3.0.0rc2

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)

3.0.0rc1

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)

2.5.1

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)

2.5.0

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

2.4.1

Bug fix release for the 2.4.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.

2.4.1 (Monday 27 May 2019)

Contributions from Egor Pafilov, Jath Palasubramaniam, Richard Nemec, and
Dave Allured.

Enhancements

• Enable mmap, keep_file_open options when loading any
  DataobjImage (pr/759) (CM, reviewed by PM)

Bug fixes

• Ensure loaded GIFTI files expose writable data arrays (pr/750) (CM,
  reviewed by PM)
• Safer warning registry manipulation when checking for overflows (pr/753)
  (CM, reviewed by MB)
• Correctly write .annot files with duplicate lables (pr/763) (Richard Nemec
  with CM)

Maintenance

• Fix typo in coordinate systems doc (pr/751) (Egor Panfilov, reviewed by
  CM)
• Replace invalid MINC1 test file with fixed file (pr/754) (Dave Allured
  with CM)
• Update Sphinx config to support recent Sphinx/numpydoc (pr/749) (CM,
  reviewed by PM)
• Pacify FutureWarning and DeprecationWarning from h5py, numpy
  (pr/760) (CM)
• Accommodate Python 3.8 deprecation of collections.MutableMapping
  (pr/762) (Jath Palasubramaniam, reviewed by CM)

API changes and deprecations

• Deprecate keep_file_open == 'auto' (pr/761) (CM, reviewed by PM)

2.4.0

New feature release for the 2.4.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.

2.4.0 (Monday 1 April 2019)

New features

• Alternative Axis-based interface for manipulating CIFTI-2 headers (#641) (Michiel Cottaar, reviewed by Demian Wassermann, CM, SG)

Enhancements

• Accept TCK files produced by tools with other delimiter/EOF defaults (#720) (Soichi Hayashi, reviewed by CM, MB, MC)
• Allow BrainModels or Parcels to contain a single vertex in CIFTI (#739) (Michiel Cottaar, reviewed by CM)
• Support for NIFTI_XFORM_TEMPLATE_OTHER xform code (#743) (CM)

Bug fixes

• Skip refcheck in ArraySequence construction/extension (#719) (Ariel Rokem, reviewed by CM, MC)
• Use safe resizing for ArraySequence extension (#724) (CM, reviewed by MC)
• Fix typo in error message (#726) (Jon Haitz Legarreta Gorroño, reviewed by CM)
• Support DICOM slice sorting in Python 3 (#728) (Samir Reddigari, reviewed by CM)
• Correctly reorient dim_info when reorienting NIfTI images (#744) (Konstantinos Raktivan, CM, reviewed by CM)

Maintenance

• Import updates to reduce upstream deprecation warnings (#711, #705, #738) (EL, YOH, reviewed by CM)
• Delay import of nibabel.testing, nose and mock to speed up import (#699) (CM)
• Increase coverage testing, drop coveralls (#722, #732) (CM)
• Add Zenodo metadata, sorted by commits (#732) (CM + others)
• Update author listing and copyrights (#742) (MB, reviewed by CM)

2.3.3

Bug fix release for the 2.3 series.

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

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

2.3.3 (Wednesday 16 January 2019)

Maintenance

• Restore six dependency (pr/714) (CM, reviewed by Gael Varoquaux, MB)

2.3.2

Bug fix release for the 2.3 series.

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

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

2.3.2 (Wednesday 2 January 2019)

Enhancements

• Enable toggling crosshair with Ctrl-x in OrthoSlicer3D viewer (pr/701)
  (Miguel Estevan Moreno, reviewed by CM)

Bug fixes

• Read .PAR files corresponding to ADC maps (pr/685) (Gregory R. Lee, reviewed
  by CM)
• Increase maximum number of items read from Siemens CSA format (Igor Solovey,
  reviewed by CM, MB)
• Check boolean dtypes with numpy.issubdtype(..., np.bool_) (pr/707)
  (Jon Haitz Legarreta Gorroño, reviewed by CM)

Maintenance

• Fix small typos in parrec2nii help text (pr/682) (Thomas Roos, reviewed by
  MB)
• Remove deprecated calls to numpy.asscalar (pr/686) (CM, reviewed by
  Gregory R. Lee)
• Update QA directives to accommodate Flake8 3.6 (pr/695) (CM)
• Update DOI links to use https://doi.org (pr/703) (Katrin Leinweber,
  reviewed by CM)
• Remove deprecated calls to numpy.fromstring (pr/700) (Ariel Rokem,
  reviewed by CM, MB)
• Drop distutils support, require bz2file for Python 2.7 (pr/700)
  (CM, reviewed by MB)
• Replace mutable bytes hack, disabled in numpy pre-release, with
  bytearray/readinto strategy (pr/700) (Ariel Rokem, CM, reviewed by
  CM, MB)

API changes and deprecations

• Add Opener.readinto method to read file contents into pre-allocated buffers
  (pr/700) (Ariel Rokem, reviewed by CM, MB)

2.3.1

Bug fix release for the 2.3 series.

