CHANGELOG.rst

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

3.18.3 (Friday 3rd May 2024)

Fixed

• Fixed an issue with :mod:fsl.wrappers functions not finding output files when $FSLOUTPUTTYPE is set to something other than NIFTI_GZ (!452).

3.18.2 (Wednesday 3rd April 2024)

Fixed

• Made some changes to the :mod:`fsl.utils.run` module to improve compatibility with [dill](https://github.com/uqfoundation/dill/) (!449).

3.18.1 (Tuesday 5th March 2024)

Fixed

• Fixed an issue which could cause :mod:`fsl.wrappers` functions to crash when being executed concurrently (!446).

3.18.0 (Thursdday 22nd February 2024)

Added

• New wrapper function for the FLIRT midtrans command (!443).
• The :class:`.Image` class now accepts a version parameter, as an easy way of specifying the NIfTI file format version (!443).

3.17.0 (Friday 9th February 2024)

Added

• New wrapper function for the FLIRT makerot command (!441).
• New wrapper functions for the imcp, immv, imrm, imln, imglob and imtest commands. These are all implemented within fslpy, so the wrapper functions invoke them directly (i.e. within the same process) (!441).

3.16.1 (Wednesday 17th January 2024)

Added

• The :func:`run` function now allows the log{'stdout'] and log{'stderr'} options (used for capturing the standard output/error streams of a called process) to be either file-likes or callables (!438).

3.16.0 (Thursday 21st December 2023)

Added

• Added more functions to the :class:`.fslmaths` wrapper (!431).
• New :func:`.smoothest` wrapper function (!432).
• New :func:`.get_standard` wrapper function (!433).
• New :func:`.vecreg` wrapper function (!434).

3.15.4 (Monday 27th November 2023)

Added

• New silent option to the :func:`.run` function = passing silent=True is equivalent to passing log={'tee':False} (!428).
• New prefix option to the :func:`.tempdir` function, which is passed through to tempfile.mkdtemp (!429).

3.15.3 (Thursday 16th November 2023)

Changed

• Adjusted the :func:`.loadLabelFile` function to accept files with missing entries, and files which only contain the MELODIC directory path and list of noisy components (!424, !425).

Fixed

• Fixed a bug in the :func:`.run.hold` function (!426).

3.15.2 (Wednesday 4th October 2023)

Fixed

• Removed the obsolete :func:`fsl.wrappers.misc.cluster` wrapper function (!422).

3.15.1 (Monday 25th September 2023)

Fixed

• Fixed a problem with some unit tests (!420).

3.15.0 (Monday 25th September 2023)

Added

• New :func:`.cluster` wrapper function for the FSL cluster / fsl-cluster command (!417).

Changed

• All metadata stored in GIfTI files is now copied by :class:`.GiftiMesh` instances into their :class:`.Meta` store (!416).

3.14.1 (Thursday 31st August 2023)

Fixed

• Fixed a bug in :meth:`.Image.__setitem__` - change listeners were being passed an un-normalised slice object (with slices for trailing dimensions of length 1 present) (!414).

3.14.0 (Wednesday 30th August 2023)

Added

• New :func:`.affine.flip` function, for applying a flip/inversion to the axes of an affine transformation (!403).

Changed

• The sform/qform fields of a :class:`.DeformationField` instance are automatically set from the reference image if they are not already set (!402).
• Replaced setup.py-based build system with pyproject.toml (!402).
• Tests have been moved into the fsl/tests/ package (!402).
• Updated the `immv/imcp scripts to support FSLOUTPUTTYPE=ANALYZE (!405).

Fixed

• Updated the `immv/imcp scripts to honour the $FSLOUTPUTTYPE environment variable more closely - conversions between NIFTI1 and NIFTI2 were not being performed correctly (!405).

3.13.3 (Monday 17th July 2023)

Changed

• Callback functions registered with :class:`.Notifier` instances no longer need to accept three arguments (!400).

3.13.2 (Monday 3rd July 2023)

Added

• New scaleAtOrigin option to the :func:`.affine.compose` function, which allows the origin to be preserved by scaling parameters (!398).

3.13.1 (Tuesday 13th June 2023)

Fixed

• Fixed some minor issues with API documentation (!396).

3.13.0 (Monday 12th June 2023)

Added

• New :func:`.runfunc` function which can be used to execute a Python function in a separate process (or as a submitted cluster job), via the :func:`~fsl.utils.run.func_to_cmd` function (!390).
• New keys(), values(), and items() methods on the :class:`.Cache` class (!391).

Changed

• The :func:`.run.func_to_cmd`, :func:`.run.hold`, and :func:`.run.job_output` functions have been moved from :mod:`fsl.utils.fslsub` to the :mod:`fsl.utils.run` module (!390).

Deprecated

• The :mod:`fsl.utils.fslsub` module has been deprecated, and scheduled for removal in fslpy 4.0.0 (!390).

3.12.1 (Tuesday 23rd May 2023)

Fixed

• The :mod:`fsl.scripts.Text2Vest` now handles column vector inputs correctly (!387, !388).
• The :func:`.tempdir` function was not changing back to the original working directory when the override argument was used (!388).

3.12.0 (Friday 19th May 2023)

Added

• New :func:`.randomise` wrapper function.

Changed

• The :func:`.fslmaths` wrapper function now allows the -dt and -odt options to be set (!381).
• Assertions (from the :mod:`.assertions` module) called within wrapper functions are now disabled if the command is to be submitted via fsl_sub (!382).
• The :class:`.Image` class will now resolve symlinks when loading images from file (!383).

Fixed

• The :func:`.fslstats` wrapper no longer overwrites the log option that is passed to :func:`~.run.run`, if a :func:`.wrapperconfig` context is active (!381).