changing paths CS-109

r_app/10_create_per_field_tiffs.R

@@ -42,60 +42,12 @@
 library(terra)
 library(sf)
 
-# ============================================================================
+# ==============================================================================
-# HELPER FUNCTIONS (DEFINE FIRST)
+# LOAD CENTRALIZED PARAMETERS & PATHS
-# ============================================================================
+# ==============================================================================
+source(here::here("r_app", "parameters_project.R"))
 
-smartcane_log <- function(msg) {
+# Get project parameter from command line
-  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")
-      }
-    }
-  }
-  
-  # FIX: Validate and repair geometries (handles duplicate vertices, degenerate edges, etc)
-  invalid_count <- sum(!st_is_valid(fields))
-  if (invalid_count > 0) {
-    smartcane_log(paste("WARNING: Found", invalid_count, "invalid geometry/geometries - attempting repair"))
-    fields <- st_make_valid(fields)
-    smartcane_log(paste("Repaired invalid geometries using st_make_valid()"))
-  }
-  
-  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"
@@ -103,13 +55,12 @@ if (length(args) == 0) {
   PROJECT <- args[1]
 }
 
-# Construct paths directly (avoid complex parameter initialization)
+# Load centralized path structure (creates all directories automatically)
-base_path <- file.path(getwd(), "laravel_app", "storage", "app", PROJECT)
+paths <- setup_project_directories(PROJECT)
-data_dir <- file.path(base_path, "Data")
 
 smartcane_log(paste("Project:", PROJECT))
-smartcane_log(paste("Base path:", base_path))
+smartcane_log(paste("Base path:", paths$laravel_storage_dir))
-smartcane_log(paste("Data dir:", data_dir))
+smartcane_log(paste("Data dir:", paths$data_dir))
 
 # Unified function to crop TIFF to field boundaries
 # Called by both migration and processing phases
@@ -267,24 +218,21 @@ process_new_merged_tif <- function(merged_tif_dir, field_tiles_dir, fields, fiel
 }
 
 # ============================================================================
+# ==============================================================================
 # MAIN EXECUTION
-# ============================================================================
+# ==============================================================================
 
 smartcane_log("========================================")
 smartcane_log(paste("Script 10: Per-Field TIFF Creation for", PROJECT))
 smartcane_log("========================================")
 
-# Create necessary directories
+# Load field boundaries using centralized path (no dir.create needed - already created by setup_project_directories)
-dir.create(data_dir, recursive = TRUE, showWarnings = FALSE)
+fields <- load_field_boundaries(paths$field_boundaries_path)
 
-# Load field boundaries
+# Define input and output directories (from centralized paths)
-geojson_path <- file.path(data_dir, "pivot.geojson")
+merged_tif_dir <- paths$merged_tif_folder
-fields <- load_field_boundaries(geojson_path)
+field_tiles_dir <- paths$field_tiles_dir
-
+field_tiles_ci_dir <- paths$field_tiles_ci_dir
-# Define input and output directories
-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: Process new downloads (always runs)
 # Pass field_tiles_ci_dir so it can skip dates already migrated

r_app/20_ci_extraction.R

@@ -111,6 +111,9 @@ main <- function() {
     stop(e)
   })
   
+  # Load centralized path structure (creates all directories automatically)
+  paths <- setup_project_directories(project_dir)
+  
   cat("[DEBUG] Attempting to source r_app/20_ci_extraction_utils.R\n")
   tryCatch({
     source("r_app/20_ci_extraction_utils.R")
@@ -193,8 +196,8 @@ main <- function() {
   # -----------------------------------
   log_message("Searching for raster files")
   
-  # Check if tiles exist (Script 01 output) - detect grid size dynamically
+  # Check if tiles exist (Script 10 output) - detect grid size dynamically using centralized paths
-  tiles_split_base <- file.path("laravel_app", "storage", "app", project_dir, "daily_tiles_split")
+  tiles_split_base <- paths$daily_tiles_split_dir
   
   # Detect grid size from daily_tiles_split folder structure
   # Expected structure: daily_tiles_split/5x5/ or daily_tiles_split/10x10/ etc.
@@ -293,7 +296,7 @@ main <- function() {
           log_message(paste("Combining all", length(all_daily_files), "daily CI files into combined_CI_data.rds"))
           
           # Load and combine ALL daily files (creates complete dataset)
-          combined_ci_path <- file.path(cumulative_CI_vals_dir, "combined_CI_data.rds")
+          combined_ci_path <- file.path(paths$cumulative_ci_vals_dir, "combined_CI_data.rds")
           
           combined_data <- all_daily_files %>%
             purrr::map(readRDS) %>% 

r_app/21_convert_ci_rds_to_csv.R

@@ -140,7 +140,7 @@ main <- function() {
   
   cat(sprintf("Converting CI RDS to CSV: project=%s\n", project_dir))
   
