Contents

function data = viz_sv(varargin)

About viz_sv

viz_sv is a 'Matlab' based function to read and visualise IMOS SOOP-BA NetCDF file.

For more information about IMOS SOOP-BA project: http://imos.org.au/facilities/shipsofopportunity/bioacoustic/

Syntax for usage

viz_sv
viz_sv(ncfile)
viz_sv(ncfile, imagefile)
viz_sv(ncfile, imagefile, 'channel', channel)
viz_sv(ncfile, imagefile, 'all')
viz_sv(ncfile, imagefile, 'depth', [min max])
viz_sv(ncfile, imagefile, 'noplots')
viz_sv(ncfile, imagefile, 'sun')
viz_sv(data_struct,data_array)
viz_sv(...,'title',title)
viz_sv(...,'location',{start end})
viz_sv(...,'channel', channel)
viz_sv(...,'range',[min max])
viz_sv(...,'depth',[min max])
viz_sv(...,'cmap',cmap)
viz_sv(...,'image',imagefile)
viz_sv(...,'axis',ticktype)
viz_sv(...,'ypos',ypos)
viz_sv(...,'noplots')
viz_sv(...,'sun')
viz_sv(...,'csv',filename)
viz_sv(...,'inf')
viz_sv(...,'sv.csv')
viz_sv(data_struct,data_array, title)

Description

The viz_sv function reads data from an IMOS_SOOP-BA*.nc file and plots the raw and processed Sv values in dB and the percentage good for each cell along with a plot of the vessel track and raw and processed NASC.

viz_sv returns a data structure containing the data extracted from the NetCDF file. This data structure may be passed to later calls of viz_sv to plot other data sets.

Examples

If viz_sv is called without arguments or the ncfile argument is not a file (e.g. is empty or a directory) the user will be asked to select the file to read.

If imagefile is specified and image of the plot will be written to file depending on the imagefile argument: [] - no file is written '' - empty string - the plot will be written to a file with the same name and directory as ncfile with a '.png' extension added. dir - if imagefile is a valid directory the image will be written to that directory with the same file name as ncfile with a '.png' extension added. '-dformat' - an image of the specified format will be written to a file with the same name as ncfile with a .format extension. See print for a list of supported formats. filename - anything else is treated as the name of the file to write the image to.

If the 'all' option is specified the data structure returned will contain all numeric (float or double) fields of the netCDF file.

If the 'noplots' option is specified the data will be read and returned but no plots will be generated on screen - a plot will still be written to file if imagefile is specified.

viz_sv(data_struct, data_array) will plot the data in data_array according to the axis found in data_struct. data_struct should be the output of an earlier viz_sv call (data read from a SOOP-BA NetCDF file). data_array may be a field of the data_struct or derived from a field of data_struct but must have the dimensions of the data_struct arrays.

title will printed (along with the file name) as part of the plot title, e.g. title({data_struct.file ; title}).

channel identifies which channel of a multi-channel (multi-frequency) data set is to be displayed. Channel may be either the integer index of the channel (1 for first channel), the name of the channel or the frequency of the channel (the first channel with that frequency). If the channel can not be identified or there is only one channel, the first channel is used.

range will set the range for the color bar, e.g. caxis(range). An empty range will be replaced by the default Sv range [-84, -48].

depth will limit the range for the vertical axis. An empty range will be replaced by the range covering valid (non-NaN) Sv data. A scalar range of 0 will go from 0 to cover the valid data. A non-zero scalar range will go from 0 to the value given.

cmap will be used as the colourmap for the plot, e.g. colormap(cmap). Use of the EK500 colourmap may cause matlab to use coarse colourmaps to overcome this explicitly state the number of colours to use e.g. viz_sv(...,'cmap',jet(64))

ticktype is one of 'time', 'lat', 'lon', 'latm', 'lonm'

ypos is the number of graph heights from the bottom of the screen to place the plot.

'sun' will use suncyle to calculate the sunrise and sunset times for each interval and add these values to the return structure as data.sun. It will also calculate whether each interval is in daylight (data.day). If a plot is requested it will draw a line on the plot showing day/night. This option requires suncycle.m to be in your path http://mooring.ucsd.edu/software/matlab/doc/toolbox/geo/suncycle.html Note: this option is fairly slow. Bugs: 'sun' does not yet plot day/night on image files.

'csv' will write a .csv file of the time, longitude and latitude and layer summary indices to the file specified. If the file name is empty then '.csv' will be added to the netCDF file name. Requires struct2txt in path.

'inf' will generate MBSystem style .inf files and echoview style .gps.csv files for the data.

'sv.csv' will generate echoview style .sv.csv and .gps.csv files for the data. One .sv.csv file will be created for each channel.

The minimum requirements for a data_struct is that it must have two fields depth and time containing vectors. data_array must be a 2 or 3 dimensional array length(depth) x length(time) [x length(channels)].

Other fields which may be used if present in data_struct are: longitude - vector with same size as time latitude - vector with same size as time file - string (usually containing filename) used in title location - cell array of two strings to label start and end of plot

Author and version

             Tim Ryan <tim.ryan@csiro.au>
             Gordon Keith <gordon.keith@csiro.au>
Contributor:  Haris Kunnath <haris.kunnath@csiro.au>
             Version: 2.6
             Date: 2019-06-20

Set defaults

TIME=0;
LAT=1;
LONG=2;
INTERVAL=3;
tickformat=TIME;

DEG=0;
MIN=1;
degformat = DEG;
min_sv = -84;
range = 36;
max_sv = min_sv + range;

Input arguments to the function

if nargin == 0
    ncfile = '';

% If first argument is a data structure plot the second arg

elseif isstruct(varargin{1})
    data = varargin{1};
    plotdata = varargin{2};
    time = data.time;
    depth = data.depth;
    if isfield(data,'latitude')
        latitude = data.latitude;
    else
        latitude = zeros(size(time));
    end
    if isfield(data, 'longitude')
        longitude = data.longitude;
    else
        longitude = zeros(size(time));
    end

    if size(plotdata,1) ~= length(depth) || size(plotdata,2) ~= length(time)
        error('Data array size (%d x %d) does not match axis size (%d x %d)', ...
            size(plotdata,1), size(plotdata,2), length(depth), length(time));
    end

    filename = '';
    ttle = '';
    chn = '';
    range = [floor(min(min(min(plotdata)))) ceil(max(max(max(plotdata)))) ];
    if range(1) == -Inf ; range(1) = -100; end
    if range(2) ==  Inf ; range(2) =  100; end
    if range(1) == range(2) ; range(2) = range(2) + 1; end
    drange = [data.depth(1) data.depth(end)];
    location = {'' ''};
    imagefile = [];
    cmap = [];
    channel = 1;
    ypos = 2;
    plt = true;
    sun = false;
    write_csv = false;
    csv_file = '';
    inf_file = false;
    sv_csv = false;

    if isfield(data, 'file')
        fullpath = strsplit(data.file,'\');
        filename = fullpath{end};
    end
    if isfield(data, 'location');
        location = data.location;
    end
    if isfield(data, 'grid_distance')
        grid_distance = data.grid_distance;
    else
        grid_distance = '1 km';
    end

    if nargin == 3
        ttle = varargin{3};
    else
        arg = 2;
        while  arg < nargin
            arg = arg + 1;
            if strcmpi('title', varargin{arg})
                arg = arg+1;
                ttle = varargin{arg};
            elseif strncmpi('location', varargin{arg},3)
                arg = arg+1;
                location = varargin{arg};
            elseif strcmpi('range', varargin{arg})
                if arg < nargin && isnumeric(varargin{arg+1})
                    arg = arg+1;
                    range = varargin{arg};
                else
                    range = [];
                end
                if isempty(range)
                    range = [min_sv, max_sv];
                end
            elseif strcmpi('depth', varargin{arg})
                if arg < nargin && isnumeric(varargin{arg+1})
                    arg = arg+1;
                    drange = varargin{arg};
                else
                    drange = [];
                end
            elseif strncmpi('image', varargin{arg},5)
                arg = arg+1;
                imagefile = varargin{arg};
            elseif strcmpi('cmap', varargin{arg})
                arg = arg+1;
                cmap = varargin{arg};
            elseif strncmpi('channel', varargin{arg},2)
                arg = arg+1;
                channel = varargin{arg};
            elseif strncmpi('ypos', varargin{arg},2)
                arg = arg+1;
                ypos = varargin{arg};
            elseif strncmpi('noplots', varargin{arg},3)
                plt = false;
            elseif strncmpi('sun', varargin{arg},3)
                sun = true;
            elseif strncmpi('csv', varargin{arg},3)
                write_csv = true;
                if arg < nargin
                    arg = arg + 1;
                    csv_file = varargin{arg};
                end
            elseif strncmpi('inf', varargin{arg},3)
                inf_file = true;
            elseif strncmpi('sv.csv', varargin{arg},2)
                sv_csv = true;
            elseif strcmpi('axis', varargin{arg})
                arg = arg+1;
                form = varargin{arg};
                if strncmpi(form, 'lat',3)
                    tickformat = LAT;
                elseif strncmpi(form, 'lon',3)
                    tickformat = LONG;
                elseif strncmpi(form, 'int',3)
                    tickformat = INTERVAL;
                end
                if max(form == 'm') || max(form == 'M')
                    degformat = MIN;
                end
            end
        end
    end
    % Do we need sun data

    if sun
        if isfield(data,'day')
            daynight = -(data.day - 4) / 3; % data.day 1=day 4=night; daynight 1=day 0=night
        else
            % calculate whether sun is above horizon
            data.sun=zeros(length(data.time),2);
            for itvl=1:length(data.time)
                data.sun(itvl,:)=suncycle(data.latitude(itvl), data.longitude(itvl), data.time(itvl));
            end
            hour = mod(data.time,1) * 24;
            daynight = xor(min(data.sun,[],2) < hour & hour < max(data.sun,[],2), ...
                data.sun(:,1) > data.sun(:,2));
            data.day = 4 - 3 * daynight; % data.day 1=day 4=night; daynight 1=day 0=night
        end
    else
        daynight = [];
    end

