CHANGELOG.rst

This document contains the fslpy release history in reverse chronological order.

2.0.0 (Under development)

Added

• New :mod:`fsl.utils.filetree` package for defining and working with file/directory templates (Michiel Cottaar).
• Simple built-in :mod:`.deprecated` decorator.

Changed

• Removed support for Python 2.7 and 3.4.
• Minimum required version of nibabel is now 2.3.
• The :class:`.Image` class now fully delegates to nibabel for managing file handles.
• The :meth:`.Image.resample` method now supports images with more than three dimensions.
• The :func:`fsl.utils.fslsub.submit` now returns the job-id as a string rather than a one-element tuple. It now also accepts a nested sequence of job ids rather than just a flat sequence. This will also changes the output from the function wrappers in :mod:`fsl.wrappers` if submitted.

Removed

• Many deprecated items removed.

Fixed

• Added a missing image attribute in the :class:`.VoxelwiseConfoundEV` class.
• Make sure that FEAT Cluster objects (created by the :func:`.loadClusterResults` function) contain p and logp attributes, even when cluster thresholding was not used.
• Fix to the :class:`.ImageWrapper` regarding complex data types.

1.13.0 (Thursday 22nd November 2018)

Added

• New wrapper functions for :func:`.fsl_anat`, :func:`.applytopup` (Martin Craig).
• New :func:`.fileOrText` decorator for use in wrapper functions (Martin Craig).

Changed

• Various minor changes and enhancements to the FSL function :mod:`.wrappers` interfaces (Martin Craig).

Fixed

• The immv and imcp scripts now accept incorrect file extensions on input arguments.

1.12.0 (Sunday October 21st 2018)

Changed

• The extract_noise script has been renamed to :mod:`.fsl_ents`.
• Increased the minimum required version of dcm2niix in the :mod:`fsl.data.dicom` module.

Deprecated

• The extract_noise script.

1.11.1 (Friday September 14th 2018

Fixed

• Fixed a Python 2 incompatibility in the :mod:`.settings` module.

1.11.0 (Thursday September 13th 2018)

Added

• A couple of new convenience functions to the :mod:`.settings` module.

Changed

• Development (test and documentation dependencies) are no longer listed in setup.py - they now need to be installed manually.
• Removed conda build infrastructure.

1.10.3 (Sunday September 9th 2018)

Added

• The :func:`.parseVersionString` function accepts (and ignores) local version identifer strings.

1.10.2 (Friday September 7th 2018)

Fixed

• The :meth:`.Image.save` method was not handling memory-mapped images correctly.

1.10.1 (Friday August 3rd 2018)

Changed

• Minor adjustmenets to improve Windows compatibility.

Fixed

• The :mod:`.FEATImage.getCOPE` method was returning PE images.

1.10.0 (Wednesday July 18th 2018)

Added

• A new script, :mod:`.extract_noise`, which can be used to extract ICA component time courses from a MELODIC ICA analysis.
• New :func:`.path.allFiles` function which returns all files underneath a directory.
• The :func:`.fileOrImage` and :func:`.fileOrArray` decorators now support loading of files which are specified with an output basename.
• New :mod:`.fast` wrapper function for the FSL FAST tool.

Changed

• When using the :func:`.run.run` function, the command output/error streams are now forwarded immediately.
• Removed dependency on pytest-runner.

1.9.0 (Monday June 4th 2018)

Added

• New :meth:`.Image.data` property method, for easy access to image data as a numpy array.
• New log option to the :func:`.run.run` function, allowing more fine-grained control over sub-process output streams.
• New :meth:`.Platform.fsldevdir` property, allowing the $FSLDEVDIR environment variable to be queried/changed.

Changed

• :meth:`.Image.ndims` has been renamed to :meth:`.Image.ndim`, to align more closely with numpy naming conventions.
• The err and ret parameters to the :func:`.run.run` function have been renamed to stderr and exitcode respectively.
• The :func:`.runfsl` function will give priority to the $FSLDEVDIR environment variable if it is set.

Deprecated

• :meth:`.Image.ndims`.
• The err and ret parameters to :func:`.run.run`.

1.8.1 (Friday May 11th 2018)

Changed

• The :func:`.fileOrImage` decorator function now accepts :class:`.Image` objects as well as nibabel image objects.

1.8.0 (Thursday May 3rd 2018)

Added

• New :mod:`.wrappers` package, containing wrapper functions for a range of FSL tools.
• New :mod:`fsl.utils.run` module, to replace the :mod:`fsl.utils.callfsl` module.
• New :mod:`fsl.utils.fslsub` module, containing a :func:`.fslsub.submit` function which submits a cluster job via fsl_sub.
• Assertions (in the :mod:`.assertions` module) can be disabled with the new :func:`.assertions.disabled` context manager.
• New :mod:`fsl.utils.parse_data` module containing various neuroimaging data constructors for use with argparse.
• The :func:`.memoize.skipUnchanged` decorator has an invalidate function which allows its cache to be cleared.

Changed

• The :func:`.tempdir` function has an option to not change to the newly created directory.

Deprecated

• The :mod:`fsl.utils.callfsl` module (replaced with :mod:`fsl.utils.run`).

1.7.2 (Monday March 19th 2018)

Added

• Added the :meth:`.MGHImage.voxToSurfMat` and related properties, giving access to the voxel-to-surface affine for an MGH image.

1.7.1 (Monday March 12th 2018)

Changed

• Adjusted :func:`.parseVersionString` so it accepts .dev* suffixes.

Fixed

• Removed deprecated use of :func:`.imagewrapper.canonicalShape`.

1.7.0 (Tuesday March 6th 2018)

Added

• The :mod:`fsl.utils.assertions` module contains a range of functions which can be used to assert that some condition is met.
• The :mod:`fsl.utils.ensure` module contains a range of functions (currently just one) which can be used to ensure that some condiution is met.

Changed

• The :mod:`.settings` module now saves its files in a format that is compatible with Python 2 and 3.
• The :func:`.tempdir` function now accepts a root argument, which specifies the location in which the temporary directory should be created.
• An image's data source can now be set via :meth:`.Image.__init__`.
• :meth:`.MGHImage` objects now have a :meth:`.MGHImage.save` method.
• Adjustments to the conda package build and deployment process.
• The :func:`.ImageWrapper.canonicalShape` function has been moved to the :mod:`.image` class.
• The :func:`.ImageWrapper.naninfrange` function has been moved into its own :mod:`.naninfrange` module.

Fixed

• Fixed a bug in the :class:`.MutexFactory` class.

Deprecated

• :func:`.ImageWrapper.canonicalShape` (moved to the :mod:`.image` module)
• :func:`.ImageWrapper.naninfrange` function (moved to the :mod:`.naninfrange` module)

1.6.8 (Monday February 12th 2018)

• The atlasq, immv, imcp and imglob scripts suppress some warnings.

1.6.7 (Friday February 9th 2018)

• More further adjustments to the conda package build.
• Adjustments to pypi source distribution - the requirements-extra.txt file was not being included.

1.6.6 (Thursday February 8th 2018)