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Mar 31 2023

a178n added a comment to T28675: Boolean Operations in Segmentation utilities are slow.

Hi everyone,
I did some basic profiling on this issue to see where the issue might be and how the python vs c++ compute comparison looks like.
TL;DR: MITK computes aren't slow at all. Problem is in conversion of results to LabelSetImage via InitializeByLabeledImage method.

Mar 31 2023, 9:37 AM · MITK (v2024.06), Request for Discussion

Mar 30 2023

kalali added a comment to T25057: Check IContextMenuActions and extension points.

I rebased this to the latest develop and pushed new branch to rMITK MITK: feature/T25057-Clean-IContextMenuActions for someone else to take over.

Mar 30 2023, 7:20 PM · MITK (v2024.06)
kalali closed T29403: [mxn multi widget] Concept for crosshair data type as Resolved.
Mar 30 2023, 5:02 PM · MITK (v2023.04)
kalali triaged T29512: [mxn multi widget] Share crosshairs between individual render windows as Normal priority.
Mar 30 2023, 5:01 PM · MITK (v2024.06)
kalali triaged T29511: [mxn multi widget] Provide more information with crosshair data as Normal priority.
Mar 30 2023, 4:53 PM · MITK (v2024.06)
kalali removed a subtask for T29403: [mxn multi widget] Concept for crosshair data type: T29386: [mxn multi widget] StdDisplay unnecessarily uses the crosshair manager.
Mar 30 2023, 4:23 PM · MITK (v2023.04)
kalali removed a parent task for T29386: [mxn multi widget] StdDisplay unnecessarily uses the crosshair manager: T29403: [mxn multi widget] Concept for crosshair data type.
Mar 30 2023, 4:23 PM · MITK (v2024.06)
floca added a comment to T29403: [mxn multi widget] Concept for crosshair data type.

@floca Part of this task is done with landing the related diff, introducing the new crosshair-data.

We can either leave it open or create dedicated tasks to tackle the remaining issues, like extending the crosshair-data with additional geometry-information or showing multiple crosshairs in a single render window etc.

Mar 30 2023, 1:09 PM · MITK (v2023.04)
kalali added a comment to T29403: [mxn multi widget] Concept for crosshair data type.

@floca Part of this task is done with landing the related diff, introducing the new crosshair-data.

Mar 30 2023, 1:00 PM · MITK (v2023.04)
kalali updated the task description for T29403: [mxn multi widget] Concept for crosshair data type.
Mar 30 2023, 12:59 PM · MITK (v2023.04)
kalali committed rMITK184f3f8c6929: New crosshair data type (authored by kalali).
New crosshair data type
Mar 30 2023, 12:57 PM
kalali committed rMITK84bb066ffd84: Fix bug such that the menu is not connected multiple times (authored by kalali).
Fix bug such that the menu is not connected multiple times
Mar 30 2023, 12:57 PM
kalali committed rMITK451fb28b14e9: Clean code to not store smart pointers unnecessarily (authored by kalali).
Clean code to not store smart pointers unnecessarily
Mar 30 2023, 12:57 PM
kalali committed rMITK71a88fbbb1a3: Clean plane geometry data mapper (authored by kalali).
Clean plane geometry data mapper
Mar 30 2023, 12:57 PM
kalali committed rMITK971711f21d22: Adapt depending classes to use the new crosshair data (authored by kalali).
Adapt depending classes to use the new crosshair data
Mar 30 2023, 12:57 PM
kalali committed rMITKcd75ba971e46: Add crosshair data and new vtk mapper (authored by kalali).
Add crosshair data and new vtk mapper
Mar 30 2023, 12:57 PM
kislinsk updated the task description for T29160: [Segmentation] Worklist specification, data structure and io functions.
Mar 30 2023, 12:02 PM · MITK (v2022.10)
s434n added a comment to T26555: [mxn multi widget] Provide different default layouts.

This task is basically done with D778, which introduced a mechanism to save/load custom layouts, as well as select from provided presets. The only thing we could further add would be more presets, as there is only one at the moment (two rows with each view direction each).

