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May 8 2024

kompan added a comment to T18489: Help perspective cannot be closed.

Since this issue was pointed out by a user recently (and I also found it confusing before reading this task description), I would like to re-open this task for discussion.

May 8 2024, 9:40 AM · MITK (v2024.12), Request for Discussion
kislinsk claimed T30414: [Documentation] Help contents have wrong titles and root pages.
May 8 2024, 9:04 AM · Checklist, MITK (v2024.06)

May 7 2024

kislinsk assigned T30421: [SEG] Undo/Redo problems with Fill/Erase tool reported to floca.
May 7 2024, 9:58 PM · Missing Info, Checklist, MITK (v2024.06)
floca committed rMITK303cdff5e506: Fixed T29526 (authored by floca).
Fixed T29526
May 7 2024, 6:28 PM
floca committed rMITK88164071fbca: Fixed T29526 (authored by floca).
Fixed T29526
May 7 2024, 6:28 PM
floca closed T29526: [Segmentation] Workbench crashes when closing render window part with active tool as Resolved by committing rMITK88164071fbca: Fixed T29526.
May 7 2024, 6:28 PM · MITK (v2024.06)
kislinsk added a comment to T30417: [Segmentation] Invisible labels are highlighted leading to confusing UX.

This is a good idea.

May 7 2024, 4:31 PM · Request for Discussion, Checklist, MITK (v2024.06)
floca added a comment to T30417: [Segmentation] Invisible labels are highlighted leading to confusing UX.

hm. I see.
May be:
B + if you press shift while hovering, then always highlight?

May 7 2024, 4:08 PM · Request for Discussion, Checklist, MITK (v2024.06)
kislinsk added a comment to T30417: [Segmentation] Invisible labels are highlighted leading to confusing UX.

That you cannot tell. You don't know how testers would react to option A. May be it is equaly irritating to them. And may be they would missing the highlighting of invisible labels if the realy would work with it... 🤔

May 7 2024, 3:57 PM · Request for Discussion, Checklist, MITK (v2024.06)
floca added a comment to T30417: [Segmentation] Invisible labels are highlighted leading to confusing UX.

but the disadvantages proved to outweigh.

That you cannot tell. You don't know how testers would react to option A. May be it is equaly irritating to them. And may be they would missing the highlighting of invisible labels if the realy would work with it... 🤔
If we want to base it on user feedback in such an unclear situation, one would need to offer/explain all options and let them choose/poll.

May 7 2024, 3:51 PM · Request for Discussion, Checklist, MITK (v2024.06)
a178n added a comment to T30426: [SEG] Highlight importance of level window in Segment Anything.

Pushed new branch to rMITK MITK: feature/T30426-doc-updates.

May 7 2024, 3:50 PM · Checklist, MITK (v2024.06)
floca added a comment to T30412: [Statistics] Planar figure cannot be set as ROI for askew images.

Hm, yes, As we also define a reference image like in the segmentation view. I think it is the most pragmatic and consistent approach to introduce the same/simelar behavior:
warn users if the rendering is not alligned with the reference image and only allow making planar figures if the geometry was reinit.
I am not sure if reinit as soon as the click on a planar figure button wouldn't be irritating.

May 7 2024, 3:45 PM · Moved to git.dkfz.de, MITK (v2024.12)
kislinsk added a revision to T29526: [Segmentation] Workbench crashes when closing render window part with active tool: Unknown Object (Differential Revision).
May 7 2024, 3:36 PM · MITK (v2024.06)
floca committed rMITK02992e94b8ae: T30411-Fix_wrong_label_color_display_after_instance_addition (authored by floca).
T30411-Fix_wrong_label_color_display_after_instance_addition
May 7 2024, 3:20 PM
floca closed T30411: [SEG] Label color is off unitl first refresh when instances are used as Resolved by committing rMITK36f6b8c0d855: Fixed T30411.
May 7 2024, 3:20 PM · Checklist, MITK (v2024.06)
floca committed rMITK36f6b8c0d855: Fixed T30411 (authored by floca).
Fixed T30411
May 7 2024, 3:20 PM
floca committed rMITK109886894aa4: Fixed T30420 (authored by floca).
Fixed T30420
May 7 2024, 3:19 PM
floca closed T30420: [SEG] Fill/Erase tool does not work due to geometry error, a subtask of T30421: [SEG] Undo/Redo problems with Fill/Erase tool reported, as Resolved.
May 7 2024, 3:19 PM · Missing Info, Checklist, MITK (v2024.06)
floca closed T30420: [SEG] Fill/Erase tool does not work due to geometry error as Resolved by committing rMITKd52112aa4083: Fixed T30420.
May 7 2024, 3:19 PM · Checklist, MITK (v2024.06)
floca committed rMITKd52112aa4083: Fixed T30420 (authored by floca).
Fixed T30420
May 7 2024, 3:19 PM
floca committed rMITKd97f4d532271: T30419-Fix_growcut_confirm_btn (authored by floca).
T30419-Fix_growcut_confirm_btn
May 7 2024, 3:18 PM
floca closed T30419: [Segmentation] "Preview" button of GrowCut tools needs to be clicked twice before "Confirm segmentation" button gets active as Resolved by committing rMITK551e8c93dbfc: Fixed T30419.
May 7 2024, 3:18 PM · Checklist, MITK (v2024.06)
floca committed rMITK551e8c93dbfc: Fixed T30419 (authored by floca).
Fixed T30419
May 7 2024, 3:18 PM
kislinsk added a revision to T30420: [SEG] Fill/Erase tool does not work due to geometry error: Unknown Object (Differential Revision).
May 7 2024, 3:03 PM · Checklist, MITK (v2024.06)
kislinsk added a comment to T30412: [Statistics] Planar figure cannot be set as ROI for askew images.