    % select a single channel to plot
    if ndims(plotdata) == 3
        chn = channel;
        if ischar(channel) && isfield(data, 'channels')
            channel=strtrim(channel);
            for c=1:length(data.channels)
                if strcmpi(channel,data.channels{c})
                    channel = c;
                    break;
                end
            end
        end
        if ischar(channel)
            channel = str2double(channel);
        end

        if channel > length(data.channels) && isfield(data, 'frequency')
            channel=strtrim(channel);
            for c=1:length(data.frequency)
                if channel == data.frequency(c)
                    channel = c;
                    break;
                end
            end
        end

        if isnan(channel) || channel > size(plotdata,3) || channel < 1 || mod(channel,1) ~= 0
            fprintf('Using channel 1\n');
            channel = 1;
        end

        plotdata = plotdata(:,:,channel);
        if isfield(data, 'channels')
            chn = data.channels{channel};
        end
    end

    % determine range of valid data, if requested
    if length(drange) < 2
        if drange > 0
            drange = [0 drange];
        else
            if isfield(data, 'Sv')
                dptdata = data.Sv(:,:,channel);
            else
                dptdata = plotdata;
            end
            hasdata = any(isfinite(dptdata),2);
            if isempty(drange)
                drange(1) = depth(find(hasdata,1, 'first'));
            end
            drange(2) = depth(find(hasdata,1, 'last'));
            if isempty(drange)
                error('No valid data to plot');
            end
        end
    end

    % trim data to selected depth range
    if drange(end) < depth(end) || drange(1) > depth(1)
        select = depth >= drange(1) & depth <= drange(end);
        plotdata = plotdata(select,:);
    end

    if plt
        echogram(plotdata, ypos, { [filename ' ' chn];  ttle }, location, range, cmap, daynight);
    end

    if ischar(imagefile)
        write_echogram(plotdata, imagefile, filename, chn, ttle, location, range, cmap);
    end

    if write_csv
        csv(data, csv_file)
    end

    if inf_file
        info(data);
    end

    if sv_csv
        svcsv(data);
    end
    return

% first arg is not a struct - it is an ncfile to plot

else
    ncfile = varargin{1};
end

if nargin < 2
    imagefile = [];
else
    imagefile = varargin{2};
end

channel = '';
all_data = false;
plots = true;
sun = false;
write_csv = false;
csv_file = '';
inf_file = false;
sv_csv = false;
dpthrange = [-Inf Inf];

arg = 2;
while arg < nargin
    arg = arg + 1;
    if strcmpi('channel', varargin{arg})
        arg = arg + 1;
        channel = varargin{arg};
    end
    if strcmpi('all', varargin{arg})
        all_data = true;
    end
    if strncmpi('noplots', varargin{arg},3)
        plots = false;
    end
    if strncmpi('sun', varargin{arg},3)
        sun = true;
    end
    if strncmpi('csv', varargin{arg},3)
        write_csv = true;
        if arg < nargin
            arg = arg + 1;
            csv_file = varargin{arg};
        end
    end
    if strncmpi('inf', varargin{arg},3)
        inf_file = true;
    end
    if strncmpi('sv.csv', varargin{arg},2)
        sv_csv = true;
    end
    if strcmpi('depth', varargin{arg})
        if arg < nargin && isnumeric(varargin{arg+1})
            arg = arg + 1;
            dpthrange = varargin{arg};
            if isscalar(dpthrange) && dpthrange > 0
                dpthrange = [0 dpthrange];      %#ok<AGROW>
            end
        else
            dpthrange = [];
        end
    end
end

% Ask user for NetCDF file if not provided
if exist(ncfile, 'file') ~= 2
    [filename, pathname] = uigetfile(...
        {'*.nc' '*.nc NetCDF file'; '*' 'All files'}, ...
        'IMOS-SOOP-BA NetCDF file', ncfile);
    if isequal(filename,0)
        error('NetCDF filename required');
    end
    ncfile = fullfile(pathname,filename);
end

% View NetCDF in Echoview

% Haris 12/07/2019 - Implementing Tim's 'nc2ev' created EV file viewing
% option.
if plots
    try
        ques = questdlg('Do you want to view NetCDF in Echoview?','View in Echoview?','Yes','No','Yes');
        if isequal(ques,'Yes')
            [dir_root, file] = fileparts(ncfile);
            ev_dir = strcat(dir_root,'\echoview_ascii\');
            ev_file_name = dir(fullfile(ev_dir,'*.ev'));
            if exist(ev_dir, 'dir') && ~isempty(ev_file_name)
                if numel(ev_file_name) == 1
                    ev_file_open = strcat(ev_dir,ev_file_name.name);
                    winopen(ev_file_open)
                else
                    cd (ev_dir)
                    file = uigetfile('*.ev','Select an ev file to open'); % select ev file
                    ev_file_open = strcat(ev_dir,file);
                    winopen(ev_file_open)
                    cd (dir_root)
                end
            else
                uiwait(msgbox('Analyst not created an EV file for you.','NetCDF in Echoview','warn'))
            end
        end
    catch
        msgbox('It looks like Echoview unable to open the EV file in "echoview_ascii" folder. Check your Echoview version and update if needed.','NetCDF view in Echoview','error')
    end

    uiwait(msgbox('Click OK to continue with Matlab plots.'))
end

if ischar(imagefile) && isempty(imagefile) && isempty(channel)
    imagefile = [ncfile '.png'];
end

% Open the netcdf file
if exist(ncfile, 'file') ~= 2
    fprintf('\n-----------------------------------------------------\n');
    fprintf('\nnetcdf file %s \ncannot be found, check location\n',ncfile);
    fprintf('\n-----------------------------------------------------\n');
else

    ncid = netcdf.open(ncfile, 'NC_NOWRITE');
    data.file = ncfile;
    [~, filename, ~] = fileparts(ncfile);

    try
        location{1} = netcdf.getAtt(ncid, ...
            netcdf.getConstant('NC_GLOBAL'), 'transit_start_locality');
    catch e     %#ok<NASGU>
        location{1} = '';
    end
    try
        location{2} = netcdf.getAtt(ncid, ...
            netcdf.getConstant('NC_GLOBAL'), 'transit_end_locality');
    catch e     %#ok<NASGU>
        location{2} = '';
    end
    data.location = location;

    try
        grid_distance = netcdf.getAtt(ncid, ...
            netcdf.getConstant('NC_GLOBAL'), 'dataset_ping_axis_size');
    catch e     %#ok<NASGU>
        grid_distance = '1 km';
    end
    data.grid_distance = grid_distance;

