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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,62 +1,95 @@ | ||
| # Define a file to log errors | ||
| error_log="error_log_funcanat.txt" | ||
| ## TODO: change the file so that the dup is the earlier scan | ||
| ## the latter scan should be better. always. | ||
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| # Define a file to log errors | ||
| # error_log="error_log_funcanat.txt" | ||
| LOG_FILE="fmap_error_log.txt" | ||
| # mapfile -t dup_files < <(find . -type f -name '*__dup-*') | ||
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| dup_files=() | ||
| while IFS= read -r -d $'\n' file; do | ||
| dup_files+=("$file") | ||
| done < <(find . -type f -name '*fmap__dup-*') | ||
| done < <(find . -type f -name '**/fmap/*__dup-*') | ||
| # done < <(find . -type f -path '*/func/*__dup-*') | ||
| # Loop through each file found. | ||
| for DUPJSON in "${dup_files[@]}"; do | ||
| # Use jq to extract TR values. | ||
| DUPJSON_TR=$(jq '.dcmmeta_shape[3]' "${DUPJSON}") | ||
| BOLDJSON=$(echo "${DUPJSON}" | sed 's/__dup-[0-9]*//') | ||
| BOLDJSON_TR=$(jq '.dcmmeta_shape[3]' "${BOLDJSON}") | ||
| if [[ "$BOLDJSON_TR" == "null" || "$BOLDJSON_TR" =~ "error" ]]; then | ||
| echo "$BOLDJSON: Error extracting TR value." >> "$error_log" | ||
| DUPJSON_TR=$(jq '.AcquisitionTime' "${DUPJSON}") | ||
| PRIMARYJSON=$(echo "${DUPJSON}" | sed 's/__dup-[0-9]*//') | ||
| PRIMARYJSON_TR=$(jq '.AcquisitionTime' "${PRIMARYJSON}") | ||
| if [[ "$PRIMARYJSON_TR" == "null" || "$PRIMARYJSON_TR" =~ "error" ]]; then | ||
| echo "$PRIMARYJSON: Error extracting TR value." >> "$error_log" | ||
| continue | ||
| fi | ||
| # Initialize a flag to indicate a matching key has been found. | ||
| found_match=0 | ||
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| # Attempt to extract a meaningful part of the filename to match against array keys. | ||
| filename=$(basename "$DUPJSON") | ||
| filename=${filename%__dup-*} | ||
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| # Iterate over keys in myArray. | ||
| for key in "${!myArray[@]}"; do | ||
| if [[ "$filename" == *"$key"* ]]; then | ||
| found_match=1 | ||
| EXPECTED_TR=${myArray[$key]} | ||
| echo "Found matching key: $key with TR: $EXPECTED_TR for file $DUPJSON" | ||
| if [[ "$BOLDJSON_TR" -eq "$EXPECTED_TR" && "$DUPJSON_TR" -lt "$BOLDJSON_TR" ]]; then | ||
| echo "Conditions met for $DUPJSON. Removing file." | ||
| # Uncomment the next line to perform file removal | ||
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| # generic_filename=$(echo "$DUPJSON" | sed -E 's/(run-[0-9]+_).+(__dup-.+)/\1*\2/') | ||
| generic_filename=$(echo "$DUPJSON" | sed -E 's/(run-[0-9]+_).+(__dup-[0-9]+).*/\1*\2.*/') | ||
| read -a files_to_remove <<< "$generic_filename" | ||
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| # Loop through the array and remove each file | ||
| for rm_file in "${files_to_remove[@]}"; do | ||
| git rm "$rm_file" | ||
| done | ||
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| else | ||
| # Handle errors | ||
| if [[ "$DUPJSON_TR" -ge "$BOLDJSON_TR" ]]; then | ||
| echo "$DUPJSON: DUPJSON_TR (${DUPJSON_TR}) is not smaller than BOLDJSON_TR (${BOLDJSON_TR})." >> "$error_log" | ||
| fi | ||
| if [[ "$BOLDJSON_TR" -ne "$EXPECTED_TR" ]]; then | ||
| echo "$BOLDJSON: BOLDJSON_TR (${BOLDJSON_TR}) does not match EXPECTED_TR ($EXPECTED_TR)." >> "$error_log" | ||
| fi | ||
| fi | ||
| break | ||
| fi | ||
| done | ||
| if [[ $found_match -eq 0 ]]; then | ||
