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@effigies effigies released this Jun 30, 2020 · 71 commits to master since this release

DOI

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.

3.1.1 (Friday 26 June 2020)

Bug-fix release in the 3.1.x series.

These are small compatibility fixes that support ARM64 architecture and indexed_gzip>=1.3.0.

Bug fixes

  • Detect IndexedGzipFile as compressed file type (pr/925) (PM, reviewed by CM)
  • Correctly cast nan when testing array_to_file, fixing ARM64 builds (pr/862) (CM, reviewed by MB)
Assets 2

@effigies effigies released this Apr 20, 2020 · 93 commits to master since this release

DOI

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.

3.1.0 (Monday 20 April 2020)

New feature release in the 3.1.x series.

New features

  • Conformation function (processing.conform) and CLI tool (nib-conform) to apply shape, orientation and zooms (pr/853) (Jakub Kaczmarzyk, reviewed by CM, YOH)
  • Affine rescaling function (affines.rescale_affine) to update dimensions and voxel sizes (pr/853) (CM, reviewed by Jakub Kaczmarzyk)

Bug fixes

  • Delay import of h5py until neded (pr/889) (YOH, reviewed by CM)

Maintenance

  • Fix typo in documentation (pr/893) (Zvi Baratz, reviewed by CM)
  • Tests converted from nose to pytest (pr/865 + many sub-PRs) (Dorota Jarecka, Krzyzstof Gorgolewski, Roberto Guidotti, Anibal Solon, Or Duek, CM)

API changes and deprecations

  • kw_only_meth/kw_only_func decorators are deprecated (pr/848) (RM, reviewed by CM)
Assets 2

@effigies effigies released this Apr 8, 2020 · 694 commits to master since this release

DOI

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, and Stephan Gerhard.

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

2.5.2 (Wednesday 8 April 2020)

Bug-fix release in the 2.5.x series. This is an extended-support series, providing bug fixes for Python 2.7 and 3.4.

This and all future releases in the 2.5.x series will be incompatible with Python 3.9. The last compatible series of numpy and scipy are 1.16.x and 1.2.x, respectively.

If you are able to upgrade to Python 3, it is recommended to upgrade to NiBabel 3.

Bug fixes

  • Change strings with invalid escapes to raw strings (pr/827) (EL, reviewed by CM)
  • Re-import externals/netcdf.py from scipy to resolve numpy deprecation (pr/821) (CM)

Maintenance

  • Set maximum numpy to 1.16.x, maximum scipy to 1.2.x (pr/901) (CM)
Assets 2

@effigies effigies released this Mar 9, 2020 · 413 commits to master since this release

DOI

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, and Stephan Gerhard.

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

3.0.2 (Monday 9 March 2020)

Bug fixes

  • Attempt to find versioneer version when building docs (pr/894) (CM)
  • Delay import of h5py until neded (backport of pr/889) (YOH, reviewed by CM)

Maintenance

  • Fix typo in documentation (backport of pr/893) (Zvi Baratz, reviewed by CM)
  • Set minimum matplotlib to 1.5.3 to ensure wheels are available on all supported Python versions. (backport of pr/887) (CM)
  • Remove pyproject.toml for now. (issue/859) (CM)
Assets 2

@effigies effigies released this Jan 27, 2020 · 428 commits to master since this release

DOI

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, and Stephan Gerhard.

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

3.0.1 (Monday 27 January 2020)

Bug fixes

  • Test failed by using array method on tuple. (pr/860) (Ben Darwin, reviewed by CM)
  • Validate ExpiredDeprecationErrors, promoted by 3.0 release from DeprecationWarnings. (pr/857) (CM)

Maintenance

  • Remove logic accommodating numpy without float16 types. (pr/866) (CM)
  • Accommodate new numpy dtype strings. (pr/858) (CM)
Assets 2

@effigies effigies released this Dec 18, 2019 · 445 commits to master since this release

DOI

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, and Stephan Gerhard.

