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Recent Activity

Mon, Sep 6

kalali closed T28635: [Segmentation] Remove deprecated classes as Resolved.
Mon, Sep 6, 9:18 AM · Cleared, MITK (v2021.10)

Wed, Sep 1

kalali raised the priority of T28134: [Multilabel Segmentation] No warning triggered when using different mask geometries in Utilities View from Normal to High.
Wed, Sep 1, 10:35 AM · Restricted Project, Cleared, MITK (v2021.10)
kalali raised the priority of T27810: [Multilabel Segmentation] Inconsistencies and unclear functionality in operations of Utilities view from Normal to High.
Wed, Sep 1, 10:34 AM · Cleared, MITK (v2021.10), Restricted Project

Aug 12 2021

kalali updated the task description for T28635: [Segmentation] Remove deprecated classes.
Aug 12 2021, 4:21 PM · Cleared, MITK (v2021.10)
kalali closed T28490: Segmentation plugin: "new" segmentation should not run reinit! as Resolved.

Has been solved for the segmentation plugin and the multilabel segmentation plugin.
A general reformatting of the resetting-functionality will happen in T27613: Improve reinit behavior.

Aug 12 2021, 3:37 PM · Cleared, MITK (v2021.10)

Jul 29 2021

kalali added a comment to T28635: [Segmentation] Remove deprecated classes.

A first differential was created. There is another class QmitkThresholdAction that is not included anywhere and has not been touched for a long time. I don't see any reason for keeping this class. So I updated the differential with the removal of this class as well.

Jul 29 2021, 4:38 PM · Cleared, MITK (v2021.10)
kalali added a revision to T28635: [Segmentation] Remove deprecated classes: Restricted Differential Revision.
Jul 29 2021, 4:36 PM · Cleared, MITK (v2021.10)
kalali added a comment to T28635: [Segmentation] Remove deprecated classes.

When I look for occurrences of mitkOverwriteSliceImageFilter, I see a description inside ApplyDiffImageOperation and DiffImageApplier that says

At the moment, ApplyDiffImageOperations are only created by OverwriteSliceImageFilter.

or

Instances of this class are created e.g. by OverwriteSliceImageFilter.

However, the mentioned mitkOverwriteSliceImageFilter is nowhere used and was replaced by mitkVtkImageOverwrite. I found occurrences of ApplyDiffImageOperation and DiffImageApplier inside QmitkSlicesInterpolator.cpp, so I changed the description accordingly.

Jul 29 2021, 4:35 PM · Cleared, MITK (v2021.10)
kalali claimed T28635: [Segmentation] Remove deprecated classes.
Jul 29 2021, 12:37 PM · Cleared, MITK (v2021.10)
kalali moved T28635: [Segmentation] Remove deprecated classes from Segmentation to Cycle on the MITK (v2021.10) board.
Jul 29 2021, 12:37 PM · Cleared, MITK (v2021.10)

Jul 28 2021

floca triaged T28641: [Segmentation] Improve Watershed tool documentation as Normal priority.
Jul 28 2021, 12:47 PM · Cleared, MITK (v2021.10)
floca moved T28641: [Segmentation] Improve Watershed tool documentation from Backlog to Segmentation on the MITK (v2021.10) board.
Jul 28 2021, 12:47 PM · Cleared, MITK (v2021.10)
floca created T28641: [Segmentation] Improve Watershed tool documentation.
Jul 28 2021, 12:47 PM · Cleared, MITK (v2021.10)
kleina claimed T28464: [Segmentation] New Add/Remove tool.
Jul 28 2021, 10:24 AM · Cleared, MITK (v2021.10)

Jul 27 2021

floca added projects to T28134: [Multilabel Segmentation] No warning triggered when using different mask geometries in Utilities View: Cleared, Restricted Project.
Jul 27 2021, 9:54 AM · Restricted Project, Cleared, MITK (v2021.10)
floca added a project to T27810: [Multilabel Segmentation] Inconsistencies and unclear functionality in operations of Utilities view: Cleared.
Jul 27 2021, 9:50 AM · Cleared, MITK (v2021.10), Restricted Project
floca added a project to T27637: [Segmentation] Multilabel label name dialoge on label creation is a UX problem: Cleared.
Jul 27 2021, 9:48 AM · Cleared, MITK (v2021.10)
floca raised the priority of T28464: [Segmentation] New Add/Remove tool from Normal to High.
Jul 27 2021, 9:46 AM · Cleared, MITK (v2021.10)
floca added a project to T28635: [Segmentation] Remove deprecated classes: Cleared.
Jul 27 2021, 9:45 AM · Cleared, MITK (v2021.10)
floca added a project to T28264: [Segmentation Utilities] Various issues: Cleared.

Comment: One should seperate the open todos into sub tasks, I think.

