function adr2cdf(advFile, cdfFile, DataType, minBurst, maxBurst);
% ADR2CDF - Converts Sontek ADV files to netCDF format
% adr2cdf(infile, outfile, DataType, minBurst, maxBurst);
%
% where:
%		advFile	= input Sontek ADV file (ex: 'CA1001.adr')
%		cdfFile = netCDF file name (ex: 'C1001.cdf')
%       DataType = 'Burst' | 'Stats' | 'Both'
%		minBusrt = Burst number at which to start converting
%		maxBurst = Burst number at which to stop converting
%
% note that if both stats and bursts are requested, time will only be
% stored as a [burst sample] shape
%
% Version 2-Apr-2004
%   Add batch capability
% Version 15-Mar-2004
%   will not work with multiple sampling schemes
%   generated time stamps for each sample when burst data is requested
%   removed pressure normalization, fixed conversion to frequency
% Version 04-Dec-2003
 

% Proposed changes
% 1) acommodate the three different sampling schemes... record and use the
% sample rate in each burst header

% Written by Andree L. Ramsey
% Heavily based on adr2mat.m written by Jingping Xu
% for the U.S. Geological Survey
% Marine and Coastal Program
% Woods Hole Center, Woods Hole, MA
% http://woodshole.er.usgs.gov/
% Please report bugs to aramsey@usgs.gov
%
% netCDF attributes and variable names follow EPIC conventions
%
% information on netCDF may be obtained at
% http://www.unidata.ucar.edu
% it's free!!
%
%

% need valid ranges for CTD data
% Someone please check CTD data- seems good to me
% Someone please check OBS data - seems good to me
% what about addtional samples per burst? Can have three sets? Need test
% data
% add batch ability when all processing files are completed for ADVToolbox

prog_ver = 'Beta Limited Burst Version 15-Mar-2004';
disp(['adr2cdf_beta_burst.m version ',prog_ver]);
 
tic
if running(batch)
    advFile = get(batch);
    eval(['advFile = ' advFile ';'])
    cdfFile = get(batch);
    eval(['cdfFile = ' cdfFile ';'])
    DataType = get(batch);
    eval(['DataType = ' DataType ';'])
    minBurst = get(batch);
    eval(['minBurst = ' minBurst ';'])
    maxBurst = get(batch);
    eval(['maxBurst = ' maxBurst ';'])
    %     def     = {'0','01-jan-2003','01-jan-2004','0','0','0','0'};
    batchline = get(batch);
    eval(['metadata{1} = ' batchline ';']) % mooring number
    batchline = get(batch);
    eval(['metadata{2} = ' batchline ';']) % deployment date
    batchline = get(batch);
    eval(['metadata{3} = ' batchline ';']) % recovery date
    batchline = get(batch);
    eval(['metadata{4} = ' batchline ';']) % Longitude, decimal degrees, W is negative
    batchline = get(batch);
    eval(['metadata{5} = ' batchline ';']) % Latitude, decimal degrees
    batchline = get(batch);
    eval(['metadata{6} = ' batchline ';']) % Magnetic Var.
    batchline = get(batch);
    eval(['metadata{7} = ' batchline ';']) % Probe offset, m
else
    % Open file and determine file size
    if nargin < 1, help(mfilename), end
    if nargin < 1, advFile = ''; end
    if nargin < 2, cdfFile = ''; end
    if nargin < 3, DataType = []; end
    if nargin < 4, minBurst = ''; end
    if nargin < 5, maxBurst = ''; end
end

if isempty(advFile), advFile = '*'; end
if isempty(cdfFile), cdfFile = '*'; end

% Get raw ADV filename.
if any(advFile == '*')
	[theFile, thePath] = uigetfile(advFile, 'Select ADV Data File:');
	if ~any(theFile), return, end

	if thePath(end) ~= filesep, thePath(end+1) = filesep; end
	advFile = [thePath theFile];
end

if isempty(DataType),
    % Choice to create a stats only flie, a data only file, or both
    DataType = menu('What type of file do you want to create?','Statistics Only','Burst Data Only','Burst and Statistics Data');
    % DataType = 1 is stats only; DataType = 2 is burst data only; DataType = 3 is both
    if DataType == 1
        disp(' ')
        disp('Only the statistics data will be converted')
    elseif DataType == 2
        disp(' ')
        disp('Only the burst data will be converted')
    elseif DataType ==3
        disp(' ')
        disp('Both the burst and the statistics data will be converted')
    end
elseif ischar(DataType),
    switch DataType,
        case 'Stats', DataType = 1;
        case 'Burst', DataType = 2;
        otherwise, DataType = 3;
    end
end

[path,name,ext,ver]=fileparts(advFile);

% Get ADV netCDF filename.
switch DataType
    case 1
        if any(cdfFile == '*')
            suggest=[name 's.cdf'];
			[theFile, thePath] = uiputfile(suggest, 'Save ADV netCDF Statistics File As:');
			if ~any(theFile), return, end
			if thePath(end) ~= filesep, thePath(end+1) = filesep; end
			cdfFile = [thePath theFile];
		end
        
    case 2
        if any(cdfFile == '*')
            suggest=[name 'b.cdf'];
			[theFile, thePath] = uiputfile(suggest, 'Save ADV netCDF Burst File As:');
			if ~any(theFile), return, end
			if thePath(end) ~= filesep, thePath(end+1) = filesep; end
			cdfFile = [thePath theFile];
		end
        
    case 3
		if any(cdfFile == '*')
            suggest=[name '.cdf'];
			[theFile, thePath] = uiputfile(suggest, 'Save ADV netCDF Whole Data File As:');
			if ~any(theFile), return, end
			if thePath(end) ~= filesep, thePath(end+1) = filesep; end
			cdfFile = [thePath theFile];
		end
end %end switch

fid=fopen(advFile);
fseek(fid,0,1);
filesize=ftell(fid);
disp(sprintf('The file is %d bytes',filesize))
fseek(fid,0,-1); %rewind file

%Create netCDF file
nc=netcdf(cdfFile,'clobber');

%Read and write global attributes from the hardware config block (441 bytes)
% Hardware Configuration (24 bytes)
nc.CreationDate = datestr(now); 
nc.cpuSoftWareVerNum = (fread(fid,1,'uchar')) * 0.1;
nc.dspSoftWareVerNum = (fread(fid,1,'uchar')) * 0.1;
nc.Inst_Type = 'Sontek ADV';
a = fread(fid,6,'char');
ADVType = {'10MHz_5cm','10MHz_10cm','OCEAN'}; %Using Jingping's code, this seems to be reading incorrectly
%nc.ADVType = ADVType{1+a(1)};
SensorOrientation = {'down','up','side'};
nc.SensorOrietnation = SensorOrientation{1+a(2)};
CompassInstalled = {'No','Yes'};
nc.CompassInstalled = CompassInstalled{1+a(3)};
RecorderInstalled = {'No','Yes'};
nc.RecorderInstalled = RecorderInstalled{1+a(4)};
TempInstalled = {'No','Yes'};
nc.TempInstalled = TempInstalled{1+a(5)};
PressInstalled = {'No','Yes'};
nc.PressInstalled = PressInstalled{1+a(6)};
clear PressInstalled TempInstalled RecorderInstalled CompassInstalled SensorOrientation ADVType a

nc.PressScale = fread(fid,1,'int32');
nc.PressOffset = fread(fid,1,'int32');
nc.CompassOffset = fread(fid,1,'int16');
nc.PressFreqOffset = fread(fid,1,'char');

a = fread(fid,2,'char');
ExtSensorInstalled = {'None','Standard','OBS_Ch1','OBS_Ch2','OBS_Ch3'};
nc.ExtSenosrInstalled = ExtSensorInstalled{1+a(1)};
ExtPressInstalled = {'Paros','Druck','ParosFreq'};
nc.ExtPressInstalled = ExtPressInstalled{a(2)};
clear ExtPressInstalled ExtSensorInstalled a

nc.PressScale_2 = fread(fid,1,'int16');
a = fread(fid,1,'char');
CTDInstalled = {'MicroCat CTD','LISST'};
nc.CTDInstalled = CTDInstalled{a};
clear CTDInstalled a

