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Use this project to tag tasks and other stuff that should be discussed in the weekly MITK meeting.

Recent Activity

Fri, May 20

kalali moved T26399: Workbench crash on simple tree model update from Backlog to MITK Meeting on the Request for Discussion board.

I'm not sure if this is the reason (T24348: Invalid pointer exception due to invalid QModelIndex in QmitkDataStorageTreeModel) for the decision. I would go the route to deprecate the QmitkDataStorageModel and replace it with the QmitkDataStorageSimpleTreeModel. However, the QmitkDataStorageSimpleTreeModel probably needs to be extended (e.g. dropping, changing hierarchy). Do we already have a task for this / should we tackle this in this release-phase?
I stumbled upon these different tasks because of T26394: [Render window manager] Provide tree view / model, which is related to the mxnMultiWidget.

Fri, May 20, 9:39 AM · MITK (v2022.10), Request for Discussion

Thu, May 19

kalali added a comment to T29094: Deleting a data node causes global reset.

See T16165: Reinit after deletion for a reasoning. Both tasks are justified but maybe we should highlight / utilize the general preference "Call global reinit if node is deleted" more.

Thu, May 19, 7:04 PM · MITK (v2022.10), Request for Discussion, Checklist
kalali added a comment to T27613: Improve reinit behavior.

My changes related to this task were mainly to clear some classes and remove uncertainty (see T28617: Inconsistent view initialization in rendering manager).
As far as I see it some changes have been made in the subtask T28490: Segmentation plugin: "new" segmentation should not run reinit! and the respective D523: This was mainly concerned with NOT resetting the view / camera using a newly introduced parameter "resetCamera".

Thu, May 19, 6:48 PM · Request for Discussion, Next Milestone, MITK
kalali added subtasks for T27613: Improve reinit behavior: T29094: Deleting a data node causes global reset, Unknown Object (Maniphest Task).
Thu, May 19, 6:48 PM · Request for Discussion, Next Milestone, MITK
kalali added a parent task for T29094: Deleting a data node causes global reset: T27613: Improve reinit behavior.
Thu, May 19, 6:48 PM · MITK (v2022.10), Request for Discussion, Checklist
kalali added a comment to T26399: Workbench crash on simple tree model update.

I quickly tested the second suggestion and I was not able to reproduce the bug anymore.

Thu, May 19, 4:45 PM · MITK (v2022.10), Request for Discussion
kalali claimed T26399: Workbench crash on simple tree model update.
Thu, May 19, 1:34 PM · MITK (v2022.10), Request for Discussion
kalali updated subscribers of T26399: Workbench crash on simple tree model update.

@floca : Ilooked into this again and found the following:
After a node has been removed, inside QmitkDataStorageSimpleTreeModel::NodeRemoved the function QmitkDataStorageSimpleTreeModel::UpdateModelData is called. Here the data storage pointer is used to retrieve the data node subset of a given node predicate. The returned nodeset still returns 6 nodes in my case, although only 5 should exists, since one node was removed.
The node still exists in the data storage, because the signal for a node being removed (RemoveNodeEvent) is sent before the actual removal of the node from the list of nodes inside StandaloneDataStorage (data member m_SourceNodes)).

Thu, May 19, 1:34 PM · MITK (v2022.10), Request for Discussion
a178n added a comment to T29154: Show available Tasks for Download in the nnUnet GUI.

Instead of command output string parsing, the plan is to export available models' information and place it in a machine-readable format (eg. JSON) in the RESULTS_FOLDER.
This file can be further read by MITK and shown in GUI.
So, this involves making changes on the Python side, as well, for the dumping of the information in a machine-readable format (eg. JSON) natively.

Thu, May 19, 12:32 PM · MITK (v2022.10)
kalali placed T29077: [Segmentation] Showing / hiding labels using the labelsetwidget selects them up for grabs.
Thu, May 19, 11:09 AM · Request for Discussion, MITK (v2022.10), Checklist
floca moved T28866: [Segmentation] Redundant label "recomputation" for Otsu/Watershed (& nnUNet) when any of the Preview-generated labels are selected to Confirm from Backlog to Cycle on the MITK (v2022.10) board.
Thu, May 19, 8:11 AM · MITK (v2022.10), Request for Discussion
floca claimed T28866: [Segmentation] Redundant label "recomputation" for Otsu/Watershed (& nnUNet) when any of the Preview-generated labels are selected to Confirm.
Thu, May 19, 8:11 AM · MITK (v2022.10), Request for Discussion

Wed, May 18

s349i added a project to T29184: Replace itkContourExtractor2DImageFilter : MITK.
Wed, May 18, 1:01 PM · MITK, Request for Discussion
s349i created T29184: Replace itkContourExtractor2DImageFilter .
Wed, May 18, 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.
Wed, May 18, 12:08 PM · MITK (v2022.10)
a178n added a comment to T29154: Show available Tasks for Download in the nnUnet GUI.

The output of the abovementioned command, for reference:

Wed, May 18, 11:50 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.

