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Mar 29 2021

isensee updated the task description for T28422: Multilabel color map does not produce unique colors.
Mar 29 2021, 1:20 PM · MITK (v2021.10)
isensee updated the task description for T28421: Use whole image grey value must always be executed when switching colormap to 'Multilabel'.
Mar 29 2021, 1:20 PM · MITK (v2021.10)
isensee updated the task description for T28422: Multilabel color map does not produce unique colors.
Mar 29 2021, 1:17 PM · MITK (v2021.10)
isensee created T28422: Multilabel color map does not produce unique colors.
Mar 29 2021, 1:17 PM · MITK (v2021.10)
isensee renamed T28421: Use whole image grey value must always be executed when switching colormap to 'Multilabel' from Use whole image grey value must always be executed when switching colormap to to Use whole image grey value must always be executed when switching colormap to 'Multilabel'.
Mar 29 2021, 1:07 PM · MITK (v2021.10)
isensee created T28421: Use whole image grey value must always be executed when switching colormap to 'Multilabel'.
Mar 29 2021, 12:59 PM · MITK (v2021.10)

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 (v2024.06)
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

Mar 26 2021

kislinsk closed T28420: 2021 Week 12 (Late March) as Resolved.
Mar 26 2021, 4:44 PM · MITK
kislinsk edited the content of Changelog.
Mar 26 2021, 4:43 PM · MITK
kislinsk added a comment to T28420: 2021 Week 12 (Late March).

Deleted branch from rMITK MITK: release/T28420-2021-Week-12.

Mar 26 2021, 4:40 PM · MITK
kislinsk committed rMITK9ccbc4d1310b: Merge branch 'master' into develop (authored by kislinsk).
Merge branch 'master' into develop
Mar 26 2021, 4:40 PM
kislinsk committed rMITK4bf9b4da41b5: Make build system aware of a new patch for ITK (authored by kislinsk).
Make build system aware of a new patch for ITK
Mar 26 2021, 4:39 PM
kislinsk committed rMITK3447b0ecffd5: Multilabel segmentation label visibility (authored by thomass).
Multilabel segmentation label visibility
Mar 26 2021, 4:39 PM
kislinsk committed rMITK0a6dee813c1e: Merge remote-tracking branch 'origin/develop' into release/T28420-2021-Week-12 (authored by kislinsk).
Merge remote-tracking branch 'origin/develop' into release/T28420-2021-Week-12
Mar 26 2021, 4:39 PM
kislinsk committed rMITKd77d800c1ace: Merge branch 'arcpatch-D477' into release/T28420-2021-Week-12 (authored by kislinsk).
Merge branch 'arcpatch-D477' into release/T28420-2021-Week-12
Mar 26 2021, 4:39 PM
kislinsk committed rMITKaadc05393e01: 2021 Week 12 (Late March) (authored by kislinsk).
2021 Week 12 (Late March)
Mar 26 2021, 4:39 PM
kislinsk edited the content of 2021 Week 12 (Late March).
Mar 26 2021, 4:34 PM
kislinsk edited the content of MITK v2021.02.
Mar 26 2021, 3:54 PM
kislinsk added a comment to T28420: 2021 Week 12 (Late March).

Pushed new branch to rMITK MITK: release/T28420-2021-Week-12.

Mar 26 2021, 3:09 PM · MITK
kislinsk triaged T28420: 2021 Week 12 (Late March) as Normal priority.
Mar 26 2021, 3:08 PM · MITK
kislinsk created an object: 2021 Week 12 (Late March).
Mar 26 2021, 3:07 PM
floca committed rMITK165ad5f01412: T28356 Make_use_of_coordinate_precision_check (authored by floca).
T28356 Make_use_of_coordinate_precision_check
Mar 26 2021, 12:41 PM
floca committed rMITK453b6b57f01c: Fixe review remarks (typos) (authored by floca).
Fixe review remarks (typos)
Mar 26 2021, 12:41 PM
floca closed T28356: MITK v2021.02 does not recognize loaded mask as segmentation as Resolved by committing rMITKc2c4e9649bfc: BREAKING!!!.
Mar 26 2021, 12:41 PM · Next Milestone, MITK
floca committed rMITKc2c4e9649bfc: BREAKING!!! (authored by floca).
BREAKING!!!
Mar 26 2021, 12:41 PM
kislinsk added a comment to T28413: MITK (resp. OpenJPEG in ITK) doesn't build with Visual Studio 16.9 2019 (Release configuration).

