Merge branch 'feature/nifti-merge' into develop
0a5bf1c22320
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Merge branch 'feature/nifti-merge' into develop

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schererj	Authored on Mar 5 2021, 3:49 PM
schererj	Pushed on Mar 5 2021, 3:47 PM

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rKAAPANAcb458885ff01: merges develop branch
rKAAPANA19e0411e6ccc: bug fix env variables in KaaapanaBaseOperator

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schererj committed rKAAPANA0a5bf1c22320: Merge branch 'feature/nifti-merge' into develop (authored by schererj).Mar 5 2021, 3:49 PM

Merged Changes

cb458885ff01 merges develop branch
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833204b9d7e7 DCMQI single-label-fix and included a check for 'slash' in filenames
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5dd4708e5fc0 nnunet ensemble improvements
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7042bcc3cf41 merged dev
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c80e4d6010b6 raised mem limit for dcm2nrrd converter
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58353d78c566 merged develop
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76cbf184425e adjusted CTP workflow to Aiflow DICOM send
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c39f4c7f8fec training adjustments
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ebc41d34ed5d create dataset rework
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ca8e9ce1cc1e Merge remote-tracking branch 'origin/develop' into feature/nifti-merge
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55790324dd21 fixed seg_info if segmentation for label was not found
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2dd3d66b6966 LocalDiceOperator adjustments
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92aaf80bbb06 nnunet simple_predict batch-level skip if processed-counter > 0
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312ef4a1e0ff ensemble improvements
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426f548b1746 first ensemble workflow
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6f9b4c371f73 Merge branch 'develop' into feature/nifti-merge
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72269d96ca81 Merge branch 'develop' into feature/nifti-merge
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0d088e16257f merged develop
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94712cf78f1e Merge branch 'develop' of https://phabricator.mitk.org/source/kaapana into…
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8bc6bfd5fe42 Merge branch 'develop' into feature/nifti-merge
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1eb97669132c nnunet ensemble init
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84f2c044bddf Merge branch 'develop' into feature/nifti-merge
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ffd0d14e9288 fixed nnunet results study_uid
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1e89252771fc nnunet install / uninstall working
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bcf7d019e9a5 merge working
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5dd018aac974 swtich work-setup
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Changes (76)

