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CHANGELOG.rst 29.45 KiB

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

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:`.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).