Deleted branch from rMITK MITK: bugfix/T28413-PatchOpenJPEGInITKForMSVC16.9.

Mar 26 2021, 12:41 PM · MITK
kislinsk committed rMITK9e9737797b79: Patch ITK/OpenJPEG to work with MSVC 16.9 (authored by kislinsk).
Patch ITK/OpenJPEG to work with MSVC 16.9
Mar 26 2021, 12:40 PM
kislinsk closed T28413: MITK (resp. OpenJPEG in ITK) doesn't build with Visual Studio 16.9 2019 (Release configuration) as Resolved by committing rMITK2f8b1fac95e7: Patch ITK/OpenJPEG to work with MSVC 16.9.
Mar 26 2021, 12:40 PM · MITK
kislinsk committed rMITK2f8b1fac95e7: Patch ITK/OpenJPEG to work with MSVC 16.9 (authored by kislinsk).
Patch ITK/OpenJPEG to work with MSVC 16.9
Mar 26 2021, 12:40 PM
isensee created T28419: better rounding and cleaner overview table.
Mar 26 2021, 11:53 AM · LSF GPU Cluster Monitoring
kislinsk added a revision to T28413: MITK (resp. OpenJPEG in ITK) doesn't build with Visual Studio 16.9 2019 (Release configuration): Unknown Object (Differential Revision).
Mar 26 2021, 5:08 AM · MITK
kislinsk added a comment to T28413: MITK (resp. OpenJPEG in ITK) doesn't build with Visual Studio 16.9 2019 (Release configuration).

Pushed new branch to rMITK MITK: bugfix/T28413-PatchOpenJPEGInITKForMSVC16.9.

Mar 26 2021, 5:02 AM · MITK
kislinsk triaged T28413: MITK (resp. OpenJPEG in ITK) doesn't build with Visual Studio 16.9 2019 (Release configuration) as High priority.
Mar 26 2021, 4:59 AM · MITK

Mar 25 2021

floca renamed T28410: MPISolverWrapper's direct call of blackbox internal seems wrong from MPISolverWrapperdirect call of blackbox internal seems wrong to MPISolverWrapper's direct call of blackbox internal seems wrong.
Mar 25 2021, 11:14 PM · Hyppopy
floca triaged T28411: Blackbox callback function is never use as Normal priority.
Mar 25 2021, 11:14 PM
floca triaged T28410: MPISolverWrapper's direct call of blackbox internal seems wrong as High priority.
Mar 25 2021, 11:04 PM · Hyppopy
s669m added a comment to T28387: Testing Gvisor with Kube8s.
ubuntu@gvisor-san:~$ minikube start --container-runtime=containerd      --docker-opt containerd=/var/run/containerd/containerd.sock
😄  minikube v1.18.1 on Ubuntu 18.04 (amd64)
✨  Using the docker driver based on existing profile
👍  Starting control plane node minikube in cluster minikube
🏃  Updating the running docker "minikube" container ...
🌐  Found network options:
    ▪ NO_PROXY=localhost,127.0.0.1,169.254.169.254,dkfz-heidelberg.de,192.168.49.2,10.96.0.0/12,192.168.99.0/24,192.168.39.0/24
    ▪ http_proxy=http://www-int2.dkfz-heidelberg.de:80
    ▪ https_proxy=http://www-int2.dkfz-heidelberg.de:80
    ▪ no_proxy=localhost,127.0.0.1,169.254.169.254,dkfz-heidelberg.de,192.168.49.2,10.96.0.0/12,192.168.99.0/24,192.168.39.0/24
❗  This container is having trouble accessing https://k8s.gcr.io
Mar 25 2021, 1:37 PM · Restricted Project
thomass added a parent task for T28383: [Multilabel Segmentation] In case of two layers, a change of visibility is not updated automatically: Unknown Object (Maniphest Task).
Mar 25 2021, 12:31 PM · Next Milestone, MITK
thomass added a parent task for T28406: [Segmentation] Examine Live-wire tool for different costfunctions/behavior: Unknown Object (Maniphest Task).
Mar 25 2021, 12:30 PM · MITK
thomass triaged T28406: [Segmentation] Examine Live-wire tool for different costfunctions/behavior as Wishlist priority.
Mar 25 2021, 12:29 PM · MITK
k656s moved T28049: DataUpload fails with Firefox from Resolved to Discussion on the Kaapana (internal) board.

