Calculate a vertical profile (vp) from a polar volume (pvol) file

Calculates a vertical profile of biological scatterers (vp) from a polar volume (pvol) file using the algorithm vol2bird (Dokter et al. 2011 doi:10.1098/rsif.2010.0116 ).

Usage

calculate_vp(
  file,
  vpfile = "",
  pvolfile_out = "",
  autoconf = FALSE,
  verbose = FALSE,
  warnings = TRUE,
  sd_vvp_threshold,
  rcs = 11,
  dual_pol = TRUE,
  rho_hv = 0.95,
  single_pol = TRUE,
  elev_min = 0,
  elev_max = 90,
  azim_min = 0,
  azim_max = 360,
  range_min = 5000,
  range_max = 35000,
  n_layer = 20,
  h_layer = 200,
  height_reference = "sea",
  ground_height_param = "HGHT",
  dealias = TRUE,
  nyquist_min = if (dealias) 5 else 25,
  nyquist_max_dealias = 25,
  dbz_quantity = "DBZH",
  eta_max = 36000,
  mistnet = FALSE,
  mistnet_elevations = c(0.5, 1.5, 2.5, 3.5, 4.5),
  local_mistnet
)

Arguments

file: Character (vector). Either a path to a single radar polar volume (pvol) file containing multiple scans/sweeps, or multiple paths to scan files containing a single scan/sweep. Or a single pvol object. The file data format should be either 1) ODIM format, which is the implementation of the OPERA data information model in the HDF5 format, 2) a format supported by the RSL library or 3) Vaisala IRIS (IRIS RAW) format.
vpfile: Character. File name. When provided, writes a vertical profile file (vpfile) either in the VPTS CSV or ODIM HDF5 format to disk.
pvolfile_out: Character. File name. When provided, writes a polar volume (pvol) file in the ODIM HDF5 format to disk. Useful for converting RSL formats to ODIM.
autoconf: Logical. When TRUE, default optimal configuration settings are selected automatically and other user settings are ignored.
verbose: Logical. When TRUE, vol2bird stdout is piped to the R console.
warnings: Logical. When TRUE, vol2bird warnings are piped to the R console.
sd_vvp_threshold: Numeric. Lower threshold for the radial velocity standard deviation (profile quantity sd_vvp) in m/s. Biological signals with sd_vvp < sd_vvp_threshold are set to zero. Defaults to 2 m/s for C-band radars and 1 m/s for S-band radars.
rcs: Numeric. Radar cross section per bird to use, in cm^2.
dual_pol: Logical. When TRUE, uses dual-pol mode, in which meteorological echoes are filtered using the correlation coefficient threshold rho_hv.
rho_hv: Numeric. Lower threshold in correlation coefficient to use for filtering meteorological scattering.
single_pol: Logical. When TRUE, uses precipitation filtering in single polarization mode based on reflectivity and radial velocity quantities.
elev_min: Numeric. Minimum elevation angle to include, in degrees.
elev_max: Numeric. Maximum elevation angle to include, in degrees.
azim_min: Numeric. Minimum azimuth to include, in degrees clockwise from north.
azim_max: Numeric. Maximum azimuth to include, in degrees clockwise from north.
range_min: Numeric. Minimum range to include, in m.
range_max: Numeric. Maximum range to include, in m.
n_layer: Numeric. Number of altitude layers to use in generated profile.
h_layer: Numeric. Width of altitude layers to use in generated profile, in m.
height_reference: Character. One of sea, antenna or ground for specifying the reference height for the profile altitude bins. Default sea level.
ground_height_param: Character. The scan parameter name of the polar volume containing ground height information. Default HGHT.
dealias: Logical. Whether to dealias radial velocities. This should typically be done when the scans in the polar volume have low Nyquist velocities (below 25 m/s).
nyquist_min: Numeric. Minimum Nyquist velocity of scans to include, in m/s.
nyquist_max_dealias: Numeric. When all scans have nyquist velocity higher than this value, dealiasing is suppressed. Default 25 m/s.
dbz_quantity: Name of the available reflectivity factor to use if not DBZH (e.g. DBZV, TH, TV).
eta_max: Maximum reflectivity in cm^2/km^3 for single gates containing birds. Default 36000 cm^2/km^3, corresponding to approximately 20 dBZ at C-band and 32 dBZ at S-band. Gates with reflectivities above this threshold will be discarded prior to profile estimation.
mistnet: Logical. Whether to use the MistNet segmentation model.
mistnet_elevations: Numeric vector of length 5. Elevation angles to feed to the MistNet segmentation model, which expects exactly 5 elevation scans at 0.5, 1.5, 2.5, 3.5 and 4.5 degrees. Specifying different elevation angles may compromise segmentation results.
local_mistnet: Character. Path to local MistNet segmentation model in PyTorch format (e.g. /your/path/mistnet_nexrad.pt).

