fsleyes
release history
This document contains the fsleyes
release history in reverse
chronological order.
1.3.3 (Thursday 23rd December 2021)
Fixed
Fixed an issue with black screenshot images in some environments (e.g. SSH sessions in mobaxterm) (!301).
Removed
pyobj-core
andpyobjc-framework-cocoa
from the list of dependencies (!302).
1.3.2 (Thursday 9th December 2021)
Fixed
Fixed an issue with line vector display when running FSLeyes in an environment which doesn’t support floating point textures (!299).
1.3.1 (Thursday 2nd December 2021)
Fixed
Updated Jupyter notebook integration to work with newer versions of
ipykernel
(!297).Various small tweaks for Python 3.10 compatibility (!297).
1.3.0 (Monday 18th October 2021)
Added
The 3D view now allows the display location to be set to the corresponding location under the mouse on a volume overlay, by shift+clicking (!290).
The display range for a
volume
overlay can now be adjusted interactively by ⌘ + ⇧ + right clicking (⌃ + ⇧ on Linux) and dragging to select a region - the display range will be set to the minimum/maximum voxel intensities within that region (!293).
Changed
The Sample along line tool now supports 2D and multi-channel (e.g. RGB) images (currently plotting the mean intensity across channels for the latter).
Small improvementsto the File ⇒ Add from XNAT dialog (!291).
Fixed
The Display space ⇒ Scaled voxel coordinates setting no longer applies a L/R flip for images with neurological data storage order (!289).
The high clipping range is no longer set when loading a Melodic image with the
--autoDisplay
/-ad
option.(!293).
1.2.0 (Monday 13th September 2021)
Added
The Display space setting can now be set to Scaled voxel coordinates on ortho and lightbox views. This causes all images to be displayed in scaled voxels, with the origin for each image set to the centre of voxel
(0, 0, 0)
(!286).
Changed
The scale vectors to unit length option for line vector overlays now scales the vector colouring, in addition to lengths (!285).
Fixed
Fixed an issue on macOS / Big Sur whereby an image specified on the command-line could be loaded twice (!285).
Fixed some rendering issues for images stored as type
NIFTI_TYPE_RGB24
(!285).
1.1.0 (Friday 6th August 2021)
Added
New
--interpolation
option formesh
overlays, which allows nearest-neighbour or linear interpolation to be selected when colouring meshes with vertex data. This replaces the--flatShading
option (!278).
Changed
The Location panel now displays the region label associated with the current vertex for mesh overlays which are being coloured with a lookup table (!278).
Fixed
Fixed a bug which was preventing the same colour map or lookup table file to be specified more than once on the command line (!278).
Fixed the Check for updates menu item - it now queries
conda-forge
for the latest available FSLeyes version (!279).Fixed a bug which had broken volume navigation in the time series view (!283).
Deprecated
The
--flatShading
option formesh
overlays is equivalent to using--interpolation nearest
(!278).
1.0.15 (Thursday 22nd July 2021)
Fixed
Fixed a subtle bug affecting
fsleyes render
, where taking a screenshot of a large 4D image could result in an infinite loop or segmentation fault (!275).
1.0.14 (Friday 16th July 2021)
Fixed
Fixed an issue with image copying, which could cause pixdims to be changed slightly (!270).
The x-axis of the power spectrum view can can now show frequencies of ICA power spectra for for MELODIC overlays (!271).
1.0.13 (Tuesday 6th July 2021)
Fixed
Fixed a circular import issue, affecting programmatic use of FSLeyes (!268).
1.0.12 (Monday 28th June 2021)
Fixed
Fixed an issue with Jupyter Notebook integration on macOS (!266).
1.0.11 (Monday 14th June 2021)
Fixed
Fixed a compatibility issue with NoMachine/x2go-like remote environments (!264).
1.0.10 (Wednesday 2nd June 2021)
Fixed
Fixed an issue with removing data series from plot views (!262).
1.0.9 (Wednesday 2nd June 2021)
Fixed
Fixed an issue with opening the overlay display panel in 3D views (!260).