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

3.0.0 (Wednesday 18 December 2019)

New features

  • ArrayProxy __array__() now accepts a dtype parameter, allowing numpy.array(dataobj, dtype=...) calls, as well as casting directly with a dtype (for example, numpy.float32(dataobj)) to control the output type. Scale factors (slope, intercept) are applied, but may be cast to narrower types, to control memory usage. This is now the basis of img.get_fdata(), which will scale data in single precision if the output type is float32. (pr/844) (CM, reviewed by Alejandro de la Vega, Ross Markello)
  • GiftiImage method agg_data() to return usable data arrays (pr/793) (Hao-Ting Wang, reviewed by CM)
  • Accept os.PathLike objects in place of filenames (pr/610) (Cameron Riddell, reviewed by MB, CM)
  • Function to calculate obliquity of affines (pr/815) (Oscar Esteban, reviewed by MB)

Enhancements

  • Improve testing of data scaling in ArrayProxy API (pr/847) (CM, reviewed by Alejandro de la Vega)
  • Document SpatialImage.slicer interface (pr/846) (CM)
  • get_fdata(dtype=np.float32) will attempt to avoid casting data to np.float64 when scaling parameters would otherwise promote the data type unnecessarily. (pr/833) (CM, reviewed by Ross Markello)
  • ArraySequence now supports a large set of Python operators to combine or update in-place. (pr/811) (MC, reviewed by Serge Koudoro, Philippe Poulin, CM, MB)
  • Warn, rather than fail, on DICOMs with unreadable Siemens CSA tags (pr/818) (Henry Braun, reviewed by CM)
  • Improve clarity of coordinate system tutorial (pr/823) (Egor Panfilov, reviewed by MB)

Bug fixes

  • Sliced Tractograms no longer apply_affine to the original Tractogram's streamlines. (pr/811) (MC, reviewed by Serge Koudoro, Philippe Poulin, CM, MB)
  • Re-import externals/netcdf.py from scipy to resolve numpy deprecation (pr/821) (CM)

Maintenance

  • Remove replicated metadata for packaged data from MANIFEST.in (pr/845) (CM)
  • Support Python >=3.5.1, including Python 3.8.0 (pr/787) (CM)
  • Manage versioning with slightly customized Versioneer (pr/786) (CM)
  • Reference Nipy Community Code and Nibabel Developer Guidelines in GitHub community documents (pr/778) (CM, reviewed by MB)

API changes and deprecations

  • Fully remove deprecated checkwarns and minc modules. (pr/852) (CM)
  • The keep_file_open argument to file load operations and ArrayProxys no longer acccepts the value "auto", raising a ValueError. (pr/852) (CM)
  • Deprecate ArraySequence.data in favor of ArraySequence.get_data(), which will return a copy. ArraySequence.data now returns a read-only view. (pr/811) (MC, reviewed by Serge Koudoro, Philippe Poulin, CM, MB)
  • Deprecate DataobjImage.get_data() API, to be removed in nibabel 5.0 (pr/794, pr/809) (CM, reviewed by MB)
Assets 2

@effigies effigies released this Dec 12, 2019 · 447 commits to master since this release

DOI

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, and Stephan Gerhard.

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

3.0.0rc2 (Wednesday 11 December 2019)

New features

  • ArrayProxy __array__() now accepts a dtype parameter, allowing numpy.array(dataobj, dtype=...) calls, as well as casting directly with a dtype (for example, numpy.float32(dataobj)) to control the output type. Scale factors (slope, intercept) are applied, but may be cast to narrower types, to control memory usage. This is now the basis of img.get_fdata(), which will scale data in single precision if the output type is float32. (pr/844) (CM, reviewed by Alejandro de la Vega, Ross Markello)
  • GiftiImage method agg_data() to return usable data arrays (pr/793) (Hao-Ting Wang, reviewed by CM)
  • Accept os.PathLike objects in place of filenames (pr/610) (Cameron Riddell, reviewed by MB, CM)
  • Function to calculate obliquity of affines (pr/815) (Oscar Esteban, reviewed by MB)