% Probe Confirguration (164 bytes)
fseek(fid,10,0);
a=fread(fid,[1,6],'char');
a(a==0)=[];
nc.SerialNum=char(a); 

% This is from adr2mat.m written by Jingping Xu
ProbeConfiguration = {'Down XYZ 5cm','Down XYZ 5cm','Up XYZ 5cm','Side XYZ 5cm',...
      'Down XZ 5cm','Up XZ 5cm','Side XY 5cm','Cable XYZ 5cm',...
      'Down XYZ 10cm','Up XYZ 10cm','Side XYZ 10cm',...
      'Down XZ 10cm','Up XZ 10cm','Side XY 10cm','Cable XYZ 10cm',...
      'Ocean Probe','Micro Down XYZ 5cm','Micro Up XYZ 5cm',...
      'Micro Side XYZ 5cm','Micro Down XZ 5cm','Micro Up XZ 5cm',...
      'Micro Sdie XY 5cm','Micro Cable XYZ 5cm'};
ProbeIndex = [0 1 2 3 4 5 6 10 17 18 19 20 21 22 26 41 81 82 83 84 85 86 90];
a=fread(fid,2,'char');
index=find(ProbeIndex==a(1));
nc.ProbeConfiguration=ProbeConfiguration{index};
clear ProbeIndex a index ProbeConfiguration

fseek(fid,102,0);
nc.xfercoeff=fread(fid,[3,3],'float32');
nc.xmtrecdist=fread(fid,1,'float32');
nc.calcw=fread(fid,1,'float32');

% Deployment Parameters (253 bytes)

nc.ConfigType = fread(fid,1,'uchar');
nc.ConfigVer = fread(fid,1,'uchar');
Nbytes = fread(fid,1,'uint16');
clear Nbytes
% Skip Configuration time
fseek(fid,8,0);
nc.Temp = fread(fid,1,'int16') * 0.1; %degrees Celcius
nc.Salinity = fread(fid,1,'int16') * 0.1; %ppt
nc.CW = fread(fid,1,'int16') * 0.1; %m/s
a = fread(fid,1,'uchar');
TempMode = {'User Value','Measured'};
nc.TempMode = TempMode{a+1}; 
nc.VelRangeIndex = fread(fid,1,'uchar');
a = fread(fid,1,'char');
SyncMode = {'Diable','Start','Sample'};
nc.SyncMode = SyncMode{a+1}; 
a = fread(fid,1,'char');
CoordSystem = {'Beam','XYZ','ENU'};
nc.CoordSystem = CoordSystem{a+1}; 
SampleRate = fread(fid,[1,3],'uint16') *0.01; %Hz
nc.SampleRate = SampleRate; 
nc.BurstInterval = fread(fid,[1,3],'uint16');  %seconds
nSamples = fread(fid,[1,3],'uint16');
nc.SamplesPerBurst = nSamples;
clear CoordSystem SyncMode TempMode a

%recored data for sampling 1
recordedData = fread(fid,1,'uchar'); 
recdata = dec2bin(recordedData);
b = '00000000';
b(8-length(recdata)+1:8) = recdata;
rflag = str2num(b(:));
bitsize = [0 3 4 0 0 4 6 4];
BytesPerSample = 8+sum(bitsize(rflag>0));
b = fliplr(b);

fseek(fid,1,0);
%%%%%   Don't know if this is needed or not??
%recorded data for sampling 2
%recordedData = fread(fid,1,'uchar'); 
%recdata = dec2bin(recordedData);
%b = '00000000';
%b(8-length(recdata)+1:8) = recdata;
%rflag = str2num(b(:));
%bitsize = [0 3 4 0 0 4 6 4];
%BytesPerSample2 = 8+sum(bitsize(rflag>0));

fseek(fid,1,0);
%recorded data for sampling 3
%recordedData = fread(fid,1,'uchar'); 
%recdata = dec2bin(recordedData);
%b = '00000000';
%b(8-length(recdata)+1:8) = recdata;
%rflag = str2num(b(:));
%bitsize = [0 3 4 0 0 4 6 4];
%BytesPerSample3 = 8+sum(bitsize(rflag>0));

%BytesPerSample = BytesPerSample1 + BytesPerSample2 + BytesPerSample3;

a = fread(fid,1,'char');
OutMode = {'Auto','Polled'};
nc.OutMode = OutMode {a+1};
a = fread(fid,1,'char');
OutFormat = {'Binary','Ascii'};
nc.OutFormat = OutFormat {a+1}; 
a = fread(fid,1,'char');
RecorderEnabled = {'Disabled','Enabled'};
nc.RecorderEnabled = RecorderEnabled {a+1}; 
a = fread(fid,1,'char');
RecorderMode = {'Normal Mode','Buffer Mode'};
nc.RecorderMode = RecorderMode {a+1}; 
a = fread(fid,1,'char');
DeploymentMode = {'Disabled','Enabled'};
nc.DeploymentMode = DeploymentMode {a+1}; 
clear DeploymentMode RecorderMode RecorderEnabled OutFormat OutMode a

DeploymentName = char(fread(fid,[1,9],'char')); 
DN = cellstr(DeploymentName);newDN = DN{:}; %gets rid of blank spaces
nc.DeploymentName = newDN; 
clear newDN DN DeploymentName

year = fread(fid,1,'int16');
day = fread(fid,1,'char');
month = fread(fid,1,'char');
minute = fread(fid,1,'char');
hour = fread(fid,1,'char');
hs = fread(fid,1,'char');
sec = fread(fid,1,'char');
nc.BeginDeployment = [day month year hour minute sec hs];
clear year day month minute hour hs sec

Comment1 = char(fread(fid,[1,60],'char'));
c1 = cellstr(Comment1);newc1 = c1{:}; %gets rid of blanks spaces
Comment2 = char(fread(fid,[1,60],'char'));
c2 = cellstr(Comment2);newc2 = c2{:};  %gets rid of blank spaces
Comment3 = char(fread(fid,[1,60],'char'));
c3 = cellstr(Comment3);newc3 = c3{:}; %gets rid of blanks spaces
nc.ADRComments = [newc1 newc2 newc3];  
clear Comment* c1 c2 c3 newc*

AutoSleep = fread(fid,1,'char'); 
clear AutoSleep
fseek(fid,7,0); %skip spare

if ~running(batch)
    %%  User Input Metadta
    %   Get Mooring Information
    prompt  = {'Enter 4-digit mooring number:',...
            'Enter the deployment date (dd-mmm-yyyy):',...
            'Enter the recovery date (dd-mmm-yyyy):',...
            'Enter the Longitude (decimal degrees):',...
            'Enter the Latitude (decimal degrees):',...
            'Enter the magnetic variation at the mooring location in degrees',...
            'Enter the distance between the ADV probe and the sea bed in meters:'};
    def     = {'0','01-jan-2003','01-jan-2004','0','0','0','0'};
    title   = 'Input metadata from the mooring data';
    lineNo  = 1;
    metadata  = inputdlg(prompt,title,lineNo,def);
    nc.Mooring = metadata{1};
    nc.Deployment_date = metadata{2};
    nc.Recovery_date = metadata{3};
    nc.Longitude = str2num(metadata{4});
    nc.Latitude = str2num(metadata{5});
    nc.mag_var = str2num(metadata{6});
    nc.probe_offset = str2num(metadata{7});
else
    nc.Mooring = metadata{1};
    nc.Deployment_date = metadata{2};
    nc.Recovery_date = metadata{3};
    nc.Longitude = metadata{4};
    nc.Latitude = metadata{5};
    nc.mag_var = metadata{6};
    nc.probe_offset = metadata{7};
end

