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Fri, Jun 11

kislinsk closed T28546: Fix macOS CI builds as Resolved.
Fri, Jun 11, 3:50 PM · CI, MITK
kislinsk added a comment to T28546: Fix macOS CI builds.

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

Fri, Jun 11, 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
Fri, Jun 11, 3:48 PM
kislinsk committed rMITK9eb477901e8e: Fix regex for extraction of macOS codename (authored by kislinsk).
Fix regex for extraction of macOS codename
Fri, Jun 11, 3:48 PM
kislinsk committed rMITKa0fecae44195: Merge branch 'bugfix/T28546-macOSCatalina' into develop (authored by kislinsk).
Merge branch 'bugfix/T28546-macOSCatalina' into develop
Fri, Jun 11, 3:48 PM
kislinsk added a comment to T28546: Fix macOS CI builds.

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

Fri, Jun 11, 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
Fri, Jun 11, 3:41 PM · CI, MITK
kislinsk triaged T28546: Fix macOS CI builds as Unbreak Now! priority.
Fri, Jun 11, 3:37 PM · CI, MITK

Fri, Jun 4

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.

Fri, Jun 4, 9:52 AM · 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.
Fri, Jun 4, 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.
Fri, Jun 4, 9:48 AM · MITK

Wed, Jun 2

kislinsk added a comment to T28491: Slice interpolation 'confirm for all slices' not working for large images.

A few things that impact the handling of huge images:

Wed, Jun 2, 12:48 PM · MITK (v2021.10)
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.

Wed, Jun 2, 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.
Wed, Jun 2, 11:42 AM · CI, Kaapana (internal), Request for Discussion, MITK
kislinsk moved T28491: Slice interpolation 'confirm for all slices' not working for large images from Backlog to Cycle on the MITK (v2021.10) board.
Wed, Jun 2, 10:51 AM · MITK (v2021.10)
kislinsk claimed T28491: Slice interpolation 'confirm for all slices' not working for large images.
Wed, Jun 2, 10:51 AM · MITK (v2021.10)
kislinsk added a comment to T28491: Slice interpolation 'confirm for all slices' not working for large images.

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

Wed, Jun 2, 10:40 AM · MITK (v2021.10)
kislinsk added a comment to T28491: Slice interpolation 'confirm for all slices' not working for large images.

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.

Wed, Jun 2, 10:37 AM · MITK (v2021.10)
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().

Wed, Jun 2, 9:03 AM · MITK

Fri, May 28

kislinsk moved T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations from Backlog to Segmentation on the MITK (v2021.10) board.
Fri, May 28, 11:10 AM · MITK (v2021.10)
kislinsk triaged T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations as High priority.
Fri, May 28, 11:10 AM · MITK (v2021.10)

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)

Apr 30 2021

kislinsk closed T28473: 2021 Week 17 (Very Late April) as Resolved.
Apr 30 2021, 1:01 PM · MITK
kislinsk added a comment to T28473: 2021 Week 17 (Very Late April).

Deleted branch from rMITK MITK: release/T28473-2021-Week-17.

Apr 30 2021, 1:01 PM · MITK
kislinsk committed rMITKda43923045ff: Merge branch 'master' into develop (authored by kislinsk).
Merge branch 'master' into develop
Apr 30 2021, 1:00 PM
kislinsk committed rMITK72edfba9cc00: 2021 Week 17 (Very Late April) (authored by kislinsk).
2021 Week 17 (Very Late April)
Apr 30 2021, 1:00 PM
kislinsk edited the content of Changelog.
Apr 30 2021, 12:55 PM · MITK
kislinsk edited the content of 2021 Week 17 (Very Late April).
Apr 30 2021, 12:55 PM
kislinsk edited the content of 2021 Week 12 (Late March).
Apr 30 2021, 12:42 PM
kislinsk added a comment to T28473: 2021 Week 17 (Very Late April).

Pushed new branch to rMITK MITK: release/T28473-2021-Week-17.

