crop_all.sh

#!/bin/sh

# crop_all.sh
# Script to run Rscript crop.R for all TIF files in data directory and subdirectories

# Colors for output
RED='\033[0;31m'
GREEN='\033[0;32m'
YELLOW='\033[1;33m'
NC='\033[0m' # No Color

echo "Starting batch croping of TIF files..."
echo "=========================================="

# Check if R packages are available
printf "Checking R package dependencies...\n"
if ! R -e "library(terra)" >/dev/null 2>&1; then
    printf "${RED}Error: terra package is not installed${NC}\n"
    printf "Please install required R packages by running:\n"
    printf "  R -e \"install.packages(c('terra', 'sf', 'ggplot2', 'tidyverse'))\"\n"
    printf "Or install them through RStudio's package manager.\n"
    exit 1
fi
printf "${GREEN}✓ R package dependencies found${NC}\n"
echo

# Find all .tif files in data directory and subdirectories
tif_files=$(find data -name "*.tif" -type f)

# Check if any TIF files were found
if [ -z "$tif_files" ]; then
    printf "${RED}No TIF files found in data directory${NC}\n"
    exit 1
fi

# Count total files
total_files=$(echo "$tif_files" | wc -l)
printf "${YELLOW}Found $total_files TIF files to crop${NC}\n"
echo

# Initialize counters
croped=0
failed=0

# crop each TIF file
while IFS= read -r tif_file; do
    croped=$((croped + 1))
    printf "${YELLOW}croping ($croped/$total_files): $tif_file${NC}\n"
    
    # Check if corresponding .txt file exists
    txt_file="${tif_file}.txt"
    if [ ! -f "$txt_file" ]; then
        printf "${RED}  Error: Missing coordinate file: $txt_file${NC}\n"
        failed=$((failed + 1))
        continue
    fi
    
    # Run Rscript crop.R with the TIF file
    # Set R library path to include common RStudio package locations
    if Rscript crop.R "$tif_file"; then
        printf "${GREEN}  ✓ Successfully croped: $tif_file${NC}\n"
    else
        printf "${RED}  ✗ Failed to crop: $tif_file${NC}\n"
        failed=$((failed + 1))
    fi
    
    echo
done <<< "$tif_files"

# Summary
echo "=========================================="
printf "${YELLOW}croping complete!${NC}\n"
printf "Total files: $total_files\n"
printf "${GREEN}Successfully croped: $((croped - failed))${NC}\n"
if [ $failed -gt 0 ]; then
    printf "${RED}Failed: $failed${NC}\n"
    exit 1
else
    printf "${GREEN}All files croped successfully!${NC}\n"
fi