Jul 27 2021, 9:43 AM · Cleared, MITK (v2021.10)

Jul 21 2021

kalali removed a project from T28490: Segmentation plugin: "new" segmentation should not run reinit!: Request for Discussion.
Jul 21 2021, 9:55 AM · Cleared, MITK (v2021.10)

Jul 16 2021

kalali added a comment to T28490: Segmentation plugin: "new" segmentation should not run reinit!.

Also, this solution still does not preserve the zoom but that's the next step.

Jul 16 2021, 1:00 PM · Cleared, MITK (v2021.10)

Jul 15 2021

kalali added a revision to T28490: Segmentation plugin: "new" segmentation should not run reinit!: Restricted Differential Revision.
Jul 15 2021, 10:38 PM · Cleared, MITK (v2021.10)
kalali updated subscribers of T28490: Segmentation plugin: "new" segmentation should not run reinit!.

We discussed this and two important points were made:

  • The difference between RenderWindowManager::InitializeViews(RenderingManager::GetInstance(), image->GetTimeGeometry()); and RenderWindowManager::InitializeViewsByBoundingObjects(RenderingManager::GetInstance(), dataStorage); is reasonable and important - even for a single data node (e.g. brain.nrrd, where the image itself is somehow rotated / tilted).
  • We definitely want to reset the geometry automatically such that the current view geometry of the renderer matches with the segmentation geometry. That way the user can immediately start drawing. We don't want the user to have to care for the correct geometry aligning manually.
Jul 15 2021, 10:35 PM · Cleared, MITK (v2021.10)

Jul 12 2021

kalali moved T28490: Segmentation plugin: "new" segmentation should not run reinit! from Backlog to MITK Meeting on the Request for Discussion board.

We need to look deeper into the segmentation plugin to find out if it is possible to create and draw a segmentation without a correctly initialized reference image.

Jul 12 2021, 6:13 PM · Cleared, MITK (v2021.10)

Jul 9 2021

kislinsk added a comment to T28385: [Segmentation] Erosion crashes the MITK Workbench after interpolation.

Deleted branch from rMITK MITK: bugfix/T28385-AddNullptrCheck.

Jul 9 2021, 9:56 AM · Cleared, MITK (v2021.10)
kislinsk added a comment to T28385: [Segmentation] Erosion crashes the MITK Workbench after interpolation.

Pushed new branch to rMITK MITK: bugfix/T28385-AddNullptrCheck.

Jul 9 2021, 9:55 AM · Cleared, MITK (v2021.10)
kislinsk added a comment to T28385: [Segmentation] Erosion crashes the MITK Workbench after interpolation.

Deleted branch from rMITK MITK: bugfix/T28385-InterpolationCrashOnMorphologicalOperations.

Jul 9 2021, 7:49 AM · Cleared, MITK (v2021.10)
kislinsk closed T28385: [Segmentation] Erosion crashes the MITK Workbench after interpolation as Resolved by committing rMITKb7299f54c209: Handle uninitialized segmentations in interpolator.
Jul 9 2021, 7:49 AM · Cleared, MITK (v2021.10)

Jul 8 2021

kislinsk renamed T28385: [Segmentation] Erosion crashes the MITK Workbench after interpolation from [Segmentation Utilities] Erosion crashes the MITK Workbench after interpolation to [Segmentation] Erosion crashes the MITK Workbench after interpolation.
Jul 8 2021, 12:23 PM · Cleared, MITK (v2021.10)
kislinsk added a revision to T28385: [Segmentation] Erosion crashes the MITK Workbench after interpolation: Restricted Differential Revision.
Jul 8 2021, 7:57 AM · Cleared, MITK (v2021.10)

Jul 7 2021

kislinsk added a comment to T28385: [Segmentation] Erosion crashes the MITK Workbench after interpolation.

Pushed new branch to rMITK MITK: bugfix/T28385-InterpolationCrashOnMorphologicalOperations.

Jul 7 2021, 10:55 PM · Cleared, MITK (v2021.10)
kalali added a comment to T28490: Segmentation plugin: "new" segmentation should not run reinit!.

So I dug a little bit deeper using brain.nrrd as test data:

Jul 7 2021, 5:39 PM · Cleared, MITK (v2021.10)
kislinsk added a comment to T28385: [Segmentation] Erosion crashes the MITK Workbench after interpolation.

We can fix it in the SegmentationInterpolationController by explicitly handling the situation that the modified image is not initialized (IsInitialized() == false).

Jul 7 2021, 5:23 PM · Cleared, MITK (v2021.10)
kislinsk claimed T28385: [Segmentation] Erosion crashes the MITK Workbench after interpolation.
Jul 7 2021, 5:14 PM · Cleared, MITK (v2021.10)
kalali added a comment to T28490: Segmentation plugin: "new" segmentation should not run reinit!.

So my conclusion from this: [...] It seems as there is a difference between the initialization that is performed when loading the image and the initialization that is performed when calling InitializeViews or using the reinit-action from the context menu.