Checked again, no idea how to fix it. The Browser seems to remove the mime type of the object... so either i remove the file check completely or we find a way of how the browser can be enabled to deal with mime types:

Mar 25 2021, 12:04 PM · Kaapana (internal)
floca added a project to T28232: Shapemodels: Kaapana (internal).

Is this ticket then realy priority "wishlist"? (Stefan put it there because it was not triaged at all) A solution (what ever it maybe) seems to be more relevant to Kaapana then just wishlist.

Mar 25 2021, 10:16 AM · Auto-closed, Kaapana (internal), Request for Discussion, MITK
s669m moved T28402: gvisor pods are crashing (CrashLoopBackOff) from Discussion to In Progress on the Kaapana (internal) board.
Mar 25 2021, 10:16 AM · Request for Discussion, Kaapana (internal)
s669m added a comment to T28402: gvisor pods are crashing (CrashLoopBackOff).

Discussion from Tech meeting (Hanno, Klaus, Marco)

Mar 25 2021, 10:16 AM · Request for Discussion, Kaapana (internal)
nolden added a comment to T28232: Shapemodels.

The topic came up in the Kaapana tech meeting again, because the current situation is causing problems there.

Mar 25 2021, 10:01 AM · Auto-closed, Kaapana (internal), Request for Discussion, MITK
s669m triaged T28402: gvisor pods are crashing (CrashLoopBackOff) as Normal priority.
Mar 25 2021, 9:21 AM · Request for Discussion, Kaapana (internal)

Mar 24 2021

k656s reopened T28049: DataUpload fails with Firefox as "Open".

I was able to reproduce the error. I will take a look

Mar 24 2021, 9:23 PM · Kaapana (internal)

Mar 23 2021

floca closed T28388: mitk::PropertyPersistenceDeserialization::deserializeXMLToScalarListLookupTableProperty does not work correctly with empty strings as Resolved.
Mar 23 2021, 5:29 PM · MITK
floca committed rMITK70ef2b890652: T28388 deserializeXMLToScalarListLookupTableProperty_does_not_work_correctly_wi… (authored by floca).
T28388 deserializeXMLToScalarListLookupTableProperty_does_not_work_correctly_wi…
Mar 23 2021, 5:29 PM
floca committed rMITKfa62e395070e: fixed review remarks (authored by floca).
fixed review remarks
Mar 23 2021, 5:28 PM
floca committed rMITK274f278f5725: Fixed behavior of serialization function (authored by floca).
Fixed behavior of serialization function
Mar 23 2021, 5:28 PM
isensee added a member for Deep Learning: s522r.
Mar 23 2021, 2:51 PM
isensee added a member for MIC: s522r.
Mar 23 2021, 2:51 PM
isensee moved T28396: scale the GPU memory graph to [0, GPU_MAX_MEMORY] instead of [0, max_used_memory * 1.05] from Backlog to Open on the LSF GPU Cluster Monitoring board.
Mar 23 2021, 2:15 PM · LSF GPU Cluster Monitoring
isensee moved T28397: display horizontal line in GPU memory plot to show requested GPU memory from Backlog to Open on the LSF GPU Cluster Monitoring board.
Mar 23 2021, 2:15 PM · LSF GPU Cluster Monitoring
isensee moved T28398: somehow use the run time reported by lsf instead of my own from Backlog to Open on the LSF GPU Cluster Monitoring board.
Mar 23 2021, 2:15 PM · LSF GPU Cluster Monitoring
isensee claimed T28398: somehow use the run time reported by lsf instead of my own.
Mar 23 2021, 2:14 PM · LSF GPU Cluster Monitoring
isensee created T28398: somehow use the run time reported by lsf instead of my own.
Mar 23 2021, 2:14 PM · LSF GPU Cluster Monitoring
isensee claimed T28397: display horizontal line in GPU memory plot to show requested GPU memory.
Mar 23 2021, 2:12 PM · LSF GPU Cluster Monitoring
isensee created T28397: display horizontal line in GPU memory plot to show requested GPU memory.
Mar 23 2021, 2:12 PM · LSF GPU Cluster Monitoring
isensee renamed T28396: scale the GPU memory graph to [0, GPU_MAX_MEMORY] instead of [0, max_used_memory * 1.05] from Todo Fabian: scale the GPU memory graph to [0, GPU_MAX_MEMORY] instead of [0, max_used_memory * 1.05] to scale the GPU memory graph to [0, GPU_MAX_MEMORY] instead of [0, max_used_memory * 1.05].
Mar 23 2021, 2:12 PM · LSF GPU Cluster Monitoring
isensee created T28396: scale the GPU memory graph to [0, GPU_MAX_MEMORY] instead of [0, max_used_memory * 1.05].
Mar 23 2021, 2:11 PM · LSF GPU Cluster Monitoring
kislinsk added a member for MITK-MBI: kahl.
Mar 23 2021, 10:30 AM

