SmartCane/r_app/40_mosaic_creation_per_field.R

# 40_MOSAIC_CREATION_PER_FIELD.R
# ===============================
# Per-Field Weekly Mosaic Creation
#
# Creates weekly mosaics FROM per-field daily CI TIFFs (output from Script 20)
# TO per-field weekly CI TIFFs (input for Scripts 90/91 reporting).
#
# ARCHITECTURE:
#   Input:  field_tiles_CI/{FIELD}/{DATE}.tif (5-band daily, per-field from Script 20)
#   Output: weekly_mosaic/{FIELD}/week_WW_YYYY.tif (5-band weekly, per-field)
#
# USAGE:
#   & "C:\Program Files\R\R-4.4.3\bin\x64\Rscript.exe" r_app/40_mosaic_creation_per_field.R [end_date] [offset] [project_dir]
#
# ARGUMENTS:
#   end_date:   End date for processing (YYYY-MM-DD format, default: today)
#   offset:     Days to look back from end_date (typically 7 for one week, default: 7)
#   project_dir: Project directory (e.g., "aura", "angata", "chemba", "esa", default: "angata")
#
# EXAMPLES:
#   & "C:\Program Files\R\R-4.4.3\bin\x64\Rscript.exe" r_app/40_mosaic_creation_per_field.R 2026-01-12 7 aura
#   & "C:\Program Files\R\R-4.4.3\bin\x64\Rscript.exe" r_app/40_mosaic_creation_per_field.R 2025-12-31 7 angata

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

# 2. Main execution function
# -------------------------
main <- function() {
  
  cat("\n")
  cat("========================================================\n")
  cat("  Script 40: Per-Field Weekly Mosaic Creation\n")
  cat("========================================================\n\n")
  
  # Capture command line arguments
  args <- commandArgs(trailingOnly = TRUE)
  
  # ==== Process Arguments ====
  
  # Project directory
  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"
    message("[INFO] No project_dir provided. Using default: angata")
  }
  
  assign("project_dir", project_dir, envir = .GlobalEnv)
  message(paste("[INFO] Project:", project_dir))
  
  # End date
  if (length(args) >= 1 && !is.na(args[1])) {
    end_date <- as.Date(args[1], format = "%Y-%m-%d")
    if (is.na(end_date)) {
      message("[WARNING] Invalid end_date. Using current date.")
      end_date <- Sys.Date()
    }
  } else {
    end_date <- Sys.Date()
    message(paste("[INFO] No end_date provided. Using current date:", format(end_date)))
  }
  
  # Offset (days back)
  if (length(args) >= 2 && !is.na(args[2])) {
    offset <- as.numeric(args[2])
    if (is.na(offset) || offset <= 0) {
      message("[WARNING] Invalid offset. Using default: 7 days")
      offset <- 7
    }
  } else {
    offset <- 7
    message("[INFO] No offset provided. Using default: 7 days")
  }
  
  # ==== Load Configuration ====
  
  # Set working directory if needed
  if (basename(getwd()) == "r_app") {
    setwd("..")
  }
  
  tryCatch({
    source("r_app/parameters_project.R")
    message("[INFO] ✓ Loaded parameters_project.R")
  }, error = function(e) {
    stop("[ERROR] Failed to load parameters_project.R: ", e$message)
  })
  
  tryCatch({
    source("r_app/40_mosaic_creation_per_field_utils.R")
    message("[INFO] ✓ Loaded 40_mosaic_creation_per_field_utils.R")
  }, error = function(e) {
    stop("[ERROR] Failed to load utilities: ", e$message)
  })
  
  # ==== Get Project Directories ====
  
  setup <- setup_project_directories(project_dir)
  
  # Determine input/output directories
  # Input: field_tiles_CI/ (from Script 20)
  field_tiles_ci_dir <- setup$field_tiles_ci_dir
  
  # Output: weekly_mosaic/ (for Scripts 90/91)
  weekly_mosaic_output_dir <- file.path(setup$laravel_storage_dir, "weekly_mosaic")
  
  message(paste("[INFO] Input directory:", field_tiles_ci_dir))
  message(paste("[INFO] Output directory:", weekly_mosaic_output_dir))
  
  # ==== Validate Input Directory ====
  
  if (!dir.exists(field_tiles_ci_dir)) {
    stop(paste("[ERROR] Input directory not found:", field_tiles_ci_dir,
               "\nScript 20 (CI extraction) must be run first to create per-field TIFFs."))
  }
  
  # Check if directory has any TIFFs
  field_dirs <- list.dirs(field_tiles_ci_dir, full.names = FALSE, recursive = FALSE)
  if (length(field_dirs) == 0) {
    stop(paste("[ERROR] No field subdirectories found in:", field_tiles_ci_dir))
  }
  
  message(paste("[INFO] Found", length(field_dirs), "field directories"))
  
  # ==== Generate Date Range ====
  
  dates <- date_list(end_date, offset)
  
  # ==== Create Per-Field Weekly Mosaics ====
  
  created_files <- create_all_field_weekly_mosaics(
    dates = dates,
    field_tiles_ci_dir = field_tiles_ci_dir,
    output_dir = weekly_mosaic_output_dir
  )
  
  # ==== Summary ====
  
  message("\n")
  message("========================================================")
  message(paste("  COMPLETED"))
  message(paste("  Created:", length(created_files), "weekly field mosaics"))
  message("========================================================\n")
  
  if (length(created_files) > 0) {
    message("[SUCCESS] Weekly mosaics ready for reporting (Scripts 90/91)")
  } else {
    message("[WARNING] No mosaics created - check input data")
  }
  
  return(invisible(created_files))
}

# Execute main if script is run directly
if (sys.nframe() == 0) {
  tryCatch({
    created <- main()
    quit(save = "no", status = 0)
  }, error = function(e) {
    message(paste("\n[FATAL ERROR]", e$message))
    quit(save = "no", status = 1)
  })
}