CHANGELOG.rst

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

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:`.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.