Mar 30 2023, 11:07 AM · MITK
s434n committed rMITKff61541ae92d: Introduce saving and loading of custom and preset window layouts (authored by s434n).
Introduce saving and loading of custom and preset window layouts
Mar 30 2023, 11:05 AM
s434n committed rMITK51364988ffb6: Merge branch 'develop' into feature/T26555-mxn-default-layouts (authored by s434n).
Merge branch 'develop' into feature/T26555-mxn-default-layouts
Mar 30 2023, 11:05 AM
s434n committed rMITK08f94571dd80: correctly set view plane selection in utility widgets (authored by s434n).
correctly set view plane selection in utility widgets
Mar 30 2023, 11:05 AM
s434n committed rMITKcad68daa40c7: make required connection type clearer for save signal (authored by s434n).
make required connection type clearer for save signal
Mar 30 2023, 11:05 AM
s434n committed rMITKce36b832b6ad: replace filename in SaveLayout function with an ostream (authored by s434n).
replace filename in SaveLayout function with an ostream
Mar 30 2023, 11:05 AM
s434n committed rMITKdd4691c235ac: Add default name to custom window layouts (authored by s434n).
Add default name to custom window layouts
Mar 30 2023, 11:05 AM
s434n committed rMITK0b9302b9c098: improve error handling and slight restructuring for simplification (authored by s434n).
improve error handling and slight restructuring for simplification
Mar 30 2023, 11:05 AM
s434n committed rMITKf21434068e4e: make window layout presets more distinct by name prefix (authored by s434n).
make window layout presets more distinct by name prefix
Mar 30 2023, 11:05 AM
s434n committed rMITKa9657c01042c: unify CustomLayoutLoad and PresetLayoutLoad in general LoadLayout (authored by s434n).
unify CustomLayoutLoad and PresetLayoutLoad in general LoadLayout
Mar 30 2023, 11:05 AM
s434n committed rMITKa39d22d1d7d1: fix dependency and unusable QT ui parameter (authored by s434n).
fix dependency and unusable QT ui parameter
Mar 30 2023, 11:05 AM
s434n committed rMITK57bdb4e383f8: make integer counter unsigned to get rid of comparison warnings (authored by s434n).
make integer counter unsigned to get rid of comparison warnings
Mar 30 2023, 11:05 AM
s434n committed rMITK118762582cc7: introduce saving and loading of custom and preset window layouts (authored by s434n).
introduce saving and loading of custom and preset window layouts
Mar 30 2023, 11:05 AM
a178n triaged T29510: Migrate installer from Qt GUI level to MITK level as Normal priority.
Mar 30 2023, 10:19 AM · MITK
kislinsk added a comment to T29160: [Segmentation] Worklist specification, data structure and io functions.

Did you consider using JSON Schema to formalize the definition? It is a bit hard to grasp it right now, but admittedly I probably didn't spend enough time looking over the various resources provided.

Mar 30 2023, 8:56 AM · MITK (v2022.10)
fedorov added a comment to T29160: [Segmentation] Worklist specification, data structure and io functions.

Did you consider using JSON Schema to formalize the definition? It is a bit hard to grasp it right now, but admittedly I probably didn't spend enough time looking over the various resources provided.

Mar 30 2023, 4:29 AM · MITK (v2022.10)
kislinsk added a revision to T29445: Make Segmentation Tasks Lists fully available in the MITK Workbench: Unknown Object (Differential Revision).
Mar 30 2023, 12:04 AM · MITK (v2023.04)

Mar 29 2023

s434n added a subtask for T28578: [mxn multi widget] Optimization of the mxn multi widget: T29509: [mxn multi widget] Clicking a render window utility toolbar does not change focus.
Mar 29 2023, 4:38 PM · MITK
s434n added a parent task for T29509: [mxn multi widget] Clicking a render window utility toolbar does not change focus: T28578: [mxn multi widget] Optimization of the mxn multi widget.
Mar 29 2023, 4:38 PM · MITK (v2024.06)
s434n triaged T29509: [mxn multi widget] Clicking a render window utility toolbar does not change focus as Low priority.
Mar 29 2023, 4:38 PM · MITK (v2024.06)
floca moved T29130: [WorkBench] Segmentation fault when "Close Project" is invoked and QmitkDataStorageComboBox widget is in UI from Segmentation to Cycle on the MITK (v2023.04) board.
Mar 29 2023, 3:53 PM · MITK
a178n triaged T29508: Replace QmitkDataStorageComboBox widget SingleNodeSelectionWidget. as Normal priority.
Mar 29 2023, 3:16 PM · MITK (v2023.04)
s434n added a comment to T29492: [mxn multi widget] Update and extend checklist.

