refactored 10 20

r_app/10_create_per_field_tiffs.R

@@ -0,0 +1,328 @@
+# ==============================================================================
+# SmartCane Script 10: Create Per-Field TIFFs
+# ==============================================================================
+#
+# PURPOSE:
+#   Split full-farm satellite TIFFs into per-field file structure across TWO phases:
+#
+#   PHASE 1 - MIGRATION (Legacy Data):
+#     Input:  merged_final_tif/{DATE}.tif (5-band: R,G,B,NIR,CI - with CI calculated)
+#     Output: field_tiles_CI/{FIELD}/{DATE}.tif
+#     Status: One-time reorganization of existing data; will be removed after 2-3 weeks
+#
+#   PHASE 2 - PROCESSING (New Downloads):
+#     Input:  merged_tif/{DATE}.tif (4-band: R,G,B,NIR - raw from Planet API)
+#     Output: field_tiles/{FIELD}/{DATE}.tif
+#     Status: Ongoing for all new downloads; always runs (not conditional)
+#
+#   INTEGRATION WITH DOWNSTREAM SCRIPTS:
+#   - Script 20 (CI Extraction):
+#     Reads from field_tiles/{FIELD}/{DATE}.tif
+#     Adds CI calculation → outputs to field_tiles_CI/{FIELD}/{DATE}.tif (5-band)
+#   - Script 40 (Mosaic Creation):
+#     Reads from field_tiles_CI/{FIELD}/{DATE}.tif (via per-field weekly aggregation)
+#     Creates weekly_mosaic/{FIELD}/week_{WW}.tif
+#
+#   ARCHITECTURE:
+#   This script uses field/date folder organization:
+#     field_tiles/
+#       ├── field_1/
+#       │   ├── 2024-01-15.tif
+#       │   └── 2024-01-16.tif
+#       └── field_2/
+#           ├── 2024-01-15.tif
+#           └── 2024-01-16.tif
+#
+#   Benefits: Upstream scripts iterate per-field → per-date, enabling clean
+#   aggregation for mosaics (Script 40) and KPIs (Script 80/90).
+#
+# ==============================================================================
+
+
+library(terra)
+library(sf)
+
+# ============================================================================
+# HELPER FUNCTIONS (DEFINE FIRST)
+# ============================================================================
+
+smartcane_log <- function(msg) {
+  cat(paste0("[", Sys.time(), "] ", msg, "\n"))
+}
+
+# Load field boundaries from GeoJSON
+load_field_boundaries <- function(geojson_path) {
+  smartcane_log(paste("Loading field boundaries from:", geojson_path))
+  
+  if (!file.exists(geojson_path)) {
+    stop("GeoJSON file not found:", geojson_path)
+  }
+  
+  fields <- st_read(geojson_path, quiet = TRUE)
+  
+  # Standardize field name property
+  if (!"field_name" %in% names(fields)) {
+    if ("field" %in% names(fields)) {
+      fields$field_name <- fields$field
+    } else if ("FIELD_ID" %in% names(fields)) {
+      fields$field_name <- fields$FIELD_ID
+    } else if ("Name" %in% names(fields)) {
+      fields$field_name <- fields$Name
+    } else {
+      # Default: use first non-geometry column
+      field_col <- names(fields)[!names(fields) %in% c("geometry", "geom")]
+      if (length(field_col) > 0) {
+        fields$field_name <- fields[[field_col[1]]]
+      } else {
+        stop("No suitable field name column found in GeoJSON")
+      }
+    }
+  }
+  
+  smartcane_log(paste("Loaded", nrow(fields), "field(s)"))
+  return(fields)
+}
+
+# ============================================================================
+# PROJECT SETUP
+# ============================================================================
+
+# Get project parameter
+args <- commandArgs(trailingOnly = TRUE)
+if (length(args) == 0) {
+  PROJECT <- "angata"
+} else {
+  PROJECT <- args[1]
+}
+
+# Construct paths directly (avoid complex parameter initialization)
+base_path <- file.path(getwd(), "laravel_app", "storage", "app", PROJECT)
+data_dir <- file.path(base_path, "Data")
+
