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Jul 4 2023

floca added a project to T28181: [Segmentation] Should warning messages be passed on to the UI?: Request for Discussion.
Jul 4 2023, 5:21 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca closed T27182: Extend CLMatchPointReg MiniApp and move from Classification to Matchpoint module as Wontfix.

There is now a dedicated mini app for matching.

Jul 4 2023, 5:17 PM · MITK (v2023.12), Restricted Project
floca moved T27718: Miniapp for basic DICOM testing from Backlog to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:16 PM · MITK (v2023.12), Kaapana (internal)
floca moved T27809: [Segmentation Utilities] "Labels" tabs in operations of Utilities view is empty from Backlog to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:15 PM · MITK (v2023.12), Request for Discussion
floca moved T28797: [Segmentation[MultiLabel][Utilities] Using 4D data with dynamic segmentations results in 3D data from Backlog to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:15 PM · MITK (v2024.06), Checklist
floca moved T28796: [Segmentation][Utilities] Morphological Operations behave unexpectedly from Backlog to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:15 PM · MITK (v2024.06), Checklist
floca moved T29098: [3D Segmentation] UL Threshold Tool - 0 intensity value not include in slider range? from Backlog to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:14 PM · MITK (v2024.12), Restricted Project, Checklist
floca moved T29204: [SEG] Rework properties of Label class + add instance information from Backlog to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:13 PM · Moved to git.dkfz.de, MITK (v2024.12), Breaking Change
floca moved T29639: [Registration] Mapping crashes when super-sampling is activated from Backlog to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:13 PM · Moved to git.dkfz.de, MITK (v2024.12), Missing Info
floca moved T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations from Backlog to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:12 PM · MITK (v2024.06), Missing Info
floca moved T28798: [Segmentation][MultiLabel][Utilities] UI is inconsistent / unstable from Backlog to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:12 PM · MITK (v2024.06), Checklist
floca moved T29535: Reinit of scene with planar figure while the Display is closed leads to crash from Backlog to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:11 PM · Moved to git.dkfz.de, MITK (v2024.12), Known Issue
floca moved T29616: [DICOM] Add option to save images as DICOM from Backlog to MITK Meeting on the Request for Discussion board.
Jul 4 2023, 5:10 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca added a comment to T29130: [WorkBench] Segmentation fault when "Close Project" is invoked and QmitkDataStorageComboBox widget is in UI.

Is this still an open thing?

Jul 4 2023, 5:08 PM · Moved to git.dkfz.de, MITK
floca moved T29569: [Checklist] Update TotalSegmentator & nnUNet checklist from Tests/Checklists to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:07 PM · MITK (v2023.12), Checklist
floca moved T29578: [Segmentation] Removing last selected region in picking tool does not update preview from Segmentation to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:06 PM · Moved to git.dkfz.de, MITK (v2024.12), Checklist
floca moved T29590: [Segmentation] [Erase] Erasing everything of the selected label when clicking on background is surprising from Segmentation to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:06 PM · Moved to git.dkfz.de, MITK (v2024.12), Checklist
floca moved T29583: [Interpolation] Interpolation is not triggered correctly from Segmentation to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:06 PM · MITK (v2024.06), Checklist
floca moved T29584: [Interpolation] Confirming 3D interpolation does not set mode to "disabled" from Segmentation to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:06 PM · Moved to git.dkfz.de, MITK (v2024.12), Checklist
floca moved T29594: Improve MITK help text for nnUNet tool from Segmentation to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:05 PM · Moved to git.dkfz.de, MITK (v2024.12), Checklist, Request for Discussion
floca moved T29540: SAM as 2D tool in MITK from Segmentation to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:04 PM · MITK (v2024.06)
floca moved T29549: [Segmentation] Label search does not work from Segmentation to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:04 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca closed T29495: [SEG] Rework segmentation view UX as Resolved.
Jul 4 2023, 5:04 PM · MITK (v2023.12)
floca moved T29526: [Segmentation] Workbench crashes when closing render window part with active tool from Segmentation to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:02 PM · MITK (v2024.06)
floca moved T29396: [Segmentation] Newly created labelset image has wrong image type from Segmentation to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:00 PM · MITK (v2024.12)
floca moved T29392: [SEG] Add dedicated writer to store multi-label images in nifti from Segmentation to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:00 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca moved T29591: [Segmentation] [Live Wire] Multiple reports of a crash due to image access out of bounds from Segmentation to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:00 PM · MITK (v2023.12), Checklist
s434n moved T29641: [Movie Maker] Allow rotation around different axes from Backlog to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 4:59 PM · Moved to git.dkfz.de, MITK (v2024.12)
gaoh created T30148: MITK FlowBench v2023.04 - crashes on "Accept segmentation".
Jul 4 2023, 11:12 AM · MITK (v2023.12)

