38 lines
1 KiB
Bash
Executable file
38 lines
1 KiB
Bash
Executable file
#/bin/bash
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#
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# create CVS for atlases included in CAT peprocessing and get QC
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#
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### use 'true' as input var if dataset containes sites: "./doCSV+QC_ses.sh true"
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sites=$1
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mkdir outputs
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DS=$(basename $PWD)
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### if there are sites, things get complicated ###
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if ( ${sites} ); then
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datalad get */sub*/ses*/report/cat_*.xml */sub*/ses*/label/cat*.xml
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for site in *; do
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if [ -d ${site} ] && [ ${site} != "logs" ] && [ ${site} != "code" ] \
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&& [ ${site} != "inputs" ] && [ ${site} != "outputs" ]; then
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echo ${site}
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cd ${site}
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echo "table name: ${DS2}"
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for sub in sub-*; do
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for subses in $sub/ses-*; do
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echo "./../code/xml2csv_ses.py ../outputs/${site} ${subses}"
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./../code/xml2csv.py ../outputs/${site} ${subses}
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done
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done
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cd ..
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fi
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done
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else
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datalad get sub*/ses*/report/cat_*.xml sub*/ses*/label/cat*.xml
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for sub in sub-*; do
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for subses in $sub/ses-*; do
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./code/xml2csv.py outputs/${DS} ${subses}
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done
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done
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fi
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