Apr 30 2021, 12:40 PM · MITK
kislinsk triaged T28473: 2021 Week 17 (Very Late April) as Normal priority.
Apr 30 2021, 12:38 PM · MITK
kislinsk created an object: 2021 Week 17 (Very Late April).
Apr 30 2021, 12:37 PM
kislinsk committed rMITKf1783ce42601: Allow custom background values in Image Masking segmentation utility (authored by kislinsk).
Allow custom background values in Image Masking segmentation utility
Apr 30 2021, 12:25 PM
kislinsk closed T28439: [Segmentation] Support custom background/outside values in image masking as Resolved by committing rMITKf1783ce42601: Allow custom background values in Image Masking segmentation utility.
Apr 30 2021, 12:25 PM · MITK (v2021.10)
kislinsk committed rMITK2e6ddbbcb3d5: Ask user for permission before correcting their custom pixel value (authored by kislinsk).
Ask user for permission before correcting their custom pixel value
Apr 30 2021, 12:25 PM
kislinsk committed rMITK8301d14b11ef: Allow custom background values in Image Masking segmentation utility (authored by kislinsk).
Allow custom background values in Image Masking segmentation utility
Apr 30 2021, 12:25 PM
kislinsk committed rMITK95fca4c5cba6: Set correct image rendering mode when applying multilabel colormap (authored by kislinsk).
Set correct image rendering mode when applying multilabel colormap
Apr 30 2021, 10:44 AM
kislinsk closed T28421: Use whole image grey value must always be executed when switching colormap to 'Multilabel' as Resolved by committing rMITK4375f606e8ea: Set correct image rendering mode when applying multilabel colormap.
Apr 30 2021, 10:44 AM · MITK (v2021.10)
kislinsk closed T28422: Multilabel color map does not produce unique colors as Resolved by committing rMITK4375f606e8ea: Set correct image rendering mode when applying multilabel colormap.
Apr 30 2021, 10:44 AM · MITK (v2021.10)
kislinsk committed rMITK4375f606e8ea: Set correct image rendering mode when applying multilabel colormap (authored by kislinsk).
Set correct image rendering mode when applying multilabel colormap
Apr 30 2021, 10:44 AM

Apr 28 2021

kislinsk added a comment to T28118: Refactoring of SegTool2D.

@floca Please delete the feature branch mentioned above if this task is resolved.

Apr 28 2021, 1:53 PM · MITK (v2021.02)

Apr 26 2021

kislinsk edited the content of MITK v2021.02.
Apr 26 2021, 9:52 AM
kislinsk added a comment to T27437: Migrate MITK to use ITK 5.x .

Can this also be matched with this other task I created?

https://phabricator.mitk.org/T28454

I only need help in one place if that part is cleared then I already refactored the Core to reflect the changes suitable for version 3.6.0 of CppMicroServices.

Apr 26 2021, 9:18 AM · MITK (v2021.10)

Apr 21 2021

kislinsk added a comment to T27437: Migrate MITK to use ITK 5.x .

Is this task finished or if not when is it planned?

Apr 21 2021, 10:19 PM · MITK (v2021.10)
kislinsk added a comment to T27437: Migrate MITK to use ITK 5.x .

Pushed new branch to rMITK MITK: feature/T27437-ITK-v5.1.

Apr 21 2021, 10:16 PM · MITK (v2021.10)
kislinsk closed T28446: Migrate MatchPoint to ITK v5.1, a subtask of T27437: Migrate MITK to use ITK 5.x , as Resolved.
Apr 21 2021, 6:50 AM · MITK (v2021.10)
kislinsk closed T28446: Migrate MatchPoint to ITK v5.1 as Resolved.
Apr 21 2021, 6:50 AM · MatchPoint, MITK (v2021.10)

