As far as SAM/MedSAM is concerned, we can add numpy<2 in our agent-sam repo and fix the issue without code changes to MITK.
Perhaps we should think about creating Totalsegmentator "agents" scripts to deal with such production issues.

Jun 25 2024, 12:07 PM · MITK

a178n added a comment to T30479: [Seg] Totalseg and SAM/MedSAM tool fails.

The numpy version upgrade seems disruptive. The current latest torch version 2.3.1 is incompatible with numpy v2 while running torch.from_numpy conversions
Since the numpy v2 release, Totalsegmentator repo has updated its dependency specification. See: https://github.com/wasserth/TotalSegmentator/commit/e648b08445434585511a8a7c8118e34f5309ce05
However, new a release hasn't occurred on pypi.

Jun 25 2024, 12:01 PM · MITK

a178n updated the task description for T30479: [Seg] Totalseg and SAM/MedSAM tool fails.

Jun 25 2024, 11:28 AM · MITK

a178n triaged T30479: [Seg] Totalseg and SAM/MedSAM tool fails as High priority.

Jun 25 2024, 11:27 AM · MITK

floca closed T30478: MITKFileConverter multiple output index before last extension as Invalid.

damn. you are right. Than i will revert it and change AVID to add in front of the first '.'.

Jun 25 2024, 11:02 AM · MITK (v2024.12), Request for Discussion, Breaking Change

kislinsk added a comment to T30478: MITKFileConverter multiple output index before last extension.

Wouldn't that break support of compressed files like foo.nii.gz for example?

Jun 25 2024, 9:57 AM · MITK (v2024.12), Request for Discussion, Breaking Change

floca moved T30478: MITKFileConverter multiple output index before last extension from Backlog to MITK Meeting on the Request for Discussion board.

Jun 25 2024, 9:17 AM · MITK (v2024.12), Request for Discussion, Breaking Change

floca triaged T30478: MITKFileConverter multiple output index before last extension as Normal priority.

Jun 25 2024, 9:17 AM · MITK (v2024.12), Request for Discussion, Breaking Change

kislinsk added a revision to T29421: Finding CppRestSDK library alternative: Unknown Object (Differential Revision).

Jun 25 2024, 4:31 AM · MITK (v2024.12)

kislinsk added a comment to T29421: Finding CppRestSDK library alternative.

Pushed new branch to rMITK MITK: bugfix/T29421-RemoveCPPRestSDK.

Jun 25 2024, 4:30 AM · MITK (v2024.12)

kislinsk edited projects for T29421: Finding CppRestSDK library alternative, added: MITK (v2024.12); removed MITK.

Jun 25 2024, 4:26 AM · MITK (v2024.12)

kislinsk edited projects for T30430: [TotalSeg] Add check if python venv exists before installation, added: MITK (v2024.06); removed MITK (v2024.12).

Jun 25 2024, 4:03 AM · MITK (v2024.06)

kislinsk closed T30430: [TotalSeg] Add check if python venv exists before installation as Resolved.

Jun 25 2024, 4:03 AM · MITK (v2024.06)

Jun 24 2024

floca updated subscribers of T30475: Add app for Splitting dynamic data sets.

FYI

Jun 24 2024, 11:39 AM · MITK

floca added a revision to T30477: Remove MiniApp suffix from ModelFit cmdapps: Unknown Object (Differential Revision).

Jun 24 2024, 11:38 AM · Breaking Change, MITK (v2024.12)

floca added a revision to T30475: Add app for Splitting dynamic data sets: Unknown Object (Differential Revision).

Jun 24 2024, 11:38 AM · MITK

floca triaged T30477: Remove MiniApp suffix from ModelFit cmdapps as Normal priority.

Jun 24 2024, 9:59 AM · Breaking Change, MITK (v2024.12)

floca updated subscribers of T30476: Expose information of the DICOM reader why blocks where splitted.

FYI

Jun 24 2024, 9:50 AM · MITK (v2024.12)

floca triaged T30476: Expose information of the DICOM reader why blocks where splitted as Normal priority.

Jun 24 2024, 9:49 AM · MITK (v2024.12)

floca triaged T30475: Add app for Splitting dynamic data sets as High priority.

Jun 24 2024, 9:44 AM · MITK

Jun 19 2024

kislinsk added a comment to T29390: How to ease the handling of external generated segmentations.

Deleted branch from rMITK MITK: feature/T29390-Improve_conversion_for_multilabel.

Jun 19 2024, 11:39 AM · MITK (v2024.06)

kislinsk added a comment to T30469: Build MITK CoreCmdApps on CentOS 7.

Deleted branch from rMITK MITK: feature/T30469-SupportExperimentalFilesystem.

Jun 19 2024, 11:38 AM · MITK (v2024.06)

kislinsk added a comment to T30387: [SEG] More visual feedback by supporting highlighted labels in render window..

