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Adding workflow to use the example notebook in /e02/notebooks
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‎e02/schema/notebook_Schema.json‎

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{
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"type": "object",
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"description": "inputs for ePSIC notebook which calibrates 4D STEM data",
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"properties": {
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"sample": {
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"default": null,
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"maxLength": 128,
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"minLength": 1,
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"title": "Sample name",
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"type": "string"
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},
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"timestamp": {
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"default": null,
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"maxLength": 1,
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"minLength": 128,
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"title": "Time stamp",
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"type": "string"
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},
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"thresh_lower": {
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"default": 0.05,
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"maximum": 0.95,
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"minimum": 0,
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"title": "The lower threshold",
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"type": "number"
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},
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"thresh_upper": {
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"default": 0.2,
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"maximum": 1,
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"minimum": 0.05,
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"title": "The upper threshold",
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"type": "number"
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}
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},
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"title": "Calibration of 4D STEM data notebook"
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}
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‎e02/schema/notebook_ui.json‎

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{
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"type": "VerticalLayout",
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"options": {
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"formWidth": "80%"
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},
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"elements": [
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{
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"type": "Group",
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"label": "ePSIC notebook which calibrates 4D STEM data",
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"elements": [
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{
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"type": "VerticalLayout",
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"elements": [
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{
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"type": "Control",
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"label": "Name of the sample",
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"scope": "#/properties/sample"
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},
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{
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"type": "Control",
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"label": "Time stamp of the data to process",
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"scope": "#/properties/timestamp"
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},
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{
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"type": "Control",
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"label": "The lower threshold",
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"scope": "#/properties/thresh_lower"
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},
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{
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"type": "Control",
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"label": "The upper threshold",
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"scope": "#/properties/thresh_upper"
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}
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]
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}
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]
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}
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]
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}

‎e02/templates/Notebook.yaml‎

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apiVersion: argoproj.io/v1alpha1
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kind: ClusterWorkflowTemplate
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metadata:
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name: Calibrate4DSTEM
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labels:
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workflows.diamond.ac.uk/science-group-imaging: "true"
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annotations:
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workflows.argoproj.io/title: Calibrate 4D STEM data
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workflows.argoproj.io/description: |
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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).
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workflows.diamond.ac.uk/repository: "https://github.com/DiamondLightSource/imaging-workflows"
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workflows.diamond.ac.uk/parameter-schema: |
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{{- .Files.Get "schema/Calibrate4DSTEMSchema.json" | nindent 6 }}
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workflows.diamond.ac.uk/ui-schema: |
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{{- .Files.Get "schema/Calibrate4DSTEMUISchema.json" | nindent 6 }}
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spec:
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entrypoint: mount-files
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arguments:
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parameters:
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- name: visitdir
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valueFrom:
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configMapKeyRef:
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name: sessionspaces
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key: data_directory
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volumeClaimTemplates:
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- metadata:
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name: tmp
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spec:
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accessModes:
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- ReadWriteOnce
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resources:
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requests:
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storage: 2Gi
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storageClassName: netapp
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templates:
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- name: calibration-notebook
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steps:
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- - name: copy-notebook
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template: mount-files
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- - name: run-notebook
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template: notebook
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- name: mount-files
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script:
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image: debian:stable-slim
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volumeMounts:
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- name: tmp
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mountPath: /tmp
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- name: session
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mountPath: "{{`{{ workflow.parameters.visitdir }}`}}"
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command: [bash]
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source: |
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OUTPUT="{{`{{workflow.parameters.visitdir}}`}}"/processing/workflows/
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mkdir -p $OUTPUT
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echo "something!"
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echo '{{ .Files.Get "notebooks/Ptycho_calibration.ipynb" | b64enc }}' | base64 -d > $OUTPUT/Ptycho_calibration.ipynb
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- name: notebook
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inputs:
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parameters:
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- name: sample
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value: "{{`{{workflow.parameters.sample}}`}}"
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- name: timestamp
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value: "{{`{{workflow.parameters.timestamp}}`}}"
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- name: outpath
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value: "{{`{{workflow.parameters.outpath}}`}}"
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- name: thresh_lower
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value: "{{`{{workflow.parameters.thresh_lower}}`}}"
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- name: thresh_upper
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value: "{{`{{workflow.parameters.thresh_upper}}`}}"
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script:
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image: gitlab.diamond.ac.uk:5050/scisoft/ptychography/dimtools/mib2x
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volumeMounts:
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- name: session
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mountPath: "{{`{{ workflows.parameters.visitdir }}`}}"
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- name: tmp
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mountPath: /tmp
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- name: software
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mountPath: /dls_sw/e02/medipix_mask
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command: [bash]
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source: |
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ERROR_TXT="raise error"
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ERROR_STR="An error occured within the notebook. Please open the output file to check"
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OUTPUT="{{`{{workflow.parameters.visitdir}}`}}"/processing/workflows/
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python -m papermill "{{`{{workflow.parameters.visitdir}}`}}"/processing/workflows/Ptycho_calibration.ipynb $OUTPUT/Calibrate-notebook.ipynb \
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-p visit "{{`{{ workflow.parameters.visitdir }}`}}"
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-p sample "{{`{{ workflows.parameters.sample }}`}}"
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-p timestamp "{{`{{workflows.parameters.timestamp}}`}}"
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-p maskpath /software/29042024_12bitmask2.h5
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-p outpath "{{`{{workflows.parameters.outpath}}`}}"
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-p lower "{{`{{workflows.parameters.thresh_lower}}`}}"
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-p upper "{{`{{workflows.parameters.thresh_upper}}`}}"
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> $OUTPUT/papermill.log 2>&1
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python -m jupyter nbconvert $OUTPUT/Calibrate-notebook.ipynb \
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--to html
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outputs:
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artifacts:
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- name: phase-output
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path: "{{`{{ inputs.parameters.outpath }}`}}/phase-output.html"
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archive:
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none: {}
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- name: notebook-log
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path: "{{`{{ inputs.parameters.outpath }}`}}/papermill.log"
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archive:
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none: {}
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podSpecPatch: |
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containers:
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- name: main
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resources:
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requests:
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cpu: 10
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memory: 30Gi
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limits:
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cpu: 10
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memory: 30Gi
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