With a reinit it works but boy is this unintuitive for users. Like when starting the Workbench and opening brain.nrrd, there's no indication that a reinit is necessary (and what a reinit is and where to find it is another story). You can draw a planar figure on it just fine.

May 7 2024, 3:00 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca claimed T29526: [Segmentation] Workbench crashes when closing render window part with active tool.
May 7 2024, 2:59 PM · MITK (v2024.06)
kislinsk added a comment to T30417: [Segmentation] Invisible labels are highlighted leading to confusing UX.

Yes, I agree. Well, not completely I guess, since I vote for B. The current state confused all testers (and me at first when I double-checked what's going on, and after I understood I still would consider it a bug in this state). I see the good intentions why you changed it from initial B to something else, but the disadvantages proved to outweigh.

May 7 2024, 2:53 PM · Request for Discussion, Checklist, MITK (v2024.06)
floca moved T30412: [Statistics] Planar figure cannot be set as ROI for askew images from Backlog to Cycle on the MITK (v2024.06) board.
May 7 2024, 2:50 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca added a project to T30412: [Statistics] Planar figure cannot be set as ROI for askew images: Missing Info.

I cannot reproduce the "bug".
But it is not realy a bug but correct. If you do not reinit on brain.nrrd before making the planar figure, it is tilted. Therefore no statistics can be computed.

May 7 2024, 2:49 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca claimed T30412: [Statistics] Planar figure cannot be set as ROI for askew images.
May 7 2024, 2:37 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca merged T30418: [Segmentation / Pixel Value] Pixel values only shown for active group into T29525: Pixel Value View should be aware of label set images.
May 7 2024, 2:36 PM · MITK
floca merged task T30418: [Segmentation / Pixel Value] Pixel values only shown for active group into T29525: Pixel Value View should be aware of label set images.
May 7 2024, 2:36 PM · Checklist, MITK (v2024.06)
floca added a revision to T30419: [Segmentation] "Preview" button of GrowCut tools needs to be clicked twice before "Confirm segmentation" button gets active: Unknown Object (Differential Revision).
May 7 2024, 2:30 PM · Checklist, MITK (v2024.06)
kislinsk added a revision to T30416: [Measurement] Selecting a shape enforces drawing it / finishing a path not obvious: Unknown Object (Differential Revision).
May 7 2024, 12:00 PM · MITK (v2024.06), Checklist
kislinsk added a comment to T30416: [Measurement] Selecting a shape enforces drawing it / finishing a path not obvious.

Pushed new branch to rMITK MITK: bugfix/T30416-AddUsageHintsToMeasurementView.

May 7 2024, 11:58 AM · MITK (v2024.06), Checklist
kislinsk added a comment to T30416: [Measurement] Selecting a shape enforces drawing it / finishing a path not obvious.

The Measurement view is quite a historically grown abomination that would greatly benefit from a complete overhaul. Hence, to keep complexity down to a minimum for the upcoming release, I suggest to not implement canceling but instead to add a hint to the GUI on how to finish continuous planar figures.