%% Define dimensions
tBursts = floor((filesize-441)/(BytesPerSample*nSamples(1)));
disp(['There are approximately ',num2str(tBursts),' bursts in the file'])
disp(['Each burst contains ',num2str(nSamples(1)),' samples'])

% Marinna changed this section to accommodate partial bursts and batch input
if exist('minBurst')~=1, minBurst = []; burstdim=1; else burstdim=0; end
if exist('maxBurst')~=1, maxBurst = []; burstdim=1; else burstdim=0; end
if ~isempty(minBurst) & ~isempty(maxBurst)
    nBursts = (maxBurst - minBurst) + 1;
    disp([num2str(nBursts),' bursts will be processed'])
else
    nBursts = floor((filesize-441)/(BytesPerSample*nSamples(1)));  
    minBurst = 1;
    maxBurst = nBursts;
    disp([num2str(nBursts),' bursts will be processed'])
end
disp(sprintf('Writing bursts %d to %d to %s', minBurst, maxBurst, cdfFile))
disp('Now defining netCDF file, this may take some time...')

if burstdim,
    % user wants all the bursts
    nc('burst') = nBursts; % this will take the time to write the entire filespace to disk first
else
    % yser wants only part of the bursts
    nc('burst') = 0; % this is faster if only a subset of the bursts are desired
end
nc('sample') = nSamples(1);
nc('axis') = 3;
clear tBursts

%% Define Variables and attributes
nc{'burstNum'} = ncfloat('burst'); 
nc{'burstNum'}.units = ncchar('counts');
nc{'burstNum'}.samplerate = SampleRate;
nc{'burstNum'}.sampleperburst = nSamples;

% removed by Marinna
% nc{'time'} = ncdouble('burst'); 
% nc{'time'}.units = ncchar('decimal days');
% nc{'time'}.long_name = ncchar('JULIAN DAYS');
% nc{'time'}.FillValue_ = ncdouble(1e+035);
% nc{'time'}.epic_code = nclong(627);
% nc{'time'}.valid_min = nclong(0);

switch DataType
    case 1
        % added by Marinna
        nc{'time'} = ncdouble('burst'); 
        nc{'time'}.units = ncchar('decimal days');
        nc{'time'}.long_name = ncchar('JULIAN DAYS');
        nc{'time'}.FillValue_ = ncdouble(1e+035);
        nc{'time'}.epic_code = nclong(627);
        nc{'time'}.valid_min = nclong(0);
        
        nc{'time2'} = ncdouble('burst'); 
        nc{'time2'}.FORTRAN_format = ncchar('F10.2');
        nc{'time2'}.units = ncchar('msec');
        nc{'time2'}.type = ncchar('UNEVEN');
        nc{'time2'}.long_name = ncchar('msec since 0:00 GMT');
        nc{'time2'}.FillValue_ = ncdouble(1e+035);
        nc{'time2'}.epic_code = nclong(624);
        nc{'time2'}.valid_min = nclong(0);
        
        nc{'MeanAmp'} = ncfloat('burst','axis');
        nc{'MeanAmp'}.long_name = ncchar('Mean Amplitude for Burst');
        nc{'MeanAmp'}.units = ncchar('counts');
        nc{'MeanAmp'}.valid_range = ncfloat([-32768 32767]);
        nc{'MeanAmp'}.FillValue_ = ncfloat(1.0e+035);
        
        nc{'MeanCorr'} = ncfloat('burst','axis');
		nc{'MeanCorr'}.long_name = ncchar('Mean Correlation for Burst');
		nc{'MeanCorr'}.units = ncchar('counts');
		nc{'MeanCorr'}.valid_range = ncfloat([-32768 32768]);
		nc{'MeanCorr'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'MeanHeading'} = ncfloat('burst');
		nc{'MeanHeading'}.long_name = ncchar('Mean Heading for Burst');
		nc{'MeanHeading'}.units = ncchar('degrees');
		nc{'MeanHeading'}.valid_range = ncfloat([0 359.9999]);
		nc{'MeanHeading'}.FillValue_ = ncfloat(1.0e+035);

		nc{'MeanPitch'} = ncfloat('burst');
		nc{'MeanPitch'}.long_name = ncchar('Mean Pitch for Burst');
		nc{'MeanPitch'}.units = ncchar('degrees');
		nc{'MeanPitch'}.valid_range = ncfloat([-20 20]);
		nc{'MeanPitch'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'MeanRoll'} = ncfloat('burst');
		nc{'MeanRoll'}.long_name = ncchar('Mean Roll for Burst');
		nc{'MeanRoll'}.units = ncchar('degrees');
		nc{'MeanRoll'}.valid_range = ncfloat([-20 20]);
		nc{'MeanRoll'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'MeanTemperature'} = ncfloat('burst'); 
		nc{'MeanTemperature'}.units = ncchar('degrees');
		nc{'MeanTemperature'}.long_name = ncchar('Mean Transducer Temperature for Burst');
		nc{'MeanTemperature'}.FillValue_ = ncfloat(1.0e+035);
		nc{'MeanTemperature'}.valid_range = ncfloat([-5 40]);
		
		nc{'MeanPressure'} = ncfloat('burst'); 
		nc{'MeanPressure'}.long_name = ncchar('Mean Pressure for Burst');
		nc{'MeanPressure'}.units = ncchar('counts');
		nc{'MeanPressure'}.valid_range = ncfloat([0 4095]);
		nc{'MeanPressure'}.FillValue_ = ncfloat(1.0e+035);

		nc{'MeanVelx'} = ncfloat('burst');
		nc{'MeanVelx'}.long_name = ncchar('Mean velocity in instrument coordinate x for Burst');
		nc{'MeanVelx'}.units = ncchar('cm s-1');
		nc{'MeanVelx'}.valid_range = ncfloat([-32768 32767]);
		nc{'MeanVelx'}.FillValue_ = ncfloat(1.0e+035);

		nc{'MeanVely'} = ncfloat('burst');
		nc{'MeanVely'}.long_name = ncchar('Mean velocity in instrument coordinate y for Burst');
		nc{'MeanVely'}.units = ncchar('cm s-1');
		nc{'MeanVely'}.valid_range = ncfloat([-32768 32767]);
		nc{'MeanVely'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'MeanVelz'} = ncfloat('burst');
		nc{'MeanVelz'}.long_name = ncchar('Mean velocity in instrument coordinate z for Burst');
		nc{'MeanVelz'}.units = ncchar('cm s-1');
		nc{'MeanVelz'}.valid_range = ncfloat([-32768 32767]);
		nc{'MeanVelz'}.FillValue_ = ncfloat(1.0e+035);

		nc{'StdAmp'} = ncfloat('burst','axis');
		nc{'StdAmp'}.long_name = ncchar('Amplitude Standard Deviation for Burst');
		nc{'StdAmp'}.units = ncchar('counts');
		nc{'StdAmp'}.valid_range = ncfloat([-32768 32767]);
		nc{'StdAmp'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'StdCorr'} = ncfloat('burst','axis');
		nc{'StdCorr'}.long_name = ncchar('Correlation Standard Deviation for Burst');
		nc{'StdCorr'}.units = ncchar('counts');
		nc{'StdCorr'}.valid_range = ncfloat([-32768 32768]);
		nc{'StdCorr'}.FillValue_ = ncfloat(1.0e+035);

