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Feb 1 2024

floca added a project to T30314: MedSAM in MITK: Request for Discussion.

Reason: see my comment above.

Feb 1 2024, 10:50 AM · Moved to git.dkfz.de, MITK (v2024.12)
floca updated subscribers of T30314: MedSAM in MITK.

Thank you for looking into that. Let's discuss it further in the next meeting, but I think we should try to get it available in the next release.
For Boundingboxes, I would align with the Bounding Box interactions we have to build up at some point for generating detection labels.

Feb 1 2024, 10:49 AM · Moved to git.dkfz.de, MITK (v2024.12)

Jan 29 2024

floca added a comment to T30294: {SEG] Remove label set structure.

Pushed new branch to rMITK MITK: feature/T30294-Remove_LabelSet_class.

Jan 29 2024, 9:41 AM · Breaking Change, MITK (v2024.06)

Jan 26 2024

floca added a comment to T30314: MedSAM in MITK.

I think the slicer plugin is not so interesting, but the MedSAM branch it used LiteMedSAM https://github.com/bowang-lab/MedSAM/blob/LiteMedSAM/README.md.

Jan 26 2024, 2:23 PM · Moved to git.dkfz.de, MITK (v2024.12)

Jan 25 2024

floca added a comment to T30309: [SEG] Last label of label preset is sometimes not stored.

I think I found the problem while doing the refactoring of the LabelSetImage (T30294). Should be verified as soon as T30294 is tested/merged.

Jan 25 2024, 11:54 AM · MITK (v2024.06)

Jan 24 2024

floca closed T29454: Clarify the versions/editions we publish as installer as Resolved.

Closed, we put everythin in own installer and solve it by configuration:
T30284
T30310

Jan 24 2024, 10:48 AM · MITK (v2024.06), Request for Discussion

Jan 19 2024

floca edited projects for T30309: [SEG] Last label of label preset is sometimes not stored, added: MITK (v2024.06); removed Missing Info, MITK.
Jan 19 2024, 10:09 AM · MITK (v2024.06)
floca updated the task description for T30309: [SEG] Last label of label preset is sometimes not stored.
Jan 19 2024, 10:09 AM · MITK (v2024.06)

Jan 18 2024

floca moved T30310: Add new views, e.g. for Seg Task List or Perfusion from Backlog to MITK Meeting on the Request for Discussion board.
Jan 18 2024, 6:02 PM · Moved to git.dkfz.de, Missing Info, MITK
floca created T30310: Add new views, e.g. for Seg Task List or Perfusion.
Jan 18 2024, 6:02 PM · Moved to git.dkfz.de, Missing Info, MITK
floca edited projects for T30309: [SEG] Last label of label preset is sometimes not stored, added: MITK, Missing Info; removed MITK (v2024.06).
Jan 18 2024, 5:32 PM · MITK (v2024.06)
floca triaged T30309: [SEG] Last label of label preset is sometimes not stored as Normal priority.
Jan 18 2024, 5:31 PM · MITK (v2024.06)

Jan 10 2024

floca updated subscribers of T30307: Join the dcmqi planning at NA-MIC/Project week..

@fedorov I added you to "warn" 😉 you, that will join the effort. Great idea!

Jan 10 2024, 9:36 AM · Request for Discussion, MITK
floca moved T30307: Join the dcmqi planning at NA-MIC/Project week. from Backlog to MITK Meeting on the Request for Discussion board.
Jan 10 2024, 9:34 AM · Request for Discussion, MITK
floca added a project to T30307: Join the dcmqi planning at NA-MIC/Project week.: Request for Discussion.
Jan 10 2024, 9:34 AM · Request for Discussion, MITK
floca created T30307: Join the dcmqi planning at NA-MIC/Project week..
Jan 10 2024, 9:34 AM · Request for Discussion, MITK

Dec 19 2023

floca committed rMPc519619a3e9a: Prepared the new algorithm. (authored by floca).
Prepared the new algorithm.
Dec 19 2023, 6:24 PM

Dec 11 2023

floca closed T24795: ModelFit visualization bug? as Invalid.
Dec 11 2023, 10:52 AM · Auto-closed, MITK, Restricted Project

Dec 5 2023

floca reopened T24795: ModelFit visualization bug? as "Open".

@kompan Could you check if this is still a problem/can be replicated, as you look into the fit inspector view anyways. If it cannot be reproduce, we know at least that we may close it for good.

Dec 5 2023, 5:51 PM · Auto-closed, MITK, Restricted Project
floca added a comment to T24962: Refactor of LevelWindow and serialization of LevelWindowProperty.