Read data variabes

    try
        latitude = getNetcdfVar(ncid, 'LATITUDE');
        data.latitude = latitude;
        longitude = getNetcdfVar(ncid, 'LONGITUDE');
        data.longitude = longitude;

        try
            depthid =  netcdf.inqVarID(ncid, 'DEPTH');
        catch e     %#ok<NASGU>
            depthid =  netcdf.inqVarID(ncid, 'RANGE');
        end
        depth = netcdf.getVar(ncid, depthid);
        data.depth = depth;
        timeid =  netcdf.inqVarID(ncid, 'TIME');
        time = netcdf.getVar(ncid, timeid);
        try
            time_base = netcdf.getAtt(ncid, timeid, 'units');
            if strncmpi(time_base, 'days since', 10)
                time = time + datenum(time_base(12:31));
            end
        catch e     %#ok<NASGU>
            time = time + datenum([1950 01 01]);
        end
        data.time = time;

        try
            svid = netcdf.inqVarID(ncid, 'Sv');
            try
                bnid  = netcdf.inqVarID(ncid, 'background_noise');  % identfier for background noise. TER 14/11/16
            catch
                bnid = -1;
            end
            try
                snrid = netcdf.inqVarID(ncid, 'signal_noise');  % identfier for signal to noise. TER 14/11/16
            catch
                snrid = -1;
            end
            try
                motid = netcdf.inqVarID(ncid, 'motion_correction_factor');  % identfier for motion correction factor. Haris 14/06/2019
            catch
                motid = -1;
            end
            qcid = netcdf.inqVarID(ncid, 'Sv_quality_control');
            pgid = netcdf.inqVarID(ncid, 'Sv_pcnt_good');
            svrawid = netcdf.inqVarID(ncid,'Sv_unfilt');
        catch e     %#ok<NASGU>
            % support old variable names
            if isempty(channel)
                channel = '38';
            end
            svid = netcdf.inqVarID(ncid, ['Sv_' channel]);
            qcid = netcdf.inqVarID(ncid, ['Sv_' channel '_quality_control']);
            pgid = netcdf.inqVarID(ncid, ['Sv_pcnt_good_' channel]);
            svrawid = netcdf.inqVarID(ncid,['Sv_unfilt_' channel]);
        end

        % TER 14/11/16 - signal to noise added
        % check, template versions prior to about June 2016 would not be outputting SNR and BN data
        % these next 10 lines will prevent program crashing on earlier
        % versions of netCDF's that do not have SNR and BN

        data.sv = getNetcdfVar(ncid, svid);
        data.qc = netcdf.getVar(ncid, qcid);
        data.pg = getNetcdfVar(ncid, pgid);
        data.svraw = getNetcdfVar(ncid,svrawid);
        if bnid > 0
            try
                data.background_noise = getNetcdfVar(ncid,bnid); % add background noise to data variable. TER 14/11/16
            catch bn_e
                % continue on, no background noise vector present
                fprintf('%s\n',bn_e.message)
            end
        end
        if snrid > 0
            try
                data.snr = getNetcdfVar(ncid,snrid); % add signal-to-noise to data variable. TER 14/11/16
            catch snr_e
                % continue on, no snr matrix present.
                fprintf('%s\n',snr_e.message)
            end
        end
        if motid > 0
            try
                data.motion_correction_factor = getNetcdfVar(ncid,motid); % add motion correction factor to data variable. Haris 14/06/2019
            catch mot_e
                % continue on, no motion correction factor matrix present.
                fprintf('%s\n',mot_e.message)
            end
        end

    catch exception
        warning('VIZ_SV:BAD_READ', [ 'Unable to read Sv: ' exception.message ])
    end

    if ndims(data.sv) == 3
        try
            data.frequency = getNetcdfVar(ncid, 'frequency');
            channels = getNetcdfVar(ncid, 'CHANNEL')';
            for c = size(channels,1):-1:1
                ch = channels(c,:);
                ch(ch == 0) = [];
                data.channels{c} = strtrim(ch);
            end
        catch
            try
                data.frequency = netcdf.getAtt(ncid,netcdf.getConstant('NC_GLOBAL'), 'frequency');
                data.channels = {netcdf.getAtt(ncid,netcdf.getConstant('NC_GLOBAL'), 'channel')};
            catch
                if ~isfield(data, 'frequency')
                    data.frequency = zeros(size(data.sv,3),1);
                end
                data.channels = cellstr(num2str(data.frequency));
            end
        end

        if ischar(channel)
            channel=strtrim(channel);
            for c=1:length(data.channels)
                if strcmpi(channel,data.channels{c})
                    channel = c;
                    break;
                end
            end
        end

        if isempty(channel)
            channel = 1:length(data.channels);
        end

        if ischar(channel)
            channel = str2double(channel);
        end

        if max(channel) > length(data.channels)
            for c=1:length(data.frequency)
                channel(channel == data.frequency(c)) = c;
            end
        end

    else
        channel = 1;
        try
            data.frequency = netcdf.getAtt(ncid,netcdf.getConstant('NC_GLOBAL'), 'frequency');
            data.channels = {netcdf.getAtt(ncid,netcdf.getConstant('NC_GLOBAL'), 'channel')};
        catch
            if ~isfield(data, 'frequency')
                data.frequency = 38;
            end
            data.channels = {''};
        end
    end

% Get all data variables, if requested
    if all_data
        [~,nvars,~,~] = netcdf.inq(ncid);
        for varid = 0:nvars-1
            [varname,xtype,~,~] = netcdf.inqVar(ncid,varid);
            if xtype == netcdf.getConstant('NC_FLOAT') || ...
                    xtype == netcdf.getConstant('NC_DOUBLE') || ...
                    xtype == netcdf.getConstant('NC_SHORT')
                if ~isfield(data, varname)
                     data.(varname) = getNetcdfVar(ncid,varid);
                end
            end
        end
    end

% Read temperature, salinity, and intermediate results if present
    try
        data.temperature = getNetcdfVar(ncid,'temperature' );
        data.salinity = getNetcdfVar(ncid, 'salinity');

        % read intermediate results if present in file
        data.soundspeed = getNetcdfVar(ncid, 'sound_speed');
        data.soundabsorption = getNetcdfVar(ncid, 'absorption') * 1000;

        data.abs_sv =  getNetcdfVar(ncid, 'abs_corrected_sv');
        data.abs_Sv = 10 * log10(data.abs_sv);

        data.uncorrected_sv = getNetcdfVar(ncid, 'uncorrected_Sv');
        data.uncorrected_sv(data.qc>2)=NaN;
        data.uncorrected_Sv = 10 * log10(data.uncorrected_sv);

        data.history = netcdf.getAtt(ncid,netcdf.getConstant('NC_GLOBAL'), 'history');
    catch e     %#ok<NASGU>
    end

% Read summary layer metrics if available
    try
        data.epipelagic = getNetcdfVar(ncid, 'epipelagic');
        data.upper_mesopelagic = getNetcdfVar(ncid, 'upper_mesopelagic');
        data.lower_mesopelagic = getNetcdfVar(ncid, 'lower_mesopelagic');
        data.day = getNetcdfVar(ncid, 'day');
    catch e %#ok<NASGU>
    end

    netcdf.close(ncid);

    if ndims(data.sv) == 3
        fields = fieldnames(data);
        for f = 1:length(fields)
            if ndims(data.(fields{f})) == 3
                data.(fields{f}) = shiftdim(data.(fields{f}),1);
            end
        end
    end

    try
        % Ignore bad data
        data.sv(data.qc>2)=NaN;

        % convert to dB
        data.Sv = 10 * log10(data.sv);
        data.Svraw = 10 * log10(data.svraw);

        % calculate NASC
        data.mean_Sv = 10*log10(nmean(data.sv));
        data.NASC = 4*pi*1852*1852*10.^(data.mean_Sv./10)*1200;

        data.mean_Svraw = 10*log10(nmean(data.svraw));
        data.NASCraw = 4*pi*1852*1852*10.^(data.mean_Svraw./10)*1200;
    catch exception
        warning('VIZ_SV:BAD_SV', [ 'Unable to compute Sv ' exception.message])
    end

    if sun
        if isfield(data,'day')
            daynight = -(data.day - 4) / 3;  % data.day 1=day 4=night; daynight 1=day 0=night
        else
            % calculate whether sun is above horizon
            data.sun=zeros(length(data.time),2);
            for itvl=1:length(data.time)
                data.sun(itvl,:)=suncycle(data.latitude(itvl), data.longitude(itvl), data.time(itvl));
            end
            hour = mod(data.time,1) * 24;
            daynight = xor(min(data.sun,[],2) < hour & hour < max(data.sun,[],2), ...
                data.sun(:,1) > data.sun(:,2));
            data.day = 4 - 3 * daynight; % data.day 1=day 4=night; daynight 1=day 0=night
        end
    else
        daynight = [];
    end

    if write_csv
        csv(data, csv_file);
    end

    if inf_file
        info(data);
    end

    if sv_csv
        svcsv(data);
    end

    imagefig = [];

    for c = 1: length(channel)

        chann = channel(c);

        % determine range of valid data, if requested
        drange = dpthrange;
        if length(drange) < 2
            hasdata = any(isfinite(data.Sv(:,:,chann)),2);
            if isempty(drange)
                drange(1) = depth(find(hasdata,1, 'first'));
            end
            drange(2) = depth(find(hasdata,1, 'last'));
            if isempty(drange)
                error('No valid data to plot');
            end
        end

        % trim data to selected depth range
        select = depth >= drange(1) & depth <= drange(end);

        % pull the data out on a per-channel basis
        Sv = data.Sv(select,:,chann);
        pg = data.pg(select,:,chann);
        Svraw = data.Svraw(select,:,chann);
        NASC = data.NASC(:,:,chann);
        NASCraw = data.NASCraw(:,:,chann);