		nc{'StdHeading'} = ncfloat('burst');
		nc{'StdHeading'}.long_name = ncchar('Heading Standard Deviation for Burst');
		nc{'StdHeading'}.units = ncchar('degrees');
		nc{'StdHeading'}.valid_range = ncfloat([0 359.9999]);
		nc{'StdHeading'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'StdPitch'} = ncfloat('burst');
		nc{'StdPitch'}.long_name = ncchar('Pitch Standard Deviation for Burst');
		nc{'StdPitch'}.units = ncchar('degrees');
		nc{'StdPitch'}.valid_range = ncfloat([-20 20]);
		nc{'StdPitch'}.FillValue_ = ncfloat(1.0e+035);

		nc{'StdRoll'} = ncfloat('burst');
		nc{'StdRoll'}.long_name = ncchar('Roll Standard Deviation for Burst');
		nc{'StdRoll'}.units = ncchar('degrees');
		nc{'StdRoll'}.valid_range = ncfloat([-20 20]);
		nc{'StdRoll'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'StdTemperature'} = ncfloat('burst'); 
		nc{'StdTemperature'}.units = ncchar('degrees');
		nc{'StdTemperature'}.long_name = ncchar('Transducer Temperature Standard Deviation for Burst');
		nc{'StdTemperature'}.FillValue_ = ncfloat(1.0e+035);
		nc{'StdTemperature'}.valid_range = ncfloat([-5 40]);

		nc{'StdPressure'} = ncfloat('burst'); 
		nc{'StdPressure'}.long_name = ncchar('Pressure Standard Deviation for Burst');
		nc{'StdPressure'}.units = ncchar('counts');
		nc{'StdPressure'}.valid_range = ncfloat([0 4095]);
		nc{'StdPressure'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'StdVelx'} = ncfloat('burst');
		nc{'StdVelx'}.long_name = ncchar('Velocity Std Deviation in instrument coordinate x for Burst');
		nc{'StdVelx'}.units = ncchar('cm s-1');
		nc{'StdVelx'}.valid_range = ncfloat([-32768 32767]);
		nc{'StdVelx'}.FillValue_ = ncfloat(1.0e+035);

		nc{'StdVely'} = ncfloat('burst');
		nc{'StdVely'}.long_name = ncchar('Velocity Std Deviation in instrument coordinate y for Burst');
		nc{'StdVely'}.units = ncchar('cm s-1');
		nc{'StdVely'}.valid_range = ncfloat([-32768 32767]);
		nc{'StdVely'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'StdVelz'} = ncfloat('burst');
		nc{'StdVelz'}.long_name = ncchar('Velocity Std Deviation in instrument coordinate z for Burst');
		nc{'StdVelz'}.units = ncchar('cm s-1');
		nc{'StdVelz'}.valid_range = ncfloat([-32768 32767]);
		nc{'StdVelz'}.FillValue_ = ncfloat(1.0e+035);

		nc{'soundspd'} = ncfloat('burst');
		nc{'soundspd'}.long_name = ncchar('sound velocity (m/s)');
		nc{'soundspd'}.units = ncchar('m s-1');
		nc{'soundspd'}.FillValue_ = ncfloat(1.0e+035);
		nc{'soundspd'}.epic_code = nclong(80);
		nc{'soundspd'}.valid_range = nclong([1400 1600]);
        
    case 2
        % added by Marinna
        nc{'time'} = ncdouble('burst','sample'); 
        nc{'time'}.units = ncchar('decimal days');
        nc{'time'}.long_name = ncchar('JULIAN DAYS');
        nc{'time'}.FillValue_ = ncdouble(1e+035);
        nc{'time'}.epic_code = nclong(627);
        nc{'time'}.valid_min = nclong(0);
        
        nc{'time2'} = ncdouble('burst','sample'); 
        nc{'time2'}.FORTRAN_format = ncchar('F10.2');
        nc{'time2'}.units = ncchar('msec');
        nc{'time2'}.type = ncchar('UNEVEN');
        nc{'time2'}.long_name = ncchar('msec since 0:00 GMT');
        nc{'time2'}.FillValue_ = ncdouble(1e+035);
        nc{'time2'}.epic_code = nclong(624);
        nc{'time2'}.valid_min = nclong(0);

        nc{'Vx'} = ncfloat('burst','sample'); 
		nc{'Vx'}.units = ncchar('cm s-1');
		nc{'Vx'}.long_name = ncchar('velocity in instrument coordinate x');
		nc{'Vx'}.FillValue_ = nclong(1.0e+035);
		nc{'Vx'}.valid_range = ncfloat([-32768 32767]);

		nc{'Vy'} = ncfloat('burst','sample'); 
		nc{'Vy'}.units = ncchar('cm s-1');
		nc{'Vy'}.long_name = ncchar('velocity in instrument coordinate y');
		nc{'Vy'}.FillValue_ = nclong(1.0e+035);
		nc{'Vy'}.valid_range = ncfloat([-32768 32767]);

		nc{'Vz'} = ncfloat('burst','sample'); 
		nc{'Vz'}.units = ncchar('cm s-1');
		nc{'Vz'}.long_name = ncchar('velocity in instrument coordinate z');
		nc{'Vz'}.FillValue_ = nclong(1.0e+035);
		nc{'Vz'}.valid_range = ncfloat([-32768 32767]);

		nc{'amp'} = ncfloat('burst','sample','axis'); 
		nc{'amp'}.units = ncchar('');
		nc{'amp'}.long_name = ncchar('Beam amplitude');
		nc{'amp'}.FillValue_ = ncfloat(1.0e+035);
		nc{'amp'}.valid_range = ncfloat([-32768 32767]);
         
		nc{'corr'} = ncfloat('burst','sample','axis'); 
		nc{'corr'}.units = ncchar('');
		nc{'corr'}.long_name = ncchar('Beam correlation');
		nc{'corr'}.FillValue_ = ncfloat(1.0e+035);
		nc{'corr'}.valid_range = ncfloat([-32768 32767]);
		
		nc{'heading'} = ncfloat('burst','sample'); 
		nc{'heading'}.units = ncchar('degrees');
		nc{'heading'}.long_name = ncchar('INST Heading');
		nc{'heading'}.epic_code = nclong(1215);
		nc{'heading'}.FillValue_ = ncfloat(1.0e+035);
		nc{'heading'}.valid_range = ncfloat([0 359.9999]);
         
		nc{'pitch'} = ncfloat('burst','sample'); 
		nc{'pitch'}.units = ncchar('degrees');
		nc{'pitch'}.long_name = ncchar('INST Pitch');
		nc{'pitch'}.epic_code = nclong(1216);
		nc{'pitch'}.FillValue_ = ncfloat(1.0e+035);
		nc{'pitch'}.valid_range = ncfloat([-20 20]);
         
		nc{'roll'} = ncfloat('burst','sample'); 
		nc{'roll'}.units = ncchar('degrees');
		nc{'roll'}.long_name = ncchar('INST roll');
		nc{'roll'}.epic_code = nclong(1217);
		nc{'roll'}.FillValue_ = ncfloat(1.0e+035);
		nc{'roll'}.valid_range = ncfloat([-20 20]);
		
		nc{'temperature'} = ncfloat('burst','sample'); 
		nc{'temperature'}.units = ncchar('degrees');
		nc{'temperature'}.long_name = ncchar('ADV Transducer Temperature');
		nc{'temperature'}.epic_code = nclong(20);
		nc{'temperature'}.FillValue_ = ncfloat(1.0e+035);
		nc{'temperature'}.valid_range = ncfloat([-5 40]);

