maybe now

TryForestTools/data.R

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+# 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
+chm_path <- "/Users/taekim/ecohackathon/first_try_lidar/ForestTools/TryForestTools/first-flight/chmtiles/chm_tile_1892_2880.tif"
+if (file.exists(chm_path)) {
+  chm <- terra::rast(chm_path)
+} else {
+  stop("CHM file does not exist")
+}
+
+# Check the CHM data
+print("Summary of CHM:")
+summary(chm)
+print(paste("Number of NA values in CHM:", sum(is.na(values(chm)))))
+plot(chm, main = "Canopy Height Model")
+
+# Function for defining dynamic window size
+lin <- function(x) { x * 0.05 + 0.6 }
+
+# Detect treetops
+ttops <- vwf(chm, winFun = lin, minHeight = 2)
+print("Treetops detected:")
+print(head(ttops))
+
+# Plot CHM and treetops
+plot(chm, xlab = "", ylab = "", xaxt = 'n', yaxt = 'n', main = "CHM with Treetops")
+plot(ttops$geometry, col = "blue", pch = 20, cex = 0.5, add = TRUE)
+print(paste("Mean height of treetops:", mean(ttops$height)))
+
+# Create crown map
+crowns_ras <- mcws(treetops = ttops, CHM = chm, minHeight = 1.5)
+
+# Plot crowns
+plot(crowns_ras, col = sample(rainbow(50), length(unique(values(crowns_ras))), replace = TRUE), legend = FALSE, xlab = "", ylab = "", xaxt = 'n', yaxt = 'n', main = "Crown Map")
+
+# Create polygon crown map
+crowns_poly <- mcws(treetops = ttops, CHM = chm, format = "polygons", minHeight = 1.5)
+print("Crown polygons:")
+print(head(crowns_poly))
+
+# Plot CHM and crown outlines
+plot(chm, xlab = "", ylab = "", xaxt = 'n', yaxt = 'n', main = "CHM with Crown Outlines")
+plot(crowns_poly$geometry, border = "blue", lwd = 0.5, add = TRUE)
+
+# Compute area and diameter
+crowns_poly[["area"]] <- st_area(crowns_poly)
+crowns_poly[["diameter"]] <- sqrt(crowns_poly[["area"]] / pi) * 2
+print(paste("Mean crown diameter:", mean(crowns_poly$diameter)))