+smartcane_log(paste("Project:", PROJECT))
+smartcane_log(paste("Base path:", base_path))
+smartcane_log(paste("Data dir:", data_dir))
+
+# Unified function to crop TIFF to field boundaries
+# Called by both migration and processing phases
+crop_tiff_to_fields <- function(tif_path, tif_date, fields, output_base_dir) {
+  
+  created <- 0
+  skipped <- 0
+  errors <- 0
+  
+  # Load raster
+  if (!file.exists(tif_path)) {
+    smartcane_log(paste("ERROR: TIFF not found:", tif_path))
+    return(list(created = 0, skipped = 0, errors = 1))
+  }
+  
+  rast <- tryCatch({
+    rast(tif_path)
+  }, error = function(e) {
+    smartcane_log(paste("ERROR loading raster:", e$message))
+    return(NULL)
+  })
+  
+  if (is.null(rast)) {
+    return(list(created = 0, skipped = 0, errors = 1))
+  }
+  
+  # Create raster bounding box in raster CRS
+  rast_bbox <- st_as_sfc(st_bbox(rast))
+  st_crs(rast_bbox) <- st_crs(rast)
+  
+  # Reproject fields to match raster CRS
+  fields_reprojected <- st_transform(fields, st_crs(rast_bbox))
+  
+  # Find which fields intersect this raster (CRITICAL: raster bbox first, then fields)
+  overlapping_indices <- st_intersects(rast_bbox, fields_reprojected, sparse = TRUE)
+  overlapping_indices <- unique(unlist(overlapping_indices))
+  
+  if (length(overlapping_indices) == 0) {
+    smartcane_log(paste("No fields intersect TIFF:", basename(tif_path)))
+    return(list(created = 0, skipped = 0, errors = 0))
+  }
+  
+  # Process each overlapping field
+  for (field_idx in overlapping_indices) {
+    field_name <- fields$field_name[field_idx]
+    field_geom <- fields_reprojected[field_idx, ]
+    
+    # Create field directory
+    field_dir <- file.path(output_base_dir, field_name)
+    if (!dir.exists(field_dir)) {
+      dir.create(field_dir, recursive = TRUE, showWarnings = FALSE)
+    }
+    
+    # Output file path
+    output_path <- file.path(field_dir, paste0(tif_date, ".tif"))
+    
+    # Check if file already exists (idempotent)
+    if (file.exists(output_path)) {
+      skipped <- skipped + 1
+      next
+    }
+    
+    # Crop raster to field boundary
+    tryCatch({
+      field_rast <- crop(rast, field_geom)
+      writeRaster(field_rast, output_path, overwrite = TRUE)
+      created <- created + 1
+    }, error = function(e) {
+      smartcane_log(paste("ERROR cropping field", field_name, ":", e$message))
+      errors <<- errors + 1
+    })
+  }
+  
+  return(list(created = created, skipped = skipped, errors = errors))
+}
+
+# Migrate legacy 5-band TIFFs with CI from merged_final_tif
+migrate_old_merged_final_tif <- function(merged_final_dir, field_tiles_ci_dir, fields) {
+  
+  smartcane_log("\n========================================")
+  smartcane_log("PHASE 1: MIGRATING LEGACY DATA")
+  smartcane_log("========================================")
+  
+  # Check if legacy directory exists
+  if (!dir.exists(merged_final_dir)) {
+    smartcane_log("No legacy merged_final_tif/ directory found - skipping migration")
+    return(list(total_created = 0, total_skipped = 0, total_errors = 0))
+  }
+  
+  # Create output directory
+  if (!dir.exists(field_tiles_ci_dir)) {
+    dir.create(field_tiles_ci_dir, recursive = TRUE, showWarnings = FALSE)
+  }
+  
+  # Find all date-pattern TIFFs in root of merged_final_tif
+  tiff_files <- list.files(
+    merged_final_dir,
+    pattern = "^[0-9]{4}-[0-9]{2}-[0-9]{2}\\.tif$",
+    full.names = TRUE
+  )
+  
+  smartcane_log(paste("Found", length(tiff_files), "legacy TIFF(s) to migrate"))
+  
+  if (length(tiff_files) == 0) {
+    smartcane_log("No legacy TIFFs found - skipping migration")
+    return(list(total_created = 0, total_skipped = 0, total_errors = 0))
+  }
