# 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)
})

# =============================================================================
# Load utility functions from 20_ci_extraction_utils.R
# =============================================================================
source("r_app/20_ci_extraction_utils.R")

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

main <- function() {
  # IMPORTANT: Set working directory to project root (smartcane/)
  # This ensures here() functions resolve relative to /smartcane, not /smartcane/r_app
  if (basename(getwd()) == "r_app") {
    setwd("..")
  }
  
  # Parse command-line arguments
  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
  
  # IMPORTANT: Make project_dir available globally for parameters_project.R
  assign("project_dir", project_dir, envir = .GlobalEnv)
  
  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))
  
  # 1. Load parameters (includes field boundaries setup)
  # ---------------------------------------------------
  tryCatch({
    source("r_app/parameters_project.R")
    safe_log("Loaded parameters_project.R")
  }, error = function(e) {
    safe_log(sprintf("Error loading parameters: %s", e$message), "ERROR")
    stop(e)
  })
  
  # 2. Set up directory paths from parameters FIRST (before using setup$...)
  # -----------------------------------------------------------------------
  setup <- setup_project_directories(project_dir)
  
  # 3. 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)
  })
  
  # 4. 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_vals_per_field_dir))
  
  # 5. 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)))
  
  # 6. Process each field
  # ----------------------
  total_success <- 0
  total_error <- 0
  ci_results_by_date <- list()
  
  for (field in fields) {
    safe_log(sprintf("\n--- Processing field: %s ---", field))
    
    field_tiles_path <- file.path(field_tiles_dir, field)
    field_ci_path <- file.path(field_tiles_ci_dir, field)
    field_daily_vals_path <- file.path(setup$daily_vals_per_field_dir, field)
    
    # Create output subdirectories for this field
    dir.create(field_ci_path, showWarnings = FALSE, recursive = TRUE)
    dir.create(field_daily_vals_path, showWarnings = FALSE, recursive = TRUE)
    
    # 5a. Process each date for this field
    # -----------------------------------
    for (date_str in dates$days_filter) {
      input_tif <- file.path(field_tiles_path, sprintf("%s.tif", date_str))
      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))
      
      # Skip if both outputs already exist
      if (file.exists(output_tif) && file.exists(output_rds)) {
        safe_log(sprintf("  %s: Already processed (skipping)", date_str))
        next
      }
      
      # Check if input TIFF exists
      if (!file.exists(input_tif)) {
        safe_log(sprintf("  %s: Input TIFF not found (skipping)", date_str))
        next
      }
      
      tryCatch({
        # Load 4-band TIFF
        raster_4band <- terra::rast(input_tif)
        
        # 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)
          safe_log(sprintf("  %s: ✓ Processed (%d sub-fields)", date_str, nrow(ci_stats)))
          
          # 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
        } else {
          safe_log(sprintf("  %s: ⚠ No CI data extracted", date_str))
        }
        
        total_success <- total_success + 1
        
      }, error = function(e) {
        safe_log(sprintf("  %s: ✗ Error - %s", date_str, e$message), "ERROR")
        total_error <<- total_error + 1
      })
    }
  }
  
  # 7. 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_vals_per_field_dir))
  }
  
  # 8. Aggregate per-field daily RDS files into combined_CI_data.rds
  # ----------------------------------------------------------------
  # This creates the wide-format (fields × dates) file that Script 30 and
  # other downstream scripts expect for backward compatibility
  safe_log("\n=== Aggregating Per-Field Daily RDS into combined_CI_data.rds ===")
  
  tryCatch({
    # Find all daily RDS files (recursively from daily_vals/{FIELD}/{DATE}.rds)
    all_daily_files <- list.files(
      path = setup$daily_vals_per_field_dir,
      pattern = "\\.rds$",
      full.names = TRUE,
      recursive = TRUE
    )
    
    if (length(all_daily_files) == 0) {
      safe_log("No daily RDS files found to aggregate", "WARNING")
    } else {
      safe_log(sprintf("Aggregating %d daily RDS files into combined_CI_data.rds", length(all_daily_files)))
      
      # Read and combine all daily RDS files
      combined_data <- all_daily_files %>%
        purrr::map(readRDS) %>%
        purrr::list_rbind() %>%
        dplyr::group_by(sub_field)
      
      # Create output directory if needed
      dir.create(setup$cumulative_CI_vals_dir, showWarnings = FALSE, recursive = TRUE)
      
      # Save combined data
      combined_ci_path <- file.path(setup$cumulative_CI_vals_dir, "combined_CI_data.rds")
      saveRDS(combined_data, combined_ci_path)
      
      safe_log(sprintf("✓ Created combined_CI_data.rds with %d rows from %d files", 
                         nrow(combined_data), length(all_daily_files)))
      safe_log(sprintf("  Location: %s", combined_ci_path))
    }
  }, error = function(e) {
    safe_log(sprintf("⚠ Error aggregating to combined_CI_data.rds: %s", e$message), "WARNING")
    safe_log("  This is OK - Script 30 can still use per-field RDS files directly", "WARNING")
  })
}

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