Timon
bb2a599075
Added explanatory text for all visualizations Fixed priority map color scheme (red=high priority, green=low priority) Improved error handling in farm health data calculations Added fallback mechanisms for missing data
112 lines
3.6 KiB
R
112 lines
3.6 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]
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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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#
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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 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 <- "2023-10-01" # Default date for testing
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}
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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 <- "2023-10-01" # 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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# 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 {
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# Default project directory
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project_dir <- "chemba"
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message("No project_dir provided. Using default:", project_dir)
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}
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# 3. Initialize project configuration
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# --------------------------------
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tryCatch({
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source("parameters_project.R")
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source("ci_extraction_utils.R")
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}, error = function(e) {
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warning("Default source files not found. Attempting to source from 'r_app' directory.")
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tryCatch({
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source("r_app/parameters_project.R")
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source("r_app/ci_extraction_utils.R")
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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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log_message(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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log_message(paste("Output will be saved as:", file_name_tif))
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# 5. Create weekly mosaic using the function from utils
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# -------------------------------------------------
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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 = weekly_CI_mosaic,
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file_name_tif = file_name_tif,
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create_plots = TRUE
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)
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}
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# Run the main function if the script is executed directly
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main()
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