Timon
d5fd4bb463
Major Changes: - NEW: Scripts 09 & 10 for KPI calculation and enhanced reporting - NEW: Shell script wrappers (01-10) for easier execution - NEW: R packages flextable and officer for enhanced Word reports - NEW: DEPLOYMENT_README.md with complete deployment guide - RENAMED: Numbered R scripts (02, 03, 04) for clarity - REMOVED: Old package management scripts (using renv only) - UPDATED: Workflow now uses scripts 09->10 instead of 05 Files Changed: 90+ files New Packages: flextable, officer New Scripts: 09_run_calculate_kpis.sh, 10_run_kpi_report.sh Documentation: DEPLOYMENT_README.md, EMAIL_TO_ADMIN.txt See DEPLOYMENT_README.md for full deployment instructions.
121 lines
3.9 KiB
R
121 lines
3.9 KiB
R
# CI_EXTRACTION.R
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# ==============
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# This script processes satellite imagery to extract Canopy Index (CI) values for agricultural fields.
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# It handles image processing, masking, and extraction of statistics by field/sub-field.
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#
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# Usage: Rscript ci_extraction.R [end_date] [offset] [project_dir]
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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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#
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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(exactextractr)
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library(readxl)
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library(here)
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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])) {
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end_date <- as.Date(args[1])
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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 {
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project_dir <- "esa" # Changed default from "aura" to "esa"
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}
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# Make project_dir available globally so parameters_project.R can use it
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assign("project_dir", project_dir, envir = .GlobalEnv)
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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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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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warning(paste("Successfully sourced files from 'r_app' directory."))
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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 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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# 5. Find and filter raster files by date
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# -----------------------------------
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log_message("Searching for raster files")
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tryCatch({
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# Use the new utility function to find satellite images
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existing_files <- find_satellite_images(planet_tif_folder, dates$days_filter)
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log_message(paste("Found", length(existing_files), "raster files for processing"))
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# 6. Process raster files and create VRT
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# -----------------------------------
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# Use the new utility function for batch processing
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vrt_list <- process_satellite_images(existing_files, field_boundaries, merged_final, daily_vrt)
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# 7. Process and combine CI values
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# ------------------------------
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# Call the process_ci_values function from utils with all required parameters
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process_ci_values(dates, field_boundaries, merged_final,
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field_boundaries_sf, daily_CI_vals_dir, cumulative_CI_vals_dir)
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}, error = function(e) {
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log_message(paste("Error in main processing:", e$message), level = "ERROR")
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stop(e$message)
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})
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}
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if (sys.nframe() == 0) {
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main()
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}
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