Value

A vertical profile object of class vp. When defined, output files vpfile and pvolfile_out are saved to disk.

Details

Typical use

Common arguments set by users are file, vpfile and autoconf. Turn on autoconf to automatically select the optimal parameters for a given radar file. The default for C-band data is to apply rain-filtering in single polarization mode and dual polarization mode when available. The default for S-band data is to apply precipitation filtering in dual-polarization mode only.

Arguments that sometimes require non-default values are: rcs, sd_vvp_threshold, range_max, dual_pol, dealias. Other arguments are typically left at their defaults.

sd_vvp_threshold

For altitude layers with a VVP-retrieved radial velocity standard deviation value below the threshold sd_vvp_threshold, the bird density dens is set to zero (see vertical profile vp class). This threshold might be dependent on radar processing settings. Results from validation campaigns so far indicate that 2 m/s is the best choice for this parameter for most C-band weather radars, which is used as the C-band default. For S-band, the default threshold is 1 m/s.

rcs

The default radar cross section (rcs) (11 cm^2) corresponds to the average value found by Dokter et al. (2011) in a calibration campaign of a full migration autumn season in western Europe at C-band. Its value may depend on radar wavelength. rcs will scale approximately \(M^{2/3}\) with M the bird's mass.

dual_pol

For S-band (radar wavelength ~ 10 cm), currently only dual_pol = TRUE mode is recommended.

azim_min / azim_max

azim_min and azim_max only affects reflectivity-derived estimates in the profile (DBZH, eta, dens), not radial-velocity derived estimates (u, v, w, ff, dd, sd_vvp), which are estimated on all azimuths at all times. azim_min, azim_max may be set to exclude an angular sector with high ground clutter.

range_min / range_max

Using default values of range_min and range_max is recommended. Ranges closer than 5 km tend to be contaminated by ground clutter, while range gates beyond 35 km become too wide to resolve the default altitude layer width of 200 meter (see beam_width()). range_max may be extended up to 40 km (40000) for volumes with low elevations only, in order to extend coverage to higher altitudes.

h_layer

The algorithm has been tested and developed for altitude layers with h_layer = 200m. Smaller widths than 100 m are not recommended as they may cause instabilities of the volume velocity profiling (VVP) and dealiasing routines, and effectively lead to pseudo-replicated altitude data, since altitudinal patterns smaller than the beam width cannot be resolved.

dealias

Dealiasing uses the torus mapping method by Haase et al. (2004).

Use parameter nyquist_min to discard specific elevation scans with very low Nyquist velocity (by default smaller than 5 m/s). The Haase et al. algorithm is known to not provide accurate estimates for heavily folded velocity data, therefore these elevation scans are best removed entirely.

