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CHANGELOG.rst 17.24 KiB

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

2.0.0 (Under development)

Changed

  • Removed support for Python 2.7 and 3.4.

Removed

  • Many deprecated items

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

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:`.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)