Mar 22 2021

gaoh placed T27968: CTP gets stuck on large import up for grabs.

after tests of the system, the problem might be at the airflow part, this has to be tested

Mar 22 2021, 2:53 PM · Kaapana (internal)

Mar 20 2021

floca added a comment to T28356: MITK v2021.02 does not recognize loaded mask as segmentation.

@j038k Hi I you look for the problem, keep in mind that the rounding error can occure when it serialized into the file (if it is in text mode). E.g. some code that saves nrrd only does it with standard precission which is in some cases 8 characters (including the dot, sign etc. this can then be not enough and you loose decimal places).

Mar 20 2021, 12:03 PM · Next Milestone, MITK
j038k added a comment to T28356: MITK v2021.02 does not recognize loaded mask as segmentation.

@floca André is on vacation. The original mask in nifty was produced by nnUNet, but we are using some of our Python scripts to split segmented tissues to different labels and to convert it into .nrrd format. Maybe there could be a rounding error during loading and saving the image header, we have to look at it.

Mar 20 2021, 9:43 AM · Next Milestone, MITK

Mar 19 2021

floca added a comment to T28356: MITK v2021.02 does not recognize loaded mask as segmentation.

@kleina Even though the problem is now fix by being less pedantic, I realy would identify the reason for the fidelty loss in the mask geometry. So the information which tool produced the mask is still welcome. Especially if it one of our tools/nets so that we can fix it.

Mar 19 2021, 10:14 PM · Next Milestone, MITK
thomass triaged T28389: [Multilabelsegmentation] Locking all labels can only be reversed by unlock all as Normal priority.
Mar 19 2021, 11:08 AM · Auto-closed, MITK
thomass claimed T28383: [Multilabel Segmentation] In case of two layers, a change of visibility is not updated automatically.
Mar 19 2021, 10:36 AM · Next Milestone, MITK

Mar 18 2021

floca added a revision to T28388: mitk::PropertyPersistenceDeserialization::deserializeXMLToScalarListLookupTableProperty does not work correctly with empty strings: Unknown Object (Differential Revision).
Mar 18 2021, 8:41 PM · MITK
floca added a revision to T28356: MITK v2021.02 does not recognize loaded mask as segmentation: Unknown Object (Differential Revision).
Mar 18 2021, 8:41 PM · Next Milestone, MITK
floca triaged T28388: mitk::PropertyPersistenceDeserialization::deserializeXMLToScalarListLookupTableProperty does not work correctly with empty strings as Normal priority.
Mar 18 2021, 6:54 PM · MITK
floca added a comment to T28356: MITK v2021.02 does not recognize loaded mask as segmentation.

@kleina Do they use multi label segmentation view or the old one?

Mar 18 2021, 6:37 PM · Next Milestone, MITK
s669m created T28387: Testing Gvisor with Kube8s.
Mar 18 2021, 4:40 PM · Restricted Project
s669m updated the task description for T28382: Testing Kata and Gvisor on Local .
Mar 18 2021, 4:40 PM · Restricted Project
thomass added a comment to T28385: [Segmentation] Erosion crashes the MITK Workbench after interpolation.

On a first glance, the interpolation seems to affect the result.

