trying new version

TryForestTools/data.R

@@ -11,48 +11,46 @@ 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")
-}
+lin <- function(x) { x * 0.05 + 0.5 }
 
-# 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")
+chm_folder <- "/Users/taekim/ecohackathon/first_try_lidar/ForestTools/TryForestTools/first-flight/chm_tiles"  # Update this with the path to your CHM tiles folder
 
-# Function for defining dynamic window size
-lin <- function(x) { x * 0.05 + 0.6 }
+# 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()
 
-# Detect treetops
-ttops <- vwf(chm, winFun = lin, minHeight = 2)
-print("Treetops detected:")
-print(head(ttops))
+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
+}
 
-# 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)))
+# Combine all sf objects into one
+all_crowns <- do.call(rbind, crown_polygons_list)
 
-# Create crown map
-crowns_ras <- mcws(treetops = ttops, CHM = chm, minHeight = 1.5)
+# Resolve overlapping polygons using spatial union
+merged_crowns <- st_union(all_crowns)
 
-# 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")
+# Compute additional attributes such as area and diameter
+merged_crowns[["area"]] <- st_area(merged_crowns)
+merged_crowns[["diameter"]] <- sqrt(merged_crowns[["area"]] / pi) * 2
 
-# Create polygon crown map
-crowns_poly <- mcws(treetops = ttops, CHM = chm, format = "polygons", minHeight = 1.5)
-print("Crown polygons:")
-print(head(crowns_poly))
+# Save the combined and merged crown polygons to a shapefile
+st_write(merged_crowns, "path_to_save/merged_crown_polygons.shp")
 
-# Plot CHM and crown outlines
-plot(chm, xlab = "", ylab = "", xaxt = 'n', yaxt = 'n', main = "CHM with Crown Outlines")
-plot(crowns_poly$geometry, border = "blue", lwd = 0.5, add = TRUE)
+# Plot the merged crown polygons for visualization
+plot(merged_crowns$geometry, col = 'green', main = "Merged Crown Polygons")
 
-# 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)))

TryForestTools/first-flight/convert_to_chm.ipynb

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:7084dfd519992356f53c2a0a6c186ee9598c252a19136c878c18c8c475cb3a68
-size 32612
+oid sha256:d654d63e3f7db465503e60e4e8336f909d0512975ec7cebe0e0972680d9e2f36
+size 155374