fsleyes issueshttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues2018-08-18T01:35:57+01:00https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/34Better management of texture resources2018-08-18T01:35:57+01:00Paul McCarthyBetter management of texture resourcesThe texture resource naming convention is ad-hoc, and large texture resources are not shared as much as they could be.
Texture resources should be accessed by their properties (e.g. the image itself, resolution, interpolation, etc), so ...The texture resource naming convention is ad-hoc, and large texture resources are not shared as much as they could be.
Texture resources should be accessed by their properties (e.g. the image itself, resolution, interpolation, etc), so that different things which need an equivalent texture will naturally end up sharing the same texture, instead of creating a duplicate.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/31Re-factor props/syncable functionality.2018-08-18T01:35:57+01:00Paul McCarthyRe-factor props/syncable functionality.(This is a ``props`` issue).
The parent-child relationships between DisplayContexts, Displays, and DisplayOpts is continuing to be a cause of bugs and kludgy workarounds.
Both parent and child instances register listeners on themselve...(This is a ``props`` issue).
The parent-child relationships between DisplayContexts, Displays, and DisplayOpts is continuing to be a cause of bugs and kludgy workarounds.
Both parent and child instances register listeners on themselves, but parent instances are really only necessary for property value synchronisation.
The ``syncable`` module should be re-written (or a new module written) which just proivides synchronisation capability. A solution similar to the ``fsl.fsleyes.group`` module might work.
Another thing ... I would like to be able to run ``FSLeyes`` (or parts thereof) without having to create a hierarchy of DisplayContexts (and associated classes).Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/30Overlay blending2018-08-18T01:35:57+01:00Paul McCarthyOverlay blendingHave a look at how the colours of transparent overlays are blended.
For example, if we have two mask overlays, one yellow and one blue, both at 50%, shouldn't the mask intersection be the same colour (hopefully a shade of green), no ma...Have a look at how the colours of transparent overlays are blended.
For example, if we have two mask overlays, one yellow and one blue, both at 50%, shouldn't the mask intersection be the same colour (hopefully a shade of green), no matter what the order?Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/120Jupyter notebook misbehaving under VNC2018-08-30T16:40:38+01:00Paul McCarthyJupyter notebook misbehaving under VNCIn Fidel's VNC session on jalapeno18, firefox didn't open, and the `screenshot` function produced corrupt resultsIn Fidel's VNC session on jalapeno18, firefox didn't open, and the `screenshot` function produced corrupt resultsPaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/29Mask intersection overlay2018-11-08T22:15:08+00:00Paul McCarthyMask intersection overlayPotentially useful feature: a new overlay type, a 'mask container' which allows the user to add mask images to it, and control how the intersection of the different masks are coloured.
Slightly related: fsl/fslpy#136Potentially useful feature: a new overlay type, a 'mask container' which allows the user to add mask images to it, and control how the intersection of the different masks are coloured.
Slightly related: fsl/fslpy#136Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/25Real time tractography display?2018-11-08T22:15:08+00:00Paul McCarthyReal time tractography display?Choose a location, and display (pre-calculated) probabilistic tractography resultsChoose a location, and display (pre-calculated) probabilistic tractography resultsPaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/22Plot motion parameters in Melodic mode2019-03-19T14:54:36+00:00Paul McCarthyPlot motion parameters in Melodic modeIf motion parameters have been estimated for a melodic data set, it would be useful to be able to plot them in the time series panel, along with component time courses. Related to fsl/fslpy#32If motion parameters have been estimated for a melodic data set, it would be useful to be able to plot them in the time series panel, along with component time courses. Related to fsl/fslpy#32Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/21'Remove trimmings' option2019-03-19T14:54:36+00:00Paul McCarthy'Remove trimmings' optionWhen setting up FSLeyes for more complicated screen shots (e.g. lightbox + time series + power spectrum), it would be useful to toggle on/off all window decorations (scrollbars, title bars, etc etc).When setting up FSLeyes for more complicated screen shots (e.g. lightbox + time series + power spectrum), it would be useful to toggle on/off all window decorations (scrollbars, title bars, etc etc).Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/20RIght click on a view panel should show the view panel menu2019-03-19T14:54:36+00:00Paul McCarthyRIght click on a view panel should show the view panel menuAllow view panel menu to be accessed via a right-click context menu popup.Allow view panel menu to be accessed via a right-click context menu popup.