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updating mib2x-auto-virtual-images.yaml to test functionality #187

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Merged
fallars merged 5 commits into from
Apr 29, 2026
Merged

updating mib2x-auto-virtual-images.yaml to test functionality #187

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6f7cc6f
Merge pull request #185 from DiamondLightSource/main
fallars Apr 29, 2026
46309bb
Merge pull request #5 from DiamondLightSource/E02_auto_mib
fallars Apr 29, 2026
8cea6c4
turning off hard coded visit path and enabling container operation on…
fallars Apr 29, 2026
ce8dd24
adding repository to template
fallars Apr 29, 2026
03ce716
Merge pull request #186 from fallars/E02_auto_mib
fallars Apr 29, 2026
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9 changes: 6 additions & 3 deletions e02/templates/mib2x-auto-virtual-images.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ metadata:
labels:
workflows.diamond.ac.uk/science-group-imaging: "true"
annotations:
workflows.diamond.ac.uk/repository: https://github.com/DiamondLightSource/imaging-workflows
workflows.argoproj.io/title: ePSIC Parallel virtual image generation
workflows.argoproj.io/description: |
This workflow takes a 4DSTEM hdf5 file and perfroms post-processing in order to make varoius vitual images. Such as virtual bright/dark field images, differential phase constrast images and parrallax images
Expand Down Expand Up @@ -62,7 +63,7 @@ spec:
inputs:
parameters:
- name: sample_name
value: workflows_testing
value: "{{`{{workflow.parameters.sample_name}}`}}"
outputs:
artifacts:
- name: find_files_logging
Expand Down Expand Up @@ -139,7 +140,7 @@ spec:
verbose = True

#start search for MIB files
os.chdir('%s/processing/Merlin/%s' % ("{{`{{workflow.parameters.visitdir}}`}}", 'workflows_testing'))
os.chdir('%s/processing/Merlin/%s' % ("{{`{{workflow.parameters.visitdir}}`}}", "{{`{{ workflow.parameters.sample_name }}`}}"))


source_path = os.getcwd() + '/'
Expand Down Expand Up @@ -220,7 +221,9 @@ spec:
command: [sh]
source: |
#!/bin/sh
echo "{{`{{inputs.parameters.hdf5_files}}`}}"
cmd=("{{`{{inputs.parameters.hdf5_files}}`}}")
echo "Executing: ${cmd}"
exec "${cmd}"
#set -e
podSpecPatch: |
containers:
Expand Down