This could be potentially solved with T30293 if we also provide a writer (at least a very simple one that does the old style, besides that change.

Dec 5 2023, 5:47 PM · Moved to git.dkfz.de, Auto-closed, MITK
floca added a subtask for T24962: Refactor of LevelWindow and serialization of LevelWindowProperty: T30293: Introduce new interoperability/developer-friendly scene file format (including reader).
Dec 5 2023, 5:35 PM · Moved to git.dkfz.de, Auto-closed, MITK
floca added a parent task for T30293: Introduce new interoperability/developer-friendly scene file format (including reader): T24962: Refactor of LevelWindow and serialization of LevelWindowProperty.
Dec 5 2023, 5:35 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca reopened T24962: Refactor of LevelWindow and serialization of LevelWindowProperty as "Open".
Dec 5 2023, 5:34 PM · Moved to git.dkfz.de, Auto-closed, MITK
floca triaged T30294: {SEG] Remove label set structure as High priority.
Dec 5 2023, 9:08 AM · Breaking Change, MITK (v2024.06)

Dec 4 2023

floca added a parent task for T30293: Introduce new interoperability/developer-friendly scene file format (including reader): Unknown Object (Maniphest Task).
Dec 4 2023, 2:43 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca renamed T30293: Introduce new interoperability/developer-friendly scene file format (including reader) from Introduce new interoperability/developer-friendly scene file format to Introduce new interoperability/developer-friendly scene file format (including reader).
Dec 4 2023, 2:42 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca updated subscribers of T30293: Introduce new interoperability/developer-friendly scene file format (including reader).

@gaoh With that already help you? Especially the last option with in file property lists and modify mode?
I would like to keep it in XML for now because it’s much faster to realize as we do not have to change complete reader infrastructure.

Dec 4 2023, 2:39 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca triaged T30293: Introduce new interoperability/developer-friendly scene file format (including reader) as Normal priority.
Dec 4 2023, 2:37 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca closed T29650: mitk-flow " Please reinitialize the selected segmentation image!" problem as Resolved.

@gaoh PLease feel free to reopen if there is still a problem.

Dec 4 2023, 2:22 PM · Next Milestone, Request for Discussion, MITK

Nov 29 2023

floca committed rMITKd40973bca0c3: - fixed regression in QmitkSliceNavigationListener that was (authored by floca).
- fixed regression in QmitkSliceNavigationListener that was
Nov 29 2023, 5:59 PM
floca committed rMITK22173bffdaea: T30287-DICOM_inspector_init (authored by floca).
T30287-DICOM_inspector_init
Nov 29 2023, 5:59 PM
floca committed rMITK76a3107afedb: - fixed T30287 (authored by floca).
- fixed T30287
Nov 29 2023, 5:59 PM
floca triaged T30286: Update to DCMQI 1.3.1 as Normal priority.
Nov 29 2023, 11:59 AM · MITK (v2024.06)
floca closed T30207: Add org.mitk.gui.qt.dicominspector to release as Resolved.
Nov 29 2023, 9:53 AM · Request for Discussion, MITK (v2023.12)
floca committed rMITK101ce291f680: T30207-Add_dicom_inspector_plugin (authored by floca).
T30207-Add_dicom_inspector_plugin
Nov 29 2023, 9:53 AM
floca committed rMITK2a8634dd0c03: Activated dicominspector and DICOMCmdApps in the workbench config. (authored by floca).
Activated dicominspector and DICOMCmdApps in the workbench config.
Nov 29 2023, 9:53 AM
floca committed rMITKeabf9fa3ade9: Optimized predicates to prohibit from selecting helper or hidden nodes. (authored by floca).
Optimized predicates to prohibit from selecting helper or hidden nodes.
Nov 29 2023, 9:53 AM
floca committed rMITKcf7f4a2ad5c5: Updated icon of the view (authored by floca).
Updated icon of the view
Nov 29 2023, 9:53 AM

Nov 28 2023

floca added a revision to T30207: Add org.mitk.gui.qt.dicominspector to release: Unknown Object (Differential Revision).
Nov 28 2023, 6:42 PM · Request for Discussion, MITK (v2023.12)

Nov 24 2023

floca triaged T29640: Verboseness in MatchPoint Algorithm Control as Low priority.
Nov 24 2023, 2:46 PM · MITK (v2024.12), Missing Info

Nov 20 2023

floca updated subscribers of T29562: [GrowCut] "Undo" only changes slices with seed images.

