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index.qmd
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---
title: "ITD Animator Tutorial"
format: html
editor: visual
author: "Liam Irwin - [email protected]"
output-dir: docs
date: 2024-02-05
---
## Individual Tree Detection Animator - Tutorial
This code allows the user to visualize the working operation of the local maxima finder tree detection algorithm by creating a beautiful GIF of the process.
The code works by taking an input CHM, performing local maxima tree detection with lidR [locate_trees](https://rdrr.io/cran/lidR/man/locate_trees.html "lidR info page on locate_trees"), and subsequently plotting the moving window as it proceeds through the CHM cells.
This work is based on the demonstration by [ptompalski](https://github.com/ptompalski) his original code can be viewed [here](https://gist.github.com/ptompalski/94904eca2e1628fb52010c2890431715).
For more information on local maxima tree top detection using a variable window size based on canopy height see the original [Popescu and Wynne 2004 publication](https://doi.org/10.14358/PERS.70.5.589).
## Using the animator
Load the necessary packages
```{r, message=FALSE, warning=FALSE}
library(lidR) # Used to locate maxima
library(dplyr) # Used to manage dataframes
library(terra) # Used to extract raster values
library(glue) # Used to print progress updates
library(gifski) # Used to compile GIF
library(tictoc) # Used to print elapsed time
library(ggplot2) # Used to generate plots
library(ggforce) # Used to draw circular window
# Load the lmf_animator function in your R environment
```
Generate a Canopy Height Model (or load your own)
```{r}
# Load pre-created CHM
# chm <- rast('chm_dir/your_chm.tif')
# Use built in LAS file from lidR
LASfile <- system.file("extdata", "MixedConifer.laz", package="lidR")
# Crop to small area while reading
las <- readLAS(LASfile, filter = "-inside 481320 3812981 481350 3813011")
# Generate 0.50m CHM
chm <- rasterize_canopy(las, res = 0.5, algorithm = pitfree(c(0,2,5,10,15), c(0, 1.5)))
plot(chm, col = viridis::viridis(50))
```
Determine your aesthetic parameters and run the animator
```{r, eval = FALSE}
# Generate subset animation using Z values as background
lmf_animator(chm, # Input CHM
dir_out = "output", # Directory where GIF and frames are saved
gif_out_name = "example_z.gif", # Output file name of GIF
buffer = 2.5, # Buffer around plot
delay = 0.1, # Time (ms) between frames in GIF
circular = T, # Circular or square lmf window
subset = TRUE, # Subset frames of the CHM (otherwise takes a long time)
sub_range = 1:800, # Range of CHM cells to subset
col_pal = scale_fill_viridis_c(), # Colour pallette for plotting CHM/hillshade
clear_frames = F, # Delete frames after GIF is created?
skip_cells = 3, # Skip cells to speed up processing and GIF playback (1 = do not skip)
ttop_size = 3, # plot.sf option size
ttop_shape = 3, # plot.sf option shape
ttop_col = "red", # plot.sf option for colour
hillshade = F # plot hillshade instead of Z values?
)
```
Resulting GIF
```{r, eval = FALSE}
# Generate subset animation using hillshade as background
lmf_animator(chm, # Input CHM
dir_out = "output", # Directory where GIF and frames are saved
gif_out_name = "example_hs.gif", # Output file name of GIF
buffer = 2.5, # Buffer around plot
delay = 0.1, # Time (ms) between frames in GIF
circular = T, # Circular or square lmf window
subset = TRUE, # Subset frames of the CHM (otherwise takes a long time)
sub_range = 1:800, # Range of CHM cells to subset
col_pal = scale_fill_viridis_c(), # Colour pallette for plotting CHM/hillshade
clear_frames = F, # Delete frames after GIF is created?
skip_cells = 3, # Skip cells to speed up processing and GIF playback (1 = do not skip)
ttop_size = 3, # plot.sf option size
ttop_shape = 3, # plot.sf option shape
ttop_col = "red", # plot.sf option for colour
hillshade = T # plot hillshade instead of Z values?
)
```
Resulting GIF
