367 lines
15 KiB
R
367 lines
15 KiB
R
# ============================================================================
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# SCRIPT 20: Canopy Index (CI) Extraction from Satellite Imagery
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# ============================================================================
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# PURPOSE:
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# Extract Canopy Index (CI) from 4-band or 8-band satellite imagery and
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# mask by field boundaries. Supports automatic band detection, cloud masking
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# with UDM2 (8-band), and per-field CI value extraction. Produces both
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# per-field TIFFs and consolidated CI statistics for growth model input.
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#
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# INPUT DATA:
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# - Source: laravel_app/storage/app/{project}/field_tiles/{FIELD}/{DATE}.tif
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# - Format: GeoTIFF (4-band RGB+NIR from Planet API, or 8-band with UDM2)
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# - Requirement: Field boundaries (pivot.geojson) for masking
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#
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# OUTPUT DATA:
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# - Destination: laravel_app/storage/app/{project}/field_tiles_CI/{FIELD}/{DATE}.tif
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# - Format: GeoTIFF (5-band: R,G,B,NIR,CI as float32)
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# - Also exports: combined_CI/combined_CI_data.rds (wide format: fields × dates)
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#
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# USAGE:
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# Rscript 20_ci_extraction.R [end_date] [offset] [project] [data_source]
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#
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# Example (Windows PowerShell):
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# & "C:\Program Files\R\R-4.4.3\bin\x64\Rscript.exe" r_app/20_ci_extraction.R 2026-01-02 7 angata merged_tif
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#
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# PARAMETERS:
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# - end_date: End date for processing (character, YYYY-MM-DD format)
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# - offset: Days to look back from end_date (numeric, default 7)
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# - project: Project name (character) - angata, chemba, xinavane, esa, simba
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# - data_source: Data source directory (character, optional) - "merged_tif" (default), "merged_tif_8b", "merged_final_tif"
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#
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# CLIENT TYPES:
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# - cane_supply (ANGATA): Yes - core data processing
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# - agronomic_support (AURA): Yes - supports field health monitoring
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#
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# DEPENDENCIES:
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# - Packages: terra, sf, tidyverse, lubridate, readxl, furrr, future
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# - Utils files: parameters_project.R, 00_common_utils.R, 20_ci_extraction_utils.R
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# - External data: Field boundaries (pivot.geojson), harvest data (harvest.xlsx)
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# - Data directories: field_tiles/, field_tiles_CI/, combined_CI/
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#
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# NOTES:
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# - CI formula: (NIR - Red) / (NIR + Red); normalized to 0-5 range
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# - 8-band data automatically cloud-masked using UDM2 (band 7-8)
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# - 4-band data assumes clear-sky Planet PSScene imagery
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# - Parallel processing via furrr for speed optimization
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# - Output RDS uses wide format (fields as rows, dates as columns) for growth model
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# - Critical dependency for Script 30 (growth model) and Script 80 (KPIs)
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#
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# RELATED ISSUES:
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# SC-112: Utilities restructuring
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# SC-108: Core pipeline improvements
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#
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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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# Spatial data handling
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library(sf) # For reading/manipulating field boundaries (GeoJSON)
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library(terra) # For raster operations (CI extraction from TIFFs)
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# Data manipulation
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library(tidyverse) # For dplyr, ggplot2, readr (data wrangling and visualization)
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library(lubridate) # For date/time operations (parsing satellite dates)
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# File I/O
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library(readxl) # For reading harvest.xlsx (harvest dates for field mapping)
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library(here) # For relative path resolution (platform-independent file paths)
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})
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# 2. Process command line arguments
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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
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if (length(args) >= 1 && !is.na(args[1]) && args[1] != "") {
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# Parse date explicitly in YYYY-MM-DD format from command line
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end_date <- as.Date(args[1], format = "%Y-%m-%d")
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if (is.na(end_date)) {
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warning("Invalid end_date provided. Using default (current date).")
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end_date <- Sys.Date()
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#end_date <- "2023-10-01"
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}
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} else {
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end_date <- Sys.Date()
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#end_date <- "2023-10-01"
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}
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# Process offset argument
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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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warning("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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offset <- 7
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}
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# Process project_dir argument
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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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project_dir <- "angata" # Changed default from "aura" to "esa"
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}
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# Process data_source argument (optional, for specifying merged_tif_8b vs merged_tif vs merged_final_tif)
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if (length(args) >= 4 && !is.na(args[4])) {
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data_source <- as.character(args[4])
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# Validate data_source is a recognized option
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if (!data_source %in% c("merged_tif_8b", "merged_tif", "merged_final_tif")) {
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warning(paste("Data source", data_source, "not in standard list. Using as-is."))