+  
+  # Process each legacy TIFF
+  total_created <- 0
+  total_skipped <- 0
+  total_errors <- 0
+  
+  for (tif_path in tiff_files) {
+    tif_date <- gsub("\\.tif$", "", basename(tif_path))
+    
+    smartcane_log(paste("Migrating:", tif_date))
+    
+    result <- crop_tiff_to_fields(tif_path, tif_date, fields, field_tiles_ci_dir)
+    total_created <- total_created + result$created
+    total_skipped <- total_skipped + result$skipped
+    total_errors <- total_errors + result$errors
+  }
+  
+  smartcane_log(paste("Migration complete: created =", total_created,
+                     ", skipped =", total_skipped, ", errors =", total_errors))
+  
+  return(list(total_created = total_created, total_skipped = total_skipped,
+              total_errors = total_errors))
+}
+
+# Process new 4-band raw TIFFs from merged_tif
+process_new_merged_tif <- function(merged_tif_dir, field_tiles_dir, fields) {
+  
+  smartcane_log("\n========================================")
+  smartcane_log("PHASE 2: PROCESSING NEW DOWNLOADS")
+  smartcane_log("========================================")
+  
+  # Check if download directory exists
+  if (!dir.exists(merged_tif_dir)) {
+    smartcane_log("No merged_tif/ directory found - no new data to process")
+    return(list(total_created = 0, total_skipped = 0, total_errors = 0))
+  }
+  
+  # Create output directory
+  if (!dir.exists(field_tiles_dir)) {
+    dir.create(field_tiles_dir, recursive = TRUE, showWarnings = FALSE)
+  }
+  
+  # Find all date-pattern TIFFs in root of merged_tif
+  tiff_files <- list.files(
+    merged_tif_dir,
+    pattern = "^[0-9]{4}-[0-9]{2}-[0-9]{2}\\.tif$",
+    full.names = TRUE
+  )
+  
+  smartcane_log(paste("Found", length(tiff_files), "TIFF(s) to process"))
+  
+  if (length(tiff_files) == 0) {
+    smartcane_log("No new TIFFs found - nothing to process")
+    return(list(total_created = 0, total_skipped = 0, total_errors = 0))
+  }
+  
+  # Process each new TIFF
+  total_created <- 0
+  total_skipped <- 0
+  total_errors <- 0
+  
+  for (tif_path in tiff_files) {
+    tif_date <- gsub("\\.tif$", "", basename(tif_path))
+    
+    smartcane_log(paste("Processing:", tif_date))
+    
+    result <- crop_tiff_to_fields(tif_path, tif_date, fields, field_tiles_dir)
+    total_created <- total_created + result$created
+    total_skipped <- total_skipped + result$skipped
+    total_errors <- total_errors + result$errors
+  }
+  
+  smartcane_log(paste("Processing complete: created =", total_created,
+                     ", skipped =", total_skipped, ", errors =", total_errors))
+  
+  return(list(total_created = total_created, total_skipped = total_skipped,
+              total_errors = total_errors))
+}
+
+# ============================================================================
+# MAIN EXECUTION
+# ============================================================================
+
+smartcane_log("========================================")
+smartcane_log(paste("Script 10: Per-Field TIFF Creation for", PROJECT))
+smartcane_log("========================================")
+
+# Create necessary directories
+dir.create(data_dir, recursive = TRUE, showWarnings = FALSE)
+
+# Load field boundaries
+geojson_path <- file.path(data_dir, "pivot.geojson")
+fields <- load_field_boundaries(geojson_path)
+
+# Define input and output directories
+merged_final_dir <- file.path(base_path, "merged_final_tif")
+merged_tif_dir <- file.path(base_path, "merged_tif")
+field_tiles_dir <- file.path(base_path, "field_tiles")
+field_tiles_ci_dir <- file.path(base_path, "field_tiles_CI")
+
+# PHASE 1: Migrate legacy data (if exists)
+migrate_result <- migrate_old_merged_final_tif(merged_final_dir, field_tiles_ci_dir, fields)