        % TER 14/11/16 - signal to noise added check, template versions
        % prior to about June 2016 would not be outputting SNR and BN data
        % these next 10 lines will prevent program crashing on earlier
        % versions of netCDF's that do not have SNR and BN

        if isfield(data,'snr');
            snr = data.snr(:,:,chann);
        end

        if isfield(data,'background_noise')
            if exist('channels') % we have mfreq data (TER)
                bn = data.background_noise(chann,:);
            else
                bn = data.background_noise(:,chann);
            end
        end

        if isfield(data,'motion_correction_factor'); % Added motion correction factor Haris 14/06/2019
            mot = data.motion_correction_factor(:,:,chann);
        end
        % -----------------------------------------------
        ttle = [filename ' ' data.channels{chann}];

        % If second argument was given write Sv image to file
        if ischar(imagefile)
            if c == length(channel)
                write_echogram(Sv, imagefile, ncfile, data.channels{chann}, 'Sv mean (dB re 1 m-1)', ...
                    location, [min_sv max_sv], EK500colourmap(), imagefig);
            else
                imagefig = write_echogram(Sv, '-', ncfile, data.channels{chann}, 'Sv mean (dB re 1 m-1)', ...
                    location, [min_sv max_sv], EK500colourmap(), imagefig);
            end

        end

% Finish if no plots are wanted.
        if ~plots
            continue
        end

Plot 'processed', 'unprocessed' Sv data, and percentage of Sv retained (%)

        echogram(Sv, 2, { ttle ;  'Processed Sv (dB re 1 m-1)' }, ...
            location, [min_sv max_sv], [], daynight);

        echogram(Svraw, 1, { ttle ;  'Unprocessed Sv (dB re 1 m-1)' }, ...
            location, [min_sv max_sv], [], daynight)

        echogram(pg,  0.1, { ttle ;  'Percentage of Sv retained (%)' }, location, [0 100], jet(100), daynight);

Plot signal-to-noise ratio

% TER 14/11/16
        if exist('snr','var')
            echogram(snr,2,{ ttle ;  'Signal-to-noise-ratio (dB)' },location,[0 36], jet(12),''); % signal to noise ratio
        end

Plot motion correction factor

% Haris 14/06/2019
%         if exist('mot')
%             echogram(mot,2,{ ttle ;  'Motion correction factor (%)' },location,[0 50], [],''); % motion correction factor
%         end

% Haris 15/06/2019. The commented lines below were creating NASC plot for
% each channel as seprate figures. viz_sv is getting busy these days
% particularly for multi-frequency data, and user is presented with
% multiple figures. The below code has been placed out of the for loop so
% that single figure with subplots can be used for display. Below part is
% not deleted. Revert if needed, and delete \ comment new addition.

% %% Plot echointegration NASC values
%
% % Haris modified- 22 December 2018. Now plotting with time.
%         figure;
%         hold on; box on; grid on
%         plot(data.time,NASC,'g');
%         plot(data.time,NASCraw,'r');
%         legend('Processed NASC', 'Raw NASC');
% %         xlabel(['Distance (' grid_distance ')']);
%         xlabel('Time (UTC)')
%         datetick('x',19)
%         ylabel('NASC (m^2 nmi^-^2)');
%         title({ ttle ; 'NASC (sv integrated between 0–1200 m) for each ping axis interval' }, 'Interpreter', 'none');
%         p=get(0,'ScreenSize');
%         set(gcf,'Position',[50 50 p(3)*0.75 p(4)*0.25])
%         zoom(gcf, 'reset');
%         if max(NASC) > 0
%             ylim([0, max(NASC)]);
%         end
%         xlim([min(data.time) max(data.time)])
%
% % Haris- same plot with distance - only for checking purpose and referencing to EV files
%         figure;
%         hold on; box on; grid on
%         plot(NASC,'g');
% %         plot(NASCraw,'r');
%         legend('Processed NASC');
% %         xlabel(['Distance (' grid_distance ')']);
%         xlabel('GPS distance (m)');
%         ylabel('NASC (m^2 nmi^-^2)');
%         title({ ttle ; 'NASC vs GPS distance for checking purpose and referencing to EV files only' }, 'Interpreter', 'none');
%         p=get(0,'ScreenSize');
%         set(gcf,'Position',[50 50 p(3)*0.75 p(4)*0.25])
%         zoom(gcf, 'reset');
%         if max(NASC) > 0
%             ylim([0, max(NASC)]);
%         end

    end

    if plots

Plot echointegration NASC values

% Haris 15/06/2019 to plot on single figure

        if length(channel) == 1 % single frequency
            figure;
            hold on; box on; grid on
            plot(data.time,data.NASC,'g');
            plot(data.time,data.NASCraw,'r');
            legend('Processed NASC', 'Raw NASC');
            xlabel('Time (UTC)')
            datetick('x',19)
            ylabel('NASC (m^2 nmi^-^2)');
            title(sprintf('NASC (sv integrated between 0–1200 m) - %s',data.channels{chann}))
            p=get(0,'ScreenSize');
            set(gcf,'Position',[50 50 p(3)*0.75 p(4)*0.25])
            zoom(gcf, 'reset');
            if max(data.NASC) > 0
                ylim([0, max(data.NASC)]);
            end
            xlim([min(data.time) max(data.time)])
        else % multi-frequency
            figure;
            p=get(0,'ScreenSize'); % Set figure size
            set(gcf,'Position',[50 50 p(3)*0.75 p(4)*0.60])
            for n = 1: length(channel)
                chann_n = channel(n);
                subplot(length(channel),1,chann_n)
                plot(data.time,data.NASC(:,:,chann_n),'g');
                hold on; box on; grid on
                plot(data.time,data.NASCraw(:,:,chann_n),'r');
                if n == max(length(channel)) % keep legend for last panel only
                   legend('Processed NASC', 'Raw NASC');
                end
                xlabel('Time (UTC)')
                datetick('x',19)
                ylabel('NASC (m^2 nmi^-^2)');
                title(sprintf('NASC (sv integrated between 0–1200 m) - %s',data.channels{chann_n}))
                if max(data.NASC(:,:,chann_n)) > 0
                    ylim([0, max(data.NASC(:,:,chann_n))]);
                end
                xlim([min(data.time) max(data.time)])
            end
        end

% same plot with distance - only for checking purpose and referencing to EV files

        if length(channel) == 1 % single frequency
            figure;
            hold on; box on; grid on
            plot(data.NASC,'g');
            legend('Processed NASC');
            xlabel('GPS distance (m)');
            ylabel('NASC (m^2 nmi^-^2)');
            title(sprintf('NASC vs GPS distance for checking purpose and referencing to EV files - %s',data.channels{chann}))
            p=get(0,'ScreenSize');
            set(gcf,'Position',[50 50 p(3)*0.75 p(4)*0.25])
            zoom(gcf, 'reset');
            if max(data.NASC) > 0
                ylim([0, max(data.NASC)]);
            end
            xlim([1 length(data.NASC)])
        else % multi-frequency
            figure;
            p=get(0,'ScreenSize'); % Set figure size
            set(gcf,'Position',[50 50 p(3)*0.75 p(4)*0.60])
            for n = 1: length(channel)
                chann_n = channel(n);
                subplot(length(channel),1,chann_n)
                plot(data.NASC(:,:,chann_n),'g');
                box on; grid on
                if n == max(length(channel)) % keep legend for last panel only
                   legend('Processed NASC');
                end
                xlabel('GPS distance (m)');
                ylabel('NASC (m^2 nmi^-^2)');
                title(sprintf('NASC vs GPS distance for checking purpose and referencing to EV files - %s',data.channels{chann_n}))
                if max(data.NASC(:,:,chann_n)) > 0
                    ylim([0, max(data.NASC(:,:,chann_n))]);
                end
                xlim([1 length(data.NASC(:,:,chann_n))])
            end
        end

Plot background noise per interval

% TER 14/11/16. Modified by Haris on 05 February 2019 to plot as a single figure for all channels

        if isfield(data, 'background_noise')
            figure;
            plot(data.time, data.background_noise','.','MarkerSize',10);
            title({filename; 'Background noise for each ping axis interval'}, 'Interpreter', 'none')
            xlabel('Time (UTC)');ylabel('dB re 1 m^-^1');
            datetick('x',19)
            p=get(0,'ScreenSize');
            set(gcf,'Position',[50 50 p(3)*0.75 p(4)*0.25])
            xlim([min(data.time) max(data.time)])
            legend(data.channels)
            grid on
        end

