# 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
  # If in migration mode, dates_to_process is provided by the pipeline runner
  if (exists("dates_to_process") && !is.null(dates_to_process)) {
    # Migration mode: Use provided list of dates (process ALL available dates)
    dates_filter <- sort(dates_to_process)
    safe_log(sprintf("Migration mode: Processing %d specified dates", length(dates_filter)))
  } else {
    # Normal mode: Use 7-day offset window
    dates <- date_list(end_date, offset)
    dates_filter <- dates$days_filter
    safe_log(sprintf("Normal mode: Processing dates: %s to %s (%d dates)", 
                      dates$start_date, dates$end_date, length(dates_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 (load merged TIFF once, extract all fields from it)
  total_processed_dates <- 0
  total_skipped_dates <- 0
  total_already_complete_dates <- 0
  total_error <- 0
  
  for (date_str in dates_filter) {
    input_tif_merged <- file.path(setup$merged_tif_folder, sprintf("%s.tif", date_str))
    output_tifs <- file.path(setup$field_tiles_ci_dir, fields, sprintf("%s.tif", date_str))
    output_rds <- file.path(setup$daily_ci_vals_dir, fields, sprintf("%s.rds", date_str))
    names(output_tifs) <- fields
    names(output_rds) <- fields
    tif_exists <- file.exists(output_tifs)
    rds_exists <- file.exists(output_rds)
    fields_need_rds_only <- fields[tif_exists & !rds_exists]
    fields_need_raster <- fields[!tif_exists]
    
    if (length(fields_need_rds_only) == 0 && length(fields_need_raster) == 0) {
      total_already_complete_dates <- total_already_complete_dates + 1
      safe_log(sprintf("  %s: All field outputs already exist (skipping)", date_str))
      next
    }
    
    fields_processed_this_date <- 0
    rds_only_processed <- 0
    raster_processed_this_date <- 0
    
    if (length(fields_need_rds_only) > 0) {
      for (field in fields_need_rds_only) {
        tryCatch({
          extract_rds_from_ci_tiff(output_tifs[[field]], output_rds[[field]], field_boundaries_sf, field)
          fields_processed_this_date <- fields_processed_this_date + 1
          rds_only_processed <- rds_only_processed + 1
        }, error = function(e) {
          safe_log(sprintf("    Error regenerating RDS for field %s: %s", field, e$message), "WARNING")
        })
      }
    }
    
    if (length(fields_need_raster) == 0) {
      total_processed_dates <- total_processed_dates + 1
      safe_log(sprintf("  %s: Regenerated %d RDS files from existing CI TIFFs", date_str, rds_only_processed))
      next
    }
    
    if (!file.exists(input_tif_merged)) {
      safe_log(sprintf("  %s: merged_tif not found (skipping)", date_str))
      total_skipped_dates <- total_skipped_dates + 1
      next
    }
    
    tryCatch({
      # Load the merged TIFF only when at least one field still needs a CI TIFF.
      raster_4band <- terra::rast(input_tif_merged)
      safe_log(sprintf("  %s: Loaded merged TIFF, processing %d fields...", date_str, length(fields_need_raster)))
      
      # Calculate CI from 4-band
      ci_raster <- calc_ci_from_raster(raster_4band)
      
      # Create 5-band (R, G, B, NIR, CI)
      # Explicitly set band names after combining to ensure proper naming
      five_band <- c(raster_4band, ci_raster)
      names(five_band) <- c("Red", "Green", "Blue", "NIR", "CI")
      
      # Now process only the fields that still need CI TIFF output for this date.
      for (field in fields_need_raster) {
        output_tif_path <- output_tifs[[field]]
        output_rds_path <- output_rds[[field]]
        
        tryCatch({
          # Crop 5-band TIFF to field boundary
          field_geom <- field_boundaries_sf %>% filter(field == !!field)
          five_band_cropped <- terra::crop(five_band, field_geom, mask = TRUE)

          # Skip empty tiles: cloud-masked pixels are stored as 0 in uint16
          # (NaN cannot be represented in that format). Sum of RGBNIR bands == 0
          # means no valid satellite data was captured for this field on this date.
          rgbnir_sum <- sum(
            terra::global(five_band_cropped[[1:4]], fun = "sum", na.rm = TRUE)$sum,
            na.rm = TRUE
          )
          if (rgbnir_sum == 0) {
            safe_log(sprintf("    SKIP (no data): field %s on %s", field, date_str), "WARNING")
          } else {
            # Save 5-band field TIFF
            terra::writeRaster(five_band_cropped, output_tif_path, overwrite = TRUE)

            # Extract CI statistics by sub_field (from cropped CI raster)
            ci_cropped <- five_band_cropped[[5]]  # 5th band is CI
            ci_stats <- extract_ci_by_subfield(ci_cropped, field_boundaries_sf, field)

            # Save RDS
            if (!is.null(ci_stats) && nrow(ci_stats) > 0) {
              saveRDS(ci_stats, output_rds_path)
            }

            fields_processed_this_date <- fields_processed_this_date + 1
            raster_processed_this_date <- raster_processed_this_date + 1
          }
        }, error = function(e) {
          # Error in individual field, continue to next
          safe_log(sprintf("    Error processing field %s: %s", field, e$message), "WARNING")
        })
      }
      
      if (fields_processed_this_date > 0) {
        total_processed_dates <- total_processed_dates + 1
        safe_log(sprintf(
          "  %s: Processed %d fields (%d CI TIFFs created, %d RDS-only regenerated)",
          date_str,
          fields_processed_this_date,
          raster_processed_this_date,
          rds_only_processed
        ))
      } else {
        total_error <- total_error + 1
        safe_log(sprintf("  %s: No field outputs were created; see warnings above", date_str), "ERROR")
      }
      
    }, error = function(e) {
      total_error <- total_error + 1
      safe_log(sprintf("  %s: Error loading or processing merged TIFF - %s", date_str, e$message), "ERROR")
    })
  }
  
  # Summary
  safe_log(sprintf("\n=== Processing Complete ==="))
  safe_log(sprintf("Dates processed: %d", total_processed_dates))
  safe_log(sprintf("Dates skipped (missing merged_tif): %d", total_skipped_dates))
  safe_log(sprintf("Dates already complete: %d", total_already_complete_dates))
  safe_log(sprintf("Errors encountered: %d", total_error))
  
  if (total_processed_dates > 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()
}