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May 18 2022

floca closed T28991: [Segmentation] 3D tools overwrite / remove previous mask if reconfirmed as Resolved.

Solved in context of i.a. T28982. Now this is handled correctly and user can also configure the behavior.

May 18 2022, 3:37 PM · MITK (v2022.10)
franza added a comment to T29082: MITK-IGT: XML logging is broken.

I would say some code in Modules\IGT\IO has to be adapted to fix this bug. Possibly the class mitk::NavigationDataRecorderDeprecated, if it is still in use.

May 18 2022, 3:33 PM · MITK (v2022.10), Pull Request, IGT
a178n edited projects for T29063: When all the folds are selected in "Folds" dropdown box, then show "All Folds" instead of "All", added: MITK (v2022.10); removed MITK.
May 18 2022, 2:18 PM · MITK (v2024.06)
a178n changed the status of T28808: [Properties] Some Pointset 2D shape selection not shown in the image views from Resolved to Invalid.
May 18 2022, 2:17 PM · MITK (v2022.10)
a178n edited projects for T29063: When all the folds are selected in "Folds" dropdown box, then show "All Folds" instead of "All", added: MITK; removed MITK (v2022.10).
May 18 2022, 2:15 PM · MITK (v2024.06)
a178n removed a project from T29063: When all the folds are selected in "Folds" dropdown box, then show "All Folds" instead of "All": Request for Discussion.
May 18 2022, 2:15 PM · MITK (v2024.06)
s349i added a project to T29184: Replace itkContourExtractor2DImageFilter : MITK.
May 18 2022, 1:01 PM · MITK, Request for Discussion
s349i created T29184: Replace itkContourExtractor2DImageFilter .
May 18 2022, 1:00 PM · MITK, Request for Discussion
a178n lowered the priority of T29063: When all the folds are selected in "Folds" dropdown box, then show "All Folds" instead of "All" from Normal to Wishlist.
May 18 2022, 12:08 PM · MITK (v2024.06)
a178n added a comment to T29154: Show available Tasks for Download in the nnUnet GUI.

The output of the abovementioned command, for reference:

May 18 2022, 11:50 AM · MITK (v2022.10)
floca removed a project from T29183: [SEG] Removal of "create as new segmentation": Request for Discussion.

Discussion result: yes makes sens.

May 18 2022, 11:50 AM · MITK
s434n claimed T28464: [Segmentation] New Add/Remove tool.
May 18 2022, 11:37 AM · MITK (v2022.10)
floca added a comment to T29077: [Segmentation] Showing / hiding labels using the labelsetwidget selects them.

Started dicussion about it. Current discussion result: We should go for a new model view based implementation instead of try to fix the current boiler plate code.
Have to discuss design of the model view pattern in detail in the next MITK meeting.

May 18 2022, 11:28 AM · MITK (v2023.04), Checklist
floca removed a project from T28936: [Segmentation] Remove utilities redundancy with MultiLabelSegmentation: Request for Discussion.
May 18 2022, 11:16 AM · MITK (v2022.10), Breaking Change
floca moved T29154: Show available Tasks for Download in the nnUnet GUI from Segmentation to Cycle on the MITK (v2022.10) board.
May 18 2022, 10:51 AM · MITK (v2022.10)
floca moved T27319: [Segmentation] Correctly implement interpolation features for Multilabel Segmentation View from Segmentation to Cycle on the MITK (v2022.10) board.
May 18 2022, 10:51 AM · MITK (v2023.04), Restricted Project
floca moved T26172: 2D interpolation in MultiLabelSegmentation Editor only works for 1. label from Segmentation to Cycle on the MITK (v2022.10) board.
May 18 2022, 10:51 AM · MITK (v2023.04)
holzwart updated the task description for T29176: IMSY-Poster for "Arbeitsgruppeninspirationsmesse".
May 18 2022, 10:37 AM · Restricted Project
kalali closed T29142: [Segmentation] Previews stay invisible if label was hidden as Resolved.
May 18 2022, 9:44 AM · MITK (v2022.10), Checklist
kalali committed rMITKb28140233b8b: Correctly show preview nodes (authored by kalali).
Correctly show preview nodes
May 18 2022, 9:43 AM
kalali committed rMITK4dfb2f180948: Set the label of the preview node to visible (authored by kalali).
Set the label of the preview node to visible
May 18 2022, 9:43 AM
floca moved T26959: [Segmentation] Newly created LabelSet segmentation is not displayed as "outline binary" from Backlog to MITK Meeting on the Request for Discussion board.
May 18 2022, 9:22 AM · MITK (v2024.06), Checklist, Request for Discussion
floca moved T29094: Deleting a data node causes global reset from Backlog to MITK Meeting on the Request for Discussion board.
May 18 2022, 9:22 AM · MITK, Checklist
floca moved T28936: [Segmentation] Remove utilities redundancy with MultiLabelSegmentation from Backlog to MITK Meeting on the Request for Discussion board.
May 18 2022, 9:21 AM · MITK (v2022.10), Breaking Change
floca moved T29077: [Segmentation] Showing / hiding labels using the labelsetwidget selects them from Backlog to MITK Meeting on the Request for Discussion board.
May 18 2022, 9:18 AM · MITK (v2023.04), Checklist
kalali closed T28815: [Segmentation] Segmentation is still rendered after "clear" was clicked as Invalid.

