CHANGELOG.rst

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

3.1.0 (Under development)

Fixed

• Updated the :func:`.fast` wrapper to support some single-character command-line flags.

3.0.1 (Wednesday 15th April 2020)

Changed

• The :func:`.isMelodicDir` function now accepts directories that do not end with .ica, as long as all required files are present.

3.0.0 (Sunday 29th March 2020)

Added

• New wrapper functions for the FSL :class:`.fslstats`, :func:`.prelude` and :func:`applyxfm4D` commands.
• New firstDot option to the :func:`.path.getExt`, :func:`.path.removeExt`, and :func:`.path.splitExt`, functions, offering rudimentary support for double-barrelled filenames.
• The :func:`.nonlinear.applyDeformation` function now accepts a premat affine, which is applied to the input image before the deformation field.
• New :class:`.SubmitParams` class, providing a higer level interface for cluster submission.
• New :meth:`.FileTree.load_json` and :meth:`.FileTree.save_json` methods.

Changed

• fslpy now requires a minimum Python version of 3.7.
• The default value for the partial_fill option to :meth:`.FileTree.read` has been changed to False. Accordingly, the :class:`.FileTreeQuery` calls the :meth:`.FileTree.partial_fill` method on the FileTree it is given.
• The :func:`.gifti.relatedFiles` function now supports files with BIDS-style naming conventions.
• The :func:`.run.run` and :func:`.run.runfsl` functions now pass through any additional keyword arguments to subprocess.Popen or, if submit=True, to :func:`fslsub.submit`.
• The :func:`.fslsub.submit` function now accepts an env option, allowing environment variables to be specified.
• The :func:`.run.runfsl` function now raises an error on attempts to run a command which is not present in $FSLDIR/bin/ (e.g. ls).
• The :mod:`.bids` module has been updated to support files with any extension, not just those in the core BIDS specification (.nii, .nii.gz, .json, .tsv).
• The return value of a function decorated with :func:`.fileOrImage`, :func:`.fileOrArray`, or :func:`.fileOrText` is now accessed via an attribute called stdout, instead of output.
• Output files of functions decorated with :func:`.fileOrImage`, :func:`.fileOrArray`, or :func:`.fileOrText`, which have been loaded via the :attr:`.LOAD` symbol, can now be accessed as attributes of the returned results object, in addition to being accessed as dict items.
• Wrapper functions decorated with the :func:`.fileOrImage`, :func:`.fileOrArray`, or :func:`.fileOrText` decorators will now pass all arguments and return values through unchanged if an argument called submit is passed in, and is set to True (or any non-False value). Furthermore, in such a scenario a :exc:`ValueError` will be raised if any in-memory objects or LOAD symbols are passed.
• The :func:`.fileOrText` decorator has been updated to work with input values - file paths must be passed in as pathlib.Path objects, so they can be differentiated from input values.
• Loaded :class:`.Image` objects returned by :mod:`fsl.wrappers` functions are now named according to the wrapper function argument name.

Fixed

• Updated the :func:`.prepareArgs` function to use shlex.split when preparing shell command arguments, instead of performing a naive whitespace split.
• Fixed some bugs in the :func:`.fslsub.info` and :func:`.fslinfo.wait` functions.
• Fixed the :func:`.DeformationField.transform` method so it works with a single set of coordinates.
• :class:`.Image` creation does not fail if loadMeta is set, and a sidecar file containing invalid JSON is present.

Removed

• Removed the deprecated .StatisticAtlas.proportions, .StatisticAtlas.coordProportions, and .StatisticAtlas.maskProportions methods.
• Removed the deprecated indexed option to :meth:`.Image.__init__`.
• Removed the deprecated .Image.resample method.
• Removed the deprecated .image.loadIndexedImageFile function.
• Removed the deprecatd .FileTreeQuery.short_names and .Match.short_name properties.
• Removed the deprecated .idle.inIdle, .idle.cancelIdle, .idle.idleReset, .idle.getIdleTimeout, and .idle.setIdleTimeout functions.
• Removed the deprecated resample.calculateMatrix function.

2.8.4 (Monday 2nd March 2020)

Added

• Added a new partial_fill option to :meth:`.FileTree.read`, which effectively eliminates any variables which only have one value. This was added to accommodate some behavioural changes that were introduced in 2.8.2.

2.8.3 (Friday 28th February 2020)

Fixed

• Fixed a bug in the :meth:`.Image.save` method.

2.8.2 (Thursday 27th February 2020)

Fixed

• Fixed some subtle bugs in the :func:`.filetree.utils.get_all` function.

2.8.1 (Thursday 20th February 2020)

Fixed

• Fixed a bug where an error would be raised on attempts to load an image file without a BIDS-compatible name from a BIDS-like directory.