[CREATE] Final Source Code

Author: FMCalisto

scripts/check_missing_patients.sh

@@ -0,0 +1,120 @@
+#!/bin/bash
+#
+# Author: Francisco Maria Calisto
+# Maintainer: Francisco Maria Calisto
+# Email: francisco.calisto@tecnico.ulisboa.pt
+# License: ACADEMIC & COMMERCIAL
+# Created Date: 2024-09-28
+# Revised Date: 2024-09-28
+# Version: 1.3
+# Status: Development
+# Usage: ./check_missing_patients.sh
+# Description: This script checks whether each anonymized Patient ID from the CSV file exists in any DICOM file within the "unexplored" folder.
+
+# Exit script immediately if any command fails
+set -e
+
+# Configuration: Define key directories and file paths
+home="$HOME"  # User's home directory
+root_dir="$home/Git"  # Root directory where the project is located
+# unchecked_dir="$root_dir/dataset-multimodal-breast/data/curation/unexplored"  # Directory with unprocessed DICOM files
+unchecked_dir="$root_dir/dataset-multimodal-breast/data/curation/checking"  # TO DELETE
+csv_file="$root_dir/dataset-multimodal-breast/data/birads/anonymized_patients_birads_curation.csv"  # CSV file with anonymized patient IDs
+LOG_DIR="$root_dir/dataset-multimodal-breast/data/logs"  # Directory for log files
+LOG_FILE="$LOG_DIR/check_missing_patients_$(date +'%Y%m%d_%H%M%S').log"  # Unique log file with timestamp
+
+# Ensure the log directory exists (if not, create it)
+mkdir -p "$LOG_DIR"
+
+# Function to log messages to both the console and log file with a timestamp
+log_message() {
+  echo "$(date +'%Y-%m-%d %H:%M:%S') - $1" | tee -a "$LOG_FILE"
+}
+
+# Function to validate the existence of required paths (directories or files)
+# Arguments:
+#   $1: Path to validate
+#   $2: Friendly name for the error message
+validate_path() {
+  if [ ! -e "$1" ]; then
+    log_message "Error: $2 ($1) does not exist. Exiting."
+    exit 1  # Terminate script if the path is missing
+  fi
+}
+
+# Ensure essential directories and CSV file exist before continuing
+validate_path "$unchecked_dir" "Unchecked folder (DICOM directory)"
+validate_path "$csv_file" "CSV file (Patient data)"
+
+# Initialize arrays to store unique Patient IDs and Patient IDs not found in DICOM files
+unique_patients=()  # Array to store unique Patient IDs
+not_found_patients=()  # Array to store Patient IDs not found in DICOM files
+
+# Function to check if an element exists in an array
+# Arguments:
+#   $1: Element to search
+#   $2: Array to search in
+element_in_array() {
+  local element="$1"
+  shift
+  for item in "$@"; do
+    if [[ "$item" == "$element" ]]; then
+      return 0  # Element found
+    fi
+  done
+  return 1  # Element not found
+}
+
+# Function to check if a given Patient ID exists in any DICOM file within the "unexplored" directory
+# Arguments:
+#   $1: The anonymized Patient ID to search for in the DICOM files
+check_patient_in_dicom_files() {
+  local patient_id="$1"
+
+  # Search for the Patient ID in the filenames of the DICOM files
+  if find "$unchecked_dir" -type f -name "*.dcm" | grep -q "$patient_id"; then
+    log_message "Patient ID: $patient_id found in DICOM files."
+  else
+    log_message "Patient ID: $patient_id NOT found in any DICOM file."
+    not_found_patients+=("$patient_id")  # Add to the list of missing Patient IDs
+  fi
+}
+
+# Function to process the CSV and check for Patient IDs
+process_csv() {
+  log_message "Starting to process the CSV file: $csv_file"
+
+  # Read the CSV file line by line, assuming Patient ID is in the second column
+  while IFS=',' read -r col1 patient_id rest; do
+    if [ -n "$patient_id" ]; then  # Ensure the Patient ID is not empty
+      # Only process if the Patient ID is unique (not already in the array)
+      if ! element_in_array "$patient_id" "${unique_patients[@]}"; then
+        unique_patients+=("$patient_id")  # Add to unique list
+        log_message "Checking Patient ID: $patient_id from CSV"
+        check_patient_in_dicom_files "$patient_id"  # Call function to check if the Patient ID exists in DICOM files
+      else
+        log_message "Skipping duplicate Patient ID: $patient_id"
+      fi
+    fi
+  done < "$csv_file"
+}
+
+# Start the process of checking Patient IDs from the CSV
+process_csv
+
+# After checking all Patient IDs, report any that were not found
+if [ ${#not_found_patients[@]} -ne 0 ]; then
+  log_message "Summary: The following Patient IDs were NOT found in any DICOM files:"
+  for patient_id in "${not_found_patients[@]}"; do
+    log_message "$patient_id"
+  done
+else
+  log_message "All Patient IDs from the CSV were found in the DICOM files."
+fi
+
+# Log the total number of unique Patient IDs processed
+log_message "Total number of unique Patient IDs processed: ${#unique_patients[@]}"
+
+log_message "Patient ID check completed successfully."
+
+# End of script

scripts/explorer.sh

@@ -5,7 +5,7 @@
 # Email: francisco.calisto@tecnico.ulisboa.pt
 # License: ACADEMIC & COMMERCIAL
 # Created Date: 2024-09-22
-# Revised Date: 2024-09-29  # Improved logging, error handling, and optimized Patient ID processing
+# Revised Date: 2024-09-28  # Improved logging, error handling, and optimized Patient ID processing
 # Version: 2.28
 # Status: Development
 # Usage: ./explorer.sh
@@ -16,7 +16,7 @@
 set -e
 
 # Configuration: Set the maximum number of DICOM files to process in one run
-FILE_LIMIT=1  # You can adjust this for testing or set higher for production
+FILE_LIMIT=50000  # You can adjust this for testing or set higher for production
 
 # Define key directories and file paths for processing
 home="$HOME"  # User's home directory