R/ReadSampleData.R

In leachth/ReadEKRaw_updated:

#function sampledata = readEKRaw_ReadSampledata(fid, sampledata)
#readEKRaw_ReadSampledata  Read EK/ES RAW0 datagram
#   sampledata = readEKRaw_ReadSampledata(fid, sampledate) returns a structure
#       containing the data from a EK/ES RAW0 datagram.
#
#   REQUIRED INPUT:
#               fid:    file handle id of raw file
#        sampledata:    pre-allocated sampledata data structure
#
#   OPTIONAL PARAMETERS:    None
#
#   OUTPUT:
#       Output is a data structure containing the RAW0 datagram data
#
#   REQUIRES:   None
#

#   Rick Towler
#   NOAA Alaska Fisheries Science Center
#   Midwater Assesment and Conservation Engineering Group
#   rick.towler@noaa.gov
#
#   Based on code by Lars Nonboe Andersen, Simrad.

#-

#sampledata.channel = fread(fid,1,'int16', 'l');
#mode_low = fread(fid,1,'int8', 'l');
#mode_high = fread(fid,1,'int8', 'l');
#sampledata.mode = 256 * mode_high + mode_low;
#sampledata.transducerdepth = fread(fid,1,'float32', 'l');
#sampledata.frequency = fread(fid,1,'float32', 'l');
#sampledata.transmitpower = fread(fid,1,'float32', 'l');
#sampledata.pulselength = fread(fid,1,'float32', 'l');
#sampledata.bandwidth = fread(fid,1,'float32', 'l');
#sampledata.sampleinterval = fread(fid,1,'float32', 'l');
#sampledata.soundvelocity = fread(fid,1,'float32', 'l');
#sampledata.absorptioncoefficient = fread(fid,1,'float32', 'l');
#sampledata.heave = fread(fid,1,'float32', 'l');
#sampledata.roll = fread(fid,1,'float32', 'l');
#sampledata.pitch = fread(fid,1,'float32', 'l');
#sampledata.temperature = fread(fid,1,'float32', 'l');
#sampledata.trawlupperdepthvalid = fread(fid,1,'int16', 'l');
#sampledata.trawlopeningvalid = fread(fid,1,'int16', 'l');
#sampledata.trawlupperdepth = fread(fid,1,'float32', 'l');
#sampledata.trawlopening = fread(fid,1,'float32', 'l');
#sampledata.offset = fread(fid,1,'int32', 'l');
#sampledata.count = fread(fid,1,'int32', 'l');

#sampledata.power = [];
#sampledata.alongship = [];
#sampledata.athwartship = [];
#if (sampledata.count > 0)
#    %  check length of arrays - grow if necessary
#    if (length(sampledata.power) < sampledata.count)
#        nSampAdd = sampledata.count - length(sampledata.power);
#        sampledata.power(end + 1:end + nSampAdd) = -999;
#        sampledata.alongship(end + 1:end + nSampAdd) = 0;
#        sampledata.athwartship(end + 1:end + nSampAdd) = 0;
#    end
#    if (sampledata.mode ~= 2)
#        power = fread(fid,sampledata.count,'int16', 'l');
#        %  power * 10 * log10(2) / 256
#        sampledata.power(1:sampledata.count) = (power * 0.011758984205624);
#    end
#    if (sampledata.mode > 1)
#        angle = fread(fid,[2 sampledata.count],'int8', 'l'); # this is two row matrix with the number of columns equal to the sample count, this fills a whole column first
#        sampledata.athwartship(1:sampledata.count) = angle(1,:)';
#        sampledata.alongship(1:sampledata.count) = angle(2,:)';
#    end
#end


# R Code
ReadSampleData = function(fid) {
  sampledata = list()
	sampledata$channel 					= readBin(con = fid, what = "integer", n = 1, size = 2, endian = "little")
	mode_low 							= readBin(con = fid, what = "integer", n = 1, size = 1, endian = "little")
	mode_high 							= readBin(con =fid, what = "integer", n = 1, size = 1, endian = "little")
	sampledata$mode 					= 256 * mode_high + mode_low
	sampledata$transducerdepth 			= readBin(con = fid, what = 'double', n = 1, size = 4, endian = "little")
	sampledata$frequency 				= readBin(con = fid, what = 'double', n = 1, size = 4, endian = "little")
	sampledata$transmitpower 			= readBin(con = fid, what = 'double', n = 1, size = 4, endian = "little")
	sampledata$pulselength 				= readBin(con = fid, what = 'double', n = 1, size = 4, endian = "little")
	sampledata$bandwidth 				= readBin(con = fid, what = 'double', n = 1, size = 4, endian = "little")
	sampledata$sampleinterval 			= readBin(con = fid, what = 'double', n = 1, size = 4, endian = "little")
	sampledata$soundvelocity 			= readBin(con = fid, what = 'double', n = 1, size = 4, endian = "little")
	sampledata$absorptioncoefficient 	= readBin(con = fid, what = 'double', n = 1, size = 4, endian = "little")
	sampledata$heave 					= readBin(con = fid, what = 'double', n = 1, size = 4, endian = "little")
	sampledata$roll 					= readBin(con = fid, what = 'double', n = 1, size = 4, endian = "little")
	sampledata$pitch 					= readBin(con = fid, what = 'double', n = 1, size = 4, endian = "little")
	sampledata$temperature 				= readBin(con = fid, what = 'double', n = 1, size = 4, endian = "little")
	sampledata$trawlupperdepthvalid 	= readBin(con = fid, what = "integer", n = 1, size = 2, endian = "little")
	sampledata$trawlopeningvalid 		= readBin(con = fid, what = "integer", n = 1, size = 2, endian = "little")
	sampledata$trawlupperdepth 			= readBin(con = fid, what = 'double', n = 1, size = 4, endian = "little")
	sampledata$trawlopening 			= readBin(con = fid, what = 'double', n = 1, size = 4, endian = "little")
	sampledata$offset 					= readBin(con = fid, what = 'integer', n = 1, size = 4, signed = TRUE, endian = "little")
	sampledata$count					= readBin(con = fid, what = 'integer', n = 1, size = 4, signed = TRUE, endian = "little")

	sampledata$power 					= c() # create empty vectors that get filled below
	sampledata$alongship 				= c()
	sampledata$athwartship 				= c()

	if (sampledata$mode !=2) {
		power = readBin(con = fid, what = "integer", n = sampledata$count, size = 2, endian = "little")
			# power * 10 * log10(2)/256
		sampledata$power = power * 0.011758984205624
	}

	if (sampledata$mode > 1) {
		angle = readBin(con = fid, what = "integer", n = 2 * sampledata$count, size = 1, endian = "little")
		anglematrix = matrix(angle, nrow = 2)
		sampledata$alongship =  anglematrix[1,] #1st column of the matrix
		sampledata$athwartship =  anglematrix[2,] # 2nd column of the matrix
	}
  sampledata
}