+
+# PHASE 2: Process new downloads (always runs)
+process_result <- process_new_merged_tif(merged_tif_dir, field_tiles_dir, fields)
+
+smartcane_log("\n========================================")
+smartcane_log("FINAL SUMMARY")
+smartcane_log("========================================")
+smartcane_log(paste("Migration: created =", migrate_result$total_created,
+                   ", skipped =", migrate_result$total_skipped,
+                   ", errors =", migrate_result$total_errors))
+smartcane_log(paste("Processing: created =", process_result$total_created,
+                   ", skipped =", process_result$total_skipped,
+                   ", errors =", process_result$total_errors))
+smartcane_log("Script 10 complete")
+smartcane_log("========================================\n")

r_app/20_ci_extraction_per_field.R

@@ -0,0 +1,240 @@
+# CI_EXTRACTION_PER_FIELD.R
+# =========================
+# Script 20 (Refactored for Per-Field Architecture)
+# 
+# This script reads per-field TIFFs from Script 10 output and:
+# 1. Calculates Canopy Index (CI) from 4-band imagery (RGB + NIR)
+# 2. Outputs 5-band TIFFs with CI as the 5th band to field_tiles_CI/{FIELD}/{DATE}.tif
+# 3. Outputs per-field per-date RDS files to daily_vals/{FIELD}/{DATE}.rds
+#
+# Key differences from legacy Script 20:
+# - Input: field_tiles/{FIELD}/{DATE}.tif (4-band, from Script 10)
+# - Output: field_tiles_CI/{FIELD}/{DATE}.tif (5-band with CI)
+# - Output: daily_vals/{FIELD}/{DATE}.rds (per-field CI statistics)
+# - Directly extracts CI statistics per sub_field within each field
+# 
+# Usage:
+#   Rscript 20_ci_extraction_per_field.R [project_dir] [end_date] [offset]
+#   Example: Rscript 20_ci_extraction_per_field.R angata 2026-01-02 7
+
+suppressPackageStartupMessages({
+  library(sf)
+  library(terra)
+  library(tidyverse)
+  library(lubridate)
+  library(here)
+})
+
+# =============================================================================
+# Load utility functions from 20_ci_extraction_utils.R
+# =============================================================================
+source("r_app/20_ci_extraction_utils.R")
+
+# =============================================================================
+# Main Processing
+# =============================================================================
+
+main <- function() {
+  # IMPORTANT: Set working directory to project root (smartcane/)
+  # This ensures here() functions resolve relative to /smartcane, not /smartcane/r_app
+  if (basename(getwd()) == "r_app") {
+    setwd("..")
+  }
+  
+  # Parse command-line arguments
+  args <- commandArgs(trailingOnly = TRUE)
+  
+  project_dir <- if (length(args) >= 1 && args[1] != "") args[1] else "angata"
+  end_date <- if (length(args) >= 2 && args[2] != "") as.Date(args[2]) else Sys.Date()
+  offset <- if (length(args) >= 3 && !is.na(as.numeric(args[3]))) as.numeric(args[3]) else 7
+  
+  # IMPORTANT: Make project_dir available globally for parameters_project.R
+  assign("project_dir", project_dir, envir = .GlobalEnv)
+  
+  safe_log(sprintf("=== Script 20: CI Extraction Per-Field ==="))
+  safe_log(sprintf("Project: %s | End Date: %s | Offset: %d days", 
+                      project_dir, format(end_date, "%Y-%m-%d"), offset))
+  
+  # 1. Load parameters (includes field boundaries setup)
+  # ---------------------------------------------------
+  tryCatch({
+    source("r_app/parameters_project.R")
+    safe_log("Loaded parameters_project.R")
+  }, error = function(e) {
+    safe_log(sprintf("Error loading parameters: %s", e$message), "ERROR")
+    stop(e)
+  })
+  
+  # 2. Set up directory paths from parameters FIRST (before using setup$...)
