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  </style></head><body><div class="content"><pre class="codeinput">clear <span class="string">all</span>
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close <span class="string">all</span>

<span class="comment">%cd('/home/bandma01/Documents/WERAs/')</span>
cd(<span class="string">'/home/bandma01/hfr-data-processing/calibrations/'</span>)

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site = <span class="string">'PAO'</span>;
<span class="comment">% site = 'PAB';</span>

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cd(site)

<span class="comment">% system</span>
<span class="keyword">for</span> sys = 1:2
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    <span class="keyword">if</span> sys == 1
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        systm = <span class="string">'Helzel'</span>;
    <span class="keyword">elseif</span> sys == 2
        systm = <span class="string">'Flament'</span>;
    <span class="keyword">end</span>

    clear <span class="string">J</span> <span class="string">I</span> <span class="string">E</span> <span class="string">Phase</span> <span class="string">calib_file</span> <span class="string">calib_hr</span> <span class="string">calib_jd</span> <span class="string">calib_min</span> <span class="string">calib_time</span> <span class="string">calib_value</span>
    clear <span class="string">calib_year</span> <span class="string">d</span> <span class="string">data</span> <span class="string">delta_phase_obs</span> <span class="string">delta_phase_th</span> <span class="string">gps_data</span> <span class="string">index_timecalib</span>
    clear <span class="string">theta_pairs</span>

    <span class="keyword">if</span> strcmp(site,<span class="string">'PAO'</span>) == 1

        load(<span class="string">'HelzelPAO_Track_29-OCT-14 183138.mat'</span>)

    <span class="keyword">elseif</span> strcmp(site,<span class="string">'PAB'</span>) == 1

        <span class="keyword">if</span> strcmp(systm,<span class="string">'Helzel'</span>) == 1
            load(<span class="string">'HelzelPAB_Track_30-OCT-14 175446.mat'</span>)
        <span class="keyword">elseif</span> strcmp(systm,<span class="string">'Flament'</span>) == 1
            load(<span class="string">'FlamentPAB_Track_30-OCT-14 182008.mat'</span>)
        <span class="keyword">end</span>

    <span class="keyword">end</span>
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    <span class="comment">% phases and time of calibration</span>
    <span class="keyword">if</span> strcmp(site,<span class="string">'PAO'</span>) == 1
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        cd(<span class="string">'2014302'</span>)
    <span class="keyword">elseif</span> strcmp(site,<span class="string">'PAB'</span>) == 1
        cd(<span class="string">'2014303'</span>)
    <span class="keyword">end</span>

    <span class="comment">% list files</span>
    clear <span class="string">d</span>
    d = dir(<span class="string">'*.mat'</span>);       <span class="comment">% returns a structure with name, date, bytes, isdir, datenum</span>
    Nfiles = length(d);     <span class="comment">% nombre de fichiers a analyser</span>


    <span class="comment">% look at the names of files and extract information</span>
    <span class="keyword">for</span> c = 1:Nfiles
        calib_year(c) = str2double(d(c).name(1:4));
        calib_jd(c) = str2double(d(c).name(5:7));
        calib_hr(c) = str2double(d(c).name(8:9));
        calib_min(c) = str2double(d(c).name(10:11));

        load(d(c).name,<span class="string">'phase'</span>)

        Phase(:,c) = phase;
    <span class="keyword">end</span>
    clear <span class="string">phase</span>

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    <span class="comment">% for each time stamp (column) compute phase difference between 2</span>
    <span class="comment">% consecutive antennas (row)</span>
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    delta_phase_obs = modsym(diff(Phase,1),180);

    To = datenum(2014,01,01,0,0,0);

    <span class="comment">% add 20 sec to center calibration time</span>
    calib_time = To + calib_jd -1 + calib_hr./24 + calib_min/24/60 + 20/24/3600;
    <span class="comment">% datevec(calib_time)</span>

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        clear <span class="string">calib_year</span> <span class="string">calib_jd</span> <span class="string">calib_hr</span> <span class="string">calib_min</span>

