing on ARM64 Mac OS runners (#1320) (CM)
• Proactively address deprecations in coming Python versions (#1329, #1332, #1333) (Jon Haitz Legarreta Gorroño, reviewed by CM)
• Replace nose-era setup() and teardown() functions with pytest equivalents (#1325) (Sandro from the Fedora Project, reviewed by Étienne Mollier and CM)
• Transitioned from blue/isort/flake8 to ruff. (#1289) (Dimitri Papadopoulos, reviewed by CM)
• Vetted and added various rules to the ruff configuration for auto-formatting and style guide enforcement. (#1321, #1351, #1352, #1353, #1354, #1355, #1357, #1358, #1359, #1360, #1361, #1362, #1363, #1364, #1368, #1369) (Dimitri Papadopoulos, reviewed by CM)
• Fixing typos when found. (#1313, #1370) (MB, Dimitri Papadopoulos)
• Applied Repo-Review suggestions (Dimitri Papadopoulos, reviewed by CM)

• Raise HeaderDataError from set_qform if the affine fails to decompose. This would previously result in numpy.linalgLinAlgError. (#1227) (CM)
• The nibabel.onetime.auto_attr module can be replaced by functoolscached_property in all supported versions of Python. This alias may be removed in future versions. (#1341) (CM)
• Removed the deprecated nisext (setuptools extensions) package. (#1290) (CM, reviewed by MB)

• @joshuacwnewton made their first contribution in #1310
• @gjpcbecq made their first contribution in #1319

Full Changelog: 5.2.1...5.3.0

Bug-fix release in the 5.2.x series.

• Support "flat" ASCII-encoded GIFTI DataArrays (#1298) (PM, reviewed by CM)

• Tolerate missing git when reporting version info (#1286) (CM, reviewed by Yuri Victorovich)
• Handle Siemens XA30 derived DWI DICOMs (#1296) (CM, reviewed by YOH and Mathias Goncalves)

• Add tool for generating GitHub-friendly release notes (#1284) (CM)
• Accommodate pytest 8 changes (#1297) (CM)

Full Changelog: 5.2.0...5.2.1

New feature release in the 5.2.x series.

This release requires a minimum Python of 3.8 and NumPy 1.20, and has been tested up to Python 3.12 and NumPy 1.26.

• Add generic Pointset and regularly spaced Grid data structures in preparation for coordinate transformation and resampling (#1251) (CM, reviewed by Oscar Esteban)

• Add copy method to ArrayProxy (#1255) (CM, reviewed by Paul McCarthy)
• Permit to_xml to pass keyword arguments to tostring (#1258) (CM)
• Allow user expansion (e.g., ~/...) in strings passed to functions that accept paths (#1260) (Reinder Vos de Wael, reviewed by CM)
• Expand CIFTI-2 brain structures to permit synonyms (#1256) (CM, reviewed by Mathias Goncalves)
• Annotate SpatialImage as accepting affine=None argument (#1253) (Blake Dewey, reviewed by CM)
• Warn on invalid MINC2 spacing declarations, treat as missing (#1237) (Peter Suter, reviewed by CM)
• Refactor find_private_section for improved readability and maintainability (#1228) (MB, reviewed by CM)

• Resolve test failure related to randomly generated invalid case (#1221) (CM)

• Remove references to NiPy data packages from documentation (#1275) (Dimitri Papadopoulos, reviewed by CM, MB)

• Quality of life improvements for CI, including color output and OIDC publishing (#1282) (CM)
• Patch for NumPy 2.0 pre-release compatibility (#1250) (Mathieu Scheltienne and EL, reviewed by CM)
• Add spellchecking to tox, CI and pre-commit (#1266) (CM)
• Add py312-dev-x64 environment to Tox to test NumPy 2.0 pre-release compatibility (#1267) (CM, reviewed by EL)
• Resurrect tox configuration to cover development workflows and CI checks (#1262) (CM)
• Updates for Python 3.12 support (#1247, #1261, #1273) (CM)
• Remove uses of deprecated numpy.compat.py3k module (#1243) (Eric Larson, reviewed by CM)
• Various fixes for typos and style issues detected by Codespell, pyupgrade and refurb (#1263, #1269, #1270, #1271, #1276) (Dimitri Papadopoulos, reviewed by CM)
• Use stable argsorts in PARREC tests to ensure consistent behavior on systems with AVX512 SIMD instructions and numpy 1.25 (#1234) (CM)
• Resolve CodeCov submission failures (#1224) (CM)
• Link to logo with full URL to avoid broken links in PyPI (#1218) (CM, reviewed by Zvi Baratz)

