CHANGELOG.rst

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

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.

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)

Added

• New :mod:`.image.roi` module, for extracting an ROI of an image, or expanding its field-of-view.

Changed

• The :mod:`.resample_image` script has been updated to support resampling of images with more than 3 dimensions.

2.3.1 (Friday July 5th 2019)

Fixed

• The :class:`.Bitmap` class now supports greyscale images and palette images.

2.3.0 (Tuesday June 25th 2019)

Added

• New :class:`.Bitmap` class, for loading bitmap images. The :meth:`.Bitmap.asImage` method can be used to convert a Bitmap into an :class:`.Image`.
• The :class:`.Image` class now has support for the RGB24 and RGBA32 NIfTI data types.
• New :attr:`.Image.nvals` property, for use with RGB24/RGBA32 images.
• New :meth:`.LabelAtlas.get` and :meth:`ProbabilisticAtlas.get` methods, which return an :class:`.Image` for a specific region.
• The :meth:`.AtlasDescription.find` method also now a name parameter, allowing labels to be looked up by name.
• New :meth:`.FileTree.defines` and :meth:`.FileTree.on_disk` methods, to replace the :func:`.FileTree.exists` method.

Fixed

• The :func:`.makeWriteable` function will always create a copy of an array if its base is a bytes object.
• Fixed a bug in the :meth:`.GitfitMesh.loadVertices` method.
• Fixed a bug in the :meth:`.Mesh.addVertices` method where the wrong face normals could be used for newly added vertex sets.

2.2.0 (Wednesday May 8th 2019)

Added

• New :mod:`.resample_image` script.
• New :mod:`.resample` module (replacing the :func:`.Image.resample` method), containing functions to resample an :class:`.Image`.
• New :func:`.resample.resampleToPixdim` and :func:`.resample.resampleToReference` functions, convenience wrappers around :func:`.resample.resample`.
• New :func:`.idle.block` function.

Changed

• The :func:`.resample` function (formerly :meth:`.Image.resample`) now accepts origin and matrix parameters, which can be used to adjust the alignment of the voxel grids of the input and output images.
• The :func:`.transform.decompose` function now accepts both (3, 3) and (4, 4) matrices.

Fixed

• Minor fixes to some :mod:`.filetree.filetree` tree definitions.

Deprecated

• The :meth:`.Image.resample` method has been deprecated in favour of the :func:`.resample.resample` function.

2.1.0 (Saturday April 13th 2019)

Added

• New tensor conversion routines in the :mod:`.dtifit` module (Michiel Cottaar).
• New :func:`.makeWriteable` function which ensures that a numpy.array is writeable, and creates a copy if necessary

Changed

• The :class:`.GiftiMesh` class no longer creates copies of the mesh vertex/index arrays. This means that, these arrays will be flagged as read-only.
• The :class:`.Mesh` class handles vertex data sets requiring different triangle unwinding orders, at the cost of potentially having to store two copies of the mesh indices.

Fixed

• The :class:`.FeatDesign` class now handles "compressed" voxelwise EV files, such as those generated by PNM.

2.0.1 (Monday April 1st 2019)

Fixed

• Fixed a bug with the :func:`.gifti.relatedFiles` function returning duplicate files.

2.0.0 (Friday March 20th 2019)

Added

• New :mod:`fsl.utils.filetree` package for defining and working with file/directory templates (Michiel Cottaar).
• Simple built-in :mod:`.deprecated` decorator.
• New :mod:`fsl.data.utils` module, which currently contains one function :func:`.guessType`, which guesses the data type of a file/directory path.
• New :func:`.commonBase` function for finding the common prefix of a set of file/directory paths.

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 :class:`.GiftiMesh` class can now load surface files which contain vertex data, and will accept surface files which end in .gii, rather than requiring files which end in .surf.gii.
• The name property of :class:`.Mesh` instances can now be updated.

Removed

• Many deprecated items removed.

Deprecated

• Deprecated the :func:`.loadIndexedImageFile` function, and the indexed flag to the :class:`.Image` constructor.

1.13.3 (Friday February 8th 2019)

Fixed

• Fixed an issue with the :func:`.dicom.loadSeries` using memory-mapping for image files that would subsequently be deleted.
• Fixed an issue in the :class:`.GiftiMesh` class, where numpy/nibabel was returning read-only index arrays.

1.13.2 (Friday November 30th 2018)

Changed

• 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.

Fixed

• Fix to the :class:`.ImageWrapper` regarding complex data types.

1.13.1 (Friday November 23rd 2018)

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.

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:`.data.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:`.data.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)

• Further adjustments to the conda package build.

1.6.5 (Tuesday February 6th 2018)

• Adjustments to the conda package build.

1.6.4 (Monday February 5th 2018)

• The :mod:`.platform` module emits a warning if it cannot import wx.