1.0.8 (Wednesday 26th May 2021)
Changed
Gamma correction is no longer disabled when log scaling is active (!256).
Fixed
Fixed a problem with API documentation generation (!256, !258).
1.0.7 (Monday 24th May 2021)
Added
New logarithmic scaling option (
--logScale
on the command-line) for volume overlays, which causes voxel intensities to be mapped to the colour map logarithmically, rather than linearly (!254).
1.0.6 (Monday 24th May 2021)
Changed
Overlay display options which refer to other overlays (e.g. Clip by) now use the display name of the other overlay, rather than their file base name (!251).
Restored compatibiilty with wxPython 4.0.* (!250).
Fixed
Fixed a bug related to positioning of line vectors, tensors and FODs for images with non-isotropic voxels (!250).
1.0.5 (Thursday 6th May 2021)
Fixed
Fixed some issues with shutting down cleanly (!248).
Fixed a bug when saving a layout with plugin-provided view panels (!248).
1.0.4 (Tuesday 4th May 2021)
Changed
Improved ortho edit mode performance on large images (!246).
Suppressed some warning messages (!246).
Fixed
Fixed an issue with the
PlotCanvas.limits
becoming out of sync with thematplotlib.Axes
limits (!246).The
file-tree
library is now optional (!246).
1.0.3 (Friday 23rd April 2021)
Fixed
Fixed an issue with the management of built-in asset files (e.g. icons, colour maps, etc). Asset files are now located inside the
fsleyes
package directory (!244).
1.0.2 (Thursday 22nd April 2021)
Fixed
Fixed some issues with FSLeyes plugin management (!242).
Fixed some issues with GL initialisations on GTK2 versions of
wxpython
(!242).New
--annotations
command-line option, allowing annotations to be loaded from a file into an ortho view (!242).
1.0.1 (Tuesday 20th April 2021)
Fixed
Fixed compatibility issues with recent versions of matplotlib (!240).
1.0.0 (Monday 19th April 2021)
Added
The lighting effect in the 3D view is now applied to
volume
overlays (OpenGL 2.1 or newer only) (!222).New
--lightDistance
option (for 3D view), allowing the distance of the light source from the centre of the display bounding box to be set (!222).New
--noBlendByIntensity
option, forvolume
overlays in the 3D view, allowing the modulation of samples by voxel intensity to be disabled (!222).New
-ixh
,-ixv
,-iyh
,-iyv
,-izh
, and-izv
options, allowing ortho canvases to be inverted vertically or horizontally (!225).New
--modulateMode
option forrgbvector
,linevector
,tensor
andsh
overlays, allowing modulation to be applied to either brightness or transparency (!231).New option to copy/paste 2D selections between slices when editing a NIFTI image (!232).
New annotation panel, allowing simple shapes and text to be overlaid on the canvases of an ortho view. Annotations can be saved to/loaded from file, via new options in the Tools menu (!233).
New Sample along line tool, allowing data from an image to be sampled along a line and plotted (!235).
Changed
Text labels drawn on GL canvases are now created using
matplotilb
rather than [Free]GLUT (!221).Removed dependence on [Free]GLUT - this means that
fsleyes render
can now be used on headless systems without usingxvfb-run
, as long as OSMesa is installed (!221).The
--lightPos
command-line option (for the 3D view) has been changed to expect three rotation values (in degrees), which specify the position of the light source with respect to the centre of the display bounding box. This can be combined with the new--lightDistance
option to specify the position of the light source (!222).FSLeyes no longer ignores the
LIBGL_ALWAYS_INDIRECT
environment variable (!222).FSLeyes attempts to determine a suitable value for
PYOPENGL_PLATFORM
if it is not already set (!222).FSLeyes should now work with both Wayland/EGL and X11/GLX builds of wxPython on Linux (!222).
The normalisation method used in the power spectrum panel has been adjusted so that, instead of the data being normalised to unit variance before the fourier transform, the fourier-transformed data itself is normalised to the range [-1, 1] (!224).
The Show command line for scene option will display a warning if any overlays are not saved (!226).
