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Maniphest T30359

MITK MiniApps in Kaapana
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Description

Currently in Kaapana we are using different MITK Miniapps based on an old installer/configuration:
https://www.mitk.org/download/kaapana/phenotyping/
To stay updated, it would be good to change to a current MITK version:
Therefore here a list of usage of this Miniapps:
Installer Container: https://codebase.helmholtz.cloud/kaapana/kaapana/-/blob/develop/data-processing/base-images/base-mitk-phenotyping/Dockerfile
Usage:
MitkFileConverter - https://codebase.helmholtz.cloud/kaapana/kaapana/-/tree/develop/data-processing/kaapana-plugin/processing-containers/mitk-fileconverter
MitkCLResampleImageToReference - https://codebase.helmholtz.cloud/kaapana/kaapana/-/tree/develop/data-processing/kaapana-plugin/processing-containers/mitk-resample
MitkCLResampleImageToReference - https://codebase.helmholtz.cloud/kaapana/kaapana/-/tree/develop/data-processing/processing-pipelines/nnunet/processing-containers/seg-check
MitkCLGlobalImageFeatures - https://codebase.helmholtz.cloud/kaapana/kaapana/-/blob/develop/data-processing/processing-pipelines/radiomics/processing-containers/radiomics/files/radiomics.sh

To reduce image size, it would be good to replace the old configuration in https://ci.mitk.org/job/MITK/job/Kaapana/job/Phenotyping/ with a configuration, that only build the required MITK executables.

Event Timeline

gaoh assigned this task to floca.Mar 6 2024, 11:34 AM
gaoh created this task.
floca added a comment.Mar 7 2024, 11:28 AM

If I haven't missed something we can directly replace MitkCLResampleImageToReference with MitkMapImage. I can patch the according Kaapana files as soon as we have the new MITK installer. Do we have tests for the containers?

Regarding the reduced size: That means you would like to have an installer with just commandline apps. Or would it be also OK if you could use also the normal MITK installer?

gaoh added a comment.Mar 7 2024, 11:40 AM
In T30359#257187, @floca wrote:

If I haven't missed something we can directly replace MitkCLResampleImageToReference with MitkMapImage. I can patch the according Kaapana files as soon as we have the new MITK installer. Do we have tests for the containers?

The CI runs some workflows, but I don't think that all piplines (in extenstions e.g. radiomics) have a workflow CI test. So some manual testing would be requiered.

Regarding the reduced size: That means you would like to have an installer with just commandline apps. Or would it be also OK if you could use also the normal MITK installer?

I don't know the size of the normal installer. But if it is not that big, it does not matter. But less is always better:)

kislinsk triaged this task as Normal priority.Jun 17 2024, 2:40 PM
gaoh added a comment.Jul 10 2024, 3:29 PM

What is with MitkCLGlobalImageFeatures, it is not expected to be part of MITK anymore? Or is it still part of it?

floca added a comment.Jul 10 2024, 3:32 PM
In T30359#260125, @gaoh wrote:

What is with MitkCLGlobalImageFeatures, it is not expected to be part of MITK anymore? Or is it still part of it?

It is still a part of MITK. So far we haven't deprecated it as it is still a used dependency. It is one of 4 CL apps that we kept.

MITK · MIC · IMSY · DKFZ