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Wed, May 15

a178n closed T29197: [Segmentation] Is the classificationsegmentation-plugin used / required? as Resolved.

Already removed

Wed, May 15, 11:29 AM · MITK (v2024.06)
a178n removed a project from T30412: [Statistics] Planar figure cannot be set as ROI for askew images: Request for Discussion.
Wed, May 15, 11:29 AM · MITK, Next Milestone
a178n closed T30447: [TotalSeg] Levelwindow effect, a subtask of T29437: [SEG] Add TotalSegmentator, as Wontfix.
Wed, May 15, 11:18 AM · MITK
a178n closed T30447: [TotalSeg] Levelwindow effect as Wontfix.

Have in base class and decide wich tools will have it or not. Not ideal for Totalsegmentator

Wed, May 15, 11:18 AM · MITK

Tue, May 14

a178n added a comment to T30447: [TotalSeg] Levelwindow effect.

Pushed new branch to rMITK MITK: feature/T30447-totalseg-levelwindow.

Tue, May 14, 5:49 PM · MITK
a178n triaged T30447: [TotalSeg] Levelwindow effect as Normal priority.
Tue, May 14, 5:38 PM · MITK
a178n claimed T30430: [TotalSeg] Add check if python venv exists before installation.
Tue, May 14, 5:33 PM · MITK (v2024.06)
a178n added a comment to T30430: [TotalSeg] Add check if python venv exists before installation.

Pushed new branch to rMITK MITK: feature/T30430-python-venv-check.

Tue, May 14, 5:21 PM · MITK (v2024.06)
a178n claimed T30426: [SEG] Highlight importance of level window in Segment Anything.
Tue, May 14, 10:10 AM · Checklist, MITK (v2024.06)
a178n added a revision to T30426: [SEG] Highlight importance of level window in Segment Anything: Unknown Object (Differential Revision).
Tue, May 14, 10:07 AM · Checklist, MITK (v2024.06)

Wed, May 8

a178n added a project to T30429: Bounding box Corner control: Next Milestone.
Wed, May 8, 11:33 AM · Next Milestone, Checklist, MITK (v2024.06)
a178n added a comment to T30431: [TotalSeg] Installation status for user.

The task will be addressed after migrating the install options into Preferences. Then the status update for installation will be implemented for all "AI" tools.

Wed, May 8, 11:32 AM · Next Milestone, MITK (v2024.06)
a178n removed a project from T30422: [SEG] Erase tool double click is irritating: Request for Discussion.

RFD result: Remove the functionality

Wed, May 8, 11:16 AM · Checklist, MITK (v2024.06)
a178n added a project to T30431: [TotalSeg] Installation status for user: Next Milestone.
Wed, May 8, 11:05 AM · Next Milestone, MITK (v2024.06)
a178n assigned T30432: [Perfusion] Possible to write text into info box to kompan.
Wed, May 8, 10:59 AM · Next Milestone, MITK (v2024.06)
a178n added projects to T30433: [Perfusion] Inconsistent appearance of info box message "Cannot compute parameters. No node selected.": Next Milestone, MITK.
Wed, May 8, 10:57 AM · MITK, Next Milestone
a178n added a project to T30434: [Perfusion] Concentration curve converter VFA box tab key skips flip angles: Next Milestone.
Wed, May 8, 10:57 AM · Next Milestone, Checklist, MITK (v2024.06)
a178n edited projects for T30435: Rename "Time" to "Timestep" in Image Navigator?, added: Next Milestone, MITK; removed Request for Discussion, MITK (v2024.06).
Wed, May 8, 10:56 AM · MITK, Next Milestone, Checklist
a178n lowered the priority of T30410: [Segmentation] 2-d interpolation does not interpolate between multiple slices from Unbreak Now! to Normal.
Wed, May 8, 10:34 AM · MITK, Next Milestone

Tue, May 7

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.