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

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

2.3.1 (Tuesday 16 October 2018)

New features

• nib-diff command line tool for comparing image files (pr/617, pr/672,
  pr/678) (CC, reviewed by YOH, Pradeep Raamana and CM)

Enhancements

• Speed up reading of numeric arrays in CIFTI2 (pr/655) (Michiel Cottaar,
  reviewed by CM)
• Add ndim property to ArrayProxy and DataobjImage (pr/674) (CM,
  reviewed by MB)

Bug fixes

• Deterministic deduction of slice ordering in degenerate cases (pr/647)
  (YOH, reviewed by CM)
• Allow 0ms TR in MGH files (pr/653) (EL, reviewed by CM)
• Allow for PPC64 little-endian long doubles (pr/658) (MB, reviewed by CM)
• Correct construction of FreeSurfer annotation labels (pr/666) (CM, reviewed
  by EL, Paul D. McCarthy)
• Fix logic for persisting filehandles with indexed-gzip (pr/679) (Paul D.
  McCarthy, reviewed by CM)

Maintenance

• Fix semantic error in coordinate systems documentation (pr/646) (Ariel
  Rokem, reviewed by CM, MB)
• Test on Python 3.7, minor associated fixes (pr/651) (CM, reviewed by Gregory
  R. Lee, MB)

2.3.0

New feature release for the 2.3 series.

Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke (MH)
Ben Cipollini (BC), Marc-Alexandre Côté (MC), Chris Markiewicz (CM), Stephan
Gerhard (SG) and Eric Larson (EL).

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

New features

• TRK <=> TCK streamlines conversion CLI tools (pr/606) (MC, reviewed by CM)
• Image slicing for SpatialImages (pr/550) (CM)

Enhancements

• Simplfiy MGHImage and add footer fields (pr/569) (CM, reviewed by MB)
• Force sform/qform codes to be ints, rather than numpy types (pr/575) (Paul
  McCarthy, reviewed by MB, CM)
• Auto-fill color table in FreeSurfer annotation file (pr/592) (Paul McCarthy,
  reviewed by CM, MB)
• Set default intent code for CIFTI2 images (pr/604) (Mathias Goncalves,
  reviewed by CM, Satra Ghosh, MB, Tim Coalson)
• Raise informative error on empty files (pr/611) (Pradeep Raamana, reviewed
  by CM, MB)
• Accept degenerate filenames such as .nii (pr/621) (Dimitri
  Papadopoulos-Orfanos, reviewed by Yaroslav Halchenko)
• Take advantage of IndexedGzipFile drop_handles flag to release
  filehandles by default (pr/614) (Paul McCarthy, reviewed by CM, MB)

Bug fixes

• Preserve first point of LazyTractogram (pr/588) (MC, reviewed by Nil
  Goyette, CM, MB)
• Stop adding extraneous metadata padding (pr/593) (Jon Stutters, reviewed by
  CM, MB)
• Accept lower-case orientation codes in TRK files (pr/600) (Kesshi Jordan,
  MB, reviewed by MB, MC, CM)
• Annotation file reading (pr/592) (Paul McCarthy, reviewed by CM, MB)
• Fix buffer size calculation in ArraySequence (pr/597) (Serge Koudoro,
  reviewed by MC, MB, Eleftherios Garyfallidis, CM)
• Resolve UnboundLocalError in Python 3 (pr/607) (Jakub Kaczmarzyk,
  reviewed by MB, CM)
• Do not crash on non-ImportError failures in optional imports (pr/618)
  (Yaroslav Halchenko, reviewed by CM)
• Return original array from get_fdata for array image, if no cast
  required (pr/638, MB, reviewed by CM)

Maintenance

• Use SSH address to use key-based auth (pr/587) (CM, reviewed by MB)
• Fix doctests for numpy 1.14 array printing (pr/591) (MB, reviewed by CM)
• Refactor for pydicom 1.0 API changes (pr/599) (MB, reviewed by CM)
• Increase test coverage, remove unreachable code (pr/602) (CM, reviewed by
  Yaroslav Halchenko, MB)
• Move nib-ls and other programs to a new cmdline module (pr/601, pr/615)
  (Chris Cheng, reviewed by MB, Yaroslav Halchenko)
• Remove deprecated numpy indexing (EL, reviewed by CM)
• Update documentation to encourage get_fdata over get_data (pr/637,
  MB, reviewed by CM)

API changes and deprecations

• Support for keep_file_open = 'auto' as a parameter to Opener() will
  be deprecated in 2.4, for removal in 3.0. Accordingly, support for
  openers.KEEP_FILE_OPEN_DEFAULT = 'auto' will be dropped on the same
  schedule.
• Drop-in support for indexed_gzip < 0.7 has been removed.