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Bash script to ignore save errors when processing multiple images from command line with Cell Profiler
#!/bin/bash
n=1 #Image Set number to start processing batch
final_image=826 #Last Image Set number in your batch
cellprofiler -p ML/Batch_data.h5 -c -r -f $n -l $final_image |& tee log.txt #Here the output from terminal is save to log.txt.
while [ $? -ne 1 ]; do
#Parse log.txt file, extracting the image set # at which the error occurs
no_save_error_image=$(sed -n '/^.*ValueError:/{n;p}' log.txt | sed -n -e 's/^.Image # //p' | sed -n -e 's/, module SaveImages.$//p')
n_=$(($no_save_error_image + 1))
#Restart CellProfiler at the next image set
echo 'Restarting at Image set #' $n_
cellprofiler -p ML/Batch_data.h5 -c -r -f $n_ -l $final_image |& tee log.txt
#Once the final image set is reached stop the script
if ((n_==$final_image)); then
echo 'The last image set #:' $n_', has been processed. All images have been processed. The script will now exit.'
break
fi
done
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