Thats because 3D Tools in total do not support undo redo currently.
Sofar we havent dared due to the memory footprint (as it would mean storing copies of the volume); but also never tested it.
May be we should ceck if it is OK in conjunction with compression (introduced by @kislinsk some time ago) and if needed limitations (a max step limit, or clearing the history if the segmentation is finished), to avoid extrem memory consumption due to long undo/redo history.

Nov 20 2023, 11:23 AM · Moved to git.dkfz.de, Request for Discussion, MITK

Nov 18 2023

floca committed rMPd9be8415db3d: Add feature for ITKImageRegistrationAlgorithms to allow (authored by floca).
Add feature for ITKImageRegistrationAlgorithms to allow
Nov 18 2023, 2:56 PM
floca committed rMPbcd7dcb79b37: Added algorithm Rigid2DMSAlgorithm (authored by floca).
Added algorithm Rigid2DMSAlgorithm
Nov 18 2023, 2:56 PM

Nov 16 2023

floca renamed T30249: [Py] UC2.3 - Load images and explore properties from UC5 - Load and save images out of a pthon script to [Py] UC5 - Load and save images out of a pthon script.
Nov 16 2023, 4:30 PM · Moved to git.dkfz.de, MITK
floca triaged T30171: [Py] View to execute scripts that interact with the rest of the workbench as Normal priority.
Nov 16 2023, 4:30 PM · Moved to git.dkfz.de, MITK
floca triaged T30172: [Py] UC1.1 - Selected image can be manipulated with simpleITK and updated as Normal priority.
Nov 16 2023, 4:29 PM · Moved to git.dkfz.de, MITK
floca triaged T30174: [Py] UC1.3 - Selected image can be manipulated with simpleITK and added to data storage as Normal priority.
Nov 16 2023, 4:29 PM · Moved to git.dkfz.de, MITK
floca triaged T30173: [Py] UC1.2 - Selected image are stored as Normal priority.
Nov 16 2023, 4:29 PM · Moved to git.dkfz.de, MITK
floca triaged T30175: [Py] UC1.4 - All images in data storage that are visible are set opacity 50% in a specific render window as Normal priority.
Nov 16 2023, 4:29 PM · Moved to git.dkfz.de, MITK
floca triaged T30249: [Py] UC2.3 - Load images and explore properties as High priority.
Nov 16 2023, 4:29 PM · Moved to git.dkfz.de, MITK
floca triaged T30170: [Py] Python in MITK as High priority.
Nov 16 2023, 4:27 PM · Moved to git.dkfz.de, MITK

Nov 14 2023

floca created T30249: [Py] UC2.3 - Load images and explore properties.
Nov 14 2023, 12:02 PM · Moved to git.dkfz.de, MITK

Nov 9 2023

floca committed rMITKe882a330a799: T30243 - Crash/Freeze when selection in DataManager is changed while MatchPoint… (authored by floca).
T30243 - Crash/Freeze when selection in DataManager is changed while MatchPoint…
Nov 9 2023, 11:57 AM
floca closed T30243: Crash/Freeze when selection in DataManager is changed while MatchPoint controller is open. as Resolved by committing rMITK476723c66866: Fixed T30243.
Nov 9 2023, 11:57 AM · MITK (v2023.12)
floca committed rMITK476723c66866: Fixed T30243 (authored by floca).
Fixed T30243
Nov 9 2023, 11:57 AM

Nov 8 2023

floca added a revision to T30243: Crash/Freeze when selection in DataManager is changed while MatchPoint controller is open.: Unknown Object (Differential Revision).
Nov 8 2023, 8:51 PM · MITK (v2023.12)
floca triaged T30243: Crash/Freeze when selection in DataManager is changed while MatchPoint controller is open. as Unbreak Now! priority.
Nov 8 2023, 8:49 PM · MITK (v2023.12)

Nov 7 2023

floca added a comment to T30240: MonaiLabel: How to support more apps.

I would lean to adding a preference "allow unsupported models" (default ==false). If people activate it, they can see all models (that are not blacklisted) and not just the white listed (verified) once.
If the risk is communicated and users are willing to take it, then I would not actively prevent people from using models (as long as they don't crash MITK or so).