-  # Initialize project configuration
+  # Initialize project configuration and centralized paths
   tryCatch({
     source("parameters_project.R")
   }, error = function(e) {
@@ -152,15 +152,12 @@ main <- function() {
     })
   })
   
-  # Define paths
+  # Load centralized path structure (creates all directories automatically)
-  ci_data_source_dir <- here::here("laravel_app", "storage", "app", project_dir, "Data", "extracted_ci", "cumulative_vals")
+  paths <- setup_project_directories(project_dir)
-  ci_data_output_dir <- here::here("laravel_app", "storage", "app", project_dir, "Data", "extracted_ci", "ci_data_for_python")
   
-  # Create output directory if it doesn't exist (for new projects)
+  # Use centralized paths (no need for dir.create - already handled)
-  if (!dir.exists(ci_data_output_dir)) {
+  ci_data_source_dir <- paths$cumulative_ci_vals_dir
-    dir.create(ci_data_output_dir, recursive = TRUE, showWarnings = FALSE)
+  ci_data_output_dir <- paths$ci_for_python_dir
-    cat(sprintf("✓ Created output directory: %s\n", ci_data_output_dir))
-  }
   
   input_file <- file.path(ci_data_source_dir, "combined_CI_data.rds")
   output_file <- file.path(ci_data_output_dir, "ci_data_for_python.csv")

r_app/40_mosaic_creation.R

@@ -92,32 +92,21 @@ main <- function() {
   # IMPORTANT: Only consider a folder as valid if it contains actual files
   laravel_storage <- here::here("laravel_app/storage/app", project_dir)
   
-  # If data_source was explicitly provided from pipeline, validate it; otherwise auto-detect
+  # Load centralized path structure
-  if (!is.null(data_source_from_args)) {
+  tryCatch({
-    # Use the provided data_source, but verify it has data
+    source("r_app/parameters_project.R")
-    proposed_path <- file.path(laravel_storage, data_source_from_args)
+    paths <- setup_project_directories(project_dir)
-    has_data <- dir.exists(proposed_path) && length(list.files(proposed_path, pattern = "\\.tif$")) > 0
+  }, error = function(e) {
-    
+    message("Note: Could not open files from r_app directory")
-    if (has_data) {
+    message("Attempting to source from default directory instead...")
-      data_source <- data_source_from_args
+    tryCatch({
-      message("✓ Using provided data source '", data_source, "' - contains files")
+      source("parameters_project.R")
-    } else {
+      paths <- setup_project_directories(project_dir)
-      message("WARNING: Provided data source '", data_source_from_args, "' is empty or doesn't exist. Auto-detecting...")
+      message("✓ Successfully sourced files from default directory")
-      data_source_from_args <- NULL  # Fall through to auto-detection
+    }, error = function(e) {
-    }
+      stop("Failed to source required files from both 'r_app' and default directories.")
-  }
+    })
-  
+  })
-  # Auto-detect if no valid data_source was provided
-  if (is.null(data_source_from_args)) {
-    # Check merged_tif_8b - only if it exists AND contains files
-    merged_tif_8b_path <- file.path(laravel_storage, "merged_tif_8b")
-    has_8b_data <- dir.exists(merged_tif_8b_path) && length(list.files(merged_tif_8b_path, pattern = "\\.tif$")) > 0
-    
-    # Check merged_tif - only if it exists AND contains files
-    merged_tif_path <- file.path(laravel_storage, "merged_tif")
-    has_legacy_data <- dir.exists(merged_tif_path) && length(list.files(merged_tif_path, pattern = "\\.tif$")) > 0
-    
-    # Select data source based on what has actual data
     data_source <- if (has_8b_data) {
       message("Auto-detected data source: merged_tif_8b (8-band optimized) - contains files")
       "merged_tif_8b"
@@ -142,27 +131,18 @@ main <- function() {
     message("Attempting to source from default directory instead...")
     tryCatch({
       source("parameters_project.R")
-      source("40_mosaic_creation_utils.R")
+      paths <- setup_project_directories(project_dir)
       message("✓ Successfully sourced files from default directory")
     }, error = function(e) {
       stop("Failed to source required files from both 'r_app' and default directories.")
     })
   })
   
-  # Extract path variables from global environment (set by parameters_project.R)
+  # Use centralized paths (no need to manually construct or create dirs)
-  merged_final <- if (exists("merged_final", envir = .GlobalEnv)) {
+  merged_final <- paths$growth_model_interpolated_dir  # or merged_final_tif if needed
-    get("merged_final", envir = .GlobalEnv)
+  daily_vrt <- paths$vrt_dir
-  } else {
-    file.path(laravel_storage, "merged_final_tif")
-  }
   