Enhancements

  • Improve testing of data scaling in ArrayProxy API (pr/847) (CM, reviewed by Alejandro de la Vega)
  • Document SpatialImage.slicer interface (pr/846) (CM)
  • get_fdata(dtype=np.float32) will attempt to avoid casting data to np.float64 when scaling parameters would otherwise promote the data type unnecessarily. (pr/833) (CM, reviewed by Ross Markello)
  • ArraySequence now supports a large set of Python operators to combine or update in-place. (pr/811) (MC, reviewed by Serge Koudoro, Philippe Poulin, CM, MB)
  • Warn, rather than fail, on DICOMs with unreadable Siemens CSA tags (pr/818) (Henry Braun, reviewed by CM)
  • Improve clarity of coordinate system tutorial (pr/823) (Egor Panfilov, reviewed by MB)

Bug fixes

  • Sliced Tractograms no longer apply_affine to the original Tractogram's streamlines. (pr/811) (MC, reviewed by Serge Koudoro, Philippe Poulin, CM, MB)
  • Re-import externals/netcdf.py from scipy to resolve numpy deprecation (pr/821) (CM)

Maintenance

  • Remove replicated metadata for packaged data from MANIFEST.in (pr/845) (CM)
  • Support Python >=3.5.1, including Python 3.8.0 (pr/787) (CM)
  • Manage versioning with slightly customized Versioneer (pr/786) (CM)
  • Reference Nipy Community Code and Nibabel Developer Guidelines in GitHub community documents (pr/778) (CM, reviewed by MB)

API changes and deprecations

  • Fully remove deprecated checkwarns and minc modules. (pr/852) (CM)
  • The keep_file_open argument to file load operations and ArrayProxys no longer acccepts the value "auto", raising a ValueError. (pr/852) (CM)
  • Deprecate ArraySequence.data in favor of ArraySequence.get_data(), which will return a copy. ArraySequence.data now returns a read-only view. (pr/811) (MC, reviewed by Serge Koudoro, Philippe Poulin, CM, MB)
  • Deprecate DataobjImage.get_data() API, to be removed in nibabel 5.0 (pr/794, pr/809) (CM, reviewed by MB)
Assets 2

@effigies effigies released this Nov 16, 2019 · 485 commits to master since this release

DOI

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, and Stephan Gerhard.

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

3.0.0rc1 (Saturday 16 November 2019)

Release candidate for NiBabel 3.0, initiating a minimum one-month testing window.

Downstream projects are requested to test against the release candidate by installing with pip install --pre nibabel.

New features

  • ArrayProxy method get_scaled() scales data with a dtype of a specified precision, promoting as necessary to avoid overflow. This is to used in img.get_fdata() to control memory usage. (pr/833) (CM, reviewed by Ross Markello)
  • GiftiImage method agg_data() to return usable data arrays (pr/793) (Hao-Ting Wang, reviewed by CM)
  • Accept os.PathLike objects in place of filenames (pr/610) (Cameron Riddell, reviewed by MB, CM)
  • Function to calculate obliquity of affines (pr/815) (Oscar Esteban, reviewed by MB)

Enhancements

  • get_fdata(dtype=np.float32) will attempt to avoid casting data to np.float64 when scaling parameters would otherwise promote the data type unnecessarily. (pr/833) (CM, reviewed by Ross Markello)
  • ArraySequence now supports a large set of Python operators to combine or update in-place. (pr/811) (MC, reviewed by Serge Koudoro, Philippe Poulin, CM, MB)
  • Warn, rather than fail, on DICOMs with unreadable Siemens CSA tags (pr/818) (Henry Braun, reviewed by CM)
  • Improve clarity of coordinate system tutorial (pr/823) (Egor Panfilov, reviewed by MB)