+  # -----------------------------------------------------------------------
+  setup <- setup_project_directories(project_dir)
+  
+  # 3. Load field boundaries directly from field_boundaries_path in setup
+  # ------------------------------------------------------------------
+  tryCatch({
+    field_boundaries_sf <- st_read(setup$field_boundaries_path, quiet = TRUE)
+    safe_log(sprintf("Loaded %d field/sub_field polygons from %s", nrow(field_boundaries_sf), setup$field_boundaries_path))
+  }, error = function(e) {
+    safe_log(sprintf("Error loading field boundaries from %s: %s", setup$field_boundaries_path, e$message), "ERROR")
+    stop(e)
+  })
+  
+  # 4. Get list of dates to process
+  dates <- date_list(end_date, offset)
+  safe_log(sprintf("Processing dates: %s to %s (%d dates)", 
+                      dates$start_date, dates$end_date, length(dates$days_filter)))
+  
+  safe_log(sprintf("Input directory: %s", setup$field_tiles_dir))
+  safe_log(sprintf("Output TIF directory: %s", setup$field_tiles_ci_dir))
+  safe_log(sprintf("Output RDS directory: %s", setup$daily_vals_per_field_dir))
+  
+  # 5. Process each field
+  # ----------------------
+  if (!dir.exists(setup$field_tiles_dir)) {
+    safe_log(sprintf("Field tiles directory not found: %s", setup$field_tiles_dir), "ERROR")
+    stop("Script 10 output not found. Run Script 10 first.")
+  }
+  
+  fields <- list.dirs(setup$field_tiles_dir, full.names = FALSE, recursive = FALSE)
+  fields <- fields[fields != ""]  # Remove empty strings
+  
+  if (length(fields) == 0) {
+    safe_log("No fields found in field_tiles directory", "WARNING")
+    return()
+  }
+  
+  safe_log(sprintf("Found %d fields to process", length(fields)))
+  
+  # 6. Process each field
+  # ----------------------
+  total_success <- 0
+  total_error <- 0
+  ci_results_by_date <- list()
+  
+  for (field in fields) {
+    safe_log(sprintf("\n--- Processing field: %s ---", field))
+    
+    field_tiles_path <- file.path(field_tiles_dir, field)
+    field_ci_path <- file.path(field_tiles_ci_dir, field)
+    field_daily_vals_path <- file.path(setup$daily_vals_per_field_dir, field)
+    
+    # Create output subdirectories for this field
+    dir.create(field_ci_path, showWarnings = FALSE, recursive = TRUE)
+    dir.create(field_daily_vals_path, showWarnings = FALSE, recursive = TRUE)
+    
+    # 5a. Process each date for this field
+    # -----------------------------------
+    for (date_str in dates$days_filter) {
+      input_tif <- file.path(field_tiles_path, sprintf("%s.tif", date_str))
+      output_tif <- file.path(field_ci_path, sprintf("%s.tif", date_str))
+      output_rds <- file.path(field_daily_vals_path, sprintf("%s.rds", date_str))
+      
+      # Skip if both outputs already exist
+      if (file.exists(output_tif) && file.exists(output_rds)) {
+        safe_log(sprintf("  %s: Already processed (skipping)", date_str))
+        next
+      }
+      
+      # Check if input TIFF exists
+      if (!file.exists(input_tif)) {
+        safe_log(sprintf("  %s: Input TIFF not found (skipping)", date_str))
+        next
+      }
+      
+      tryCatch({
+        # Load 4-band TIFF
+        raster_4band <- terra::rast(input_tif)
+        
+        # Calculate CI
+        ci_raster <- calc_ci_from_raster(raster_4band)
+        
+        # Create 5-band TIFF (R, G, B, NIR, CI)