May 7 2024, 11:08 AM · MITK (v2024.06), Checklist
kislinsk claimed T30416: [Measurement] Selecting a shape enforces drawing it / finishing a path not obvious.
May 7 2024, 11:05 AM · MITK (v2024.06), Checklist
kompan triaged T30437: [Perfusion] Provide example start parameter image for checklists as Low priority.
May 7 2024, 10:49 AM · Moved to git.dkfz.de, MITK (v2024.12), Checklist
kompan triaged T30436: [Perfusion] Checkbox for Start Parameters instead of radio button as Low priority.
May 7 2024, 10:43 AM · Moved to git.dkfz.de, MITK (v2024.12), Checklist
kompan added a project to T30435: Rename "Time" to "Timestep" in Image Navigator?: Request for Discussion.
May 7 2024, 10:40 AM · Moved to git.dkfz.de, MITK (v2024.12), Checklist
kompan triaged T30435: Rename "Time" to "Timestep" in Image Navigator? as Normal priority.
May 7 2024, 9:48 AM · Moved to git.dkfz.de, MITK (v2024.12), Checklist
kompan triaged T30434: [Perfusion] Concentration curve converter VFA box tab key skips flip angles as Normal priority.
May 7 2024, 9:40 AM · Moved to git.dkfz.de, MITK (v2024.12), Checklist
kompan triaged T30433: [Perfusion] Inconsistent appearance of info box message "Cannot compute parameters. No node selected." as Normal priority.
May 7 2024, 9:11 AM · Moved to git.dkfz.de, MITK (v2024.12)
kompan updated the task description for T30432: [Perfusion] Possible to write text into info box.
May 7 2024, 9:03 AM · Moved to git.dkfz.de, MITK (v2024.12)
kompan triaged T30432: [Perfusion] Possible to write text into info box as Normal priority.
May 7 2024, 8:57 AM · Moved to git.dkfz.de, MITK (v2024.12)
kislinsk added a revision to T29525: Pixel Value View should be aware of label set images: Unknown Object (Differential Revision).
May 7 2024, 8:50 AM · MITK
kislinsk added a comment to T29525: Pixel Value View should be aware of label set images.

Pushed new branch to rMITK MITK: bugfix/T29525-IgnoreLabelSetImagesInPixelValueView.

May 7 2024, 8:46 AM · MITK
kislinsk claimed T29525: Pixel Value View should be aware of label set images.

For now, I suggest the most simple solution which is to ignore label set images all together, as long as we do not correctly support probing pixel values at a certain location. This is a much more complex problem that can be tackled in the future if requested, for example:

May 7 2024, 8:43 AM · MITK

May 6 2024

floca moved T30419: [Segmentation] "Preview" button of GrowCut tools needs to be clicked twice before "Confirm segmentation" button gets active from Backlog to Cycle on the MITK (v2024.06) board.
May 6 2024, 12:11 PM · Checklist, MITK (v2024.06)
floca moved T30411: [SEG] Label color is off unitl first refresh when instances are used from Backlog to Cycle on the MITK (v2024.06) board.
May 6 2024, 12:11 PM · Checklist, MITK (v2024.06)
floca moved T30420: [SEG] Fill/Erase tool does not work due to geometry error from Backlog to Cycle on the MITK (v2024.06) board.
May 6 2024, 12:11 PM · Checklist, MITK (v2024.06)
floca claimed T30419: [Segmentation] "Preview" button of GrowCut tools needs to be clicked twice before "Confirm segmentation" button gets active.
May 6 2024, 12:10 PM · Checklist, MITK (v2024.06)
a178n triaged T30431: [TotalSeg] Installation status for user as Normal priority.
May 6 2024, 11:59 AM · Moved to git.dkfz.de, MITK (v2024.12)
a178n triaged T30430: [TotalSeg] Add check if python venv exists before installation as Normal priority.
May 6 2024, 11:44 AM · MITK (v2024.06)
a178n triaged T30429: Bounding box Corner control as Normal priority.
May 6 2024, 11:20 AM · Moved to git.dkfz.de, MITK (v2024.12), Checklist
kompan added a comment to T30428: DCE MR Perfusion DataFit View: Selected Mask widget can't find DICOM segmentation nodes.

It seems to be an issue with this specific dataset. I made new set of segmentations (Prostate label and AIF label) and stored them each as DICOM segmentation. And now I find that the segmentation nodes are found as expected. It needs to be determined if the old data set is somehow corrupted or if it is a backwards compatibility issue (the masks were initially created in 2019).