Tue, May 7, 3:50 PM · Checklist, MITK (v2024.06)

Mon, May 6

a178n triaged T30431: [TotalSeg] Installation status for user as Normal priority.
Mon, May 6, 11:59 AM · Next Milestone, MITK (v2024.06)
a178n triaged T30430: [TotalSeg] Add check if python venv exists before installation as Normal priority.
Mon, May 6, 11:44 AM · MITK (v2024.06)
a178n triaged T30429: Bounding box Corner control as Normal priority.
Mon, May 6, 11:20 AM · Next Milestone, Checklist, MITK (v2024.06)
a178n updated the task description for T30428: DCE MR Perfusion DataFit View: Selected Mask widget can't find DICOM segmentation nodes.
Mon, May 6, 10:54 AM · Next Milestone, MITK (v2024.06)
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.
Mon, May 6, 10:53 AM · Next Milestone, MITK (v2024.06)
a178n updated the task description for T30428: DCE MR Perfusion DataFit View: Selected Mask widget can't find DICOM segmentation nodes.
Mon, May 6, 10:53 AM · Next Milestone, MITK (v2024.06)
a178n triaged T30428: DCE MR Perfusion DataFit View: Selected Mask widget can't find DICOM segmentation nodes as Normal priority.
Mon, May 6, 10:52 AM · Next Milestone, 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.

Mon, May 6, 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.
Mon, May 6, 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.
Mon, May 6, 9:55 AM · MITK

Sat, May 4

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

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

Sat, May 4, 1:37 PM · MITK
a178n closed T30398: 3D interpolation using SAM tool, a subtask of T29524: SAM in MITK, as Invalid.
Sat, May 4, 1:37 PM · MITK

Thu, May 2

a178n added a comment to T30353: [TotalSeg] Add confirmation dialog before exiting the tool .

Deleted branch from rMITK MITK: feature/T30353-tool-confirm-exit.

Thu, May 2, 8:36 AM · MITK (v2024.06)
a178n added a comment to T30403: 3D interpolation UX improvement using SAM tool.

Deleted branch from rMITK MITK: feature/T30403-clear-zombie-preview.

Thu, May 2, 8:35 AM · MITK (v2024.06)
a178n added a comment to T30391: [Segmentation] Python 3.12 support for installable AI tools.

Deleted branch from rMITK MITK: feature/T30391-python312-update.

Thu, May 2, 8:34 AM · MITK (v2024.06)
a178n closed T30403: 3D interpolation UX improvement using SAM tool as Resolved.
Thu, May 2, 8:25 AM · MITK (v2024.06)
a178n closed T30403: 3D interpolation UX improvement using SAM tool, a subtask of T29524: SAM in MITK, as Resolved.
Thu, May 2, 8:25 AM · MITK
a178n closed T30391: [Segmentation] Python 3.12 support for installable AI tools as Resolved.
Thu, May 2, 8:25 AM · MITK (v2024.06)
a178n closed T30353: [TotalSeg] Add confirmation dialog before exiting the tool as Resolved.
Thu, May 2, 8:22 AM · MITK (v2024.06)
a178n closed T30353: [TotalSeg] Add confirmation dialog before exiting the tool , a subtask of T29437: [SEG] Add TotalSegmentator, as Resolved.
Thu, May 2, 8:22 AM · MITK
a178n added a revision to T30353: [TotalSeg] Add confirmation dialog before exiting the tool : Unknown Object (Differential Revision).
Thu, May 2, 8:22 AM · MITK (v2024.06)

Mon, Apr 29

a178n committed rMITK79f421965c87: Reset preview before adding point to a new plane (authored by a178n).
Reset preview before adding point to a new plane
Mon, Apr 29, 5:41 PM
a178n committed rMITK16e0e7a3536a: Reset preview logic update (authored by a178n).
Reset preview logic update
Mon, Apr 29, 5:41 PM
a178n committed rMITK3855327865b5: SAM tool Reset old preview before setting new geomtery (authored by a178n).
SAM tool Reset old preview before setting new geomtery
Mon, Apr 29, 5:41 PM
a178n added a revision to T30403: 3D interpolation UX improvement using SAM tool: Unknown Object (Differential Revision).
Mon, Apr 29, 2:30 PM · MITK (v2024.06)
a178n added a comment to T30403: 3D interpolation UX improvement using SAM tool.

