# CI_EXTRACTION_PER_FIELD.R
# =========================
# Script 20 (Refactored for Per-Field Architecture)
# 
# This script reads per-field TIFFs from Script 10 output and:
# 1. Calculates Canopy Index (CI) from 4-band imagery (RGB + NIR)
# 2. Outputs 5-band TIFFs with CI as the 5th band to field_tiles_CI/{FIELD}/{DATE}.tif
# 3. Outputs per-field per-date RDS files to daily_vals/{FIELD}/{DATE}.rds
#
# Key differences from legacy Script 20:
# - Input: field_tiles/{FIELD}/{DATE}.tif (4-band, from Script 10)
# - Output: field_tiles_CI/{FIELD}/{DATE}.tif (5-band with CI)
# - Output: daily_vals/{FIELD}/{DATE}.rds (per-field CI statistics)
# - Directly extracts CI statistics per sub_field within each field
# 
# Usage:
#   Rscript 20_ci_extraction_per_field.R [project_dir] [end_date] [offset]
#   Example: Rscript 20_ci_extraction_per_field.R angata 2026-01-02 7

suppressPackageStartupMessages({
  library(sf)
  library(terra)
  library(tidyverse)
  library(lubridate)
  library(here)
})

# =============================================================================
# Main Processing
# =============================================================================

main <- function() {
  # STEP 1: Set working directory to project root (smartcane/)
  # This ensures all relative paths resolve correctly
  if (basename(getwd()) == "r_app") {
    setwd("..")
  }
  
  # STEP 2: SOURCE ALL UTILITY SCRIPTS (before any operations)
  # Parse command-line arguments FIRST
  args <- commandArgs(trailingOnly = TRUE)
  project_dir <- if (length(args) >= 1 && args[1] != "") args[1] else "angata"
  end_date <- if (length(args) >= 2 && args[2] != "") as.Date(args[2]) else Sys.Date()
  offset <- if (length(args) >= 3 && !is.na(as.numeric(args[3]))) as.numeric(args[3]) else 7
  
  # Make project_dir available globally for parameters_project.R
  assign("project_dir", project_dir, envir = .GlobalEnv)
  
  # Load parameters_project.R (provides safe_log, date_list, setup_project_directories, etc.)
  tryCatch({
    source("r_app/parameters_project.R")
  }, error = function(e) {
    cat(sprintf("Error loading parameters_project.R: %s\n", e$message))
    stop(e)
  })
  
  # Load CI extraction utilities
  tryCatch({
    source("r_app/20_ci_extraction_utils.R")
  }, error = function(e) {
    cat(sprintf("Error loading 20_ci_extraction_utils.R: %s\n", e$message))
    stop(e)
  })
  
  # STEP 3: Now all utilities are loaded, proceed with script logic
  safe_log(sprintf("=== Script 20: CI Extraction Per-Field ==="))
  safe_log(sprintf("Project: %s | End Date: %s | Offset: %d days", 
                      project_dir, format(end_date, "%Y-%m-%d"), offset))
  
  # Set up directory paths from parameters
  setup <- setup_project_directories(project_dir)
  
  # Load field boundaries directly from field_boundaries_path in setup
  tryCatch({
    field_boundaries_sf <- st_read(setup$field_boundaries_path, quiet = TRUE)
    safe_log(sprintf("Loaded %d field/sub_field polygons from %s", nrow(field_boundaries_sf), setup$field_boundaries_path))
  }, error = function(e) {
    safe_log(sprintf("Error loading field boundaries from %s: %s", setup$field_boundaries_path, e$message), "ERROR")
    stop(e)
  })
  
  # Get list of dates to process
  dates <- date_list(end_date, offset)
  safe_log(sprintf("Processing dates: %s to %s (%d dates)", 
                      dates$start_date, dates$end_date, length(dates$days_filter)))
  
  safe_log(sprintf("Input directory: %s", setup$field_tiles_dir))
  safe_log(sprintf("Output TIF directory: %s", setup$field_tiles_ci_dir))
  safe_log(sprintf("Output RDS directory: %s", setup$daily_ci_vals_dir))
  
  # Process each field
  if (!dir.exists(setup$field_tiles_dir)) {
    safe_log(sprintf("Field tiles directory not found: %s", setup$field_tiles_dir), "ERROR")
    stop("Script 10 output not found. Run Script 10 first.")
  }
  
  fields <- list.dirs(setup$field_tiles_dir, full.names = FALSE, recursive = FALSE)
  fields <- fields[fields != ""]  # Remove empty strings
  
  if (length(fields) == 0) {
    safe_log("No fields found in field_tiles directory", "WARNING")
    return()
  }
  
  safe_log(sprintf("Found %d fields to process", length(fields)))
  