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    <span class="keyword">if</span> strcmp(site,<span class="string">'PAO'</span>) == 1
        <span class="comment">% calib time 2min34sec late wrt GPS</span>
        calib_time = calib_time + 2/24/60 + 34/24/3600;
    <span class="keyword">end</span>
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    disp([<span class="string">'calibrations started at '</span> datestr(calib_time(1)) <span class="string">' and ended at '</span> datestr(calib_time(end))])
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    <span class="comment">% separate between calibrations made with Helzel's system and Flament's system</span>
    <span class="comment">% date of new calibration files</span>
    <span class="comment">% Helzel 2014-10-30 16:52 to 17:54</span>
    <span class="comment">% Flament 2014-10-30 17:55 to 18:20</span>
    T1 = datenum(2014,10,30,17,55,00);
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        clear <span class="string">J</span>
        <span class="keyword">if</span> strcmp(systm,<span class="string">'Helzel'</span>) == 1
            J = find(calib_time &gt; T1);
        <span class="keyword">elseif</span> strcmp(systm,<span class="string">'Flament'</span>) == 1
            J = find(calib_time &lt; T1);
        <span class="keyword">end</span>
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        <span class="comment">% remove unwanted data to avoid confusion!</span>
<span class="comment">%         calib_year(J)=[];</span>
<span class="comment">%         calib_jd(J)=[];</span>
<span class="comment">%         calib_hr(J)=[];</span>
<span class="comment">%         calib_min(J)=[];</span>
        Phase(:,J)=[];
        delta_phase_obs(:,J)=[];
        calib_time(J)=[];
        d(J)=[];
        clear <span class="string">c</span> <span class="string">Nfiles</span>
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    <span class="comment">%+++++++++++++++++++++++++++++++++++++++++</span>
    <span class="comment">% for each calibration file  (series# 1)</span>
    <span class="comment">%+++++++++++++++++++++++++++++++++++++++++</span>
    <span class="keyword">for</span> calib_file = 1:length(calib_time)

        time_calib = calib_time(calib_file);

        <span class="comment">% find corresponding file in gps data</span>
        clear <span class="string">I</span>
        I = find(data(:,1) &gt; time_calib);
        <span class="comment">% take closest point for now</span>
        I = I(1);

        <span class="comment">% datevec(data(I,1))</span>
        <span class="comment">% datevec(time_calib)</span>

        index_timecalib(calib_file) = I;
    <span class="keyword">end</span>

    <span class="comment">% check</span>
    <span class="comment">% datevec(data(index_timecalib,1))</span>

    <span class="comment">% isolate gps calibration data</span>
    gps_data = data(index_timecalib,:); <span class="comment">% time lat lon</span>

    figure(1)
    hold <span class="string">on</span>
    h1=plot(gps_data(:,2),gps_data(:,3),<span class="string">'.'</span>);
    grid <span class="string">on</span>
        <span class="keyword">if</span> strcmp(systm,<span class="string">'Helzel'</span>) == 1
            set(h1,<span class="string">'marker'</span>,<span class="string">'.'</span>,<span class="string">'color'</span>,<span class="string">'b'</span>)
        <span class="keyword">elseif</span> strcmp(systm,<span class="string">'Flament'</span>) == 1
            set(h1,<span class="string">'marker'</span>,<span class="string">'x'</span>,<span class="string">'color'</span>,<span class="string">'k'</span>)
        <span class="keyword">end</span>

    <span class="comment">% load antenna coordinates</span>
    cd <span class="string">..</span>
    load([site <span class="string">'_Rx_coords.mat'</span>])

    hold <span class="string">on</span>
    plot(lon,lat,<span class="string">'x'</span>)
    grid <span class="string">on</span>
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    legend(<span class="string">'gps'</span>,<span class="string">'antennas'</span>,<span class="string">'location'</span>,<span class="string">'southeast'</span>)
    xlabel(<span class="string">'longitude'</span>)
    ylabel(<span class="string">'latitude'</span>)
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    title([<span class="string">'site = '</span> site ])
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    <span class="comment">% compute theoretical phase values</span>
    <span class="comment">% wavelength</span>
    lambda = 3E8/16.15E6;
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    <span class="comment">% initialize variables</span>
    theta_pairs = nan(11,length(gps_data));

    <span class="comment">% for each gps point</span>
    <span class="keyword">for</span> pt = 1:length(gps_data)

        <span class="comment">% compute distance between GPS and antennas</span>
        <span class="keyword">for</span> ant = 1:12
            clear <span class="string">E</span> <span class="string">W</span>
            [E,W] = lonlat2km(gps_data(pt,2),gps_data(pt,3),lon(ant),lat(ant));
            ddist = sqrt(E.^2+W.^2);
            r(ant) = ddist*1000;    <span class="comment">%meters</span>
        <span class="keyword">end</span>


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        <span class="comment">% for each pair of antennas</span>
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        <span class="keyword">for</span> p = 1:11

            <span class="comment">%delta_r</span>
            delta_r(p) = r(p+1) - r(p);

            <span class="comment">% theoretical phase</span>
            delta_phase_th(p,pt) = modsym((delta_r(p)*360./lambda),180);


