From 204b818a0e2e35f76261e1d71cdb600091caf50a Mon Sep 17 00:00:00 2001 From: frederick Date: Wed, 6 May 2026 10:49:38 +0100 Subject: [PATCH 1/2] check the current directory of the container --- e02/templates/mib2x-auto-virtual-images.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/e02/templates/mib2x-auto-virtual-images.yaml b/e02/templates/mib2x-auto-virtual-images.yaml index eb99db0..07b904a 100644 --- a/e02/templates/mib2x-auto-virtual-images.yaml +++ b/e02/templates/mib2x-auto-virtual-images.yaml @@ -222,6 +222,7 @@ spec: source: | #!/bin/sh #set -e + pwd cmd=("{{`{{inputs.parameters.hdf5_files}}`}}") echo "Executing: ${cmd}" exec "${cmd}" From b45d48a1b79eb504bf24b15b21f3dffa90ca89c1 Mon Sep 17 00:00:00 2001 From: frederick Date: Wed, 6 May 2026 17:00:27 +0100 Subject: [PATCH 2/2] fixing relative path of python function --- 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 07b904a..de4f83a 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 /home/ruska/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 /home/ruska/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