199 lines
7.4 KiB
R
199 lines
7.4 KiB
R
# CI_EXTRACTION_PER_FIELD.R
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# =========================
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# Script 20 (Refactored for Per-Field Architecture)
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#
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# This script reads per-field TIFFs from Script 10 output and:
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# 1. Calculates Canopy Index (CI) from 4-band imagery (RGB + NIR)
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# 2. Outputs 5-band TIFFs with CI as the 5th band to field_tiles_CI/{FIELD}/{DATE}.tif
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# 3. Outputs per-field per-date RDS files to daily_vals/{FIELD}/{DATE}.rds
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#
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# Key differences from legacy Script 20:
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# - Input: field_tiles/{FIELD}/{DATE}.tif (4-band, from Script 10)
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# - Output: field_tiles_CI/{FIELD}/{DATE}.tif (5-band with CI)
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# - Output: daily_vals/{FIELD}/{DATE}.rds (per-field CI statistics)
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# - Directly extracts CI statistics per sub_field within each field
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#
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# Usage:
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# Rscript 20_ci_extraction_per_field.R [project_dir] [end_date] [offset]
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# Example: Rscript 20_ci_extraction_per_field.R angata 2026-01-02 7
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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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# =============================================================================
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# Load utility functions from 20_ci_extraction_utils.R
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# =============================================================================
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source("r_app/20_ci_extraction_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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end_date <- if (length(args) >= 2 && args[2] != "") as.Date(args[2]) else Sys.Date()
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offset <- if (length(args) >= 3 && !is.na(as.numeric(args[3]))) as.numeric(args[3]) else 7
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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 20: CI Extraction Per-Field ==="))
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safe_log(sprintf("Project: %s | End Date: %s | Offset: %d days",
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project_dir, format(end_date, "%Y-%m-%d"), offset))
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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$message), "ERROR")
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stop(e)
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})
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# 2. Set up directory paths from parameters FIRST (before using setup$...)
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# -----------------------------------------------------------------------
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setup <- setup_project_directories(project_dir)
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# 3. Load field boundaries directly from field_boundaries_path in setup
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# ------------------------------------------------------------------
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tryCatch({
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field_boundaries_sf <- st_read(setup$field_boundaries_path, quiet = TRUE)
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safe_log(sprintf("Loaded %d field/sub_field polygons from %s", nrow(field_boundaries_sf), setup$field_boundaries_path))
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}, error = function(e) {
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safe_log(sprintf("Error loading field boundaries from %s: %s", setup$field_boundaries_path, e$message), "ERROR")
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stop(e)
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})
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# 4. Get list of dates to process
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dates <- date_list(end_date, offset)
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safe_log(sprintf("Processing dates: %s to %s (%d dates)",
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dates$start_date, dates$end_date, length(dates$days_filter)))
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safe_log(sprintf("Input directory: %s", setup$field_tiles_dir))
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safe_log(sprintf("Output TIF directory: %s", setup$field_tiles_ci_dir))
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safe_log(sprintf("Output RDS directory: %s", setup$daily_vals_per_field_dir))
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# 5. Process each field
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# ----------------------
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if (!dir.exists(setup$field_tiles_dir)) {
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safe_log(sprintf("Field tiles directory not found: %s", setup$field_tiles_dir), "ERROR")
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stop("Script 10 output not found. Run Script 10 first.")
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}
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fields <- list.dirs(setup$field_tiles_dir, full.names = FALSE, recursive = FALSE)
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fields <- fields[fields != ""] # Remove empty strings
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if (length(fields) == 0) {
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safe_log("No fields found in field_tiles directory", "WARNING")
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return()
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}
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safe_log(sprintf("Found %d fields to process", length(fields)))
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# 6. Process each field
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# ----------------------
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total_success <- 0
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total_error <- 0
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ci_results_by_date <- list()
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for (field in fields) {
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safe_log(sprintf("\n--- Processing field: %s ---", field))
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field_tiles_path <- file.path(field_tiles_dir, field)
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field_ci_path <- file.path(field_tiles_ci_dir, field)
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field_daily_vals_path <- file.path(setup$daily_vals_per_field_dir, field)
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# Create output subdirectories for this field
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dir.create(field_ci_path, showWarnings = FALSE, recursive = TRUE)
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dir.create(field_daily_vals_path, showWarnings = FALSE, recursive = TRUE)
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# 5a. Process each date for this field
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# -----------------------------------
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for (date_str in dates$days_filter) {
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input_tif <- file.path(field_tiles_path, sprintf("%s.tif", date_str))
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output_tif <- file.path(field_ci_path, sprintf("%s.tif", date_str))
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output_rds <- file.path(field_daily_vals_path, sprintf("%s.rds", date_str))
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# Skip if both outputs already exist
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if (file.exists(output_tif) && file.exists(output_rds)) {
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safe_log(sprintf(" %s: Already processed (skipping)", date_str))
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next
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}
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# Check if input TIFF exists
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if (!file.exists(input_tif)) {
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safe_log(sprintf(" %s: Input TIFF not found (skipping)", date_str))
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next
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}
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tryCatch({
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# Load 4-band TIFF
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raster_4band <- terra::rast(input_tif)
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# Calculate CI
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ci_raster <- calc_ci_from_raster(raster_4band)
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# Create 5-band TIFF (R, G, B, NIR, CI)
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five_band <- c(raster_4band, ci_raster)
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# Save 5-band TIFF
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terra::writeRaster(five_band, output_tif, overwrite = TRUE)
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# Extract CI statistics by sub_field
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ci_stats <- extract_ci_by_subfield(ci_raster, field_boundaries_sf, field)
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# Save RDS
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if (!is.null(ci_stats) && nrow(ci_stats) > 0) {
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saveRDS(ci_stats, output_rds)
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safe_log(sprintf(" %s: ✓ Processed (%d sub-fields)", date_str, nrow(ci_stats)))
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# Store for daily aggregation
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ci_stats_with_date <- ci_stats %>% mutate(date = date_str)
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key <- sprintf("%s_%s", field, date_str)
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ci_results_by_date[[key]] <- ci_stats_with_date
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} else {
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safe_log(sprintf(" %s: ⚠ No CI data extracted", date_str))
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}
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total_success <- total_success + 1
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}, error = function(e) {
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safe_log(sprintf(" %s: ✗ Error - %s", date_str, e$message), "ERROR")
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total_error <<- total_error + 1
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})
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}
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}
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# 7. Summary
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# ----------
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safe_log(sprintf("\n=== Processing Complete ==="))
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safe_log(sprintf("Successfully processed: %d", total_success))
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safe_log(sprintf("Errors encountered: %d", total_error))
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if (total_success > 0) {
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safe_log("Output files created in:")
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safe_log(sprintf(" TIFFs: %s", setup$field_tiles_ci_dir))
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safe_log(sprintf(" RDS: %s", setup$daily_vals_per_field_dir))
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}
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}
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# Execute main if called from command line
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if (sys.nframe() == 0) {
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main()
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}
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