Wed, May 18, 11:28 AM · Request for Discussion, MITK (v2022.10), Checklist
floca moved T29154: Show available Tasks for Download in the nnUnet GUI from Segmentation to Cycle on the MITK (v2022.10) board.
Wed, May 18, 10:51 AM · MITK (v2022.10)
floca moved T26172: 2D interpolation in MultiLabelSegmentation Editor only works for 1. label from Segmentation to Cycle on the MITK (v2022.10) board.
Wed, May 18, 10:51 AM · MITK (v2022.10), Request for Discussion
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.
Wed, May 18, 9:22 AM · MITK (v2022.10), 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.
Wed, May 18, 9:22 AM · MITK (v2022.10), Request for Discussion, Checklist
floca moved T28936: [Segmentation] Remove utilities redundancy with MultiLabelSegmentation from Backlog to MITK Meeting on the Request for Discussion board.
Wed, May 18, 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.
Wed, May 18, 9:18 AM · Request for Discussion, 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.
Wed, May 18, 8:17 AM · MITK
floca triaged T29183: [SEG] Removal of "create as new segmentation" as Normal priority.
Wed, May 18, 8:17 AM · MITK

Tue, May 17

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 🙈 .

Tue, May 17, 8:03 PM · MITK (v2022.10), Request for Discussion
kalali updated subscribers of T28140: [MultiLabel Segmentation] Default parameter (unsigned int layer = 0) is unnecessary and causes problems.

I just stumbled upon the following:

Tue, May 17, 6:07 PM · MITK (v2022.10), Request for Discussion
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".

Tue, May 17, 3:34 PM · Request for Discussion, MITK (v2022.10), Kaapana (internal)
floca closed T28982: Weak Label Annotation Picking Tool as Resolved by committing rMITKb907c41570e1: Added relabel mode to PickingTool.
Tue, May 17, 10:47 AM · MITK (v2022.10), Request for Discussion
floca closed T29146: Union Mode for the picking tool, a subtask of T28982: Weak Label Annotation Picking Tool, as Resolved.
Tue, May 17, 10:47 AM · MITK (v2022.10), Request for Discussion
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.

Tue, May 17, 9:48 AM · Request for Discussion, MITK (v2022.10), Kaapana (internal)
floca added a revision to T28982: Weak Label Annotation Picking Tool: Restricted Differential Revision.
Tue, May 17, 8:12 AM · MITK (v2022.10), Request for Discussion
floca closed T29177: [Segmentation] TransferLabelToImage function should support to ignore locks, a subtask of T28982: Weak Label Annotation Picking Tool, as Resolved.
Tue, May 17, 8:11 AM · MITK (v2022.10), Request for Discussion

Mon, May 16

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.
Mon, May 16, 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.
Mon, May 16, 4:01 PM · MITK (v2022.10)
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.

Mon, May 16, 1:24 PM · MITK (v2022.10), Request for Discussion
s349i claimed T26172: 2D interpolation in MultiLabelSegmentation Editor only works for 1. label .
Mon, May 16, 1:23 PM · MITK (v2022.10), Request for Discussion
floca moved T26172: 2D interpolation in MultiLabelSegmentation Editor only works for 1. label from Backlog to Segmentation on the MITK (v2022.10) board.
Mon, May 16, 12:32 PM · MITK (v2022.10), Request for Discussion
floca moved T25445: MultiLabel segmentation mapper is very slow from Backlog to Segmentation on the MITK (v2022.10) board.
Mon, May 16, 12:32 PM · MITK (v2022.10), Request for Discussion
floca moved T28139: [LabelSetImage] Ambigious meaning of "layer" in LabelSetImage from Backlog to Segmentation on the MITK (v2022.10) board.
Mon, May 16, 12:31 PM · MITK (v2022.10), 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.
Mon, May 16, 12:31 PM · MITK (v2022.10), Request for Discussion
floca moved T28691: AutoSegmentationWithPreviewTool tool manager won't support multi threading from Backlog to Segmentation on the MITK (v2022.10) board.
Mon, May 16, 12:31 PM · MITK (v2022.10), Request for Discussion
floca moved T28763: [Multilabel Segmentation] Fill / Erase tool does not fully respect multiple labels from Backlog to Segmentation on the MITK (v2022.10) board.
Mon, May 16, 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.
Mon, May 16, 12:31 PM · Request for Discussion, MITK (v2022.10), Kaapana (internal)
floca moved T28989: [Segmentation] CanHandle functions seem to be inconsistent from Backlog to Segmentation on the MITK (v2022.10) board.
Mon, May 16, 12:30 PM · MITK (v2022.10), 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.
Mon, May 16, 12:30 PM · MITK (v2022.10), Request for Discussion
floca moved T28982: Weak Label Annotation Picking Tool from Backlog to Cycle on the MITK (v2022.10) board.
Mon, May 16, 12:30 PM · MITK (v2022.10), Request for Discussion
floca moved T29154: Show available Tasks for Download in the nnUnet GUI from Backlog to Segmentation on the MITK (v2022.10) board.
Mon, May 16, 12:30 PM · MITK (v2022.10)
gaoh lowered the priority of T28884: MITK Flowbench -Save Seg not working, due to file naming issues from Normal to Low.

Yes, so I changed it already, and I am using the seriesUID as name for the images. Additionally, I had to add the layer property: Because by introducing the image name property, somehow the layer is also set (to a high number, probably). When I create a new SEG without setting the layer of the image to 0, the SEG is only put on top, when opening the data manager.

Mon, May 16, 10:02 AM · Request for Discussion, MITK (v2022.10), Kaapana (internal)

Fri, May 13

floca edited projects for T28989: [Segmentation] CanHandle functions seem to be inconsistent, added: MITK (v2022.10); removed Next Milestone, MITK.
Fri, May 13, 7:35 PM · MITK (v2022.10), Request for Discussion