The Fast Marching tool hast been removed with 2ef49f51d547. Also, no other tools exist that have a "Clear"-button.

May 18 2022, 9:08 AM · MITK (v2022.10), Checklist
kalali updated the task description for T28815: [Segmentation] Segmentation is still rendered after "clear" was clicked.
May 18 2022, 9:06 AM · MITK (v2022.10), Checklist
floca moved T29183: [SEG] Removal of "create as new segmentation" from Backlog to MITK Meeting on the Request for Discussion board.
May 18 2022, 8:17 AM · MITK
floca triaged T29183: [SEG] Removal of "create as new segmentation" as Normal priority.
May 18 2022, 8:17 AM · MITK

May 17 2022

floca added a comment to T28140: [MultiLabel Segmentation] Default parameter (unsigned int layer = 0) is unnecessary and causes problems.

in the new data structure it won't happen as there is no active label anymore. But you are right I thought the same when I looked through the class. My motiviation to refine this obsolete class was only limited 🙈 .

May 17 2022, 8:03 PM · MITK (v2024.06)
kalali moved T29142: [Segmentation] Previews stay invisible if label was hidden from Tests/Checklists to Cycle on the MITK (v2022.10) board.
May 17 2022, 6:36 PM · MITK (v2022.10), Checklist
kalali claimed T29142: [Segmentation] Previews stay invisible if label was hidden.

I can confirm the behavior.
I debugged a little bit and found the following:
The preview-image is an own data node (e.g. Threshold preview), stored in the data storage / shown in the data manager. The QmitkLabelSetWidget::OnVisibleButtonClicked-function only retrieves the current working image and sets its visible-state.

May 17 2022, 6:35 PM · MITK (v2022.10), Checklist
kalali updated subscribers of T28140: [MultiLabel Segmentation] Default parameter (unsigned int layer = 0) is unnecessary and causes problems.

I just stumbled upon the following:

May 17 2022, 6:07 PM · MITK (v2024.06)
a178n closed T28808: [Properties] Some Pointset 2D shape selection not shown in the image views as Resolved.
May 17 2022, 5:57 PM · MITK (v2022.10)
gaoh added a comment to T28884: MITK Flowbench -Save Seg not working, due to file naming issues.

yes, that will help. Also, this worklist will be quite helpful, allowing a new form of "batch-processing".

May 17 2022, 3:34 PM · MITK (v2023.04), Request for Discussion, Kaapana (internal)
floca created T29182: Extend TransferLabelContent.
May 17 2022, 2:38 PM · MITK
kalali added a revision to T29142: [Segmentation] Previews stay invisible if label was hidden: Unknown Object (Differential Revision).
May 17 2022, 2:10 PM · MITK (v2022.10), Checklist
kalali closed T28978: [MultiLabel Segmentation] Create segmentation action always creates a dynamic segmentation as Resolved.

The fix was updated and landed onto develop. I will close this now but the question remains in which scenario this datamanager-contextmenu entry / action could be relevant - I don't see any need for this.

