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CHANGELOG.rst 33.86 KiB

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.

2.8.0 (Wednesday 29th January 2020)

Added

  • New :meth:`.Nifti.adjust` method, for creating a copy of a :class:`.Nifti` header with adjusted shape, pixdims, and affine. This can be useful for creating a resampling reference.
  • New :func:`.affine.rescale` function, for adjusting a scaling matrix.
  • New :func:`.mghimage.voxToSurfMat` function, for creating a voxel-to-freesurfer affine transform from any image.

Changed

  • The :class:`.ImageWrapper` now maintains its own image data cache, rather than depending on nibabel.
  • Internal changes to avoid using the deprecated nibabel.dataobj_images.DataobjImage.get_data method.

Fixed

  • Improved the algorithm used by the :func:`.mesh.needsFixing` function.
  • The :meth:`.fslmaths.run` method now accepts :attr:`.wrappers.LOAD` as an output specification.
  • Fixed a bug in the :class:`.Mesh` class to prevent indices from being loaded as floating point type.
  • Fixed a bug in the :func:`.resample` function.
  • Fixed a bug in the :class:`.MGHImage` class, which was causing pixdims to be overridden by scales derived from the affine.

Deprecated

  • :func:`.calculateMatrix` - its functionality has been moved to the :func:`.affine.rescale` function.

2.7.0 (Wednesday 6th November 2019)

Added

  • New until option to the :func:`.idle.block` function.
  • New :meth:`.Idle.neverQueue` setting, which can be used to force all tasks passed to :func:`.idle.idle` to be executed synchronously.
  • New :meth:`.IdleLoop.synchronous` context manager, to temporarily change the value of :meth:`.IdleLoop.neverQueue`.
  • New :mod:`.bids` module, containing a few simple functions for working with BIDS datasets.
  • New :func:`.image.loadMetadata` function, and loadMeta option to the :class:`.Image` class, to automatically find and load any sidecar JSON files associated with an image file.

Changed

  • Internal reorganisation in the :mod:`.idle` module.

Fixed

  • Fixed incorrect usage of setuptools.find_packages, which was causing unit tests to be installed.

Deprecated

  • :func:`.idle.inIdle` - replaced by :meth:`.IdleLoop.inIdle`.
  • :func:`.idle.cancelIdle` - replaced by :meth:`.IdleLoop.cancelIdle`.
  • :func:`.idle.idleReser` - replaced by :meth:`.IdleLoop.idleReset`.
  • :func:`.idle.getIdleTimeout` - replaced by :meth:`.IdleLoop.callRate`.
  • :func:`.idle.setIdleTimeout` - replaced by :meth:`.IdleLoop.callRate`.

2.6.2 (Monday 7th October 2019)

Changed

  • Added a debugging hook in the :mod:`.idle` module.
  • The :func:`.fslsub.submit` function is now more flexible in the way it accepts the command and input arguments.
  • The :func:`.run.prepareArgs` function has been renamed (from _prepareArgs).

2.6.1 (Thursday 19th September 2019)

Changed

  • fslpy is no longer tested against Python 3.5, and is now tested against Python 3.6, 3.7, and 3.8.

2.6.0 (Tuesday 10th September 2019)

Added

  • New :meth:`.Image.iscomplex` attribute.
  • Support for a new Statistic atlas type.

Changed

  • The :class:`.Cache` class has a new lru option, allowing it to be used as a least-recently-used cache.
  • The :mod:`fsl.utils.filetree` module has been refactored to make it easier for the :mod:`.query` module to work with file tree hierarchies.
  • The :meth:`.LabelAtlas.get` method has a new binary flag, allowing either a binary mask, or a mask with the original label value, to be returned.
  • The :mod:`.dicom` module has been updated to work with the latest version of dcm2niix.

Deprecated

  • :meth:`.ProbabilisticAtlas.proportions`, :meth:`.ProbabilisticAtlas.maskProportions`, and :meth:`.ProbabilisticAtlas.labelProportions` have been deprecated in favour of :meth:`.StatisticAtlas.values`, :meth:`.StatisticAtlas.maskValues`, and :meth:`.StatisticAtlas.labelValues`

2.5.0 (Tuesday 6th August 2019)

Added

  • New :meth:`.Image.getAffine` method, for retrieving an affine between any of the voxel, FSL, or world coordinate systems.
  • New :mod:`fsl.transforms` package, which contains classes and functions for working with linear and non-linear FLIRT and FNIRT transformations.
  • New static methods :meth:`.Nifti.determineShape`, :meth:`.Nifti.determineAffine`, :meth:`.Nifti.generateAffines`, and :meth:`.Nifti.identifyAffine`.
  • New prototype :mod:`fsl.transforms.x5` module, for reading/writing linear and non-linear X5 files (preliminary release, subject to change).
  • New prototype :mod:`.fsl_convert_x5` :mod:`.fsl_apply_x5` programs, for working with X5 transformations (preliminary release, subject to change).

Changed

  • The :mod:`.vest.looksLikeVestLutFile` function has been made slightly more lenient.
  • h5py has been added to the fslpy dependencies.

Deprecated

  • The :mod:`fsl.utils.transform` module has been deprecated; its functions can now be found in the :mod:`fsl.transforms.affine` and :mod:`fsl.transform.flirt` modules.

2.4.0 (Wednesday July 24th 2019)