123 lines
4.4 KiB
R
123 lines
4.4 KiB
R
# filepath: c:\Users\timon\Resilience BV\4020 SCane ESA DEMO - Documenten\General\4020 SCDEMO Team\4020 TechnicalData\WP3\smartcane\r_app\interpolate_growth_model.R
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#
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# INTERPOLATE_GROWTH_MODEL.R
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# =========================
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# This script interpolates CI (Chlorophyll Index) values between measurement dates
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# to create a continuous growth model. It generates daily values and cumulative
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# CI statistics for each field.
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#
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# Usage: Rscript interpolate_growth_model.R [project_dir] [data_source]
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# - project_dir: Project directory name (e.g., "chemba")
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# - data_source: (Optional) Data source directory - "merged_tif" (default), "merged_tif_8b"
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# & 'C:\Program Files\R\R-4.4.3\bin\x64\Rscript' r_app/30_interpolate_growth_model.R angata merged_tif
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# 1. Load required packages
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# -----------------------
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suppressPackageStartupMessages({
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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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# =============================================================================
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# Load utility functions from 30_growth_model_utils.R
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# =============================================================================
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source("r_app/30_growth_model_utils.R")
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# =============================================================================
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# Main Processing
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# =============================================================================
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main <- function() {
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# IMPORTANT: Set working directory to project root (smartcane/)
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# This ensures here() functions resolve relative to /smartcane, not /smartcane/r_app
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if (basename(getwd()) == "r_app") {
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setwd("..")
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}
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# Parse command-line arguments
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args <- commandArgs(trailingOnly = TRUE)
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project_dir <- if (length(args) >= 1 && args[1] != "") args[1] else "angata"
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# IMPORTANT: Make project_dir available globally for parameters_project.R
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assign("project_dir", project_dir, envir = .GlobalEnv)
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safe_log(sprintf("=== Script 30: Growth Model Interpolation ==="))
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safe_log(sprintf("Project: %s", project_dir))
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# 1. Load parameters (includes field boundaries setup)
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# ---------------------------------------------------
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tryCatch({
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source("r_app/parameters_project.R")
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safe_log("Loaded parameters_project.R")
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}, error = function(e) {
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safe_log(sprintf("Error loading parameters: %s", e$message), "ERROR")
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stop(e)
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})
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# 2. Set up directory paths from parameters
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# -----------------------------------------------
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setup <- setup_project_directories(project_dir)
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# For per-field architecture: read from daily_vals_per_field_dir (Script 20 per-field output)
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daily_vals_dir <- setup$daily_vals_per_field_dir
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safe_log(sprintf("Using per-field daily CI directory: %s", daily_vals_dir))
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safe_log("Starting CI growth model interpolation")
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# 3. Load and process the data
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# ----------------------------
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tryCatch({
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# Load the combined CI data (created by Script 20 per-field)
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# Script 20 per-field outputs: daily_vals/{FIELD_NAME}/{YYYY-MM-DD}.rds
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CI_data <- load_combined_ci_data(daily_vals_dir)
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# Validate harvesting data
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if (is.null(harvesting_data) || nrow(harvesting_data) == 0) {
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safe_log("No harvesting data available", "ERROR")
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stop("No harvesting data available")
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}
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# Get the years from harvesting data
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years <- harvesting_data %>%
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filter(!is.na(season_start)) %>%
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distinct(year) %>%
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pull(year)
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safe_log(paste("Processing data for years:", paste(years, collapse = ", ")))
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# Generate interpolated CI data for each year and field
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CI_all <- generate_interpolated_ci_data(years, harvesting_data, CI_data)
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# CI_all <- CI_all %>%
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# group_by(Date, field, season) %>%
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# filter(!(field == "00F25" & season == 2023 & duplicated(DOY)))
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# Calculate growth metrics and save the results
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if (nrow(CI_all) > 0) {
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# Add daily and cumulative metrics
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CI_all_with_metrics <- calculate_growth_metrics(CI_all)
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# Save the processed data to cumulative_vals directory
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save_growth_model(
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CI_all_with_metrics,
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setup$cumulative_CI_vals_dir,
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"All_pivots_Cumulative_CI_quadrant_year_v2.rds"
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)
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} else {
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safe_log("No CI data was generated after interpolation", "WARNING")
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}
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safe_log("Growth model interpolation completed successfully")
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}, error = function(e) {
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safe_log(paste("Error in growth model interpolation:", e$message), "ERROR")
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stop(e$message)
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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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