• The nibabel.pydicom_compat module is deprecated and will be removed in NiBabel 7.0. (#1280)
• The int_to_float and as_int functions are no longer needed to work around NumPy deficiencies and have been deprecated (#1272) (CM, reviewed by EL)

• @petsuter made their first contribution in #1237
• @blakedewey made their first contribution in #1253
• @ReinderVosDeWael made their first contribution in #1260
• @mscheltienne made their first contribution in #1250

Full Changelog: 5.1.0...5.2.0

New feature release in the 5.1.x series.

Most work on NiBabel so far has been by Matthew Brett (MB), Chris Markiewicz (CM), Michael Hanke (MH), Marc-Alexandre Côté (MC), Ben Cipollini (BC), Paul McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh (SG), Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).

References like "pr/298" refer to github pull request numbers.

• Make imagestats available with import nibabel (pr/1208) (Fabian Perez, reviewed by CM)
• Use symmetric threshold for identifying unit quaternions on qform calculations (pr/1182) (CM, reviewed by MB)
• Type annotations for nibabel.loadsave (pr/1213) and nibabel.spatialimages.SpatialImage APIs (pr/1179), nibabel.deprecated, nibabel.deprecator, nibabel.onetime and nibabel.optpkg modules (pr/1188), nibabel.volumeutils (pr/1189), nibabel.filename_parser and nibabel.openers (pr/1197) (CM, reviewed by Zvi Baratz)

• Require explicit overrides to write GIFTI files that contain data arrays with data types not permitted by the GIFTI standard (pr/1199) (CM, reviewed by Alexis Thual)

• Move compression detection logic into a private nibabel._compression module, resolving unexpected errors from pyzstd. (pr/1212) (CM)
• Improved consistency of docstring formatting (pr/1200) (Zvi Baratz, reviewed by CM)
• Modernized README text (pr/1195) (Zvi Baratz, reviewed by CM)
• Updated README badges to include package distributions (pr/1192) (Horea Christian, reviewed by CM)
• Removed all dependencies on distutils and setuptools (pr/1190) (CM, reviewed by Zvi Baratz)
• Add a _version.pyi stub to allow mypy to run without building nibabel (pr/1210) (CM)

• @TheChymera made their first contribution in #1192
• @Factral made their first contribution in #1208

Full Changelog: 5.0.1...5.1.0

Bug-fix release in the 5.0.x series.

Most work on NiBabel so far has been by Matthew Brett (MB), Chris Markiewicz (CM), Michael Hanke (MH), Marc-Alexandre Côté (MC), Ben Cipollini (BC), Paul McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh (SG), Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).

References like "pr/298" refer to github pull request numbers.

• Support ragged voxel arrays in ParcelsAxis (pr/1194) (Michiel Cottaar, reviewed by CM)
• Return to cwd on exception in InTemporaryDirectory (pr/1184) (CM)

• Add py.typed to module root to enable use of types in downstream projects (pr/1196) (CM, reviewed by Fernando Pérez-Garcia)
• Cache git-archive separately from Python packages in GitHub Actions (pr/1186) (CM, reviewed by Zvi Baratz)

New feature release in the 5.0.x series.

Most work on NiBabel so far has been by Matthew Brett (MB), Chris Markiewicz (CM), Michael Hanke (MH), Marc-Alexandre Côté (MC), Ben Cipollini (BC), Paul McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh (SG), Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).

• SerializableImage now has to_stream() and from_stream() methods to read/write streams implementing the io.IOBase interface. A from_url() method enables loading images from URLs. (pr/1129) (CM, reviewed by MB)
• TrkFile supports TRKv3, an undocumented but generally compatible variant of TRKv2. (pr/1125) (CM)

• Support multiline header fields in TCKFile (pr/1175) (CM, reviewed by Matt Cieslak)
• Make layout order an initialization parameter of ArrayProxy (pr/1131) (CM, reviewed by MB)
• Initial support for type annotations. (pr/1115, pr/1178) (CM, reviewed by Zvi Baratz)

