fsleyes release history

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

0.24.2 (Friday June 8th 2018)

Changed

  • Changed the Jupyter notebook server management so it can be easily run within a frozen version of FSLeyes.

0.24.1 (Wednesday June 6th 2018)

Changed

  • Reduced the size of the PyPi source distribution files.

0.24.0 (Tuesday June 5th 2018)

Added

  • Integration with Jupyter Notebook is now available via the FileOpen notebooks menu option.
  • Support for high-resolution (e.g. retina) displays under macOS.
  • fslpy FSL wrapper functions are now available in the Python shell and Jupyter notebooks.
  • A colour bar preview is now shown in the overlay display panel.

Changed

  • The gamma display setting now accepts values between -1 and +1.
  • Minor improvements to 3D volumetric raycasting.
  • The fsleyes.perspectives module has been renamed to fsleyes.layouts. All associated functions and classes have been renamed accordingly.
  • The fsleyes.state module has been re-written - the getState() and setState() functions can be used to save/restore the full FSLeyes state (layout and overlays).

Deprecated

  • The fsleyes.perspectives, fsleyes.actions.clearperspective, fsleyes.actions.loadperspective, and fsleyes.actions.saveperspective modules.
  • The fsleyes.views.shellpanel has been deprecated in favour of using Jupyter notebooks.

Fixed

  • Regression in handling 3D textures from on-disk image files.

0.23.0 (Friday May 4th 2018)

Added

  • The Nudge tool now allows users to change the centre of rotation.
  • New gamma correction display setting for volume and mesh overlays.
  • New smoothing display setting for 3D volume rendering.
  • New normalise display setting for SH FODs, to normalise individual FODs to voxel size.
  • New fill tool in orthographic edit mode, which allows a bounded region to be filled or selected.

Changed

  • Plot view interaction changed - left click to pan, right click to zoom, and hold down ⌃ (⌘ under macOS) and click for secondary behaviour (e.g. changing the current volume on a time series panel).
  • In edit mode, when a new image is created, it is now selected.

Fixed

  • Freesurfer surface files could not be selectd in macOS open file dialogs.
  • Freesurfer surfaces were causing an error in overlay information panel.
  • Fixed issue where edit mode selection overlay could become out of date when display space was changed.
  • Show/hide button in a plot view’s overlay list no longer toggles overlay visibility on other (e.g. ortho) views.
  • Selecting an item in a plot view’s overlay list no longer shows/hides its data plot - the eye_icon button needs to be clicked.

Removed

  • Removed all code and resources related to standalone versions of FSLeyes - this is now managed in a separate project.

0.22.6 (Wednesday April 18th 2018)

  • Fixed more libspatialindex issues with macOS standalone builds.

0.22.5 (Tuesday April 17th 2018)

Fixed

  • Fixed an issue with macOS standalone builds (problems with libspatialindex).

0.22.4 (Thursday March 29th 2018)

Fixed

  • Fixed a couple of bugs in FOD rendering.

0.22.3 (Tuesday March 19th 2018)

Added

  • A new option for the MeshOpts.coordSpace property - this fixes an issue with display alignemnt of freesurfer surfaces.

Deprecated

  • MeshOpts.getCoordSpaceTransform() - the MeshOpts.getTransform() should be used instead.

0.22.2 (Sunday March 18th 2018)

Fixed

  • Fixed an error with the Override data range not being applied correctly.

0.22.1 (Thursday March 15th 2018)

Fixed

  • Fixed an error which was being raised on attempts to add (“hold”) a data series to a plot.

0.22.0 (Tuesday March 13th 2018)

Added

  • New Freesurfer lookup table (freesurfercolorlut.lut, provided by Vincent Koppelmans) to replace the incomplete mgh-cma-freesurfer.lut lookup table.
  • FSLeyes can now load and save non-FLIRT affine transformation files.
  • Infrastructure for buildling FSLeyes conda packages.
  • Ortho view keyboard navigation shortcuts now work in edit mode.

