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Merge pull request #18 from GSTT-CSC/aide-workflows
Adds Clinical Workflow and Argo Workflow files for running on AIDE
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| metadata: | ||
| name: totalsegmentator-argo-template | ||
| generateName: totalsegmentator-argo-template- | ||
| namespace: argo | ||
| spec: | ||
| templates: | ||
| - name: totalsegmentator | ||
| inputs: | ||
| artifacts: | ||
| - name: input-dicom | ||
| path: /var/monai/input | ||
| s3: | ||
| accessKeySecret: | ||
| name: my-minio-cred | ||
| key: accesskey | ||
| secretKeySecret: | ||
| name: my-minio-cred | ||
| key: secretkey | ||
| key: argo/inputs/artifacts/input-dicom | ||
| outputs: | ||
| artifacts: | ||
| - name: output | ||
| path: /var/monai/output | ||
| s3: | ||
| bucket: bucket1 | ||
| accessKeySecret: | ||
| name: my-minio-cred | ||
| key: accesskey | ||
| secretKeySecret: | ||
| name: my-minio-cred | ||
| key: secretkey | ||
| key: /var/monai/output | ||
| metadata: {} | ||
| container: | ||
| name: '' | ||
| image: ghcr.io/gstt-csc/totalsegmentator-aide/map:0.1.2 | ||
| command: | ||
| - /bin/bash | ||
| - '-c' | ||
| args: | ||
| - python3 -u /opt/monai/app/app.py | ||
| resources: | ||
| limits: | ||
| cpu: '20' | ||
| memory: 128Gi | ||
| nvidia.com/gpu: '1' | ||
| requests: | ||
| cpu: '0' | ||
| memory: '0' | ||
| nvidia.com/gpu: '1' | ||
| imagePullPolicy: IfNotPresent | ||
| podSpecPatch: >- | ||
| {"initContainers":[{"name":"init","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}],"containers":[{"name":"wait","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}]} | ||
| entrypoint: totalsegmentator | ||
| arguments: {} |
55 changes: 55 additions & 0 deletions
55
app/workflows/totalsegmentator-argo-template-high-resource.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| metadata: | ||
| name: totalsegmentator-argo-template | ||
| generateName: totalsegmentator-argo-template- | ||
| namespace: argo | ||
| spec: | ||
| templates: | ||
| - name: totalsegmentator | ||
| inputs: | ||
| artifacts: | ||
| - name: input-dicom | ||
| path: /var/monai/input | ||
| s3: | ||
| accessKeySecret: | ||
| name: my-minio-cred | ||
| key: accesskey | ||
| secretKeySecret: | ||
| name: my-minio-cred | ||
| key: secretkey | ||
| key: argo/inputs/artifacts/input-dicom | ||
| outputs: | ||
| artifacts: | ||
| - name: output | ||
| path: /var/monai/output | ||
| s3: | ||
| bucket: bucket1 | ||
| accessKeySecret: | ||
| name: my-minio-cred | ||
| key: accesskey | ||
| secretKeySecret: | ||
| name: my-minio-cred | ||
| key: secretkey | ||
| key: /var/monai/output | ||
| metadata: {} | ||
| container: | ||
| name: '' | ||
| image: ghcr.io/gstt-csc/totalsegmentator-aide/map:0.1.2 | ||
| command: | ||
| - /bin/bash | ||
| - '-c' | ||
| args: | ||
| - python3 -u /opt/monai/app/app.py | ||
| resources: | ||
| limits: | ||
| cpu: '8' | ||
| memory: 64000Mi | ||
| nvidia.com/gpu: '1' | ||
| requests: | ||
| cpu: '0' | ||
| memory: '0' | ||
| nvidia.com/gpu: '1' | ||
| imagePullPolicy: IfNotPresent | ||
| podSpecPatch: >- | ||
| {"initContainers":[{"name":"init","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}],"containers":[{"name":"wait","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}]} | ||
