Was adapted for the 2021.10 release with the following findings:

• T28826: [Segmentation][Interpolation] Color of 2D interpolated slice is not yellow but segmentation color
• T28827: [Segmentation][Interpolation] Color of 3D interpolated segmentations is red, not green
• T28829: [Segmentation][Interpolation] Interpolation area is still enabled, when segmentation node is hidden.

Was adapted for the 2021.10 release with the following findings:

• T28798: [Segmentation][MultiLabel][Utilities] UI is inconsistent / unstable
• T28796: [Segmentation][Utilities] Morphological Operations behave unexpectedly
• T28797: [Segmentation[MultiLabel][Utilities] Using 4D data with dynamic segmentations results in 3D data

Was adapted for the 2021.10 release with the following findings:

• T26959: [Segmentation] Newly created LabelSet segmentation is not displayed as "outline binary"
• T28766: [Segmentation] Preferences / properties for "Smoothed surface creation" do not seem to have any effect
• T28789: [Segmentation][Multilabel][Options] Auto-selection mode is unclear in checklist or broken
• T28791: [Segmentation][Multilabel][Options]"Create polygon model" issues for large images
• T28793: [Segmentation][Multilabel][Options] Changing only decimation rate has no visible effect in "Create smoothed polygon model"

@kahl I hope it is ok, that I assigned you, since you are working on this anyways.

In the same line of reasoning (see discussion above). We could also remove the label name dialoge, when you add a new layer, couldn't we. In the current tests there was a remark, that when adding a new layer, you first are queried if you realy want to make a new layer and then you are asked for the label name...

Pushed new branch to rMITK MITK: feature/T28464-new-add-tool.

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.

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.

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.

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

In T28490#226519, @kalali wrote:

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

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.

In T28490#226107, @kalali wrote:

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.

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

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

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

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

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

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

In T28490#226107, @kalali wrote:

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.

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: