Adding workflow to use the example notebook in /e02/notebooks

e02/schema/notebook_Schema.json

@@ -0,0 +1,36 @@
+{
+  "type": "object",
+    "description": "inputs for ePSIC notebook which calibrates 4D STEM data",
+    "properties": {
+        "sample": {
+            "default": null,
+            "maxLength": 128,
+            "minLength": 1,
+            "title": "Sample name",
+            "type": "string"
+        },
+        "timestamp": {
+            "default": null,
+            "maxLength": 1,
+            "minLength": 128,
+            "title": "Time stamp",
+            "type": "string"
+        },
+        "thresh_lower": {
+            "default": 0.05,
+            "maximum": 0.95,
+            "minimum": 0,
+            "title": "The lower threshold",
+            "type": "number"
+        },
+        "thresh_upper": {
+            "default": 0.2,
+            "maximum": 1,
+            "minimum": 0.05,
+            "title": "The upper threshold",
+            "type": "number"
+        }
+    },
+    "title": "Calibration of 4D STEM data notebook"
+}
+

e02/schema/notebook_ui.json

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

e02/templates/Notebook.yaml

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