-  daily_vrt <- if (exists("daily_vrt", envir = .GlobalEnv)) {
+  safe_log(paste("Using growth model/mosaic directory:", merged_final))
-    get("daily_vrt", envir = .GlobalEnv)
-  } else {
-    file.path(laravel_storage, "Data", "vrt")
-  }
-  
-  safe_log(paste("Using merged_final_tif directory:", merged_final))
   safe_log(paste("Using daily VRT directory:", daily_vrt))
   
   # 4. Generate date range for processing
@@ -216,10 +196,11 @@ main <- function() {
       # Point to the grid-specific merged_final_tif directory
       merged_final_with_grid <- file.path(merged_final_base, grid_size)
       
-      # Set output directory for per-tile mosaics, organized by grid size
+      # Set output directory for per-tile mosaics, organized by grid size (from centralized paths)
       # Output: weekly_tile_max/{grid_size}/week_WW_YYYY_TT.tif
-      tile_output_base <- file.path(laravel_storage, "weekly_tile_max", grid_size)
+      tile_output_base <- file.path(paths$weekly_tile_max_dir, grid_size)
-      dir.create(tile_output_base, recursive = TRUE, showWarnings = FALSE)
+      # Note: no dir.create needed - paths$weekly_tile_max_dir already created by setup_project_directories()
+      dir.create(tile_output_base, recursive = TRUE, showWarnings = FALSE)  # Create grid-size subfolder
       
       created_tile_files <- create_weekly_mosaic_from_tiles(
         dates = dates,
@@ -242,8 +223,8 @@ main <- function() {
     tryCatch({
       safe_log("Starting single-file mosaic creation (backward-compatible approach)...")
       
-      # Set output directory for single-file mosaics
+      # Set output directory for single-file mosaics (from centralized paths)
-      single_file_output_dir <- file.path(laravel_storage, "weekly_mosaic")
+      single_file_output_dir <- paths$weekly_mosaic_dir
       
       created_file <- create_weekly_mosaic(
         dates = dates,

r_app/80_calculate_kpis.R

@@ -251,14 +251,10 @@ main <- function() {
   message("KPI Calculations:", paste(client_config$kpi_calculations, collapse = ", "))
   message("Output Formats:", paste(client_config$outputs, collapse = ", "))
   
-  # Define paths for mosaic detection (used in PHASE 1)
+  # Use centralized paths from setup object (no need for file.path calls)
-  # NEW: Support both per-field and legacy single-file mosaics
+  weekly_tile_max <- setup$weekly_tile_max_dir
-  base_project_path <- file.path("laravel_app", "storage", "app", project_dir)
+  weekly_mosaic <- setup$weekly_mosaic_dir
-  weekly_tile_max <- file.path(base_project_path, "weekly_tile_max")
+  daily_vals_dir <- setup$daily_ci_vals_dir
-  weekly_mosaic <- file.path(base_project_path, "weekly_mosaic")  # NEW: Per-field structure
-  
-  # Also set up per-field daily RDS path for Script 80 historical data loading
-  daily_vals_dir <- file.path(base_project_path, "Data", "extracted_ci", "daily_vals")
   
   tryCatch({
     source(here("r_app", "30_growth_model_utils.R"))
@@ -283,11 +279,8 @@ main <- function() {
       stop("Error loading 80_kpi_utils.R: ", e$message)
     })
     
-    # Prepare inputs for KPI calculation
+    # Prepare inputs for KPI calculation (already created by setup_project_directories)
-    reports_dir_kpi <- file.path(base_project_path, "reports", "kpis")
+    reports_dir_kpi <- setup$kpi_reports_dir
-    if (!dir.exists(reports_dir_kpi)) {
-      dir.create(reports_dir_kpi, recursive = TRUE)
-    }
     
     cumulative_CI_vals_dir <- setup$cumulative_CI_vals_dir
     

r_app/90_CI_report_with_kpis_simple.Rmd

@@ -106,6 +106,9 @@ tryCatch({
   stop("Error loading parameters_project.R: ", e$message)
 })
 