The
FileTreePanel
has been updated to work with the new file-tree library (!230).Change to the interface for copying/pasting data between images - there is now a single button for copying, pasting, and clearing the clipboard (!232).
annotations.TextAnnotation
objects can now be positioned in the display coordinate system, in addition to being positioned at pixel locations on a canvas (!232).Changes to the FSLeyes plugin system to ease the development of FSLeyes controls that use custom interaction profiles, and to improve switching between different interaction proflies (!234).
The FSLeyes plugin system now supports tools which are bound to a specific view panel (!234).
Many built-in FSLeyes control panels and tools have been migrated into the FSLeyes plugin system so that they are dynamically loaded as plugins, rather than being hard-coded (!234).
It is now possible to save and re-load view/control panel layouts with plugin-provided views and control panels (!234).
Fixed
Various fixes and improvements to the lighting effect on
mesh
overlays in the 3D view (!222).When opening a
melodic_IC.nii.gz
file with the--autoDisplay'`/
-ad``, option, themelodic_IC
file is now selected by default, instead of themean
underlay (!219).Fixed a bug in image texture preparation for complex data types, when running in a limited GL environment (e.g. VNC) (!220).
Compatibility fixes for newer versions of Jupyter notebook (!227).
Fixed a problem with macOS desktop integration - it should now be possible to open a file with FSLeyes as the default application, and to drag a file onto the FSLeyes.app icon (!228).
Improved stability when running under macOS+XQuartz (!229).
Fixed an issue with screenshots generated by
fsleyes render
containing transparent pixels (!233).Fixed a collision between the
-mc
and-a
command-line options for mesh overlays (!233).
0.34.2 (Tuesday 14th July 2020)
Fixed
Added support for high-DPI scaling under macOS with wxPython >= 4.1.0 (!217).
0.34.1 (Monday 13th July 2020)
Fixed
Fixed an issue with Jupyter Notebook integration on conda+macOS installations (!215).
Fixed an issue with the high-DPI option not appearing in the view settings panel under macOS (!215).
0.34.0 (Wednesday 8th July 2020)
Added
New option under the Tools menu which allows data from an image overlay to be projected onto a surface overlay (!213).
New Flat shading display option when viewing surfaces in 3D (!213).
Changed
Tweaked GL initialisation to avoid errors when running via XQuartz (!211).
Minor adjustment to Jupyter Notebook integration (!213).
NaN values in mesh overlay vertex data are now handled in the same manner as clipped values - previously they would be displayed in the low colour from the selected colour map (!213).
0.33.2 (Tuesday 23rd June 2020)
Added
Added some more line styles to the plotting panels (!206).
Added a new “accessible” lookup table, courtesy of Paul Tol (https://personal.sron.nl/~pault/) (!206).
Changed
Increased the default plotting line width (!206).
The default plot colours are now from a pre-generated accessible palette, rather than being randomly generated (!206).
The default plot line style is also rotated, in addition the plot colour (!206).
Adjusted the histogram panel so that, when plotting a probability histogram, the values are normalised by bin-width (!203).
A minor adjustment to the default font, to improve readability on some platforms (!202).
Fixed
Fixed an issue with FSLeyes not shutting down cleanly (!204).
0.33.1 (Monday 8th June 2020)
Changed
Changed the
embed()
function so that a parentwx
object is not required.
0.33.0 (Tuesday 26th May 2020)
Added
New modulate alpha option for volume and mesh overlays, which causes opacity to be modulated by voxel/vertex intensity (!193).
Changed
The minimum supported Python version is now 3.7, due to reliance upon a recent version of fslpy (!190).
The
embed()
function accepts amkFrame
argument, allowing it to be called without creating aFSLeyesFrame
(!195).A warning is now displayed in the location panel when images with different orientations, resolutions and/or fields-of-view are being displayed (!198).
Fixed
Fixed a bug in the Export data series action, which was causing a crash on macOS (!190).
Importing modules from the current directory in the Notebook/shell environments is now possible within standalone versions of FSLeyes (!189).
Fixed a small bug in the
embed()
function (!189).Fixed a bug in the Add from XNAT action (!192).