Apr 20 2021

kislinsk committed rMP3e771a0f9115: Replace more itk::ImageIOBase enums with itk::IO...Enum enums (authored by kislinsk).
Replace more itk::ImageIOBase enums with itk::IO...Enum enums
Apr 20 2021, 7:30 AM
kislinsk committed rMPf7699d1ec6c8: Migrate TransformCategoryType to TransformCategoryEnum (authored by kislinsk).
Migrate TransformCategoryType to TransformCategoryEnum
Apr 20 2021, 7:30 AM

Apr 14 2021

kislinsk reassigned T28446: Migrate MatchPoint to ITK v5.1 from kislinsk to floca.

https://phabricator.mitk.org/source/matchpoint/history/T28446-MigrateToITKv5.1/

Apr 14 2021, 2:31 PM · MatchPoint, MITK (v2021.10)
kislinsk committed rMPe001b8fbc029: Do more mutex fixes (authored by kislinsk).
Do more mutex fixes
Apr 14 2021, 2:30 PM
kislinsk committed rMP7da4216a857d: MappingTaskBatch needs a more thorough migration (authored by kislinsk).
MappingTaskBatch needs a more thorough migration
Apr 14 2021, 2:30 PM
kislinsk committed rMP110d8364c3b5: Fix more NULL smart pointer initializations (authored by kislinsk).
Fix more NULL smart pointer initializations
Apr 14 2021, 2:30 PM
kislinsk committed rMP15b61e51f6ae: Do more enum replacements (authored by kislinsk).
Do more enum replacements
Apr 14 2021, 2:30 PM
kislinsk committed rMP6ecafd4d4b7a: Adapt threading-related API to ITK v5 (authored by kislinsk).
Adapt threading-related API to ITK v5
Apr 14 2021, 2:30 PM
kislinsk committed rMPad4619bd536d: [DOUBLE-CHECK THIS COMMIT] Migrate spatial objects (authored by kislinsk).
[DOUBLE-CHECK THIS COMMIT] Migrate spatial objects
Apr 14 2021, 2:30 PM
kislinsk committed rMP255e513cf781: Replace unsigned long return type of GetMTime() with itk::ModifiedTimeType (authored by kislinsk).
Replace unsigned long return type of GetMTime() with itk::ModifiedTimeType
Apr 14 2021, 2:30 PM
kislinsk committed rMP38d25ea84a08: Replace itksys::String with std::string (authored by kislinsk).
Replace itksys::String with std::string
Apr 14 2021, 2:30 PM
kislinsk committed rMP0837e06d97ff: Replace vcl_ math functions with std:: math functions (authored by kislinsk).
Replace vcl_ math functions with std:: math functions
Apr 14 2021, 2:30 PM
kislinsk committed rMP1a3628a9c04b: Replace ITK smart pointer NULL initialization with (implicit) nullptr… (authored by kislinsk).
Replace ITK smart pointer NULL initialization with (implicit) nullptr…
Apr 14 2021, 2:30 PM
kislinsk committed rMPc733cb3de98f: Replace itk::ImageIOBase enums with itk::IO...Enum enums (authored by kislinsk).
Replace itk::ImageIOBase enums with itk::IO...Enum enums
Apr 14 2021, 2:30 PM
kislinsk committed rMPeb6be9df7d3f: Replace itk::LoggerBase::PriorityLevelType with itk::LoggerBaseEnums… (authored by kislinsk).
Replace itk::LoggerBase::PriorityLevelType with itk::LoggerBaseEnums…
Apr 14 2021, 2:30 PM
kislinsk committed rMP9168cd710920: Replace ITK mutexes with std mutexes (authored by kislinsk).
Replace ITK mutexes with std mutexes
Apr 14 2021, 2:30 PM
kislinsk added a member for MatchPoint: kislinsk.
Apr 14 2021, 2:30 PM
kislinsk triaged T28446: Migrate MatchPoint to ITK v5.1 as High priority.
Apr 14 2021, 9:56 AM · MatchPoint, MITK (v2021.10)
kislinsk claimed T27437: Migrate MITK to use ITK 5.x .
Apr 14 2021, 9:19 AM · MITK (v2021.10)