• Handle extension/file-format mismatches implemented incompletely in pr/1013 (pr/1138) (CM, reviewed by Thomas Phil)
• Improve handling of invalid TCK files, which could sometimes cause an infinite loop (pr/1140) (Anibal Solon, reviewed by CM)
• Clean up ECAT test case that left filehandle open and failed to use class variables (pr/1155) (Dimitri Papadopoulos, reviewed by CM)

• Simplify TCK reading code by assuming files are open in binary mode (pr/1142) (Anibal Solon, reviewed by MC, CM)
• Code support for tests covering deprecated functionality (pr/1159) (CM)
• Miscellaneous code cleanups (pr/1148, pr/1149, pr/1153, pr/1154, pr/1156) (Dimitri Papadopoulos, reviewed by CM)
• Update CI to build, test and deploy PyPI artifacts (pr/1134) (CM, reviewed by MB)
• Transition from setup.cfg to pyproject.toml package configuration (pr/1133) (CM, reviewed by MB)
• Addressed race conditions preventing running tests with pytest-xdist. (pr/1157, pr/1158) (CM, reviewed by Christian Haselgrove)
• Apply blue and isort auto-formatters and provide pre-commit configuration to reduce human burden of style guidelines. (pr/1124, pr/1165, pr/1169) (CM and Zvi Baratz)
• Manage versioning with setuptools_scm (pr/1171) (CM, reviewed by Zvi Baratz)
• Reduce installed package size by excluding very large test file (pr/1176) (CM, reviewed by Zvi Baratz)

• Passing an int64 array to Nifti1Image without a header or dtype argument will raise a ValueError. (pr/1173) (CM)

• tmpdirs.TemporaryDirectory is deprecated in favor of tempfile.TemporaryDirectory. (pr/1172) (CM, reviewed by Zvi Baratz)

• The nisext package is deprecated and will be removed in NiBabel 6.0. (pr/1170) (CM, reviewed by MB)

• Drop support for Python 3.7, Numpy < 1.19 (pr/1177) (CM)

• The following deprecated functions and methods will now raise ExpiredDeprecationErrors

  • nibabel.loadsave.read_img_data
  • nibabel.dataobj_images.DataobjImage.get_data
  • nibabel.loadsave.guessed_image_type
  • nibabel.onetime.setattr_on_read
  • nibabel.orientations.flip_axis

• Modules, classes and functions that expired at 4.0 were fully removed. ExpiredDeprecationError\s will now be AttributeError\s.

Most work on NiBabel so far has been by Matthew Brett (MB), Chris Markiewicz
(CM), Michael Hanke (MH), Marc-Alexandre Côté (MC), Ben Cipollini (BC), Paul
McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh (SG),
Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).

References like "pr/298" refer to github pull request numbers.

New feature release in the 4.0.x series.

• Add 'mask', 'compat' and 'smallest' dtype aliases to NIfTI images
  to allow for dtype specifications that can depend on the contents of the data.
  'mask' is a synonym for uint8. 'compat' will find the nearest
  Analyze-compatible (therefore widely supported) dtype that will not truncate
  the data. 'smallest' attempts to find the smallest integer dtype that will
  contain the data. (pr/1096) (CM, reviewed by Chris Rorden and Josh Teves)
• Add dtype arguments to Cifti2Image (pr/1111) (CM)
• Allow dtypes to be passed to Analyze-like images at __init__() and
  to_filename() to provide better control over output images. (pr/1082)
  (CM, following discussions with Chris Rorden, Josh Teves, Jerome Dockes, and MB)
• Allow compressed GIFTI images (MB, reviewed by CM)
• Add zstd compression support (pr/1005) (Andrew Van, reviewed by CM)
• Support ExternalFileBinary GIFTI data arrays (PM, reviewed by CM)

• Document InTemporaryDirectory as non-thread-safe (pr/1103) (Jacob Roberts,
  reviewed by MB)
• Unify Caret-XML-style metadata structure (GiftiMetaData, Cifti2MetaData)
  as dict-like (pr/1091) (CM, reviewed by Josh Teves and Hao-Ting Wang)
• Add __repr__ methods to GIFTI objects (pr/1092) (CM,
  reviewed by Josh Teves and Hao-Ting Wang)
• Create gzip header deterministically by default (pr/1024) (CM, reviewed by YOH)
• Provide clear error message when files with zip extensions don't match
  file contents (pr/1013) (Jérôme Dockès, reviewed by CM)

