gediWFMetrics.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/C_processExtractMetrics.R
\name{gediWFMetrics}
\alias{gediWFMetrics}
\title{GEDI full waveform data processing}
\usage{
gediWFMetrics(
  input,
  outRoot,
  writeFit = FALSE,
  writeGauss = FALSE,
  bounds = NULL,
  ground = FALSE,
  useInt = FALSE,
  useFrac = FALSE,
  rhRes = 5,
  laiRes = 10,
  laiH = 30,
  noRHgauss = FALSE,
  gTol = 0,
  fhdHistRes = 0.001,
  forcePsigma = FALSE,
  bayesGround = FALSE,
  dontTrustGround = FALSE,
  noRoundCoord = FALSE,
  noCanopy = FALSE,
  dcBias = 0,
  nSig = 0,
  seed = NULL,
  hNoise = 0,
  linkNoise = NULL,
  linkFsig = NULL,
  linkPsig = NULL,
  trueSig = NULL,
  bitRate = NULL,
  maxDN = NULL,
  renoise = FALSE,
  newPsig = -1,
  oldPsig = 0.764331,
  addDrift = NULL,
  missGround = FALSE,
  minGap = NULL,
  photonCount = FALSE,
  pcl = FALSE,
  nPhotons = 2.1,
  photonWind = 200,
  noiseMult = 0.1,
  rhoVrhoG = 1,
  nPhotC = 2.1,
  nPhotG = -1,
  photHDF = FALSE,
  meanN = 0,
  thresh = 1e-14,
  varNoise = FALSE,
  varScale = NULL,
  statsLen = NULL,
  noiseTrack = FALSE,
  sWidth = NULL,
  psWidth = 0,
  msWidth = NULL,
  preMatchF = FALSE,
  postMatchF = FALSE,
  pFile = NULL,
  gWidth = 1.2,
  minGsig = 0.764331,
  minWidth = 0,
  medNoise = FALSE,
  varDrift = NULL,
  driftFac = NULL,
  rhoG = 0.4,
  rhoC = 0.57,
  pSigma = NULL,
  gold = FALSE,
  deconTol = NULL
)
}
\arguments{
\item{input}{\code{\link[rGEDI:gedi.level1bSim-class]{gedi.level1bSim}} (may be a list of objects). Simulated waveform input object(s).}

\item{outRoot}{name. output filename root}

\item{writeFit}{write fitted waveform}

\item{writeGauss}{write Gaussian parameters}

\item{bounds}{minX minY maxX maxY. only analyse data within bounds}

\item{ground}{read true ground from file}

\item{useInt}{use discrete intensity instead of count}

\item{useFrac}{use fractional hits rather than counts}

\item{rhRes}{r. percentage energy resolution of RH metrics}

\item{laiRes}{res. lai profile resolution in metres}

\item{laiH}{h. height to calculate LAI to}

\item{noRHgauss}{do not fit Gaussians}

\item{gTol}{tol. ALS ground tolerance. Used to calculate slope.}

\item{fhdHistRes}{res. waveform intensity resolution to use when calculating FHD from histograms}

\item{forcePsigma}{do not read pulse sigma from file}

\item{bayesGround}{use Bayseian ground finding}

\item{dontTrustGround}{don't trust ground in waveforms, if included}

\item{noRoundCoord}{do not round up coords when outputting}

\item{noCanopy}{do not calculate FHD histograms and LAI profiles}

\item{dcBias}{n. mean noise level}

\item{nSig}{sig. noise sigma}

\item{seed}{n. random number seed}

\item{hNoise}{n. hard threshold noise as a fraction of integral}

\item{linkNoise}{linkM cov. apply Gaussian noise based on link margin at a cover}

\item{linkFsig}{sig. footprint width to use when calculating and applying signal noise}

\item{linkPsig}{sig. pulse width to use when calculating and applying signal noise}

\item{trueSig}{sig. true sigma of background noise}

\item{bitRate}{n. digitisation bit rate}

\item{maxDN}{max. maximum DN}

\item{renoise}{remove noise from truth before applying new noise level}

\item{newPsig}{sig. new value for pulse width, when lengthening pulse}

\item{oldPsig}{sig. old value for pulse width if not defined in waveform file, when lengthening pulse}

\item{addDrift}{xi. apply detector background drift}

\item{missGround}{assume ground is missed to assess RH metrics}

\item{minGap}{gap. delete signal beneath min detectable gap fraction}

\item{photonCount}{output point cloud from photon counting}

\item{pcl}{convert to photon counting pulsecompressed}

\item{nPhotons}{n. mean number of photons}

\item{photonWind}{x. window length for photon counting search, metres}

\item{noiseMult}{x. noise multiplier for photoncounting}

\item{rhoVrhoG}{x. ratio of canopy to ground reflectance at this wavelength. Not different from rhoV and rhoG}