Jul 3 2023

a178n renamed T30147: MONAI Label: New approach using python wrapper?? from MONAI Label: New approach using python wrapper??q to MONAI Label: New approach using python wrapper??.
Jul 3 2023, 4:48 PM · Moved to git.dkfz.de, MITK (v2024.12), Request for Discussion
a178n renamed T30147: MONAI Label: New approach using python wrapper?? from MONAI Label: New approach using python wrapper to MONAI Label: New approach using python wrapper??q.
Jul 3 2023, 4:47 PM · Moved to git.dkfz.de, MITK (v2024.12), Request for Discussion

Jul 2 2023

a178n triaged T30147: MONAI Label: New approach using python wrapper?? as Normal priority.
Jul 2 2023, 11:34 PM · Moved to git.dkfz.de, MITK (v2024.12), Request for Discussion

Jun 30 2023

a178n added a comment to T30146: SAMtool: Problem while downloading pretrained models.

A practical solution is to shift the download feature into the python wrapper.

Jun 30 2023, 1:00 PM · MITK (v2023.12)
a178n added a comment to T30146: SAMtool: Problem while downloading pretrained models.

After discussion with @kislinsk, it's presumed that Ubuntu 22.04 comes with OpenSSL 3 which is incompatible to OpenSSL 1.1.1. Qt from the online installer was built against OpenSSL 1.1.1, though. That's why it is not working. It probably works Ubuntu setups with system Qt 5 which I guess is patched to work with system OpenSSL 3.
Therefore, so the way out, without any fixes to get this running on Ubuntu 22.04 is on the actual build machine when using system Qt5.

Jun 30 2023, 12:59 PM · MITK (v2023.12)
kislinsk added a comment to T30146: SAMtool: Problem while downloading pretrained models.

Qt 5.15 is built against OpenSSL 1.1.1, however, Ubuntu 22.04 provides only the incompatible OpenSSL 3, which is why the calls cannot be resolved. The Qt 5 apt packages (resp. system Qt 5) is probably patched to work with OpenSSL 3, though, which is why it works on build machines that use system Qt 5 instead of the Qt5 online installer. System libs are not packed into installers, though, so it only works in the build tree and installers will be broken on other systems.

Jun 30 2023, 12:50 PM · MITK (v2023.12)
a178n triaged T30146: SAMtool: Problem while downloading pretrained models as Normal priority.
Jun 30 2023, 12:19 PM · MITK (v2023.12)
kompan committed rMITK58c69a1eb97f: Unit tests for curve descriptive parameter calculation. (authored by kompan).
Unit tests for curve descriptive parameter calculation.
Jun 30 2023, 9:09 AM
kompan committed rMITK104a74fad5c0: Unit tests for curve descriptive parameter calculation. (authored by kompan).
Unit tests for curve descriptive parameter calculation.
Jun 30 2023, 9:09 AM

Jun 29 2023

a178n removed a project from T29655: SAM tool: Enable 2D RGB image support: Request for Discussion.
Jun 29 2023, 2:31 PM · MITK (v2023.12)
a178n closed T29655: SAM tool: Enable 2D RGB image support, a subtask of T29524: SAM in MITK, as Resolved.
Jun 29 2023, 2:31 PM · Moved to git.dkfz.de, MITK
a178n closed T29655: SAM tool: Enable 2D RGB image support as Resolved.

Code test and patched for 2D image support.

