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.

Create the segmentation with interpolation -> save it -> reload segmentation -> erosion = no crash
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

floca edited parent tasks for T25496: Visualize RTDOSE correctly, added: Unknown Object (Maniphest Task); removed: Unknown Object (Maniphest Task).

Mar 15 2021, 11:19 PM · MITK

floca added a parent task for T25496: Visualize RTDOSE correctly: Unknown Object (Maniphest Task).

Mar 15 2021, 11:18 PM · MITK

floca merged Restricted Maniphest Task into T25496: Visualize RTDOSE correctly.

Mar 15 2021, 11:17 PM · MITK

a178n added a comment to T28354: Update MITK documentation on CMAKE build for plugins.

I want to use a plugin, how do I activate it?

Mar 15 2021, 4:55 PM · Next Milestone, MITK (v2021.10)

nolden added a comment to T27968: CTP gets stuck on large import.

Not sure if this is related:

Mar 15 2021, 1:47 PM · Kaapana (internal)

nolden removed a project from T28374: Workbench crashes after DICOM retrieval : Missing Info.

Mar 15 2021, 9:52 AM · Next Milestone, DICOM, MITK

nolden closed T28374: Workbench crashes after DICOM retrieval as Resolved.

@gaoh thanks for pointing there, I will close this one as a duplicate

Mar 15 2021, 9:51 AM · Next Milestone, DICOM, MITK

nolden added a comment to T28207: MITK DicomBrowser q/r Retrieve part crash.

Another option for testing is to use dicomserver.co.uk , I think it is preconfigured in the Workbench. It's a public DICOM endpoint and the data there differs, but 5 min ago I was able to reproduce the crash with a retrieval from there. Just activate the checkbox in the MITK config table , query last month, select a few patients and retrieve. Worked for me to reproduce the crash.

Mar 15 2021, 9:50 AM · MITK, Checklist

gaoh added a comment to T28374: Workbench crashes after DICOM retrieval .

T28207 describes how to test it without the wDB. When searching for DICOM query retrieve there are already different tasks open with all similar problems

Mar 15 2021, 9:39 AM · Next Milestone, DICOM, MITK