Adjusted the Jupyter Notebook integration so it does not rely on the existence of a command called
jupyter-notebook
(!191).Fixed a couple of bugs in the RGB vector overlay code (!194).
Fixed a bug in ortho edit mode (!196).
0.32.3 (Monday 2nd March 2020)
Fixed
Fixed a bug which occurred when using 3D mode on platforms with limited OpenGL capabilities.
Fixed some minor issues in the file tree panel.
0.32.1 (Thursday 20th February 2020)
Changed
Any mesh overlay can now be displayed in the Freesurfer mesh coordinate system - not just Freesurfer meshes.
Internal changes to avoid using the deprecated
nibabel.dataobj_images.DataobjImage.get_data
method.
Fixed
Fixed a bug which caused mesh display to be corrupted when changing rows in the file tree panel.
Added support for high-DPI displays on platforms other than macOS.
Fixed a bug in animated GIF generation.
Fixed a bug which occurred when editing 4D images.
0.32.0 (Thursday 7th November 2019)
Added
New
--notebookFile
command-line option, which starts the Jupyter notebook server, and opens a specified notebook file.New option to change the location of the Notes column in the file treee panel.
New
--unitLength
option for the RGB vector overlay type, which scales the vector data to unit length.Metadata from JSON sidecar files (e.g. in BIDS data sets) is now displayed in the overlay information panel.
Changed
The
main.embed()
function has been changed so that it now works in a synchronous manner, rather than using an asynchronous callback function.The Jupyter notebook server is now configured so that its root directory is the current working directory.
Small valued regions are no longer shown in the atlas information panel. They are thresholded according to the
lower
threshold in theAtlasDescription
.
Fixed
Fixed a bug in
MeshOpts
bounds calculation.Fixed a bug in Jupyter notebook integration, where an error in the notebook would stop the kernel from executing any more commands.
The Robust FOV and load/export affine transformation options now work with in-memory images.
0.31.2 (Tuesday October 22nd 2019)
Changed
FSLeyes is now more lenient towards NIfTI images with extreme qform affines.
Various changes to improve GTK3 compatibility.
Various changes to reduce warnings and unnecessary output messages.
Fixed
Image texture data is now prepared off the main thread; this was the behaviour before version 0.30.0, but was accidentally disabled for that release.
0.31.1 (Tuesday October 8th 2019)
Fixed
Fixed a bug in edit mode where the image texture would not get updated correctly in restricted environments (e.g. VNC) with certain image data types.
0.31.0 (Thursday September 10th 2019)
Added
New File tree control panel, for viewing data contained in structured directories.
New
complex
overlay type, for displaying images with a complex data type.Support in plot panels for complex images - data from the real, imaginary, magnitude, and/or phase components can be plotted.
New plot panel options to invert axes, and to apply scale/offsets.
New power spectrum panel options to apply phase correction to complex image data.
The atlas panel has basic support for more general “Statistic” atlas types.
New File ⇒ New image menu option, a shortcut to create a new empty image.
Changed
Images with a complex data type are no longer split into separate real and imaginary
volume
overlays - they are loaded as a single image, and displayed ascomplex
overlays.The Overlay ⇒ Copy menu option now supports complex and RGB(A) images.
The plugin interface for tools has changed slightly - tools provided by FSLeyes plugins are now passed references to the
OverlayList
, theDisplayContext
, and to the mainFSLeyesFrame
, to their__init__
method.
Fixed
Fixed a bug in the
OverlayGroup
where old display settings were mistakenly being applied to newly added overlays.Fixed a number of minor bugs in the plot panel logic.
0.30.1 (Wednesday 7th August 2019)
Changed
The Crop tool can now be used to expand the field-of-view of an image, in addition to cropping an image.
The label overlay
--lut
command-line option will accepts colour map files.
Fixed
Added support for editing 2D images.
Fixed a bug in the mesh vertex picking logic which would occur when multiple views were open.
0.30.0 (Thursday 27th June 2019)
Added
The volume overlay type now has support for NIfTI images of type
RGB24
andRGBA32
, via a new Channel setting.New RGB(A) overlay type, for displaying the above image types.
