Timon
fabbf3214d
- Updated `detect_mosaic_mode` function to check for grid-size subdirectories in addition to tile-named files. - Added comprehensive tests for DOY reset logic in `test_doy_logic.py`. - Implemented feature extraction tests in `test_feature_extraction.py`. - Created tests for growing window method in `test_growing_window_only.py`. - Developed a complete model inference test in `test_model_inference.py`. - Added a debug script for testing two-step refinement logic in `test_script22_debug.py`.
217 lines
8.4 KiB
R
217 lines
8.4 KiB
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
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#
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# MOSAIC_CREATION.R
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# ===============
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# This script creates weekly mosaics from daily satellite imagery.
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# It handles command-line arguments and initiates the mosaic creation process.
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#
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# Usage: Rscript mosaic_creation.R [end_date] [offset] [project_dir] [file_name] [use_tiles] [tile_size]
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# - end_date: End date for processing (YYYY-MM-DD format)
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# - offset: Number of days to look back from end_date
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# - project_dir: Project directory name (e.g., "chemba")
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# - file_name: Optional custom output file name
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# - use_tiles: Use tile-based processing for memory efficiency (TRUE/FALSE, default: FALSE)
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# - tile_size: Tile size in km (default: 5, only used if use_tiles=TRUE)
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#
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# Examples:
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# & "C:\Program Files\R\R-4.4.3\bin\x64\Rscript.exe" r_app/40_mosaic_creation.R 2026-01-12 7 angata
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#
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# 1. Load required packages
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# -----------------------
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suppressPackageStartupMessages({
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library(sf)
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library(terra)
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library(tidyverse)
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library(lubridate)
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library(here)
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})
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# 2. Process command line arguments and run mosaic creation
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# ------------------------------------------------------
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main <- function() {
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# Capture command line arguments
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args <- commandArgs(trailingOnly = TRUE)
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# Process project_dir argument with default
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if (length(args) >= 3 && !is.na(args[3])) {
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project_dir <- as.character(args[3])
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} else if (exists("project_dir", envir = .GlobalEnv)) {
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project_dir <- get("project_dir", envir = .GlobalEnv)
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} else {
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# Default project directory
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project_dir <- "angata"
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message("No project_dir provided. Using default:", project_dir)
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}
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# Make project_dir available globally so parameters_project.R can use it
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assign("project_dir", project_dir, envir = .GlobalEnv)
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# Process end_date argument with default
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if (length(args) >= 1 && !is.na(args[1])) {
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end_date <- as.Date(args[1])
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if (is.na(end_date)) {
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message("Invalid end_date provided. Using current date.")
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end_date <- Sys.Date()
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end_date <- "2026-01-01" # Default date for testing
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}
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} else if (exists("end_date_str", envir = .GlobalEnv)) {
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end_date <- as.Date(get("end_date_str", envir = .GlobalEnv))
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} else {
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# Default to current date if no argument is provided
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end_date <- Sys.Date()
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end_date <- "2026-01-01" # Default date for testing
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message("No end_date provided. Using current date: ", format(end_date))
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}
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# Process offset argument with default
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if (length(args) >= 2 && !is.na(args[2])) {
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offset <- as.numeric(args[2])
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if (is.na(offset) || offset <= 0) {
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message("Invalid offset provided. Using default (7 days).")
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offset <- 7
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}
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} else {
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# Default to 7 days if no argument is provided
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offset <- 7
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message("No offset provided. Using default:", offset, "days")
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}
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# 3. Initialize project configuration
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# --------------------------------
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# Detect which data source directory exists (merged_tif or merged_tif_8b)
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laravel_storage <- here::here("laravel_app/storage/app", project_dir)
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data_source <- if (dir.exists(file.path(laravel_storage, "merged_tif_8b"))) {
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message("Detected data source: merged_tif_8b (8-band optimized)")
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"merged_tif_8b"
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} else if (dir.exists(file.path(laravel_storage, "merged_tif"))) {
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message("Detected data source: merged_tif (legacy 4-band)")
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"merged_tif"
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} else {
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message("Warning: No data source found. Using default: merged_tif_8b")
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"merged_tif_8b"
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}
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# Set global data_source for parameters_project.R
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assign("data_source", data_source, envir = .GlobalEnv)
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tryCatch({
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source("parameters_project.R")
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source("40_mosaic_creation_utils.R")
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safe_log(paste("Successfully sourced files from default directory."))
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}, error = function(e) {
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message("Note: Could not open files from default directory (expected on some systems)")
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message("Attempting to source from 'r_app' directory instead...")