Nov 7 2023, 12:02 PM · Moved to git.dkfz.de, MITK (v2024.12)

Nov 3 2023

floca committed rMITK8dcc50cc2600: T27718 Added DICOM Volume Diagnostics app (authored by floca).
T27718 Added DICOM Volume Diagnostics app
Nov 3 2023, 7:27 PM
floca committed rMITK4293212e5fa7: Fixed review remarks (authored by floca).
Fixed review remarks
Nov 3 2023, 7:26 PM
floca committed rMITK4220dc3ebb22: fixed gcc compiler error (authored by floca).
fixed gcc compiler error
Nov 3 2023, 7:26 PM
floca closed T27718: Miniapp for basic DICOM testing as Resolved by committing rMITK51d7f4f13072: Added DICOM Volume Diagnostics app.
Nov 3 2023, 7:26 PM · MITK (v2023.12), Kaapana (internal)
floca committed rMITK51d7f4f13072: Added DICOM Volume Diagnostics app (authored by floca).
Added DICOM Volume Diagnostics app
Nov 3 2023, 7:26 PM

Oct 27 2023

floca placed T28499: Refactor/rewrite RegionGrowing3D tool up for grabs.
Oct 27 2023, 1:12 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca placed T28275: [Segmentation] AdaptiveRegionGrowingTool must be refactored / 4D Segmentation returns error message when point is not on the correct timestep up for grabs.
Oct 27 2023, 1:12 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca moved T28275: [Segmentation] AdaptiveRegionGrowingTool must be refactored / 4D Segmentation returns error message when point is not on the correct timestep from Backlog to MITK Meeting on the Request for Discussion board.
Oct 27 2023, 1:11 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca moved T28499: Refactor/rewrite RegionGrowing3D tool from Backlog to MITK Meeting on the Request for Discussion board.
Oct 27 2023, 1:11 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca closed T30222: [Registration] Enable use of parameters for command line MiniApp as Resolved.
Oct 27 2023, 1:08 PM · MITK (v2023.12)

Oct 26 2023

floca added a comment to T29454: Clarify the versions/editions we publish as installer.

We should also have a look on eMITK plugins. Maybe not for that release, but for the next.
E.g. would the MRI tools make sense?
SUV would also be a candidate... may RT (but there we have to double check the state...

Oct 26 2023, 10:04 PM · MITK (v2024.06), Request for Discussion

Oct 25 2023

floca committed rMITKed4fb2550811: Added option to pass parameters to MatchImageMiniApp (authored by floca).
Added option to pass parameters to MatchImageMiniApp
Oct 25 2023, 3:36 PM
floca committed rMITK34e229f7a4cc: removed wrong parameters (copyNpaste error) (authored by floca).
removed wrong parameters (copyNpaste error)
Oct 25 2023, 3:36 PM
floca committed rMITKc3283e082481: BREAKING Removed superfluous "MiniApp" suffix (authored by floca).
BREAKING Removed superfluous "MiniApp" suffix
Oct 25 2023, 3:36 PM
floca committed rMITKb8a3d2391605: T30222 Add parameter feature to MatchImageMiniApp (authored by floca).
T30222 Add parameter feature to MatchImageMiniApp
Oct 25 2023, 3:36 PM
floca committed rMITK5537bee6651c: Fixed review comments. (authored by floca).
Fixed review comments.
Oct 25 2023, 3:36 PM

Oct 24 2023

floca added a project to T29454: Clarify the versions/editions we publish as installer: Request for Discussion.

So now we have to clarify the name for the bigger edition. And if we want to have just one extended edition or if we will in the end have it focused on topics. As we only have currently fitting stuf added.

Oct 24 2023, 12:09 PM · MITK (v2024.06), Request for Discussion
floca added a comment to T29454: Clarify the versions/editions we publish as installer.

NOT included will be (@floca as far is I understood these plugins were tailored for specific applications and are not really of interest to the users in general, correct? ):

  • org.mitk.gui.qt.fit.demo
  • org.mitk.gui.qt.pharmacokinetics.simulation
Oct 24 2023, 12:07 PM · MITK (v2024.06), Request for Discussion

Oct 13 2023

floca added a comment to T30222: [Registration] Enable use of parameters for command line MiniApp.

Pushed new branch to rMITK MITK: feature/T30222-MatchImageMiniApp_add_parameter_support.

Oct 13 2023, 9:23 PM · MITK (v2023.12)

Oct 11 2023

floca added a revision to T27718: Miniapp for basic DICOM testing: Unknown Object (Differential Revision).
Oct 11 2023, 2:20 PM · MITK (v2023.12), Kaapana (internal)
floca added a project to T29639: [Registration] Mapping crashes when super-sampling is activated: Missing Info.

Not clear when and how it happens. Need to narrow it down more.

Oct 11 2023, 11:57 AM · Moved to git.dkfz.de, MITK (v2024.12), Missing Info
floca added a project to T29098: [3D Segmentation] UL Threshold Tool - 0 intensity value not include in slider range?: Restricted Project.
Oct 11 2023, 11:55 AM · MITK (v2024.12), Restricted Project, Checklist
floca added a project to T29535: Reinit of scene with planar figure while the Display is closed leads to crash: Known Issue.
Oct 11 2023, 11:49 AM · Moved to git.dkfz.de, MITK (v2024.12), Known Issue
floca lowered the priority of T29130: [WorkBench] Segmentation fault when "Close Project" is invoked and QmitkDataStorageComboBox widget is in UI from Unbreak Now! to Normal.