Apr 12 2021

kislinsk raised the priority of T27437: Migrate MITK to use ITK 5.x from Normal to High.
Apr 12 2021, 10:55 AM · MITK (v2021.10)
kislinsk edited projects for T27437: Migrate MITK to use ITK 5.x , added: MITK (v2021.10); removed MITK.
Apr 12 2021, 10:54 AM · MITK (v2021.10)

Apr 8 2021

kislinsk added a revision to T28439: [Segmentation] Support custom background/outside values in image masking: Unknown Object (Differential Revision).
Apr 8 2021, 7:19 PM · MITK (v2021.10)
kislinsk triaged T28439: [Segmentation] Support custom background/outside values in image masking as Normal priority.
Apr 8 2021, 7:10 PM · MITK (v2021.10)
kislinsk raised the priority of T28264: [Segmentation Utilities] Various issues from Normal to High.
Apr 8 2021, 7:08 PM · MITK (v2021.10)
kislinsk triaged T28437: 3D region growing may have issues when the seed point is on a pixel with value 0 as High priority.
Apr 8 2021, 9:44 AM · MITK (v2021.10)
kislinsk added a comment to T28422: Multilabel color map does not produce unique colors.

Will be fixed with D480.

Apr 8 2021, 8:03 AM · MITK (v2021.10)
kislinsk added a revision to T28422: Multilabel color map does not produce unique colors: Unknown Object (Differential Revision).
Apr 8 2021, 8:03 AM · MITK (v2021.10)
kislinsk added a comment to T28421: Use whole image grey value must always be executed when switching colormap to 'Multilabel'.

Hm, while D480 resolves the issue, I think that the original approach for handling the Multilabel colormap in T23589 is already a workaround. Changing the level window to the maximum possible range is just an emulation of "do not use the level window". We actually have that mode in MITK already. The Image Rendering.Mode property is usually set to LOOKUPTABLE_LEVELWINDOW_COLOR but there is also LOOKUPTABLE_COLOR which is exactly what we need here. The thing is, that LOOKUPTABLE_COLOR is not implemented correctly in the 2-d image mapper, as the level window filter is not reset and instead is using the previously set range. So I will extent D480 to actually use the correct mode and fix the 2-d image mapper.

Apr 8 2021, 7:27 AM · MITK (v2021.10)
kislinsk added a comment to T28422: Multilabel color map does not produce unique colors.

If the image is converted to a segmentation (context menu -> Convert to segmentation), it is rendered correctly even though the very same lookup table is used. So I guess the issue is to be found within the 2d image mapper.

Apr 8 2021, 6:25 AM · MITK (v2021.10)
kislinsk added a comment to T28422: Multilabel color map does not produce unique colors.

The lookup table is set correctly but the rendered colors do not match.

Apr 8 2021, 6:16 AM · MITK (v2021.10)
kislinsk claimed T28422: Multilabel color map does not produce unique colors.

This really shouldn't happen. A first look at the code revealed that the intention is to have at least 25 different colors for values 1-26 and after that repeatedly cycle through 12 colors.

Apr 8 2021, 5:32 AM · MITK (v2021.10)
kislinsk added a revision to T28421: Use whole image grey value must always be executed when switching colormap to 'Multilabel': Unknown Object (Differential Revision).
Apr 8 2021, 5:27 AM · MITK (v2021.10)
kislinsk added a comment to T28421: Use whole image grey value must always be executed when switching colormap to 'Multilabel'.

Found the issue. After setting the colormap to "Multilabel" in QmitkDataNodeColorMapAction::OnActionTriggered, the previous LUT is checked if it is a "Multilabel" LUT, instead of the new LUT. Hence the observation above that it works when applying it twice.

Apr 8 2021, 5:20 AM · MITK (v2021.10)
kislinsk claimed T28421: Use whole image grey value must always be executed when switching colormap to 'Multilabel'.