Changed

  • The x-axis in a time series view now defaults to showing volumes, rather than being scaled by time. This can be toggled via the Use pixdims option in the time series control panel.
  • MGH images should no longer be displayed as unsaved. When an MGH image is copied/edited and saved, it will be saved as a NIfTI image.
  • Labels in FSLeyes .lut files no longer need to be in ascending order.
  • The FSLeyes settings directory should now be compatible across Python 2 and 3.
  • An error message is now displayed on attempts to load an invalid lookup table file.
  • Adjustments to standalone Linux builds, hopefully fixing libxcb related compatibility issues.

Fixed

  • FSLeyes should now run on macOS systems which have FreeGLUT installed.
  • Fixed a bug where viewing outlines of mask or label overlays would cause a GLXBadRenderRequest error.
  • Fixed a bug where mask overlays were not shown in a lightbox view over a SSH/X11 connection.
  • Fixed a problem with colour maps/luts not being listed in command line help.
  • Fixed a bug with the location panel History tab when running under Python 2.

Deprecated

  • fsleyes.overlay.PropCache - an equivalent class is now available in fsleyes-props.

0.21.1 (Monday February 5th 2018)

  • Adjustments to standalone linux builds, hopefully fixing the module 'wx' has no attribute '__version__' issue.

0.21.0 (Tuesday January 30th 2018)

  • FSLeyes is now able to load Freesurfer surface files, and mgh / mgz images.
  • The vertices of a 3D mesh (VTK, GIFTI, or Freesurfer file) can now be selected in both 3D and ortho views by holding down the shift key. If data is associated with the mesh vertices, it will be shown in the location panel, the time series panel, and the power spectrum panel. This feature is dependent on the presence of the Trimesh library, a new optional dependency.
  • Mesh vertex data is now shown on the histogram panel.
  • It is now possible to associate multiple vertex files with mesh overlays. For Freesurfer/GIFTI surfaces, if other vertex files are found (e.g. pial, white matter, inflated), they will be added as options.
  • Docked FSLeyes control panels can now be minimised by dragging the dock separator.
  • The 3D view now has a toolbar, and standard panels when it is opened.
  • The --version, --help and --fullhelp command line arguments can now be used on systems which do not have a display, and without Xvfb.
  • Initial display range for all volume overlays can now be set as a percentile, via the global --initialDisplayRange command line argument.
  • A small bugfix to 2D mesh outline drawing with weird reference image orientations.
  • Default 3D volume settings have been increased when running in an SSH/X11 environment.
  • Fixed some bugs with mask outline view.

0.20.1 (Friday January 11th 2018)

  • Fixed an issue with label overlays - the outline and width settings defaulted to being synchronised across images.
  • FSLeyes dependencies are now separated into core, optional and development dependencies.
  • Adjustments to standalone build environment.

0.20.0 (Wednesday January 10th 2018)

  • The location panel now has a history section, which contains a list of previously visited locations.
  • Volume display range can now be specified as a percentile on the command line
  • Colour maps and lookup table files can now be specified on the command line.
  • The --vertexData command line argument, for mesh overlays, can be specified multiple times. All vertex data files will be pre-loaded, and the first one will be selected.
  • New options on mask overlays to display the mask outline, and to apply interpolation on the display.
  • The threshold range for mask overlays is now exclusive - now, only values which are within the threshold limits are displayed. Previously, values which were within or equal to the limits were displayed.
  • Profile instances can now notify arbitrary listeners of mouse and keyboard events, instead of only notifying via sub-class methods.

0.19.1 (Wednesday January 3rd 2018)

  • Small fix related to per-view selected overlays.
  • Adjustments to per-view volume linking.

