This document contains the ``fslpy`` release history in reverse chronological order. 3.2.2 (Thursday 9th July 2020) ------------------------------ Changed ^^^^^^^ * The :func:`.fslsub.func_to_cmd` function allows more fine-grained control over whether the script file is removed after the job has finished running. 3.2.1 (Tuesday 23rd June 2020) ------------------------------ Changed ^^^^^^^ * Minor updates to documentation. 3.2.0 (Thursday 11th June 2020) ------------------------------- Added ^^^^^ * A new :func:`.fslsub.hold` function to wait on previously submitted jobs, to be used in place of the ``wait`` function. Removed ^^^^^^^ * The :func:`.fslsub.wait` (and :func:`.run.wait`) function has been removed, as repeated calls to ``qstat`` can adversely affect the cluster job submission system. 3.1.0 (Thursday 21st May 2020) ------------------------------ Added ^^^^^ * New :mod:`.cifti` module, providing classes and functions for working with `CIFTI `_ data. * New :func:`.winpath` and :func:`wslpath` functions for working with paths when using FSL in a Windows Subsystem for Linux (WSL) environment. * New :func:`.wslcmd` function for generating a path to a FSL command installed in a WSL environment. * New :meth:`.Platform.fslwsl` attribute for detecting whether FSL is installed in a WSL environment. * New :meth:`.Image.niftiDataType` property. * The :class:`.FileTree` class has been updated to allow creation of deep copies via the new :meth:`.FileTree.copy` method. Changed ^^^^^^^ * :func:`.Image` objects created from ``numpy`` arrays will be NIFTI1 or NIFTI2, depending on the value of the ``$FSLOUTPUTTYPE`` environment variable. Fixed ^^^^^ * Updated the :func:`.fast` wrapper to support some single-character command-line flags. 3.0.1 (Wednesday 15th April 2020) --------------------------------- Changed ^^^^^^^ * The :func:`.isMelodicDir` function now accepts directories that do not end with ``.ica``, as long as all required files are present. * Added the ``dataclasses`` backport, so ``fslpy`` is now compatible with Python 3.6 again. 3.0.0 (Sunday 29th March 2020) ------------------------------ Added ^^^^^ * New wrapper functions for the FSL :class:`.fslstats`, :func:`.prelude` and :func:`applyxfm4D` commands. * New ``firstDot`` option to the :func:`.path.getExt`, :func:`.path.removeExt`, and :func:`.path.splitExt`, functions, offering rudimentary support for double-barrelled filenames. * The :func:`.nonlinear.applyDeformation` function now accepts a ``premat`` affine, which is applied to the input image before the deformation field. * New :class:`.SubmitParams` class, providing a higer level interface for cluster submission. * New :meth:`.FileTree.load_json` and :meth:`.FileTree.save_json` methods. Changed ^^^^^^^ * ``fslpy`` now requires a minimum Python version of 3.7. * The default value for the ``partial_fill`` option to :meth:`.FileTree.read` has been changed to ``False``. Accordingly, the :class:`.FileTreeQuery` calls the :meth:`.FileTree.partial_fill` method on the ``FileTree`` it is given. * The :func:`.gifti.relatedFiles` function now supports files with BIDS-style naming conventions. * The :func:`.run.run` and :func:`.run.runfsl` functions now pass through any additional keyword arguments to ``subprocess.Popen`` or, if ``submit=True``, to :func:`fslsub.submit`. * The :func:`.fslsub.submit` function now accepts an ``env`` option, allowing environment variables to be specified. * The :func:`.run.runfsl` function now raises an error on attempts to run a command which is not present in ``$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. * :class:`.Image` creation does not fail if ``loadMeta`` is set, and a sidecar file containing invalid JSON is present. 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