Deleted branch from rMITK MITK: bugfix/T28739-UpdateSupportedTier1Platforms.

Pushed new branch to rMITK MITK: bugfix/T28739-UpdateSupportedTier1Platforms.

Pushed new branch to rMITK MITK: bugfix/T28737-RemovePicSupport.

see T28736, does not really work for me

Unfortunately still slow. Just checked with 2021-10-01 shapshot on Ubuntu 18.04 (same system as tests above).
13.6s for intersection
14s for difference
didn't bother clocking union

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?

Maybe related to / has similarities to {T28633}.

All Differential clients include MITK-ProjectTemplate builds.

In T28142#228390, @kalali wrote:

Since we are now in the "final" release phase I suggest to use the corresponding checklists to check the new / modified behavior of D533 and simultaneously verify the checklists and test the UI behavior of both segmentation plugin views.

Since we are now in the "final" release phase I suggest to use the corresponding checklists to check the new / modified behavior of D533 and simultaneously verify the checklists and test the UI behavior of both segmentation plugin views.

This function is also available in the preferences (Ctrl+P). There, just select "Draw as transparent overlay" (see image below).

Seems like you were right. I was doing a Debug build, yes. Changing the lib name to lz4 instead of lz4d fixed the issue on my end too.

Deleted branch from rMITK MITK: bugfix/T28706-LZ4DebugUnix.

Pushed new branch to rMITK MITK: bugfix/T28706-LZ4DebugUnix.

Thanks for giving it a try. I see that optimized;/work1/patmjen/MITK/MITK-superbuild-test/ep/lib64/liblz4.so is indeed added to the dependencies. So it is strange that it is not picked up by the linker. Or, did you do a Debug build? That would explain it at least since there is only a library specified for Release builds.

Thank you very much for your quick response.

Oh, I think I might have found the issue. Ignore the comment above and in CMake/Findlz4.cmake please add lib64 to the PATH_SUFFIXES of the two calls to find_library() in lines 11 and 18 like PATH_SUFFIXES lib lib64. Does it work?

Thanks for the comprehensive report. Can you do me a favor and add message(FATAL_ERROR "include dirs: ${lz4_INCLUDE_DIR} libraries: ${lz4_LIBRARIES}") as last line to CMake/PackageDepends/MITK_lz4_Config.cmake and configure MITK (not superbuild) to get the output?

With both subtasks done, we have successfully implemented the main goal of this task. The remaining bug that deactivating a segmentation tool resets the interaction to an earlier state (the one at which the tool was activated) has been split off into T28630 because it is not critical and can be easily handled with the new feature of deactivating PACS tools.

This could be connected to the undo/redo implementation of MITK and the creation of difference images for the undo stack. I do not know your version of MITK but the use of LZ4 compression for difference images in the latest versions could already be the or part of the solution. I agree that the operations should be much faster but they might be already as fast as the python implementation so whoever is working on this task should clock the different parts of the operation first to see what is actually taking so long and as said, if it is still the case in the latest version of MITK.

This is already possible in the Properties view but I guess it is a good candidate to be more accessible from within the segmentation view or preference page.

Deleted branch from rMITK MITK: bugfix/T28680-removed-old-style-cast-error.

Pushed new branch to rMITK MITK: bugfix/T28680-removed-old-style-cast-error.

2. Exception Handling: leading to Segmentation fault and Workbench crash

I did some debugging and found some more insights into the situation and workarounds.

Possible duplicate of T28278? That task's description is not very clear about the problem, but could be referencing the same thing

I started working on T28142: [Segmentation] Remove plugin redundancy with MultiLabelSegmentation which makes this task and some mentioned bugs invalid. We can close this task, once D533 is landed. The "New"-button is correctly enabled / disabled using the mentioned changes / differential and some warning messages were removed / simplified.

2- Tests using tmp_cropped.nii.gz

1- Tests using tmp.nii.gz
We tested multiple times the following workflow:

I did some testing (with Amir) on ubuntu 20.04 (32GB RAM). The issue could be replicated with a questionable increase in the utilization of RAM.
Fabian provided us a couple of files for testing, viz. tmp.nii.gz and tmp_cropped.nii.gz (same content, just removed some of the zeros around the ROI)

I looked into this using the latest Develop-branch on Windows. Using the Debug build I was able to see the stack trace after a crash (using the small, cropped image):

Exception Unhandled:
Unhandled exception at 0x00007FF96A63AFAC (ucrtbased.dll) in MitkWorkbench.exe: An invalid parameter was passed to a function that considers invalid parameters fatal.

This is still not fixed, can we please re-open it?

I refactored both views massively. What I did was to somehow bring both plugins in line with each other to see the differences and the similarities. This simplifies to understand how things are implemented and what needs to be done to remove redundancy. I will highlight some points that I find striking:

• the multilabel plugin view did not compare the world geometry to the selected segmentation node
  • I was able to draw a mask which was then positioned somewhere else (jumped) because of this (e.g. using brain.nrrd)
• hiding the selected segmentation node disables the tools for the segmentation plugin but not for the multilabel segmentation plugin
• the auto selection mode for showing / hiding the selected / not selected nodes in the data manager / render windows if the node selection is changed does not work anymore for the segmentation plugin (was already mentioned in T28256: [Segmentation] Auto-selection preference was hijacked for something else)
• the multilabel segmentation plugin did not listen to render window part changes (no subclass of IRenderWindowPartListener)
• the multilabel segmentation plugin lists some segmentation tools that don't even exist (FastMarching2D, Two Thresholds Auto Threshold Multiple Otsu)
• the multilabel segmentation view plugin is not able to accept binary images as a segmentation

T28650: [Selection concept] (Re)setting a data storage does not automatically check for matching nodes was opened during the review-process.

In T26172#227071, @floca wrote:

For now, I wouldn't try to patch in multi-label support into the interpolation class. Instead I would ensure that only a label image (so an image that just contains the active label) is passed to the interpolation class.
I think that that is the most pragmatic approach to it, procure the current implementation will never work properly when multiple labels are present, due to the assumptions already stated by @kalali.

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.

So I'm trying to replace the ExtractImageFilter with the ExtractSliceFilter by doing the following:

const PlaneGeometry *planarFigurePlaneGeometry = m_PlanarFigure->GetPlaneGeometry();

As of now, we will remain with Qt 5.12 for a while, since it is a well maintained long-term version