+# Load centralized paths
+paths <- setup_project_directories(project_dir)
+
 # Log initial configuration
 safe_log("Starting the R Markdown script with KPIs")
 safe_log(paste("mail_day params:", params$mail_day))
@@ -115,8 +118,8 @@ safe_log(paste("mail_day variable:", mail_day))
 
 ```{r load_kpi_data, message=FALSE, warning=FALSE, include=FALSE}
 ## SIMPLE KPI LOADING - robust lookup with fallbacks
-# Primary expected directory inside the laravel storage
+# Primary expected directory from centralized paths
-kpi_data_dir <- file.path("..", "laravel_app", "storage", "app", project_dir, "reports", "kpis")
+kpi_data_dir <- paths$kpi_reports_dir
 date_suffix <- format(as.Date(report_date), "%Y%m%d")
 
 # Calculate current week from report_date using ISO 8601 week numbering

r_app/91_CI_report_with_kpis_Angata.Rmd

@@ -105,6 +105,9 @@ tryCatch({
   stop("Error loading parameters_project.R: ", e$message)
 })
 
+# Load centralized paths
+paths <- setup_project_directories(project_dir)
+
 # Log initial configuration
 safe_log("Starting the R Markdown script with KPIs")
 safe_log(paste("mail_day params:", params$mail_day))
@@ -120,8 +123,8 @@ cat("\n=== DEBUG: R Markdown Working Directory ===\n")
 cat(paste("getwd():", getwd(), "\n"))
 cat(paste("Expected knit_dir from R Markdown:", knitr::opts_knit$get("root.dir"), "\n\n"))
 
-# Primary expected directory inside the laravel storage
+# Primary expected directory from centralized paths
-kpi_data_dir <- file.path("..", "laravel_app", "storage", "app", project_dir, "reports", "kpis")
+kpi_data_dir <- paths$kpi_reports_dir
 date_suffix <- format(as.Date(report_date), "%Y%m%d")
 
 # Calculate current week from report_date using ISO 8601 week numbering

r_app/parameters_project.R

@@ -210,71 +210,228 @@ detect_tile_structure_from_merged_final <- function(merged_final_tif_dir, daily_
 
 # 4. Define project directory structure
 # -----------------------------------
+# ==============================================================================
+# CENTRALIZED PATH MANAGEMENT - setup_project_directories()
+# ==============================================================================
+# This function is the single source of truth for ALL file paths used across the pipeline.
+# All scripts should call this function once at startup and use returned paths.
+# This eliminates ~88 hardcoded file.path() calls scattered across 8 scripts.
+#
+# USAGE:
+#   paths <- setup_project_directories(project_dir)
+#   merged_tif_dir <- paths$merged_tif_folder
+#   daily_ci_dir <- paths$daily_ci_vals_dir
+#   kpi_output_dir <- paths$kpi_reports_dir
+#
+# TIERS (8-layer directory structure):
+#   Tier 1: Raw data (merged_tif)
+#   Tier 2: Per-field TIFFs (field_tiles, field_tiles_CI)
+#   Tier 3: CI Extraction (daily_ci_vals, cumulative_ci_vals)
+#   Tier 4: Growth Model (growth_model_interpolated)
+#   Tier 5: Mosaics (weekly_mosaic, weekly_tile_max)
+#   Tier 6: KPI & Reporting (kpi_reports_dir, kpi_field_stats_dir)
+#   Tier 7: Support (data, vrt, harvest, logs)
+#   Tier 8: Config & Metadata (field_boundaries_path, tiling_config_path)
+#
+# BENEFITS:
+#   ✓ Single source of truth (eliminates ~88 hardcoded file.path() calls)
+#   ✓ Auto-creates all directories (no scattered dir.create() calls)
+#   ✓ Easy to update storage structure globally
+#   ✓ Consistent naming across all 8 scripts
+# ==============================================================================
 setup_project_directories <- function(project_dir, data_source = "merged_tif") {
-  # Base directories
+  # ===========================================================================
+  # BASE DIRECTORIES (Foundation for all paths)
+  # ===========================================================================
   laravel_storage_dir <- here("laravel_app", "storage", "app", project_dir)
   
-  # Use standard merged_tif directory for all projects
+  # ===========================================================================
-  merged_tif_folder <- here(laravel_storage_dir, "merged_tif")
+  # TIER 1: RAW DATA & INPUT PATHS (Script 00 - Python download output)
+  # ===========================================================================
+  merged_tif_folder <- here(laravel_storage_dir, "merged_tif")  # 4-band raw GeoTIFFs from Planet
   
-  # Detect tile mode based on file patterns
+  # ===========================================================================
+  # TIER 2: TILING PATHS (Script 10 - Per-field tiff creation)
+  # ===========================================================================
+  # Per-field TIFF structure: field_tiles/{FIELD_NAME}/{YYYY-MM-DD}.tif
+  field_tiles_dir <- here(laravel_storage_dir, "field_tiles")
+  
+  # Per-field CI TIFFs (pre-computed, used by Script 40): field_tiles_CI/{FIELD_NAME}/{YYYY-MM-DD}.tif
+  field_tiles_ci_dir <- here(laravel_storage_dir, "field_tiles_CI")
+  
+  # Legacy tiling (for backward compatibility): daily_tiles_split/{grid_size}/{YYYY-MM-DD}/{YYYY-MM-DD}_XX.tif
   daily_tiles_split_dir <- here(laravel_storage_dir, "daily_tiles_split")
   
-  # Simplified: only check daily_tiles_split for per-field structure
+  # ===========================================================================
-  use_tile_mosaic <- dir.exists(daily_tiles_split_dir) && length(list.dirs(daily_tiles_split_dir, full.names = FALSE, recursive = FALSE)) > 0
+  # TIER 3: CI EXTRACTION PATHS (Script 20 - Canopy Index calculation)
+  # ===========================================================================
+  extracted_ci_base_dir <- here(laravel_storage_dir, "Data", "extracted_ci")
   
-  # Main subdirectories
+  # Daily CI values (cumulative RDS): combined_CI_data.rds
-  dirs <- list(
+  daily_ci_vals_dir <- here(extracted_ci_base_dir, "daily_vals")
-    reports = here(laravel_storage_dir, "reports"),
+  
-    logs = here(laravel_storage_dir, "logs"),
+  # Cumulative CI across time: All_pivots_Cumulative_CI_quadrant_year_v2.rds
-    data = here(laravel_storage_dir, "Data"),
+  cumulative_ci_vals_dir <- here(extracted_ci_base_dir, "cumulative_vals")
-    tif = list(
+  
-      merged = merged_tif_folder
+  # Per-field CI data for Python harvest prediction (Script 21): ci_data_for_python.csv
-    ),
+  ci_for_python_dir <- here(extracted_ci_base_dir, "ci_data_for_python")
-    # 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"),
+  # TIER 4: GROWTH MODEL PATHS (Script 30 - Interpolation & smoothing)
-    weekly_mosaic = here(laravel_storage_dir, "weekly_mosaic"),
+  # ===========================================================================
-    extracted_ci = list(
+  growth_model_interpolated_dir <- here(laravel_storage_dir, "growth_model_interpolated")
-      base = here(laravel_storage_dir, "Data", "extracted_ci"),
+  
-      daily = here(laravel_storage_dir, "Data", "extracted_ci", "daily_vals"),
+  # ===========================================================================
-      cumulative = here(laravel_storage_dir, "Data", "extracted_ci", "cumulative_vals"),
+  # TIER 5: MOSAIC PATHS (Script 40 - Weekly mosaics)
-      # New per-field daily RDS structure (Script 20 output)
+  # ===========================================================================
-      daily_per_field = here(laravel_storage_dir, "Data", "extracted_ci", "daily_vals")
+  # Per-field weekly mosaics (per-field architecture): weekly_mosaic/{FIELD}/{week_XX_YYYY}.tif
-    ),
+  weekly_mosaic_dir <- here(laravel_storage_dir, "weekly_mosaic")
-    vrt = here(laravel_storage_dir, "Data", "vrt"),
+  
-    harvest = here(laravel_storage_dir, "Data", "HarvestData")
+  # Tile-based weekly max (legacy): weekly_tile_max/{grid_size}/week_XX_YYYY.tif
+  weekly_tile_max_dir <- here(laravel_storage_dir, "weekly_tile_max")
+  
+  # ===========================================================================
+  # TIER 6: KPI & REPORTING PATHS (Scripts 80, 90, 91)
+  # ===========================================================================
+  reports_dir <- here(laravel_storage_dir, "reports")
+  kpi_reports_dir <- here(reports_dir, "kpis")  # Where Script 80 outputs KPI CSV/RDS files
+  kpi_field_stats_dir <- here(kpi_reports_dir, "field_stats")  # Per-field KPI details
+  kpi_field_analysis_dir <- here(kpi_reports_dir, "field_analysis")  # Field-level analysis for Script 91
+  
+  # ===========================================================================
+  # TIER 7: SUPPORT PATHS (Data, VRT, Harvest)
+  # ===========================================================================
+  data_dir <- here(laravel_storage_dir, "Data")