Plot motion correction factor, box plot or line plot

% Haris 15/06/2019

        if exist('mot')

            depth_bin = floor(depth./100)*100;

            if length(channel) == 1 % & ~all(isnan(mot)) % single frequency, uncomment ~all(isnan(mot)) if plot is not needed
                if license('test','statistics_toolbox') % try box plot
                    figure;
                    boxplot(mot', -depth_bin, 'orientation','horizontal');
                    xlabel('Percentage (%) correction')
                    ylabel('Depth (m)')
                    title({ data.channels{chann} ; 'Motion correction factor' })
                    box on; grid on
                else % if box plot is not available
                    warning('No box plot for motion correction factor')
                    figure;
                    plot(mot,-depth);
                    xlabel('Percentage (%) correction')
                    ylabel('Depth (m)')
                    title({ data.channels{chann} ; 'Motion correction factor' })
                    box on; grid on
                end
            end

            if length(channel) > 1 % & ~all(isnan(mot)) % multi frequency, uncomment ~all(isnan(mot)) if plot is not needed
                if license('test','statistics_toolbox') % try box plot
                    figure;
                    p = get(0,'ScreenSize'); % Set figure size
                    set(gcf,'Position',[50 50 p(3)*0.4 p(4)*0.5])
                    for m = 1: length(channel)
                        chann_m = channel(m);
                        subplot(1,length(channel),chann_m)
                        boxplot(data.motion_correction_factor(:,:,chann_m)', -depth_bin, 'orientation','horizontal');
                        xlabel('Percentage (%) correction')
                        ylabel('Depth (m)')
                        title({ data.channels{chann_m} ; 'Motion correction factor' })
                        hold on; box on; grid on
                    end
                else % if box plot is not available
                    warning('No box plot for motion correction factor')
                    figure;
                    p = get(0,'ScreenSize'); % Set figure size
                    set(gcf,'Position',[50 50 p(3)*0.4 p(4)*0.5])
                    for m = 1: length(channel)
                        chann_m = channel(m);
                        subplot(1,length(channel),chann_m)
                        plot(data.motion_correction_factor(:,:,chann_m), -depth);
                        xlabel('Percentage (%) correction')
                        ylabel('Depth (m)')
                        title({ data.channels{chann_m} ; 'Motion correction factor' })
                        hold on; box on; grid on
                    end
                end
            end
        end

Plot summary layer metrics

% Haris modified- 22 December 2018. Now plotting with time and modified
% condition. Updated on 30 April 2019.

        if isfield(data, 'lower_mesopelagic') & isfield(data, 'day')

            figure
            p = get(0,'ScreenSize'); % Set figure size
            set(gcf,'Position',[50 50 p(3)*0.75 p(4)*0.6])
            try % yyaxis right option is introduced in R2016a
                subplot(3,1,1)
                plot(data.time,data.epipelagic')
%                 xlabel(['Distance (' grid_distance ')']);
                xlabel('Time (UTC)')
                datetick('x',19)
                ylabel('{\itS_v} (dB re 1 m^2 m^-^3)')
                title({filename; 'Epipelagic layer (20-200 m)'}, 'Interpreter', 'none')
                hold on
%                 ylm = ylim;
%                 scal = 0.5 * (ylm(2) - ylm(1));
%                 offs = ylm(1) + 0.25 * (ylm(2) - ylm(1));
%                 plot(daynight * scal + offs, 'y')
%                 legend([data.channels {'Daylight'}])

                yyaxis right
                b2 = plot(data.time,data.day);
                datetick('x',19)
                xlabel('Time (UTC)')
                ylabel('Diurnal sun cycle')
                legend(b2,'1-Day o 2-Sunset+/-1 hr o 3-Sunrise+/-1 hr o 4-Night')
                grid on
                xlim([min(data.time) max(data.time)])
                ylim([0 5])
            catch % color will not match with rest of the subplots
                warning('Try using Matlab version R2016a or later for better display of summary metrics plot')
                subplot(3,1,1)
                [hAx,hLine1,hLine2] = plotyy(data.time,data.epipelagic',data.time,data.day);
                datetick('x',19)
                xlabel('Time (UTC)')
                xlim(hAx(1),[min(data.time) max(data.time)]) % should be same limit
                xlim(hAx(2),[min(data.time) max(data.time)]) % should be same limit
                ylabel(hAx(1),'{\itS_v} (dB re 1 m^2 m^-^3)') % left y-axis
                ylabel(hAx(2),'Diurnal sun cycle') % right y-axis
                legend(hLine2,'1-Day o 2-Sunset+/-1 hr o 3-Sunrise+/-1 hr o 4-Night')
                grid on
            end

            subplot(3,1,2)
            plot(data.time,data.upper_mesopelagic')
%             xlabel(['Distance (' grid_distance ')']);
            xlabel('Time (UTC)')
            datetick('x',19)
            ylabel('{\itS_v} (dB re 1 m^2 m^-^3)')
            title('Upper mesopelagic layer (200-400 m)')
            grid on
            xlim([min(data.time) max(data.time)])

            subplot(3,1,3)
            plot(data.time,data.lower_mesopelagic')
            legend(data.channels)
%             xlabel(['Distance (' grid_distance ')']);
            xlabel('Time (UTC)')
            datetick('x',19)
            ylabel('{\itS_v} (dB re 1 m^2 m^-^3)')
            title('Lower mesopelagic layer (400-800 m)')
            grid on
            xlim([min(data.time) max(data.time)])
        end

% Haris- same plots with distance - only for checking purpose and referencing to EV files
        if isfield(data, 'lower_mesopelagic')
            figure
            p = get(0,'ScreenSize'); % Set figure size
            set(gcf,'Position',[50 50 p(3)*0.75 p(4)*0.6])
            subplot(3,1,1)
            plot(data.epipelagic')
%             xlabel(['Distance (' grid_distance ')']);
            xlabel('GPS distance (m)');
            ylabel('{\itS_v} (dB re 1 m^2 m^-^3)')
            title('Epipelagic layer vs GPS distance for checking purpose and referencing to EV files only')
            xlim([1 length(data.epipelagic)])
            hold on
            grid on

            subplot(3,1,2)
            plot(data.upper_mesopelagic')
%             xlabel(['Distance (' grid_distance ')']);
            xlabel('GPS distance (m)');
            ylabel('{\itS_v} (dB re 1 m^2 m^-^3)')
            xlim([1 length(data.upper_mesopelagic)])
            title('Upper mesopelagic layer vs GPS distance for checking purpose and referencing to EV files only')
            grid on

            subplot(3,1,3)
            plot(data.lower_mesopelagic')
            legend(data.channels)
%             xlabel(['Distance (' grid_distance ')']);
            xlabel('GPS distance (m)');
            ylabel('{\itS_v} (dB re 1 m^2 m^-^3)')
            xlim([1 length(data.lower_mesopelagic)])
            title('Lower mesopelagic layer vs GPS distance for checking purpose and referencing to EV files only')
            grid on
        end

Plot voyage track

% Haris - 20 June 2018. Plot voyage track on globe without using mapping toolbox
% based on: https://au.mathworks.com/matlabcentral/answers/350195-how-can-you-plot-lines-of-latitude-and-longitude-on-a-globe-without-using-the-mapping-toolbox

        figure % Plot voyage track on globe
        p = get(0,'ScreenSize'); % Set figure size
        set(gcf,'Position',[50 50 p(3)*0.64 p(4)*0.6])

        R = 6371; % earth radius in km
        latspacing = 10;
        lonspacing = 20;

        % lines of longitude:
        [lon1,lat1] = meshgrid(-180:lonspacing:180,linspace(-90,90,300));
        [x1,y1,z1] = sph2cart(lon1*pi/180,lat1*pi/180,R);
        subplot(1,2,1)
        plot3(x1,y1,z1,'-','color',0.8*[1 1 1])
        hold on

        % lines of latitude:
        [lat2,lon2] = meshgrid(-90:latspacing:90,linspace(-180,180,300));
        [x2,y2,z2] = sph2cart(lon2*pi/180,lat2*pi/180,R);
        plot3(x2,y2,z2,'-','color',0.8*[1 1 1])
        axis equal tight off

        [X,Y,Z] = sphere(100);
        surf(X*R*.99,Y*R*.99,Z*R*.99,'facecolor','w','edgecolor','none')

        % Coastline data is predefined to avoid dependency
        coastlat = 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        [xtmp,ytmp,ztmp] = sph2cart(deg2rad(coastlon),deg2rad(coastlat),R);
        plot3(xtmp,ytmp,ztmp,'b','linewidth', 0.85)% plot coastline

        [xtmpn,ytmpn,ztmpn] = sph2cart(deg2rad(data.longitude),deg2rad(data.latitude),R);
        plot3(xtmpn,ytmpn,ztmpn,'r','linewidth', 1.25)% plot voyage track

        % Set azimuth and elevation for southern ocean
        view(-153, -36);
        title({filename; 'Voyage track'}, 'Interpreter', 'none');

        % Standard plot (as subplot)
        subplot(1,2,2)
        hold on; box on; grid on
        plot(data.longitude,data.latitude,'r.');