Jun 29 2023, 2:31 PM · MITK (v2023.12)
floca raised the priority of T27718: Miniapp for basic DICOM testing from Wishlist to Normal.
Jun 29 2023, 11:48 AM · MITK (v2023.12), Kaapana (internal)

Jun 28 2023

Unknown Object (User) added a comment to rMITKfb81d8a8d92f: Added feature of anisotropic super sampling.
Jun 28 2023, 9:52 AM
Unknown Object (User) added a comment to rMITKfb81d8a8d92f: Added feature of anisotropic super sampling.
Jun 28 2023, 9:52 AM
Unknown Object (User) added a comment to rMITKffcd7442e2fc: Fixed review comments.
Jun 28 2023, 9:52 AM
Unknown Object (User) added a comment to rMITK6059a719c7ac: Add MiniApps for MatchPoint registration and mapping.
Jun 28 2023, 9:52 AM
Unknown Object (User) added a comment to T29076: [Segmentation] Pressing DEL should delete a label.
Jun 28 2023, 9:51 AM · MITK (v2024.06), Checklist
Unknown Object (User) added a comment to T29371: [Registration] Improve view icons.
Jun 28 2023, 9:51 AM · MITK
Unknown Object (User) added a comment to T29521: Should all MITK.IO infos be stored in serialzed file?.
Jun 28 2023, 9:51 AM · Moved to git.dkfz.de, Request for Discussion, MITK
Unknown Object (User) added a subtask for T26959: [Segmentation] Newly created LabelSet segmentation is not displayed as "outline binary": Unknown Object (Maniphest Task).
Jun 28 2023, 9:32 AM · Moved to git.dkfz.de, MITK (v2024.12), Checklist, Request for Discussion
Unknown Object (User) added a subtask for T24925: Compile Technical Paper - Methods: Unknown Object (Maniphest Task).
Jun 28 2023, 9:32 AM · CSI-HD
Unknown Object (User) added a subtask for T27162: How to activate the features: Unknown Object (Maniphest Task).
Jun 28 2023, 9:32 AM
Unknown Object (User) added a subtask for T29076: [Segmentation] Pressing DEL should delete a label: Unknown Object (Maniphest Task).
Jun 28 2023, 9:32 AM · MITK (v2024.06), Checklist
Unknown Object (User) added a subtask for T28206: [Image Statistics] Renaming segmentation or planar figure based ROI nodes breaks histogram: Unknown Object (Maniphest Task).
Jun 28 2023, 9:32 AM · MITK (v2024.12)
Unknown Object (User) added a subtask for T29521: Should all MITK.IO infos be stored in serialzed file?: Unknown Object (Maniphest Task).
Jun 28 2023, 9:32 AM · Moved to git.dkfz.de, Request for Discussion, MITK
Unknown Object (User) added a subtask for T29371: [Registration] Improve view icons: Unknown Object (Maniphest Task).
Jun 28 2023, 9:32 AM · MITK

Jun 27 2023

a178n added a comment to T29655: SAM tool: Enable 2D RGB image support.

I am not sure what happens when 2D 3 channel is loaded for segmentation. Never tested the behaviour of the SegWithPreviewTool API. From my side, I need to update the wrapper to accommodate for 3 channel images. Of course, it's a straightforward change but at the moment, 3-channel won't work.

Jun 27 2023, 6:06 PM · MITK (v2023.12)
floca updated subscribers of T29650: mitk-flow " Please reinitialize the selected segmentation image!" problem.
In T29650#248947, @gaoh wrote:

@k656s has an example dataset. I am still at the release version before (I think 2022.10?) but I will update to the current release. Could this already help?

Yes, it could. I thought something like this was already introduced. @kislinsk, or?

Jun 27 2023, 5:46 PM · Next Milestone, Request for Discussion, MITK
floca added a comment to T29655: SAM tool: Enable 2D RGB image support.

what is the problem here/where do you lose the other channels? shouldn't it work out of the box already?