This was briefly touched upon in the group meeting today. An idea that came up was to include a section in some checklists to gather feedback on existing and suggestions for new features / UX in general.

Mar 29 2023, 11:26 AM · MITK (v2023.04)
s434n claimed T29492: [mxn multi widget] Update and extend checklist.
Mar 29 2023, 11:24 AM · MITK (v2023.04)

Mar 28 2023

t470h created T29506: Create list of awards that IMSY people can apply to.
Mar 28 2023, 1:34 PM · Restricted Project
floca added a project to T29505: [SEG] New NRRD file formate for MultiLabelSegmentation + IO classes + introduction of legacy reader: Breaking Change.
Mar 28 2023, 9:34 AM · Breaking Change, MITK (v2023.04)
floca claimed T29505: [SEG] New NRRD file formate for MultiLabelSegmentation + IO classes + introduction of legacy reader.
Mar 28 2023, 8:57 AM · Breaking Change, MITK (v2023.04)
floca added a subtask for T29392: [SEG] Add dedicated writer to store multi-label images in nifti: T29505: [SEG] New NRRD file formate for MultiLabelSegmentation + IO classes + introduction of legacy reader.
Mar 28 2023, 8:56 AM · MITK (v2024.06)
floca added a parent task for T29505: [SEG] New NRRD file formate for MultiLabelSegmentation + IO classes + introduction of legacy reader: T29392: [SEG] Add dedicated writer to store multi-label images in nifti.
Mar 28 2023, 8:56 AM · Breaking Change, MITK (v2023.04)
floca triaged T29505: [SEG] New NRRD file formate for MultiLabelSegmentation + IO classes + introduction of legacy reader as Unbreak Now! priority.
Mar 28 2023, 8:56 AM · Breaking Change, MITK (v2023.04)

Mar 27 2023

kalali committed rMITKc744ead52c26: Optimize data accessibility using a new data node model (authored by kalali).
Optimize data accessibility using a new data node model
Mar 27 2023, 6:14 PM
kalali committed rMITKf581179e09e3: Extend layer utilities to delete / transfer property values (authored by kalali).
Extend layer utilities to delete / transfer property values
Mar 27 2023, 6:14 PM
kalali committed rMITK4071c66b46c1: Clean render window layer utilities (authored by kalali).
Clean render window layer utilities
Mar 27 2023, 6:14 PM
kalali committed rMITKa8287902cd00: Clean render window layer controller class (authored by kalali).
Clean render window layer controller class
Mar 27 2023, 6:14 PM
kalali committed rMITK89dbd59ad284: Use the new table model / selection widget (authored by kalali).
Use the new table model / selection widget
Mar 27 2023, 6:14 PM
kalali committed rMITK2965dc193fb5: Add table model / selection widget for render window data management (authored by kalali).
Add table model / selection widget for render window data management
Mar 27 2023, 6:14 PM
gaoh closed T28884: MITK Flowbench -Save Seg not working, due to file naming issues as Invalid.

theoretically yes, but I guess it is not relevant. Since we now use the tasklist feature. And before that, I used the described workaround. So this is not needed anymore.

Mar 27 2023, 5:11 PM · MITK (v2023.04), Request for Discussion, Kaapana (internal)
kalali triaged T29504: Initialize QmitkSlicesInterpolator with render windows instead of slice navigation controllers as Normal priority.
Mar 27 2023, 4:58 PM · MITK (v2024.06)
kompan closed T29503: Add ModelFit testing helper data to MITK-Data as Resolved.
Mar 27 2023, 12:59 PM · MITK
kompan committed rMD3937e12e3d1f: Add model fit JSON helper files (T2DecayModel). (authored by kompan).
Add model fit JSON helper files (T2DecayModel).
Mar 27 2023, 12:57 PM
kompan committed rMD1017394b5e44: Remove files (authored by kompan).
Remove files
Mar 27 2023, 12:57 PM
kompan committed rMD41e8b3b25dc3: Add JSON testing helper files for th2 T2 decay model. (authored by kompan).
Add JSON testing helper files for th2 T2 decay model.
Mar 27 2023, 12:57 PM
kompan triaged T29503: Add ModelFit testing helper data to MITK-Data as Normal priority.
Mar 27 2023, 10:56 AM · MITK

Mar 25 2023

a178n added a comment to T29130: [WorkBench] Segmentation fault when "Close Project" is invoked and QmitkDataStorageComboBox widget is in UI.