May 17 2022, 1:34 PM · MITK (v2022.10)
kalali committed rMITK3f7a773b1790: Create dynamic / static segmentation action (authored by kalali).
Create dynamic / static segmentation action
May 17 2022, 1:27 PM
kalali committed rMITK1b2969ff5eb1: Use new segmentation creation dialog (authored by kalali).
Use new segmentation creation dialog
May 17 2022, 1:27 PM
kalali committed rMITK210e293e188f: Add dialog for static / dynamic segmentation creation (authored by kalali).
Add dialog for static / dynamic segmentation creation
May 17 2022, 1:27 PM
kalali updated subscribers of T29110: [Segmentation] Optimize new segmentation view.
In T29110, @kalali wrote:
  • A newly created label is automatically selected?
    • Was mentioned in a checklist and should be checked, as this is relevant when it comes to using the label and observing the drawn mask color
May 17 2022, 1:26 PM · MITK (v2022.10)
kalali closed T29141: [Segmentation] Color change not immediately applied as Resolved.
May 17 2022, 1:24 PM · MITK (v2022.10), Checklist
kalali committed rMITKbb5195b4587d: Fix labelset widget issues (authored by kalali).
Fix labelset widget issues
May 17 2022, 12:55 PM
kalali committed rMITK3fbd2c338e0b: Get active label on active layer (authored by kalali).
Get active label on active layer
May 17 2022, 12:55 PM
kalali committed rMITKe53bc4de30ff: Do not explicitly react on label changes (authored by kalali).
Do not explicitly react on label changes
May 17 2022, 12:55 PM
kalali committed rMITKdfcef20e5356: Observe relevant event for new layers (authored by kalali).
Observe relevant event for new layers
May 17 2022, 12:55 PM
floca committed rMITK445b45bebf34: Fixed wrong include (authored by floca).
Fixed wrong include
May 17 2022, 12:13 PM
floca committed rMITK4adbf8a0b84c: Fixed wrong include (authored by floca).
Fixed wrong include
May 17 2022, 12:13 PM
a178n added a comment to T28808: [Properties] Some Pointset 2D shape selection not shown in the image views.

Ok, I got it working as well. Thanks!
We can mark it resolved.

Screenshot 2022-05-17 at 12.05.34.png (2×3 px, 996 KB)

May 17 2022, 12:08 PM · MITK (v2022.10)
neher committed rMITKDIFF2849e4058199: Merge branch 'T29109-DynamicItkThreading' (authored by neher).
Merge branch 'T29109-DynamicItkThreading'
May 17 2022, 11:52 AM
neher committed rMITKDIFFf06091d9c699: using new dynmic threading (authored by neher).
using new dynmic threading
May 17 2022, 11:51 AM
s434n claimed T29093: [Image Cropper] Warning of rotated geometry not removed after reinit.
May 17 2022, 11:23 AM · MITK (v2022.10), Checklist
neher committed rMD5d36bd874a80: tensor tracking test data (authored by neher).
tensor tracking test data
May 17 2022, 11:14 AM
s434n added a comment to T28808: [Properties] Some Pointset 2D shape selection not shown in the image views.

I expect a circle in the cross-hairs, akin to Shape: cross or vertex. But there is None. Is this expected behaviour?

May 17 2022, 11:10 AM · MITK (v2022.10)
s434n added a comment to T29141: [Segmentation] Color change not immediately applied.

Is this the same (T29110, see description point 3) and specifically T29110#235991?
If so, I have a fix for the > layer 0 problem which can be tested and reviewed in D632.

May 17 2022, 10:49 AM · MITK (v2022.10), Checklist
floca committed rMITK5846ba3200a0: T28982 Added option to control MergeStyle and OverwriteStyle of an… (authored by floca).
T28982 Added option to control MergeStyle and OverwriteStyle of an…
May 17 2022, 10:47 AM
floca closed T28982: Weak Label Annotation Picking Tool as Resolved by committing rMITKb907c41570e1: Added relabel mode to PickingTool.
May 17 2022, 10:47 AM · MITK (v2022.10), Request for Discussion
floca closed T28982: Weak Label Annotation Picking Tool, a subtask of T29157: NCT ISSO Annotation Support with MITK Segmentation Flow, as Resolved.
May 17 2022, 10:47 AM · MITK (v2024.06)
floca closed T29146: Union Mode for the picking tool, a subtask of T28982: Weak Label Annotation Picking Tool, as Resolved.
May 17 2022, 10:47 AM · MITK (v2022.10), Request for Discussion
floca closed T29146: Union Mode for the picking tool as Resolved by committing rMITKb907c41570e1: Added relabel mode to PickingTool.
May 17 2022, 10:47 AM · MITK (v2022.10)
floca committed rMITK5ba5b9e3c5e8: fixed review comments (authored by floca).
fixed review comments
May 17 2022, 10:47 AM
floca committed rMITKb907c41570e1: Added relabel mode to PickingTool (authored by floca).
Added relabel mode to PickingTool
May 17 2022, 10:47 AM
floca committed rMITKe9bca1de8d69: Added option to control MergeStyle and OverwriteStyle of an AutoSegmentationTool (authored by floca).
Added option to control MergeStyle and OverwriteStyle of an AutoSegmentationTool
May 17 2022, 10:47 AM
floca added a comment to T28884: MITK Flowbench -Save Seg not working, due to file naming issues.

