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do papermill injection in-place #124

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Merged
daurer merged 1 commit into from
Mar 3, 2026
Merged

do papermill injection in-place #124

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14 changes: 8 additions & 6 deletions i14/templates/xrf-tomo-template.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ spec:
- name: outputFolder
value: "testing"
- name: multiScan
value: '[{"multiScan":{"start":423844,"end":423934,"excluded":[423908,423909,423911,423916,423917]}},{"multiScan":{"start":423938,"end":423941,"excluded":[423940]}},{"multiScan":{"start":423946,"end":423947,"excluded":[]}}]'
value: '[{"multiScan":{"start":423844,"end":423947,"excluded":[423908,423909,423911,423916,423917,423935,423936,423937,423940,423942,423943,423944,423945]}}]'
- name: multiEdge
value: '[{"edgeElement":"Pb","edgeTransition":"La"},{"edgeElement":"Br","edgeTransition":"Ka"}]'
- name: elementToAlign
Expand Down Expand Up @@ -131,14 +131,15 @@ spec:

cd $OUTPUT
python -m papermill \
$OUTPUT/align_initial.ipynb $OUTPUT/align_initial_with_params.ipynb \
$OUTPUT/align_initial.ipynb $OUTPUT/align_initial.ipynb \
-p inpath "tomo_xrf_${START}_${END}_${EDGE}.nxs" \
-p outpath_nexus "${EDGE}_aligned_initial.nxs" \
-p outpath_shifts "${EDGE}_shifts.txt" \
-p alignment_section "{{`{{ workflow.parameters.alignmentSection }}`}}" \
-p alignment_band "{{`{{ workflow.parameters.alignmentBand }}`}}"
--prepare-only

python -m jupyter nbconvert --to html --execute --output align_initial --output-dir $OUTPUT/_assets --embed-images $OUTPUT/align_initial_with_params.ipynb
python -m jupyter nbconvert --to html --execute --output align_initial --output-dir $OUTPUT/_assets --embed-images $OUTPUT/align_initial.ipynb
volumeMounts:
- name: session
mountPath: "{{`{{ workflow.parameters.visitdir }}`}}"
Expand Down Expand Up @@ -206,13 +207,14 @@ spec:

cd $OUTPUT
python -m papermill \
$OUTPUT/align_and_normalise.ipynb $OUTPUT/align_and_normalise_with_params.ipynb \
$OUTPUT/align_and_normalise.ipynb $OUTPUT/align_and_normalise.ipynb \
-p inpath "tomo_xrf_${START}_${END}_${ELEMENT}-${TRANSITION}.nxs" \
-p inpath_shifts "${EDGE2ALIGN}_shifts.txt"
-p inpath_shifts "${EDGE2ALIGN}_shifts.txt" \
-p outpath_nexus "${ELEMENT}-${TRANSITION}_aligned.nxs" \
-p normalise "{{`{{ workflow.parameters.normalise }}`}}" \
--prepare-only \

python -m jupyter nbconvert --to html --execute --output align_and_normalise --output-dir $OUTPUT/_assets --embed-images $OUTPUT/align_and_normalise_with_params.ipynb
python -m jupyter nbconvert --to html --execute --output align_and_normalise --output-dir $OUTPUT/_assets --embed-images $OUTPUT/align_and_normalise.ipynb
volumeMounts:
- name: session
mountPath: "{{`{{ workflow.parameters.visitdir }}`}}"
Expand Down