CHANGELOG.rst

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

2.6.0 (Under development)

Added

• New :meth:`.Image.iscomplex` attribute.

Changed

• The :class:`.Cache` class has a new lru option, allowing it to be used as a least-recently-used cache.
• The :mod:`.filetree` module has been refactored to make it easier for the :mod:`.query` module to work with file tree hierarchies.

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.