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function spectrum_analyzer = E4440a_take_data(varargin)
% This script reads data from E440a spectrum analyzer and saves it to a file
%
% Eugeniy E. Mikhailov eemikh@wm.edu
% Gleb Romanov   gromanov@hellok.org
% 6/20/2013
% 7/20/2015 added a choice for saving and plotting
% 7/27/2015 added a choice to save only specific channels 

%% some sane defaults

nVarargs = length(varargin);
if (nVarargs > 3 )
    error ('wrong number of arguments');
end
if (nVarargs < 3 )
    channels_to_grab_flag = [ true, true, true];  % grab all channels
else
    channels_to_grab_flag = varargin{3};
end
if (nVarargs < 2 )
    data_plot_flag = true;  % Default to plot Data 
else
    data_plot_flag = varargin{2};
end
if (nVarargs < 1 )
    data_save_flag = true; % Default to save data
else
    data_save_flag = varargin{1};
end




%% Data file parameters
data_prefix = 'S';
data_path = 'Z:\qol_comp_data\data\';
run_number_file = 'Z:\qol_comp_data\data\autofile\runnum.dat';

%% Windows computer parameters
if ispc 
    % Define instrument parameters
    board_index = 0;
    gpib_address = 21;
    bufSize = 100000;

    %% Find and initialize instrument
    obj1 = instrfind('Type', 'gpib', 'BoardIndex', board_index, 'PrimaryAddress', gpib_address, 'Tag', '');
    % alternatively
    % obj1 = instrfind('Type', 'visa-gpib', 'RsrcName', 'GPIB0::21::INSTR', 'Tag', '');

    % Create the GPIB object if it does not exist
    % otherwise use the object that was found.
    if isempty(obj1)
        obj1 = gpib('NI', board_index, gpib_address);
    else
        fclose(obj1);
        obj1 = obj1(1);
    end

    % Adjust the buffers so the traces fit.
    % Do this before fopen(obj1);
    obj1.InputBufferSize  = bufSize;
    obj1.OutputBufferSize = bufSize;

    %% Connect to instrument object, obj1.
    fopen(obj1);
end

%% Unix specific parameters
if isunix 
    obj1=lgpib('Agilent_E4405b')
end

%disp('--------------------')
device_string = query(obj1, '*IDN?');
%disp(horzcat('Connected to ', device_string));

% Communicating with instrument object, obj1.
%
% You can send commands using:
% fprintf(obj1, '_command_');
%
% Or read stuff using:
% _data_ = query(obj1, '_command_');
%disp('Reading traces...');

%% Find number of points
Npoints_string = query(obj1, ':SENSe:SWEep:POINts?');
Npoints = sscanf(Npoints_string, '%f');
%Npoints=4695;

tr1 = NaN(Npoints,1);   %  prefill traces with NaN 
tr2 = NaN(Npoints,1);
tr3 = NaN(Npoints,1);

%% Read traces
% switch to ASCII trace transfer
fwrite(obj1, ':FORMAT:TRACE:DATA ASCII');

if channels_to_grab_flag(1);      
tr1_string = query(obj1, ':TRACE:DATA? TRACE1;'); % select traces to grab
end 

if channels_to_grab_flag(2);
tr2_string = query(obj1, ':TRACE:DATA? TRACE2;');

end
if channels_to_grab_flag(3); 
tr3_string = query(obj1, ':TRACE:DATA? TRACE3;');
end 

%disp('Reading Spectrum Analyzer parameters...');
%% Read various spectrum analyzer parameters
freq_start_string = query(obj1, ':SENSE:FREQUENCY:START?');
freq_stop_string = query(obj1, ':SENSE:FREQUENCY:STOP?');
freq_center_string = query(obj1, ':SENSE:FREQUENCY:CENTER?');
freq_span_string = query(obj1, ':SENSE:FREQUENCY:SPAN?');
amplitude_units_string = query(obj1, ':UNIT:POWER?');
attenuation_string = query(obj1, ':SENSE:POWER:RF:ATTenuation?');
ref_level_string = query(obj1, ':DISPLAY:WINDOW:TRACE:Y:SCALE:RLEVEL?');

log_scale_string = query(obj1, ':DISPlAY:WINDOW:TRACE:Y:SCALE:PDIVISION?');

rbw_string = query(obj1, 'SENSE:BANDWIDTH:RESOLUTION?');
vbw_string = query(obj1, 'SENSE:BANDWIDTH:VIDEO?');
sweep_time_string = query(obj1, ':SENSE:SWEEP:TIME?');

%% Disconnect from instrument object, obj1.
if ispc
    % windows needs to close the file
    fclose(obj1);
end

%disp('Spectrum Analyzer data communincation is done');