Bug fixes

  • Sliced Tractograms no longer apply_affine to the original Tractogram's streamlines. (pr/811) (MC, reviewed by Serge Koudoro, Philippe Poulin, CM, MB)
  • Re-import externals/netcdf.py from scipy to resolve numpy deprecation (pr/821) (CM)

Maintenance

  • Support Python >=3.5.1, including Python 3.8.0 (pr/787) (CM)
  • Manage versioning with slightly customized Versioneer (pr/786) (CM)
  • Reference Nipy Community Code and Nibabel Developer Guidelines in GitHub community documents (pr/778) (CM, reviewed by MB)

API changes and deprecations

  • Deprecate ArraySequence.data in favor of ArraySequence.get_data(), which will return a copy. ArraySequence.data now returns a read-only view. (pr/811) (MC, reviewed by Serge Koudoro, Philippe Poulin, CM, MB)
  • Deprecate DataobjImage.get_data() API, to be removed in nibabel 5.0 (pr/794, pr/809) (CM, reviewed by MB)
Assets 2

@effigies effigies released this Sep 23, 2019 · 708 commits to master since this release

DOI

Bug fix release for the 2.5.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, and Stephan Gerhard.

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

2.5.1 (Monday 23 September 2019)

The 2.5.x series is the last with support for either Python 2 or Python 3.4. Extended support for this series 2.5 will last through December 2020.

Enhancements

  • Ignore endianness in nib-diff if values match (pr/799) (YOH, reviewed by CM)

Bug fixes

  • Correctly handle Philips DICOMs w/ derived volume (pr/795) (Mathias Goncalves, reviewed by CM)
  • Raise CSA tag limit to 1000, parametrize for future relaxing (pr/798, backported to 2.5.x in pr/800) (Henry Braun, reviewed by CM, MB)
  • Coerce data types to match NIfTI intent codes when writing GIFTI data arrays (pr/806) (CM, reported by Tom Holroyd)

Maintenance

  • Require h5py 2.10 for Windows + Python < 3.6 to resolve unexpected dtypes in Minc2 data (pr/804) (CM, reviewed by YOH)

API changes and deprecations

  • Deprecate nicom.dicomwrappers.Wrapper.get_affine() in favor of affine property; final removal in nibabel 4.0 (pr/796) (YOH, reviewed by CM)
Assets 2

@effigies effigies released this Aug 5, 2019 · 751 commits to master since this release

DOI

New feature release in the 2.5.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, and Stephan Gerhard.

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

2.5.0 (Sunday 4 August 2019)

The 2.5.x series is the last with support for either Python 2 or Python 3.4. Extended support for this series 2.5 will last through December 2020.

Thanks for the test ECAT file and fix provided by Andrew Crabb.

Enhancements

  • Add SerializableImage class with to/from_bytes methods (#644) (CM, reviewed by MB)
  • Check CIFTI-2 data shape matches shape described by header (#774) (Michiel Cottaar, reviewed by CM)

Bug fixes

  • Handle stricter numpy casting rules in tests (#768) (CM, reviewed by PM)
  • TRK header fields flipped in files written on big-endian systems (#782) (CM, reviewed by YOH, MB)
  • Load multiframe ECAT images with Python 3 (CM and Andrew Crabb)

Maintenance

  • Fix CodeCov paths on Appveyor for more accurate coverage (#769) (CM)
  • Move to setuptools and reduce use nisext functions (#764) (CM, reviewed by YOH)
  • Better handle test setup/teardown (#785) (CM, reviewed by YOH)

API changes and deprecations

  • Effect threatened warnings and set some deprecation timelines (#755) (CM)
    • Trackvis methods now default to v2 formats
    • nibabel.trackvis scheduled for removal in nibabel 4.0
    • nibabel.minc and nibabel.MincImage will be removed in nibabel 3.0
Assets 2
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