May 6 2024, 11:10 AM · Moved to git.dkfz.de, MITK (v2024.12)
a178n updated the task description for T30428: DCE MR Perfusion DataFit View: Selected Mask widget can't find DICOM segmentation nodes.
May 6 2024, 10:54 AM · Moved to git.dkfz.de, MITK (v2024.12)
a178n renamed T30428: DCE MR Perfusion DataFit View: Selected Mask widget can't find DICOM segmentation nodes from DCE MR Perfusion DataFit View: Selection Mask widget can't find DICOM segmentation nodes to DCE MR Perfusion DataFit View: Selected Mask widget can't find DICOM segmentation nodes.
May 6 2024, 10:53 AM · Moved to git.dkfz.de, MITK (v2024.12)
a178n updated the task description for T30428: DCE MR Perfusion DataFit View: Selected Mask widget can't find DICOM segmentation nodes.
May 6 2024, 10:53 AM · Moved to git.dkfz.de, MITK (v2024.12)
a178n triaged T30428: DCE MR Perfusion DataFit View: Selected Mask widget can't find DICOM segmentation nodes as Normal priority.
May 6 2024, 10:52 AM · Moved to git.dkfz.de, MITK (v2024.12)
floca added a project to T30417: [Segmentation] Invisible labels are highlighted leading to confusing UX: Request for Discussion.

The first version had option B.
I changed it because I thought that UX is better if you have still the posibility to peek/see also the highlight of invisible labels. E.g. in order to pick the right one to make visible again.

May 6 2024, 10:26 AM · Request for Discussion, Checklist, MITK (v2024.06)
floca claimed T30420: [SEG] Fill/Erase tool does not work due to geometry error.
May 6 2024, 10:10 AM · Checklist, MITK (v2024.06)
kompan added a subtask for T29524: SAM in MITK: T30427: [SEG] No status change message after changing model type to ‘vit_l’..
May 6 2024, 10:02 AM · Moved to git.dkfz.de, MITK
kompan added a parent task for T30427: [SEG] No status change message after changing model type to ‘vit_l’.: T29524: SAM in MITK.
May 6 2024, 10:02 AM · Moved to git.dkfz.de, MITK (v2024.12), Checklist
kompan triaged T30427: [SEG] No status change message after changing model type to ‘vit_l’. as Normal priority.
May 6 2024, 10:02 AM · Moved to git.dkfz.de, MITK (v2024.12), Checklist
kompan added a subtask for T29524: SAM in MITK: T30426: [SEG] Highlight importance of level window in Segment Anything.
May 6 2024, 9:58 AM · Moved to git.dkfz.de, MITK
kompan added a parent task for T30426: [SEG] Highlight importance of level window in Segment Anything: T29524: SAM in MITK.
May 6 2024, 9:58 AM · Checklist, MITK (v2024.06)
kompan triaged T30426: [SEG] Highlight importance of level window in Segment Anything as Normal priority.
May 6 2024, 9:57 AM · Checklist, MITK (v2024.06)
a178n added a comment to T30423: [SEG] Segment Anything misleading GPU message for first time users.

Agree. SAM and MedSAM can work reasonably well even without GPU. Sorry can be removed.

May 6 2024, 9:57 AM · Checklist, MITK (v2024.06)
a178n added a parent task for T30423: [SEG] Segment Anything misleading GPU message for first time users: T29524: SAM in MITK.
May 6 2024, 9:55 AM · Checklist, MITK (v2024.06)
a178n added a subtask for T29524: SAM in MITK: T30423: [SEG] Segment Anything misleading GPU message for first time users.
May 6 2024, 9:55 AM · Moved to git.dkfz.de, MITK
kompan triaged T30425: [SEG] Segment Anything - Loading errors occur when opening the preferences as Normal priority.
May 6 2024, 9:54 AM · Moved to git.dkfz.de, MITK (v2024.12), Checklist
kompan updated the task description for T30424: [SEG] Reduce size of dots in Segment Anything.
May 6 2024, 9:44 AM · Moved to git.dkfz.de, MITK (v2024.12), Checklist
kompan triaged T30424: [SEG] Reduce size of dots in Segment Anything as Normal priority.
May 6 2024, 9:42 AM · Moved to git.dkfz.de, MITK (v2024.12), Checklist
kompan triaged T30423: [SEG] Segment Anything misleading GPU message for first time users as Normal priority.
May 6 2024, 9:33 AM · Checklist, MITK (v2024.06)
floca triaged T30422: [SEG] Erase tool double click is irritating as Normal priority.
May 6 2024, 9:31 AM · Checklist, MITK (v2024.06)
floca added a comment to T30421: [SEG] Undo/Redo problems with Fill/Erase tool reported.

Have to check if T30420 is fixed.