%% Convert the grabbed traces from strings into vectors 
if channels_to_grab_flag(1);
tr1 = sscanf(tr1_string, '%f,');
end

if channels_to_grab_flag(2);
tr2 = sscanf(tr2_string, '%f,');
end 

if channels_to_grab_flag(3);
tr3 = sscanf(tr3_string, '%f,');
end 

% Transpose the vectors
tr1 = tr1';
tr2 = tr2';
tr3 = tr3';

% Create the frequency vector
freq_start = sscanf(freq_start_string, '%f');
freq_stop = sscanf(freq_stop_string, '%f');
freq = linspace(freq_start,freq_stop, Npoints);



% Create spectrum analyzer structure
spectrum_analyzer.traces=[tr1',tr2', tr3'];
spectrum_analyzer.freq=freq';
spectrum_analyzer.RBW=sscanf(rbw_string, '%f');
spectrum_analyzer.VBW=sscanf(vbw_string, '%f');
spectrum_analyzer.sweep_time=sscanf(sweep_time_string, '%f');

%% Save data to a file
if (data_save_flag)
    % Get full path of the file to save
    save_to_file = qol_get_next_data_file( data_prefix, data_path, run_number_file );
    %
    % Write the data to a file
    %disp(' ');
    disp(horzcat('Saving data to ',save_to_file));
    save_to_file_handle = fopen(save_to_file,'wt');
    fprintf(save_to_file_handle,'%s',horzcat('# ', datestr(clock)));
    fprintf(save_to_file_handle,'\n');
    fprintf(save_to_file_handle,'%s',horzcat('# Device:', '   ', device_string));
    fprintf(save_to_file_handle,'%s',horzcat('# Frequency center, Hz', '   ', freq_center_string));
    fprintf(save_to_file_handle,'%s',horzcat('# Frequency span, Hz', '   ', freq_span_string));
    fprintf(save_to_file_handle,'%s',horzcat('# Frequency start, Hz', '   ', freq_start_string));
    fprintf(save_to_file_handle,'%s',horzcat('# Frequency stop, Hz', '   ', freq_stop_string));
    fprintf(save_to_file_handle,'%s',horzcat('# Amplitude units      ', amplitude_units_string));
    fprintf(save_to_file_handle,'%s',horzcat('# Attenuation      ', attenuation_string));
    fprintf(save_to_file_handle,'%s',horzcat('# Reference level     ', ref_level_string));
    fprintf(save_to_file_handle,'%s',horzcat('# Log scale    ', log_scale_string));
    fprintf(save_to_file_handle,'%s',horzcat('# Resolution bandwidth, Hz', '   ', rbw_string));
    fprintf(save_to_file_handle,'%s',horzcat('# Video bandwidth, Hz', '   ', vbw_string));
    fprintf(save_to_file_handle,'%s',horzcat('# Sweep time, seconds', '   ', sweep_time_string));
    
    % saving traces data
    data = [freq; tr1; tr2; tr3];
    fprintf(save_to_file_handle,'%f\t%f\t%f\t%f\n',data);
    % Close the file
    fclose(save_to_file_handle);
end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


if (data_plot_flag)
    %% Plot raw traces
    %
    % Open a window
    figure111 = figure(111);
    %close(figure111);
    %figure1 = figure(111);
    %
    % Create axes
%     axes1 = axes('Parent',figure111,'YGrid','on','XGrid','on','FontSize',14);
%     box(axes1,'on');
%     hold(axes1,'all');
    %ylim([-2,12])
    %ylim([-85,-70])
    %
    % Create plot
    plot(freq/1e6, tr1, 'Color', [1 0 0], 'DisplayName', 'Trace 1'); hold on
    plot(freq/1e6, tr2, 'Color', [0 0 0], 'DisplayName', 'Trace 2');
    plot(freq/1e6, tr3, 'Color', [0 0 1], 'DisplayName', 'Trace 3'); hold off
    
%     plot(freq/1e6,tr1,'Color',[1 0 0],'Parent',axes1,'DisplayName','Trace 1')
%     plot(freq/1e6,tr2,'Color',[0 0 0],'Parent',axes1,'DisplayName','Trace 2')
%     plot(freq/1e6,tr3,'Color',[0 0 1],'Parent',axes1,'DisplayName','Trace 3')
%     
    % Create xlabel
    xlabel('Detection frequency, MHz','FontSize',14);
    %
    % Create ylabel
    ylabel('Noise power, dBm','FontSize',14);
    %
    % Show legend
    legend('show');
    grid on;
    
    
   
end

%drawnow;



%% Finish up and cleanup
% Close all opened files
fclose('all');

% Bring focus back to the command window
%commandwindow;