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tryCatch({
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source(here::here("r_app", "parameters_project.R"))
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source(here::here("r_app", "40_mosaic_creation_utils.R"))
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message("✓ Successfully sourced files from 'r_app' directory")
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}, error = function(e) {
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stop("Failed to source required files from both default and 'r_app' directories.")
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})
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})
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# 4. Generate date range for processing
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# ---------------------------------
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dates <- date_list(end_date, offset)
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safe_log(paste("Processing data for week", dates$week, "of", dates$year))
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# Create output filename
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file_name_tif <- if (length(args) >= 4 && !is.na(args[4])) {
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as.character(args[4])
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} else {
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paste0("week_", sprintf("%02d", dates$week), "_", dates$year, ".tif")
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}
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safe_log(paste("Output will be saved as:", file_name_tif))
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# 5. Create weekly mosaics - route based on project tile detection
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# ---------------------------------------------------------------
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# The use_tile_mosaic flag is auto-detected by parameters_project.R
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# based on whether tiles exist in merged_final_tif/
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if (!exists("use_tile_mosaic")) {
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# Fallback detection if flag not set (shouldn't happen)
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merged_final_dir <- file.path(laravel_storage, "merged_final_tif")
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tile_detection <- detect_mosaic_mode(merged_final_dir)
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use_tile_mosaic <- tile_detection$has_tiles
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}
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if (use_tile_mosaic) {
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# TILE-BASED APPROACH: Create per-tile weekly MAX mosaics
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# This is used for projects like Angata with large ROIs requiring spatial partitioning
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# Input data comes from merged_final_tif/{grid_size}/{DATE}/{DATE}_XX.tif (5-band tiles from script 20)
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tryCatch({
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safe_log("Starting per-tile mosaic creation (tile-based approach)...")
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# Detect grid size from merged_final_tif folder structure
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# Expected: merged_final_tif/5x5/ or merged_final_tif/10x10/ etc.
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merged_final_base <- file.path(laravel_storage, "merged_final_tif")
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grid_subfolders <- list.dirs(merged_final_base, full.names = FALSE, recursive = FALSE)
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# Look for grid size patterns like "5x5", "10x10", "20x20"
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grid_patterns <- grep("^\\d+x\\d+$", grid_subfolders, value = TRUE)
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if (length(grid_patterns) == 0) {
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stop("No grid size subfolder found in merged_final_tif/ (expected: 5x5, 10x10, etc.)")
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}
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grid_size <- grid_patterns[1] # Use first grid size found
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safe_log(paste("Detected grid size:", grid_size))
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# Point to the grid-specific merged_final_tif directory
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merged_final_with_grid <- file.path(merged_final_base, grid_size)
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# Set output directory for per-tile mosaics, organized by grid size
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# Output: weekly_tile_max/{grid_size}/week_WW_YYYY_TT.tif
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tile_output_base <- file.path(laravel_storage, "weekly_tile_max", grid_size)
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dir.create(tile_output_base, recursive = TRUE, showWarnings = FALSE)
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created_tile_files <- create_weekly_mosaic_from_tiles(
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dates = dates,
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merged_final_dir = merged_final_with_grid,
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tile_output_dir = tile_output_base,
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field_boundaries = field_boundaries
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)
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safe_log(paste("✓ Per-tile mosaic creation completed - created",
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length(created_tile_files), "tile files"))
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}, error = function(e) {
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safe_log(paste("ERROR in tile-based mosaic creation:", e$message), "ERROR")
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traceback()
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stop("Mosaic creation failed")
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})
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} else {
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# SINGLE-FILE APPROACH: Create single weekly mosaic file
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# This is used for legacy projects (ESA, Chemba, Aura) expecting single-file output
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tryCatch({
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safe_log("Starting single-file mosaic creation (backward-compatible approach)...")
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# Set output directory for single-file mosaics
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single_file_output_dir <- file.path(laravel_storage, "weekly_mosaic")
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created_file <- create_weekly_mosaic(
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dates = dates,
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field_boundaries = field_boundaries,
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daily_vrt_dir = daily_vrt,
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merged_final_dir = merged_final,
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output_dir = single_file_output_dir,
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file_name_tif = file_name_tif,
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create_plots = FALSE
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)
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safe_log(paste("✓ Single-file mosaic creation completed:", created_file))
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}, error = function(e) {
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safe_log(paste("ERROR in single-file mosaic creation:", e$message), "ERROR")
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traceback()
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stop("Mosaic creation failed")
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})
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}
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}
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if (sys.nframe() == 0) {
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main()
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}
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