R/getLevel1BGeo.R

In rGEDI: NASA's Global Ecosystem Dynamics Investigation (GEDI) Data Visualization and Processing

#'Get GEDI Full Waveform Geolocations (GEDI Level1B)
#'
#'@description This function extracts Pulse Full Waveform Geolocations from GEDI Level1B data
#'
#'@usage getLevel1BGeo(level1b, select)
#'
#'@param level1b A GEDI Level1B object (output of \code{\link[rGEDI:readLevel1B]{readLevel1B}} function).
#'An S4 object of class "gedi.level1b".
#'@param select A character vector specifying the fields to extract from GEDI Level1B data. If NULL,
#'by default it will extract \emph{latitude_bin0}, \emph{latitude_lastbin}, \emph{longitude_bin0}, \emph{longitude_lastbin}, and \emph{shot_number}. See details for more options.
#'
#'@return Returns an S4 object of class \code{\link[data.table:data.table]{data.table-class}} containing the GEDI Full Waveform Geolocations
#'
#'
#'@seealso https://lpdaac.usgs.gov/products/gedi01_bv001/
#'
#'@details Additional fields to be extracted from GEDI level 1B:
#'\itemize{
#'\item \emph{all_samples_sum} Sum of all values within the 10 km range window.
#'\item \emph{beam} Beam number	Number.
#'\item \emph{channel} Channel number.
#'\item \emph{master_frac} Master time, fractional part.
#'\item \emph{master_int} Master time, integer part.
#'\item \emph{noise_mean_corrected} Noise mean.
#'\item \emph{noise_stddev_corrected} Corrected noise standard deviation.
#'\item \emph{nsemean_even} Noise mean of the beam's detector channel from even sub-converter.
#'\item \emph{nsemean_odd} Noise mean of the beam's odd sub-converter.
#'\item \emph{rx_energy} Integrated energy in receive (RX) waveform after subtracting the noise mean.
#'\item \emph{rx_offset} Time interval from first stored sample to first downloaded RX sample.
#'\item \emph{rx_open} Time interval from time 0 to first stored RX sample.
#'\item \emph{rx_sample_count} The number of sample intervals (elements) in each RX waveform.
#'\item \emph{rx_sample_start_index} The index in the rxwaveform dataset of the first element of each RX waveform starting at 1.
#'\item \emph{selection_stretchers_x} Commanded number of samples added to the algorithm section on the left.
#'\item \emph{selection_stretchers_y} Commanded number of samples added to the algorithm section on the right.
#'\item \emph{shot_number} Unique shot identifier.
#'\item \emph{stale_return_flag} Indicates that a "stale" cue point from the coarse search algorithm is being used.
#'\item \emph{th_left_used} Count values for the left threshold used in fine search where two consecutive points at or above this value indicate pulse detection.
#'\item \emph{tx_egamplitude} Amplitude of the extended Gaussian fit to the transmit (TX) waveform.
#'\item \emph{tx_egamplitude_error} Error on tx_egamplitude.
#'\item \emph{tx_egbias} Bias of the extended Gaussian fit to the TX waveform.
#'\item \emph{tx_egbias_error} Error on tx_egbias.
#'\item \emph{tx_egflag} Extended Gaussian fit status flag.
#'\item \emph{tx_eggamma} Gamma value of the extended Gaussian fit to the TX waveform.
#'\item \emph{tx_eggamma_error} Error on tx_eggamma.
#'\item \emph{tx_egsigma} Sigma of the extended Gaussian fit to the TX waveform.
#'\item \emph{tx_egsigma_error} Error on tx_egsigma.
#'\item \emph{tx_gloc} Location (mean) of the Gaussian fit to the TX waveform.
#'\item \emph{tx_gloc_error} Error on tx_gloc.
#'\item \emph{tx_pulseflag} Set to 1 if a pulse is detected in the TX waveform.
#'\item \emph{tx_sample_count} The number of sample intervals (elements) in each transmit waveform.
#'\item \emph{tx_sample_start_index} The index in the rxwaveform dataset of the first element of each RX waveform starting at 1.
#'\item \emph{altitude_instrument} Height of the instrument diffractive optical element (DOE) above the WGS84 ellipsoid.
#'\item \emph{altitude_instrument_error} Error on altitude_instrument.
#'\item \emph{bounce_time_offset_bin0} The difference between the TX time and the time at the start of the RX window.
#'\item \emph{bounce_time_offset_bin0_error} Error on bounce_time_offset_bin0.
#'\item \emph{bounce_time_offset_lastbin} The difference between the TX time and the time at the end of the RX window.
#'\item \emph{bounce_time_offset_lastbin_error} Error on bounce_time_offset_lastbin.
#'\item \emph{degrade} Greater than zero if the shot occurs during a degrade period, zero otherwise.
#'\item \emph{delta_time} Transmit time of the shot, measured in seconds since 2018-01-01.
#'\item \emph{digital_elevation_model} Digital elevation model height above the WGS84 ellipsoid.
#'\item \emph{elevation_bin0} Height of the start of the RX window, relative to the WGS-84 ellipsoid.
#'\item \emph{elevation_bin0_error} Error on elevation_bin0.
#'\item \emph{elevation_lastbin} Height of the end of the RX window, relative to the WGS-84 ellipsoid.
#'\item \emph{elevation_lastbin_error} Error on elevation_lastbin.
#'\item \emph{latitude_bin0} Latitude of the start of the RX window.
#'\item \emph{latitude_bin0_error} Error on latitude_bin0.
#'\item \emph{latitude_lastbin} Latitude of the end of the RX window.
#'\item \emph{latitude_lastbin_error} Error on latitude_lastbin.
#'\item \emph{latitude_instrument} Latitude of the instrument diffractive optical element (DOE) at laser transmit time.
#'\item \emph{latitude_instrument_error} Error on latitude_instrument.
#'\item \emph{local_beam_azimuth} Azimuth of the unit pointing vector for the laser in the local East, North, Up (ENU) frame.
#'\item \emph{local_beam_azimuth_error} Error on local_beam_azimuth.
#'\item \emph{local_beam_elevation} Elevation of the unit pointing vector for the laser in the local ENU frame.
#'\item \emph{local_beam_elevation_error} Error on local_beam_elevation.
#'\item \emph{longitude_bin0} Longitude of the start of the RX window.
#'\item \emph{longitude_bin0_error} Error on longitude_bin0.
#'\item \emph{longitude_lastbin} Longitude of the end of the RX window.
#'\item \emph{longitude_lastbin_error} Error on longitude_lastbin.
#'\item \emph{longitude_instrument} Longitude of the instrument diffractive optical element (DOE) at laser transmit time.
#'\item \emph{longitude_instrument_error} Error on longitude_instrument.
#'\item \emph{mean_sea_surface} Mean sea surface height above the WGS84 ellipsoid, includes the geoid	.
#'\item \emph{neutat_delay_derivative_bin0} Change in neutral atmospheric delay per height change for the start of the RX window.
#'\item \emph{neutat_delay_derivative_lastbin} Change in neutral atmospheric delay per height change for the end of the RX window.
#'\item \emph{neutat_delay_total_bin0} Total neutral atmosphere delay correction (wet+dry) from the TX pulse to the start of the RX window.
#'\item \emph{neutat_delay_total_lastbin} Total neutral atmosphere delay correction (wet+dry) from the TX pulse to the end of the RX window.
#'\item \emph{range_bias_correction} The range bias applied to the range measurement.
#'\item \emph{shot_number} Unique shot identifier	Number.
#'\item \emph{solar_azimuth} The azimuth of the sun position vector.
#'\item \emph{solar_elevation} The elevation of the sun position vector.
#'\item \emph{surface_type} Flags describing which surface types.
#'\item \emph{dynamic_atmosphere_correction} Dynamic Atmospheric Correction (DAC) includes inverted barometer (IB) effect.
#'\item \emph{geoid} Geoid height above WGS-84 reference ellipsoid.
#'\item \emph{tide_earth} Solid Earth tides.
#'\item \emph{tide_load} Load Tide - Local displacement due to Ocean Loading.
#'\item \emph{tide_ocean} Ocean Tides including diurnal and semi-diurnal, and longerperiod tides.
#'\item \emph{tide_ocean_pole} Oceanic surface rotational deformation due to polar motion.
#'\item \emph{tide_pole} Solid Earth Pole Tide. Rotational deformation due to polar motion.
#'}
#'
#'@examples
#'# specify the path to GEDI level1B data (zip file)
#'outdir = tempdir()
#'level1B_fp_zip <- system.file("extdata",
#'                   "GEDI01_B_2019108080338_O01964_T05337_02_003_01_sub.zip",
#'                   package="rGEDI")
#'
#'# Unzipping GEDI level1B data
#'level1Bpath <- unzip(level1B_fp_zip,exdir = outdir)
#'
#'# Reading GEDI level1B data (h5 file)
#'level1b<-readLevel1B(level1Bpath=level1Bpath)
#'
#'# Extracting GEDI level1B geolocations
#'level1bGeo<-getLevel1BGeo(level1b,select=c("elevation_bin0", "elevation_lastbin"))
#'head(level1bGeo)
#'
#'close(level1b)
#'@export
getLevel1BGeo<-function(level1b,select=c("elevation_bin0", "elevation_lastbin")) {