Pushed new branch to rMITK MITK: feature/T30403-clear-zombie-preview.

Mon, Apr 29, 2:25 PM · MITK (v2024.06)
a178n triaged T30403: 3D interpolation UX improvement using SAM tool as Normal priority.
Mon, Apr 29, 10:53 AM · MITK (v2024.06)
a178n closed T30354: [MedSAM] Update SAM python daemon script for MedSAM as Resolved.

Find the updated script here: https://github.com/MIC-DKFZ/agent-sam.git@v0.2

Mon, Apr 29, 10:44 AM · MITK (v2024.06)
a178n closed T30354: [MedSAM] Update SAM python daemon script for MedSAM, a subtask of T30314: MedSAM in MITK, as Resolved.
Mon, Apr 29, 10:44 AM · MITK (v2024.06)
a178n closed T30355: [Seg] MedSAM as new 2D Tool in MITK as Resolved.
Mon, Apr 29, 10:43 AM · MITK (v2024.06)
a178n closed T30355: [Seg] MedSAM as new 2D Tool in MITK, a subtask of T30314: MedSAM in MITK, as Resolved.
Mon, Apr 29, 10:43 AM · MITK (v2024.06)
a178n closed T30356: [MedSAM] Create Test user checklist, a subtask of T30314: MedSAM in MITK, as Resolved.
Mon, Apr 29, 10:42 AM · MITK (v2024.06)
a178n closed T30356: [MedSAM] Create Test user checklist as Resolved.
Mon, Apr 29, 10:42 AM · MITK (v2024.06)
a178n closed T30357: [MedSAM] Add user documentaiton, a subtask of T30314: MedSAM in MITK, as Resolved.
Mon, Apr 29, 10:42 AM · MITK (v2024.06)
a178n closed T30357: [MedSAM] Add user documentaiton as Resolved.
Mon, Apr 29, 10:42 AM · MITK (v2024.06)
a178n committed rMITK2e3082856c36: MedSAM tool doxygen documention changes (authored by a178n).
MedSAM tool doxygen documention changes
Mon, Apr 29, 9:06 AM
a178n committed rMITK983859188caa: MedSAM doku update (authored by a178n).
MedSAM doku update
Mon, Apr 29, 9:05 AM
a178n committed rMITK816f8de12342: Minor typo fixes (authored by a178n).
Minor typo fixes
Mon, Apr 29, 9:05 AM
a178n committed rMITKfb467b3b9102: MedSAM & SAM screenshot update (authored by a178n).
MedSAM & SAM screenshot update
Mon, Apr 29, 9:05 AM
a178n committed rMITKfbb453143d00: MedSAM tool user documention (authored by a178n).
MedSAM tool user documention
Mon, Apr 29, 9:05 AM