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}
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} else if (exists("data_source", envir = .GlobalEnv)) {
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data_source <- get("data_source", envir = .GlobalEnv)
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} else {
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data_source <- "merged_tif_8b" # Default to 8-band (newer data with cloud masking)
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}
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# Make project_dir and data_source available globally
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assign("project_dir", project_dir, envir = .GlobalEnv)
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assign("data_source", data_source, envir = .GlobalEnv)
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cat(sprintf("CI Extraction: project=%s, end_date=%s, offset=%d days, data_source=%s\n",
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project_dir, format(end_date, "%Y-%m-%d"), offset, data_source))
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# Set flag to use pivot_2.geojson for ESA (extra fields for yield prediction)
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ci_extraction_script <- TRUE
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assign("ci_extraction_script", ci_extraction_script, envir = .GlobalEnv)
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# 3. Initialize project configuration
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# --------------------------------
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new_project_question <- TRUE
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cat("[DEBUG] Attempting to source r_app/parameters_project.R\n")
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tryCatch({
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source("r_app/parameters_project.R")
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cat("[DEBUG] Successfully sourced r_app/parameters_project.R\n")
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}, error = function(e) {
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cat("[ERROR] Failed to source r_app/parameters_project.R:\n", e$message, "\n")
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stop(e)
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})
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# Load centralized path structure (creates all directories automatically)
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paths <- setup_project_directories(project_dir)
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cat("[DEBUG] Attempting to source r_app/00_common_utils.R\n")
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tryCatch({
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source("r_app/00_common_utils.R")
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cat("[DEBUG] Successfully sourced r_app/00_common_utils.R\n")
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}, error = function(e) {
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cat("[ERROR] Failed to source r_app/00_common_utils.R:\n", e$message, "\n")
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stop(e)
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})
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cat("[DEBUG] Attempting to source r_app/20_ci_extraction_utils.R\n")
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tryCatch({
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source("r_app/20_ci_extraction_utils.R")
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cat("[DEBUG] Successfully sourced r_app/20_ci_extraction_utils.R\n")
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}, error = function(e) {
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cat("[ERROR] Failed to source r_app/20_ci_extraction_utils.R:\n", e$message, "\n")
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stop(e)
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})
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# 4. Generate date list for processing
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# ---------------------------------
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dates <- date_list(end_date, offset)
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log_message(paste("Processing data for week", dates$week, "of", dates$year))
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# 4a. CHECK DAILY CI EXTRACTION - Skip dates that already have extracted files
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# -------------------------------------------------------------------------
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log_message("\n===== CHECKING DAILY CI EXTRACTION STATUS =====")
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# Check which dates already have extracted CI files
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already_extracted <- c()
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missing_extraction <- c()
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if (dir.exists(daily_CI_vals_dir)) {
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existing_ci_files <- list.files(daily_CI_vals_dir, pattern = "^extracted_.*\\.rds$")
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# Extract dates from filenames like "extracted_2025-12-31_quadrant.rds"
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already_extracted <- sub("^extracted_(.+)_.*\\.rds$", "\\1", existing_ci_files)
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}
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# Find which dates in our processing range need extraction
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missing_extraction <- dates$days_filter[!(dates$days_filter %in% already_extracted)]
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cat(sprintf("[CI CHECK] Already extracted: %d dates\n", length(already_extracted)))
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cat(sprintf("[CI CHECK] Need extraction: %d dates (from %s to %s)\n",
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length(missing_extraction),
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if(length(missing_extraction) > 0) min(missing_extraction) else "N/A",
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if(length(missing_extraction) > 0) max(missing_extraction) else "N/A"))
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# If any dates need extraction, we'll extract them
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# If NO dates need extraction, we'll skip extraction but ALWAYS rebuild combined_CI_data.rds
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skip_extraction <- (length(missing_extraction) == 0)
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if (skip_extraction) {
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log_message("✓ All dates in processing range already have extracted CI files - skipping extraction")
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log_message("⚠ Will rebuild combined_CI_data.rds to ensure completeness")
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}
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# 4b. CHECK SOURCE DATA AVAILABILITY
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# ---------------------------------------------------------------
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# Verify that source data exists for dates we're going to extract
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# If a date is missing from source, we'll skip it gracefully
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log_message("\n===== CHECKING SOURCE DATA AVAILABILITY =====")
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dates_with_source <- c()
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dates_missing_source <- c()
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if (!skip_extraction && length(missing_extraction) > 0) {
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# Check which source dates are actually available
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for (date_str in missing_extraction) {
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# Look for the date in merged_tif directory
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source_file_pattern <- sprintf("%s\\.tif$", date_str)
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files_for_date <- list.files(planet_tif_folder, pattern = source_file_pattern)
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if (length(files_for_date) > 0) {
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dates_with_source <- c(dates_with_source, date_str)
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} else {
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dates_missing_source <- c(dates_missing_source, date_str)
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}
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}
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cat(sprintf("[SOURCE CHECK] Dates with available source data: %d\n", length(dates_with_source)))
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cat(sprintf("[SOURCE CHECK] Dates missing from source (will skip): %d\n", length(dates_missing_source)))
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if (length(dates_missing_source) > 0) {
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log_message(paste("⚠ Skipping extraction for missing source dates:", paste(dates_missing_source, collapse = ", ")))
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}
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}
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# 5. Find and filter raster files by date - with grid size detection
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# -----------------------------------
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log_message("Searching for raster files")
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# Check if tiles exist (Script 10 output) - detect grid size dynamically using centralized paths
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tiles_split_base <- paths$daily_tiles_split_dir
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# Detect grid size from daily_tiles_split folder structure
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# Expected structure: daily_tiles_split/5x5/ or daily_tiles_split/10x10/ etc.
