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Jul 7 2021

kislinsk claimed T28385: [Segmentation] Erosion crashes the MITK Workbench after interpolation.

Jul 7 2021, 5:14 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)

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

@floca I just tested it with my latest changes and the issue still persists. The connection to interpolation seems to be that the SegmentationInterpolationController is still holding a reference to the image and is notified about a modification. When changing the segmentation volume to the new segmentation eventually the ImageTimeSelector crashes when trying to clone an ImageDataItem that already seems to be null (this is 0x00000000). Here's a part of the call stack:

Jul 7 2021, 12:00 PM · Cleared, MITK (v2021.10)

Jul 5 2021

kislinsk added a comment to T28606: [Segmentation] Accelerate do/undo mechanism for segmentations.

Pushed new branch to rMITK MITK: bugfix/T28606-UseLZ4InCompressedImageContainerClass.

Jul 5 2021, 11:32 PM · MITK (v2021.10)

kislinsk added a comment to T28606: [Segmentation] Accelerate do/undo mechanism for segmentations.

With the same test data as in T28491, I was already able to virtually eliminate the time spent on compression with LZ4.

Jul 5 2021, 11:03 PM · MITK (v2021.10)

kislinsk moved T28606: [Segmentation] Accelerate do/undo mechanism for segmentations from Backlog to Segmentation on the MITK (v2021.10) board.

Jul 5 2021, 10:51 PM · MITK (v2021.10)

kislinsk triaged T28606: [Segmentation] Accelerate do/undo mechanism for segmentations as Normal priority.

Jul 5 2021, 10:51 PM · MITK (v2021.10)

Jul 2 2021

kislinsk closed T28602: 2021 Week 26 (Very Early July) as Resolved.

Jul 2 2021, 10:50 AM · MITK

kislinsk edited the content of Changelog.

Jul 2 2021, 10:49 AM · MITK

kislinsk added a comment to T28602: 2021 Week 26 (Very Early July).

Deleted branch from rMITK MITK: release/T28602-2021-Week-26.

Jul 2 2021, 10:45 AM · MITK

kislinsk committed rMITK3349cb419412: Merge branch 'master' into develop (authored by kislinsk).

Merge branch 'master' into develop

Jul 2 2021, 10:45 AM

kislinsk committed rMITKce85d3e8c908: 2021 Week 26 (Very Early July) (authored by kislinsk).

2021 Week 26 (Very Early July)

Jul 2 2021, 10:44 AM

kislinsk edited the content of 2021 Week 26 (Very Early July).

Jul 2 2021, 10:36 AM

kislinsk edited the content of 2021 Week 17 (Very Late April).

Jul 2 2021, 9:45 AM

kislinsk added a comment to T28602: 2021 Week 26 (Very Early July).

Pushed new branch to rMITK MITK: release/T28602-2021-Week-26.

Jul 2 2021, 9:42 AM · MITK

kislinsk triaged T28602: 2021 Week 26 (Very Early July) as Normal priority.

Jul 2 2021, 9:40 AM · MITK

kislinsk created T28602: 2021 Week 26 (Very Early July).

Jul 2 2021, 9:40 AM · MITK

kislinsk created an object: 2021 Week 26 (Very Early July).

Jul 2 2021, 9:40 AM

Jul 1 2021

kislinsk closed T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes as Resolved.

I will create another task for an optimization of the diff image operations in the do/undo stack.

Jul 1 2021, 10:10 AM · MITK (v2023.12)

kislinsk added a comment to T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes.

Deleted branch from rMITK MITK: bugfix/T28491-SpeedUp2DInterpolationsOfLargeSegmentations.

Jul 1 2021, 10:08 AM · MITK (v2023.12)

kislinsk committed rMITK014bc90c3796: Cleanup QmitkSlicesInterpolator::AcceptAllInterpolations() (authored by kislinsk).

Cleanup QmitkSlicesInterpolator::AcceptAllInterpolations()

Jul 1 2021, 10:08 AM

kislinsk committed rMITKc92776202a35: Clean up mitk::SegmentationInterpolationController::Interpolate() (authored by kislinsk).

Clean up mitk::SegmentationInterpolationController::Interpolate()

Jul 1 2021, 10:08 AM

kislinsk committed rMITK83e828cf2778: Implement simple caching of distance images (authored by kislinsk).

Implement simple caching of distance images

Jul 1 2021, 10:08 AM

kislinsk committed rMITK7814683ed6f3: Add optional parameter to allow caching of calculations (authored by kislinsk).

Add optional parameter to allow caching of calculations

Jul 1 2021, 10:08 AM

kislinsk committed rMITK72a664bc86d6: Cache some calculations for repeated 2d-interpolation (authored by kislinsk).