Path

Size

build-scripts/

build-configuration.yaml

build_helper/

charts_build_and_push_all.py

containers_build_and_push_all.py

start_build.py

platforms/

kaapana-platform/

platform-installation/

install_platform.sh

services/

applications/

code-server/

code-server-chart/

templates/

deployment.yaml

docker/

Dockerfile

files/

requirements.txt

flow/

airflow/

docker/

files/

scripts/

init_pools.py

ctp/

ctp-chart/

templates/

docker/

files/

kaapana-core/

louketo-proxy/

louketo-proxy-chart/

templates/

louketo_deployment.yaml

templates_and_examples/

templates/

workflows/

processing-container/

DockerPythonTemplate/

files/

	start_simple.py
	process.py

workflows/

airflow-components/

dags/

dag_nnunet_ensemble.py

dag_nnunet_inference.py

dag_nnunet_install_model.py

	dag_nnunet_model_install.py
	dag_nnunet_install_model.py

dag_nnunet_model_uninstall.py

dag_nnunet_training.py

dag_nnunet_training_5fold.py

dag_service_clean_tmp_dag_data.py

dag_service_extract_metadata.py

nnunet/

GetTaskModelOperator.py

LocalDataorganizerOperator.py

LocalDiceOperator.py

LocalSegCheckOperator.py

NnUnetOperator.py

getTasks.py

radiomics/

RadiomicsOperator.py

plugins/

kaapana/

kubetools/

pod_launcher.py

operators/

Bin2DcmOperator.py

DcmConverterOperator.py

DcmSeg2ItkOperator.py

HelperDcmWeb.py

Itk2DcmSegOperator.py

KaapanaBaseOperator.py

KaapanaPythonBaseOperator.py

LocalDeleteFromPacsOperator.py

LocalGetInputDataOperator.py

LocalGetRefSeriesOperator.py

LocalJson2MetaOperator.py

ResampleOperator.py

dag-installer/

nnunet/

Dockerfile.shapemodel

processing-container/

dcmqi/

Dockerfile

files/

code_lookup_table.csv

code_lookup_table.json

itkimage2segimage.py

segimage2itkimage.py

dcmtk-bin2dcm/

files/

start.py

template.xml

dicom-web-send/

files/

dcmweb.py

mitk-fileconverter/

files/

mitk_fileconverter.sh

mitk-phenotyping/

mitk-resample/

files/

nnunet/

nnunet-get-models/

files/

nnunet/

files/

radiomics/

files/

radiomics.sh

rKAAPANA0a5bf1c22320

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build-scripts/build-configuration.yaml

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build-scripts/build_helper/charts_build_and_push_all.py

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build-scripts/build_helper/containers_build_and_push_all.py

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build-scripts/start_build.py

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platforms/kaapana-platform/platform-installation/install_platform.sh

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services/applications/code-server/code-server-chart/templates/deployment.yaml

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services/applications/code-server/docker/Dockerfile

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services/applications/code-server/docker/files/requirements.txt

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services/flow/airflow/docker/files/scripts/init_pools.py

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services/flow/ctp/ctp-chart/templates/configmap.yaml

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services/flow/ctp/ctp-chart/templates/deployment.yaml

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services/flow/ctp/docker/Dockerfile

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services/flow/ctp/docker/files/Launcher.properties

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services/kaapana-core/louketo-proxy/louketo-proxy-chart/templates/louketo_deployment.yaml

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templates_and_examples/templates/workflows/processing-container/DockerPythonTemplate/Dockerfile

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templates_and_examples/templates/workflows/processing-container/DockerPythonTemplate/files/process.py

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templates_and_examples/templates/workflows/processing-container/DockerPythonTemplate/files/requirements.txt

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templates_and_examples/templates/workflows/processing-container/DockerPythonTemplate/files/start.py

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templates_and_examples/templates/workflows/processing-container/DockerPythonTemplate/files/start_simple.py

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workflows/airflow-components/dags/dag_nnunet_ensemble.py

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workflows/airflow-components/dags/dag_nnunet_inference.py

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workflows/airflow-components/dags/dag_nnunet_install_model.py

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workflows/airflow-components/dags/dag_nnunet_model_install.py

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workflows/airflow-components/dags/dag_nnunet_model_uninstall.py

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workflows/airflow-components/dags/dag_nnunet_training.py

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workflows/airflow-components/dags/dag_nnunet_training_5fold.py

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workflows/airflow-components/dags/dag_service_clean_tmp_dag_data.py

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workflows/airflow-components/dags/dag_service_extract_metadata.py

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workflows/airflow-components/dags/nnunet/GetTaskModelOperator.py

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workflows/airflow-components/dags/nnunet/LocalDataorganizerOperator.py

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workflows/airflow-components/dags/nnunet/LocalDiceOperator.py

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workflows/airflow-components/dags/nnunet/LocalSegCheckOperator.py

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workflows/airflow-components/dags/nnunet/NnUnetOperator.py

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workflows/airflow-components/dags/nnunet/getTasks.py

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workflows/airflow-components/dags/radiomics/RadiomicsOperator.py

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workflows/airflow-components/plugins/kaapana/kubetools/pod_launcher.py

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workflows/airflow-components/plugins/kaapana/operators/Bin2DcmOperator.py

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workflows/airflow-components/plugins/kaapana/operators/DcmConverterOperator.py

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workflows/airflow-components/plugins/kaapana/operators/DcmSeg2ItkOperator.py

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workflows/airflow-components/plugins/kaapana/operators/HelperDcmWeb.py

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workflows/airflow-components/plugins/kaapana/operators/Itk2DcmSegOperator.py

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workflows/airflow-components/plugins/kaapana/operators/KaapanaBaseOperator.py

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workflows/airflow-components/plugins/kaapana/operators/KaapanaPythonBaseOperator.py

