# Install the ForestTools package if it's not already installed
if (!require(ForestTools)) install.packages("ForestTools")
if (!require(terra)) install.packages("terra")
if (!require(sf)) install.packages("sf")
if (!require(imager)) install.packages("imager")

# Load the necessary libraries
library(ForestTools)
library(terra)
library(sf)
library(imager)

# Load sample canopy height model provided by ForestTools
lin <- function(x) { x * 0.05 + 0.5 }

chm_folder <- "/Users/taekim/ecohackathon/first_try_lidar/ForestTools/TryForestTools/first-flight/chm_tiles"  # Update this with the path to your CHM tiles folder

# List all TIFF files in the directory
tile_paths <- list.files(path = chm_folder, pattern = "\\.tif$", full.names = TRUE)
print(tile_paths)
# Initialize an empty list to store sf objects for each tile
crown_polygons_list <- list()

for (chm_path in tile_paths) {
  # Load the CHM file
  chm <- terra::rast(chm_path)
  if (nlyr(chm) > 1) {
    chm <- chm[[1]]  # Select the first layer if necessary
  }
  
  # Detect treetops using the VWF algorithm
  ttops <- vwf(chm, winFun = lin, minHeight = 2)
  
  # Create crown polygons using the MCWS method
  crowns_poly <- mcws(treetops = ttops, CHM = chm, format = "polygons", minHeight = 1.5)
  
  # Add the results to the list
  crown_polygons_list[[chm_path]] <- crowns_poly
}

# Combine all sf objects into one
all_crowns <- do.call(rbind, crown_polygons_list)

# Resolve overlapping polygons using spatial union
merged_crowns <- st_union(all_crowns)

# Compute additional attributes such as area and diameter
merged_crowns[["area"]] <- st_area(merged_crowns)
merged_crowns[["diameter"]] <- sqrt(merged_crowns[["area"]] / pi) * 2

# Save the combined and merged crown polygons to a shapefile
st_write(merged_crowns, "path_to_save/merged_crown_polygons.shp")

# Plot the merged crown polygons for visualization
plot(merged_crowns$geometry, col = 'green', main = "Merged Crown Polygons")