DEV: find dups

spacetop_prep/datalad/remove_dups_anatfmap.sh

@@ -17,12 +17,11 @@ 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=()
 while IFS= read -r -d $'\n' file; do
     dup_files+=("$file")
-done < <(find . -type f -path "*/fmap/*__dup-*.json")
+done < <(find . -path "*/fmap/*__dup-*.json")
 
 # Loop through each file found.
 for DUPJSON in "${dup_files[@]}"; do

spacetop_prep/datalad/remove_dups_fmap_sub-0057.sh

@@ -0,0 +1,33 @@
+#!/bin/bash
+
+# Function to handle renaming for a given direction
+rename_fmapdup() {
+    local DIRECTION="$1"
+    local RUN_NUM_ORIG="$2"
+    local RUN_NUM_NEW="$3"
+
+    # Construct original and new JSON filenames based on direction and run numbers
+    local DUPJSON="./sub-0057/ses-01/fmap/sub-0057_ses-01_acq-mb8_dir-${DIRECTION}_run-${RUN_NUM_ORIG}_epi__dup-01.json"
+    local RENAMEJSON="./sub-0057/ses-01/fmap/sub-0057_ses-01_acq-mb8_dir-${DIRECTION}_run-${RUN_NUM_NEW}_epi.json"
+
+    # Rename the JSON file
+    datalad run ../../../code/rename_file "${DUPJSON}" "${RENAMEJSON}"
+
+    # Construct the corresponding .nii.gz filenames
+    local ORIGINAL_NII_GZ="${DUPJSON%.json}.nii.gz"
+    local NEW_NII_GZ="${RENAMEJSON%.json}.nii.gz"
+
+    # Check if the original .nii.gz file exists before attempting to rename
+    if [ -f "$ORIGINAL_NII_GZ" ]; then
+        # Rename the .nii.gz file
+        git mv "$ORIGINAL_NII_GZ" "$NEW_NII_GZ"
+        echo "Renamed $ORIGINAL_NII_GZ to $NEW_NII_GZ"
+    else
+        echo "File $ORIGINAL_NII_GZ does not exist, skipping..."
+    fi
+}
+
+# Run the renaming for both directions
+# Adjust RUN_NUM_ORIG and RUN_NUM_NEW as needed for each case
+rename_fmapdup "ap" "02" "03"
+rename_fmapdup "pa" "02" "03" # Update RUN_NUM_ORIG and RUN_NUM_NEW as per your requirements for the pa direction

spacetop_prep/datalad/remove_dups_func.sh

@@ -34,13 +34,11 @@ done
 # Define a file to log errors
 error_log="error_log.txt"
 
-# mapfile -t dup_files < <(find . -type f -name '*__dup-*')
-
 dup_files=()
 while IFS= read -r -d $'\n' file; do
     dup_files+=("$file")
-done < <(find . -type f -name '*bold__dup-*')
-# done < <(find . -type f -path '*/func/*__dup-*')
+done < <(find . -name '*bold__dup-*')
+# done < <(find .  -path '*/func/*__dup-*')
 # Loop through each file found.
 for DUPJSON in "${dup_files[@]}"; do
     # Use jq to extract TR values.

spacetop_prep/datalad/remove_fmap_sub-0122.sh

@@ -0,0 +1,35 @@
+#NEED TO REMOVE PRIMARY and rename DUP as PRIMARY
+# PRIMARYJSON="sub-0122_ses-03_acq-mb8_dir-ap_run-01_epi.json"
+DUPJSON="./sub-0122/ses-03/fmapsub-0122_ses-03_acq-mb8_dir-ap_run-01_epi__dup-01.json"
+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
+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) + $3 }')
+
+if [ "$PRIMARYJSON_SEC" -lt "$DUPJSON_SEC" ]; then
+echo -e "\n${DUPJSON}\nPRIMARYJSON acquisition time is earlier." >> $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
+     $(dirname "$0")/rename_file "${PRIMARYJSON}" CRAPJSON; 
+     $(dirname "$0")/rename_file "${DUPJSON}" "${PRIMARYJSON}"; 
+     $(dirname "$0")/rename_file CRAPJSON "${DUPJSON}"
+     # # RENAME fmap
+     $(dirname "$0")/rename_file "${PRIMARYGZ}" CRAPNII; 
+     $(dirname "$0")/rename_file "${DUPGZ}" "${PRIMARYGZ}"; 
+     $(dirname "$0")/rename_file CRAPNII "${DUPGZ}"
+     # DELETE files
+     git rm "${DUPGZ}"
+     git rm "${DUPJSON}"
+
+fi