		nc{'pressure'} = ncfloat('burst','sample'); 
		nc{'pressure'}.long_name = ncchar('PRESSURE');
		nc{'pressure'}.units = ncchar('counts');
		nc{'pressure'}.epic_code = nclong(1);
		nc{'pressure'}.valid_range = ncfloat([0 4095]);
		nc{'pressure'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'extsensor1'} = ncfloat('burst','sample'); 
		nc{'extsensor1'}.units = ncchar('counts');
		nc{'extsensor1'}.long_name = ncchar('raw data from external sensor channel 1');
		nc{'extsensor1'}.valid_range = ncfloat([0 10000]);
		nc{'extsensor1'}.FillValue_ = ncfloat(1.0e+035);

		nc{'extsensor2'} = ncfloat('burst','sample'); 
		nc{'extsensor2'}.units = ncchar('counts');
		nc{'extsensor2'}.long_name = ncchar('raw data from external sensor channel 2');
		nc{'extsensor2'}.valid_range = ncfloat([0 10000]);
		nc{'extsensor2'}.FillValue_ = ncfloat(1.0e+035);
         
		nc{'extpress'} = ncfloat('burst','sample');
		nc{'extpress'}.long_name = ncchar('raw data from external pressure sensor');
		nc{'extpress'}.units = ncchar('counts');
		nc{'extpress'}.valid_range = ncfloat([0 10000]);
		nc{'extpress'}.FillValue_ = ncfloat(1.0e+035);

		nc{'extpressfreq'} = ncfloat('burst','sample'); 
		nc{'extpressfreq'}.long_name = ncchar('pressure frequency');
		nc{'extpressfreq'}.units = ncchar('Hz');
		nc{'extpressfreq'}.epic_code = nclong(1);
		nc{'extpressfreq'}.valid_range = ncfloat([10000 40000]);
		nc{'extpressfreq'}.FillValue_ = ncfloat(1.0e+035);

		nc{'CTD_temp'} = ncfloat('burst');
		nc{'CTD_temp'}.long_name = ncchar('CTD Temperature Probe');
		nc{'CTD_temp'}.units = ncchar('Degrees Celcius');
		nc{'CTD_temp'}.valid_range = ncfloat([-5 40]);
		nc{'CTD_temp'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'CTD_cond'} = ncfloat('burst');
		nc{'CTD_cond'}.long_name = ncchar('CTD Conductivity Probe');
		nc{'CTD_cond'}.units = ncchar('siemens');
		%nc{'CTD_cond'}.valid_range = ncfloat([ ]);  NEED
		nc{'CTD_cond'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'CTD_press'} = ncfloat('burst');
		nc{'CTD_press'}.long_name = ncchar('CTD Pressure Sensor');
		nc{'CTD_press'}.units = ncchar('dbar');
		%nc{'CTD_press'}.valid_range = ncfloat([ ]);  NEED
		nc{'CTD_press'}.FillValue_ = ncfloat(1.0e+035);

		nc{'CTD_sal'} = ncfloat('burst');
		nc{'CTD_sal'}.long_name = ncchar('CTD Salinity Reading');
		nc{'CTD_sal'}.units = ncchar('PSU');
		%nc{'CTD_sal'}.valid_range = ncfloat([ ]);  NEED
		nc{'CTD_sal'}.FillValue_ = ncfloat(1.0e+035);
        
    case 3
        % added by Marinna
        nc{'time'} = ncdouble('burst','sample'); 
        nc{'time'}.units = ncchar('decimal days');
        nc{'time'}.long_name = ncchar('JULIAN DAYS');
        nc{'time'}.FillValue_ = ncdouble(1e+035);
        nc{'time'}.epic_code = nclong(627);
        nc{'time'}.valid_min = nclong(0);
        
        nc{'time2'} = ncdouble('burst','sample'); 
        nc{'time2'}.FORTRAN_format = ncchar('F10.2');
        nc{'time2'}.units = ncchar('msec');
        nc{'time2'}.type = ncchar('UNEVEN');
        nc{'time2'}.long_name = ncchar('msec since 0:00 GMT');
        nc{'time2'}.FillValue_ = ncdouble(1e+035);
        nc{'time2'}.epic_code = nclong(624);
        nc{'time2'}.valid_min = nclong(0);

		nc{'Vx'} = ncfloat('burst','sample'); 
		nc{'Vx'}.units = ncchar('cm s-1');
		nc{'Vx'}.long_name = ncchar('velocity in instrument coordinate x');
		nc{'Vx'}.FillValue_ = nclong(1.0e+035);
		nc{'Vx'}.valid_range = ncfloat([-32768 32767]);

		nc{'Vy'} = ncfloat('burst','sample'); 
		nc{'Vy'}.units = ncchar('cm s-1');
		nc{'Vy'}.long_name = ncchar('velocity in instrument coordinate y');
		nc{'Vy'}.FillValue_ = nclong(1.0e+035);
		nc{'Vy'}.valid_range = ncfloat([-32768 32767]);

		nc{'Vz'} = ncfloat('burst','sample'); 
		nc{'Vz'}.units = ncchar('cm s-1');
		nc{'Vz'}.long_name = ncchar('velocity in instrument coordinate z');
		nc{'Vz'}.FillValue_ = nclong(1.0e+035);
		nc{'Vz'}.valid_range = ncfloat([-32768 32767]);

		nc{'amp'} = ncfloat('burst','sample','axis'); 
		nc{'amp'}.units = ncchar('');
		nc{'amp'}.long_name = ncchar('Beam amplitude');
		nc{'amp'}.FillValue_ = ncfloat(1.0e+035);
		nc{'amp'}.valid_range = ncfloat([-32768 32767]);
         
		nc{'corr'} = ncfloat('burst','sample','axis'); 
		nc{'corr'}.units = ncchar('');
		nc{'corr'}.long_name = ncchar('Beam correlation');
		nc{'corr'}.FillValue_ = ncfloat(1.0e+035);
		nc{'corr'}.valid_range = ncfloat([-32768 32767]);
		
		nc{'heading'} = ncfloat('burst','sample'); 
		nc{'heading'}.units = ncchar('degrees');
		nc{'heading'}.long_name = ncchar('INST Heading');
		nc{'heading'}.epic_code = nclong(1215);
		nc{'heading'}.FillValue_ = ncfloat(1.0e+035);
		nc{'heading'}.valid_range = ncfloat([0 359.9999]);
         
		nc{'pitch'} = ncfloat('burst','sample'); 
		nc{'pitch'}.units = ncchar('degrees');
		nc{'pitch'}.long_name = ncchar('INST Pitch');
		nc{'pitch'}.epic_code = nclong(1216);
		nc{'pitch'}.FillValue_ = ncfloat(1.0e+035);
		nc{'pitch'}.valid_range = ncfloat([-20 20]);
         
		nc{'roll'} = ncfloat('burst','sample'); 
		nc{'roll'}.units = ncchar('degrees');
		nc{'roll'}.long_name = ncchar('INST roll');
		nc{'roll'}.epic_code = nclong(1217);
		nc{'roll'}.FillValue_ = ncfloat(1.0e+035);
		nc{'roll'}.valid_range = ncfloat([-20 20]);
		
		nc{'temperature'} = ncfloat('burst','sample'); 
		nc{'temperature'}.units = ncchar('degrees');
		nc{'temperature'}.long_name = ncchar('ADV Transducer Temperature');
		nc{'temperature'}.epic_code = nclong(20);
		nc{'temperature'}.FillValue_ = ncfloat(1.0e+035);
		nc{'temperature'}.valid_range = ncfloat([-5 40]);

		nc{'pressure'} = ncfloat('burst','sample'); 
		nc{'pressure'}.long_name = ncchar('PRESSURE');
		nc{'pressure'}.units = ncchar('counts');
		nc{'pressure'}.epic_code = nclong(1);
		nc{'pressure'}.valid_range = ncfloat([0 4095]);
		nc{'pressure'}.FillValue_ = ncfloat(1.0e+035);
		