FSLeyes can now load bitmap images (e.g.
.jpg
,.png
, etc.). When a bitmap file is loaded it is internally converted into a 2D NIfTI image.New alternative main function
fsleyes.filtermain.main()
, which filters out useless warnings that originate from underlying libraries (e.g.wx
, GTK, Cocoa, etc).New
--cliserver
option, allowing command-line arguments to be passed to a single FSLeyes instance.
Changed
The
fsleyes.gl.textures
package has been cleaned up and refactored without any attempt to preserve backwards compatibility. Much of the texture data handling code is now shared by theTexture2D
andTexture3D
classes.The
NiftiOpts
class has been moved into a separate module.2D NIfTI images are now displayed with a 2D texture - this means that the maximum dimension size for 2D images is now 16384 on typical hardware.
The Freesurfer coordinates coordinate space option is no longer available on non-freesurfer mesh overlays.
0.29.0 (Sunday May 12th 2019)
Added
The Tools ⇒ Resample image option now allows an image to be resampled to the space of another image.
New
-stdb
and-std1mmb
command-line options for loading brain-extracted versions of the MNI152 templtes.
Fixed
Fixed an issue where images with unconventional voxel storage orders were being transformed into the display coordinate system in a slightly inaccurate manner.
FIxed an issue with orthographic edit mode being incorrectly disabled when the selected overlay is changed.
0.28.2 (Sunday April 14th 2019)
Changed
The update check option does not verify SSL certificates when downloading the latest version string.
0.28.0 (Friday April 5th 2019)
Added
Added metadata to allow better integration with Linux desktop environments.
Added ability to drag-and-drop files onto the FSLeyes window to open them.
The
--vertexSet
and--vertexData
command-line options now cause the last vertex set/data to be selected, and also support GIFTI surface files which contain multiple vertex sets and vertex data.New
ControlMixin.defaultLayout()
method, which can be overridden by control panels (including plugins) to customise the default panel positioning/layout.
Changed
FSLeyes no longer depends on the
deprecation
library.
Fixed
Jupyter Notebook integration has been updated to work with newer versions of the
ipykernel
library.Fixed bug with initial directory shown in open file dialogs.
Fixed a bug which would sometimes cause 4D image data display to be corrupted on macOS.
Fixed a bug which was preventing image textures from being updated when non-3D data regions were changed.
Deprecated
The
fsleyes.overlay.guessDataSourceType()
function has been deprecated, as it has been replaced by thefsl.data.utils.guessType()
function.
0.27.3 (Friday February 8th 2019)
Fixed
Fixed initialisation bug on platforms with a non-English language.
0.27.2 (Friday February 8th 2019)
Changed
Small display range values are forced to 0 on the colour bar.
0.27.1 (Friday January 18th 2019)
Fixed
Updated the
render
command so it incoporates the recent enhancments to colour bar display.
0.27.0 (Monday December 3rd 2018)
Added
Complex image types are now supported - the real and imaginary components are loaded as separate overlays.
New Set $FSLDIR menu option, for updating the FSL installation directory.
Changed
FSLeyes is no longer tested against Python 2, or wxPython 3.
The Tools ⇒ Resample image menu option now supports images with more than three dimensions.
Increased range of colour bar tick labels.
When the negative colour map is enabled, and the display range minimum is 0.0, only a single central tick label is displayed on the colour bar.
Fixed
FSLeyes should fail more gracefully when unrecognised files/directories are specified on the command line.
Fixed a bug in the
--fullhelp
/-fh
command line option.
0.26.5 (Monday November 26th 2018)
Added
New option to change the colour bar width/height - this is available in the ortho/lightbox/3D settings panel (the
button).
The Label size option now adjusts the colour bar font size, in addition to the orientation label font size.
Fixed
Fixed a bug in the time series panel when viewing a FEAT analysis with voxelwise confound EVs.
Fixed a bug in the FEAT cluster panel when viewing a FEAT analysis which had not used cluster-based thresholding.
