SmartCane/r_app/04_mosaic_creation.R

# filepath: c:\Users\timon\Resilience BV\4020 SCane ESA DEMO - Documenten\General\4020 SCDEMO Team\4020 TechnicalData\WP3\smartcane\r_app\mosaic_creation.R
#
# MOSAIC_CREATION.R
# ===============
# This script creates weekly mosaics from daily satellite imagery.
# It handles command-line arguments and initiates the mosaic creation process.
#
# Usage: Rscript mosaic_creation.R [end_date] [offset] [project_dir] [file_name] [use_tiles] [tile_size]
#   - 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")
#   - file_name: Optional custom output file name
#   - use_tiles: Use tile-based processing for memory efficiency (TRUE/FALSE, default: FALSE)
#   - tile_size: Tile size in km (default: 5, only used if use_tiles=TRUE)
#
# Examples:
#   Rscript 04_mosaic_creation.R 2025-12-21 7 angata
#   Rscript 04_mosaic_creation.R 2025-12-21 7 angata week_51.tif TRUE 5  [tile-based]
#

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

# 2. Process command line arguments and run mosaic creation
# ------------------------------------------------------
main <- function() {
  # Capture command line arguments
  args <- commandArgs(trailingOnly = TRUE)
  
    # Process project_dir argument with default
  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 {
    # Default project directory
    project_dir <- "angata"
    message("No project_dir provided. Using default:", project_dir)
  }
  
  # Make project_dir available globally so parameters_project.R can use it
  assign("project_dir", project_dir, envir = .GlobalEnv)
  
  # Process end_date argument with default
  if (length(args) >= 1 && !is.na(args[1])) {
    end_date <- as.Date(args[1])
    if (is.na(end_date)) {
      message("Invalid end_date provided. Using current date.")
      end_date <- Sys.Date()
      end_date <- "2026-01-01"  # Default date for testing
    }
  } else if (exists("end_date_str", envir = .GlobalEnv)) {
    end_date <- as.Date(get("end_date_str", envir = .GlobalEnv))
  } else {
    # Default to current date if no argument is provided
    end_date <- Sys.Date()
    end_date <-  "2026-01-01"   # Default date for testing
    message("No end_date provided. Using current date: ", format(end_date))
  }
  
  # Process offset argument with default
  if (length(args) >= 2 && !is.na(args[2])) {
    offset <- as.numeric(args[2])
    if (is.na(offset) || offset <= 0) {
      message("Invalid offset provided. Using default (7 days).")
      offset <- 7
    }
  } else {
    # Default to 7 days if no argument is provided
    offset <- 7
    message("No offset provided. Using default:", offset, "days")
  }
  
  # 3. Initialize project configuration
  # --------------------------------
  
  # Detect which data source directory exists (merged_tif or merged_tif_8b)
  laravel_storage <- here::here("laravel_app/storage/app", project_dir)
  data_source <- if (dir.exists(file.path(laravel_storage, "merged_tif_8b"))) {
    message("Detected data source: merged_tif_8b (8-band optimized)")
    "merged_tif_8b"
  } else if (dir.exists(file.path(laravel_storage, "merged_tif"))) {
    message("Detected data source: merged_tif (legacy 4-band)")
    "merged_tif"
  } else {
    message("Warning: No data source found. Using default: merged_tif_8b")
    "merged_tif_8b"
  }
  
  # Set global data_source for parameters_project.R
  assign("data_source", data_source, envir = .GlobalEnv)
  
  tryCatch({
    source("parameters_project.R")
    source("mosaic_creation_utils.R")
    safe_log(paste("Successfully sourced files from default directory."))
  }, error = function(e) {
    message("Note: Could not open files from default directory (expected on some systems)")
    message("Attempting to source from 'r_app' directory instead...")
    tryCatch({
      source(here::here("r_app", "parameters_project.R"))
      source(here::here("r_app", "mosaic_creation_utils.R"))
      message("✓ 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 range for processing
  # ---------------------------------
  dates <- date_list(end_date, offset)  
  safe_log(paste("Processing data for week", dates$week, "of", dates$year))
  
  # Create output filename
  file_name_tif <- if (length(args) >= 4 && !is.na(args[4])) {
    as.character(args[4])
  } else {
    paste0("week_", sprintf("%02d", dates$week), "_", dates$year, ".tif")
  }
  
  safe_log(paste("Output will be saved as:", file_name_tif))
  
  # 5. Create weekly per-tile MAX mosaics
  # ----------------------------------
  
  tryCatch({
    safe_log("Starting per-tile mosaic creation...")
    
    # Set output directory for per-tile mosaics
    tile_output_base <- file.path(laravel_storage, "weekly_tile_max")
    
    created_tile_files <- create_weekly_mosaic_from_tiles(
      dates = dates,
      merged_final_dir = merged_final,
      tile_output_dir = tile_output_base,
      field_boundaries = field_boundaries
    )
    
    safe_log(paste("✓ Per-tile mosaic creation completed - created", 
                   length(created_tile_files), "tile files"))
  }, error = function(e) {
    safe_log(paste("ERROR in mosaic creation:", e$message), "WARNING")
    traceback()
    stop("Mosaic creation failed")
  })
}

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