        % midnight positions
        begin = floor(time(1));
        fin = floor(time(end)) - begin;

        lt = zeros(fin, 1);
        ln = zeros(fin, 1);

        for d = 1:fin
            midnight = find(time >= begin + d, 1);
            lt(d) = data.latitude(midnight);
            ln(d) = data.longitude(midnight);
            text(ln(d), lt(d), datestr(time(midnight), 'yyyy-mm-dd'));
        end
        plot(ln, lt, '+');

        xlabel('Longitude');
        ylabel('Latitude');

        lat = median(data.latitude);
        set(gca, 'DataAspectRatio', [1 cosd(lat) 1 ]);

    end

end

Function for generating echogram plots of the dataset as an image

    function echogram(dataset, position, ttle, location, range, cmap, sun)
    %   echogram plots the dataset as an image.
    %   INPUTS
    %   dataset     2D data to plot (if more than 2D only first slice is
    %               plotted)
    %   position    number of plot heights from bottom of screen to place
    %               plot
    %   ttle        Title of plot
    %   location    String array of labels for start and end of plot
    %   range       Range of colortable used to display data.
    %   cmap        Colormap used to display data [EK500colourmap]
    %   sun         Optional vector drawn on image, usually 1 = day 0 = night

        screen = getScreen();
        [dheight, dwidth] = size(dataset);
        if screen(3) - screen(1) < dwidth + 100
            ll = { location{1}, '2 -->' };
            if nargin < 6
                cmap=EK500colourmap();
            end
            swidth=screen(3) - screen(1) - 200;
            page=0;
            while page * swidth < dwidth
                dstart = page * swidth + 1;
                page = page + 1;
                dend = page * swidth;
                if dend >= dwidth
                    dend = dwidth;
                    ll{2} = location{2};
                end
                ds=dataset(:,dstart:dend,1);
                if nargin < 7 || isempty(sun)
                    sn = [];
                else
                    sn = sun(dstart:dend);
                end
                echogram(ds, position, ttle, ll, range, cmap, sn)
                set(gcf, 'User', dstart-1);
                ticks(gcf);

                ll ={ ['<-- ' num2str(page)], [num2str(page + 2) ' -->']};
            end

            return
        end

        figure
        drawnow     % need to draw figure before setting position on dual screen systems

        imagesc(dataset(:,:,1), range)
        if nargin < 6 || isempty(cmap)
            colormap(EK500colourmap())
        else
            colormap(cmap)
        end

        if nargin > 6 && ~isempty(sun)
            % plot sun between 1/4 and 3/4 height of image.
            hold on
            yl = ylim;
            scl = 0.5 * (yl(1) - yl(2)) / (max(sun) - min(sun));
            off = yl(2) + 0.25 * (yl(1) - yl(2)) - min(sun) * scl;
            plot(sun * scl + off, 'r')
        end

        set(zoom,'ActionPostCallback',@ticks)
        set(pan,'ActionPostCallback',@ticks)

        if tickformat == LAT
            xlabel('Latitude')
        elseif tickformat == LONG
            xlabel('Longitude')
        elseif tickformat == INTERVAL
            xlabel(['Distance (' grid_distance ')'])
        else
            xlabel('Time (UTC)')
        end

        ylabel('Depth (m)')
        title(ttle, 'Interpreter','none');
        colorbar;

        % fit figure on "screen"
        % calculate image size
        left = 80;
        bot  = 50;
        width = dwidth + 2 * left;
        height = dheight + 2 * bot;
        base = 100 + floor(position * 1.4 * height);
        set(gcf, 'Position',  [screen(1) base width height]);
        pos = get(gcf, 'Position');

        text(0, -10, location{1});
        text(dwidth, -10, location{2}, 'HorizontalAlignment', 'right');

        % keep figure from going over top of screen
        opos = get(gcf, 'OuterPosition');
        above = opos(2) + opos(4) - screen(4);
        if above > 0
            pos(2) = pos(2) - above;
            set(gcf, 'Position', pos);
        end

        % if figure is too wide for screen
        if screen(3) - screen(1) < width
            left = (screen(3) - screen(1) - opos(3) + pos(3) - dwidth) / 2;
            if left < 30
                left = 30;
            end
        end

        % set image to one pixel per cell
        set(gca, 'Units', 'pixels');
        set(gca, 'Position', [left, bot, dwidth, dheight]);
        set(gca, 'Units', 'normalized');

        button_panel = uibuttongroup(gcf, ...
            'SelectionChangeFcn', @xFormat, ...
            'Units',        'pixels', ...
            'Position',     [0 0 600 20]);

        uicontrol(button_panel, ...
            'Style',        'radiobutton', ...
            'TooltipString', 'Show time across X axis', ...
            'Tag',          'time', ...
            'String',       'Time', ...
            'Value',        tickformat == TIME, ...
            'User',         TIME, ...
            'Units',        'pixels', ...
            'Position',     [0 0 100 20]);
        uicontrol(button_panel, ...
            'Style',        'radiobutton', ...
            'TooltipString', 'Show latitude across X axis', ...
            'Tag',          'latitude', ...
            'String',       'Latitude', ...
            'Value',        tickformat == LAT && degformat == DEG, ...
            'User',         LAT, ...
            'Units',        'pixels', ...
            'Position',     [100 0 100 20]);
        uicontrol(button_panel, ...
            'Style',        'radiobutton', ...
            'TooltipString', 'Show longitude across X axis', ...
            'Tag',          'longitude', ...
            'String',       'Longitude', ...
            'Value',        tickformat == LONG && degformat == DEG, ...
            'User',         LONG, ...
            'Units',        'pixels', ...
            'Position',     [200 0 100 20]);
        uicontrol(button_panel, ...
            'Style',        'radiobutton', ...
            'TooltipString', 'Show latitude across X axis in deg:min', ...
            'Tag',          'lat:min', ...
            'String',       'Lat (d:m)', ...
            'Value',        tickformat == LAT && degformat == MIN, ...
            'User',         LAT, ...
            'Units',        'pixels', ...
            'Position',     [300 0 100 20]);
        uicontrol(button_panel, ...
            'Style',        'radiobutton', ...
            'TooltipString', 'Show longitude across X axis in deg:min', ...
            'Tag',          'long:min', ...
            'String',       'Long (d:m)', ...
            'Value',        tickformat == LONG && degformat == MIN, ...
            'User',         LONG, ...
            'Units',        'pixels', ...
            'Position',     [400 0 100 20]);
        uicontrol(button_panel, ...
            'Style',        'radiobutton', ...
            'TooltipString', 'Show distance number across X axis', ...
            'Tag',          'distance', ...
            'String',       'Distance', ...
            'Value',        tickformat == INTERVAL, ...
            'User',         INTERVAL, ...
            'Units',        'pixels', ...
            'Position',     [500 0 100 20]);

        % update axis
        ticks(gcf)
    end

    function [EK500cmap]=EK500colourmap()
    % EK500colourmap is the colour map used by EK500

        EK500cmap = [255   255   255   % white
            159   159   159   % light grey
            95    95    95   % grey
            0     0   255   % dark blue
            0     0   127   % blue
            0   191     0   % green
            0   127     0   % dark green
            255   255     0   % yellow
            255   127     0   % orange
            255     0   191   % pink
            255     0     0   % red
            166    83    60   % light brown
            120    60    40]./255;  % dark brown
    end

    function xFormat(panel,event)
    % Callback used when the user selects a different X axis label

        tickformat = get(event.NewValue, 'User');

        if tickformat == LAT
            xlabel('Latitude')
        elseif tickformat == LONG
            xlabel('Longitude')
        elseif tickformat == INTERVAL
            xlabel(['Distance (' grid_distance ')'])
        else
            xlabel('Time (UTC)')
        end

        tag = get(event.NewValue, 'Tag');
        if length(tag) > 3 && strcmp(tag(end-2:end), 'min')
            degformat = MIN;
        else
            degformat = DEG;
        end

        fig = get(panel, 'Parent');
        ticks(fig, event)
    end

    function ticks(figure,~)
    % Callback used to draw tick marks
        caxes=get(figure,'CurrentAxes');

        % depth ticks
        ytick=get(caxes,'YTick');

        set(caxes,'YTickLabel',depth(floor(ytick)));

        offset = 0;
        x_lim=get(caxes,'XLim');
        set(caxes,'Units','Pixels');
        pos = get(caxes, 'Position');
        width = pos(3);
        user = get(figure, 'User');
        if ~isempty(user) && isfloat(user)
            offset = user;
        end
        x_lim = x_lim + offset;