Sun, Apr 28

a178n committed rMITKcbaf43055a1d: Python 3.12 support for TotalSeg & SAM installations (authored by a178n).
Python 3.12 support for TotalSeg & SAM installations
Sun, Apr 28, 11:29 PM
a178n committed rMITK44ce61b1d410: Python version range specification update (authored by a178n).
Python version range specification update
Sun, Apr 28, 11:29 PM
a178n committed rMITKa36de41cac3b: Python 3.12 support for TotalSeg & SAM (authored by a178n).
Python 3.12 support for TotalSeg & SAM
Sun, Apr 28, 11:29 PM
a178n committed rMITKbf359a964484: MedSAM tool inital changes (authored by a178n).
MedSAM tool inital changes
Sun, Apr 28, 10:18 PM
a178n committed rMITKc0fc994e4e12: MedSAM tool minor update for testing (authored by a178n).
MedSAM tool minor update for testing
Sun, Apr 28, 10:18 PM
a178n committed rMITK2f44c0c6d55e: MedSAM Bounding box changes (authored by a178n).
MedSAM Bounding box changes
Sun, Apr 28, 10:18 PM
a178n committed rMITK064236383068: MedSAM boundingbox bugfixes (authored by a178n).
MedSAM boundingbox bugfixes
Sun, Apr 28, 10:18 PM
a178n committed rMITK135db56eddb6: Register boundbox in segmentation plugin (authored by a178n).
Register boundbox in segmentation plugin
Sun, Apr 28, 10:18 PM
a178n committed rMITK3b1949e21053: Add MedSAM code documentation (authored by a178n).
Add MedSAM code documentation
Sun, Apr 28, 10:18 PM
a178n committed rMITK11a0ed742065: MedSAM Preference UI update (authored by a178n).
MedSAM Preference UI update
Sun, Apr 28, 10:18 PM
a178n committed rMITK2f365d2ccca4: Merge branch 'develop' into feature/T30355-medsam-tool (authored by a178n).
Merge branch 'develop' into feature/T30355-medsam-tool
Sun, Apr 28, 10:18 PM
a178n committed rMITKeb4eacd02549: Merge branch 'develop' into feature/T30355-medsam-tool (authored by a178n).
Merge branch 'develop' into feature/T30355-medsam-tool
Sun, Apr 28, 10:18 PM
a178n committed rMITK7e92989d521f: MedSAM "Reset RoI" will also clear preview segmentation if any (authored by a178n).
MedSAM "Reset RoI" will also clear preview segmentation if any
Sun, Apr 28, 10:18 PM
a178n committed rMITK527b63478043: MedSAM boundingbox coordinate extraction logic update (authored by a178n).
MedSAM boundingbox coordinate extraction logic update
Sun, Apr 28, 10:18 PM
a178n committed rMITK555bca428914: Model type preference change don't need reinit anymore (authored by a178n).
Model type preference change don't need reinit anymore
Sun, Apr 28, 10:18 PM
a178n committed rMITK8691a73a8e78: SAM tool install check updates (authored by a178n).
SAM tool install check updates
Sun, Apr 28, 10:18 PM
a178n committed rMITKa768f541e094: Reset Preview will be more responsive (authored by a178n).
Reset Preview will be more responsive
Sun, Apr 28, 10:18 PM
a178n committed rMITK85eb9f1c4e42: Merge branch 'develop' into feature/T30355-medsam-tool (authored by a178n).
Merge branch 'develop' into feature/T30355-medsam-tool
Sun, Apr 28, 10:17 PM
a178n committed rMITK06812e8f1a0f: Kill process immediately when stderr event to prevent invalid ProcessID pointer (authored by a178n).
Kill process immediately when stderr event to prevent invalid ProcessID pointer
Sun, Apr 28, 10:17 PM
a178n committed rMITK547fe487ac24: Medsam code refactoring changes (authored by a178n).
Medsam code refactoring changes
Sun, Apr 28, 10:17 PM
a178n committed rMITK7c26ba08e742: Change std::stringstream for std::string (authored by a178n).
Change std::stringstream for std::string
Sun, Apr 28, 10:17 PM
a178n committed rMITK110279e34d11: MedSAM tool code (authored by a178n).
MedSAM tool code
Sun, Apr 28, 10:17 PM

Thu, Apr 25

a178n triaged T30398: 3D interpolation using SAM tool as Normal priority.
Thu, Apr 25, 9:11 AM · MITK

Wed, Apr 24

a178n committed rMITKfddfdc182dc2: IsPreviewGenerated set to false when tool is activated (authored by a178n).
IsPreviewGenerated set to false when tool is activated
Wed, Apr 24, 4:27 PM
a178n committed rMITK7f413c922d0e: Confirm Segmentation button bugfix (authored by a178n).
Confirm Segmentation button bugfix
Wed, Apr 24, 4:27 PM
a178n committed rMITKb884b24c25b4: TotalSeg nnUNet Confirm Segmentation button bugfix (authored by a178n).
TotalSeg nnUNet Confirm Segmentation button bugfix
Wed, Apr 24, 4:27 PM

Tue, Apr 23

a178n added a revision to T30392: [Segmentation] Totalsegmentator & Otsu is buggy: Unknown Object (Differential Revision).
Tue, Apr 23, 11:30 PM · MITK (v2024.06)
a178n added a comment to T30392: [Segmentation] Totalsegmentator & Otsu is buggy.