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workflows/airflow-components/plugins/kaapana/operators/LocalDeleteFromPacsOperator.py

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workflows/airflow-components/plugins/kaapana/operators/LocalGetInputDataOperator.py

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workflows/airflow-components/plugins/kaapana/operators/LocalGetRefSeriesOperator.py

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workflows/airflow-components/plugins/kaapana/operators/LocalJson2MetaOperator.py

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workflows/airflow-components/plugins/kaapana/operators/ResampleOperator.py

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workflows/dag-installer/nnunet/Dockerfile.shapemodel

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workflows/processing-container/dcmqi/Dockerfile

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workflows/processing-container/dcmqi/files/code_lookup_table.csv

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workflows/processing-container/dcmqi/files/code_lookup_table.json

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workflows/processing-container/dcmqi/files/itkimage2segimage.py

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workflows/processing-container/dcmqi/files/segimage2itkimage.py

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workflows/processing-container/dcmtk-bin2dcm/files/start.py

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workflows/processing-container/dcmtk-bin2dcm/files/template.xml

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workflows/processing-container/dicom-web-send/files/dcmweb.py

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workflows/processing-container/mitk-fileconverter/files/mitk_fileconverter.sh

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workflows/processing-container/mitk-phenotyping/Dockerfile

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workflows/processing-container/mitk-resample/Dockerfile

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workflows/processing-container/mitk-resample/files/requirements.txt

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workflows/processing-container/mitk-resample/files/start.py

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workflows/processing-container/mitk-resample/files/start.sh

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workflows/processing-container/nnunet/nnunet-get-models/files/process.py

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workflows/processing-container/nnunet/nnunet/Dockerfile

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workflows/processing-container/nnunet/nnunet/files/create_dataset.py

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workflows/processing-container/nnunet/nnunet/files/create_report.py

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workflows/processing-container/nnunet/nnunet/files/ensemble.py

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workflows/processing-container/nnunet/nnunet/files/monitoring.py

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workflows/processing-container/nnunet/nnunet/files/nnUNetTrainerV2.py

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workflows/processing-container/nnunet/nnunet/files/preparation.py

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workflows/processing-container/nnunet/nnunet/files/run_training.py

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workflows/processing-container/nnunet/nnunet/files/simple_predict.py

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workflows/processing-container/nnunet/nnunet/files/start_nnunet.sh

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workflows/processing-container/nnunet/nnunet/files/write_model_info.py

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workflows/processing-container/radiomics/files/radiomics.sh

Merge branch 'feature/nifti-merge' into develop0a5bf1c22320Actions

Description

Details

Event Timeline

Merged Changes

Changes (76)

rKAAPANA0a5bf1c22320

build-scripts/build-configuration.yaml

build-scripts/build_helper/charts_build_and_push_all.py

build-scripts/build_helper/containers_build_and_push_all.py

build-scripts/start_build.py

platforms/kaapana-platform/platform-installation/install_platform.sh

services/applications/code-server/code-server-chart/templates/deployment.yaml

services/applications/code-server/docker/Dockerfile

services/applications/code-server/docker/files/requirements.txt

services/flow/airflow/docker/files/scripts/init_pools.py

services/flow/ctp/ctp-chart/templates/configmap.yaml

services/flow/ctp/ctp-chart/templates/deployment.yaml

services/flow/ctp/docker/Dockerfile

services/flow/ctp/docker/files/Launcher.properties

services/kaapana-core/louketo-proxy/louketo-proxy-chart/templates/louketo_deployment.yaml

templates_and_examples/templates/workflows/processing-container/DockerPythonTemplate/Dockerfile

templates_and_examples/templates/workflows/processing-container/DockerPythonTemplate/files/process.py

templates_and_examples/templates/workflows/processing-container/DockerPythonTemplate/files/requirements.txt

templates_and_examples/templates/workflows/processing-container/DockerPythonTemplate/files/start.py

templates_and_examples/templates/workflows/processing-container/DockerPythonTemplate/files/start_simple.py