1.6.3 (Friday February 2nd 2018)

• Minor enhancements to the :class:`.WeakFunctionRef` class.
• Some bugfixes to the :mod:`fsl.utils.imcp` module, with respect to handling relative path names, moving file groups (e.g. .img/.hdr pairs), and non-existent directories.

1.6.2 (Tuesday January 30th 2018)

• Updates to the conda installation process.
• A new script is installed when fslpy is installed via pip or conda - atlasquery, which emulates the FSL atlasquery tool.

1.6.1 (Monday January 29th 2018)

• Removed lxml as a dependency - this was necessary in older versions of trimesh.

1.6.0 (Friday January 26th 2018)

• The new :class:`.Mesh` class is now the base class for all mesh types. It has been written to allow multiple sets of vertices to be associated with a mesh object (to support e.g. white matter, inflated, spherical models for a GIFTI/freeusrfer mesh).
• The new :class:`.VTKMesh` class must now be used for loading VTK model files, instead of the old :class:`.TriangleMesh` class.
• The new :class:`.Mesh` class uses the trimesh library (https://github.com/mikedh/trimesh) to perform various geometrical operations, accessible via new :meth:`.Mesh.rayIntersection`, :meth:`.Mesh.planeIntersection`, :meth:`.Mesh.nearestVertex` methods.
• The :class:`.Nifti` and :class:`.Mesh` classes have new methods allowing arbitrary metadata to be stored with the image, as key-value pairs. These are provided by a new mixin class, :class:`.Meta`.
• Freesurer surface files and vertex data can now be loaded via the :class:`.FreesurferMesh` class, in the new :mod:`.freesurfer` module.
• Freesurfer mgz / mgh image files can now be loaded via the new :mod:`.mghimage` module. Internally, these image files are converted to NIFTI - the :class:`.MGHImage` class derives from the :class:`.Image` class.
• Meta-data access methods on the :class:`.DicomImage` class have been deprecated, as their functionality is provided by the new :class:`.Meta` mixin.
• The :class:`.TriangleMesh` class has been deprecated in favour of the new :class:`.Mesh` class.
• Optional dependencies wxpython, indexed_gzip, trimesh, and rtree are now listed separately, so fslpy can be used without them (although relevant functionality will be disabled if they are not present).

1.5.4 (Wednesday January 10th 2018)

• Actually included the fix that was supposed to be in version 1.5.3.

1.5.3 (Tuesday January 9th 2018)

• Bug fix to :meth:`.ImageWrapper.__expandCoverage` - was not correctly handling large images with lots of nan values.

1.5.2 (Tuesday January 2nd 2018)

• Fixed issue with MANIFEST.in file.

1.5.1 (Thursday December 14th 2017)

• Fixed bug in :func:`.dicom.scanDir` function related to data series ordering.

1.5.0 (Wednesday December 13th 2017)

• New module :mod:`.dicom`, which provides a thin wrapper on top of Chris Rorden's dcm2niix.
• New module :mod:`.tempdir`, which has a convenience function for creating temporary directories.
• Fixed small issue in :meth:`.Image.dtype` - making sure that it access image data via the :class:`.ImageWrapper`, rather than via the Nifti1Image object.

1.4.2 (Tuesday December 5th 2017)

• New function :func:`.transform.rmsdev` function, which implements the RMS deviation equation for comparing two affine transformations (FMRIB Technical Report TR99MJ1, available at https://www.fmrib.ox.ac.uk/datasets/techrep/).
• Some small bugfixes to the :mod:`.atlasq` and :mod:`.atlases` moduless.

1.4.1 (Thursday November 9th 2017)

• Fixed bug in setup.py.

1.4.0 (Thursday November 9th 2017)

• The :func:`.uniquePrefix` function now raises a :exc:`~.path.PathError` instead of a :exc:`.ValueError`, when an invalid path is provided.
• The :mod:`fsl.utils.async` module is now deprecated, as async will become a reserved word in Python 3.7. It has been renamed to fsl.utils.idle, with no other API changes.
• For image file pairs, the hdr extension now takes precedence over the img extension, when using the :func:`fsl.data.image.addExt` (and related) functions.
• The :func:`fsl.utils.path.addExt` function accepts a new parameter, unambiguous which causes it to allow an ambiguous prefix, and return all matching paths.
• New :mod:`~fsl.scripts.atlasq` application, intended to replace the FSL atlasquery tool.
• New :mod:`~fsl.scripts.imglob` application, intended to replace the FSL imglob tool.
• The :meth:`.Image.resample` method explicitly raises a ValueError if incompatible shapes are provided.

1.3.1 (Wednesday October 25th 2017)

• Fixed bug in :meth:`.Platform.wxPlatform` causing it to always return WX_UNKNOWN.