        nc{'extsensor1'} = ncfloat('burst','sample'); 
		nc{'extsensor1'}.units = ncchar('counts');
		nc{'extsensor1'}.long_name = ncchar('raw data from external sensor channel 1');
		nc{'extsensor1'}.valid_range = ncfloat([0 10000]);
		nc{'extsensor1'}.FillValue_ = ncfloat(1.0e+035);

		nc{'extsensor2'} = ncfloat('burst','sample'); 
		nc{'extsensor2'}.units = ncchar('counts');
		nc{'extsensor2'}.long_name = ncchar('raw data from external sensor channel 2');
		nc{'extsensor2'}.valid_range = ncfloat([0 10000]);
		nc{'extsensor2'}.FillValue_ = ncfloat(1.0e+035);
         
		nc{'extpress'} = ncfloat('burst','sample');
		nc{'extpress'}.long_name = ncchar('raw data from external pressure sensor');
		nc{'extpress'}.units = ncchar('counts');
		nc{'extpress'}.valid_range = ncfloat([0 10000]);
		nc{'extpress'}.FillValue_ = ncfloat(1.0e+035);

		nc{'extpressfreq'} = ncfloat('burst','sample'); 
		nc{'extpressfreq'}.long_name = ncchar('pressure frequency');
		nc{'extpressfreq'}.units = ncchar('Hz');
		nc{'extpressfreq'}.epic_code = nclong(1);
		nc{'extpressfreq'}.valid_range = ncfloat([10000 40000]);
		nc{'extpressfreq'}.FillValue_ = ncfloat(1.0e+035);

		nc{'CTD_temp'} = ncfloat('burst');
		nc{'CTD_temp'}.long_name = ncchar('CTD Temperature Probe');
		nc{'CTD_temp'}.units = ncchar('Degrees Celcius');
		nc{'CTD_temp'}.valid_range = ncfloat([-5 40]);
		nc{'CTD_temp'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'CTD_cond'} = ncfloat('burst');
		nc{'CTD_cond'}.long_name = ncchar('CTD Conductivity Probe');
		nc{'CTD_cond'}.units = ncchar('siemens');
		%nc{'CTD_cond'}.valid_range = ncfloat([ ]);  NEED
		nc{'CTD_cond'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'CTD_press'} = ncfloat('burst');
		nc{'CTD_press'}.long_name = ncchar('CTD Pressure Sensor');
		nc{'CTD_press'}.units = ncchar('dbar');
		%nc{'CTD_press'}.valid_range = ncfloat([ ]);  NEED
		nc{'CTD_press'}.FillValue_ = ncfloat(1.0e+035);

		nc{'CTD_sal'} = ncfloat('burst');
		nc{'CTD_sal'}.long_name = ncchar('CTD Salinity Reading');
		nc{'CTD_sal'}.units = ncchar('PSU');
		%nc{'CTD_sal'}.valid_range = ncfloat([ ]);  NEED
		nc{'CTD_sal'}.FillValue_ = ncfloat(1.0e+035);
        
		nc{'MeanAmp'} = ncfloat('burst','axis');
		nc{'MeanAmp'}.long_name = ncchar('Mean Amplitude for Burst');
		nc{'MeanAmp'}.units = ncchar('counts');
		nc{'MeanAmp'}.valid_range = ncfloat([-32768 32767]);
		nc{'MeanAmp'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'MeanCorr'} = ncfloat('burst','axis');
		nc{'MeanCorr'}.long_name = ncchar('Mean Correlation for Burst');
		nc{'MeanCorr'}.units = ncchar('counts');
		nc{'MeanCorr'}.valid_range = ncfloat([-32768 32768]);
		nc{'MeanCorr'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'MeanHeading'} = ncfloat('burst');
		nc{'MeanHeading'}.long_name = ncchar('Mean Heading for Burst');
		nc{'MeanHeading'}.units = ncchar('degrees');
		nc{'MeanHeading'}.valid_range = ncfloat([0 359.9999]);
		nc{'MeanHeading'}.FillValue_ = ncfloat(1.0e+035);

		nc{'MeanPitch'} = ncfloat('burst');
		nc{'MeanPitch'}.long_name = ncchar('Mean Pitch for Burst');
		nc{'MeanPitch'}.units = ncchar('degrees');
		nc{'MeanPitch'}.valid_range = ncfloat([-20 20]);
		nc{'MeanPitch'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'MeanRoll'} = ncfloat('burst');
		nc{'MeanRoll'}.long_name = ncchar('Mean Roll for Burst');
		nc{'MeanRoll'}.units = ncchar('degrees');
		nc{'MeanRoll'}.valid_range = ncfloat([-20 20]);
		nc{'MeanRoll'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'MeanTemperature'} = ncfloat('burst'); 
		nc{'MeanTemperature'}.units = ncchar('degrees');
		nc{'MeanTemperature'}.long_name = ncchar('Mean Transducer Temperature for Burst');
		nc{'MeanTemperature'}.FillValue_ = ncfloat(1.0e+035);
		nc{'MeanTemperature'}.valid_range = ncfloat([-5 40]);
		
		nc{'MeanPressure'} = ncfloat('burst'); 
		nc{'MeanPressure'}.long_name = ncchar('Mean Pressure for Burst');
		nc{'MeanPressure'}.units = ncchar('counts');
		nc{'MeanPressure'}.valid_range = ncfloat([0 4095]);
		nc{'MeanPressure'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'MeanVelx'} = ncfloat('burst');
		nc{'MeanVelx'}.long_name = ncchar('Mean velocity in instrument coordinate x for Burst');
		nc{'MeanVelx'}.units = ncchar('cm s-1');
		nc{'MeanVelx'}.valid_range = ncfloat([-32768 32767]);
		nc{'MeanVelx'}.FillValue_ = ncfloat(1.0e+035);

		nc{'MeanVely'} = ncfloat('burst');
		nc{'MeanVely'}.long_name = ncchar('Mean velocity in instrument coordinate y for Burst');
		nc{'MeanVely'}.units = ncchar('cm s-1');
		nc{'MeanVely'}.valid_range = ncfloat([-32768 32767]);
		nc{'MeanVely'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'MeanVelz'} = ncfloat('burst');
		nc{'MeanVelz'}.long_name = ncchar('Mean velocity in instrument coordinate z for Burst');
		nc{'MeanVelz'}.units = ncchar('cm s-1');
		nc{'MeanVelz'}.valid_range = ncfloat([-32768 32767]);
		nc{'MeanVelz'}.FillValue_ = ncfloat(1.0e+035);

		nc{'StdAmp'} = ncfloat('burst','axis');
		nc{'StdAmp'}.long_name = ncchar('Amplitude Standard Deviation for Burst');
		nc{'StdAmp'}.units = ncchar('counts');
		nc{'StdAmp'}.valid_range = ncfloat([-32768 32767]);
		nc{'StdAmp'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'StdCorr'} = ncfloat('burst','axis');
		nc{'StdCorr'}.long_name = ncchar('Correlation Standard Deviation for Burst');
		nc{'StdCorr'}.units = ncchar('counts');
		nc{'StdCorr'}.valid_range = ncfloat([-32768 32768]);
		nc{'StdCorr'}.FillValue_ = ncfloat(1.0e+035);

