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Nov 26 2021

s669m added a comment to T28847: [HACKING WEEK] - Upgrading Microk8s of Kaapana - .
Error: failed to install CRD crds/crds.yaml: CustomResourceDefinition.apiextensions.k8s.io "tlsstores.traefik.containo.us" is invalid: [spec.versions: Invalid value: []apiextensions.CustomResourceDefinitionVersion(nil): must have exactly one version marked as storage version, status.storedVersions: Invalid value: []string(nil): must have at least one stored version]
Nov 26 2021, 12:07 PM · Restricted Project, Kaapana (internal)
neher closed T27601: Fiber2DSliceThickness in fiber processing as Resolved.
Nov 26 2021, 9:34 AM · MITK Diffusion
neher closed T27699: mitkCommandLineParser should allow arbitrary types with input/output flag as Resolved.
Nov 26 2021, 9:34 AM · MITK
neher closed T28872: Diffusion registration crashes when two non-diffusion-weighted images are registered as Resolved.
Nov 26 2021, 9:33 AM · MITK Diffusion
neher closed T27419: Fix dartclient documentation build as Resolved.
Nov 26 2021, 9:33 AM · MITK Diffusion

Nov 25 2021

s434n added a comment to T28731: Update README.md of project template.

It seems to me like this was done in this commit. Can the task be closed?

Nov 25 2021, 2:57 PM · MITK (v2022.04), MITK-ProjectTemplate
neher closed T28875: Refactor ODF normalization for streamline tracking as Resolved.
Nov 25 2021, 12:01 PM · MITK Diffusion
neher committed rMITKDIFF12917e7439e4: Merge branch 'T28875-OdfNormalization' (authored by neher).
Merge branch 'T28875-OdfNormalization'
Nov 25 2021, 11:10 AM
neher added a comment to T28875: Refactor ODF normalization for streamline tracking.

Pushed new branch T28875-OdfNormalization.

Nov 25 2021, 11:09 AM · MITK Diffusion
neher committed rMITKDIFFe1364c9083b6: Using sharpening for tensor tracking. No min-max sharpening (authored by neher).
Using sharpening for tensor tracking. No min-max sharpening
Nov 25 2021, 11:09 AM
neher committed rMDf47f5098b8b0: Update streamline tracking reference (authored by neher).
Update streamline tracking reference
Nov 25 2021, 11:09 AM
neher triaged T28875: Refactor ODF normalization for streamline tracking as High priority.
Nov 25 2021, 9:33 AM · MITK Diffusion

Nov 24 2021

kahl added a revision to T24754: Volume Visualization crashes with some CT images: Unknown Object (Differential Revision).
Nov 24 2021, 1:49 PM · Restricted Project, MITK
kahl added a revision to T28274: [Volume Visualization] Volume Rendering for 4D images does only work on timestep 0 or not at all: Unknown Object (Differential Revision).
Nov 24 2021, 1:49 PM · Restricted Project, MITK (v2022.04), Request for Discussion
kahl added a comment to T28274: [Volume Visualization] Volume Rendering for 4D images does only work on timestep 0 or not at all.

I implemented a fix which includes your suggestion to extend the interfaces of the TranferFunctionWidget and QmitkTransferFunctionGeneratorWidget @floca. This resolves the issue that the histogram is not updated. Additionally, to also update the volume that is shown in the 3D render window, I extended the mitkVolumeMapperVtkSmart3D to also work with the correct timesteps. Before this change, only a volume for timestep 0 was created. With this fix, the workbench also does not crash with the Heart3D+t dataset.

Nov 24 2021, 1:37 PM · Restricted Project, MITK (v2022.04), Request for Discussion
kahl added a comment to T28274: [Volume Visualization] Volume Rendering for 4D images does only work on timestep 0 or not at all.

Pushed new branch to rMITK MITK: bugfix/T28274-volumerendering-multiple-timesteps.

Nov 24 2021, 1:27 PM · Restricted Project, MITK (v2022.04), Request for Discussion