\item{nPhotC}{n. mean number of canopy photons (replaces nPhotons and rhoVrhoG)}

\item{nPhotG}{n. mean number of ground photons (replaces nPhotons and rhoVrhoG)}

\item{photHDF}{write photoncounting}

\item{meanN}{n. mean noise level, if using a predefined mean level}

\item{thresh}{n. noise threshold, if using a predefined noise threshold}

\item{varNoise}{use a variable noise threshold}

\item{varScale}{x. variable noise threshold scale (multiple of stdev above mean to set threshold)}

\item{statsLen}{len. length to calculate noise stats over for varNoise}

\item{noiseTrack}{use noise tracking}

\item{sWidth}{sig. smoothing width, after densoising}

\item{psWidth}{sigma. smoothing width, before denoising}

\item{msWidth}{sig. smoothing width, after noise stats, before denoising}

\item{preMatchF}{matched filter before denoising}

\item{postMatchF}{matched filter after denoising}

\item{pFile}{file. read pulse file, for deconvoltuion and matched filters}

\item{gWidth}{sig. Gaussian parameter selection smoothing width}

\item{minGsig}{sig. minimum Gaussian sigma to fit}

\item{minWidth}{n. minimum feature width in bins}

\item{medNoise}{use median stats rather than mean}

\item{varDrift}{correct detector drift with variable factor}

\item{driftFac}{xi. fix drift with constant drift factor}

\item{rhoG}{rho. ground reflectance}

\item{rhoC}{rho. canopy reflectance}

\item{pSigma}{sig. pulse width to smooth by if using Gaussian pulse}

\item{gold}{deconvolve with Gold's method}

\item{deconTol}{deconvolution tolerance}
}
\value{
A S4 object of class \code{\link[hdf5r:H5File-class]{hdf5r::H5File}} in the \emph{hdf5r} package.
}
\description{
GEDI full waveform data processing and metrics extraction
}
\examples{
\dontshow{
rm(list=ls())
}

libsAvailable = require(lidR) && require(plot3D)
if (libsAvailable) {

# specify the path to ALS data (zip)
alsfile_Amazon_zip <- system.file("extdata", "Amazon.zip", package="rGEDI")
alsfile_Savanna_zip <- system.file("extdata", "Savanna.zip", package="rGEDI")

# Unzipping ALS data
alsfile_Amazon_filepath <- unzip(alsfile_Amazon_zip,exdir = dirname(alsfile_Amazon_zip))
alsfile_Savanna_filepath <- unzip(alsfile_Savanna_zip,exdir = dirname(alsfile_Savanna_zip))

# Reading and plot ALS file (las file)
als_Amazon<-readLAS(alsfile_Amazon_filepath)
als_Savanna<-readLAS(alsfile_Savanna_filepath)

# Extracting plot center geolocations
xcenter_Amazon = mean(als_Amazon@bbox[1,])
ycenter_Amazon = mean(als_Amazon@bbox[2,])
xcenter_Savanna = mean(als_Savanna@bbox[1,])
ycenter_Savanna = mean(als_Savanna@bbox[2,])

# Simulating GEDI full-waveform
wf_Amazon<-gediWFSimulator(input=alsfile_Amazon_filepath,
                          output=file.path(getwd(),"gediWF_amazon_simulation.h5"),
                          coords = c(xcenter_Amazon, ycenter_Amazon))

wf_Savanna<-gediWFSimulator(input=alsfile_Savanna_filepath,
                           output=file.path(getwd(),"gediWF_Savanna_simulation.h5"),
                           coords = c(xcenter_Savanna, ycenter_Savanna))

# Extracting GEDI full-waveform derived metrics
wf_amazon_metrics<-gediWFMetrics(input=wf_Amazon,outRoot=file.path(getwd(), "amazon"))
wf_savanna_metrics<-gediWFMetrics(input=wf_Savanna,outRoot=file.path(getwd(), "Savanna"))

close(wf_Amazon)
close(wf_Savanna)

metrics<-rbind(wf_amazon_metrics,wf_savanna_metrics)
rownames(metrics)<-c("Amazon","Savanna")
head(metrics)
}

}
\seealso{
i) Hancock, S., Armston, J., Hofton, M., Sun, X., Tang, H., Duncanson, L.I., Kellner,
J.R. and Dubayah, R., 2019. The GEDI simulator: A large‐footprint waveform lidar simulator
for calibration and validation of spaceborne missions. Earth and Space Science.
https://doi.org/10.1029/2018EA000506

ii) gediSimulator: https://bitbucket.org/StevenHancock/gedisimulator/src/master/
}