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grid_size <- NA
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if (dir.exists(tiles_split_base)) {
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subfolders <- list.dirs(tiles_split_base, full.names = FALSE, recursive = FALSE)
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# Look for grid size patterns like "5x5", "10x10", "20x20"
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grid_patterns <- grep("^\\d+x\\d+$", subfolders, value = TRUE)
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if (length(grid_patterns) > 0) {
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grid_size <- grid_patterns[1] # Use first grid size found
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log_message(paste("Detected grid size:", grid_size))
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}
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}
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# Construct tile folder path with grid size
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if (!is.na(grid_size)) {
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tile_folder <- file.path(tiles_split_base, grid_size)
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} else {
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tile_folder <- tiles_split_base
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}
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use_tiles <- dir.exists(tile_folder)
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# Make grid_size available globally for other functions
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assign("grid_size", grid_size, envir = .GlobalEnv)
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tryCatch({
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if (skip_extraction) {
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log_message("\n===== SKIPPING CI EXTRACTION (all dates already processed) =====")
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} else if (use_tiles) {
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# Use tile-based processing
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log_message(paste("Tile folder detected at", tile_folder))
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log_message("Using tile-based CI extraction")
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# Call the tile-based extraction function
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process_ci_values_from_tiles(
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dates = dates,
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tile_folder = tile_folder,
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field_boundaries = field_boundaries,
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field_boundaries_sf = field_boundaries_sf,
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daily_CI_vals_dir = daily_CI_vals_dir,
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cumulative_CI_vals_dir = cumulative_CI_vals_dir,
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merged_final_dir = merged_final,
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grid_size = grid_size
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)
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} else {
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# Use legacy full-extent processing
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log_message("No tiles found. Using legacy full-extent approach")
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# Use the existing utility function to find satellite images
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existing_files <- find_satellite_images(planet_tif_folder, dates$days_filter)
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log_message(paste("Found", length(existing_files), "raster files for processing"))
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# Process raster files and create VRT
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vrt_list <- process_satellite_images(existing_files, field_boundaries, merged_final, daily_vrt)
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# Process and combine CI values
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process_ci_values(dates, field_boundaries, merged_final,
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field_boundaries_sf, daily_CI_vals_dir, cumulative_CI_vals_dir)
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}
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}, error = function(e) {
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log_message(paste("Error in main processing:", e$message), level = "ERROR")
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stop(e$message)
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})
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# 6. REBUILD combined_CI_data.rds from ALL daily extracted files
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# -----------------------------------------------
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# This ensures the combined file is complete and up-to-date
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# even if extraction was skipped (because dates already existed)
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# NOTE: Only rebuild if new dates were successfully extracted
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# If all dates were missing from source, skip this step to avoid corrupting the file
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log_message("\n===== HANDLING combined_CI_data.rds =====")
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if (length(dates_with_source) == 0 && length(missing_extraction) > 0) {
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# All missing dates had no source data - skip combined_CI_data.rds update
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log_message("⚠ No new dates extracted (all source data missing) - skipping combined_CI_data.rds update")
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} else if (skip_extraction) {
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# All dates already extracted - optionally rebuild for consistency
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log_message("✓ All dates already extracted - combined_CI_data.rds is up-to-date")
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} else {
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# New dates were extracted - rebuild combined_CI_data.rds from ALL daily files
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log_message("Rebuilding combined_CI_data.rds from all daily extracted files...")
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tryCatch({
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if (!dir.exists(daily_CI_vals_dir)) {
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log_message("Daily CI directory does not exist yet", level = "WARNING")
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} else {
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# List ALL daily CI files (not just new ones)
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all_daily_files <- list.files(path = daily_CI_vals_dir, pattern = "^extracted_.*\\.rds$", full.names = TRUE)
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if (length(all_daily_files) == 0) {
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log_message("No daily CI files found to combine", level = "WARNING")
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} else {
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log_message(paste("Combining all", length(all_daily_files), "daily CI files into combined_CI_data.rds"))
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# Load and combine ALL daily files (creates complete dataset)
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combined_ci_path <- file.path(paths$cumulative_ci_vals_dir, "combined_CI_data.rds")
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combined_data <- all_daily_files %>%
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purrr::map(readRDS) %>%
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purrr::list_rbind() %>%
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dplyr::group_by(sub_field)
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# Save the rebuilt combined data
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saveRDS(combined_data, combined_ci_path)
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log_message(paste("✓ Rebuilt combined_CI_data.rds with", nrow(combined_data), "total rows"))
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}
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}
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}, error = function(e) {
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log_message(paste("⚠ Error rebuilding combined_CI_data.rds (will skip):", e$message), level = "WARNING")
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log_message(" Note: This is OK - Script 30 will use growth model RDS instead", level = "WARNING")
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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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