  1. Create the segmentation with interpolation -> save it -> reload segmentation -> erosion = no crash
  2. Create the segmentation with interpolation -> erosion = crash
Mar 18 2021, 2:24 PM · Cleared, MITK (v2021.10)
thomass triaged T28385: [Segmentation] Erosion crashes the MITK Workbench after interpolation as High priority.
Mar 18 2021, 2:15 PM · Cleared, MITK (v2021.10)
k656s added a member for NLP: s460g.
Mar 18 2021, 12:54 PM
s669m moved T28357: Running Isolated container in Kaapana ( Instead of Default Docker) from Discussion to In Progress on the Kaapana (internal) board.
Mar 18 2021, 10:13 AM · Restricted Project, Kaapana (internal)
s669m added a comment to T28357: Running Isolated container in Kaapana ( Instead of Default Docker).

check with microk8s - kata microk8s current system

Mar 18 2021, 10:13 AM · Restricted Project, Kaapana (internal)
s669m added a project to T28357: Running Isolated container in Kaapana ( Instead of Default Docker): Restricted Project.
Mar 18 2021, 9:42 AM · Restricted Project, Kaapana (internal)
thomass added a comment to T28383: [Multilabel Segmentation] In case of two layers, a change of visibility is not updated automatically.

The issue can indeed be solved by a mitk::RenderingManager::GetInstance()->RequestUpdateAll(); in QmitkLabelsetWidget function OnVisibleButtonClicked() but there seems to be something wrong with the lock logic when "Lock All" "Unlock All" is clicked

Mar 18 2021, 8:53 AM · Next Milestone, MITK

Mar 17 2021

s669m added a comment to T28382: Testing Kata and Gvisor on Local .

Kata-supported platforms are given below.

Mar 17 2021, 2:09 PM · Restricted Project
thomass added a project to T28383: [Multilabel Segmentation] In case of two layers, a change of visibility is not updated automatically: Next Milestone.
Mar 17 2021, 1:39 PM · Next Milestone, MITK
thomass triaged T28383: [Multilabel Segmentation] In case of two layers, a change of visibility is not updated automatically as Normal priority.
Mar 17 2021, 1:38 PM · Next Milestone, MITK
s669m triaged T28382: Testing Kata and Gvisor on Local as High priority.
Mar 17 2021, 12:02 PM · Restricted Project
s669m created T28382: Testing Kata and Gvisor on Local .
Mar 17 2021, 12:01 PM · Restricted Project
kislinsk triaged T28380: [MultLabel Segmentation, MITK FlowBench] Segmentation not recognized as segmentation in Release v2021.02 as Normal priority.
Mar 17 2021, 9:16 AM · MITK
kislinsk updated subscribers of T28380: [MultLabel Segmentation, MITK FlowBench] Segmentation not recognized as segmentation in Release v2021.02.

Yes, as soon as there is a new tag that includes your necessary changes, just change the tag and click on build.

Mar 17 2021, 9:08 AM · MITK

Mar 16 2021

gaoh updated the task description for T28380: [MultLabel Segmentation, MITK FlowBench] Segmentation not recognized as segmentation in Release v2021.02.
Mar 16 2021, 10:52 AM · MITK
gaoh created T28380: [MultLabel Segmentation, MITK FlowBench] Segmentation not recognized as segmentation in Release v2021.02.
Mar 16 2021, 10:51 AM · MITK
floca committed rMITK608a3021ae44: T28225 Fix SegTool2D WritePreviewOnWorkingImage to work correctly with any label (authored by floca).
T28225 Fix SegTool2D WritePreviewOnWorkingImage to work correctly with any label
Mar 16 2021, 8:48 AM
floca committed rMITKb6864e69493a: Fixed review feedback. (authored by floca).
Fixed review feedback.
Mar 16 2021, 8:48 AM
floca closed T28225: [Segmentation] SegTool2D::WritePreviewOnWorkingImage does not work correctly as Resolved by committing rMITK30991329cccd: BREAKING ContourModelUtils::FillSliceInSlice.
Mar 16 2021, 8:48 AM · MITK
floca committed rMITK30991329cccd: BREAKING ContourModelUtils::FillSliceInSlice (authored by floca).
BREAKING ContourModelUtils::FillSliceInSlice
Mar 16 2021, 8:48 AM

Mar 15 2021

floca raised the priority of T26805: Make the MPI master work as well from Wishlist to Low.
Mar 15 2021, 11:38 PM · Hyppopy
floca changed the visibility for T26805: Make the MPI master work as well.
Mar 15 2021, 11:36 PM · Hyppopy
floca closed T28333: Allow auto wrapping of blackbox for MPI as Resolved.
Mar 15 2021, 11:33 PM · Hyppopy