Jun 27 2023, 5:30 PM · MITK (v2023.12)
a178n triaged T29655: SAM tool: Enable 2D RGB image support as Normal priority.
Jun 27 2023, 5:01 PM · MITK (v2023.12)
floca committed rMITKd5929d7ba0a9: Added override for isEmpty (authored by floca).
Added override for isEmpty
Jun 27 2023, 4:37 PM
floca committed rMITK458e53a8e4bc: Added helper function to generate sub/super sampled geometries for mapping. (authored by floca).
Added helper function to generate sub/super sampled geometries for mapping.
Jun 27 2023, 4:37 PM
floca committed rMITKac628e8f5ff2: Added miniapp for Mapping (authored by floca).
Added miniapp for Mapping
Jun 27 2023, 4:37 PM
floca committed rMITK5cd909f761f7: Added miniapp for matching (authored by floca).
Added miniapp for matching
Jun 27 2023, 4:37 PM
floca committed rMITKb5d67c246b32: Added slabbedHead and headNeck reg algorithm (authored by floca).
Added slabbedHead and headNeck reg algorithm
Jun 27 2023, 4:37 PM
floca closed T29611: [REG] Add MatchPoint slabbedHead and HeadNeck algorithms as Resolved by committing rMITKb5d67c246b32: Added slabbedHead and headNeck reg algorithm.
Jun 27 2023, 4:37 PM · Noteworthy, MITK
floca closed T29607: [REG] Add MiniApp for MatchPoint base matching/registration as Resolved by committing rMITK6059a719c7ac: Add MiniApps for MatchPoint registration and mapping.
Jun 27 2023, 4:37 PM · MatchPoint, Noteworthy, MITK
floca committed rMITK6059a719c7ac: Add MiniApps for MatchPoint registration and mapping (authored by floca).
Add MiniApps for MatchPoint registration and mapping
Jun 27 2023, 4:37 PM
floca closed T29606: [REG] Add MiniApp for MatchPoint base mapping as Resolved by committing rMITK6059a719c7ac: Add MiniApps for MatchPoint registration and mapping.
Jun 27 2023, 4:37 PM · Noteworthy, MITK
floca committed rMITKffcd7442e2fc: Fixed review comments (authored by floca).
Fixed review comments
Jun 27 2023, 4:37 PM
floca committed rMITKfb81d8a8d92f: Added feature of anisotropic super sampling (authored by floca).
Added feature of anisotropic super sampling
Jun 27 2023, 4:37 PM
a178n closed T29635: SAM tool: Cannot Confirm segmentation properly, a subtask of T29604: SAM as 2D Tool in MITK- iteration 2, as Resolved.
Jun 27 2023, 2:41 PM · MITK (v2024.06)
a178n closed T29635: SAM tool: Cannot Confirm segmentation properly as Resolved.
Jun 27 2023, 2:41 PM · MITK (v2023.12)
a178n triaged T29654: SAM tool: Preview not fully cleared when Reset Picks button is clicked as Normal priority.
Jun 27 2023, 1:48 PM · Moved to git.dkfz.de, MITK (v2024.12)
a178n triaged T29653: SAM tool: Install process can be non-blocking as Normal priority.
Jun 27 2023, 11:06 AM · Moved to git.dkfz.de, MITK (v2024.12)
gaoh updated subscribers of T29650: mitk-flow " Please reinitialize the selected segmentation image!" problem.

@k656s has an example dataset. I am still at the release version before (I think 2022.10?) but I will update to the current release. Could this already help?
If not, I would vote for the task list view reinit after loading opiton.

Jun 27 2023, 11:05 AM · Next Milestone, Request for Discussion, MITK
a178n triaged T29652: [Preferences] Cannot open SAM preference page after tool activation as Normal priority.
Jun 27 2023, 9:52 AM · Moved to git.dkfz.de, MITK (v2024.12)
floca added a project to T29611: [REG] Add MatchPoint slabbedHead and HeadNeck algorithms: Noteworthy.
Jun 27 2023, 8:52 AM · Noteworthy, MITK
floca added projects to T29607: [REG] Add MiniApp for MatchPoint base matching/registration: Noteworthy, MatchPoint.
Jun 27 2023, 8:51 AM · MatchPoint, Noteworthy, MITK
floca added a project to T29606: [REG] Add MiniApp for MatchPoint base mapping: Noteworthy.
Jun 27 2023, 8:51 AM · Noteworthy, MITK