• Re-import externals/netcdf.py from scipy to resolve numpy API change (pr/1110)
  (CM)
• Resize ArraySequence.data without helper function to avoid reference increment
  (pr/1093) (MC, reviewed by CM)

• Update submodule URLs to use https over git protocol (pr/1097) (CM)
• Published BIAP 9: CoordinateImage API (pr/1084) (CM)
• Drop uses of deprecated distutils (pr/1073) (CM, reviewed by MB)
• Suppress LGTM false alarm "Clear-text logging of sensitive information"
  (pr/1052) (Dimitri Papadopoulos, reviewed by CM)
• Test on Python 3.10 (pr/1047) (CM)
• Fix typos found by codespell (pr/1040, pr/1044)
  (Dimitri Papadopoulos, reviewed by CM)
• Run stable tests weekly, pre-release tests nightly (pr/1025) (CM)
• Documentation updates to establish/clarify governance and decision
  making (pr/1019, pr/1020, pr/1022, pr/1018, pr/1017, pr/1016) (MB and CM)

• Writing NIfTIs with 64-bit integer dtypes is getting harder.
  Passing (u)int64 arrays to Nifti1Image and subclasses will warn unless
  a header or dtype option is passed; in the future this will become an
  error.
  Additionally, passing int or 'int' to set_data_dtype() now raises
  an error, requiring an explicit numpy dtype to make 64-bit integer images.
  (pr/1082) (CM, following discussions with Chris Rorden, Josh Teves, Jerome Dockes,
  and MB)
• Drop support for Python 3.6, Numpy < 1.17 (pr/1079) (CM)
• Fully removed the following APIs, which have raised errors on use
  since 3.0 (pr/980) (CM, reviewed by Jonathan Daniel)
  • nibabel.trackvis
  • nibabel.volumeutils.calculate_scale
  • nibabel.volumeutils.can_cast
  • nibabel.volumeutils.scale_min_max
  • nibabel.dataobj_images.DataobjImage.get_shape
  • nibabel.minc1.MincImage (use Minc1Image)
  • nibabel.minc1.MincFile (use Minc1File)
  • nibabel.filebasedimages.FileBasedImage.from_files
  • nibabel.filebasedimages.FileBasedImage.filespec_to_files
  • nibabel.filebasedimages.FileBasedImage.to_filespec
  • nibabel.filebasedimages.FileBasedImage.to_files
  • nibabel.arrayproxy.ArrayProxy.header
  • keep_file_open=="auto" parameter to load method (now must be boolean)

Most work on NiBabel so far has been by Matthew Brett (MB), Chris Markiewicz
(CM), Michael Hanke (MH), Marc-Alexandre Côté (MC), Ben Cipollini (BC), Paul
McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh (SG),
Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).

References like "pr/298" refer to github pull request numbers.

New feature release in the 4.0.x series.

• Add 'mask', 'compat' and 'smallest' dtype aliases to NIfTI images
  to allow for dtype specifications that can depend on the contents of the data.
  'mask' is a synonym for uint8. 'compat' will find the nearest
  Analyze-compatible (therefore widely supported) dtype that will not truncate
  the data. 'smallest' attempts to find the smallest integer dtype that will
  contain the data. (pr/1096) (CM, reviewed by Chris Rorden and Josh Teves)
• Add dtype arguments to Cifti2Image (pr/1111) (CM)
• Allow dtypes to be passed to Analyze-like images at __init__() and
  to_filename() to provide better control over output images. (pr/1082)
  (CM, following discussions with Chris Rorden, Josh Teves, Jerome Dockes, and MB)
• Allow compressed GIFTI images (MB, reviewed by CM)
• Add zstd compression support (pr/1005) (Andrew Van, reviewed by CM)
• Support ExternalFileBinary GIFTI data arrays (PM, reviewed by CM)

• Document InTemporaryDirectory as non-thread-safe (pr/1103) (Jacob Roberts,
  reviewed by MB)
• Unify Caret-XML-style metadata structure (GiftiMetaData, Cifti2MetaData)
  as dict-like (pr/1091) (CM, reviewed by Josh Teves and Hao-Ting Wang)
• Add __repr__ methods to GIFTI objects (pr/1092) (CM,
  reviewed by Josh Teves and Hao-Ting Wang)
• Create gzip header deterministically by default (pr/1024) (CM, reviewed by YOH)
• Provide clear error message when files with zip extensions don't match
  file contents (pr/1013) (Jérôme Dockès, reviewed by CM)