Pushed new branch to rMITK MITK: bugfix/T30392-totalseg-nnunet-confirmbutton.

Tue, Apr 23, 9:48 PM · MITK (v2024.06)

Apr 17 2024

a178n committed rMITK34b810129724: Merge branch 'develop' into feature/T30353-tool-confirm-exit (authored by a178n).
Merge branch 'develop' into feature/T30353-tool-confirm-exit
Apr 17 2024, 9:47 AM
a178n committed rMITK4e153e1b8ac0: Add confirm dialog before exiting Totalseg tool (authored by a178n).
Add confirm dialog before exiting Totalseg tool
Apr 17 2024, 9:47 AM
a178n committed rMITKdd74bf243fed: Update message text (authored by a178n).
Update message text
Apr 17 2024, 9:47 AM
a178n committed rMITK7d9ec741ede5: Rename ConfirmBeforeExit and moving its implementation to SegWithPreviewTool… (authored by a178n).
Rename ConfirmBeforeExit and moving its implementation to SegWithPreviewTool…
Apr 17 2024, 9:47 AM
a178n committed rMITK7bc53a62a36f: Update qmessage box text (authored by a178n).
Update qmessage box text
Apr 17 2024, 9:47 AM
a178n committed rMITK966e84892cf1: Confirm before tool exit (authored by a178n).
Confirm before tool exit
Apr 17 2024, 9:47 AM

Apr 15 2024

a178n renamed T30392: [Segmentation] Totalsegmentator & Otsu is buggy from [Segmentation] Totalsegmentator is buggy to [Segmentation] Totalsegmentator & Otsu is buggy.
Apr 15 2024, 10:26 AM · MITK (v2024.06)
a178n added a comment to T30392: [Segmentation] Totalsegmentator & Otsu is buggy.

Further testing/debugging reveals that the error occurs in TotalSegmentatorTool::UpdatePrepare() method at preview->RemoveLabels(preview->GetAllLabelValues()). More precisely, the LabelSetImage::RemoveLabel method has this->InvokeEvent(LabelRemovedEvent(pixelValue)); which causes the exception. This issue is also applicable for Otsu tool (hence updating the title of this task).

Apr 15 2024, 10:26 AM · MITK (v2024.06)

Apr 9 2024

a178n updated the task description for T29652: [Preferences] Cannot open SAM preference page after tool activation.
Apr 9 2024, 4:26 PM · MITK (v2024.06)
a178n added a comment to T29652: [Preferences] Cannot open SAM preference page after tool activation.

Latest testing reveals that the issue is fixed in Ubuntu 22.04.
I think the reason is Qt6 update.

Apr 9 2024, 4:23 PM · MITK (v2024.06)
a178n added a revision to T30357: [MedSAM] Add user documentaiton: Unknown Object (Differential Revision).
Apr 9 2024, 4:13 PM · MITK (v2024.06)
a178n added a comment to T30268: [Checklist] Segmentation 3D Interpolation.

After testing:

  1. Contours are still in red. Not black.❌ -> Checklist updated should suffice.
  2. Interpolation is updated immediately. No need to reinit anymore. ✔
  3. Interpolation is updated immediately. No need to reinit anymore. ✔
  4. Dropdown is still in 3-Dimensional, not on Disabled. ❌ -> Checklist updated could suffice as fix.
  5. There is no contour. Dropdown on "Disabled" ❌
Apr 9 2024, 12:25 PM · MITK (v2024.06), Checklist
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