This task can be potentially closed after T30149 is handled (that one should be done first).

Oct 11 2023, 11:37 AM · Moved to git.dkfz.de, MITK
floca added a subtask for T29130: [WorkBench] Segmentation fault when "Close Project" is invoked and QmitkDataStorageComboBox widget is in UI: T30149: nnUNet(v2) in MITK.
Oct 11 2023, 11:36 AM · Moved to git.dkfz.de, MITK
floca added a parent task for T30149: nnUNet(v2) in MITK: T29130: [WorkBench] Segmentation fault when "Close Project" is invoked and QmitkDataStorageComboBox widget is in UI.
Oct 11 2023, 11:36 AM · Moved to git.dkfz.de, MITK (v2024.12)
floca edited projects for T27413: MITK Workflow Q&A, added: Request for Discussion, MITK; removed MITK (v2023.12).
Oct 11 2023, 11:30 AM · Moved to git.dkfz.de, MITK, Request for Discussion
floca lowered the priority of T27432: Error loading DCE-MRI DICOM image from High to Low.
Oct 11 2023, 11:29 AM · MITK, DICOM, Cleared
floca placed T27655: [statistics] Logic of DataGeneratorBase blocks the UI thread up for grabs.
Oct 11 2023, 11:28 AM · MITK (v2024.06)
floca closed T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes as Resolved.
Oct 11 2023, 11:26 AM · MITK (v2023.12)
floca moved T29454: Clarify the versions/editions we publish as installer from Backlog to Cycle on the MITK (v2023.12) board.
Oct 11 2023, 11:23 AM · MITK (v2024.06), Request for Discussion
floca triaged T30164: [Segmentation] [Bug] 2D RGB image not correctly handled by SegPreviewTool API tool as Normal priority.
Oct 11 2023, 11:20 AM · Moved to git.dkfz.de, MITK (v2024.12), Request for Discussion
floca lowered the priority of T30158: [DCM][SEG] Check why unittests did not detect breaking support of DCM Seg and fix the (unit) test from Unbreak Now! to High.
Oct 11 2023, 11:17 AM · Moved to git.dkfz.de, MITK (v2024.12)
floca moved T29130: [WorkBench] Segmentation fault when "Close Project" is invoked and QmitkDataStorageComboBox widget is in UI from Backlog to Cycle on the MITK (v2023.12) board.
Oct 11 2023, 11:00 AM · Moved to git.dkfz.de, MITK
floca moved T29509: [mxn multi widget] Clicking a render window utility toolbar does not change focus from mxn MultiWidget to Cycle on the MITK (v2023.12) board.
Oct 11 2023, 11:00 AM · Moved to git.dkfz.de, MITK (v2024.12)
floca moved T29597: TotalSeg didn't remember python environment from Segmentation to Cycle on the MITK (v2023.12) board.
Oct 11 2023, 10:59 AM · Moved to git.dkfz.de, MITK (v2024.12), Checklist
floca moved T29540: SAM as 2D tool in MITK from Segmentation to Cycle on the MITK (v2023.12) board.
Oct 11 2023, 10:59 AM · MITK (v2024.06)
floca moved T29302: Movie maker plugin does not work correctly with the new mxn multi widget from Backlog to Cycle on the MITK (v2023.12) board.
Oct 11 2023, 10:58 AM · Moved to git.dkfz.de, MITK (v2024.12)
floca moved T29295: MONAI Label App as auto-segmentation tool in MITK from Backlog to Cycle on the MITK (v2023.12) board.
Oct 11 2023, 10:57 AM · Moved to git.dkfz.de, MITK (v2024.12)
floca moved T29651: [Preferences] SAM tool Preferences not rendered nicely on MacOS from Backlog to Cycle on the MITK (v2023.12) board.
Oct 11 2023, 10:57 AM · Moved to git.dkfz.de, MITK (v2024.12)
floca moved T29539: SAM Python wrapper for MITK from Backlog to Cycle on the MITK (v2023.12) board.
Oct 11 2023, 10:57 AM · MITK (v2024.06)
floca added a comment to T30220: SAM tool: Custom NRRD writer not working as expected in Ubuntu.

most likely it is due to wrong locales in the out stream operation on your OS. You have ',' in your file where '.' should be.

Oct 11 2023, 9:24 AM · MITK (v2023.12)