fslpy release history

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

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 Nifti.adjust() method, for creating a copy of a Nifti header with adjusted shape, pixdims, and affine. This can be useful for creating a resampling reference.

  • New affine.rescale() function, for adjusting a scaling matrix.

  • New mghimage.voxToSurfMat() function, for creating a voxel-to-freesurfer affine transform from any image.

Changed

  • The 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 mesh.needsFixing() function.

  • The fslmaths.run() method now accepts wrappers.LOAD as an output specification.

  • Fixed a bug in the Mesh class to prevent indices from being loaded as floating point type.

  • Fixed a bug in the resample() function.

  • Fixed a bug in the MGHImage class, which was causing pixdims to be overridden by scales derived from the affine.

Deprecated

2.7.0 (Wednesday 6th November 2019)

Added

  • New until option to the idle.block() function.

  • New Idle.neverQueue() setting, which can be used to force all tasks passed to idle.idle() to be executed synchronously.

  • New IdleLoop.synchronous() context manager, to temporarily change the value of IdleLoop.neverQueue().

  • New bids module, containing a few simple functions for working with BIDS datasets.

  • New image.loadMetadata() function, and loadMeta option to the Image class, to automatically find and load any sidecar JSON files associated with an image file.

Changed

  • Internal reorganisation in the idle module.

Fixed

  • Fixed incorrect usage of setuptools.find_packages, which was causing unit tests to be installed.

Deprecated

2.6.2 (Monday 7th October 2019)

Changed

  • Added a debugging hook in the idle module.

  • The fslsub.submit() function is now more flexible in the way it accepts the command and input arguments.

  • The 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

Changed

  • The Cache class has a new lru option, allowing it to be used as a least-recently-used cache.

  • The filetree module has been refactored to make it easier for the query module to work with file tree hierarchies.

  • The 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 dicom module has been updated to work with the latest version of dcm2niix.

Deprecated

2.5.0 (Tuesday 6th August 2019)

Added

  • New Image.getAffine() method, for retrieving an affine between any of the voxel, FSL, or world coordinate systems.

  • New fsl.transforms package, which contains classes and functions for working with linear and non-linear FLIRT and FNIRT transformations.

  • New static methods Nifti.determineShape(), Nifti.determineAffine(), Nifti.generateAffines(), and Nifti.identifyAffine().

  • New prototype fsl.transforms.x5 module, for reading/writing linear and non-linear X5 files (preliminary release, subject to change).

  • New prototype fsl_convert_x5 fsl_apply_x5 programs, for working with X5 transformations (preliminary release, subject to change).

Changed

  • The vest.looksLikeVestLutFile function has been made slightly more lenient.

  • h5py has been added to the fslpy dependencies.

Deprecated

  • The fsl.utils.transform module has been deprecated; its functions can now be found in the fsl.transforms.affine and fsl.transform.flirt modules.

2.4.0 (Wednesday July 24th 2019)

Added

  • New image.roi module, for extracting an ROI of an image, or expanding its field-of-view.

Changed

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

2.3.0 (Tuesday June 25th 2019)

Added

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

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

Deprecated

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

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

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

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

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

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

Changed

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

Deprecated

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

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

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)

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)

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)

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)

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)

1.0.1 (Sunday 4th June 2017)

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