0.26.4 (Tuesday October 23rd 2018)
Changed
Renamed the File ⇒ Add atlas menu item to Import new atlas.
Removed
Test data is not included in the FSLeyes source distribution, as it is too large for PyPi.
0.26.3 (Tuesday October 23rd 2018)
Fixed
Fixed a bug in edit mode where the selection overlay would sometimes not be displayed.
Fixed a bug in the
DiagnosticReportAction
(the FSLeyes ⇒ Diagnostic Report menu item).
0.26.2 (Friday October 5th 2018)
Changed
Development (test and documentation dependencies) are no longer listed in
setup.py
- they now need to be installed manually.Removed conda build infrastructure.
0.26.0 (Sunday September 16th 2018)
Added
New
plugins
architecture, for adding custom panels and tools to FSLeyes.The
render
tool has a new--crop
option, to auto-crop screenshots.The
VolumeOpts.overrideDataRange
is now automatically enabled for images with an extreme data range, on platforms that do not support floating point textures.New
brain_colour
colour maps provided by MRICron and Cyril Pernet.
Changed
User-added and built-in colour map/lookup table names and display order can now be customised by adding a file called
order.txt
to the FSLeyes user configuration directory.
Fixed
Updated user documentation.
Fixed a bug in the
HistogramSeries
class.Fixed a bug in the
ImportDataSeriesAction
class.Fixed a bug in the
AddMaskDataSeriesAction
class.Fixed a bug in the
AddROIHistogramAction
class.gl
initialisation can now handle non-ASCII OpenGL renderer strings.
0.25.0 (Tuesday August 28th 2018)
Added
New MIP overlay type, for displaying 2D maximum intensity projections (not available over SSH/X11).
A new movie mode option to change the canvas refresh regime between synchronised and unsynchronised, as the default synchronised regime does not work in some environments/platforms.
New
fsleyes.main.embed()
function, allowing a FSLeyes frame to be opened from within an existing application.
0.24.6 (Monday August 6th 2018)
Fixed
Fixed a small bug in detection of image/analysis types from command line arguments.
Fixed deprecation warning suppression in standalone versions of FSLeyes.
0.24.5 (Wednesday August 1st 2018)
Added
New command line flag
--notebook
/-nb
, which starts the Jupyter notebook server automatically.
Changed
Overlays loaded from
fslpy
wrapper functions are now named accordingly.
Fixed
Fixed a memory leak in the
fsleyes.displaycontext.group
module.Suppresed some deprecation warnings when running frozen versions of FSLeyes.
0.24.4 (Thursday July 19th 2018)
Fixed
Fixed an error caused when loading a Melodic IC label file containing unrecognised labels.
Changed
fslpy
wrapper functions now return a value (e.g. if output files are marked for loading) when called from a Jupyter notebook or the FSLeyes python shell.The
appnope
library is only a dependency on macOS.
0.24.3 (Monday June 11th 2018)
Fixed
Further fixes to Jupyter notebook server and kernel management for running within frozen versions of FSLeyes.
Fixed a sizing issue in the FSLeyes about dialog.
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.
0.24.0 (Tuesday June 5th 2018)
Added
Integration with Jupyter Notebook is now available via the File ⇒ Open 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 tofsleyes.layouts
. All associated functions and classes have been renamed accordingly.The
fsleyes.state
module has been re-written - thegetState()
andsetState()
functions can be used to save/restore the full FSLeyes state (layout and overlays).
Deprecated
The
fsleyes.perspectives
,fsleyes.actions.clearperspective
,fsleyes.actions.loadperspective
, andfsleyes.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
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).
0.22.3 (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()
- theMeshOpts.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 incompletemgh-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 infsleyes-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 File ⇒ Add 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 theShellPanel
, and in scripts executed by theRunScriptAction
).New command line option
--selectedOverlay
to specify the selected overlay.The
TimeSeriesPanel
honours the NIFTItoffset
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
). ThemovieGif()
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 thetransform
property to'reference'
. Volume to reference transformation is now handled by individualNiftiOpts
instances, rather than centrally by theDisplayContext
.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