Pushed new branch to rMITK MITK: feature/T29130-nnunet-widget-change.

Mar 25 2023, 6:48 PM · MITK
a178n claimed T29130: [WorkBench] Segmentation fault when "Close Project" is invoked and QmitkDataStorageComboBox widget is in UI.
Mar 25 2023, 11:42 AM · MITK
a178n added a comment to T29130: [WorkBench] Segmentation fault when "Close Project" is invoked and QmitkDataStorageComboBox widget is in UI.

Sure. I will replace the current QmitkDataStorageComboBox widget to the newly moved NodeSelectionWidget.

Mar 25 2023, 11:42 AM · MITK

Mar 24 2023

floca triaged T29502: [SEG] Optimizing MultiLabelImage widgets (context menue) action names + new actions? as Wishlist priority.
Mar 24 2023, 8:49 PM · MITK (v2024.06)
floca added a project to T29076: [Segmentation] Pressing DEL should delete a label: Request for Discussion.

Still does not work for Del. For a sequence like CTRL+L CTRL+D it works.

Mar 24 2023, 8:47 PM · MITK (v2024.06), Checklist
floca added a comment to T28884: MITK Flowbench -Save Seg not working, due to file naming issues.

@gaoh is this still an open issue?

Mar 24 2023, 8:28 PM · MITK (v2023.04), Request for Discussion, Kaapana (internal)
floca added a comment to T29076: [Segmentation] Pressing DEL should delete a label.

I think with the new widget it should be easy. What are the keys actions wanted now?

Mar 24 2023, 8:27 PM · MITK (v2024.06), Checklist
floca added a project to T29390: How to ease the handling of external generated segmentations: Request for Discussion.

is the discussion realy over now? I think this is also more an meta task, concrete actions like removing binary tag and such should be sub tasks.
@kislinsk Could you make sub tasks out of your discussion points. Thanks.

Mar 24 2023, 8:26 PM · MITK (v2024.06)
floca raised the priority of T29396: [Segmentation] Newly created labelset image has wrong image type from Normal to High.
Mar 24 2023, 8:23 PM · MITK (v2024.06)
floca raised the priority of T29130: [WorkBench] Segmentation fault when "Close Project" is invoked and QmitkDataStorageComboBox widget is in UI from High to Unbreak Now!.

@a178n can you take care of it?