Cache some calculations for repeated 2d-interpolation

Jul 1 2021, 10:08 AM

kislinsk committed rMITK1c0d3e8cba5e: Derive cache size from number of H/W threads (authored by kislinsk).

Derive cache size from number of H/W threads

Jul 1 2021, 10:08 AM

kislinsk committed rMITK7f8aff5a2781: Implement optional slice extraction cache for lower and upper slices (authored by kislinsk).

Implement optional slice extraction cache for lower and upper slices

Jul 1 2021, 10:08 AM

kislinsk committed rMITK3efa9373b497: Use slice extraction cache for repeated 2d-interpolations (authored by kislinsk).

Use slice extraction cache for repeated 2d-interpolations

Jul 1 2021, 10:08 AM

kislinsk committed rMITKedebc008c3c9: Secure caches with mutexes for safe multithreading (authored by kislinsk).

Secure caches with mutexes for safe multithreading

Jul 1 2021, 10:08 AM

kislinsk committed rMITK4b229dc7cf62: Distribute slices for interpolation to multiple threads (authored by kislinsk).

Distribute slices for interpolation to multiple threads

Jul 1 2021, 10:08 AM

kislinsk committed rMITKda3a0c2eb252: Fix atomic initialization error (authored by kislinsk).

Fix atomic initialization error

Jul 1 2021, 10:08 AM

kislinsk committed rMITKe74273d042e5: Fix incomplete type error (authored by kislinsk).

Fix incomplete type error

Jul 1 2021, 10:08 AM

kislinsk committed rMITKcf9b6e2117dd: Fix unused variable (authored by kislinsk).

Fix unused variable

Jul 1 2021, 10:07 AM

kislinsk committed rMITK90a074d4c276: Fix review remarks (authored by kislinsk).

Fix review remarks

Jul 1 2021, 10:07 AM

kislinsk committed rMITKb43019736082: Speed up "Accept all slices" 2d-interpolations of segmentations (authored by kislinsk).

Speed up "Accept all slices" 2d-interpolations of segmentations

Jul 1 2021, 10:07 AM

Jun 30 2021

kislinsk added a comment to T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes.

On my 4 cores / 8 threads workstation, I get a speedup factor of nearly 10x (or 35x, if neglecting the whole do/undo stuff during measurement). This is for a 1024³ block, where only the first and last slices contain segmentations, so the whole image block need to get interpolated.

Jun 30 2021, 3:12 PM · MITK (v2023.12)

Jun 29 2021

kislinsk added a comment to T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes.

1024³ image block 2d-interpolation
==================================
Without optimizations      392.78s
Distance image cache        53.17s
-- Speedup factor ----------- 7.4x
Distance image cache +
Extract slice cache         47.22s
-- Speedup factor ----------- 8.3x

Jun 29 2021, 5:23 PM · MITK (v2023.12)

kislinsk added a comment to T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes.

Interpolation is not done in place to build a Do and Undo operation for the Undo/Redo-Stack. In the test case above this is another 30 seconds (more than half of the time with the first optimizations). While undo/redo is important, we should consider coming up with an heuristic, or option, or something similar to disable it for the interpolation of large images.

Jun 29 2021, 12:59 PM · MITK (v2023.12)

kislinsk updated subscribers of T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes.

Jun 29 2021, 12:45 PM · MITK (v2023.12)

kislinsk added a comment to T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes.

Without looking into parallelizing the interpolation yet, I was already able to algorithmically speed up the interpolation by 7-8 times.

Jun 29 2021, 12:45 PM · MITK (v2023.12)

kislinsk added a comment to T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes.

Pushed new branch to rMITK MITK: bugfix/T28491-SpeedUp2DInterpolationsOfLargeSegmentations.

Jun 29 2021, 12:42 PM · MITK (v2023.12)

Jun 28 2021

kislinsk closed T28591: Git rid of CMake 3.20 developer warnings regarding source files without explicit extensions as Resolved.

Jun 28 2021, 10:44 PM · MITK (v2021.10)

kislinsk committed rMITKc5ad8d309d25: Fix previous commit (authored by kislinsk).

Fix previous commit

Jun 28 2021, 10:44 PM

kislinsk added a comment to T28591: Git rid of CMake 3.20 developer warnings regarding source files without explicit extensions.

Deleted branch from rMITK MITK: bugfix/T28591-SourceFileExtensions.

Jun 28 2021, 10:44 PM · MITK (v2021.10)

kislinsk committed rMITKacdd14fb9592: Merge branch 'bugfix/T28591-SourceFileExtensions' into develop (authored by kislinsk).

Merge branch 'bugfix/T28591-SourceFileExtensions' into develop

Jun 28 2021, 10:44 PM

kislinsk reopened T28591: Git rid of CMake 3.20 developer warnings regarding source files without explicit extensions as "Open".