May 6 2024, 9:08 AM · Missing Info, Checklist, MITK (v2024.06)
floca added a subtask for T30421: [SEG] Undo/Redo problems with Fill/Erase tool reported: T30420: [SEG] Fill/Erase tool does not work due to geometry error.
May 6 2024, 9:08 AM · Missing Info, Checklist, MITK (v2024.06)
floca added a parent task for T30420: [SEG] Fill/Erase tool does not work due to geometry error: T30421: [SEG] Undo/Redo problems with Fill/Erase tool reported.
May 6 2024, 9:08 AM · Checklist, MITK (v2024.06)
floca created T30421: [SEG] Undo/Redo problems with Fill/Erase tool reported.
May 6 2024, 9:08 AM · Missing Info, Checklist, MITK (v2024.06)
floca updated the task description for T30420: [SEG] Fill/Erase tool does not work due to geometry error.
May 6 2024, 9:05 AM · Checklist, MITK (v2024.06)
floca triaged T30420: [SEG] Fill/Erase tool does not work due to geometry error as Unbreak Now! priority.
May 6 2024, 9:05 AM · Checklist, MITK (v2024.06)
floca claimed T30411: [SEG] Label color is off unitl first refresh when instances are used.
May 6 2024, 8:59 AM · Checklist, MITK (v2024.06)

May 5 2024

kislinsk triaged T30419: [Segmentation] "Preview" button of GrowCut tools needs to be clicked twice before "Confirm segmentation" button gets active as High priority.
May 5 2024, 6:45 AM · Checklist, MITK (v2024.06)
kislinsk triaged T30418: [Segmentation / Pixel Value] Pixel values only shown for active group as Normal priority.
May 5 2024, 5:56 AM · Checklist, MITK (v2024.06)
kislinsk triaged T30417: [Segmentation] Invisible labels are highlighted leading to confusing UX as Normal priority.
May 5 2024, 5:49 AM · Request for Discussion, Checklist, MITK (v2024.06)
kislinsk renamed T30416: [Measurement] Selecting a shape enforces drawing it / finishing a path not obvious from [Measurement] Selecting a shape enforces drawing it to [Measurement] Selecting a shape enforces drawing it / finishing a path not obvious.
May 5 2024, 5:26 AM · MITK (v2024.06), Checklist
kislinsk triaged T30416: [Measurement] Selecting a shape enforces drawing it / finishing a path not obvious as Low priority.
May 5 2024, 5:18 AM · MITK (v2024.06), Checklist
kislinsk triaged T30415: [Level Window] Changing level window with multiple images is confusing as Normal priority.
May 5 2024, 5:10 AM · Moved to git.dkfz.de, MITK (v2024.12), Checklist
kislinsk changed the visibility for F3633453: Screenshot 2024-05-05 043710.png.
May 5 2024, 4:38 AM
kislinsk changed the visibility for F3633454: Screenshot 2024-05-05 043502.png.
May 5 2024, 4:38 AM
kislinsk triaged T30414: [Documentation] Help contents have wrong titles and root pages as High priority.
May 5 2024, 4:38 AM · Checklist, MITK (v2024.06)
kislinsk triaged T30413: [Documentation] Help pages are blank in certain situations as Normal priority.
May 5 2024, 4:32 AM · Checklist, MITK (v2024.06)
kislinsk added a comment to T30410: [Segmentation] 2-d interpolation does not interpolate between multiple slices.

thanks for the research. Are you already working on that ticket?

May 5 2024, 4:30 AM · Moved to git.dkfz.de, MITK (v2024.12)

May 4 2024

a178n closed T30398: 3D interpolation using SAM tool as Invalid.

This was not a valid issue. The real issue was T30403.

May 4 2024, 1:37 PM · MITK
a178n closed T30398: 3D interpolation using SAM tool, a subtask of T29524: SAM in MITK, as Invalid.
May 4 2024, 1:37 PM · Moved to git.dkfz.de, MITK
floca added a comment to T30410: [Segmentation] 2-d interpolation does not interpolate between multiple slices.

I also peeked into the code base. And as also 2D is a mess 🙈.
It would make sense to completle rework and align it with the chaching mechanism of the surface interpolation controler (may be refactor it to use the same interpolation base class or just cover both use cases in the same controller class, because the only difference is the interpolation strategy (generate surface or slice interpolations along a plane normal, and over a method for doing 2D interpolations).
Therfore I am inclined to opt for the following:

May 4 2024, 12:55 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca added a revision to T30411: [SEG] Label color is off unitl first refresh when instances are used: Unknown Object (Differential Revision).
May 4 2024, 12:04 PM · Checklist, MITK (v2024.06)
floca added a comment to T30398: 3D interpolation using SAM tool.

@a178n isn't that resolved?

May 4 2024, 11:59 AM · MITK
floca closed T29437: [SEG] Add TotalSegmentator, a subtask of T29191: [SEG] New segmentation tool candidates, as Resolved.
May 4 2024, 11:57 AM · Moved to git.dkfz.de, MITK (v2024.12)