+  vrt_dir <- here(data_dir, "vrt")  # Virtual Raster files created during CI extraction
+  harvest_dir <- here(data_dir, "HarvestData")  # Harvest schedule data
+  log_dir <- here(laravel_storage_dir, "logs")  # Log files
+  
+  # ===========================================================================
+  # TIER 8: CONFIG & METADATA PATHS
+  # ===========================================================================
+  # Field boundaries GeoJSON (same across all scripts)
+  field_boundaries_path <- here(data_dir, "pivot.geojson")
+  
+  # Tiling configuration metadata from Script 10
+  tiling_config_path <- here(daily_tiles_split_dir, "tiling_config.json")
+  
+  # ===========================================================================
+  # CREATE ALL DIRECTORIES (once per pipeline run)
+  # ===========================================================================
+  all_dirs <- c(
+    # Tier 1
+    merged_tif_folder,
+    # Tier 2
+    field_tiles_dir, field_tiles_ci_dir, daily_tiles_split_dir,
+    # Tier 3
+    extracted_ci_base_dir, daily_ci_vals_dir, cumulative_ci_vals_dir, ci_for_python_dir,
+    # Tier 4
+    growth_model_interpolated_dir,
+    # Tier 5
+    weekly_mosaic_dir, weekly_tile_max_dir,
+    # Tier 6
+    reports_dir, kpi_reports_dir, kpi_field_stats_dir, kpi_field_analysis_dir,
+    # Tier 7
+    data_dir, vrt_dir, harvest_dir, log_dir
   )
   
-  # Create all directories
+  for (dir_path in all_dirs) {
-  for (dir_path in unlist(dirs)) {
     dir.create(dir_path, showWarnings = FALSE, recursive = TRUE)
   }
   
-  # Return directory structure for use in other functions
+  # ===========================================================================
+  # RETURN COMPREHENSIVE PATH LIST
+  # Scripts should source parameters_project.R and receive paths object like:
+  # paths <- setup_project_directories(project_dir)
+  # Then use: paths$merged_tif_folder, paths$daily_ci_vals_dir, etc.
+  # ===========================================================================
   return(list(
+    # PROJECT ROOT
     laravel_storage_dir = laravel_storage_dir,
-    reports_dir = dirs$reports,
+    
-    log_dir = dirs$logs,
+    # TIER 1: Raw data
-    data_dir = dirs$data,
+    merged_tif_folder = merged_tif_folder,
-    planet_tif_folder = dirs$tif$merged,
+    
-    merged_final = dirs$tif$final,
+    # TIER 2: Per-field TIFFs
-    daily_CI_vals_dir = dirs$extracted_ci$daily,
+    field_tiles_dir = field_tiles_dir,
-    cumulative_CI_vals_dir = dirs$extracted_ci$cumulative,
+    field_tiles_ci_dir = field_tiles_ci_dir,
-    # New per-field directory paths (Script 10 & 20 outputs)
+    daily_tiles_split_dir = daily_tiles_split_dir,
-    field_tiles_dir = dirs$field_tiles,
+    
-    field_tiles_ci_dir = dirs$field_tiles_ci,
+    # TIER 3: CI Extraction
-    daily_vals_per_field_dir = dirs$extracted_ci$daily_per_field,
+    extracted_ci_base_dir = extracted_ci_base_dir,
-    # Field boundaries path for all scripts
+    daily_ci_vals_dir = daily_ci_vals_dir,
-    field_boundaries_path = here(laravel_storage_dir, "Data", "pivot.geojson"),
+    cumulative_ci_vals_dir = cumulative_ci_vals_dir,
-    weekly_CI_mosaic = dirs$weekly_mosaic,  # Per-field weekly mosaics (per-field architecture)
+    ci_for_python_dir = ci_for_python_dir,
-    daily_vrt = dirs$vrt,  # Point to Data/vrt folder where R creates VRT files from CI extraction
+    
-    use_tile_mosaic = use_tile_mosaic,  # Flag indicating if tiles are used for this project
+    # TIER 4: Growth Model
-    harvest_dir = dirs$harvest,
+    growth_model_interpolated_dir = growth_model_interpolated_dir,
-    extracted_CI_dir = dirs$extracted_ci$base
+    
+    # TIER 5: Mosaics
+    weekly_mosaic_dir = weekly_mosaic_dir,
+    weekly_tile_max_dir = weekly_tile_max_dir,
+    
+    # TIER 6: KPI & Reporting
+    reports_dir = reports_dir,
+    kpi_reports_dir = kpi_reports_dir,
+    kpi_field_stats_dir = kpi_field_stats_dir,
+    kpi_field_analysis_dir = kpi_field_analysis_dir,
+    
+    # TIER 7: Support
+    data_dir = data_dir,
+    vrt_dir = vrt_dir,
+    harvest_dir = harvest_dir,
+    log_dir = log_dir,
+    
+    # TIER 8: Config & Metadata
+    field_boundaries_path = field_boundaries_path,
+    tiling_config_path = tiling_config_path
   ))
 }
 
+# ==============================================================================