Deleted branch from rMITK MITK: feature/T30387-highlight_labels.

Jun 19 2024, 11:38 AM · MITK (v2024.06)

kislinsk added a comment to T29317: Clean up DICOM Browser plugin.

Deleted branch from rMITK MITK: bugfix/T29317-CleanUpDICOMBrowser.

Jun 19 2024, 11:36 AM · MITK (v2024.12)

kislinsk closed T29317: Clean up DICOM Browser plugin, a subtask of T24398: Dicom plugin: Retrieve does not work, as Wontfix.

Jun 19 2024, 11:36 AM · MITK (v2024.12)

kislinsk closed T29317: Clean up DICOM Browser plugin as Wontfix.

Meanwhile a lot of code in CTK regarding the DICOM browser changed and the branch her is outdated so much that it makes sense to start from scratch again, if really necessary at all.

Jun 19 2024, 11:36 AM · MITK (v2024.12)

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

Deleted branch from rMITK MITK: feature/T30222-MatchImageMiniApp_add_parameter_support.

Jun 19 2024, 11:33 AM · MITK (v2023.12)

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

Deleted branch from rMITK MITK: feature/T30294-Remove_LabelSet_class.

Jun 19 2024, 11:33 AM · Breaking Change, MITK (v2024.06)

kislinsk added a comment to T28487: MitkMRSignal2Concentration MiniApp does not correctly handles exceptions in app configuration step.

Deleted branch from rMITK MITK: bugfix/T28487-MitkMRSignal2Concentration_handle_exceptions.

Jun 19 2024, 11:33 AM · MITK

kislinsk added a comment to T27196: Rewrite packaging of MITK.

Deleted branch from rMITK MITK: bugfix/T27196-RewritePackaging.

Jun 19 2024, 11:31 AM · MITK, Cleared

kislinsk edited projects for T27196: Rewrite packaging of MITK, added: MITK; removed MITK (v2024.12).

Jun 19 2024, 11:30 AM · MITK, Cleared

kislinsk added a comment to T29371: [Registration] Improve view icons.

Deleted branch from rMITK MITK: bugfix/T29371-ImproveRegistrationIcons.

Jun 19 2024, 11:30 AM · MITK

kislinsk closed T29371: [Registration] Improve view icons as Wontfix.

Jun 19 2024, 11:30 AM · MITK

kislinsk added a comment to T29603: Warn (as error) in Visual Studio for unreferenced parameters and variables to match our GCC/Clang settings.

Deleted branch from rMITK MITK: bugfix/T29603-MatchVisualStudioCompilerErrorsBetterToGCCAndClang.

Jun 19 2024, 11:28 AM · MITK

kislinsk added a comment to T30321: Upgrade dependencies to be compatible with Ubuntu 23.10+.

Deleted branch from rMITK MITK: bugfix/T30321-Ubuntu_23.10_Compatibility.

Jun 19 2024, 11:26 AM · MITK

kislinsk added a comment to T30334: Images are not rendered anymore in 3-d window.

Deleted branch from rMITK MITK: bugfix/T30334-FixPlaneGeometryDataToSurfaceFilter.

Jun 19 2024, 11:26 AM · MITK

kislinsk closed T30255: Allow render window utility widgets on all sides as Wontfix.

We weren't able to get the PR working.

Jun 19 2024, 11:26 AM · MITK (v2024.12), Pull Request

kislinsk added a comment to T30255: Allow render window utility widgets on all sides .

Deleted branch from rMITK MITK: feature/T30255-RenderWindowUtilityWidgets.

Jun 19 2024, 11:25 AM · MITK (v2024.12), Pull Request

Jun 18 2024

a178n added a comment to T30300: Remember "Fast" checkbox setting.

Deleted branch from rMITK MITK: feature/T30300-totalseg-fastbox.

Jun 18 2024, 6:08 PM · MITK (v2024.06)

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

Deleted branch from rMITK MITK: feature/T30353-totalseg-update.

Jun 18 2024, 6:08 PM · MITK (v2024.06)

a178n added a comment to T30392: [Segmentation] Totalsegmentator & Otsu is buggy.

Deleted branch from rMITK MITK: bugfix/T30392-totalseg-nnunet-confirmbutton.

Jun 18 2024, 6:08 PM · MITK (v2024.06)

a178n added a comment to T30355: [Seg] MedSAM as new 2D Tool in MITK.

Deleted branch from rMITK MITK: feature/T30355-medsam-tool.

Jun 18 2024, 6:08 PM · MITK (v2024.06)

a178n added a comment to T30357: [MedSAM] Add user documentaiton.

Deleted branch from rMITK MITK: feature/T30357-medsam-doku.

Jun 18 2024, 6:08 PM · MITK (v2024.06)

a178n added a comment to T30231: Monailabel User documentation.

