# Visualize CI time series with harvest dates to validate patterns
suppressPackageStartupMessages({
  library(readxl)
  library(dplyr)
  library(tidyr)
  library(lubridate)
  library(terra)
  library(sf)
  library(here)
  library(ggplot2)
})

# Set project directory
project_dir <- "esa"
assign("project_dir", project_dir, envir = .GlobalEnv)

# Source required files
cat("Loading project configuration...\n")
source(here("r_app", "parameters_project.R"))

# Read pre-extracted CI data
ci_rds_file <- here("laravel_app/storage/app", project_dir, "Data/extracted_ci/cumulative_vals/All_pivots_Cumulative_CI_quadrant_year_v2.rds")
ci_data_raw <- readRDS(ci_rds_file) %>% ungroup()

time_series <- ci_data_raw %>%
  mutate(
    date = as.Date(Date),
    week = isoweek(date),
    year = isoyear(date)
  ) %>%
  select(
    field_id = field,
    date,
    week,
    year,
    mean_ci = FitData
  ) %>%
  filter(!is.na(mean_ci), !is.na(date), !is.na(field_id)) %>%
  arrange(field_id, date)

# Read actual harvest data
harvest_actual_all <- read_excel('laravel_app/storage/app/esa/Data/harvest.xlsx') %>%
  mutate(
    season_start = as.Date(season_start),
    season_end = as.Date(season_end)
  ) %>%
  filter(!is.na(season_end))

fields_with_data <- unique(field_boundaries_sf$field)

harvest_actual <- harvest_actual_all %>%
  filter(field %in% fields_with_data) %>%
  filter(!is.na(season_end))

cat("Creating visualizations for each field...\n\n")

# Select fields to visualize (ones with missed harvests)
fields_to_plot <- c("00302", "00F25", "00F28", "00P81", "00P82", "KHWA", "KHWB", "LOMDA")

for (field_name in fields_to_plot) {
  
  field_ts <- time_series %>%
    filter(field_id == field_name)
  
  field_harvests <- harvest_actual %>%
    filter(field == field_name) %>%
    arrange(season_end)
  
  if (nrow(field_ts) == 0 || nrow(field_harvests) == 0) {
    cat("Skipping field", field_name, "(no data)\n")
    next
  }
  
  cat("Plotting field:", field_name, "\n")
  cat("  Harvests:", nrow(field_harvests), "\n")
  cat("  CI observations:", nrow(field_ts), "\n")
  
  # Create plot
  p <- ggplot() +
    # CI time series
    geom_line(data = field_ts, aes(x = date, y = mean_ci), 
              color = "darkgreen", size = 0.5) +
    geom_point(data = field_ts, aes(x = date, y = mean_ci), 
               color = "darkgreen", size = 0.8, alpha = 0.6) +
    # Harvest dates as vertical lines
    geom_vline(data = field_harvests, aes(xintercept = season_end), 
               color = "red", linetype = "dashed", size = 0.8) +
    # Add harvest labels
    geom_text(data = field_harvests, 
              aes(x = season_end, y = max(field_ts$mean_ci) * 0.95, 
                  label = format(season_end, "%Y-%m-%d")),
              angle = 90, vjust = -0.3, size = 3, color = "red") +
    # Horizontal reference lines
    geom_hline(yintercept = 2.0, color = "blue", linetype = "dotted", alpha = 0.5) +
    geom_hline(yintercept = 2.5, color = "orange", linetype = "dotted", alpha = 0.5) +
    # Labels and theme
    labs(
      title = paste("Field", field_name, "- CI Time Series with Harvest Dates"),
      subtitle = paste("Red dashed lines = harvest dates |", 
                      "Blue dotted = CI 2.0 |", 
                      "Orange dotted = CI 2.5"),
      x = "Date",
      y = "Canopy Index (CI)"
    ) +
    theme_minimal() +
    theme(
      plot.title = element_text(face = "bold", size = 14),
      plot.subtitle = element_text(size = 10),
      axis.text.x = element_text(angle = 45, hjust = 1)
    ) +
    scale_x_date(date_breaks = "3 months", date_labels = "%Y-%m")
  
  # Save plot
  output_file <- paste0("output/harvest_ci_", field_name, ".png")
  ggsave(output_file, p, width = 14, height = 6, dpi = 150)
  cat("  Saved:", output_file, "\n\n")
  
  # Also print plot to screen
  print(p)
}

cat("\n=== SUMMARY ===\n")
cat("Plots saved to output/ folder\n")
cat("Look for patterns:\n")
cat("  1. Does CI drop below 2.0-2.5 around harvest dates?\n")
cat("  2. How long does CI stay low after harvest?\n")
cat("  3. Are there other low CI periods NOT associated with harvest?\n")
cat("  4. Is there a consistent time offset between harvest date and minimum CI?\n")