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FSL 6.0.7.3, 5th September 2023

fsleyes 1.8.1 -> 1.8.3

  • New --cmapCycle command-line option, which automatically assigns a different colour map to each volume overlay (!402).
  • Fixed an issue with overlays being interleaved when overlapping slices in the lightbox view.
  • Fixed some bugs in edit mode - crashes could occur when drawing/selecting voxels in highly anisotropic images, and the cursor size could vary for images with floating point imprecision in their pixdims.
  • Fixed an issue with loading built-in plugins - the atlas panel (amongst others) was not being loaded.

Detailed history

  • CI: Adjust pipeline rules - test 3.10 on MRs, test all pyvers on release branches
  • BF: Fix a couple of subtle bugs a) anisotropic voxels, and b) images with floating point drift in their pixdims (e.g. nifti2)
  • BF: fix log statement - display is no longer defined here
  • TEST: regression test for slice overlap issue
  • BF: Fix display artifact in lightbox view when overlapping slices, and drawing more than one overlay - the slices/overlays were being interleaved according to draw order. The only work around is to draw in order of slices, so that each slice completely overlaps previously drawn slices.
  • DOC: install page updates
  • CI: fslpy default branch is now called main
  • TEST: Test --cmapCycle
  • CI: Default branch renamed to main
  • ENH: New --cmapCycle option to automatically assign colour maps
  • DOC: Fix super script formatting
  • MNT: Add log statement back in
  • TEST: Regression test for loading builtin plugins in submodules
  • DOC: Explain atlas panel value discrepancy

fslpy 3.13.3 -> 3.14.1

  • BF: Accidentally removed tbss from fsl.wrappers namespace
  • Mnt/doc

Fix sphinx formatting/build issues

  • ENH: New option to compose function

allowing order of scale/origin translate to be changed, with the effect that the position of the origin will not be changed by the scaling parameters

  • MNT: Allow Notifier callback functions to accept no arguments

  • ENH,MNT: Automatically set sform for FNIRT displacement fields which do not have their sform set. Replace setup.py with pyproject.toml

  • Automatically set sform for FNIRT displacement fields which do not have their sform set.

  • Replace setup.py with pyproject.toml

  • Move tests into fsl/tests

  • Enh/flip

New fsl.transform.affine.flip function, for applying a flip/inversion to the axes of an affine transformation.

  • CI: id_doc_deploy no longer used

Documentation publishing is now via gitlab pages, and not via SSH key-based login to a remote host.

  • MNT: Adjust immv/imcp so that they support FSLOUTPUTTYPE=ANALYZE
  • MNT: Remove some obsolete warning suppression logic, and suppress nibabel warning when converting to NIFTI2
  • REL: 3.14.0
  • REL: 3.14.0
  • REL: 3.14.0
  • REL: 3.14.0
  • REL: 3.14.1

