fslpy release history

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

2.3.1 (Friday July 5th 2019)

Fixed

• The Bitmap class now supports greyscale images and palette images.

2.3.0 (Tuesday June 25th 2019)

Added

• New Bitmap class, for loading bitmap images. The Bitmap.asImage() method can be used to convert a Bitmap into an Image.

• The Image class now has support for the RGB24 and RGBA32 NIfTI data types.

• New Image.nvals property, for use with RGB24/RGBA32 images.

• New LabelAtlas.get() and ProbabilisticAtlas.get() methods, which return an Image for a specific region.

• The AtlasDescription.find() method also now a name parameter, allowing labels to be looked up by name.

• New FileTree.defines() and FileTree.on_disk() methods, to replace the FileTree.exists() method.

Fixed

• The makeWriteable() function will always create a copy of an array if its base is a bytes object.

• Fixed a bug in the GitfitMesh.loadVertices() method.

• Fixed a bug in the 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 resample_image script.

• New resample module (replacing the Image.resample() method), containing functions to resample an Image.

• New resample.resampleToPixdim() and resample.resampleToReference() functions, convenience wrappers around resample.resample().

• New idle.block() function.

Changed

• The resample() function (formerly 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 transform.decompose() function now accepts both (3, 3) and (4, 4) matrices.

Fixed

• Minor fixes to some filetree.filetree tree definitions.

Deprecated

• The Image.resample() method has been deprecated in favour of the resample.resample() function.

2.1.0 (Saturday April 13th 2019)

Added

• New tensor conversion routines in the dtifit module (Michiel Cottaar).

• New makeWriteable() function which ensures that a numpy.array is writeable, and creates a copy if necessary

Changed

• The GiftiMesh class no longer creates copies of the mesh vertex/index arrays. This means that, these arrays will be flagged as read-only.

• The 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 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 gifti.relatedFiles() function returning duplicate files.

2.0.0 (Friday March 20th 2019)

Added

• New fsl.utils.filetree package for defining and working with file/directory templates (Michiel Cottaar).

• Simple built-in deprecated decorator.

• New fsl.data.utils module, which currently contains one function guessType(), which guesses 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 Image class now fully delegates to nibabel for managing file handles.

• The 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 Mesh instances can now be updated.

Removed

• Many deprecated items removed.

Deprecated

• Deprecated the loadIndexedImageFile() function, and the indexed flag to the Image constructor.

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 GiftiMesh class, where numpy/nibabel was returning read-only index arrays.

1.13.2 (Friday November 30th 2018)

Changed

• The Image.resample() method now supports images with more than three dimensions.

• The 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 fsl.wrappers if submitted.

Fixed

• Fix to the ImageWrapper regarding complex data types.

1.13.1 (Friday November 23rd 2018)

Fixed

• Added a missing image attribute in the VoxelwiseConfoundEV class.

• Make sure that FEAT Cluster objects (created by the 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 fsl_anat(), applytopup() (Martin Craig).

• New fileOrText() decorator for use in wrapper functions (Martin Craig).

Changed

• Various minor changes and enhancements to the FSL function 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 fsl_ents.

• Increased the minimum required version of dcm2niix in the fsl.data.dicom module.

Deprecated

• The extract_noise script.

1.11.1 (Friday September 14th 2018

Fixed

• Fixed a Python 2 incompatibility in the settings module.

1.11.0 (Thursday September 13th 2018)

Added

• A couple of new convenience functions to the 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 parseVersionString() function accepts (and ignores) local version identifer strings.

1.10.2 (Friday September 7th 2018)

Fixed

• The 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 FEATImage.getCOPE method was returning PE images.

1.10.0 (Wednesday July 18th 2018)

Added

• A new script, extract_noise, which can be used to extract ICA component time courses from a MELODIC ICA analysis.

• New path.allFiles() function which returns all files underneath a directory.

• The fileOrImage() and fileOrArray() decorators now support loading of files which are specified with an output basename.

• New fast wrapper function for the FSL FAST tool.

Changed

• When using the 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 Image.data() property method, for easy access to image data as a numpy array.

• New log option to the run.run() function, allowing more fine-grained control over sub-process output streams.

• New Platform.fsldevdir() property, allowing the $FSLDEVDIR environment variable to be queried/changed.

Changed

• Image.ndims() has been renamed to Image.ndim(), to align more closely with numpy naming conventions.

• The err and ret parameters to the run.run() function have been renamed to stderr and exitcode respectively.

• The runfsl() function will give priority to the $FSLDEVDIR environment variable if it is set.

Deprecated

• Image.ndims().

• The err and ret parameters to run.run().

1.8.1 (Friday May 11th 2018)

Changed

• The fileOrImage() decorator function now accepts Image objects as well as nibabel image objects.

1.8.0 (Thursday May 3rd 2018)

Added

• New wrappers package, containing wrapper functions for a range of FSL tools.

• New fsl.utils.run module, to replace the fsl.utils.callfsl module.

• New fsl.utils.fslsub module, containing a fslsub.submit() function which submits a cluster job via fsl_sub.

• Assertions (in the assertions module) can be disabled with the new assertions.disabled() context manager.

• New fsl.utils.parse_data module containing various neuroimaging data constructors for use with argparse.

• The memoize.skipUnchanged() decorator has an invalidate function which allows its cache to be cleared.

Changed

• The tempdir() function has an option to not change to the newly created directory.

Deprecated

• The fsl.utils.callfsl module (replaced with fsl.utils.run).

1.7.2 (Monday March 19th 2018)

Added

• Added the 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 parseVersionString() so it accepts .dev* suffixes.