  select<-unique(c("latitude_bin0", "latitude_lastbin", "longitude_bin0", "longitude_lastbin","shot_number",select))
  level1b<-level1b@h5

  datasets<-hdf5r::list.datasets(level1b, recursive = T)
  datasets_names<-basename(datasets)

  selected<-datasets_names %in% select

  for ( i in select){
    if  ( i =="shot_number"){
      assign(i,bit64::as.integer64(NaN))
    } else {
      assign(i,numeric())
    }
  }

  dtse2<-datasets[selected][!grepl("geolocation/shot_number",datasets[selected])]


  # Set progress bar
  pb <- utils::txtProgressBar(min = 0, max = length(dtse2), style = 3)
  i.s=0

  for ( i in dtse2){
    i.s<-i.s+1
    utils::setTxtProgressBar(pb, i.s)
    name_i<-basename(i)
    if ( name_i =="shot_number"){
      assign(name_i, bit64::c.integer64(get(name_i),level1b[[i]][]))
    } else {
      assign(name_i, c(get(name_i), level1b[[i]][]))
    }
  }

  level1b.dt<-data.table::data.table(as.data.frame(get("shot_number")[-1]))
  select2<-select[!select[]=="shot_number"]

  for ( i in select2){
    level1b.dt[,i]<-get(i)
  }

  colnames(level1b.dt)<-c("shot_number",select2)
  close(pb)
  return(level1b.dt)
}