This issue was already resolved by @kalali in T23589: Multilabel Segmentations not loaded with multilabel colormap, resp. {D172} for MITK v2018.04.2 but I can confirm that the issue exists for the example image.

Apr 8 2021, 5:12 AM · MITK (v2021.10)

Apr 7 2021

kislinsk edited projects for T28039: DICOM Seg loading error, added: MITK (v2021.10); removed Next Milestone, MITK, Missing Info, Request for Discussion.
Apr 7 2021, 9:14 AM · MITK (v2021.10)
kislinsk edited projects for T24398: Dicom plugin: Retrieve does not work, added: MITK (v2021.10); removed Next Milestone, MITK.
Apr 7 2021, 9:12 AM · MITK (v2021.10)

Apr 6 2021

kislinsk edited projects for T27432: Error loading DCE-MRI DICOM image, added: MITK (v2021.10); removed MITK, Next Milestone.
Apr 6 2021, 4:29 PM · MITK (v2021.10), DICOM, Cleared
kislinsk closed T28263: [2-d surface mapper] Surface is drawn in every time step even if it has limited time bounds as Resolved.
Apr 6 2021, 4:28 PM · MITK (v2021.02)
kislinsk added a comment to T27413: MITK 2020 Workflow Q&A.

We now have some manuals but we still need an example-based guide for reviews/Arcanist.

Apr 6 2021, 4:24 PM · MITK (v2021.10)
kislinsk updated the task description for T27413: MITK 2020 Workflow Q&A.
Apr 6 2021, 4:23 PM · MITK (v2021.10)
kislinsk edited projects for T27701: Overhaul or remove PluginGenerator, added: MITK (v2021.10); removed MITK, Next Milestone.
Apr 6 2021, 4:21 PM · MITK (v2021.10)
kislinsk lowered the priority of T27578: 2021.1 Linux installer does not work on Fedora from Unbreak Now! to High.
Apr 6 2021, 4:21 PM · MITK (v2021.10)
kislinsk edited projects for T28172: Include MITK-ProjectTemplate in MITK Differential builds, added: MITK (v2021.10); removed Next Milestone, MITK.
Apr 6 2021, 4:12 PM · MITK (v2021.10), CI
kislinsk edited projects for T28422: Multilabel color map does not produce unique colors, added: MITK (v2021.10); removed MITK.
Apr 6 2021, 4:12 PM · MITK (v2021.10)
kislinsk edited projects for T28421: Use whole image grey value must always be executed when switching colormap to 'Multilabel', added: MITK (v2021.10); removed MITK.
Apr 6 2021, 4:11 PM · MITK (v2021.10)
kislinsk added a hashtag to MITK (v2021.10): #mitk-2021-10.
Apr 6 2021, 4:11 PM
kislinsk triaged T28421: Use whole image grey value must always be executed when switching colormap to 'Multilabel' as High priority.
Apr 6 2021, 12:48 AM · MITK (v2021.10)
kislinsk triaged T28422: Multilabel color map does not produce unique colors as High priority.
Apr 6 2021, 12:46 AM · MITK (v2021.10)
kislinsk created MITK (v2021.10).
Apr 6 2021, 12:41 AM
kislinsk triaged T28428: Re-enable code coverage testing in MITK CI as Normal priority.
Apr 6 2021, 12:40 AM · CI, MITK

Mar 27 2021

kislinsk closed T26969: [Segmentation] New segmentation dialog: Change color twice and aborting the second time chages color to red, a subtask of T28176: [Segmentation] Inspection of module and plugin, as Resolved.
Mar 27 2021, 4:48 PM · MITK (v2021.10)
kislinsk closed T26969: [Segmentation] New segmentation dialog: Change color twice and aborting the second time chages color to red as Resolved.
Mar 27 2021, 4:48 PM · MITK
kislinsk closed T28383: [Multilabel Segmentation] In case of two layers, a change of visibility is not updated automatically as Resolved.
Mar 27 2021, 4:47 PM · Next Milestone, MITK