Fixed

• Removed deprecated use of imagewrapper.canonicalShape().

1.7.0 (Tuesday March 6th 2018)

Added

• The fsl.utils.assertions module contains a range of functions which can be used to assert that some condition is met.

• The 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 settings module now saves its files in a format that is compatible with Python 2 and 3.

• The 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 Image.__init__().

• MGHImage() objects now have a MGHImage.save() method.

• Adjustments to the conda package build and deployment process.

• The ImageWrapper.canonicalShape() function has been moved to the data.image class.

• The ImageWrapper.naninfrange() function has been moved into its own naninfrange module.

Fixed

• Fixed a bug in the MutexFactory class.

Deprecated

• ImageWrapper.canonicalShape() (moved to the data.image module)

• ImageWrapper.naninfrange() function (moved to the 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 platform module emits a warning if it cannot import wx.

1.6.3 (Friday February 2nd 2018)

• Minor enhancements to the WeakFunctionRef class.

• Some bugfixes to the 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 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 VTKMesh class must now be used for loading VTK model files, instead of the old TriangleMesh class.

• The new Mesh class uses the trimesh library (https://github.com/mikedh/trimesh) to perform various geometrical operations, accessible via new Mesh.rayIntersection(), Mesh.planeIntersection(), Mesh.nearestVertex() methods.

• The Nifti and 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, Meta.

• Freesurer surface files and vertex data can now be loaded via the FreesurferMesh class, in the new freesurfer module.

• Freesurfer mgz / mgh image files can now be loaded via the new mghimage module. Internally, these image files are converted to NIFTI - the MGHImage class derives from the Image class.

• Meta-data access methods on the DicomImage class have been deprecated, as their functionality is provided by the new Meta mixin.

• The TriangleMesh class has been deprecated in favour of the new 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 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 dicom.scanDir() function related to data series ordering.

1.5.0 (Wednesday December 13th 2017)

• New module dicom, which provides a thin wrapper on top of Chris Rorden’s dcm2niix.

• New module tempdir, which has a convenience function for creating temporary directories.

• Fixed small issue in Image.dtype() - making sure that it access image data via the ImageWrapper, rather than via the Nifti1Image object.

1.4.2 (Tuesday December 5th 2017)

• New function 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 atlasq and atlases moduless.

1.4.1 (Thursday November 9th 2017)

• Fixed bug in setup.py.

1.4.0 (Thursday November 9th 2017)

• The uniquePrefix() function now raises a PathError instead of a ValueError, when an invalid path is provided.

• The 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 fsl.data.image.addExt() (and related) functions.

• The fsl.utils.path.addExt() function accepts a new parameter, unambiguous which causes it to allow an ambiguous prefix, and return all matching paths.

• New atlasq application, intended to replace the FSL atlasquery tool.

• New imglob application, intended to replace the FSL imglob tool.

• The Image.resample() method explicitly raises a ValueError if incompatible shapes are provided.

1.3.1 (Wednesday October 25th 2017)

• Fixed bug in Platform.wxPlatform() causing it to always return WX_UNKNOWN.

1.3.0 (Wednesday October 25th 2017)

• Atlas classes can now pass kwargs through to the Image constructor.

• LabelAtlas image values no longer need to match the index of the label into the AtlasDescription labels list. This means that label atlas XML files may contain non-sequential label values.

• Cache now implements __getitem__ and __setitem__

• The image.read_segments() function (monkey-patched into nibabel) is deprecated, as it is no longer necessary as of nibabel 2.2.0.

• 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 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 Image is passed an existing nibabel header object, it creates a copy, rather than using the original.

• New Image.resample() method, which resamples the image data to a different resolution.

• New LabelAtlas.coordLabel(), LabelAtlas.maskLabel(), ProbabilisticAtlas.coordProportions() and 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)

• fsl.data.image.Nifti.voxelsToScaledVoxels() method deprecated in favour of new Nifti.voxToScaledVoxMat() and Nifti.scaledVoxToVoxMat() properties.

1.1.0 (Monday September 11th 2017)

• The fsl package is now a pkgutil-style namespace package, so it can be used for different projects.

• Updates to fsl.data.image.Nifti and 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 fsl.utils.transform module:

• transform.rotMatToAffine() converts a (3, 3) rotation matrix into a (4, 4) affine.

• transform.transformNormal() applies an affine transform to one or more vectors.

• transform.veclength() calculates the length of a vector

• transform.normalise() normalises a vector

• transform.scaleOffsetXform() adjusted to have more flexibility with respect to inputs.

• transform.decompose() can return rotations either as three axis-angles, or as a rotation matrix

• Updates to 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.

• fsl.utils.memoize.memoize() decorator made into a class rather than a function. The new Memoize class has an invalidate method, which clears the cache.

1.0.4 (Friday July 14th 2017)

• Python 2/3 compatibility fix to fsl.utils.callfsl.

• Fix to fsl.utils.transform.scaleOffsetXform() - accepts inputs that are not lists.

• 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 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 fsl.version.patchVersion() function.

1.0.1 (Sunday 4th June 2017)

• New version number parsing functions in 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: - fsl.utils.colourbarbitmap - fsl.utils.dialog - fsl.utils.imagepanel - fsl.utils.layout - fsl.utils.platform - fsl.utils.runwindow - fsl.utils.status - fsl.utils.textbitmap - fsl.utils.typedict - fsl.utils.webpage

• 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 fsl.utils.platform is more lenient

• New AtlasLabel class

• Image.__init__() allows arguments to be passed through to nibabel.load.

• New 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