| entrypoint: totalsegmentator | ||
| arguments: {} |
55 changes: 55 additions & 0 deletions
55
app/workflows/totalsegmentator-argo-template-low-resource.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| metadata: | ||
| name: totalsegmentator-argo-template | ||
| generateName: totalsegmentator-argo-template- | ||
| namespace: argo | ||
| spec: | ||
| templates: | ||
| - name: totalsegmentator | ||
| inputs: | ||
| artifacts: | ||
| - name: input-dicom | ||
| path: /var/monai/input | ||
| s3: | ||
| accessKeySecret: | ||
| name: my-minio-cred | ||
| key: accesskey | ||
| secretKeySecret: | ||
| name: my-minio-cred | ||
| key: secretkey | ||
| key: argo/inputs/artifacts/input-dicom | ||
| outputs: | ||
| artifacts: | ||
| - name: output | ||
| path: /var/monai/output | ||
| s3: | ||
| bucket: bucket1 | ||
| accessKeySecret: | ||
| name: my-minio-cred | ||
| key: accesskey | ||
| secretKeySecret: | ||
| name: my-minio-cred | ||
| key: secretkey | ||
| key: /var/monai/output | ||
| metadata: {} | ||
| container: | ||
| name: '' | ||
| image: ghcr.io/gstt-csc/totalsegmentator-aide/map:0.1.2 | ||
| command: | ||
| - /bin/bash | ||
| - '-c' | ||
| args: | ||
| - python3 -u /opt/monai/app/app.py | ||
| resources: | ||
| limits: | ||
| cpu: '1' | ||
| memory: 8000Mi | ||
| nvidia.com/gpu: '1' | ||
| requests: | ||
| cpu: '0' | ||
| memory: '0' | ||
| nvidia.com/gpu: '1' | ||
| imagePullPolicy: IfNotPresent | ||
| podSpecPatch: >- | ||
| {"initContainers":[{"name":"init","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}],"containers":[{"name":"wait","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}]} | ||
| entrypoint: totalsegmentator | ||
| arguments: {} |
55 changes: 55 additions & 0 deletions
55
app/workflows/totalsegmentator-argo-template-med-resource.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| metadata: | ||
| name: totalsegmentator-argo-template | ||
| generateName: totalsegmentator-argo-template- | ||
| namespace: argo | ||
| spec: | ||
| templates: | ||
| - name: totalsegmentator | ||
| inputs: | ||
| artifacts: | ||
| - name: input-dicom | ||
| path: /var/monai/input | ||
| s3: | ||
| accessKeySecret: | ||
| name: my-minio-cred | ||
| key: accesskey | ||
| secretKeySecret: | ||
| name: my-minio-cred | ||
| key: secretkey | ||
| key: argo/inputs/artifacts/input-dicom | ||
| outputs: | ||
| artifacts: | ||
| - name: output | ||
| path: /var/monai/output | ||
| s3: | ||
| bucket: bucket1 | ||
| accessKeySecret: | ||
| name: my-minio-cred | ||
| key: accesskey | ||
| secretKeySecret: | ||
| name: my-minio-cred | ||
| key: secretkey | ||
| key: /var/monai/output | ||
| metadata: {} | ||
| container: | ||
| name: '' | ||
| image: ghcr.io/gstt-csc/totalsegmentator-aide/map:0.1.2 | ||
| command: | ||
| - /bin/bash | ||
| - '-c' | ||
| args: | ||
| - python3 -u /opt/monai/app/app.py | ||
| resources: | ||
| limits: | ||
| cpu: '4' | ||
| memory: 16000Mi | ||
| nvidia.com/gpu: '1' | ||
| requests: | ||
| cpu: '0' | ||
| memory: '0' | ||
| nvidia.com/gpu: '1' | ||
| imagePullPolicy: IfNotPresent | ||
| podSpecPatch: >- | ||
| {"initContainers":[{"name":"init","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}],"containers":[{"name":"wait","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}]} | ||
| entrypoint: totalsegmentator | ||