Nov 23 2021

k656s added a member for Kaapana Elevated Branching Privileges: p212r.
Nov 23 2021, 10:28 PM
s669m added a comment to T28847: [HACKING WEEK] - Upgrading Microk8s of Kaapana - .
ubuntu@vm-129-189:~$ ./install_platform.sh 
USER: ubuntu 
Check disk space: ok
SIZE:  194G 
Check if helm is available...
ok
Get helm deployments...
Error: Kubernetes cluster unreachable: the server has asked for the client to provide credentials
Nov 23 2021, 3:44 PM · Restricted Project, Kaapana (internal)
s669m added a comment to T28847: [HACKING WEEK] - Upgrading Microk8s of Kaapana - .
ubuntu@vm-129-189:~$ kubectl get pods -A
NAMESPACE     NAME                                    READY   STATUS      RESTARTS   AGE
base          code-server-7b9b68c556-fqrc9            1/1     Running     3          84m
base          landingpage-7c7bb855b-hz484             1/1     Running     3          86m
default       kaapana-exp-extensions-87rjt            0/1     Completed   0          84m
default       kaapana-plugin-kqdd2                    0/1     Completed   0          84m
default       kaapana-stab-extensions-ktk29           0/1     Completed   0          84m
flow-jobs     dcmsend-00382388                        0/1     Completed   0          81m
flow-jobs     dcmsend-2b49b0c7                        0/1     Completed   0          80m
flow-jobs     dcmsend-5ff032fb                        0/1     Completed   0          81m
flow-jobs     dcmsend-98c4d2c3                        0/1     Completed   0          81m
flow-jobs     dcmsend-e2633395                        0/1     Completed   0          81m
flow          airflow-6ddc54d9b4-hcvb6                2/2     Running     6          86m
flow          ctp-76cf9bbc9f-6nchk                    1/1     Running     3          86m
flow          postgres-airflow-64954bfb86-t2bjt       1/1     Running     3          86m
kube-system   coredns-588fd544bf-27hc8                1/1     Running     5          91m
kube-system   error-pages-57598754db-fz7bc            1/1     Running     3          86m
kube-system   keycloak-967cbfb55-8jjsv                1/1     Running     3          86m
kube-system   kube-helm-deployment-7f8464f9df-tnbmg   1/1     Running     3          86m
kube-system   kube-state-metrics-5695698777-dq864     1/1     Running     3          86m
kube-system   kubernetes-dashboard-69664c8798-4lw9j   1/1     Running     3          86m
kube-system   louketo-687bbbf6d9-cjgxs                1/1     Running     3          86m
kube-system   postgres-keycloak-5cc9b468d9-pkd82      1/1     Running     3          86m
kube-system   preinstall-extensions-init-w9jss        0/2     Completed   0          86m
kube-system   traefik-5786899dff-99q9f                1/1     Running     3          86m
kube-system   update-extensions-init-vjhtq            0/1     Completed   0          86m
meta          elastic-meta-de-9885fb5b4-wcptq         1/1     Running     3          86m
meta          init-meta-dfpdt                         0/1     Completed   0          86m
meta          kibana-meta-de-8f7c4bd6c-h7k94          1/1     Running     3          86m
monitoring    alertmanager-74fc67bd8-5zvtn            1/1     Running     3          86m
monitoring    grafana-6f6b5dc559-2jhcx                1/1     Running     3          86m
monitoring    prometheus-76bf79f68f-zcqfp             1/1     Running     3          86m
store         dcm4chee-78487774cf-86pkq               1/1     Running     3          86m
store         dicom-init-twb8d                        0/1     Completed   0          86m
store         ldap-684f697598-lzfnj                   1/1     Running     3          86m
store         minio-deployment-79dc7dd464-qv4sk       1/1     Running     3          86m
store         minio-init-76dn6                        0/1     Completed   0          86m
store         ohif-65cdcd8b87-lhcfd                   1/1     Running     3          86m
store         postgres-dcm4che-75d84848c5-rdqxq       1/1     Running     3          86m
ubuntu@vm-129-189:~$ 
ubuntu@vm-129-189:~$ 
ubuntu@vm-129-189:~$ 
ubuntu@vm-129-189:~$ 
ubuntu@vm-129-189:~$ kubectl get nodes
NAME                                  STATUS   ROLES    AGE   VERSION
vm-129-189.cloud.dkfz-heidelberg.de   Ready    <none>   92m   v1.21.6-3+dd57cd4fdc581a
Nov 23 2021, 2:57 PM · Restricted Project, Kaapana (internal)

Nov 22 2021

kislinsk added a member for MIC: o280o.
Nov 22 2021, 3:26 PM
franza added a comment to T27260: Spacing points still remain in data manager after closing calibration view.

Here is the fix of this bug as pull request at github: https://github.com/MITK/MITK/pull/253

Nov 22 2021, 1:57 PM · MITK (v2022.04), Pull Request, IGT
franza added a project to T27260: Spacing points still remain in data manager after closing calibration view: Pull Request.
Nov 22 2021, 1:55 PM · MITK (v2022.04), Pull Request, IGT
neher committed rMITKDIFF1bc1f9c63130: Merge branch 'T28872-Registration' (authored by neher).
Merge branch 'T28872-Registration'
Nov 22 2021, 12:45 PM
neher committed rMITKDIFF93ad4096f56e: Ctaching non diff images (authored by neher).
Ctaching non diff images
Nov 22 2021, 12:39 PM
neher added a comment to T28872: Diffusion registration crashes when two non-diffusion-weighted images are registered.

Pushed new branch T28872-Registration.

Nov 22 2021, 12:39 PM · MITK Diffusion
neher triaged T28872: Diffusion registration crashes when two non-diffusion-weighted images are registered as Normal priority.
Nov 22 2021, 11:14 AM · MITK Diffusion
floca added a comment to T28274: [Volume Visualization] Volume Rendering for 4D images does only work on timestep 0 or not at all.

For the histogram part the reason is (swiftly looking into the code) that Neither the TransferFunctionWidgets nor the used histogramm classes support 4D images, the assume images to be static. But as the QmitkTransferFunctionWidget want the whole node, we cannot just use a TimePointSelector filter in the view. It seems like we need to extend the interface of the TransferFunctionWidgets (same for the QmitkTransferFunctionGeneratorWidget) in order to also set the current time step and handel it internally correctly.