@gaoh maybe also the worklist feature covered by T29159 would also help/suffice? Than you could explicitly define the output path.

May 17 2022, 9:48 AM · MITK (v2023.04), Request for Discussion, Kaapana (internal)
floca updated the task description for T29159: [Segmentation] Flow bench worklist feature .
May 17 2022, 9:47 AM · MITK (v2022.10)
floca added a revision to T29146: Union Mode for the picking tool: Restricted Differential Revision.
May 17 2022, 8:12 AM · MITK (v2022.10)
floca added a revision to T28982: Weak Label Annotation Picking Tool: Restricted Differential Revision.
May 17 2022, 8:12 AM · MITK (v2022.10), Request for Discussion
floca committed rMITK27ffcb0daf95: Added OverwriteStyle modes to TransferLabelContent (authored by floca).
Added OverwriteStyle modes to TransferLabelContent
May 17 2022, 8:11 AM
floca committed rMITKd9e5c458f0de: removed unused variables (authored by floca).
removed unused variables
May 17 2022, 8:11 AM
floca committed rMITKc28d93f779ad: fixed typo (authored by floca).
fixed typo
May 17 2022, 8:11 AM
floca closed T29177: [Segmentation] TransferLabelToImage function should support to ignore locks, a subtask of T29146: Union Mode for the picking tool, as Resolved.
May 17 2022, 8:11 AM · MITK (v2022.10)
floca closed T29177: [Segmentation] TransferLabelToImage function should support to ignore locks as Resolved by committing rMITKb66ecfea8e69: Added OverwriteStyle modes to TransferLabelContent.
May 17 2022, 8:11 AM · MITK (v2022.10)
floca committed rMITKb66ecfea8e69: Added OverwriteStyle modes to TransferLabelContent (authored by floca).
Added OverwriteStyle modes to TransferLabelContent
May 17 2022, 8:11 AM
floca closed T29177: [Segmentation] TransferLabelToImage function should support to ignore locks, a subtask of T28982: Weak Label Annotation Picking Tool, as Resolved.
May 17 2022, 8:11 AM · MITK (v2022.10), Request for Discussion

May 16 2022

kausch added a member for MIC: r682g.
May 16 2022, 4:51 PM
a178n edited projects for T28866: [Segmentation] Redundant label "recomputation" for Otsu/Watershed (& nnUNet) when any of the Preview-generated labels are selected to Confirm, added: MITK (v2022.10); removed MITK.
May 16 2022, 4:22 PM · MITK (v2022.10), Request for Discussion
a178n added a project to T29063: When all the folds are selected in "Folds" dropdown box, then show "All Folds" instead of "All": Request for Discussion.
May 16 2022, 4:01 PM · MITK (v2024.06)
a178n added a comment to T29063: When all the folds are selected in "Folds" dropdown box, then show "All Folds" instead of "All".

Now regarding the requested cosmetic change (requested by Fabian during the Hackathon) -
We use CTK checkable combo box to facilitate the selection of multiple options in a dropdown.
When all the options are selected by the user in the dropdown, the display in the dropdown automatically changes to "All".
This is done by a paint event of the Combobox where the string "All" is arbitrarily assigned. Ref: https://github.com/commontk/CTK/blob/c97620f43dec6b1eac894d7d9c491d2af236dc22/Libs/Widgets/ctkCheckableComboBox.cpp#L385
Thus, any custom text would require a change from CTK side.

May 16 2022, 3:55 PM · MITK (v2024.06)
a178n added a comment to T29063: When all the folds are selected in "Folds" dropdown box, then show "All Folds" instead of "All".

The changes for the second part of the task are already incorporated in the 2022.04 release.