| arguments: {} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| metadata: | ||
| name: totalsegmentator-argo-template | ||
| generateName: totalsegmentator-argo-template- | ||
| namespace: argo | ||
| spec: | ||
| templates: | ||
| - name: totalsegmentator | ||
| inputs: | ||
| artifacts: | ||
| - name: input-dicom | ||
| path: /var/monai/input | ||
| s3: | ||
| accessKeySecret: | ||
| name: my-minio-cred | ||
| key: accesskey | ||
| secretKeySecret: | ||
| name: my-minio-cred | ||
| key: secretkey | ||
| key: argo/inputs/artifacts/input-dicom | ||
| outputs: | ||
| artifacts: | ||
| - name: output | ||
| path: /var/monai/output | ||
| s3: | ||
| bucket: bucket1 | ||
| accessKeySecret: | ||
| name: my-minio-cred | ||
| key: accesskey | ||
| secretKeySecret: | ||
| name: my-minio-cred | ||
| key: secretkey | ||
| key: /var/monai/output | ||
| metadata: {} | ||
| container: | ||
| name: '' | ||
| image: ghcr.io/gstt-csc/totalsegmentator-aide/map:0.1.2 | ||
| command: | ||
| - /bin/bash | ||
| - '-c' | ||
| args: | ||
| - python3 -u /opt/monai/app/app.py | ||
| resources: | ||
| limits: | ||
| cpu: '20' | ||
| memory: 128Gi | ||
| nvidia.com/gpu: '1' | ||
| requests: | ||
| cpu: '0' | ||
| memory: '0' | ||
| nvidia.com/gpu: '1' | ||
| imagePullPolicy: IfNotPresent | ||
| podSpecPatch: >- | ||
| {"initContainers":[{"name":"init","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}],"containers":[{"name":"wait","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}]} | ||
| entrypoint: totalsegmentator | ||
| arguments: {} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,72 @@ | ||
| { | ||
| "name": "TotalSegmentator", | ||
| "version": "0.1.2", | ||
| "description": "Clinical Workflow for TotalSegmentator", | ||
| "informatics_gateway": { | ||
| "ae_title": "MONAI", | ||
| "data_origins": [], | ||
| "export_destinations": [ | ||
| "PACS" | ||
| ] | ||
| }, | ||
| "tasks": [ | ||
| { | ||
| "id": "totalsegmentator-task", | ||
| "description": "TotalSegmentator automatic CT segmentation", | ||
| "type": "argo", | ||
| "args": { | ||
| "workflow_template_name": "totalsegmentator-argo-template", | ||
| "server_url": "http://argo-argo-workflows-server.argo:2746", | ||
| "namespace": "argo", | ||
| "allow_insecure": "true" | ||
| }, | ||
| "task_destinations": [ | ||
| { | ||
| "name": "export-rt-struct", | ||
| "conditions": [] | ||
| } | ||
| ], | ||
| "export_destinations": [], | ||
| "artifacts": { | ||
| "input": [ | ||
| { | ||
| "name": "input-dicom", | ||
| "value": "{{ context.input.dicom }}", | ||
| "mandatory": true | ||
| } | ||
| ], | ||
| "output": [ | ||
| { | ||
| "name": "output", | ||
| "value": "", | ||
| "mandatory": true | ||
| } | ||
| ] | ||
| }, | ||
| "timeout_minutes": -1 | ||
| }, | ||
| { | ||
| "id": "export-rt-struct", | ||
| "description": "Export TotalSegmentator output RT Struct DICOMs", | ||
| "type": "export", | ||
| "args": {}, | ||
| "task_destinations": [], | ||
| "export_destinations": [ | ||
| { | ||
| "name": "PACS" | ||
| } | ||
| ], | ||
| "artifacts": { | ||
| "input": [ | ||
| { | ||
| "name": "output", | ||
| "value": "{{ context.executions.totalsegmentator-task.artifacts.output }}", | ||
| "mandatory": true | ||
| } | ||
| ], | ||
| "output": [] | ||
| }, | ||
| "timeout_minutes": -1 | ||
| } | ||
| ] | ||
| } |