This document contains the ``fslpy`` release history in reverse chronological order. 2.0.0 (Under development) ------------------------- 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:`` module, which currently contains one function :func:`.guessType`, which guess the data type of a file/directory path. * New `.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. Removed ^^^^^^^ * Many deprecated items removed. 1.13.3 (Friday February 8th 2019) --------------------------------- Fixed ^^^^^ * Fixed an issue with the `.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:`` 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 ```` - 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:`` 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:`` 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:`` property method, for easy access to image data as a ``numpy`` array. * New ``log`` option to the :func:`` function, allowing more fine-grained control over sub-process output streams. * New :meth:`.Platform.fsldevdir` property, allowing the ``$FSLDEVDIR`` environment variable to be queried/changed. Changed ^^^^^^^ * :meth:`.Image.ndims` has been renamed to :meth:`.Image.ndim`, to align more closely with ``numpy`` naming conventions. * The ``err`` and ``ret`` parameters to the :func:`` function have been renamed to ``stderr`` and ``exitcode`` respectively. * The :func:`.runfsl` function will give priority to the ``$FSLDEVDIR`` environment variable if it is set. Deprecated ^^^^^^^^^^ * :meth:`.Image.ndims`. * The ``err`` and ``ret`` parameters to :func:``. 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:`` 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:``). 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:`` 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 ( 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 ```` 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 * Some small bugfixes to the :mod:`.atlasq` and :mod:`.atlases` moduless. 1.4.1 (Thursday November 9th 2017) ---------------------------------- * Fixed bug in ````. 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:`` (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:`` 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:`` and :class:`` 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:`` - ``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