+        five_band <- c(raster_4band, ci_raster)
+        
+        # Save 5-band TIFF
+        terra::writeRaster(five_band, output_tif, overwrite = TRUE)
+        
+        # Extract CI statistics by sub_field
+        ci_stats <- extract_ci_by_subfield(ci_raster, field_boundaries_sf, field)
+        
+        # Save RDS
+        if (!is.null(ci_stats) && nrow(ci_stats) > 0) {
+          saveRDS(ci_stats, output_rds)
+          safe_log(sprintf("  %s: ✓ Processed (%d sub-fields)", date_str, nrow(ci_stats)))
+          
+          # Store for daily aggregation
+          ci_stats_with_date <- ci_stats %>% mutate(date = date_str)
+          key <- sprintf("%s_%s", field, date_str)
+          ci_results_by_date[[key]] <- ci_stats_with_date
+        } else {
+          safe_log(sprintf("  %s: ⚠ No CI data extracted", date_str))
+        }
+        
+        total_success <- total_success + 1
+        
+      }, error = function(e) {
+        safe_log(sprintf("  %s: ✗ Error - %s", date_str, e$message), "ERROR")
+        total_error <<- total_error + 1
+      })
+    }
+  }
+  
+  # 7. Summary
+  # ----------
+  safe_log(sprintf("\n=== Processing Complete ==="))
+  safe_log(sprintf("Successfully processed: %d", total_success))
+  safe_log(sprintf("Errors encountered: %d", total_error))
+  
+  if (total_success > 0) {
+    safe_log("Output files created in:")
+    safe_log(sprintf("  TIFFs: %s", setup$field_tiles_ci_dir))
+    safe_log(sprintf("  RDS:   %s", setup$daily_vals_per_field_dir))
+  }
+  
+  # 8. Aggregate per-field daily RDS files into combined_CI_data.rds
+  # ----------------------------------------------------------------
+  # This creates the wide-format (fields × dates) file that Script 30 and
+  # other downstream scripts expect for backward compatibility
+  safe_log("\n=== Aggregating Per-Field Daily RDS into combined_CI_data.rds ===")
+  
+  tryCatch({
+    # Find all daily RDS files (recursively from daily_vals/{FIELD}/{DATE}.rds)
+    all_daily_files <- list.files(
+      path = setup$daily_vals_per_field_dir,
+      pattern = "\\.rds$",
+      full.names = TRUE,
+      recursive = TRUE
+    )
+    
+    if (length(all_daily_files) == 0) {
+      safe_log("No daily RDS files found to aggregate", "WARNING")
+    } else {
+      safe_log(sprintf("Aggregating %d daily RDS files into combined_CI_data.rds", length(all_daily_files)))
+      
+      # Read and combine all daily RDS files
+      combined_data <- all_daily_files %>%
+        purrr::map(readRDS) %>%
+        purrr::list_rbind() %>%
+        dplyr::group_by(sub_field)
+      
+      # Create output directory if needed
+      dir.create(setup$cumulative_CI_vals_dir, showWarnings = FALSE, recursive = TRUE)
+      
+      # Save combined data
+      combined_ci_path <- file.path(setup$cumulative_CI_vals_dir, "combined_CI_data.rds")
+      saveRDS(combined_data, combined_ci_path)
+      
+      safe_log(sprintf("✓ Created combined_CI_data.rds with %d rows from %d files", 
+                         nrow(combined_data), length(all_daily_files)))
+      safe_log(sprintf("  Location: %s", combined_ci_path))
+    }
+  }, error = function(e) {
+    safe_log(sprintf("⚠ Error aggregating to combined_CI_data.rds: %s", e$message), "WARNING")
+    safe_log("  This is OK - Script 30 can still use per-field RDS files directly", "WARNING")
+  })
+}
+
