diff --git a/e02/templates/Notebook.yaml b/e02/templates/Notebook.yaml index b676254..e82a625 100644 --- a/e02/templates/Notebook.yaml +++ b/e02/templates/Notebook.yaml @@ -5,7 +5,7 @@ metadata: 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 workflows.diamond.ac.uk/repository: "https://github.com/DiamondLightSource/imaging-workflows" @@ -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 \