# 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.
#
# Usage: Rscript ci_extraction.R [end_date] [offset] [project_dir]
#   - 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., "chemba")
#

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

# 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 {
    project_dir <- "chemba"
  }
  
  # Make project_dir available globally so parameters_project.R can use it
  assign("project_dir", project_dir, envir = .GlobalEnv)
  

  # 3. Initialize project configuration
  # --------------------------------
  new_project_question <- FALSE
  
  tryCatch({
    source("parameters_project.R")
    source("ci_extraction_utils.R")
  }, error = function(e) {
    warning("Default source files not found. Attempting to source from 'r_app' directory.")
    tryCatch({
      source(here::here("r_app", "parameters_project.R"))
      source(here::here("r_app", "ci_extraction_utils.R"))
      warning(paste("Successfully sourced files from 'r_app' directory."))

    }, error = function(e) {
      stop("Failed to source required files from both default and 'r_app' directories.")
    })
  })
  
  # 4. Generate date list for processing
  # ---------------------------------
  dates <- date_list(end_date, offset)
  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")
  
  tryCatch({
    # Use the new 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"))
    
    # 6. Process raster files and create VRT
    # -----------------------------------
    # Use the new utility function for batch processing
    vrt_list <- process_satellite_images(existing_files, field_boundaries, merged_final, daily_vrt)
    
    # 7. Process and combine CI values
    # ------------------------------
    # Call the process_ci_values function from utils with all required parameters
    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()
}