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QuPath data access via json
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| #!/bin/bash | |
| # Define the base directory | |
| BASE_DIR="/Users/cercan/Desktop/BE/NU_wholeDataset_qupath/data" # Change this to your target directory | |
| OUTPUT_CSV="/Users/cercan/Desktop/BE/NU_wholeDataset_qupath/annotationData.csv" | |
| # Write the header to the CSV file | |
| echo "Name,Unclassified,Biopsy,Flow" > "$OUTPUT_CSV" | |
| # Find all subdirectories and process the JSON files | |
| find "$BASE_DIR" -type d | while read -r dir; do | |
| # Read server.json | |
| SERVER_JSON="$dir/server.json" | |
| if [[ -f "$SERVER_JSON" ]]; then | |
| NAME=$(jq -r '.metadata.name // "N/A"' "$SERVER_JSON") | |
| else | |
| NAME="N/A" | |
| fi | |
| # Read summary.json | |
| SUMMARY_JSON="$dir/summary.json" | |
| if [[ -f "$SUMMARY_JSON" ]]; then | |
| UNCLASSIFIED=$(jq -r '.hierarchy.annotationClassificationCounts.Unclassified // "0"' "$SUMMARY_JSON") | |
| BIOPSY=$(jq -r '.hierarchy.annotationClassificationCounts.biopsy // "0"' "$SUMMARY_JSON") | |
| FLOW=$(jq -r '.hierarchy.annotationClassificationCounts.flow // "0"' "$SUMMARY_JSON") | |
| else | |
| UNCLASSIFIED="0" | |
| BIOPSY="0" | |
| FLOW="0" | |
| fi | |
| # Append the data to the CSV file | |
| echo "$NAME,$UNCLASSIFIED,$BIOPSY,$FLOW" >> "$OUTPUT_CSV" | |
| done | |
| echo "Data has been written to $OUTPUT_CSV" | |
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| #!/bin/bash | |
| # Directory to start from | |
| dir="/Volumes/rsrch6/home/trans_mol_path/yuan_lab/TIER2/barrett/roi/flow/NU/QuPath_240813/data" | |
| # Loop through all subdirectories | |
| for subdir in "$dir"/*; do | |
| if [ -d "$subdir" ]; then | |
| # Check if summary.json exists and contains "flow_new" | |
| if grep -q "flow_new" "$subdir/summary.json"; then | |
| # Extract the value of "uri" from server.json | |
| uri=$(jq -r '.uri' "$subdir/server.json") | |
| # Print the value of "uri" | |
| echo "URI in $subdir: $uri" | |
| fi | |
| fi | |
| done |
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