Deleted branch from rMITK MITK: feature/T30231-monailabel-doku.

Jun 18 2024, 6:08 PM · MITK (v2024.06)

a178n added a comment to T30426: [SEG] Highlight importance of level window in Segment Anything.

Deleted branch from rMITK MITK: feature/T30426-doc-updates.

Jun 18 2024, 6:08 PM · Checklist, MITK (v2024.06)

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

Deleted branch from rMITK MITK: feature/T30447-totalseg-levelwindow.

Jun 18 2024, 6:03 PM · MITK

a178n added a comment to T30430: [TotalSeg] Add check if python venv exists before installation.

Deleted branch from rMITK MITK: feature/T30430-python-venv-check.

Jun 18 2024, 6:03 PM · MITK (v2024.06)

a178n added a comment to T30457: Add TotalSegmentator MR image (v 2.2) support in MITK.

Deleted branch from rMITK MITK: feature/T30457-totalseg-mri.

Jun 18 2024, 6:03 PM · MITK (v2024.06)

a178n added a comment to T29295: MONAI Label App as auto-segmentation tool in MITK.

Deleted branch from rMITK MITK: feature/T29295-monai-tool-httplib.

Jun 18 2024, 6:02 PM · MITK (v2024.12)

Jun 17 2024

s434n reopened T27904: Feature request: Colorbars to interpret data in MITK as "Open".

Jun 17 2024, 4:11 PM · Request for Discussion, MITK

floca reopened T29024: [Core] Crash-inducing racing condition in TimeGeometry as "Open".

Jun 17 2024, 3:56 PM · MITK

floca reopened T28942: Ensure default properties for data nodes as "Open".

Jun 17 2024, 3:55 PM · MITK

floca reopened T28887: [Registration] MITKMatchPoint code should use PropertyRelationRules for its results as "Open".

Jun 17 2024, 3:52 PM · Next Milestone, MITK

floca reopened T29171: Replace redundant ImageTimeSelector code by SelectImageByTimeStep/TimePoint as "Open".

Jun 17 2024, 3:46 PM · Next Milestone, Restricted Project, MITK

floca edited projects for T29171: Replace redundant ImageTimeSelector code by SelectImageByTimeStep/TimePoint, added: Next Milestone; removed Auto-closed.

Jun 17 2024, 3:46 PM · Next Milestone, Restricted Project, MITK

floca reopened T27193: Introduce a NodeSelectionButton widget as "Open".

Jun 17 2024, 3:45 PM · MITK

floca reopened T24295: mitk::LocaleSwitch promotes illpossed pattern and excessive use reduces thread savety as "Open".

Jun 17 2024, 3:42 PM · Restricted Project, MITK

floca reopened T24692: Scene serialization is corrupted due to images stored with wrong locale as "Open".

Jun 17 2024, 3:41 PM · Auto-closed, Restricted Project, MITK

floca reopened T23748: Image should have a valid DICOM.0008.0018 proprety, a subtask of T23746: MITK and DICOM (realization), as Open.

Jun 17 2024, 3:39 PM · MITK

floca reopened T23748: Image should have a valid DICOM.0008.0018 proprety as "Open".

Jun 17 2024, 3:39 PM · Auto-closed, MITK

floca reopened T23748: Image should have a valid DICOM.0008.0018 proprety, a subtask of T23774: Implement helper to correctly (DICOM conformal) parameterize images (or other BaseData derived classes), as Open.

Jun 17 2024, 3:39 PM · MITK

kislinsk closed T30448: MITK snapshots/2024-05-02 Workbench not restarting as Invalid.

I close this task as invalid. We were not able to reproduce this issue at all and we never heard of if by anyone else. Feel free to reopen the task if there's a reliable recipe for reproduction.

Jun 17 2024, 2:42 PM · MITK (v2024.12), Missing Info

kislinsk triaged T30359: MITK MiniApps in Kaapana as Normal priority.

Jun 17 2024, 2:40 PM · MITK

kislinsk triaged T30310: Add new views, e.g. for Seg Task List or Perfusion as Wishlist priority.

Jun 17 2024, 2:39 PM · Missing Info, MITK

kislinsk triaged T18489: Help perspective cannot be closed as Low priority.

Jun 17 2024, 2:38 PM · MITK (v2024.12), Request for Discussion

kislinsk closed T23748: Image should have a valid DICOM.0008.0018 proprety, a subtask of T23774: Implement helper to correctly (DICOM conformal) parameterize images (or other BaseData derived classes), as Wontfix.

Jun 17 2024, 2:36 PM · MITK

kislinsk closed T28780: Levelwindow widgets - add labels to the edit field as Wontfix.

Hi there! 🙂

Jun 17 2024, 2:36 PM · Auto-closed, MITK