Timon
4cd62ab82e
- Updated `create_CI_map` and `create_CI_diff_map` functions to enforce a 1:1 aspect ratio for consistent map sizing. - Modified `ci_plot` function to adjust widths of arranged maps for better layout. - Changed raster merging method in `aggregate_per_field_mosaics_to_farm_level` from `mosaic` to `merge` for improved handling of field data. - Introduced `test_kpi_validation.R` script to validate the structure of KPI RDS files, ensuring expected KPIs are present. - Added `test_overview_maps_aggregation.R` script to test the aggregation pipeline for overview maps, including loading field mosaics, creating a farm-level mosaic, and generating visualizations.
241 lines
9.4 KiB
R
241 lines
9.4 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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# Main Processing
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# =============================================================================
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main <- function() {
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# STEP 1: Set working directory to project root (smartcane/)
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# This ensures all relative paths resolve correctly
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if (basename(getwd()) == "r_app") {
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setwd("..")
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}
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# STEP 2: SOURCE ALL UTILITY SCRIPTS (before any operations)
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# Parse command-line arguments FIRST
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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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# Make project_dir available globally for parameters_project.R
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assign("project_dir", project_dir, envir = .GlobalEnv)
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# Load parameters_project.R (provides safe_log, date_list, setup_project_directories, etc.)
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tryCatch({
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source("r_app/parameters_project.R")
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}, error = function(e) {
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cat(sprintf("Error loading parameters_project.R: %s\n", e$message))
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stop(e)
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})
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# Load CI extraction utilities
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tryCatch({
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source("r_app/20_ci_extraction_utils.R")
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}, error = function(e) {
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cat(sprintf("Error loading 20_ci_extraction_utils.R: %s\n", e$message))
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stop(e)
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})
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# STEP 3: Now all utilities are loaded, proceed with script logic
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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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# Set up directory paths from parameters
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setup <- setup_project_directories(project_dir)
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# Load field boundaries directly from field_boundaries_path in setup
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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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# Get list of dates to process
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# If in migration mode, dates_to_process is provided by the pipeline runner
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if (exists("dates_to_process") && !is.null(dates_to_process)) {
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# Migration mode: Use provided list of dates (process ALL available dates)
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dates_filter <- sort(dates_to_process)
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safe_log(sprintf("Migration mode: Processing %d specified dates", length(dates_filter)))
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} else {
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# Normal mode: Use 7-day offset window
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dates <- date_list(end_date, offset)
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dates_filter <- dates$days_filter
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safe_log(sprintf("Normal mode: Processing dates: %s to %s (%d dates)",
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dates$start_date, dates$end_date, length(dates_filter)))
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}
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safe_log(sprintf("Input directory: %s", setup$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_ci_vals_dir))
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# Process each field
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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$field_tiles_dir, full.names = FALSE, recursive = FALSE)
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fields <- fields[fields != ""] # Remove empty strings
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if (length(fields) == 0) {
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safe_log("No fields found in field_tiles directory", "WARNING")
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return()
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}
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safe_log(sprintf("Found %d fields to process", length(fields)))
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# DEBUG: Check what paths are available in setup
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safe_log(sprintf("[DEBUG] Available setup paths: %s", paste(names(setup), collapse=", ")))
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safe_log(sprintf("[DEBUG] field_tiles_ci_dir: %s", setup$field_tiles_ci_dir))
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safe_log(sprintf("[DEBUG] daily_ci_vals_dir: %s", setup$daily_ci_vals_dir))
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# Use daily_ci_vals_dir for per-field daily CI output
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# Pre-create output subdirectories for all fields
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for (field in fields) {
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dir.create(file.path(setup$field_tiles_ci_dir, field), showWarnings = FALSE, recursive = TRUE)
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if (!is.null(setup$daily_ci_vals_dir)) {
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dir.create(file.path(setup$daily_ci_vals_dir, field), showWarnings = FALSE, recursive = TRUE)
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}
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}
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# Process each DATE (load merged TIFF once, extract all fields from it)
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total_success <- 0
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total_error <- 0
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for (date_str in dates_filter) {
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# Load the MERGED TIFF (farm-wide) ONCE for this date
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input_tif_merged <- file.path(setup$merged_tif_folder, sprintf("%s.tif", date_str))
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if (!file.exists(input_tif_merged)) {
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safe_log(sprintf(" %s: merged_tif not found (skipping)", date_str))
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total_error <<- total_error + 1
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next
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}
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tryCatch({
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# Load 4-band TIFF ONCE
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raster_4band <- terra::rast(input_tif_merged)
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safe_log(sprintf(" %s: Loaded merged TIFF, processing %d fields...", date_str, length(fields)))
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# Calculate CI from 4-band
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ci_raster <- calc_ci_from_raster(raster_4band)
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# Create 5-band (R, G, B, NIR, CI)
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# Explicitly set band names after combining to ensure proper naming
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five_band <- c(raster_4band, ci_raster)
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names(five_band) <- c("Red", "Green", "Blue", "NIR", "CI")
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# Now process all fields from this single merged TIFF
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fields_processed_this_date <- 0
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for (field in fields) {
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field_ci_path <- file.path(setup$field_tiles_ci_dir, field)
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field_daily_vals_path <- file.path(setup$daily_ci_vals_dir, field)
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# Pre-create output directories
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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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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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# MODE 3: Skip if both outputs already exist
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if (file.exists(output_tif) && file.exists(output_rds)) {
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next
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}
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# MODE 2: Regeneration mode - RDS missing but CI TIFF exists
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if (file.exists(output_tif) && !file.exists(output_rds)) {
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tryCatch({
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extract_rds_from_ci_tiff(output_tif, output_rds, field_boundaries_sf, field)
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fields_processed_this_date <- fields_processed_this_date + 1
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}, error = function(e) {
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# Continue to next field
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})
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next
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}
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# MODE 1: Normal mode - crop 5-band TIFF to field boundary and save
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tryCatch({
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# Crop 5-band TIFF to field boundary
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field_geom <- field_boundaries_sf %>% filter(field == !!field)
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five_band_cropped <- terra::crop(five_band, field_geom, mask = TRUE)
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# Save 5-band field TIFF
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terra::writeRaster(five_band_cropped, output_tif, overwrite = TRUE)
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# Extract CI statistics by sub_field (from cropped CI raster)
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ci_cropped <- five_band_cropped[[5]] # 5th band is CI
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ci_stats <- extract_ci_by_subfield(ci_cropped, 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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}
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fields_processed_this_date <- fields_processed_this_date + 1
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}, error = function(e) {
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# Error in individual field, continue to next
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safe_log(sprintf(" Error processing field %s: %s", field, e$message), "WARNING")
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})
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}
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# Increment success counter if at least one field succeeded
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if (fields_processed_this_date > 0) {
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total_success <<- total_success + 1
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safe_log(sprintf(" %s: Processed %d fields", date_str, fields_processed_this_date))
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}
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}, error = function(e) {
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total_error <<- total_error + 1
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safe_log(sprintf(" %s: Error loading or processing merged TIFF - %s", date_str, e$message), "ERROR")
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})
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}
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# Summary
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safe_log(sprintf("\n=== Processing Complete ==="))
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safe_log(sprintf("Successfully processed: %d", total_success))
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safe_log(sprintf("Errors encountered: %d", total_error))
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if (total_success > 0) {
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safe_log("Output files created in:")
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safe_log(sprintf(" TIFFs: %s", setup$field_tiles_ci_dir))
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safe_log(sprintf(" RDS: %s", setup$daily_ci_vals_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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