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fixing errors: changing workflows into workflow #268

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Merged
fallars merged 2 commits into from
Jul 22, 2026
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fixing errors: changing workflows into workflow #268

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6bdf266
Merge pull request #10 from DiamondLightSource/E02_auto_mib
fallars Jul 22, 2026
10dfe83
fixing errors: changing workflows into workflow
fallars Jul 22, 2026
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14 changes: 7 additions & 7 deletions e02/templates/Notebook.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand Down Expand Up @@ -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
Expand All @@ -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 \
Expand Down