Jul 7 2021, 12:05 PM · Cleared, MITK (v2021.10)
kislinsk edited projects for T28385: [Segmentation] Erosion crashes the MITK Workbench after interpolation, added: Cleared; removed Missing Info.
Jul 7 2021, 12:02 PM · Cleared, MITK (v2021.10)

Jul 6 2021

kalali added a comment to T28490: Segmentation plugin: "new" segmentation should not run reinit!.

I see no difference between calling InitializeViews with the new Enum value NO_UPDATE and not calling InitializeViews at all, solely using mitk::RenderingManager::GetInstance()->RequestUpdateAll() to correctly set the rendering geometry without changing the view after a new segmentation nodes has been created.
However, both variants do not allow segmenting on the new segmentation node as the warning message shows, stating that a reinit should be performed on the segmentation image. The warning message appears in the scenario where I changed the camera view before creating a new segmentation:

NO_UPDATE_02.png (1×2 px, 229 KB)

Jul 6 2021, 4:49 PM · Cleared, MITK (v2021.10)

Jun 30 2021

kalali moved T28490: Segmentation plugin: "new" segmentation should not run reinit! from Segmentation to Cycle on the MITK (v2021.10) board.
Jun 30 2021, 9:41 AM · Cleared, MITK (v2021.10)

Jun 28 2021

kalali added a comment to T28490: Segmentation plugin: "new" segmentation should not run reinit!.

After a new segmentation node was been created, it is added to the data manager. This event itself will call RequestUpdateAll multiple times. However, the view will not be reset with the mentioned new value NO_UPDATE - that means, requesting a render update does not change the view / crosshair / camera orientation etc. The view is only updated / reset when InitializeViews or InitializeViewsByBoundingObjects is called (which in turn calls InternalViewInitialization and updates the slice navigation controller).

Jun 28 2021, 2:34 PM · Cleared, MITK (v2021.10)
kalali added a comment to T28490: Segmentation plugin: "new" segmentation should not run reinit!.

A first idea was mentioned here:

Just for testing purposes: I created an additional Enum value to mitk::RenderingManager::RequestType, called NO_UPDATE. [...]

This allows to disable resetting the view / crosshair etc. after a new segmentation has been created.

Jun 28 2021, 10:25 AM · Cleared, MITK (v2021.10)

Jun 25 2021

kalali claimed T28490: Segmentation plugin: "new" segmentation should not run reinit!.
Jun 25 2021, 12:19 PM · Cleared, MITK (v2021.10)
kalali added a comment to T28490: Segmentation plugin: "new" segmentation should not run reinit!.

The QmitkNewSegmentationDialog, which is used for the "New-button" does not contain any logic for resetting the render windows.
It can be used to simply create a new segmentation, e.g. when using the QmitkCreateMultiLabelSegmentationAction from the data manager context menu - here this dialog is used but no re-initialization / view resetting is done.

Jun 25 2021, 12:18 PM · Cleared, MITK (v2021.10)
kalali moved T28490: Segmentation plugin: "new" segmentation should not run reinit! from MITK Meeting to Backlog on the Request for Discussion board.
Jun 25 2021, 10:35 AM · Cleared, MITK (v2021.10)

Jun 16 2021

kalali updated subscribers of T28490: Segmentation plugin: "new" segmentation should not run reinit!.

We should look into this and focus on the mentioned related task by @kislinsk to start with separating the two processes:

  1. matching the geometry of the images for interaction
  2. resetting the view of render windows to see the new segmentation
Jun 16 2021, 12:45 PM · Cleared, MITK (v2021.10)
kalali moved T28490: Segmentation plugin: "new" segmentation should not run reinit! from Backlog to MITK Meeting on the Request for Discussion board.
Jun 16 2021, 9:46 AM · Cleared, MITK (v2021.10)
kalali added a project to T28490: Segmentation plugin: "new" segmentation should not run reinit!: Request for Discussion.
Jun 16 2021, 9:46 AM · Cleared, MITK (v2021.10)

Jun 7 2021

floca raised the priority of T27319: [Segmentation] Correctly implement interpolation features for Multilabel Segmentation View from High to Unbreak Now!.
Jun 7 2021, 9:16 AM · MITK (v2021.10), Restricted Project, Cleared
floca added a parent task for T27319: [Segmentation] Correctly implement interpolation features for Multilabel Segmentation View: T28142: [Segmentation] Remove plugin redundancy with MultiLabelSegmentation.
Jun 7 2021, 9:14 AM · MITK (v2021.10), Restricted Project, Cleared
floca moved T27319: [Segmentation] Correctly implement interpolation features for Multilabel Segmentation View from Backlog to Segmentation on the MITK (v2021.10) board.
Jun 7 2021, 9:08 AM · MITK (v2021.10), Restricted Project, Cleared