In mqueinnec/icesat2R: Downloading and processing ICESat-2 data for forest analysis

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(icesat2R)

library(dplyr)
library(tidyr)
library(ggplot2)

Data

This tutorial uses one ATL03 HDF file and one ATL08 HDF file acquired across an approximately 3-km long ground track (in the along-track direction).

xfun::embed_file("data/ATL_zipped")

The ATL08 product

Read ATL08 HDF files

The function read_ATL08() can be used to convert the HDF file into a R friendly format. The only required argument is file, which should be a path to a ATL08 .h5 file (ATL08_[yyyymmdd][hhmmss]_[ttttccss]_[vvv_rr].h5 or processed_ATL08_[yyyymmdd][hhmmss]_[ttttccss]_[vvv_rr].h5).

The ATL08 algorithm classifies ATL03 photons as noise, ground, canopy or top of canopy and generates canopy and terrain height statistics along 100-m segments (5 x 20-m ATL03 segments). Therefore, one part of the data is delivered at the ATL03 photon level (classification per )

The function converts the ATL08 data to two data.frame objects. The first data frame includes the ATL80 terrain and canopy height metrics generated at the 100-m segment intervals along with ancillary information. The second data frame includes the ATL08 classification as noise, ground, canopy or top of canopy of the ATL03 photons. Note that this data.frame does not includes the coordinates (lat/lon) of the classified photons since this information is contained in the ATL03 product. Each photon can be uniquely identified using a 20-m segment ID (ph_segment_id) and a counting index (classed_pc_indx) indicating the photon record within the given 20-m in the ATL03 product.

atl08_h5_file <- "ATL_zipped/processed_ATL08_20200821122613_08730802_004_01.h5"

atl08_dat <- read_ATL08(file = atl08_h5_file)

The functionread_ATL08() returns a list with one element per beam. For each beam, the element ATL08 contains the data.frame with 100-m terrain and canopy height metrics. The ATL08_sf contains the same information but is returned as a georeferenced spatial object (sf). The last element

Generate ground tracks from ATL08 100-m segments center points

ground_tracks <- make_transect(atl08_dat$gt1l$ATL08_sf)

ground_tracks_all <- lapply(1:length(atl08_dat), function(x) {
  obj <- atl08_dat[[x]]$ATL08_sf
  out <- make_transect(obj)
  return(out)
})

ground_tracks_all <- bind_rows(ground_tracks_all)

mapview::mapview(ground_tracks_all)

The ATL03 product

Read ATL03 HDF files

atl03_h5_file <- "ATL_zipped/processed_ATL03_20200821122613_08730802_004_01.h5"

atl03_dat <- read_ATL03(file = atl03_h5_file)

Classified ATL03 product

mqueinnec/icesat2R documentation built on Feb. 18, 2022, 2:38 a.m.