  # DEBUG: Check what paths are available in setup
  safe_log(sprintf("[DEBUG] Available setup paths: %s", paste(names(setup), collapse=", ")))
  safe_log(sprintf("[DEBUG] field_tiles_ci_dir: %s", setup$field_tiles_ci_dir))
  safe_log(sprintf("[DEBUG] daily_ci_vals_dir: %s", setup$daily_ci_vals_dir))
  
  # Use daily_ci_vals_dir for per-field daily CI output
  # Pre-create output subdirectories for all fields
  for (field in fields) {
    dir.create(file.path(setup$field_tiles_ci_dir, field), showWarnings = FALSE, recursive = TRUE)
    if (!is.null(setup$daily_ci_vals_dir)) {
      dir.create(file.path(setup$daily_ci_vals_dir, field), showWarnings = FALSE, recursive = TRUE)
    }
  }
  
  # Process each DATE (OPTIMIZED: load TIFF once, process all fields)
  total_success <- 0
  total_error <- 0
  ci_results_by_date <- list()
  
  for (date_str in dates$days_filter) {
    # Load the merged TIFF ONCE for this date
    merged_tif_path <- file.path(setup$field_tiles_dir, fields[1], sprintf("%s.tif", date_str))
    
    # Find the actual TIFF path (it's in the first field that has it)
    input_tif_full <- NULL
    for (field in fields) {
      candidate_path <- file.path(setup$field_tiles_dir, field, sprintf("%s.tif", date_str))
      if (file.exists(candidate_path)) {
        input_tif_full <- candidate_path
        break
      }
    }
    
    if (is.null(input_tif_full)) {
      safe_log(sprintf("  %s: Input TIFF not found (skipping)", date_str))
      next
    }
    
    tryCatch({
      # Load TIFF ONCE
      raster_4band <- terra::rast(input_tif_full)
      
      # Now process all fields from this single TIFF
      for (field in fields) {
        field_ci_path <- file.path(setup$field_tiles_ci_dir, field)
        field_daily_vals_path <- file.path(setup$daily_ci_vals_dir, field)
        output_tif <- file.path(field_ci_path, sprintf("%s.tif", date_str))
        output_rds <- file.path(field_daily_vals_path, sprintf("%s.rds", date_str))
        
        # MODE 3: Skip if both outputs already exist
        if (file.exists(output_tif) && file.exists(output_rds)) {
          next  # Skip to next field
        }
        
        # MODE 2: Regeneration mode - RDS missing but CI TIFF exists
        if (file.exists(output_tif) && !file.exists(output_rds)) {
          tryCatch({
            extract_rds_from_ci_tiff(output_tif, output_rds, field_boundaries_sf, field)
            total_success <<- total_success + 1
          }, error = function(e) {
            total_error <<- total_error + 1
          })
          next
        }
        
        # MODE 1: Normal mode - calculate CI from 4-band input
        tryCatch({
          # Calculate CI
          ci_raster <- calc_ci_from_raster(raster_4band)
          
          # Create 5-band TIFF (R, G, B, NIR, CI)
          five_band <- c(raster_4band, ci_raster)
          
          # Save 5-band TIFF
          terra::writeRaster(five_band, output_tif, overwrite = TRUE)
          
          # Extract CI statistics by sub_field
          ci_stats <- extract_ci_by_subfield(ci_raster, field_boundaries_sf, field)
          
          # Save RDS
          if (!is.null(ci_stats) && nrow(ci_stats) > 0) {
            saveRDS(ci_stats, output_rds)
            
            # Store for daily aggregation
            ci_stats_with_date <- ci_stats %>% mutate(date = date_str)
            key <- sprintf("%s_%s", field, date_str)
            ci_results_by_date[[key]] <<- ci_stats_with_date
          }
          
          total_success <<- total_success + 1
          
        }, error = function(e) {
          total_error <<- total_error + 1
        })
      }
      
    }, error = function(e) {
      safe_log(sprintf("  %s: ✗ Error loading TIFF - %s", date_str, e$message), "ERROR")
      total_error <<- total_error + 1
    })
  }
  
  # Summary
  safe_log(sprintf("\n=== Processing Complete ==="))
  safe_log(sprintf("Successfully processed: %d", total_success))
  safe_log(sprintf("Errors encountered: %d", total_error))
  
  if (total_success > 0) {
    safe_log("Output files created in:")
    safe_log(sprintf("  TIFFs: %s", setup$field_tiles_ci_dir))
    safe_log(sprintf("  RDS:   %s", setup$daily_ci_vals_dir))
  }
}

# Execute main if called from command line
if (sys.nframe() == 0) {
  main()
}