DEV: identify dup fmap

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