		nc{'StdHeading'} = ncfloat('burst');
		nc{'StdHeading'}.long_name = ncchar('Heading Standard Deviation for Burst');
		nc{'StdHeading'}.units = ncchar('degrees');
		nc{'StdHeading'}.valid_range = ncfloat([0 359.9999]);
		nc{'StdHeading'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'StdPitch'} = ncfloat('burst');
		nc{'StdPitch'}.long_name = ncchar('Pitch Standard Deviation for Burst');
		nc{'StdPitch'}.units = ncchar('degrees');
		nc{'StdPitch'}.valid_range = ncfloat([-20 20]);
		nc{'StdPitch'}.FillValue_ = ncfloat(1.0e+035);

		nc{'StdRoll'} = ncfloat('burst');
		nc{'StdRoll'}.long_name = ncchar('Roll Standard Deviation for Burst');
		nc{'StdRoll'}.units = ncchar('degrees');
		nc{'StdRoll'}.valid_range = ncfloat([-20 20]);
		nc{'StdRoll'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'StdTemperature'} = ncfloat('burst'); 
		nc{'StdTemperature'}.units = ncchar('degrees');
		nc{'StdTemperature'}.long_name = ncchar('Transducer Temperature Standard Deviation for Burst');
		nc{'StdTemperature'}.FillValue_ = ncfloat(1.0e+035);
		nc{'StdTemperature'}.valid_range = ncfloat([-5 40]);

		nc{'StdPressure'} = ncfloat('burst'); 
		nc{'StdPressure'}.long_name = ncchar('Pressure Standard Deviation for Burst');
		nc{'StdPressure'}.units = ncchar('counts');
		nc{'StdPressure'}.valid_range = ncfloat([0 4095]);
		nc{'StdPressure'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'StdVelx'} = ncfloat('burst');
		nc{'StdVelx'}.long_name = ncchar('Velocity Std Deviation in instrument coordinate x for Burst');
		nc{'StdVelx'}.units = ncchar('cm s-1');
		nc{'StdVelx'}.valid_range = ncfloat([-32768 32767]);
		nc{'StdVelx'}.FillValue_ = ncfloat(1.0e+035);

		nc{'StdVely'} = ncfloat('burst');
		nc{'StdVely'}.long_name = ncchar('Velocity Std Deviation in instrument coordinate y for Burst');
		nc{'StdVely'}.units = ncchar('cm s-1');
		nc{'StdVely'}.valid_range = ncfloat([-32768 32767]);
		nc{'StdVely'}.FillValue_ = ncfloat(1.0e+035);
		
		nc{'StdVelz'} = ncfloat('burst');
		nc{'StdVelz'}.long_name = ncchar('Velocity Std Deviation in instrument coordinate z for Burst');
		nc{'StdVelz'}.units = ncchar('cm s-1');
		nc{'StdVelz'}.valid_range = ncfloat([-32768 32767]);
		nc{'StdVelz'}.FillValue_ = ncfloat(1.0e+035);

		nc{'soundspd'} = ncfloat('burst');
		nc{'soundspd'}.long_name = ncchar('sound velocity (m/s)');
		nc{'soundspd'}.units = ncchar('m s-1');
		nc{'soundspd'}.FillValue_ = ncfloat(1.0e+035);
		nc{'soundspd'}.epic_code = nclong(80);
		nc{'soundspd'}.valid_range = nclong([1400 1600]);
end %end switch


%Read and write data blocks (one data block for each sampling burst)
% Burst Header Information (60 bytes) including date and time from the real-time clock
%   a time-series of samples collected during the burst, and
%   statistics calculated at the end of each burst, optional (36 bytes)
%   The size of the data block will depend on the data recording
%   parameters.
% The end of the burst is a 2-byte checksum

while ~feof(fid)
    % Reading Burst Header (60 bytes)
    fseek(fid,14,0); %skip to burst number
    BurstNumber = fread(fid,1,'uint32');
    if isempty(BurstNumber)
        break;
    end
    
    % Test for complete burst
    if BurstNumber > maxBurst
        break;
    end
   
    % Place the data in NetCDF file without blanks or fill values for
    % skipped burst numbers
    all = 1:nBursts;
    count = minBurst:maxBurst;
    placement = find(count==BurstNumber);
    index = all(placement);
   
    if BurstNumber >= minBurst & BurstNumber <= maxBurst;  
		nc{'burstNum'}(index) = BurstNumber;
		disp(['Now Reading Burst Number ',num2str(BurstNumber),'...'])
		
		y = fread(fid,1,'int16');
		d = fread(fid,1,'char');
		m = fread(fid,1,'char');
		min = fread(fid,1,'char');
		hour = fread(fid,1,'char');
		hs = fread(fid,1,'char');
		sec = fread(fid,1,'char');
        
        % Marinna made changes here
		fseek(fid,2,0); %skip Velocity range index list and spare
		%fread(fid,2,'uint16'); %sample rate and samples per burst
		sampleinterval = 1/(fread(fid,1,'uint16').*0.01); % stored by Hydra in Hz*100, converted to sec here
		nsamplesthisburst = fread(fid,1,'uint16'); %samples per burst
        % expand time so there is a time stamp for every sample
        % assume that a burst is never going to be longer than a day
        time1 = ones(1,nsamplesthisburst).*julian([y m d 0 0 0]); % julian day
        time2 = (0:sampleinterval:((nsamplesthisburst.*sampleinterval)-sampleinterval)).*1000; % in msec from start of burst
        % time2 is the start of burst in milliseconds from the start of the julian day
        time2 = time2 + hour.*(3600*1000)+... % hours to milliseconds
            min.*(60*1000)+... % minutes to milliseconds
            sec.*(1000)+... % seconds to milliseconds
            hs.*10; % hundredths of seconds to milliseconds        
        % but account for those bursts that extend over the day boundary
        rolloveridx = find(time2 >= 1000*60*60*24); % find amounts greater than the # of milliseconds in the day
        if ~isempty(rolloveridx),
            time2(rolloveridx) = time2(rolloveridx) - 1000*60*60*24; % we will add a day to time 1 for these
            time1(rolloveridx) = time1(rolloveridx) + 1; % these are technically in the next day
        end
        
        switch DataType
            case 1, % statistics only, we need time as the middle of the burst
                tjstart = time1(1)+time2(1)./(3600*24*1000);
                tjend = time1(end)+time2(end)./(3600*24*1000);
                tjmid = tjstart+(tjend-tjstart)/2;
                nc{'time'}(index) = floor(tjmid); 
                nc{'time2'}(index) = (tjmid - floor(tjmid)).*(3600*24*1000); 
            otherwise
                nc{'time'}(index,:) = time1; 
                nc{'time2'}(index,:) = time2; 
        end
        %clear y d m min hour hs sec
        
        fseek(fid,2,0); %skip coord system and recorded data
        nc{'soundspd'}(index) = fread(fid,1,'uint16')*0.1; %m/s
		nc{'brange'}(index) = fread(fid,1,'int16')*0.01; %cm/s
		nc{'vrange'}(index) = fread(fid,1,'int16')*0.01; %cm/s
		status = fread(fid,[1,20],'uchar')'; 
        clear status  %leave out of *.cdf file for now.  Don't seem to need.
	