+# Execute main if called from command line
+if (sys.nframe() == 0) {
+  main()
+}

r_app/20_ci_extraction_utils.R

@@ -6,6 +6,10 @@
 #
 # Parallel Processing: Tile-based extraction uses furrr::future_map to process
 # multiple tiles simultaneously (typically 2-4 tiles in parallel depending on CPU cores)
+#
+# Per-Field Functions (Script 20):
+#   - calc_ci_from_raster(): Calculate CI from 4-band raster (NDVI formula)
+#   - extract_ci_by_subfield(): Extract per-sub_field CI statistics from raster
 
 #' Safe logging function that works whether log_message exists or not
 #'
@@ -1013,3 +1017,93 @@ extract_ci_from_tiles <- function(tile_files, date, field_boundaries_sf, daily_C
   
   return(aggregated)
 }
+
+# =============================================================================
+# Script 20 (Per-Field) Specific Functions
+# =============================================================================
+
+#' Calculate Canopy Index (CI) from 4-band raster
+#'
+#' Computes CI = (NIR - Red) / (NIR + Red), which is equivalent to NDVI.
+#' Expects band order: Red (band 1), Green (band 2), Blue (band 3), NIR (band 4)
+#'
+#' @param raster_obj Loaded raster object with at least 4 bands
+#' @return Raster object containing CI values
+#'
+calc_ci_from_raster <- function(raster_obj) {
+  # Expected band order: Red (band 1), Green (band 2), Blue (band 3), NIR (band 4)
+  if (terra::nlyr(raster_obj) < 4) {
+    stop("Raster has fewer than 4 bands. Cannot calculate CI.")
+  }
+  
+  r <- terra::subset(raster_obj, 1)  # Red
+  nir <- terra::subset(raster_obj, 4)  # NIR
+  
+  # Canopy Index (CI) = (NIR - Red) / (NIR + Red)
+  # This is essentially NDVI - Normalized Difference Vegetation Index
+  ci <- (nir - r) / (nir + r)
+  
+  return(ci)
+}
+
+#' Extract CI statistics by sub_field from a CI raster
+#'
+#' For a given field, masks the CI raster to each sub_field polygon
+#' and calculates statistics (mean, median, sd, min, max, count).
+#'
+#' @param ci_raster Raster object containing CI values
+#' @param field_boundaries_sf SF object containing field/sub_field polygons
+#' @param field_name Character string of the field name to process
+#' @return Data frame with field, sub_field, and CI statistics; NULL if field not found
+#'
+extract_ci_by_subfield <- function(ci_raster, field_boundaries_sf, field_name) {
+  # Filter to current field
+  field_poly <- field_boundaries_sf %>%
+    filter(field == field_name)
+  
+  if (nrow(field_poly) == 0) {
+    safe_log(sprintf("Field '%s' not found in boundaries", field_name), "WARNING")
+    return(NULL)
+  }
+  
+  # Extract CI values by sub_field
+  results <- list()
+  
+  # Group by sub_field within this field
+  for (sub_field in unique(field_poly$sub_field)) {
+    sub_poly <- field_poly %>% filter(sub_field == sub_field)
+    ci_sub <- terra::mask(ci_raster, sub_poly)
+    
+    # Get statistics
+    ci_values <- terra::values(ci_sub, na.rm = TRUE)
+    
+    if (length(ci_values) > 0) {
+      result_row <- data.frame(
+        field = field_name,
+        sub_field = sub_field,
+        ci_mean = mean(ci_values, na.rm = TRUE),
+        ci_median = median(ci_values, na.rm = TRUE),
+        ci_sd = sd(ci_values, na.rm = TRUE),
+        ci_min = min(ci_values, na.rm = TRUE),
+        ci_max = max(ci_values, na.rm = TRUE),
+        ci_count = length(ci_values),
+        stringsAsFactors = FALSE