        %
        % Label X axis using latitude or longitude
        %
        if tickformat == LAT || tickformat == LONG

            if tickformat == LONG
                ticker = longitude;
            else
                ticker = latitude;
            end

            ticker = ticker(ceil(x_lim(1)):floor(x_lim(2)));
            mint = min(ticker);
            maxt = max(ticker);
            trange = (maxt - mint)/width*100;
            if degformat == MIN
                if trange > 2       % more than 2 degrees per 100 pixels
                    tock = 1;       % show whole degrees
                elseif trange > .5  % more than 1 degree per 200 pixels
                    tock = 4;       % show 15 minutes
                elseif trange > .05
                    tock = 12;      % show 5 minutes
                else
                    tock = 60;      % show minutes
                end
            else
                if trange > 10      % more than 1 degree per 10 pixels
                    tock = .1;      % show every 10 degrees
                elseif trange > 5   % more than 1 degree per 20 pixels
                    tock = .2;      % show every 5 degrees
                elseif trange > 1   % more than 1 degree per 100 pixels
                    tock = 1;       % show each degree
                elseif trange > .5  % more than 1 degree per 200 pixels
                    tock = 2;       % show half degrees
                else
                    tock = 10;      % show tenth degrees
                end
            end

            tickedge = floor(ticker * tock);
            tk=tickedge;
            tk(end) = [];
            tickedge(1) = [];
            xtick = find(tk ~= tickedge);
            xtick = xtick + 1;
            xlabels = num2str(ticker(xtick),'%4.0f');
            if tock > 1
                if degformat == MIN
                    xdeg = round(ticker(xtick)*60)/60;
                    xmin = xdeg - fix(xdeg);
                    xmin = abs(xmin) * 60;
                    colon= char(ones(length(xmin),1) * ':');
                    xlabels = [ num2str(fix(xdeg)) colon num2str(xmin, '%02.0f') ];
                else
                    if tock <= 10
                        xlabels = num2str(ticker(xtick),'%6.1f');
                    else
                        xlabels = num2str(ticker(xtick),'%7.2f');
                    end
                end
            end
            xtick = xtick + ceil(x_lim(1));

        elseif tickformat == INTERVAL
            xtick = 0:max(1,10^(floor((log10((x_lim(2) - x_lim(1))/width*2000))-1))):x_lim(2);
            xlabels = xtick;

        else
            %
            % Label X Axis using Time
            %

            start=time(ceil(x_lim(1)));
            finish=time(floor(x_lim(2)));

            len=(finish-start)/width*100;
            if len < .01
                format = 15;    % 'HH:MM'
                tock=96;        % quarter hour
            elseif len < .05
                format = 15;    % 'HH:MM'
                tock=24;        % hour
            elseif len < .2
                format = 'yyyy-mm-dd HH:MM';
                tock=4;         % 6 hr
            else
                format=29;      % 'yyyy-mm-dd'
                tock=1;         % day
            end

            xtock=(ceil(start*tock):1:finish*tock)/tock;
            if isempty(xtock); xtock = start; end
            xtick(length(xtock))=0;
            for i=1:length(xtock)
                xtick(i)=find(time>=xtock(i),1);
            end

            xtick(diff(xtick) == 0) = [];
            xlabels = datestr(time(xtick), format);
        end

        set(caxes,'XTick',xtick - offset);
        set(caxes,'XTickLabel',xlabels);
    end

    function fig = write_echogram(dataset, imagefile, file, channel, ttle, location, range, cmap, fig)
    % write_echogram writes the echogram to an image file.

    % Haris 24 January 2019 - modified: The 'PNG' image file had issues with
    % width, height, and font sizes. This was creating an image file with
    % overlapping fonts that were out of the image box.
    % Some lines below have been modified to write an image for better display.
    % Original code is commented i.e. not deleted.

        [~, name, ext] = fileparts(file);

        % size figure to hold full data set
        dotspercell = 1;
        resolution = 300;
        fontsize = 1200 * dotspercell / resolution;
        dwidth = size(dataset,2);
        wdth = dwidth*dotspercell/resolution;
        hght = size(dataset,1)*dotspercell/resolution;
%         left = 0.5 + 50 / resolution;
%         bot  = 4 * fontsize / 72;
%         width = wdth + 2 * left;
%         height = hght + 2 * bot;
        left = 0.2 + 50 / resolution;
        bot  = 5.5 * fontsize / 72;
        width = wdth + 2.8 * left;
        height = hght + 2 * bot;

        if nargin < 9 || isempty(fig)
            fig = figure;
        else
            figure(fig)
            oldpos = get(fig, 'Position');
            dheight = height;
            height = dheight + oldpos(4);
            set(fig, 'Position', [0, 0.5, width, height ] );
            children = get(fig, 'Children');
            for i = length(children):-1:1
                if ~strcmp(get(children(i), 'Tag'), 'Colorbar')
                    set(children(i), 'Units', 'inches');
                    chpos = get(children(i), 'Position');
                    chpos(2) = chpos(2) + dheight;
                    set(children(i), 'Position',chpos);
                end
            end
        end

        set(fig, 'Units', 'inches');
        set(fig, 'Position', [0, 0.5, width, height ] );

        set(fig, 'PaperUnits', 'inches');
        set(fig, 'PaperSize', [width height]);
        set(fig, 'PaperPositionMode', 'manual');
        set(fig, 'PaperPosition', [0 0 width height]);

        ax = axes('Units', 'inches', 'FontSize', fontsize, 'Position', [left, bot, wdth, hght]); % Haris-the fontsize set here is not holding after colormap
        imagesc(dataset, range);

        if isempty(cmap)
            colormap(ax, EK500colourmap)
        else
            colormap(ax, cmap)
        end

        set(ax,'FontSize',5); % Haris- added to set fontsize

        if tickformat == LAT
            xlabel('Latitude')
        elseif tickformat == LONG
            xlabel('Longitude')
        elseif tickformat == INTERVAL
            xlabel(['Distance (' grid_distance ')'])
        else
%             xlabel('TIME (UTC)')
            xlabel('Time (UTC)','FontSize', 6)
        end

%         ylabel('Depth (m)')
        ylabel('Depth (m)','FontSize', 6)

        if iscell(ttle)
%             title(ttle, 'Interpreter','none')
            title(ttle, 'Interpreter','none','FontSize', 5)
        else
%             title({ [ name ext ' ' channel ] ;  ttle }, 'Interpreter','none')
            name_n = name;
            name_n(name_n == '_') = '-'; % Haris- replace '_' with '-' for Interpreter
            title({[ name_n ext ' ' channel ];'Mean {\itS_v} (dB re 1 m^2 m^-^3)'},'FontSize', 5) % Haris - for better display of symbol and unit
        end
        step = 10^ceil(log10((range(2) - range(1)) / 6));
        if (range(2) - range(1)) / step < 1.5
            step = step / 5;
        elseif (range(2) - range(1)) / step < 3
            step = step / 2;
        end

        colorbar('EastOutside', 'peer', ax, 'FontSize', fontsize, 'YTick', step * ceil(range(1)/step):step:range(2)); % For text - color bar
        set(ax, 'Position', [left, bot, wdth, hght]);
        text(0, -15, location{1}, 'FontSize', fontsize); % For text - transect start
        text(dwidth, -15, location{2}, 'HorizontalAlignment', 'right', 'FontSize', fontsize); % For text - transect end

        ticks(fig)
        drawnow;

        if strcmp(imagefile, '-')
            % don't write file or close figure
        else
            driver = '-dpng';

            if ~isempty(channel)
                channel = ['_' channel];
            end

            % does image file end in a '?'
            ask = 0;
            if ~isempty(imagefile) && imagefile(end) == '?';
                ask = 1;
                imagefile = imagefile(1:end-1);
            end
            % is an empty character string
            if isempty(imagefile)
                imagefile = [ file channel '.png' ];
            end
            % is a driver
            if imagefile(1) == '-' && imagefile(2) == 'd'
                driver = imagefile;
                imagefile = [ file channel '.' imagefile(3:end) ];
            end
            % is a directory
            if isdir(imagefile)
                imagefile = fullfile(imagefile, [ name ext channel '.png' ]);
            end
            % ask the user if the image file ended in ?
            if ask
                [imagefile, ipath] = uiputfile(imagefile);
                if imagefile == 0
                    return
                end
                imagefile = fullfile(ipath, imagefile);
            end

            print(fig, driver, imagefile, ['-r' num2str(resolution)]);

            close;
        end
    end

    function vardata = getNetcdfVar(ncid, vid)
    % read a variable from netcdf
        if ischar(vid)
            vid = netcdf.inqVarID(ncid, vid);
        end
        vardata = netcdf.getVar(ncid, vid);
        try
            vfill = netcdf.getAtt(ncid, vid, '_FillValue');
            vardata(vardata == vfill) = NaN;
        catch
        end
    end

    function nmean = nmean(data)
    % calculate mean ignoring NaN values
        nan = isnan(data);
        data(nan) = 0;
        count = sum(~nan);
        count(count==0) = NaN;      % prevent divide by 0
        nmean = sum(data)./count;
    end

    function screen = getScreen()
    % calculate plottable area of screen, this gets hairy for multiple monitors
    % returns [left top width height]
        screen = get(0, 'ScreenSize');

        mpos = get(0,'MonitorPosition');
        if ispc
            screen(1) = min(mpos(:,1));
            screen(3) = max(mpos(:,3));
        elseif isunix
            screen(1) = min(mpos(:,1));
            screen(3) = max(mpos(:,1) + mpos(:,3));
        elseif ismac
        end
    end