workflows/airflow-components/dags/dag_nnunet_ensemble.py

workflows/airflow-components/dags/dag_nnunet_inference.py

workflows/airflow-components/dags/dag_nnunet_install_model.py

workflows/airflow-components/dags/dag_nnunet_model_install.py

workflows/airflow-components/dags/dag_nnunet_model_uninstall.py

workflows/airflow-components/dags/dag_nnunet_training.py

workflows/airflow-components/dags/dag_nnunet_training_5fold.py

workflows/airflow-components/dags/dag_service_clean_tmp_dag_data.py

workflows/airflow-components/dags/dag_service_extract_metadata.py

workflows/airflow-components/dags/nnunet/GetTaskModelOperator.py

workflows/airflow-components/dags/nnunet/LocalDataorganizerOperator.py

workflows/airflow-components/dags/nnunet/LocalDiceOperator.py

workflows/airflow-components/dags/nnunet/LocalSegCheckOperator.py

workflows/airflow-components/dags/nnunet/NnUnetOperator.py

workflows/airflow-components/dags/nnunet/getTasks.py

workflows/airflow-components/dags/radiomics/RadiomicsOperator.py

workflows/airflow-components/plugins/kaapana/kubetools/pod_launcher.py

workflows/airflow-components/plugins/kaapana/operators/Bin2DcmOperator.py

workflows/airflow-components/plugins/kaapana/operators/DcmConverterOperator.py

workflows/airflow-components/plugins/kaapana/operators/DcmSeg2ItkOperator.py

workflows/airflow-components/plugins/kaapana/operators/HelperDcmWeb.py

workflows/airflow-components/plugins/kaapana/operators/Itk2DcmSegOperator.py

workflows/airflow-components/plugins/kaapana/operators/KaapanaBaseOperator.py

workflows/airflow-components/plugins/kaapana/operators/KaapanaPythonBaseOperator.py

workflows/airflow-components/plugins/kaapana/operators/LocalDeleteFromPacsOperator.py

workflows/airflow-components/plugins/kaapana/operators/LocalGetInputDataOperator.py

workflows/airflow-components/plugins/kaapana/operators/LocalGetRefSeriesOperator.py

workflows/airflow-components/plugins/kaapana/operators/LocalJson2MetaOperator.py

workflows/airflow-components/plugins/kaapana/operators/ResampleOperator.py

workflows/dag-installer/nnunet/Dockerfile.shapemodel

workflows/processing-container/dcmqi/Dockerfile

workflows/processing-container/dcmqi/files/code_lookup_table.csv

workflows/processing-container/dcmqi/files/code_lookup_table.json

workflows/processing-container/dcmqi/files/itkimage2segimage.py

workflows/processing-container/dcmqi/files/segimage2itkimage.py

workflows/processing-container/dcmtk-bin2dcm/files/start.py

workflows/processing-container/dcmtk-bin2dcm/files/template.xml

workflows/processing-container/dicom-web-send/files/dcmweb.py

workflows/processing-container/mitk-fileconverter/files/mitk_fileconverter.sh

workflows/processing-container/mitk-phenotyping/Dockerfile

workflows/processing-container/mitk-resample/Dockerfile

workflows/processing-container/mitk-resample/files/requirements.txt

workflows/processing-container/mitk-resample/files/start.py

workflows/processing-container/mitk-resample/files/start.sh

workflows/processing-container/nnunet/nnunet-get-models/files/process.py

workflows/processing-container/nnunet/nnunet/Dockerfile

workflows/processing-container/nnunet/nnunet/files/create_dataset.py

workflows/processing-container/nnunet/nnunet/files/create_report.py

workflows/processing-container/nnunet/nnunet/files/ensemble.py

workflows/processing-container/nnunet/nnunet/files/monitoring.py

workflows/processing-container/nnunet/nnunet/files/nnUNetTrainerV2.py

workflows/processing-container/nnunet/nnunet/files/preparation.py

workflows/processing-container/nnunet/nnunet/files/run_training.py

workflows/processing-container/nnunet/nnunet/files/simple_predict.py

Merge branch 'feature/nifti-merge' into develop
0a5bf1c22320
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