+      )
+    } else {
+      result_row <- data.frame(
+        field = field_name,
+        sub_field = sub_field,
+        ci_mean = NA_real_,
+        ci_median = NA_real_,
+        ci_sd = NA_real_,
+        ci_min = NA_real_,
+        ci_max = NA_real_,
+        ci_count = 0,
+        stringsAsFactors = FALSE
+      )
+    }
+    results[[length(results) + 1]] <- result_row
+  }
+  
+  return(dplyr::bind_rows(results))
+}

r_app/parameters_project.R

@@ -212,7 +212,7 @@ detect_tile_structure_from_merged_final <- function(merged_final_tif_dir, daily_
 # -----------------------------------
 setup_project_directories <- function(project_dir, data_source = "merged_tif_8b") {
   # Base directories
-  laravel_storage_dir <- here("laravel_app/storage/app", project_dir)
+  laravel_storage_dir <- here("laravel_app", "storage", "app", project_dir)
   
   # Determine which TIF source folder to use based on data_source parameter
   # Default is merged_tif_8b for newer data with cloud masking (8-band + UDM)
@@ -238,15 +238,20 @@ setup_project_directories <- function(project_dir, data_source = "merged_tif_8b"
       merged = merged_tif_folder,  # Use data_source parameter to select folder
       final = merged_final_dir
     ),
+    # New per-field directory structure (Script 10 output)
+    field_tiles = here(laravel_storage_dir, "field_tiles"),
+    field_tiles_ci = here(laravel_storage_dir, "field_tiles_CI"),
     weekly_mosaic = here(laravel_storage_dir, "weekly_mosaic"),
     weekly_tile_max = here(laravel_storage_dir, "weekly_tile_max"),
     extracted_ci = list(
-      base = here(laravel_storage_dir, "Data/extracted_ci"),
+      base = here(laravel_storage_dir, "Data", "extracted_ci"),
-      daily = here(laravel_storage_dir, "Data/extracted_ci/daily_vals"),
+      daily = here(laravel_storage_dir, "Data", "extracted_ci", "daily_vals"),
-      cumulative = here(laravel_storage_dir, "Data/extracted_ci/cumulative_vals")
+      cumulative = here(laravel_storage_dir, "Data", "extracted_ci", "cumulative_vals"),
+      # New per-field daily RDS structure (Script 20 output)
+      daily_per_field = here(laravel_storage_dir, "Data", "extracted_ci", "daily_vals")
     ),
-    vrt = here(laravel_storage_dir, "Data/vrt"),
+    vrt = here(laravel_storage_dir, "Data", "vrt"),
-    harvest = here(laravel_storage_dir, "Data/HarvestData")
+    harvest = here(laravel_storage_dir, "Data", "HarvestData")
   )
   
   # Create all directories
@@ -264,6 +269,12 @@ setup_project_directories <- function(project_dir, data_source = "merged_tif_8b"
     merged_final = dirs$tif$final,
     daily_CI_vals_dir = dirs$extracted_ci$daily,
     cumulative_CI_vals_dir = dirs$extracted_ci$cumulative,
+    # New per-field directory paths (Script 10 & 20 outputs)
+    field_tiles_dir = dirs$field_tiles,
+    field_tiles_ci_dir = dirs$field_tiles_ci,
+    daily_vals_per_field_dir = dirs$extracted_ci$daily_per_field,
+    # Field boundaries path for all scripts
+    field_boundaries_path = here(laravel_storage_dir, "Data", "pivot.geojson"),
     weekly_CI_mosaic = if (use_tile_mosaic) dirs$weekly_tile_max else dirs$weekly_mosaic,  # SMART: Route based on tile detection
     daily_vrt = dirs$vrt,  # Point to Data/vrt folder where R creates VRT files from CI extraction
     weekly_tile_max = dirs$weekly_tile_max,  # Per-tile weekly MAX mosaics (Script 04 output)