CHANGELOG.rst

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

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

• Remobved 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:`.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:`.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)