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FSL 6.0.7.5, 15th November 2023

fsleyes 1.9.0 -> 1.10.0

  • RF: Changed the behaviour of the Modulate alpha by intensity setting for mesh overlays

Now, if the Hide clipped areas setting is enabled, the mesh transparency is modulated by intensity. But if the Hide clipped areas setting is disabled, the mesh data colour is blended with its background colour.

  • Add ${FSLEYES_SITE_CONFIG_DIR} as a place for colour maps and lookup tables

  • Add the ability to store colour maps and lookup table files in a site-specific configuration directory, which can be set by a ${FSLEYES_SITE_CONFIG_DIR} environment variable. Contributed by Rob Reid at https://github.com/pauldmccarthy/fsleyes/pull/121.

  • Change the way that FSLeyes layouts are stored - they are now saved as plain-text files in <settings-dir>/layouts/, or ${FSLEYES_SITE_CONFIG_DIR}/layouts/.
  • Default command-line arguments can now be stored in ${FSLEYES_SITE_CONFIG_DIR}/default_arguments.txt. If <settings-dir>/default_arguments.txt exists, it will take precedence.

Detailed history

  • RF: Allow mesh width to be changed if vertex data is set
  • RF: Change modulate-by-alpha behaviour on mesh overlays - if modalpha and hide clipped, use alpha modulation. Or if mod alpha and not hide clipped, blend with flat colour.
  • TEST: Update mesh modalpha tests
  • TEST: Sanity check test for overlay display panel
  • TEST: Missing benchmark
  • CI: Make test failures available as CI artifacts
  • BF: Using wrong register
  • BF: Need a depth texture, otherwise z ordering is wrong in some situations
  • BF: Whether or not to clip was being overwritten by the disacardClipped setting
  • DOC: Note about default arguments
  • MNT: avoid (harmless) crash when shutting down nb server
  • Adds $FSL_SITE_CONFIG_DIR as a place for cmaps and luts
  • s/FSL_SITE/FSLEYES_SITE/g
  • RF: Simplify cmap/lut initialisation. The getCmapDir/getLutDir functions have been renamed to getCmapDirs/getLutDirs, and each return a list of map directories in order of priority
  • DOC: Update colourmaps module documentation
  • ENH: New ability to save layouts as files, similar to cmaps/luts
  • MNT: Move key funcs into separate "utils" package.
  • RF: Save custom layouts as files rather than in pickle from now on
  • DOC: Update layouts module docs
  • BF: Changed var name
  • MNT: I've removed other functions in this refactor, so don't see the point in retaining+deprecating any. It's highly unlikely that these functions are used by third-party programs/scripts.
  • TEST: Update layout/cmaps unit tests
  • DOC: Update user documentation regarding $FSLEYES_SITE_CONFIG_DIR and custom layout files
  • DOC: Changelog, some formatting fixes
  • MNT: Allow site-wide default arguments
  • DOC: Update docs on default args
  • BF: userArgs was being left as non-existent file path
  • DOC: Some formatting fixes
  • TEST: Unit test for default arguments. Move some helper functions up to fsleyes.tests package

fsl-fugue 2201.3 -> 2201.4

  • ENH: GEHC gui options, kindly provided by Brice Fernandez

Detailed history

  • ENH: GEHC gui options, kindly provided by Brice Fernandez

fsl-nets 0.8.0 -> 0.8.1

  • BF: Use np.nanpercentile when calculating nets.groupmean plot limits in case there are any nans or infs

Detailed history

  • BF: Use nanpercentile when calculating groupmean plot limits in case there are any nans or infs
  • DOC: Readme

fsl-xtract 1.6.4.1 -> 1.6.4.2

  • fix make_subplots error

Detailed history

  • fix make_subplots error