| echo "No matching key found in the array for $DUPJSON" | ||
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| PRIMARYJSON_SEC=$(echo $PRIMARYJSON_TR | awk -F: '{ print ($1 * 3600) + ($2 * 60) + $3 }') | ||
| DUPJSON_SEC=$(echo $DUPJSON_TR | awk -F: '{ print ($1 * 3600) + ($2 * 60) + $3 }') | ||
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| # Compare the numeric values | ||
| if (( $(echo "$PRIMARYJSON_SEC < $DUPJSON_SEC" |bc -l) )); then | ||
| echo "PRIMARYJSON acquisition time is earlier." >> $LOG_FILE | ||
| echo "Error: PRIMARYJSON has an earlier time than DUPJSON" >> $LOG_FILE | ||
| elif (( $(echo "$PRIMARYJSON_SEC > $DUPJSON_SEC" |bc -l) )); then | ||
| echo "DUPJSON acquisition time is earlier." >> $LOG_FILE | ||
| echo "Info: DUPJSON is identified as the correct file due to earlier acquisition time." >> $LOG_FILE | ||
| generic_filename=$(echo "$DUPJSON" | sed -E 's/(run-[0-9]+_).+(__dup-[0-9]+).*/\1*\2.*/') | ||
| read -a files_to_remove <<< "$generic_filename" | ||
| echo "removed files: ${generic_filename}" >> $LOG_FILE | ||
| # Loop through the array and remove each file | ||
| for rm_file in "${files_to_remove[@]}"; do | ||
| echo "remove!" | ||
| # git rm "$rm_file" | ||
| done | ||
| else | ||
| echo "Acquisition times are the same." >> $LOG_FILE | ||
| # Log as error or info since times being the same might be unexpected | ||
| echo "Warning: PRIMARYJSON and DUPJSON have the same acquisition time." >> $LOG_FILE | ||
| fi | ||
| done | ||
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| # # Initialize a flag to indicate a matching key has been found. | ||
| # found_match=0 | ||
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| # # Attempt to extract a meaningful part of the filename to match against array keys. | ||
| # filename=$(basename "$DUPJSON") | ||
| # filename=${filename%__dup-*} | ||
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| # # Iterate over keys in myArray. | ||
| # for key in "${!myArray[@]}"; do | ||
| # if [[ "$filename" == *"$key"* ]]; then | ||
| # found_match=1 | ||
| # EXPECTED_TR=${myArray[$key]} | ||
| # echo "Found matching key: $key with TR: $EXPECTED_TR for file $DUPJSON" | ||
| # if [[ "$PRIMARYJSON_TR" -eq "$EXPECTED_TR" && "$DUPJSON_TR" -lt "$PRIMARYJSON_TR" ]]; then | ||
| # echo "Conditions met for $DUPJSON. Removing file." | ||
| # # Uncomment the next line to perform file removal | ||
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| # # generic_filename=$(echo "$DUPJSON" | sed -E 's/(run-[0-9]+_).+(__dup-.+)/\1*\2/') | ||
| # generic_filename=$(echo "$DUPJSON" | sed -E 's/(run-[0-9]+_).+(__dup-[0-9]+).*/\1*\2.*/') | ||
| # read -a files_to_remove <<< "$generic_filename" | ||
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| # # Loop through the array and remove each file | ||
| # for rm_file in "${files_to_remove[@]}"; do | ||
| # git rm "$rm_file" | ||
| # done | ||
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| # else | ||
| # # Handle errors | ||
| # if [[ "$DUPJSON_TR" -ge "$PRIMARYJSON_TR" ]]; then | ||
| # echo "$DUPJSON: DUPJSON_TR (${DUPJSON_TR}) is not smaller than PRIMARYJSON_TR (${PRIMARYJSON_TR})." >> "$error_log" | ||
| # fi | ||
| # if [[ "$PRIMARYJSON_TR" -ne "$EXPECTED_TR" ]]; then | ||
| # echo "$PRIMARYJSON: PRIMARYJSON_TR (${PRIMARYJSON_TR}) does not match EXPECTED_TR ($EXPECTED_TR)." >> "$error_log" | ||
| # fi | ||
| # fi | ||
| # break | ||
| # fi | ||
| # done | ||
| # if [[ $found_match -eq 0 ]]; then | ||
| # echo "No matching key found in the array for $DUPJSON" | ||
| # fi | ||
| # done |