0.19.0 (Wednesday January 3rd 2018)

  • Volumetric DICOM data series can now be loaded into FSLeyes, via the FileAdd from DICOM menu option. The DICOM to NIFTI conversion is performed using Chris Rorden’s dcm2niix tool.
  • The selected overlay can now be different in different FSLeyes views.
  • Volume/timepoint properties can now be linked across views independently of other display properties. This is accessible via a new setting Link overlay volume settings in the view settings panel.
  • All new overlays are now linked by default. This is so that the volumes for 4D images will be synchronised by default.
  • Ortho edit mode has a new Invert selection option.
  • Bug fix in time series and histogram panels regarding non-Image overlays (e.g. surfaces).
  • Work around in screenshot logic for a bug in matplotlib (see https://github.com/matplotlib/matplotlib/pull/10084).

0.18.2 (Thursday December 7th 2017)

  • Fixed another bug drawing label overlays - were not being drawn correctly when both image and LUT had low number of labels.

0.18.1 (Wednesday December 6th 2017)

  • Fixed bug in render (introduced by new --selectedOverlay command line option)

0.18.0 (Wednesday December 6th 2017)

  • Fixed issue linking to the freeglut library on linux builds.
  • Fixed bug drawing label overlays on lightbox views - outlines were not being drawn.
  • A couple of wxPython 3.0.2.0 compatibility bug-fixes.
  • Fixed bug in ResampleAction - was crashing on 4D images.
  • Fixed bug in ColourBarCanvas - was trying to draw before colour bar texture had been created.
  • The screenshot() function is now available in the shell environment (in the ShellPanel, and in scripts executed by the RunScriptAction).
  • New command line option --selectedOverlay to specify the selected overlay.
  • The TimeSeriesPanel honours the NIFTI toffset field.
  • New histogram option HistogramPanel.plotType, to choose between plotting bin edges or bin centres.
  • The HistogramSeries.nbins property now has a maximum value of 1000, and will also accept larger values.
  • The SliceCanvas no longer resets the pan/zoom settings when an overlay is added/removed.
  • The xnat and wxnatpy dependencies are now optional - the Load overlay from XNAT option will be disabled if these dependenceies are not present.
  • New option to generate animated GIFs (see the MovieGifAction). The movieGif() function is available in the shell environment.
  • Plot panels no longer draw tick lines when ticks are disabled.

0.17.2 (Wednesday November 15th 2017)

  • Fixed API documentation generation

0.17.1 (Monday Novermber 13th 2017)

  • Fixed screenhot bug (related to CanvasPanel.colourBarCanvas() property).

0.17.0 (Sunday November 12th 2017)

  • Adjustments to the use of GL_LUMINANCE textures - they are now only used as a fallback if there are are absolutely no other options, as they do not display correctly on some more recent GL drivers.
  • Improved the version update notification dialog.
  • Fixed use of the help function in the python shell.
  • The Volume3DOpts.dithering property, and the --dithering command line option are now deprecated - a suitable dithering level is now automatically determined.
  • Removed some XNAT account credentials which were accidentally hard-coded.

0.16.0 (Tuesday October 31st 2017)

  • Removed the --skipupdatecheck command line option - the default behaviour is now not to check for updates on startup. This can be enabled via the new --updatecheck option.
  • Added the ability to load images from an XNAT server.
  • Application font size can now be set via the --fontSize command line option.
  • 3D volume clipping planes can now be applied as the intersection (default), union or complement of all active clipping planes.
  • Bugfix in CLI generation - --overrideDataRange option does not get generated if data range override is disabled.
  • Display space warning popups/changes are no longer used - instead, a little warning message is shown alongside a button that allows the user to change the display space manually.

0.15.2 (Friday November 24th 2017)

  • A couple of wxPython 3.0.2.0 compatibility bug-fixes (backported from 0.18.0).

0.15.1 (Saturday October 7th 2017)

  • Crop image dialog now has ability to load/save crop parameters
  • New ‘resample’ tool, allowing an image to be resampled to another resolution.

