diff --git a/e02/schema/notebook_Schema.json b/e02/schema/notebook_Schema.json index baa6af7..fb2cfce 100644 --- a/e02/schema/notebook_Schema.json +++ b/e02/schema/notebook_Schema.json @@ -29,6 +29,13 @@ "minimum": 0.05, "title": "The upper threshold", "type": "number" + }, + "maskpath": { + "deafult": null, + "minlength": 0, + "maxlength": 100, + "title": "Mask path", + "type": "string" } }, "title": "Calibration of 4D STEM data notebook" diff --git a/e02/schema/notebook_ui.json b/e02/schema/notebook_ui.json index 24c882d..cfff84a 100644 --- a/e02/schema/notebook_ui.json +++ b/e02/schema/notebook_ui.json @@ -30,6 +30,11 @@ "type": "Control", "label": "The upper threshold", "scope": "#/properties/thresh_upper" + }, + { + "type": "Control", + "label": "The path to the mask, to be applied to the 4DSTEM data", + "scope": "#/properties/maskpath" } ] } diff --git a/e02/templates/Notebook_simple.yaml b/e02/templates/Notebook_simple.yaml index 035678d..5c754e0 100644 --- a/e02/templates/Notebook_simple.yaml +++ b/e02/templates/Notebook_simple.yaml @@ -62,6 +62,8 @@ spec: value: "{{`{{workflow.parameters.sample}}`}}" - name: timestamp value: "{{`{{workflow.parameters.timestamp}}`}}" + - name: maskpath + value: "{{`{{workflow.parameters.maskpath}}`}}" - name: thresh_lower value: "{{`{{workflow.parameters.thresh_lower}}`}}" - name: thresh_upper @@ -83,10 +85,10 @@ spec: -p visit "{{`{{ workflow.parameters.visitdir }}`}}" \ -p sample "{{`{{ workflow.parameters.sample }}`}}" \ -p timestamp "{{`{{workflow.parameters.timestamp}}`}}" \ - -p maskpath "/home/ruska/29042024_12bitmask2.h5" \ + -p maskpath "{{`{{workflow.parameters.maskpath}}`}}" \ -p lower "{{`{{workflow.parameters.thresh_lower}}`}}" \ -p upper "{{`{{workflow.parameters.thresh_upper}}`}}" \ - > $OUTPUT/papermill.log 2>&1 + > $OUTPUT/papermill.log 2>&1 -k python3 python -m jupyter nbconvert $OUTPUT/Calibrate-notebook.ipynb \ --to html