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virtual images workflow update #191

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Merged
fallars merged 7 commits into from
May 6, 2026
+4 −3
Merged

virtual images workflow update #191

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0555f29
Merge pull request #188 from DiamondLightSource/main
fallars May 5, 2026
f563508
Merge pull request #6 from DiamondLightSource/E02_auto_mib
fallars May 5, 2026
dadc0c0
updating the python call construction (find-hdf5-files) within the vi…
fallars May 5, 2026
a6dbc25
Merge pull request #189 from fallars/E02_auto_mib
fallars May 5, 2026
46ebd2f
small chnage to see if this fixes the linting errors?
fallars May 6, 2026
cca3372
Merge branch 'DiamondLightSource:E02_auto_mib' into E02_auto_mib
fallars May 6, 2026
a01f69f
Merge pull request #190 from fallars/E02_auto_mib
fallars May 6, 2026
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7 changes: 4 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 @@ -181,8 +181,8 @@ spec:

todo, checks = check_dataset(hdf5_files,hdf5_timestamps,[no_vir,no_dpc,no_par])
for item,x in enumerate(todo):
cmd_list.append('python py4DSTEM_Virtual_Image_clean.py %s --virtual-images %s --dpc-images %s --plax %s' %(hdf5_files[todo[item]],checks[0][todo[item]],checks[1][todo[item]],checks[2][todo[item]]))
logging.append('python py4DSTEM_Virtual_Image_clean.py %s --virtual-images %s --dpc-images %s --plax %s' %(hdf5_files[todo[item]],checks[0][todo[item]],checks[1][todo[item]],checks[2][todo[item]]))
cmd_list.append('python py4DSTEM_Virtual_Image.py --hdf5-path %s --disk-thrs-low %f --disk-thrs-up %f --virtual-images %s --dpc-images %s --plax %s --mask-path %s' %(hdf5_files[todo[item]],0.05,0.2,checks[0][todo[item]],checks[1][todo[item]],checks[2][todo[item]],"/home/ruska/29042024_12bitmask2.h5"))
logging.append('python py4DSTEM_Virtual_Image.py --hdf5-path %s --disk-thrs-low %f --disk-thrs-up %f --virtual-images %s --dpc-images %s --plax %s --mask-path %s' %(hdf5_files[todo[item]],0.05,0.2,checks[0][todo[item]],checks[1][todo[item]],checks[2][todo[item]],"/home/ruska/29042024_12bitmask2.h5"))

#ToDo think about this printing in the context of an Error
#this should be try statement
Expand Down Expand Up @@ -221,10 +221,11 @@ spec:
command: [sh]
source: |
#!/bin/sh
#set -e
cmd=("{{`{{inputs.parameters.hdf5_files}}`}}")
echo "Executing: ${cmd}"
exec "${cmd}"
#set -e

podSpecPatch: |
containers:
- name: main
Expand Down