Jun 28 2021, 10:43 PM · MITK (v2021.10)

kislinsk added a comment to T28591: Git rid of CMake 3.20 developer warnings regarding source files without explicit extensions.

Pushed new branch to rMITK MITK: bugfix/T28591-SourceFileExtensions.

Jun 28 2021, 10:43 PM · MITK (v2021.10)

kislinsk closed T28591: Git rid of CMake 3.20 developer warnings regarding source files without explicit extensions as Resolved.

Jun 28 2021, 9:50 PM · MITK (v2021.10)

kislinsk committed rMITK7b12369b1c06: Use explicit extensions for source files (authored by kislinsk).

Use explicit extensions for source files

Jun 28 2021, 9:50 PM

kislinsk added a comment to T28591: Git rid of CMake 3.20 developer warnings regarding source files without explicit extensions.

Deleted branch from rMITK MITK: bugfix/T28591-SourceFileExtensions.

Jun 28 2021, 9:50 PM · MITK (v2021.10)

kislinsk committed rMITKe2953332cdd3: Merge branch 'bugfix/T28591-SourceFileExtensions' into develop (authored by kislinsk).

Merge branch 'bugfix/T28591-SourceFileExtensions' into develop

Jun 28 2021, 9:50 PM

kislinsk added a comment to T28591: Git rid of CMake 3.20 developer warnings regarding source files without explicit extensions.

Pushed new branch to rMITK MITK: bugfix/T28591-SourceFileExtensions.

Jun 28 2021, 9:49 PM · MITK (v2021.10)

kislinsk triaged T28591: Git rid of CMake 3.20 developer warnings regarding source files without explicit extensions as Low priority.

Jun 28 2021, 9:48 PM · MITK (v2021.10)

kislinsk added a revision to T27437: Migrate MITK to use ITK 5.x : Restricted Differential Revision.

Jun 28 2021, 2:18 PM · MITK-ProjectTemplate, MITK (v2022.04)

Jun 25 2021

kislinsk committed rMITKa08edb0eab0c: [Segmentation] Respect null labels but do not try to save properties for them (authored by kislinsk).

[Segmentation] Respect null labels but do not try to save properties for them

Jun 25 2021, 4:55 PM

kislinsk committed rMITKaa7862cc1bba: Respect null labels but do not try to save properties for them (authored by kislinsk).

Respect null labels but do not try to save properties for them

Jun 25 2021, 4:55 PM

Jun 15 2021

kislinsk closed T28358: Data Manager context menu items added multiple times for multi-selections as Invalid.

Wasn't able to reproduce it anymore, too.

Jun 15 2021, 12:27 PM · MITK (v2021.10)

kislinsk added a revision to T28455: RT struct 3D visibility is not working correctly: Unknown Object (Differential Revision).

Jun 15 2021, 9:52 AM · MITK (v2021.10)

kislinsk closed T28546: Fix macOS CI builds as Resolved.

I reported the cmakebuilder-plugin issue to Jenkins: https://issues.jenkins.io/browse/JENKINS-65893

Jun 15 2021, 9:49 AM · CI, MITK

kislinsk added a comment to T28546: Fix macOS CI builds.

Deleted branch from rMITK MITK: bugfix/T28546-macOSCatalina-Boost.

Jun 15 2021, 9:48 AM · CI, MITK

kislinsk committed rMITK5e7000af2207: Use default project-config.jam file on macOS (authored by kislinsk).

Use default project-config.jam file on macOS

Jun 15 2021, 9:12 AM

kislinsk committed rMITKb1c7fb9eda5f: Merge branch 'bugfix/T28546-macOSCatalina-Boost' into develop (authored by kislinsk).

Merge branch 'bugfix/T28546-macOSCatalina-Boost' into develop

Jun 15 2021, 9:12 AM

kislinsk added a comment to T28546: Fix macOS CI builds.

Pushed new branch to rMITK MITK: bugfix/T28546-macOSCatalina-Boost.

Jun 15 2021, 9:12 AM · CI, MITK

kislinsk reopened T28546: Fix macOS CI builds as "Open".

We also need to fix the Boost binary build on macOS.

Jun 15 2021, 9:05 AM · CI, MITK

Jun 11 2021

kislinsk closed T28546: Fix macOS CI builds as Resolved.

Jun 11 2021, 3:50 PM · CI, MITK

kislinsk added a comment to T28546: Fix macOS CI builds.

Deleted branch from rMITK MITK: bugfix/T28546-macOSCatalina.

Jun 11 2021, 3:49 PM · CI, MITK

kislinsk committed rMITK68699eab4fb3: Do not build SWIG and PCRE on macOS anymore (authored by kislinsk).