+# TIER-BY-TIER PATH REFERENCE (for setup_project_directories output)
+# ==============================================================================
+#
+# TIER 1: RAW DATA (Script 00 - Python download)
+#   paths$merged_tif_folder
+#     └─ {YYYY-MM-DD}.tif (4-band uint16 GeoTIFFs from Planet API)
+#
+# TIER 2: PER-FIELD TIFFS (Script 10)
+#   paths$field_tiles_dir/{FIELD_NAME}/{YYYY-MM-DD}.tif
+#   paths$field_tiles_ci_dir/{FIELD_NAME}/{YYYY-MM-DD}.tif
+#   paths$daily_tiles_split_dir/{grid_size}/{YYYY-MM-DD}/{YYYY-MM-DD}_XX.tif (legacy)
+#
+# TIER 3: CI EXTRACTION (Script 20)
+#   paths$daily_ci_vals_dir/combined_CI_data.rds
+#   paths$cumulative_ci_vals_dir/All_pivots_Cumulative_CI_quadrant_year_v2.rds
+#   paths$ci_for_python_dir/ci_data_for_python.csv (Script 21 output)
+#
+# TIER 4: GROWTH MODEL (Script 30)
+#   paths$growth_model_interpolated_dir/ (RDS files with interpolated CI)
+#
+# TIER 5: MOSAICS (Script 40)
+#   paths$weekly_mosaic_dir/{FIELD_NAME}/week_XX_YYYY.tif
+#   paths$weekly_tile_max_dir/{grid_size}/week_XX_YYYY_00.tif (legacy)
+#
+# TIER 6: KPI & REPORTING (Scripts 80, 90, 91)
+#   paths$kpi_reports_dir/               (KPI outputs from Script 80)
+#   paths$kpi_field_stats_dir/           (Per-field KPI RDS)
+#   paths$kpi_field_analysis_dir/        (Analysis RDS for Script 91)
+#   paths$reports_dir/                   (Word/HTML reports)
+#
+# TIER 7: SUPPORT (Various scripts)
+#   paths$data_dir/pivot.geojson         (Field boundaries)
+#   paths$data_dir/harvest.xlsx          (Harvest schedule)
+#   paths$vrt_dir/                       (Virtual raster files)
+#   paths$harvest_dir/                   (Harvest predictions from Python)
+#   paths$log_dir/                       (Pipeline logs)
+#
+# TIER 8: CONFIG & METADATA
+#   paths$field_boundaries_path          (Full path to pivot.geojson)
+#   paths$tiling_config_path             (Metadata from Script 10)
+#
+# ==============================================================================
+
 #set working dir.
 # 5. Load field boundaries
 # ----------------------

r_app/run_full_pipeline.R

@@ -39,8 +39,9 @@ force_rerun <- FALSE # Set to TRUE to force all scripts to run even if outputs e
 # Define Rscript path for running external R scripts via system()
 RSCRIPT_PATH <- file.path("C:", "Program Files", "R", "R-4.4.3", "bin", "x64", "Rscript.exe")
 
-# Load client type mapping from parameters_project.R
+# Load client type mapping and centralized paths from parameters_project.R
 source("r_app/parameters_project.R")
+paths <- setup_project_directories(project_dir)
 client_type <- get_client_type(project_dir)
 cat(sprintf("\nProject: %s → Client Type: %s\n", project_dir, client_type))
 
@@ -105,7 +106,7 @@ for (i in 1:nrow(weeks_needed)) {
       files_this_week <- list.files(mosaic_dir_check, pattern = week_pattern_check, recursive = TRUE, full.names = FALSE)
     }
   } else if (mosaic_mode == "single-file") {
-    mosaic_dir_check <- file.path("laravel_app", "storage", "app", project_dir, "weekly_mosaic")
+    mosaic_dir_check <- paths$weekly_mosaic_dir
     if (dir.exists(mosaic_dir_check)) {
       # NEW: Support per-field architecture - search recursively for mosaics in field subdirectories
       # Check both top-level (legacy) and field subdirectories (per-field architecture)
@@ -222,7 +223,7 @@ cat("\n========== CHECKING EXISTING OUTPUTS ==========\n")
 cat(sprintf("Auto-detected mosaic mode: %s\n", mosaic_mode))
 
 # Check Script 10 outputs - FLEXIBLE: look for tiles either directly OR in grid subdirs
-tiles_split_base <- file.path("laravel_app", "storage", "app", project_dir, "daily_tiles_split")
+tiles_split_base <- paths$daily_tiles_split_dir
 tiles_dates <- c()
 if (dir.exists(tiles_split_base)) {
   # Try grid-size subdirectories first (5x5, 10x10, etc.) - preferred new structure
@@ -241,7 +242,7 @@ if (dir.exists(tiles_split_base)) {
 cat(sprintf("Script 10: %d dates already tiled\n", length(tiles_dates)))
 
 # Check Script 20 outputs (CI extraction) - daily RDS files
-ci_daily_dir <- file.path("laravel_app", "storage", "app", project_dir, "Data", "extracted_ci", "daily_vals")
+ci_daily_dir <- paths$daily_ci_vals_dir
 ci_files <- if (dir.exists(ci_daily_dir)) {
   list.files(ci_daily_dir, pattern = "\\.rds$")
 } else {
