diff --git a/spacetop_prep/datalad/remove_dups_anatfmap.sh b/spacetop_prep/datalad/remove_dups_anatfmap.sh index fc525c1..0b79187 100644 --- a/spacetop_prep/datalad/remove_dups_anatfmap.sh +++ b/spacetop_prep/datalad/remove_dups_anatfmap.sh @@ -10,6 +10,11 @@ LOG_FILE="fmap_error_log.txt" if [ -f "$LOG_FILE" ]; then rm "$LOG_FILE" fi + +SUMMARYLOG_FILE="fmap_summary_log.txt" +if [ -f "$SUMMARYLOG_FILE" ]; then + rm "$SUMMARYLOG_FILE" +fi # mapfile -t dup_files < <(find . -type f -name '*__dup-*') dup_files=() @@ -31,25 +36,38 @@ PRIMARYJSON_NODEC=${PRIMARYJSON_TR%%.*} DUPJSON_NODEC=${DUPJSON_TR%%.*} PRIMARYJSON_SEC=$(echo $PRIMARYJSON_NODEC | tr -d '"'| awk -F: '{ print ($1 * 3600) + ($2 * 60) + $3 }') DUPJSON_SEC=$(echo $DUPJSON_NODEC | tr -d '"' | awk -F: '{ print ($1 * 3600) + ($2 * 60) + $3 }') -#PRIMARYJSON_SEC=$(echo $PRIMARYJSON_TR | awk -F: '{ split($3, a, "."); print ($1 * 3600) + ($2 * 60) + a[1] }') -#DUPJSON_SEC=$(echo $DUPJSON_TR | awk -F: '{ split($3, a, "."); print ($1 * 3600) + ($2 * 60) + a[1] }') # Compare the numeric values #if (( $(echo "$PRIMARYJSON_SEC < $DUPJSON_SEC" |bc -l) )); then if [ "$PRIMARYJSON_SEC" -lt "$DUPJSON_SEC" ]; then echo -e "\n${DUPJSON}\nPRIMARYJSON acquisition time is earlier." >> $LOG_FILE - echo -e "Error: PRIMARYJSON ${PRIMARYJSON_NODEC} ${PRIMARYJSON_SEC} has an earlier time than DUPJSON ${DUPJSON_NODEC} ${DUPJSON_SEC}\n\n" >> $LOG_FILE + echo -e "\n>>>>> ERROR: PRIMARYJSON ${PRIMARYJSON_NODEC} ${PRIMARYJSON_SEC} has an earlier time than DUPJSON ${DUPJSON_NODEC} ${DUPJSON_SEC}\n\n" >> $LOG_FILE + + # SWAP DUP AND PRIMARY, THEN DELETED + PRIMARYGZ=${PRIMARYJSON} + DUPGZ=${DUPJSON} #TODO remove file extension + # RENAME JSON primary is crap, keep dup + # ../../../code/rename_file "${PRIMARYJSON}" CRAPJSON; + # ../../../code/rename_file "${DUPJSON}" "${PRIMARYJSON}"; + # ../../../code/rename_file CRAPJSON "${DUPJSON}" + # # RENAME fmap + # ../../../code/rename_file "${PRIMARYGZ}" CRAPNII; + # ../../../code/rename_file "${DUPGZ}" "${PRIMARYGZ}"; + # ../../../code/rename_file CRAPNII "${DUPGZ}" + # DELETE files + # git rm "${DUPGZ}" + # git rm "${DUPJSON}" elif [ "$PRIMARYJSON_SEC" -gt "$DUPJSON_SEC" ]; then #elif (( $(echo "$PRIMARYJSON_SEC > $DUPJSON_SEC" |bc -l) )); then echo -e "\nDUPJSON acquisition time is earlier." >> $LOG_FILE - echo -e "Info: DUPJSON is identified as the correct file due to earlier acquisition time." >> $LOG_FILE + echo -e "Info: DUPJSON is identified as the correct file due to earlier acquisition time." >> $SUMMARYLOG_FILE generic_filename=$(echo "$DUPJSON" | sed -E 's/(run-[0-9]+_).+(__dup-[0-9]+).*/\1*\2.*/') read -a files_to_remove <<< "$generic_filename" echo -e "removed files: ${generic_filename}\n\n" >> $LOG_FILE # Loop through the array and remove each file for rm_file in "${files_to_remove[@]}"; do echo "remove!" - # git rm "$rm_file" + git rm "$rm_file" done else echo -e "\n${DUPJSON}\nAcquisition times are the same." >> $LOG_FILE