From dadc0c00f31be5a82b724a76703d8c02b6b7e683 Mon Sep 17 00:00:00 2001 From: frederick Date: Tue, 5 May 2026 15:17:41 +0100 Subject: [PATCH 1/2] updating the python call construction (find-hdf5-files) within the virtual images workflow. aslo updated the inputs to the python function. these changes shouldthe number of incured errors --- e02/templates/mib2x-auto-virtual-images.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/e02/templates/mib2x-auto-virtual-images.yaml b/e02/templates/mib2x-auto-virtual-images.yaml index bda378a..b5d85b5 100644 --- a/e02/templates/mib2x-auto-virtual-images.yaml +++ b/e02/templates/mib2x-auto-virtual-images.yaml @@ -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 From 46ebd2fc3c4ee3e131f122bcf4b5fc83b33f1d0e Mon Sep 17 00:00:00 2001 From: frederick Date: Wed, 6 May 2026 09:43:55 +0100 Subject: [PATCH 2/2] small chnage to see if this fixes the linting errors? --- e02/templates/mib2x-auto-virtual-images.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/e02/templates/mib2x-auto-virtual-images.yaml b/e02/templates/mib2x-auto-virtual-images.yaml index b5d85b5..eb99db0 100644 --- a/e02/templates/mib2x-auto-virtual-images.yaml +++ b/e02/templates/mib2x-auto-virtual-images.yaml @@ -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.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")) + 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 @@ -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