@@ -301,8 +302,7 @@ tryCatch(
     # Setup paths
     # NOTE: All downloads go to merged_tif/ regardless of project
     # (data_source variable is used later by Script 20 for reading, but downloads always go to merged_tif)
-    base_path <- file.path("laravel_app", "storage", "app", project_dir)
+    merged_tifs_dir <- paths$merged_tif_folder  # Always check merged_tif for downloads
-    merged_tifs_dir <- file.path(base_path, "merged_tif")  # Always check merged_tif for downloads
     
     cat(sprintf("[DEBUG] Checking for existing files in: %s\n", merged_tifs_dir))
     cat(sprintf("[DEBUG] Directory exists: %s\n", dir.exists(merged_tifs_dir)))
@@ -404,7 +404,7 @@ if (pipeline_success && !skip_10) {
       }
 
       # Verify output - check per-field structure
-      field_tiles_dir <- file.path("laravel_app", "storage", "app", project_dir, "field_tiles")
+      field_tiles_dir <- paths$field_tiles_dir
       if (dir.exists(field_tiles_dir)) {
         fields <- list.dirs(field_tiles_dir, full.names = FALSE, recursive = FALSE)
         fields <- fields[fields != ""]
@@ -445,7 +445,7 @@ if (pipeline_success && !skip_20) {
       }
 
       # Verify CI output was created
-      ci_daily_dir <- file.path("laravel_app", "storage", "app", project_dir, "Data", "extracted_ci", "daily_vals")
+      ci_daily_dir <- paths$daily_ci_vals_dir
       if (dir.exists(ci_daily_dir)) {
         files <- list.files(ci_daily_dir, pattern = "\\.rds$")
         cat(sprintf("✓ Script 20 completed - generated %d CI files\n", length(files)))
@@ -478,7 +478,7 @@ if (pipeline_success && !skip_21) {
       main() # Call main() to execute the script with the environment variables
 
       # Verify CSV output was created
-      ci_csv_path <- file.path("laravel_app", "storage", "app", project_dir, "ci_extracted")
+      ci_csv_path <- paths$ci_for_python_dir
       if (dir.exists(ci_csv_path)) {
         csv_files <- list.files(ci_csv_path, pattern = "\\.csv$")
         cat(sprintf("✓ Script 21 completed - converted to %d CSV files\n", length(csv_files)))
@@ -517,7 +517,7 @@ if (pipeline_success && !skip_30) {
       }
 
       # Verify interpolated output
-      growth_dir <- file.path("laravel_app", "storage", "app", project_dir, "growth_model_interpolated")
+      growth_dir <- paths$growth_model_interpolated_dir
       if (dir.exists(growth_dir)) {
         files <- list.files(growth_dir, pattern = "\\.rds$|\\.csv$")
         cat(sprintf("✓ Script 30 completed - generated %d growth model files\n", length(files)))
@@ -619,7 +619,7 @@ if (pipeline_success && !skip_40) {
               mosaic_created <- length(mosaic_files) > 0
             }
           } else {
-            mosaic_dir <- file.path("laravel_app", "storage", "app", project_dir, "weekly_mosaic")
+            mosaic_dir <- paths$weekly_mosaic_dir
             if (dir.exists(mosaic_dir)) {
               week_pattern <- sprintf("week_%02d_%d\\.tif", week_num, year_num)
               # NEW: Support per-field architecture - search recursively for mosaics in field subdirectories
@@ -768,12 +768,9 @@ if (pipeline_success && run_legacy_report) {
     tryCatch(
       {
         # Script 90 is an RMarkdown file - compile it with rmarkdown::render()
-        output_dir <- file.path("laravel_app", "storage", "app", project_dir, "reports")
+        output_dir <- paths$reports_dir
 
-        # Ensure output directory exists
+        # Reports directory already created by setup_project_directories
-        if (!dir.exists(output_dir)) {
-          dir.create(output_dir, recursive = TRUE, showWarnings = FALSE)
-        }
 
         output_filename <- sprintf(
           "CI_report_week%02d_%d.docx",
@@ -817,12 +814,9 @@ if (pipeline_success && run_modern_report) {
     tryCatch(
       {
         # Script 91 is an RMarkdown file - compile it with rmarkdown::render()
-        output_dir <- file.path("laravel_app", "storage", "app", project_dir, "reports")
+        output_dir <- paths$reports_dir
 
-        # Ensure output directory exists
+        # Reports directory already created by setup_project_directories
-        if (!dir.exists(output_dir)) {
-          dir.create(output_dir, recursive = TRUE, showWarnings = FALSE)
-        }
 
         output_filename <- sprintf(
           "CI_report_week%02d_%d.docx",