Do not build SWIG and PCRE on macOS anymore

Jun 11 2021, 3:48 PM

kislinsk committed rMITK9eb477901e8e: Fix regex for extraction of macOS codename (authored by kislinsk).

Fix regex for extraction of macOS codename

Jun 11 2021, 3:48 PM

kislinsk committed rMITKa0fecae44195: Merge branch 'bugfix/T28546-macOSCatalina' into develop (authored by kislinsk).

Merge branch 'bugfix/T28546-macOSCatalina' into develop

Jun 11 2021, 3:48 PM

kislinsk added a comment to T28546: Fix macOS CI builds.

Pushed new branch to rMITK MITK: bugfix/T28546-macOSCatalina.

Jun 11 2021, 3:48 PM · CI, MITK

kislinsk added a comment to T28546: Fix macOS CI builds.

For now I will disable SWIG (and PCRE) builds on macOS and require it to be provided (for example via Homebrew brew install swig).
I already renamed everything in Jenkins, Phabricator, and Git hooks
The macOS codename extraction can be easily fixed adding the backslash to the extraction regex

Jun 11 2021, 3:41 PM · CI, MITK

kislinsk triaged T28546: Fix macOS CI builds as Unbreak Now! priority.

Jun 11 2021, 3:37 PM · CI, MITK

Jun 4 2021

kislinsk added a comment to T26427: Support software rendering.

Without looking into it yet, I think the Nvidia solution for accelerated remote desktop is currently by far the most promising as it tackles the actual issue.

Jun 4 2021, 9:52 AM · Auto-closed, MITK

kislinsk merged T28514: [Multilabel Segmentation] Changing visibility of labels on higher layers does not trigger update into T28383: [Multilabel Segmentation] In case of two layers, a change of visibility is not updated automatically.

Jun 4 2021, 9:48 AM · Next Milestone, MITK

kislinsk merged task T28514: [Multilabel Segmentation] Changing visibility of labels on higher layers does not trigger update into T28383: [Multilabel Segmentation] In case of two layers, a change of visibility is not updated automatically.

Jun 4 2021, 9:48 AM · MITK

Jun 2 2021

kislinsk added a comment to T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes.

A few things that impact the handling of huge images:

Jun 2 2021, 12:48 PM · MITK (v2023.12)

kislinsk closed T28144: CorrectorTool does not properly handle unlocked lables of LabelSet Images as Resolved.

The tool was already removed from the last release because people tend to use the Add/Subtract tool for the same tasks anyway and we could reduce code/complexity.

Jun 2 2021, 11:52 AM · Request for Discussion, MITK (v2021.10)

kislinsk moved T28159: Officially support MITK using system Qt from MITK Meeting to Backlog on the Request for Discussion board.

Jun 2 2021, 11:42 AM · Auto-closed, CI, Request for Discussion, MITK

kislinsk moved T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes from Backlog to Cycle on the MITK (v2021.10) board.

Jun 2 2021, 10:51 AM · MITK (v2023.12)

kislinsk claimed T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes.

Jun 2 2021, 10:51 AM · MITK (v2023.12)

kislinsk added a comment to T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes.

And we seem to have a huge leak here. Even after deleting all the nodes again, half of my RAM is still in use.

Jun 2 2021, 10:40 AM · MITK (v2023.12)

kislinsk added a comment to T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes.

As it is an inexpensive operation my first guess would be an issue related to the amount of used memory. For example, the image above eats 3,5 GB, Activating the interpolation already triples it. Confirming adds at least another 3,5 GB. That could also explain why it is so slow (swapping). But at this point it is just a first assumption. On a 16 GB Windows machine I was able to complete the interpolation without crash but it took a while.

Jun 2 2021, 10:37 AM · MITK (v2023.12)

kislinsk updated subscribers of T28514: [Multilabel Segmentation] Changing visibility of labels on higher layers does not trigger update.

Maybe @thomass is still reading. :) I think she reported the same thing some weeks ago but I cannot find it. It's just a missing RequestRenderWindowUpdate().

Jun 2 2021, 9:03 AM · MITK

May 28 2021

kislinsk moved T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations from Backlog to Segmentation on the MITK (v2021.10) board.

May 28 2021, 11:10 AM · MITK (v2024.06), Missing Info

kislinsk triaged T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations as High priority.

May 28 2021, 11:10 AM · MITK (v2024.06), Missing Info

May 11 2021

kislinsk added a comment to T28204: Refactor LevelWindowManagerTest.

Hm, I cannot answer this without looking into this in detail but a first step could be to improve the AssertImageForLevelWindowProperty function or maybe even encapsule the CPPUNIT_ASSERT_MESSAGE calls in that function instead the other way around since the error message one does receive currently doesn't tell much about what actually failed since it could be any or all of the three checks.

May 11 2021, 10:51 AM · MITK (v2021.10)