update

TryForestTools/first-flight/combine_tiles.ipynb

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+oid sha256:1cd5ac1077f24e427a57d393d7cfa4a45248cefea41b413a7beecaeead9ff8c1
+size 11371

TryForestTools/first-flight/convert_to_chm.ipynb

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:d654d63e3f7db465503e60e4e8336f909d0512975ec7cebe0e0972680d9e2f36
-size 155374
+oid sha256:4cc2ce9a3a51f78cb98b680cb85277354758ec1e71e00697fd88c4f255b51606
+size 249142

TryForestTools/first-flight/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")
+install.packages("dplyr")
+install.packages("ggplot2")
+
+
+# Load the necessary libraries
+library(ForestTools)
+library(terra)
+library(sf)
+library(imager)
+library(ggplot2)
+
+
+# Load sample canopy height model provided by ForestTools
+lin <- function(x) { x * 0.08 + 0.8 }
+
+chm_folder <- "/Users/taekim/ecohackathon/WeCanopy/TryForestTools/first-flight/chm_tiles_shiftxy"
+
+# List all TIFF files in the directory
+tile_paths <- list.files(path = chm_folder, pattern = "\\.tif$", full.names = TRUE)
+print(tile_paths)
+# Initialize an empty list to store sf objects for each tile
+crown_polygons_list <- list()
+
+counter <- 0
+for (chm_path in tile_paths) {
+  print(counter)
+  
+  counter <- counter + 1
+  chm <- terra::rast(chm_path)
+  if (nlyr(chm) > 1) {
+    chm <- chm[[1]]  # Select the first layer if necessary
+  }
+  
+  ttops <- vwf(chm, winFun = lin, minHeight = 2)
+  crowns_poly <- mcws(treetops = ttops, CHM = chm, format = "polygons", minHeight = 5)
+  crowns_sf <- st_as_sf(crowns_poly)
+  crowns_sf$tile_path <- chm_path
+  
+  heights_list <- lapply(seq_len(nrow(crowns_sf)), function(i) {
+    crown_mask <- mask(chm, crowns_sf[i, ])
+    max(crown_mask[], na.rm = TRUE)
+  })
+  heights <- unlist(heights_list)
+  
+  print(heights)
+  
+  base_name <- tools::file_path_sans_ext(basename(chm_path))
+  output_file_path <- file.path("/Users/taekim/ecohackathon/WeCanopy/TryForestTools/first-flight/result_polygons_shiftxy", paste0(base_name, "_crowns.geojson"))
+  
+  st_write(crowns_sf, output_file_path, driver = "GeoJSON")
+  
+  crown_polygons_list[[chm_path]] <- crowns_sf
+}
+
+  
+
+
+
+