Function for generating *.sv.csv and *.gps.csv file from data structure

    function svcsv(data)
    % generate .sv.csv and .gps.csv file from data structure
        [path,name,ext] = fileparts(data.file);

        ns = length(data.depth);
        h = (data.depth(end) - data.depth(1)) / (ns-1);
        srange = sprintf('%g, %g, %g', data.depth(1) - h/2, data.depth(end) + h/2, ns);

        if isfield(data, 'channels')
            for s = length(data.channels):-1:1
                sv(s) = fopen(fullfile(path,[name ext '_' data.channels{s} '.sv.csv']),'w');
            end
        else
            sv = fopen(fullfile(path,[name ext '.sv.csv']),'w');
        end
        for s = 1 : length(sv)
            fprintf(sv(s), 'Ping_date, Ping_time, Ping_milliseconds, Range_start, Range_stop, Sample_count,\n');
        end

        gps = fopen(fullfile(path,[name ext '.gps.csv']),'w');
        fprintf(gps,'GPS_date, GPS_time, GPS_milliseconds, Latitude, Longitude\n');
        for i=1 : length(data.time)
            timestr = datestr(data.time(i), 'yyyy-mm-dd,HH:MM:SS,FFF');
            fprintf(gps,timestr);
            fprintf(gps,'%s,%g,%g\n', timestr, data.latitude(i), data.longitude(i));
            for s = 1 : length(sv)
                fprintf(sv(s), '%s, %s', timestr, srange);
                fprintf(sv(s), ', %g', data.Sv(:,i,s));
                fprintf(sv(s), '\n');
            end
        end
        fclose(gps);
        for s = 1 : length(sv)
            fclose(sv(s));
        end
    end

Function for generating *.csv file from summary layer metrics

    function csv(data, file)
    % generate .csv file from summary indices
        csv.Time = datestr(data.time, 'yyyy-mm-dd HH:MM:SS');
        csv.Longitude = data.longitude;
        csv.Latitude = data.latitude;
        if isfield(data, 'day')
            dsrn = 'DSRN';
            csv.Daylight = dsrn(data.day)';
        end
        for layer = {'epipelagic', 'upper_mesopelagic', 'lower_mesopelagic'}
            if isfield(data, layer)
                if isfield(data, 'channels') && length(data.channels) > 1
                    for i = 1 : length(data.channels)
                        field = sprintf('%s_%s', layer{1}, data.channels{i});
                        csv.(field) = data.(layer{1})(i,:);
                    end
                end
            end
        end
        if isempty(file)
            file = [data.file '.csv'];
        end
        struct2txt(csv, file);
    end

Function for generating *.inf and *.gps.csv files from data structure

    function info(data)
    % generate .inf and .gps.csv file from data structure
        [path,name,ext] = fileparts(data.file);

        gps = fopen(fullfile(path,[name ext '.gps.csv']),'w');
        fprintf(gps,'GPS_date,GPS_time,GPS_milliseconds,Latitude,Longitude\n');
        for i=1:length(data.time)
            fprintf(gps,datestr(data.time(i), 'yyyy-mm-dd,HH:MM:SS,FFF,'));
            fprintf(gps,'%g,%g\n', data.latitude(i), data.longitude(i));
        end
        fclose(gps);

        inf = fopen(fullfile(path,[name ext '.inf']),'w');
        fprintf(inf,'\nData File:     ');
        fprintf(inf, [name ext]);

        fprintf(inf,'\n\nIntervals : %d\n', length(data.time));

        distance = length(data.time)/1000;
        scale = data.grid_distance;
        if scale(end) == 'm'
            scale(end) = [];
            if scale(end) == 'k';
                scale(end) = [];
                distance = distance * 1000;
            end
            if scale(end) == 'N'
                scale(end) = [];
                distance = distance * 1852;
            end
        end
        try
            distance = distance * str2double(scale);
        catch
            distance = distance * 1000; % if unparsable assume 1km
        end

        duration = (data.time(end) - data.time(1)) * 24;
        speed = distance / duration;
        fprintf(inf,'\nNavigation Totals:\nTotal Time:         % 9.4f hours\n', duration);
        fprintf(inf,'Total Track Length: % 9.4f km\n', distance);
        fprintf(inf,'Average Speed:    % 9.4f km/hr (%.4f knots)\n', speed, speed / 1.852);

        fprintf(inf,'\nStart of Data:\nTime:  ');
        fprintf(inf,datestr(data.time(1),'yyyy-mm-dd HH:MM:SS.FFF'));
        dv=datevec(data.time(1));
        dv(2:6)=0;
        fprintf(inf,'  JD%d\n',floor(data.time(1) - datenum(dv)));
        fprintf(inf,'Lon:  % 9.4f    Lat: % 9.4f\n', data.longitude(1), data.latitude(1));

        fprintf(inf,'\nEnd of Data:\nTime:  ');
        fprintf(inf,datestr(data.time(end),'yyyy-mm-dd HH:MM:SS.FFF'));
        dv=datevec(data.time(end));
        dv(2:6)=0;
        fprintf(inf,'  JD%d\n',floor(data.time(end) - datenum(dv)));
        fprintf(inf,'Lon:  % 9.4f    Lat: % 9.4f\n', data.longitude(end), data.latitude(end));

        fprintf(inf,'\nLimits\n');
        fprintf(inf,'Minimum Longitude:     % 9.4f   Maximum Longitude:     % 9.4f\n', ...
            min(data.longitude), max(data.longitude));
        fprintf(inf,'Minimum Latitude:      % 9.4f   Maximum Latitude:      % 9.4f\n', ...
            min(data.latitude), max(data.latitude));

        fclose(inf);
    end

end

ans = 

  struct with fields:

                        file: 'Q:\Temporary_working_area\Investigator_example_data_for_web_page\IMOS_SOOP-BA_AE_20190119T231825Z_VLMJ_FV02_Investigator-EK60-18-38-70-120_END-20190125T003711Z_C-20191015T045235Z.nc'
                    location: {'Hobart'  'Antarctica'}
               grid_distance: '1 km'
                    latitude: [2048×1 double]
                   longitude: [2048×1 double]
                       depth: [120×1 double]
                        time: [2048×1 double]
                          sv: [120×2048×4 double]
                          qc: [120×2048×4 int8]
                          pg: [120×2048×4 double]
                       svraw: [120×2048×4 double]
            background_noise: [4×2048 double]
                         snr: [120×2048×4 double]
    motion_correction_factor: [120×2048×4 double]
                   frequency: [4×1 single]
                    channels: {'18kHz'  '38kHz'  '70kHz'  '120kHz'}
                 temperature: [120×2048 double]
                    salinity: [120×2048 double]
                  soundspeed: [120×2048 double]
             soundabsorption: [120×2048×4 double]
                      abs_sv: [120×2048×4 double]
                      abs_Sv: [120×2048×4 double]
              uncorrected_sv: [120×2048×4 double]
              uncorrected_Sv: [120×2048×4 double]
                     history: '2019-06-27T05:21:31Z nau016 Inferred temperature and salinity read from \\oa-osm-03-hba.it.csiro.au\OA_OCEANDATA_LIBRARY_MAIN\climatologies\synTS\NRT06\. refer: http://dx.doi.org/10.1016/j.dsr.2010.05.010 http://www.cmar.csiro.au/cars/ http://www.marine.csiro.au/eez_data/doc/synTS.html ↵2019-06-27T05:21:31Z nau016 Environmental variables read from CARS refer: http://www.cmar.csiro.au/cars/ ↵2019-06-27T05:21:49Z nau016 Sound speed (Mackenzie 1981) and absorption (Francois and Garrison 1982) corrections applied.↵IMOS_SOOP-BA_AE_20190119T231825Z_VLMJ_FV02_Investigator-EK60-18-38-70-120_END-20190125T003711Z_C-20190627T052152Z↵ 2019-10-15T04:52:35Z  by nau016 on LOOT-HF PCWIN64 at 2019-06-27T15:18:43 local  using process_BASOOP; Matlab; IMOS toolbox; Echoview using 2.5 $Id: basoop.m 1216 2019-06-23 23:18:17Z  $; 9.4.0.813654 (R2018a); 2.5.38 - ; 10.0.255.36628'
                  epipelagic: [4×2048 double]
           upper_mesopelagic: [4×2048 double]
           lower_mesopelagic: [4×2048 double]
                         day: [2048×1 double]
                          Sv: [120×2048×4 double]
                       Svraw: [120×2048×4 double]
                     mean_Sv: [1×2048×4 double]
                        NASC: [1×2048×4 double]
                  mean_Svraw: [1×2048×4 double]
                     NASCraw: [1×2048×4 double]

Published with MATLAB® R2019b