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/17specifying intensity threshold for voxel selection in edit mode2019-03-19T14:54:36+00:00Lennart Verhagenspecifying intensity threshold for voxel selection in edit modeI encountered a few issues with specifying the intensity threshold for intensity-based voxel selection in edit mode. I really like the edit mode, and this specific selection type is a nice addition. Please see all my comments as very min...I encountered a few issues with specifying the intensity threshold for intensity-based voxel selection in edit mode. I really like the edit mode, and this specific selection type is a nice addition. Please see all my comments as very minor and friendly suggestions. When I initially enter this mode the intensity threshold is set at 10, regardless of the intensities in the actual image. For example I wanted to select voxels from an FA image. I also noticed that the down-button had no effect, I could only press "up" to go higher than 10. I could mouse-scroll, but this took a very long scroll to values below 1. The scroll speed is not dependent on the value (nor the arrow jump), so once I got below 1 it was nearly impossible to select an appropriate value between 0 and 1 with the mouse scroll. Adjusting the intensity value does not adjust the current intensity-selection, you have to click to do this again. I ended up with a set of multiple erroneous selections, so I had to clear all selections, and do it again. I see that this is a compromise, but to me an intuitive workflow would be that I make an intensity-based selection (by mouse selection), see that is it too big/small, and adjust the threshold (requiring you to move your mouse cursor away from the selection). It isn't always easy to have to move your cursor back to your initial voxel.https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/16Reset range to current volume2019-03-19T14:54:36+00:00Paul McCarthyReset range to current volumeOn display toolbar, for volume overlays, a button which allows the user to adjust the display/clipping range to the range of the current volume.On display toolbar, for volume overlays, a button which allows the user to adjust the display/clipping range to the range of the current volume.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/15Merge mask images2019-03-19T14:54:36+00:00Paul McCarthyMerge mask imagesWhen creating mask images it might be useful to allow multiple masks to be merged e.g. via union or intersection (or addition/subtraction, if a non-binary mask).When creating mask images it might be useful to allow multiple masks to be merged e.g. via union or intersection (or addition/subtraction, if a non-binary mask).Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/13Optimise seed correlation2019-03-19T14:54:36+00:00Paul McCarthyOptimise seed correlationIt's slow and force-loads the entire image (which is possibly why it is slow). Fix these things.It's slow and force-loads the entire image (which is possibly why it is slow). Fix these things.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/11Atlas panel - load affine/nonlinear transformation to query non-MNI152 images?2019-03-19T14:54:36+00:00Paul McCarthyAtlas panel - load affine/nonlinear transformation to query non-MNI152 images?Why don't we just build `Featquery_gui` into FSLeyes?Why don't we just build `Featquery_gui` into FSLeyes?Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/9IC label panel sync and focus2019-03-19T14:54:36+00:00Paul McCarthyIC label panel sync and focusWhen you select a tag in the label grid, the volume should be displayed
Focus of the specific tag should be retained .... although this might be complicatedWhen you select a tag in the label grid, the volume should be displayed
Focus of the specific tag should be retained .... although this might be complicatedPaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/6Contour overlay2019-03-19T14:54:36+00:00Paul McCarthyContour overlay1. Coloured according to a `LookupTable` which defines the contour values
2. Use a technique based on the `VolumeOpts.colourMapResolution` setting to draw the contours
3. Option to draw contour lines, or contour bands1. Coloured according to a `LookupTable` which defines the contour values
2. Use a technique based on the `VolumeOpts.colourMapResolution` setting to draw the contours
3. Option to draw contour lines, or contour bandsPaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/2props: remove attribute listeners?2019-03-19T14:54:36+00:00Paul McCarthyprops: remove attribute listeners?Is a distinction between property value listeners and property attribute listeners necessary?Is a distinction between property value listeners and property attribute listeners necessary?Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/1DisplayOpts mixin classes2019-03-19T14:54:36+00:00Paul McCarthyDisplayOpts mixin classesSimilar to the `ColourMapOpts` class, you should also add a `4DOpts` (with a better, less syntactically invalid name) class for overlay types which may be 4D, and a `LutOpts` class for overlay types with lookup tables.
This will allow ...Similar to the `ColourMapOpts` class, you should also add a `4DOpts` (with a better, less syntactically invalid name) class for overlay types which may be 4D, and a `LutOpts` class for overlay types with lookup tables.
This will allow you to remove explicit handling of different overlay types in e.g. the location panel (the volume counter), and the lookup table panel.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/69Group analysis browser2019-05-14T09:40:49+01:00Paul McCarthyGroup analysis browserA control panel which allows easy navigation of (e.g.) FEAT group analyses.
Thoughts:
- A prompt which allows the user to type in a file system path (with tab completion)
- A list which shows the contents of the current path (with th...A control panel which allows easy navigation of (e.g.) FEAT group analyses.
Thoughts:
- A prompt which allows the user to type in a file system path (with tab completion)
- A list which shows the contents of the current path (with thumbnails for `.nii` images, and maybe `.feat`/`.ica` directories)
- The ability to filter this list according to a wildcard
- The ability to recurse into sub-directories, and list all files which match a wildcard patternFSLeyes 1.0.0Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/145ability to edit multi-channel images2019-09-06T08:54:04+01:00Paul McCarthyability to edit multi-channel imagesPaul McCarthyPaul McCarthy