Deleted branch from rMITK MITK: bugfix/T28455-rt-struct-3d-visibility.

Deleted branch from rMITK MITK: feature/T28354-cmake_faq.

Deleted branch from rMITK MITK: bugfix/T28737-RemovePicSupport.

Deleted branch from rMITK MITK: bugfix/T27711-rename-image-selection-label.

Deleted branch from rMITK MITK: release/T28802-MITK-v2021.10.

Deleted branch from rMITK MITK: release/T28802-2021-Week-45.

Pushed new branch to rMITK MITK: release/T28802-2021-Week-45.

I lower the priority since the exception is caught and it results in an error message instead of a crash. It's also an academic edge case, since it hardly makes any sense in a real world scenario to convert an actual image with more than 65000 different pixel values into a segmentation. Converting binary images or segmentation-like images works as expected.

The problem is fixed by the diff. One can argue that the current solution for the histogramm widget (hide if timestep has no statistic) is not ideal from the UX perspective (very flickery).
But I think that is another problem. The question should be, why are no statistics container produced for empty masks? wouldn't make it more sense to produce a also for such time step a statistic, even if it is very trival as no pixel are evaluated.

The description of the actual but swallowed exception is "Prohibited image access: the requested image part is already in use and cannot be requested recursively!" thrown indirectly from line 315 in mitkLabelSetImage.cpp: AccessFixedDimensionByItk_n(), which eventually calls ImageToItkImage() in mitkImageToItk.h:132. There, the Update() call of the ImageToItk class throws the exception mentioned above,

In T28799#229890, @kalali wrote:

Is this related / the same (because the second label is automatically selected and then the second layer has no second label)? T28131: [MultiLabel Segmentation] 3D Threshold tool does not work with multiple labels / layers

Was also meantioned several times be testers this week.

Is this related / the same (because the second label is automatically selected and then the second layer has no second label)? T28131: [MultiLabel Segmentation] 3D Threshold tool does not work with multiple labels / layers

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...

Just a ping because it was triggered by a checklist for the upcoming release.

@isensee What exactly does not work?

• Are you not able to load the data / ML nodes in the utilities selection widgets? That is a known bug and is addressed here: T28135
• Are you not able to work with multiple labels at all? This is also a known problem, since the MultiLabel Utilities View was never correctly implemented for working with multiple labels.

Maybe @s349i can also say something to this: Did you test the Utilities with segmentation masks created by the "MultiLabel Segmentation View"?

Deleted branch from rMITK MITK: bugfix/T28771-FixNegInfInSerializedGeometryProps.

Pushed new branch to rMITK MITK: bugfix/T28771-FixNegInfInSerializedGeometryProps.

In T28135, @kalali wrote:

MultiLabel Segmentation View creates segmentation masks that are non-binary, rendering most of the operations useless.

In T28763#229375, @floca wrote:

May be I do not understand the problem right. But the described behavior sounds correct to me. Flood fill should stop on another (not the label you clicked on (including background) label boundary. The only thing you could discuss is wether it is important if another label is locked or not.

May be I do not understand the problem right. But the described behavior sounds correct to me. Flood fill should stop on another (not the label you clicked on (including background) label boundary. The only thing you could discuss is wether it is important if another label is locked or not.

Thanks for the feedback.

In T28756#229271, @floca wrote:

Found the problem. It is not a error in the picking tool.

It is in

void mitk::LabelSetImage::ClearBuffer()

Because AccessByItk (which is used there) by default only supports 2D and 3D. -> Exception when trying to reset dynamic LabelSetImages.

So far I see the following solutions:

1. Add 4D as a CMake default (but would impact a lot of code...)
2. Add in clear buffer a check if instance is 4D and if so explizitly call it for 4D (in other cases use AccessByItk as we did so far.

@kislinsk Do you see an other option? Which one would you choose?

Found the problem. It is not a error in the picking tool.

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

Testing if both Segmentation Utilities and Multilabel Segmentation Utilities have the same functionality:

• For 3d data, a surface (or surfaces, depending on the case) was created by doing a 3d-interpolation of the masks in different 2d views. Data Used: MITK-Data/brain.nrrd.

Deleted branch from rMITK MITK: bugfix/T28749-libxdamage.

Pushed new branch to rMITK MITK: bugfix/T28749-libxdamage.

In T28320#229111, @kalali wrote:

@floca, should we also add this for the upcoming release?

Has been fixed with the mentioned diff / task.

@floca, should we also add this for the upcoming release?

I already implemented something but it is not yet finished.

Good catch! Thanks

BTW I recommend to test always with the latest snapshot installer instead of the last release.

Found the bug. The lower threshold for the region growing preview is set to itk::NumericTraits<TPixel>::min() when the region growing direction is downwards. However, itk::NumericTraits<TPixel>::min() is the wrong method as it has a different meaning for floating point values than the author obviously expected (compare to min() vs. lowest() in std::numeric_limits<>). The correct method is itk::NumericTraits<TPixel>::NonpositiveMin(), which works for all cases and is the right semantic minimum of a range of values.

Is doesn't have to be in the installer - but it has to be in the final release, meaning: It will probably be a bug found by some manual checklist testing by some random people.

Workaround: (Re)open the MultiLabel Segmentation view after you converted the segmentation to make it work.

In T28732#228848, @kalali wrote:

We actually talked about the priority and I explicitly said to set it to "Unbreak Now" because it HAS to be fixed for the upcoming release. What are your thoughts?

Deleted branch from rMITK MITK: bugfix/T28740-CIBuildStatusBadges.

Pushed new branch to rMITK MITK: bugfix/T28740-CIBuildStatusBadges.