Jun 26 2023

a178n triaged T29651: [Preferences] SAM tool Preferences not rendered nicely on MacOS as Normal priority.
Jun 26 2023, 7:32 PM · Moved to git.dkfz.de, MITK (v2024.12)
a178n renamed T29539: SAM Python wrapper for MITK from Python wrapper for MITK to SAM Python wrapper for MITK.
Jun 26 2023, 7:28 PM · MITK (v2024.06)
a178n added a subtask for T29539: SAM Python wrapper for MITK: T29648: SAM Python: Improve the wrapper to be used independently without MITK.
Jun 26 2023, 7:27 PM · MITK (v2024.06)
a178n removed a subtask for T29604: SAM as 2D Tool in MITK- iteration 2: T29648: SAM Python: Improve the wrapper to be used independently without MITK.
Jun 26 2023, 7:27 PM · MITK (v2024.06)
a178n edited parent tasks for T29648: SAM Python: Improve the wrapper to be used independently without MITK, added: T29539: SAM Python wrapper for MITK; removed: T29604: SAM as 2D Tool in MITK- iteration 2.
Jun 26 2023, 7:27 PM · Moved to git.dkfz.de, MITK
a178n added a subtask for T29604: SAM as 2D Tool in MITK- iteration 2: T29648: SAM Python: Improve the wrapper to be used independently without MITK.
Jun 26 2023, 7:25 PM · MITK (v2024.06)
a178n added a parent task for T29648: SAM Python: Improve the wrapper to be used independently without MITK: T29604: SAM as 2D Tool in MITK- iteration 2.
Jun 26 2023, 7:25 PM · Moved to git.dkfz.de, MITK
kompan committed rMITKea2567c3c8e3: Add unit tests for signal to concentration conversion. (authored by kompan).
Add unit tests for signal to concentration conversion.
Jun 26 2023, 9:41 AM
kompan committed rMITK246ca15d1ea4: Correct comparison of integer expressions of different signedness errors. (authored by kompan).
Correct comparison of integer expressions of different signedness errors.
Jun 26 2023, 9:41 AM
kompan committed rMITK4e985244cece: Code refactoring. (authored by kompan).
Code refactoring.
Jun 26 2023, 9:41 AM
kompan committed rMITK0df505762712: Only generate curve generators and images when needed for test. (authored by kompan).
Only generate curve generators and images when needed for test.
Jun 26 2023, 9:41 AM
kompan committed rMITK434958d25bae: Add unit tests for signal to concentration conversion. (authored by kompan).
Add unit tests for signal to concentration conversion.
Jun 26 2023, 9:41 AM

Jun 23 2023

floca added projects to T29650: mitk-flow " Please reinitialize the selected segmentation image!" problem: Request for Discussion, Next Milestone.

@gaoh do you have example data to reproduce this situation. That would help to replicate it and search for the best solution.
Which version of MITK was it?

Jun 23 2023, 2:29 PM · Next Milestone, Request for Discussion, MITK

Jun 22 2023

gaoh created T29650: mitk-flow " Please reinitialize the selected segmentation image!" problem.
Jun 22 2023, 3:49 PM · Next Milestone, Request for Discussion, MITK
nolden added a comment to T27190: Clang format style for * and & at variables.

there is a DerivePointerAlignment option which basically unifies it on a file by file basis, in case there is no agreement. But I agree to Ralf with using the "left" style and put it next to the type

Jun 22 2023, 2:54 PM · Moved to git.dkfz.de, Request for Discussion, MITK
floca moved T29649: Classification Module clean up from Backlog to MITK Meeting on the Request for Discussion board.

That is a first shorted list. Other apps and plugins are already ruled out (e.g. due to Vigra dependency). We no shuold assess which of those can really stay in the main mitk repo.

Jun 22 2023, 1:35 PM · MITK (v2023.12), Request for Discussion
floca triaged T29649: Classification Module clean up as Normal priority.
Jun 22 2023, 1:33 PM · MITK (v2023.12), Request for Discussion
a178n triaged T29648: SAM Python: Improve the wrapper to be used independently without MITK as Normal priority.
Jun 22 2023, 9:09 AM · Moved to git.dkfz.de, MITK

Jun 21 2023

kislinsk closed T29647: [Interpolation] The 3D mesh is visible after interpolation is confirmed as Invalid.

It's a feature.

Jun 21 2023, 11:16 PM · Request for Discussion, MITK
a178n created T29647: [Interpolation] The 3D mesh is visible after interpolation is confirmed.
Jun 21 2023, 6:27 PM · Request for Discussion, MITK