# CI_EXTRACTION.R
# ==============
# This script processes satellite imagery to extract Canopy Index (CI) values for agricultural fields.
# It handles image processing, masking, and extraction of statistics by field/sub-field.
# Supports both 4-band and 8-band PlanetScope data with automatic band detection and cloud masking.
#
# Usage: Rscript 02_ci_extraction.R [end_date] [offset] [project_dir] [data_source]
#   - end_date: End date for processing (YYYY-MM-DD format)
#   - offset: Number of days to look back from end_date 
#   - project_dir: Project directory name (e.g., "angata", "aura", "chemba")
#   - data_source: Data source directory - "merged_tif_8b" (default) or "merged_tif" (4-band) or "merged_final_tif"
#                  If tiles exist (daily_tiles_split/), they are used automatically
#
# Examples:
#   # Angata 8-band data (with UDM cloud masking)
#   & 'C:\Program Files\R\R-4.4.3\bin\x64\Rscript' r_app/02_ci_extraction.R 2026-01-02 7 angata merged_tif_8b
#   
#   # Aura 4-band data
#   Rscript 02_ci_extraction.R 2025-11-26 7 aura merged_tif
#
#   # Auto-detects and uses tiles if available:
#   Rscript 02_ci_extraction.R 2026-01-02 7 angata  (uses tiles if daily_tiles_split/ exists)

# 1. Load required packages
# -----------------------
suppressPackageStartupMessages({
  library(sf)
  library(terra)
  library(tidyverse)
  library(lubridate)
  library(readxl)
  library(here)
  library(furrr)
})

# 2. Process command line arguments
# ------------------------------
main <- function() {
  # Capture command line arguments
  args <- commandArgs(trailingOnly = TRUE)
  
  # Process end_date argument
  if (length(args) >= 1 && !is.na(args[1])) {
    end_date <- as.Date(args[1])
    if (is.na(end_date)) {
      warning("Invalid end_date provided. Using default (current date).")
      end_date <- Sys.Date()
      #end_date <- "2023-10-01"
    }
  } else {
    end_date <- Sys.Date()
    #end_date <- "2023-10-01"
  }
  
  # Process offset argument
  if (length(args) >= 2 && !is.na(args[2])) {
    offset <- as.numeric(args[2])
    if (is.na(offset) || offset <= 0) {
      warning("Invalid offset provided. Using default (7 days).")
      offset <- 7
    }
  } else {
    offset <- 7
  }
  
  # Process project_dir argument
  if (length(args) >= 3 && !is.na(args[3])) {
    project_dir <- as.character(args[3])
  } else if (exists("project_dir", envir = .GlobalEnv)) {
    project_dir <- get("project_dir", envir = .GlobalEnv)
  } else {
    project_dir <- "angata"  # Changed default from "aura" to "esa"
  }
  
  # Process data_source argument (optional, for specifying merged_tif_8b vs merged_tif vs merged_final_tif)
  if (length(args) >= 4 && !is.na(args[4])) {
    data_source <- as.character(args[4])
    # Validate data_source is a recognized option
    if (!data_source %in% c("merged_tif_8b", "merged_tif", "merged_final_tif")) {
      warning(paste("Data source", data_source, "not in standard list. Using as-is."))
    }
  } else if (exists("data_source", envir = .GlobalEnv)) {
    data_source <- get("data_source", envir = .GlobalEnv)
  } else {
    data_source <- "merged_tif_8b"  # Default to 8-band (newer data with cloud masking)
  }
  
  # Make project_dir and data_source available globally
  assign("project_dir", project_dir, envir = .GlobalEnv)
  assign("data_source", data_source, envir = .GlobalEnv)
  
  cat(sprintf("CI Extraction: project=%s, end_date=%s, offset=%d days, data_source=%s\n",
              project_dir, format(end_date, "%Y-%m-%d"), offset, data_source))
  
  # Set flag to use pivot_2.geojson for ESA (extra fields for yield prediction)
  ci_extraction_script <- TRUE
  assign("ci_extraction_script", ci_extraction_script, envir = .GlobalEnv)

  # 3. Initialize project configuration
  # --------------------------------
  new_project_question <- TRUE
  
  cat("[DEBUG] Attempting to source r_app/parameters_project.R\n")
  tryCatch({
    source("r_app/parameters_project.R")
    cat("[DEBUG] Successfully sourced r_app/parameters_project.R\n")
  }, error = function(e) {
    cat("[ERROR] Failed to source r_app/parameters_project.R:\n", e$message, "\n")
    stop(e)
  })
  
  cat("[DEBUG] Attempting to source r_app/ci_extraction_utils.R\n")
  tryCatch({
    source("r_app/ci_extraction_utils.R")
    cat("[DEBUG] Successfully sourced r_app/ci_extraction_utils.R\n")
  }, error = function(e) {
    cat("[ERROR] Failed to source r_app/ci_extraction_utils.R:\n", e$message, "\n")
    stop(e)
  })
  
  # 4. Generate date list for processing
  # ---------------------------------
  dates <- date_list(end_date, 7)
  log_message(paste("Processing data for week", dates$week, "of", dates$year))
  
  # 5. Find and filter raster files by date
  # -----------------------------------
  log_message("Searching for raster files")
  
  # Check if tiles exist (Script 01 output)
  tile_folder <- file.path("laravel_app", "storage", "app", project_dir, "daily_tiles_split")
  use_tiles <- dir.exists(tile_folder)
  
  tryCatch({
    if (use_tiles) {
      # Use tile-based processing
      log_message(paste("Tile folder detected at", tile_folder))
      log_message("Using tile-based CI extraction")
      
      # Call the tile-based extraction function
      process_ci_values_from_tiles(
        dates = dates,
        tile_folder = tile_folder,
        field_boundaries = field_boundaries,
        field_boundaries_sf = field_boundaries_sf,
        daily_CI_vals_dir = daily_CI_vals_dir,
        cumulative_CI_vals_dir = cumulative_CI_vals_dir,
        merged_final_dir = merged_final
      )
      
    } else {
      # Use legacy full-extent processing
      log_message("No tiles found. Using legacy full-extent approach")
      
      # Use the existing utility function to find satellite images
      existing_files <- find_satellite_images(planet_tif_folder, dates$days_filter)
      log_message(paste("Found", length(existing_files), "raster files for processing"))
      
      # Process raster files and create VRT
      vrt_list <- process_satellite_images(existing_files, field_boundaries, merged_final, daily_vrt)
      
      # Process and combine CI values
      process_ci_values(dates, field_boundaries, merged_final, 
                       field_boundaries_sf, daily_CI_vals_dir, cumulative_CI_vals_dir)
    }
    
  }, error = function(e) {
    log_message(paste("Error in main processing:", e$message), level = "ERROR")
    stop(e$message)
  })
}

if (sys.nframe() == 0) {
  main()
}