Detailed history

  • BF: Accidentally removed tbss from fsl.wrappers namespace
  • DOC: Sphinx fixes
  • DOC: Fix references, mock dill in doc build environment
  • DOC: Changelog
  • ENH: New option to compose function allowing order of scale/origin translate to be changed, with the effect that the position of the origin will not be changed by the scaling parameters
  • CI: Allow tests to be skipped via SKIP_TESTS env var
  • TEST: Test origin preservation
  • DOC: Changelog, apidocs
  • MNT: Notifier callback functions can now be no-args
  • DOC: Changelog
  • TEST: Test noargs callback function
  • MNT: Automatically set sform for FNIRT displacement fields which do not have their sform set
  • MNT: Replace setup.py with pyproject.toml
  • CI: update doc/dist build commands, remove some cruft
  • MNT: Remove coveragerc
  • CI: id_git no longer exists
  • MNT: no more setup.py
  • MNT: pass args directly to pytest, another setup.py ref
  • TEST: Move tests into fsl package
  • CI: update test paths
  • MNT: Move conftest to root. Don't include tests in built wheels
  • TEST: More updated test paths
  • TEST: Change pytest import mode so that pytest does not mess with sys.path
  • MNT: wrong path
  • CI: sphinx-build, not sphinx build
  • MNT: Wrong path again
  • BF: Did not mean to add this
  • DOC: Changelog
  • CI: rename default branch to main
  • MNT: Use atlasquery not atlasq in cli help
  • ENH: New afffine.flip function; make scaleOffsetXform args optional
  • DOC: Update readme r.e. move to pyproject.toml
  • DOC: Changelog
  • MNT: Don't apply boundary offset
  • TEST: Basic teSt for affine.flip
  • CI: id_doc_deploy no longer used
  • MNT: change to f-strings
  • MNT: Add file type enumeration to Image class, and fileType function which infers type of a file. Adjust immv/imcp so that they support FSLOUTPUTTYPE=ANALYZE
  • TEST: Don't set FSLOUTPUTTYPE in env
  • TEST: Make sure that immv/imcp performs file type conversions correctly
  • DOC: Changelog
  • DOC: CHangelog
  • MNT: Remove some obsolete warning suppression. Suppress nibabel warning when converting to NIFTI2
  • DOC: additional entry in changelog regarding immv/imcp
  • MNT: Version
  • CI: Wrong venv path
  • CI: Wrong docker image for doc build
  • CI: fix images/commands used for pypi dist build job
  • BF: Image setitem notifier was returning the un-normalised slice object, instead of the normalised one (with trailing dimensions of length 1 removed)
  • DOC: Changelog
  • TEST: Regression test for setitem callback value
  • CI: Don't run tests on upstream/main, as they will have already been run on the MR branch
  • MNT: Post-release version bump
  • CI: allow tests to be skipped via commit message [skip-tests]

fsl-avwutils 2209.1 -> 2209.2

  • RF: Change fslchfiletype to rely on imcp doing the type conversion

In FSL 5.0.11, the imcp and immv commands were updated to honour the $FSLOUTPUTTYPE environment variable and to potentially convert image files, rather than just copying them.

Unfortunately at that time we failed to notice that fslchfiletype relied on immv performing a naive copy, and so since then fslchfiletype has not worked correctly in some circumstances.

This MR updates fslchfiletype so that it performs the file conversion by setting $FSLOUTPUTTYPE and then calling imcp. A small suite of unit tests are also included, to validate the behaviour of fslchfiletype.

The binary fslchfiletype.cc executable (installed to fslchfiletype_exe) as been removed, but a copy of the fslchfiletype script is installed to fslchfiletype_exe in case anybody was directly calling the binary.

Detailed history

  • RF: Change fslchfiletype to rely on immv doing the type conversion
  • MNT,TEST: Remove fslchfiletype binary as it is no longer used. Add fslchfiletype unit tests
  • TEST: Add additional tests to check fslchpixdim copy/inplace semantics
  • TEST: enumerate over file types for copy/inplace semantics tests

fsl-installer 3.5.5 -> 3.5.6

  • BF: Context.admin_password was returning None on first call

Detailed history

  • BF: admin_password was returning None on first call
  • DOC: changelog
  • MNT: replace setup.py with pyproject.toml
  • CI: Rename default branch to main
  • RF: Make Context.admin_password trigger evalution of need_admin. Make sure destdir is abspathed when specified at Context creation
  • TEST: fix dir in pyproject, add context test
  • TEST: Mark test which will fail if run by root user
  • CI: Run noroottests as non-root user

fsl-newimage 2203.10 -> 2203.11

  • BF: Fix NIfTI file format identifier names

It seems that file format identifier names were inadvertently changed in a search+replace mishap. This would have affected uses of the fslchfiletype command, with the NIFTI_PAIR, NIFTI_PAIR_GZ, NIFTI2_PAIR_GZ, or NIFTI2_PAIR_GZ identifiers.

Detailed history

  • BF: It seems that file format identifier names were inadvertently changed in a search+replace mishap
  • TEST: Regression test for file formats