May 16 2022, 3:33 PM · MITK (v2024.06)
amiiney added a member for IMSY: f793t.
May 16 2022, 1:52 PM
s349i added a comment to T26172: 2D interpolation in MultiLabelSegmentation Editor only works for 1. label .

Yes. My work will take care of this. Just need to finish off the label merging for individual slices.

May 16 2022, 1:24 PM · MITK (v2023.04)
s349i claimed T26172: 2D interpolation in MultiLabelSegmentation Editor only works for 1. label .
May 16 2022, 1:23 PM · MITK (v2023.04)
s349i claimed T27319: [Segmentation] Correctly implement interpolation features for Multilabel Segmentation View.
May 16 2022, 1:23 PM · MITK (v2023.04), Restricted Project
floca moved T26172: 2D interpolation in MultiLabelSegmentation Editor only works for 1. label from Backlog to Segmentation on the MITK (v2022.10) board.
May 16 2022, 12:32 PM · MITK (v2023.04)
floca moved T25445: MultiLabel segmentation mapper is very slow from Backlog to Segmentation on the MITK (v2022.10) board.
May 16 2022, 12:32 PM · MITK (v2024.06), Request for Discussion
floca moved T27319: [Segmentation] Correctly implement interpolation features for Multilabel Segmentation View from Backlog to Segmentation on the MITK (v2022.10) board.
May 16 2022, 12:31 PM · MITK (v2023.04), Restricted Project
floca moved T27872: [Segmentation] Region Growing 3D GUI does not provide a "Overwrite" checkbox from Backlog to Cycle on the MITK (v2022.10) board.
May 16 2022, 12:31 PM · MITK (v2022.10), Cleared
floca moved T27913: [Segmentation] Warnings in utilities view are inconsistent from Backlog to Segmentation on the MITK (v2022.10) board.
May 16 2022, 12:31 PM · MITK (v2024.06)
floca moved T28135: [MultiLabel Segmentation] Utilities view cannot handle non-binary multilabel segmentations from Backlog to Segmentation on the MITK (v2022.10) board.
May 16 2022, 12:31 PM · MITK (v2023.04)
floca moved T28139: [LabelSetImage] Ambigious meaning of "layer" in LabelSetImage from Backlog to Segmentation on the MITK (v2022.10) board.
May 16 2022, 12:31 PM · MITK (v2023.12), Request for Discussion
floca moved T28557: Cannot load segmentations from KITS challenge due to unknown pixel type from Backlog to Segmentation on the MITK (v2022.10) board.
May 16 2022, 12:31 PM · MITK, Request for Discussion
floca moved T28675: Boolean Operations in Segmentation utilities are slow from Backlog to Segmentation on the MITK (v2022.10) board.
May 16 2022, 12:31 PM · MITK (v2024.06), Request for Discussion
floca moved T28691: AutoSegmentationWithPreviewTool tool manager won't support multithreading from Backlog to Segmentation on the MITK (v2022.10) board.
May 16 2022, 12:31 PM · MITK
floca moved T28752: [Segmentation] Move Segmentation utilities widgets to SegmentationUI module from Backlog to Segmentation on the MITK (v2022.10) board.
May 16 2022, 12:31 PM · MITK (v2023.04)
floca moved T28763: [Multilabel Segmentation] Fill / Erase tool does not fully respect multiple labels from Backlog to Segmentation on the MITK (v2022.10) board.
May 16 2022, 12:31 PM · MITK (v2022.10), Request for Discussion
floca moved T28884: MITK Flowbench -Save Seg not working, due to file naming issues from Backlog to Segmentation on the MITK (v2022.10) board.
May 16 2022, 12:31 PM · MITK (v2023.04), Request for Discussion, Kaapana (internal)
floca moved T28886: MITK Flowbench - Reopen created segmentation not working from Backlog to Segmentation on the MITK (v2022.10) board.
May 16 2022, 12:31 PM · MITK (v2022.10), Missing Info, Kaapana (internal)
floca moved T28989: [Segmentation] CanHandle functions seem to be inconsistent from Backlog to Segmentation on the MITK (v2022.10) board.
May 16 2022, 12:30 PM · MITK, Request for Discussion
floca moved T29067: Introduce option to save the segmentation in the nnUNet tool GUI itself. from Backlog to Cycle on the MITK (v2022.10) board.
May 16 2022, 12:30 PM · MITK