It appears that toggling visibility of segmentation in slice view toggles all of the viewers, even if the views are unlinked. Is this a bug? I see the same behavior both in latest and stable. If I export segmentation as labelmap, it behaves as I would expect, where with unlinked views just the current view visibility is toggled.
This is the correct and expected behavior for every nodes in Slicer. Only display of volume nodes (scalar and labelmap) in slice views are the exception because of the limitation that you cannot easily display any number of volumes in the same slice view.
You can very easily display nodes only in selected views, by drag-and-dropping the node from the Data module to the views where you want to see them.
Thanks for the clarification. I didnât realize this is the expected behavior.
cc: @erikziegler - I was wrong, strangely, itâs not a bug.
For consistency, we could remove the segmentation node selector from the view controller (the same way as you cannot show/hide markups or models using the slice view controller). We added segmentations visibility controls there to make transitions from labelmaps easier. However, Iâm not sure how often this is used and since it does not have the limitation of volume layers, maybe it is too confusing have these controls there along with volume layer controls.
@lassoan sorry, I am removing most of my comment, since I realize it is exactly the same issue.
BUT
According to the documentation here User Interface â 3D Slicer documentation
âLayer visibility âeyeâ buttons and Layer opacity spinboxes control visibility of segmentations and volumes in the slice view.â
My interpretation of the above is that it should toggle layer visibility in a single view, not in all views.
Should this bit of the documentation be rephrased? The actual behavior is not what the documentation seems to imply.
We only added the eye icon to the slice view to keep things more familiar for people when transitioning from labelmap volume to segmentation. Segmentation visibility setting works slightly differently than volume layer selectors, because you can display any number of segmentations in a slice view, while volume display is limited to 2+1.
I see the following options to make things more clear:
I think option B is the best both in term of consistency and simplicity in usage and maintenance, but Iâm not sure if users are ready for the change, i.e., if they already use the Data moduleâs eye icon and drag-and-drop instead of the slice view controllers.
Of course documentation should always be up-to-date with latest functionality and if found to not match then it should be updated.
As it relates to these widgets in the Slice Controller:
I hope some of my thoughts here are helpful as part of gathering user behavior related to the Slice Controller to make everything easier for new users.
I have to say that I am still struggling to understand why per-slice toggle is not possible. I followed the steps, and if I drag a segmentation from Data module list to a slice viewer, and after that toggle segmentation visibility it toggles in a single view. But then I dragged it into other views, and it seemed to be toggling in all views. And I could not figure out how to remove a segmentation from a specific view if I no longer want it to be visible.
I am definitely biased, but I think toggle behavior for labelmap was very intuitive, and didnât require reading any documentation to understand. Therefore, my preference is Option C.
Would be great to hear thoughts from other users.
Yes, I looked around more and found it.
Wouldnât it be helpful if the eye button corresponding to the segmentations layers toggled visibility of all segmentations in the selector below
either in the current slice (if slice views are unlocked) or in all slices otherwise?
It would be probably helpful. However, given models, markups, volumes are set this way (from their specific module) I didnât find it very confusing. Just quite buried (like the others).
I am wondering if it would be useful to do all of this in a âdata visibilityâ module to control all these different data types using the same interface in the same place (as opposed to use the Advanced tabs of each module). Maybe even have it under the data module somehow.
It is possible, but the behavior would still not the same as the label layer selector, because that automatically hides the previously displayed label, which we donât want to do for segmentations.
Dragging to views works the same way for all nodes: if you drag a node from the Data module to a view then it is displayed in that view only (or that view group, if the views are linked). You can reset these per-view display settings in the right-click menu of the eye icon in Data module.
We could add a checkable view list to the right click menu of the eye icon, if you think that would help.
When we implement proper slice displayable managers for volumes so that we can display any number of volumes in a slice view (probably within a few years) then the layer selectors will need to go anyway. So we are looking for improving usability of the layer selectors in the short/mid term. As a long term solution, I like the way how ParaView does it: the eye icon in the Data tree only adjusts the visibility of the node in the view that has the focus (when you click on a view it gets the focus, which is indicated by a highlight of the border).
I agree with each and every point of @jamesobutler , thatâs exactly how I use these features too. But we are Slicer dinosaurs, quite set in our ways. If we had to change the UI Iâd probably remove this row from the controller to reduce confusion, however, it can be convenient for some users, so Iâd vote for Option A.
Historical reasons⌠we have been struggling with this division for many years now, that the volumes and all the rest of the data are shown in a different way. Volumes can only be shown in 2D as the foreground or background of the slice views, and these are exclusive, and quite rigid, thus the link views feature was necessary etc. Any other type, however, model, markup, segmentation, or anything else is âjust shownâ, so shown in all views or not shown, and per-view visibility is a quite special feature where you need to have multiple display nodes for the same data node telling each view whether the node is visible in that view or not (please note that volume nodes are so different this is done via a different mechanism there).
Yes, this will be the ultimate solution. Until then, we can just balance between familiar and 100% correct. Because as you, Andriy, found out, although the familiar feature is there, it works slightly differently. If we remove it, many people will be looking for it. If we implement the per-view feature there, it would be an unproportinally large time investment from developers (at least thatâs what I think), and it would then mess up the display nodes (creating multiple ones), which, I suspect, will lead to even larger issues. Iâd say fix up the documentation and focus on the ultimate solution.
One display node can manage selective display in certain views, so we would not need to add more display nodes. But it would certainly take more effort than adding some clarifications to the documentation.
@fedorov after you have tried drag-and-drop for selecting what nodes are displayed in which views, do you still want to use the slice view controllers for this?
I personally would not say it works slightly different. It just looks like a bug. To me, the reason for updating the documentation is to explain the behavior, not help discover a feature of the UI.
Sorry, I am really slow to get this. In the above, I donât understand what you mean by âthe behavior would still not the same as the label layer selector, because that automatically hides the previously displayed label, which we donât want to do for segmentationsâ. I am not suggesting to revise the behavior of the selector, but just the eye button, to toggle visibility of all segmentations/segments in the given view, when views are not linked.
Right now, toggling visibility of a segmentation per-view is already possible via âSegmentations > Advanced > Viewsâ. Thatâs why I thought implementation of the per-slice visibility toggle would not require any major development work. I didnât realize it requires significant effort, which I agree is not justified.
I personally would like to, because otherwise I need to go to Segmentations module to do this. But given there is no interest from other users, and this would be a major development effort, it is not important.
I was just trying to understand whatâs going on. Sorry for taking your time with these back and forth.
You donât need to go to Segmentation module - you can set up most commonly needed visualizations without switching modules, just using the Data module.
For example, from the tree in Data module, you can drag-and-drop any node to any view. It makes the node show up only in the view(s) the node has been dragged into. You can reset this selective display by right-clicking on the eye icon and choosing âShow in all viewsâ.
But you canât set per slice view in the Data module. If you want one segmentation in yellow slice and another in green. I donât think thatâs possible without the segmentations module. Am I mistaken? Thatâs what I think @fedorov wants/needsâŚ
You certainly can! Drag-and-drop the segmentation from the data tree to the views that you want to appear in. No need to use the segmentations module for this.
Himm, I always assumed that when I drag and drop the segmentation it showed in all slice views, but apparently not.
This is niceâŚ
If views are linked then drag-and-drop into a view displays the node in all the views in the view group. Otherwise it just shows the node in that specific view.
You can use this to set up contents of views in a few seconds, with any nodes (volumes, models, markups, segmentations, âŚ), without switching between modules.