Nov 22 2021, 10:41 AM · Restricted Project, MITK (v2022.04), Request for Discussion
s669m raised the priority of T28870: UPenn's GaNDLF Integration with Kaapana (v1) from Normal to High.
Nov 22 2021, 10:11 AM · Restricted Project, Kaapana (internal)
s669m triaged T28870: UPenn's GaNDLF Integration with Kaapana (v1) as Normal priority.
Nov 22 2021, 10:11 AM · Restricted Project, Kaapana (internal)
kahl claimed T28274: [Volume Visualization] Volume Rendering for 4D images does only work on timestep 0 or not at all.

I tried to reproduce this bug and for US4DCyl the behaviour was the same when I tested it (histogram remains the same for all timesteps). For Heart3D+t sometimes nothing is displayed at all (as described here) but also sometimes the workbench crashes as described in T24754. However, I could not find any pattern when which behaviour occurs. I tested it with the current release installer on Windows and on the current develop branch in Debug mode. I can try to narrow it down a bit.

Nov 22 2021, 9:09 AM · Restricted Project, MITK (v2022.04), Request for Discussion

Nov 19 2021

neher committed rMITKDIFF0ea02355d8f3: Merge branch 'T28867-FiberfoxTest' (authored by neher).
Merge branch 'T28867-FiberfoxTest'
Nov 19 2021, 11:11 AM
neher committed rMITKDIFF0b82b32bd2e8: Outputting gradient index (authored by neher).
Outputting gradient index
Nov 19 2021, 11:11 AM
neher added a comment to T28867: Fiberfox test randomly fails.

Pushed new branch T28867-FiberfoxTest.

Nov 19 2021, 11:11 AM · MITK Diffusion
neher triaged T28867: Fiberfox test randomly fails as High priority.
Nov 19 2021, 11:10 AM · MITK Diffusion
neher closed T28831: dMRI nonlocal means denoising crashes as Wontfix.
Nov 19 2021, 11:09 AM · MITK Diffusion
neher reopened T28831: dMRI nonlocal means denoising crashes as "Open".
Nov 19 2021, 11:08 AM · MITK Diffusion
neher closed T28831: dMRI nonlocal means denoising crashes as Wontfix.
Nov 19 2021, 11:07 AM · MITK Diffusion

Nov 18 2021

s669m moved T28175: TFDA MVP v1 from Restricted Project Column to Restricted Project Column on the Restricted Project board.
Nov 18 2021, 4:28 PM · Restricted Project
neher lowered the priority of T26413: Nifti2 support from Normal to Wishlist.
Nov 18 2021, 3:35 PM · Auto-closed, Missing Info, MITK
neher closed T26960: Fiber mapper test fails as Resolved.
Nov 18 2021, 3:34 PM · MITK Diffusion
a178n added a comment to T28866: [Segmentation] Redundant label "recomputation" for Otsu/Watershed (& nnUNet) when any of the Preview-generated labels are selected to Confirm.

After some analysis, it is understood that there is a difference in the modified time of the tool and the segmentation. This is detected in the AutoMLSegmentationWithPreviewTool.DoUpdatePreview method if-case of this->GetMTime() > m_MLPreviewNode->GetData()->GetMTime().
This change in time happens because tool->IsTimePointChangeAwareOn() is called after the tool->UpdatePreview() call is made in the tool's GUI class, eg. QmitkOtsuTool3DGUI

Nov 18 2021, 3:29 PM · MITK (v2022.10), Request for Discussion
a178n created T28866: [Segmentation] Redundant label "recomputation" for Otsu/Watershed (& nnUNet) when any of the Preview-generated labels are selected to Confirm.
Nov 18 2021, 3:17 PM · MITK (v2022.10), Request for Discussion
neher added a comment to T28831: dMRI nonlocal means denoising crashes.

I think there is a bug in the itk filter. itkPatchBasedDenoisingImageFilter normalizes the patch weights to center weigh=1, i.e. the other weights might very well become > 1. In a next step it is asserted that the weights are <=1, leading to a crash (PatchBasedDenoisingBaseImageFilter<TInputImage, TOutputImage>
::SetPatchWeights).

Nov 18 2021, 3:09 PM · MITK Diffusion
kislinsk lowered the priority of T28778: "Use constraint zooming and panning" is only applied after reinit/restart from Unbreak Now! to Low.
Nov 18 2021, 2:18 PM · MITK, Checklist
kislinsk added a comment to T28778: "Use constraint zooming and panning" is only applied after reinit/restart.

Deleted branch from rMITK MITK: bugfix/T28778-fix-rendering-tests.

Nov 18 2021, 2:18 PM · MITK, Checklist
kislinsk committed rMITK1c4db16fd159: Revert changes to directly apply correct zooming and panning (authored by kahl).
Revert changes to directly apply correct zooming and panning
Nov 18 2021, 2:17 PM

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