• Re-import externals/netcdf.py from scipy to resolve numpy API change (pr/1110)
  (CM)
• Resize ArraySequence.data without helper function to avoid reference increment
  (pr/1093) (MC, reviewed by CM)

• Update submodule URLs to use https over git protocol (pr/1097) (CM)
• Published BIAP 9: CoordinateImage API (pr/1084) (CM)
• Drop uses of deprecated distutils (pr/1073) (CM, reviewed by MB)
• Suppress LGTM false alarm "Clear-text logging of sensitive information"
  (pr/1052) (Dimitri Papadopoulos, reviewed by CM)
• Test on Python 3.10 (pr/1047) (CM)
• Fix typos found by codespell (pr/1040, pr/1044)
  (Dimitri Papadopoulos, reviewed by CM)
• Run stable tests weekly, pre-release tests nightly (pr/1025) (CM)
• Documentation updates to establish/clarify governance and decision
  making (pr/1019, pr/1020, pr/1022, pr/1018, pr/1017, pr/1016) (MB and CM)

• Writing NIfTIs with 64-bit integer dtypes is getting harder.
  Passing (u)int64 arrays to Nifti1Image and subclasses will warn unless
  a header or dtype option is passed; in the future this will become an
  error.
  Additionally, passing int or 'int' to set_data_dtype() now raises
  an error, requiring an explicit numpy dtype to make 64-bit integer images.
  (pr/1082) (CM, following discussions with Chris Rorden, Josh Teves, Jerome Dockes,
  and MB)
• Drop support for Python 3.6, Numpy < 1.17 (pr/1079) (CM)
• Fully removed the following APIs, which have raised errors on use
  since 3.0 (pr/980) (CM, reviewed by Jonathan Daniel)
  • nibabel.trackvis
  • nibabel.volumeutils.calculate_scale
  • nibabel.volumeutils.can_cast
  • nibabel.volumeutils.scale_min_max
  • nibabel.dataobj_images.DataobjImage.get_shape
  • nibabel.minc1.MincImage (use Minc1Image)
  • nibabel.minc1.MincFile (use Minc1File)
  • nibabel.filebasedimages.FileBasedImage.from_files
  • nibabel.filebasedimages.FileBasedImage.filespec_to_files
  • nibabel.filebasedimages.FileBasedImage.to_filespec
  • nibabel.filebasedimages.FileBasedImage.to_files
  • nibabel.arrayproxy.ArrayProxy.header
  • keep_file_open=="auto" parameter to load method (now must be boolean)

Most work on NiBabel so far has been by Matthew Brett (MB), Chris Markiewicz (CM), Michael Hanke (MH), Marc-Alexandre Côté (MC), Ben Cipollini (BC), Paul McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh (SG), Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).

References like "pr/298" refer to github pull request numbers.

Bug fix release in the 3.2.x series.

• Reshape CIFTI-2 affines to 4x4 when encoded as row-major sequence (pr/1059)
  (Andrew Van, reviewed by CM)
• Suggest nibabel.save() on calls to deprecated giftiio.write() (pr/1055)
  (Anibal Solon, reviewed by CM)
• Various bugs and style issues detected by LGTM (pr/1043, pr/1048)
  (Dimitri Papadopoulos, reviewed by CM)
• Resolve unclosed file warning in GiftiImage (pr/1038) (Lea Waller, reviewed by CM)
• Fix typos preventing deprecation warnings from being raised (pr/991)
  (Jonathan Daniel, reviewed by MB)
• Work around numpy SystemError to maintain expected error types (pr/1051) (CM)
• Use more constrained mock when testing optpkg (pr/983) (CM, reviewed by YOH)

• Add setuptools requirement to match usage (pr/1009)
  (Tomáš Hrnčiar, reviewed by CM)
• Fix grammar of headings in CoC (pr/996) (MB, reviewed by CM, Ariel Rokem)
• Set minimum pydicom to 1.0.0 (pr/1050) (CM)
• Submit coverage to codecov via pinned PyPI package (pr/1008) (CM)
• Upgrade versioneer to 0.19 (pr/967) (CM)
• Migrate to GitHub actions (pr/972) (CM, reviewed by Serge Koudoro)

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4