1.3.0 (Wednesday October 25th 2017)

• :class:`.Atlas` classes can now pass kwargs through to the :class:`.Image` constructor.
• :class:`.LabelAtlas` image values no longer need to match the index of the label into the :class:`.AtlasDescription` labels list. This means that label atlas XML files may contain non-sequential label values.
• :class:`.Cache` now implements __getitem__ and __setitem__
• The :func:`.image.read_segments` function (monkey-patched into nibabel) is deprecated, as it is no longer necessary as of nibabel 2.2.0.
• :func:`.platform.isWidgetAlive` is deprecated in favour of an equivalent function in the fsleyes-widgets library.
• scipy is now explicitly listed as a requirement (this should have been done in 1.2.1).

1.2.2 (Saturday October 21st 2017)

• The :func:`.image.read_segments` function is only monkey-patched into nibabel 2.1.0, as it breaks when used with 2.2.0.

1.2.1 (Saturday October 7th 2017)

• If an :class:`.Image` is passed an existing nibabel header object, it creates a copy, rather than using the original.
• New :meth:`.Image.resample` method, which resamples the image data to a different resolution.
• New :meth:`.LabelAtlas.coordLabel`, :meth:`.LabelAtlas.maskLabel`, :meth:`.ProbabilisticAtlas.coordProportions` and :meth:`.ProbabilisticAtlas.maskProportions` methods. The coord methods perform coordinate queries in voxel or world coordinates, and the mask methods perform mask-based queries.

1.2.0 (Thursday September 21st 2017)

• :meth:`fsl.data.image.Nifti.voxelsToScaledVoxels` method deprecated in favour of new :meth:`.Nifti.voxToScaledVoxMat` and :meth:`Nifti.scaledVoxToVoxMat` properties.

1.1.0 (Monday September 11th 2017)

• The :mod:`fsl` package is now a pkgutil-style namespace package, so it can be used for different projects.
• Updates to :class:`fsl.data.image.Nifti` and :class:`fsl.data.image.Image` to add support for images with more than 4 dimensions: - New ndims property - is4DImage method deprecated

1.0.5 (Thursday August 10th 2017)

• New functions and further adjustments in :mod:`fsl.utils.transform` module:

• :func:`.transform.rotMatToAffine` converts a (3, 3) rotation matrix into a (4, 4) affine.
• :func:`.transform.transformNormal` applies an affine transform to one or more vectors.
• :func:`.transform.veclength` calculates the length of a vector
• :func:`.transform.normalise` normalises a vector
• :func:`.transform.scaleOffsetXform` adjusted to have more flexibility with respect to inputs.
• :func:`.transform.decompose` can return rotations either as three axis-angles, or as a rotation matrix

• Updates to :class:`fsl.data.mesh.TriangleMesh` - vertices and indices are now property attributes. New lazily generated normals and vnormals properties (face and vertex normals respectively). Option to __init__ to fix the face winding order of a mesh.
• :func:`fsl.utils.memoize.memoize` decorator made into a class rather than a function. The new :class:`.Memoize` class has an invalidate method, which clears the cache.

1.0.4 (Friday July 14th 2017)

• Python 2/3 compatibility fix to :mod:`fsl.utils.callfsl`.
• Fix to :func:`fsl.utils.transform.scaleOffsetXform` - accepts inputs that are not lists.
• :func:`fsl.utils.transform.compose` accepts either a sequence of three axis angles, or a (3, 3) rotation matrix.

1.0.3 (Sunday June 11th 2017)

• Fix to :mod:`fsl.utils.async` which was breaking environments where multiple wx.App instances were being created.

1.0.2 (Thursday June 8th 2017)

• Python 2/3 compatibility fixes
• New :func:`fsl.version.patchVersion` function.

1.0.1 (Sunday 4th June 2017)

• New version number parsing functions in :mod:`fsl.version`.

1.0.0 (Saturday May 27th 2017)

• Removed many GUI-related modules - they have been moved to the fsleyes-widgets project. The following modules have been removed: - :mod:`fsl.utils.colourbarbitmap` - :mod:`fsl.utils.dialog` - :mod:`fsl.utils.imagepanel` - :mod:`fsl.utils.layout` - :mod:`fsl.utils.platform` - :mod:`fsl.utils.runwindow` - :mod:`fsl.utils.status` - :mod:`fsl.utils.textbitmap` - :mod:`fsl.utils.typedict` - :mod:`fsl.utils.webpage`
• :mod:`fsl.utils.settings` module rewritten. It no longer uses wx, but instead stores plain-text and pickle files in the user's home directory.
• Software GL renderer test in :mod:`fsl.utils.platform` is more lenient
• New :class:`.AtlasLabel` class
• :meth:`.Image.__init__` allows arguments to be passed through to nibabel.load.
• New :meth:`.Nifti.strval` method to handle escaped strings in NIFTI headers.
• Python 2/3 compatibility fixes

0.11.0 (Thursday April 20th 2017)

• First public release as part of FSL 5.0.10