Use parameter nyquist_max_dealias to suppress dealiasing for polar volumes for which all scans already have a high Nyquist velocity. This prevents dealiasing when the data does not require it.

height reference

Profiles are calculated by default for height bins defined relative to mean sea level. Alternatively, height bins may be defined relative to the radar antenna height by setting height_reference to antenna. This places the bottom of the lowest altitude bin at the radar antenna height. Profiles may also be calculated relative to the height of the ground level terrain. This is especiallyuseful for stopover studies focused on altitude distributions during peak exodus shortly after sunset. Estimating a profile relative to ground height requires adding information from a digital elevation map to each pixel of the input polar volume, which is accomplished easily with function add_param(). Ground heights should be stored in units of meters relative to mean sea level. Parameter ground_height_param should point to the scan parameter name containing the digital elevation information.

Local installation

You may point parameter local_mistnet to a local download of the MistNet segmentation model in PyTorch format, e.g. /your/path/mistnet_nexrad.pt. The MistNet model can be downloaded at https://s3.amazonaws.com/mistnet/mistnet_nexrad.pt.

References

Dokter et al. (2011) is the main reference for the profiling algorithm (vol2bird) underlying this function. When using the mistnet option, please also cite Lin et al. (2019). When dealiasing data (dealias), please also cite Haase et al. (2004).

Dokter AM, Liechti F, Stark H, Delobbe L,Tabary P, Holleman I (2011) Bird migration flight altitudes studied by a network of operational weather radars, Journal of the Royal Society Interface 8 (54), pp. 30-43. doi:10.1098/rsif.2010.0116
Haase G & Landelius T (2004) Dealiasing of Doppler radar velocities using a torus mapping. Journal of Atmospheric and Oceanic Technology 21(10), pp. 1566-1573. doi:10.1175/1520-0426(2004)021<1566:DODRVU>2.0.CO;2
Lin T-Y, Winner K, Bernstein G, Mittal A, Dokter AM, Horton KG, Nilsson C, Van Doren BM, Farnsworth A, La Sorte FA, Maji S, Sheldon D (2019) MistNet: Measuring historical bird migration in the US using archived weather radar data and convolutional neural networks. Methods in Ecology and Evolution 10 (11), pp. 1908-22. doi:10.1111/2041-210X.13280

Examples

# Locate and read the polar volume example file
pvolfile_source <- system.file("extdata", "volume.h5", package = "bioRad")

# Copy the file to a temporary directory with read/write permissions
pvolfile <- paste0(tempdir(),"/volume.h5")
file.copy(pvolfile_source, pvolfile)
#> [1] TRUE

# Calculate the profile
if (requireNamespace("vol2birdR", quietly = TRUE)) {
vp <- calculate_vp(pvolfile)

# Get summary info
vp

# By default profiles are calculated for bins defined relative to sea level
# To calculate a profile relative to ground level:
# \donttest{
if(requireNamespace("elevatr", quietly = TRUE)){

example_pvol <- read_pvolfile(pvolfile)

# Download digital elevation model (DEM) information:
example_pvol |>
  # extract lowest scan
  get_scan(.5) |>
  # convert to raster object
  scan_to_raster(param="DBZH") |>
  # convert to terra raster class
  terra::rast() |>
  # download digital elevation data (increase z for higher resolutions)
  elevatr::get_elev_raster(z = 5, clip = "bbox") -> data_dem
# set digital elevations for open water to mean sea level (0)
data_dem[data_dem<0]=0
# set an informative name for the DEM information
names(data_dem) <- "HGHT"

# add the DEM information as a scan parameter to the polar volume:
example_pvol <- add_param(example_pvol, data_dem, "HGHT")

# calculate a profile relative to ground level:
vp_ground <- calculate_vp(example_pvol, height_reference="ground", ground_height_param="HGHT")

}
# }

# Clean up
file.remove(pvolfile)

}
#> Running vol2birdSetUp
#> Warning: radial velocities will be dealiased...
#> Mosaicing & Projecting
#> Clipping DEM to bbox
#> Note: Elevation units are in meters.
#> Running vol2birdSetUp
#> Warning: radial velocities will be dealiased...
#> [1] TRUE

Calculate a vertical profile (`vp`) from a polar volume (`pvol`) file