diff --git a/e02/templates/Notebook.yaml b/e02/templates/Notebook.yaml index fd9c17a..e82a625 100644 --- a/e02/templates/Notebook.yaml +++ b/e02/templates/Notebook.yaml @@ -1,20 +1,20 @@ apiVersion: argoproj.io/v1alpha1 kind: ClusterWorkflowTemplate metadata: - name: Calibrate4DSTEM + name: calibrate-ptycho labels: workflows.diamond.ac.uk/science-group-imaging: "true" annotations: - workflows.argoproj.io/title: Calibrate 4D STEM data + workflows.argoproj.io/title: Calibrate ptycho STEM data workflows.argoproj.io/description: | - A utility which takes in a 4D STEM data set and outs the approximate real space pixel size, measured camera length and scan rotation (based off dpc). + A utility which takes in a 4D STEM data set and outs the approximate real space pixel size, measured camera length and scan rotation, based off dpc workflows.diamond.ac.uk/repository: "https://github.com/DiamondLightSource/imaging-workflows" workflows.diamond.ac.uk/parameter-schema: | {{- .Files.Get "schema/notebook_Schema.json" | nindent 6 }} workflows.diamond.ac.uk/ui-schema: | {{- .Files.Get "schema/notebook_ui.json" | nindent 6 }} spec: - entrypoint: mount-files + entrypoint: calibration-notebook arguments: parameters: - name: visitdir @@ -73,7 +73,7 @@ spec: image: gitlab.diamond.ac.uk:5050/scisoft/ptychography/dimtools/mib2x volumeMounts: - name: session - mountPath: "{{`{{ workflows.parameters.visitdir }}`}}" + mountPath: "{{`{{ workflow.parameters.visitdir }}`}}" - name: tmp mountPath: /tmp - name: software @@ -85,12 +85,12 @@ spec: OUTPUT="{{`{{workflow.parameters.visitdir}}`}}"/processing/workflows/ python -m papermill "{{`{{workflow.parameters.visitdir}}`}}"/processing/workflows/Ptycho_calibration.ipynb $OUTPUT/Calibrate-notebook.ipynb \ -p visit "{{`{{ workflow.parameters.visitdir }}`}}" - -p sample "{{`{{ workflows.parameters.sample }}`}}" - -p timestamp "{{`{{workflows.parameters.timestamp}}`}}" + -p sample "{{`{{ workflow.parameters.sample }}`}}" + -p timestamp "{{`{{workflow.parameters.timestamp}}`}}" -p maskpath /software/29042024_12bitmask2.h5 - -p outpath "{{`{{workflows.parameters.outpath}}`}}" - -p lower "{{`{{workflows.parameters.thresh_lower}}`}}" - -p upper "{{`{{workflows.parameters.thresh_upper}}`}}" + -p outpath "{{`{{workflow.parameters.outpath}}`}}" + -p lower "{{`{{workflow.parameters.thresh_lower}}`}}" + -p upper "{{`{{workflow.parameters.thresh_upper}}`}}" > $OUTPUT/papermill.log 2>&1 python -m jupyter nbconvert $OUTPUT/Calibrate-notebook.ipynb \ @@ -112,9 +112,9 @@ spec: resources: requests: cpu: 10 - memory: 30Gi + memory: 50Gi limits: cpu: 10 - memory: 30Gi + memory: 50Gi \ No newline at end of file