		% Reading Variables
		% Format to read variables is fread(fid,number of samples,precision,skip)
		
		%   VELOCITY
		velx = fread(fid,nSamples(1),'int16',BytesPerSample-2)*0.01; %cm/s
		fseek(fid,-BytesPerSample*nSamples(1)+2,0); %rewind to get vel2
		vely = fread(fid,nSamples(1),'int16',BytesPerSample-2)*0.01; %cm/s
		fseek(fid,-BytesPerSample*nSamples(1)+2,0); %rewind to get vel3
		velz = fread(fid,nSamples(1),'int16',BytesPerSample-2)*0.01; %cm/s
		fseek(fid,-BytesPerSample*nSamples(1)+2,0); %rewind to get amp and corr
		nc{'Vx'}(index,:) = velx;
		nc{'Vy'}(index,:) = vely;
		nc{'Vz'}(index,:) = velz;
        mnvelx = mean(velx); stdvelx = std(velx);
        mnvely = mean(vely); stdvely = std(vely);
        mnvelz = mean(velz); stdvelz = std(velz);
		clear velx vely velz
	
		%   AMPLITUDE AND CORRELATION
		if isequal(b(1),'1')
            for kk=1:6
                ampcorr(:,kk) = fread(fid,nSamples(1),'uchar',BytesPerSample-1);
                fseek(fid,-BytesPerSample*nSamples(1)+1,0); %rewind to get Heading
            end
            nc{'amp'}(index,:,:) = ampcorr(:,1:3); %amplitude for beams 1-3, counts
            nc{'corr'}(index,:,:)= ampcorr(:,4:6); %Correlation for beams 1-3, counts
		else
            for kk=1:2
                ampcorr(:,kk) = fread(fid,nSamples(1),'uchar',BytesPerSample-1);
                fseek(fid,-BytesPerSample*nSamples(1)+1,0); %rewind to get Heading
            end
            nc{'amp'}(index,:,:) = ampcorr(:,1); %Mean Amp
            nc{'corr'}(index,:,:) = ampcorr(:,2); %Mean Corr
		end
		clear ampcorr kk
	
		%   HEADING, PITCH, ROLL
		if isequal(b(2),'1')
            nc{'heading'}(index,:) = fread(fid,nSamples(1),'int16',BytesPerSample-2)*0.1; %heading degrees
            fseek(fid,-nSamples(1)*BytesPerSample+2,0); %rewind to get Pitch
            nc{'pitch'}(index,:) = fread(fid,nSamples(1),'int16',BytesPerSample-2)*0.1; %pitch degrees
            fseek(fid,-nSamples(1)*BytesPerSample+2,0); %rewind to get Roll
            nc{'roll'}(index,:) = fread(fid,nSamples(1),'int16',BytesPerSample-2)*0.1; %roll degrees
            fseek(fid,-nSamples(1)*BytesPerSample+2,0); %rewind to get Temperature
		end
	
		%   TEMPERATURE AND PRESSURE
		if isequal(b(3),'1')
            nc{'temperature'}(index,:) = fread(fid,nSamples(1),'int16',BytesPerSample-2)*0.01; %temperature degrees C
            fseek(fid,-nSamples(1)*BytesPerSample+2,0); %rewind to get Pressure
            nc{'pressure'}(index,:) = fread(fid,nSamples(1),'int16',BytesPerSample-2); %pressure in counts
            fseek(fid,-nSamples(1)*BytesPerSample+2,0); %rewind to get External Sensor Channel 1
		end
		
		%   EXTERNAL SENSORS  
		if isequal(b(6),'1')
            nc{'extsensor1'}(index,:) = fread(fid,nSamples(1),'int16',BytesPerSample-2); %external sensor channel 1 in counts
            fseek(fid,-nSamples(1)*BytesPerSample+2,0); %rewind to get External Sensor Channel 2
            nc{'extsensor2'}(index,:) = fread(fid,nSamples(1),'int16',BytesPerSample-2); %external sensor channel 2 in counts
            fseek(fid,-nSamples(1)*BytesPerSample+2,0); %rewind to get External Pressure
		end
	
        %   EXTERNAL PRESSURE

        if isequal(b(7),'1')
            pcount = fread(fid,nSamples(1),'ubit24',(BytesPerSample-3)*8); % millidbars (paros)/milliHz (Druck/ParosFreq)
            % if the user put in the wrong pressure offset, fix it
            PressFreqOffset = nc.PressFreqOffset(:);
            [pcount, nfixed] = fixparosoverflow(pcount,PressFreqOffset);
            if nfixed > 0, disp(sprintf('fixed %d pressure samples for bit overflow',nfixed)); end
            nc{'extpress'}(index,:) = pcount;
            PressFreq = (PressFreqOffset.*1000000 + pcount).*0.001; % shift left 16 bits
            nc{'extpressfreq'}(index,:) = PressFreq; % millidbars (paros)/milliHz (Druck/ParosFreq)
            fseek(fid,-nSamples(1)*BytesPerSample+3,0); %rewind to get Statistics
        end
		
		% Skip to end of burst to check for statistics
		fseek(fid,BytesPerSample*(nSamples-1),0);
	
		%   STATISTICS  (Means and Standard Deviations)
		if isequal(b(5),'1')
            means = [fread(fid,[1,6],'uchar'),...
                    fread(fid,[1,3],'int16'),...
                    fread(fid,1,'int16'),...
                    fread(fid,[1,1],'int32')];
            stds = [fread(fid,[1,6],'uchar'),...
                    fread(fid,[1,3],'int16'),...
                    fread(fid,1,'int16'),...
                    fread(fid,[1,1],'int16')];
            nc{'MeanAmp'}(index,:) = means(1:3); %mean amplitude for beams 1-3, counts
            nc{'MeanCorr'}(index,:)= means(4:6); %mean correlation for beams 1-3, counts
            nc{'MeanHeading'}(index) = means(7)*0.1; %degrees
            nc{'MeanPitch'}(index) = means(8)*0.1; %degrees
            nc{'MeanRoll'}(index) = means(9)*0.1; %degrees
            nc{'MeanTemperature'}(index) = means(10)*0.01; %degrees
            nc{'MeanPressure'}(index) = means(11); %counts
            nc{'MeanVelx'}(index) = mnvelx;
            nc{'MeanVely'}(index) = mnvely;
            nc{'MeanVelz'}(index) = mnvelz;
            
            nc{'StdAmp'}(index,:) = stds(1:3); %std deviation amplitude for beams 1-3, counts
            nc{'StdCorr'}(index,:)= stds(4:6); %std deviation correlation for beams 1-3, counts
            nc{'StdHeading'}(index) = stds(7)*0.1; %degrees
            nc{'StdPitch'}(index) = stds(8)*0.1; %degrees
            nc{'StdRoll'}(index) = stds(9)*0.1; %degrees
            nc{'StdTemperature'}(index) = stds(10)*0.01; %degrees
            nc{'StdPressure'}(index) = stds(11); %counts
            nc{'StdVelx'}(index) = stdvelx;
            nc{'StdVely'}(index) = stdvely;
            nc{'StdVelz'}(index) = stdvelz;
            SoundSpeedStat = fread(fid,1,'uint16')*0.1; % meters per second
            clear SoundSpeedStat means stds mnvel* stdvel*
		end
	
		%   CTD
		if isequal(b(8),'1')
            CTD = fread(fid,[1,4],'int32');
            nc{'CTD_temp'}(index) = CTD(1)*0.0001; %degrees C
            nc{'CTD_cond'}(index) = CTD(2)*0.00001; %siemens
            nc{'CTD_press'}(index) = CTD(3)*0.001; %dbar
            nc{'CTD_sal'}(index) = CTD(4)*0.0001; %PSU
            clear CTD
		end
		
		%   CHECKSUM - End of Sample
		fseek(fid,2,0);  %checksum
    else
        burstsize = rflag(4)*38 + rflag(1)*16 + nSamples(1)*BytesPerSample + 60-18;
        fseek(fid,burstsize,0);
    end %end if BurstNumber >= minBurst & BurstNumber <= maxBurst loop
end %end while ~feof(fid) loop

%nc.StartTime = 
%nc.StopTime = 

nc.history = ['Converted to netCDF via MATLAB by adr2cdf.m ', prog_ver];
disp('Closing netCDF file, this may take some time...')
fclose(fid);
close (nc)
disp(sprintf('Finished conversion of %d bursts in %f minutes', maxBurst-minBurst, toc/60))