CHANGELOG.rst

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

1.6.0 (Under development)

• 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 geometry files can now be loaded via the :class:`.FreesurferMesh` class.
• 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