0.15.0 (Thursday September 21st 2017)

  • Removed NiftiOpts.customXform property. Volume overlays can now be aligned to a reference image by setting the transform property to 'reference'. Volume to reference transformation is now handled by individual NiftiOpts instances, rather than centrally by the DisplayContext.
  • Fix to canvas screenshot save - was always saving to current working directory.
  • Nudge panel now displays a warning if the display space is set such that transform changes would not be seen.
  • Various bug fixes to command line generation - --orientFlip, --fgColour, --displaySpace, and overlay order.
  • Fix to pyinstaller/CentOS7 build.
  • Fix to image display on some VM environments - images were displayed at low contrast due to use of luminance texture.

0.14.2 (Wednesday September 13th 2017)

  • Bugfix to vector image handling, caused by 4D addition in 0.14.1
  • Improvements to performance of histogram panel

0.14.1 (Monday September 11th 2017)

  • Support for images with more than 4 dimensions.
  • Overlay display panel has a ‘dimension’ spin control for images, allowing the volume value to control different dimensions.

0.14.0 (Thursday August 24th 2017)

  • Display space is no longer a global setting, but can be changed independently on different views.
  • 3D view always displays in world coordinate system
  • Added command line interface for 3D view and overlay settings
  • Changes to command line for setting ortho centr
  • VEST lookup table files are no longer normalised when loaded
  • Canvases now have a foreground colour option, which controls text, cursor, etc.

0.13.1 (Monday August 14th 2017)

  • Movie mode working in 3D
  • Histogram view has ability to calculate histogram from an ROI
  • Fixes to handling of GL canvas/colour bar background colour
  • Screenshots can now be generated from a script/shell
  • Line vector width is now floating point rather than integer

0.13.0 (Thursday August 10th 2017

  • New 3D view, with volume ray-casting and mesh visualisation
  • OpenGL 1.4 ARB shader program parser now allows sub-routines with arbitrarily named parameters
  • Overlay display panel code refactored to make it easier to customise

0.12.4 (Friday July 14th 2017)

  • New ‘Tools’ menu, intended for things which don’t fit anywhere else.
  • Apply/save FLIRT transform, and seed correlation menu options moved to new Tools menu.
  • Time series view has a feature to generate mean time series from a mask
  • New HSV colour map
  • Order of paths in ‘recent paths’ menu inverted.
  • Fix an issue with py2app command line handling under python 3

0.12.3 (Monday June 12th 2017)

  • Fixes to macOS build

0.12.2 (Monday June 12th 2017)

  • Voxels with a value of NaN are now clipped for volume overlays
  • Bug fixes to melodic classification panel

0.12.1 (Sunday June 11th 2017)

  • Bug fix to histogram auto-bin option for images with no data range
  • Allow Unicode characters in GLSL shader files
  • Changes to FSLeyes build process

0.12.0 (Sunday June 4th 2017)

  • Fixed screenshot under Python 3
  • Changes to FSLeyes assets directory (icons, data files, etc)
  • Changes to FSLeyes build process

0.11.0 (Saturday May 27th 2017)

  • Re-added ‘Reset display range’ button to toolbar for volume overlays
  • Lightbox panel now defaults to Z axis
  • Fixed icon button centering under OSX
  • Fixes to execution and screenshot generation to work around issues in remote (vnc/x2go) execution environments.
  • FSLeyes settings are now stored in user’s home directory on all platforms.
  • Fixes to off-screen orthographic and lightbox rendering
  • Fixes to ortho edit mode ‘target image’ option
  • Many python 2/3, and wxPython 3/4 compatibility fixes

0.10.1 (Thursday April 20th 2017)

  • First public release as part of FSL 5.0.10
  • Melodic classificaiton panel can now be used with any 4D image, not just melodic_IC images.
  • Bug fix to edit mode - was broken for 4D images
  • Volume clipping range can now be specified as a percentile on the command line