Mar 24 2023, 8:18 PM · MITK
floca moved T29392: [SEG] Add dedicated writer to store multi-label images in nifti from Segmentation to Cycle on the MITK (v2023.04) board.
Mar 24 2023, 8:17 PM · MITK (v2024.06)
floca claimed T29392: [SEG] Add dedicated writer to store multi-label images in nifti.
Mar 24 2023, 8:16 PM · MITK (v2024.06)
floca moved T29063: When all the folds are selected in "Folds" dropdown box, then show "All Folds" instead of "All" from Cycle to Segmentation on the MITK (v2023.04) board.
Mar 24 2023, 8:14 PM · MITK (v2024.06)
floca moved T29163: [XNAT] Opening XNAT session fails from Cycle to Backlog on the MITK (v2023.04) board.
Mar 24 2023, 8:13 PM · MITK (v2024.06)
floca moved T25057: Check IContextMenuActions and extension points from Cycle to Backlog on the MITK (v2023.04) board.
Mar 24 2023, 8:13 PM · MITK (v2024.06)
floca moved T29163: [XNAT] Opening XNAT session fails from Backlog to Cycle on the MITK (v2023.04) board.
Mar 24 2023, 8:13 PM · MITK (v2024.06)
floca moved T25057: Check IContextMenuActions and extension points from Backlog to Cycle on the MITK (v2023.04) board.
Mar 24 2023, 8:13 PM · MITK (v2024.06)
floca moved T29445: Make Segmentation Tasks Lists fully available in the MITK Workbench from Backlog to Cycle on the MITK (v2023.04) board.
Mar 24 2023, 8:13 PM · MITK (v2023.04)
floca moved T29457: Introduce basic TotalSegmentator tool in Workbench from Backlog to Cycle on the MITK (v2023.04) board.
Mar 24 2023, 8:13 PM · MITK (v2023.04)
floca moved T29458: Include Advanced settings support for TotalSegmentator tool in MITK from Backlog to Cycle on the MITK (v2023.04) board.
Mar 24 2023, 8:13 PM · MITK (v2023.04)
floca moved T29463: Doxygen documentation for TotalSegmentator from Backlog to Cycle on the MITK (v2023.04) board.
Mar 24 2023, 8:13 PM · MITK (v2023.04)
floca moved T29464: Test plan for TotalSegmentator from Backlog to Cycle on the MITK (v2023.04) board.
Mar 24 2023, 8:13 PM · MITK (v2023.04)
floca moved T29476: [Segmentation] [Interpolation] Unknown exception when creating new segmentation while interpolation is active on current segmentation at layer != 0 from Backlog to Cycle on the MITK (v2023.04) board.
Mar 24 2023, 8:13 PM · MITK (v2023.04)
floca moved T29468: Let MITK handle TotalSegmentator setup from Backlog to Cycle on the MITK (v2023.04) board.
Mar 24 2023, 8:13 PM · MITK (v2023.04)
floca moved T29492: [mxn multi widget] Update and extend checklist from Backlog to Cycle on the MITK (v2023.04) board.
Mar 24 2023, 8:12 PM · MITK (v2023.04)
floca moved T29500: [SEG] SegWithPreview tools with multiple labels are broken (if the produce a 0 label) from Backlog to Cycle on the MITK (v2023.04) board.
Mar 24 2023, 8:12 PM · MITK (v2023.04)
kalali triaged T29501: mitk::Mapper needs to be explicitly set as Normal priority.
Mar 24 2023, 6:29 PM · MITK (v2024.06)
neher closed T23701: Refactor OdfVtkMapper2D as Wontfix.
Mar 24 2023, 10:08 AM · MITK Diffusion
neher closed T24297: Refactor mitkRawShModel as Wontfix.
Mar 24 2023, 10:08 AM · MITK Diffusion
neher closed T26056: [MITK Diffusion] Integrated MIC Bet update in MITK Diffusion as Wontfix.
Mar 24 2023, 10:08 AM · MITK Diffusion
neher closed T27070: Planar figure to image fails as Wontfix.
Mar 24 2023, 10:08 AM · MITK Diffusion
neher closed T29430: Flip x direction for trk files as Wontfix.
Mar 24 2023, 10:07 AM · MITK Diffusion
neher closed T28849: Remove fiber parts only removes parts if point inside mask as Wontfix.
Mar 24 2023, 10:06 AM · MITK Diffusion
floca added a parent task for T29500: [SEG] SegWithPreview tools with multiple labels are broken (if the produce a 0 label): T29495: [SEG] Rework segmentation view UX.
Mar 24 2023, 9:41 AM · MITK (v2023.04)
floca added a subtask for T29495: [SEG] Rework segmentation view UX: T29500: [SEG] SegWithPreview tools with multiple labels are broken (if the produce a 0 label).
Mar 24 2023, 9:41 AM · MITK (v2023.12)
floca added a subtask for T29451: [SEG] Response labels all not displayed on Workbench: T29500: [SEG] SegWithPreview tools with multiple labels are broken (if the produce a 0 label).
Mar 24 2023, 9:41 AM · Cleared, MITK (v2023.04)
floca added a parent task for T29500: [SEG] SegWithPreview tools with multiple labels are broken (if the produce a 0 label): T29451: [SEG] Response labels all not displayed on Workbench.
Mar 24 2023, 9:41 AM · MITK (v2023.04)
floca updated the task description for T29500: [SEG] SegWithPreview tools with multiple labels are broken (if the produce a 0 label).
Mar 24 2023, 9:41 AM · MITK (v2023.04)
floca updated the task description for T29500: [SEG] SegWithPreview tools with multiple labels are broken (if the produce a 0 label).
Mar 24 2023, 9:39 AM · MITK (v2023.04)
floca triaged T29500: [SEG] SegWithPreview tools with multiple labels are broken (if the produce a 0 label) as Unbreak Now! priority.
Mar 24 2023, 9:39 AM · MITK (v2023.04)