cplot2d.event: Plot a 2-D echogram.

Description Usage Arguments

View source: R/cplot2d.event.R

Description

This function reads TSD data from an event and plots the data as a 2-D echogram. The funciton will look for the previously read data and use these if applicable, for faster plotting of the same data using different plotting settings.

Usage

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cplot2d.event(event = 1, t = 1, cruise = 2009116, dir.data = NULL,
  max.memory = 8e+09, breaks = 40, col = "combined", colpar = list(start
  = 0, end = 0.8, flip = TRUE), null.value = NA, beamstypes = 1,
  grid = TRUE, white = 0, log = TRUE, endcol = c("white", ""),
  esnm = "MS70", var = c("vbsc", "sgsc", "pr0s", "sgs0", "sgsE", "sgsi",
  "sgsI", "psis", "tlns"), ind = list(), range = list(), subset = NULL,
  plot = TRUE, cs.xyzlim = "g", xlim = NULL, ylim = NULL, zlim = NULL,
  tlim = NULL, up = FALSE, freq = 1, wb = 1, rmar = 5,
  xaxis = c("time", "dist", "pings"), gap = median, gapthr = 10,
  tol = 0.1, heave = c("interp", "pixel", "ignore"), x0 = NULL,
  unit = NULL, date = c("unique", "all", "none"), nticksx = 10,
  lwdfact = 55, region = NULL, adds = NULL, origin = 1, clock = NULL,
  cex.clock = 1, format.clock = "Ping: indt\nyyyy-mm-dd\nHH:MM:SS.FFF",
  digits.clock = 2, col.clock = 4, tres = NULL, xres = NULL,
  zres = NULL, rres = NULL, bres = NULL, funvbsc = c("median", "mean"),
  funt = c("median", "mean"), cs = "g", ...)

Arguments

event

is the identifier of the event, either given as the number of the event, a string contained in the name of the event, or the path of the event directory.

t

is either a vector of the numbers of the pings to be returned, as listed from 1 to the number of pings in the event, or a vector of time points given as strings "yyyymmddHHMMSS.FFF" or "HHMMSS.FFF" from which the range of the time points to be read is extracted. If t=="all", all files are read and if t=="none" an empty list is returned.

cruise

is either the idenfication number of the cruise, given as specified by the IMR (yyyynnn), or the path to the directory containing the event to be read.

dir.data

is the path to the directory in which the projects are stored, defaulted by the variable Acoustics_datasets_directory().

max.memory

is the maximum memory allowed for the function to occupy.

breaks

has two possible inputs: (1) the number of breaks of the scale on which the data 'z' are arranged, equally spaced between min(z) and max(z) (or logarithmically equaly spaced when log=TRUE). (2) a vector of values for the breaks given in dB values (volume backscattering strength Sv), typically -82:-30 for EK60.

col

is either the color vector if length(col)>1, or the color function to generate the colors from. Currently the color function name must be one of "rainbow", "grey", "heat.colors", "terrain.colors", "topo.colors" and "cm.colors", but other color functions may be inplemented in the future. Set color.bar=NULL to supress plotting the color bar.

colpar

is a list of parameters used in colscale().

null.value

is is the value to set non-postitive values in the case of logarithmic plotting. The default is the only non-numeric value allowed, and implies the smallest positive value of the data.

beamstypes

***********************************

grid

***********************************

white

***********************************

log

***********************************

esnm

is the name of the acoustical instrument, given as a four character string. See sonR_implemented() for the implemented systems. May be given in 'data', and in lower case.

var

is a string specifying the variable to plot. Currently supported are "vbsc", for volume backscattering data, "sgsc"/"sgs0"/"sgsE"/"sgsi"/"sgsI", for (thresholded) segmentation data, "pr0s" or "psis" for unhtresholded not-school probability data, and "tlns" for pure estimated noise.

ind

is a list of indexes, as typed into the [] of an array, where 0 and NULL denotes all indexes.

range

is a list of elements with names matching names of 'data', specifying the range of the corresponding elements.

subset

is a numeric or logical vector/expression indicating elements or rows to keep. Missing values are taken as false, and subset=0 or subset=NULL indicates no subsetting.

plot

is FALSE to prevent plotting.

cs.xyzlim

defines the coordinate system to use when specifying the plotting frame. Given as one of "g" or "v" representing the global coordinate and the coordinate system of the vessel.

xaxis

A character defining the variable to use for the x axis, one of (1) "time", assigning time to the x axis; (2) "dist" or "x", plotting salied distance along the x axis; (3) "pings", plotting the ping indices along the x axis; (4) "compr", ; (5) "sparse", which plots only the time points given in t with no spaces where thera are gaps (ping 13 may follow directly after ping 4).

adds

is an optional list of variables overriding the variables in 'data'.

origin

***********************************

clock

is the position of the clock timing the frames, either given as a vector of length 3 representing the coordinates of the clock, as FALSE for no clock, or as one of

cex.clock

is the numeric character expansion value for the clock.

format.clock

is the format of the date and time, specified as the input to utim2ftim(). Default is "yyyy-mm-dd\nHH:MM:SS.FFF" resulting in date and time separated by a line break of width according to the value of 'lsp.clock'. All "\n" apparing in 'format.clock' cause a line break.

digits.clock

is a numeric specifying the number of digits of the seconds part of the time.

col.clock

is the color of the plotted time and date.

tres, xres, zres, rres, bres

Used when compressing data which are too large for plotting. Preferably create a compressed event by compr.event(), which places the compressed event in the same directory as the original event (named e.g. tsd_compr1), and then plot this event

funvbsc

is the function to apply in the compression, either given as function or as a string, in which case the strings "mean" and "median" represents fast versions of the functions with the corresponding names (sum()/length() and fastMedian(), respectively).

funt

is the same as funvbsc, but used for averaging vessel data in the new time/distance bins.

...

are inputs passed on to pplot2d.TSD, and cplot2d.TSD(). Also the direction of the light source in the plot is given here by the variables 'theta' and 'phi' (see rgl.light, default is to clear the light source).


arnejohannesholmin/cpplot3d documentation built on March 19, 2018, 9:15 a.m.