            <span class="comment">% position of middle of pairs</span>
            clear <span class="string">lon_mid</span> <span class="string">lat_mid</span>
            lon_mid = (lon(p+1)+lon(p))/2;
            lat_mid = (lat(p+1)+lat(p))/2;

            <span class="comment">% distance between middle of pair and one of the antenna in the pair</span>
            <span class="comment">%         clear E W</span>
            <span class="comment">%         [E,W] = lonlat2km(lon_mid,lat_mid,lon(p),lat(p));</span>
            <span class="comment">%         ddist = sqrt(E.^2+W.^2);</span>
            <span class="comment">%         a(p) = ddist*1000;    %meters</span>

            <span class="comment">% distance between middle of pair and GPS pt</span>
            clear <span class="string">ddsit</span> <span class="string">phasAng</span>
            [ddist,phasAng] = sw_dist([gps_data(pt,3) lat_mid],[gps_data(pt,2) lon_mid],<span class="string">'km'</span>);
            r_mid(p) = ddist*1000;    <span class="comment">%meters</span>
            zeta(p) = phasAng;


            <span class="comment">% distance between pair of antennas</span>
            clear <span class="string">ddsit</span> <span class="string">phasAng</span>
            [ddist,phasAng] = sw_dist([lat(p) lat(p+1)],[lon(p) lon(p+1)],<span class="string">'km'</span>);
            phi(p) = phasAng;


            <span class="comment">% azimuth</span>
            theta_pairs(p,pt) = modsym(zeta(p)-phi(p)+90,180);
            <span class="comment">%rad2deg(theta_pairs)</span>
        <span class="keyword">end</span>
    <span class="keyword">end</span>



    <span class="comment">% for each pair of antenna</span>
    <span class="keyword">for</span> p = 1:11
        figure(p+1)
        h2=plot(theta_pairs(p,:),delta_phase_th(p,:),<span class="string">'x'</span>);
        hold <span class="string">on</span>
        h3=plot(theta_pairs(p,:),-delta_phase_obs(p,:),<span class="string">'or'</span>);
        grid <span class="string">on</span>
        xlabel(<span class="string">'incidence (degrees)'</span>)
        ylabel(<span class="string">'phase difference (degrees)'</span>)
        legend(<span class="string">'theoretical'</span>,<span class="string">'observed'</span>,<span class="string">'location'</span>,<span class="string">'best'</span>)
        <span class="keyword">if</span> strcmp(systm,<span class="string">'Helzel'</span>) == 1
            set(h2,<span class="string">'color'</span>,<span class="string">'b'</span>)
            set(h3,<span class="string">'color'</span>,<span class="string">'r'</span>,<span class="string">'marker'</span>,<span class="string">'o'</span>)
        <span class="keyword">elseif</span> strcmp(systm,<span class="string">'Flament'</span>) == 1
            set(h2,<span class="string">'color'</span>,<span class="string">'k'</span>,<span class="string">'marker'</span>,<span class="string">'*'</span>)
            set(h3,<span class="string">'color'</span>,<span class="string">'r'</span>,<span class="string">'marker'</span>,<span class="string">'sq'</span>,<span class="string">'markerfacecolor'</span>,<span class="string">'r'</span>)
        <span class="keyword">end</span>
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        title([site <span class="string">' - antennas '</span> num2str(p) <span class="string">'-'</span> num2str(p+1)])
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        <span class="comment">% compute calibration value for antennas pairs</span>
        calib_value(p) = nanmean(modsym(-delta_phase_obs(p,:)-delta_phase_th(p,:),180),2);


         <span class="comment">% compute calibration value for each antenna</span>
        phi_ant(p+1,sys) = sum(calib_value);

    <span class="keyword">end</span>

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    P = ones(16,3);
    P(13:16,:) = 0;
    P(1:12,3) = phi_ant(:,1);
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    <span class="comment">% save file (we only keep results from Helzel</span>
    <span class="keyword">if</span> strcmp(site,<span class="string">'PAO'</span>) == 1
        dlmwrite(<span class="string">'calibration_pao_29OCT2014.wera'</span>,P,<span class="string">'delimiter'</span>,<span class="string">'\t'</span>,<span class="string">'precision'</span>,<span class="string">'%.7f'</span>)
    <span class="keyword">elseif</span> strcmp(site,<span class="string">'PAB'</span>) == 1
        dlmwrite(<span class="string">'calibration_pab_30OCT2014.wera'</span>,P,<span class="string">'delimiter'</span>,<span class="string">'\t'</span>,<span class="string">'precision'</span>,<span class="string">'%.7f'</span>)
    <span class="keyword">end</span>


    figure(13)
    hold <span class="string">on</span>
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    h4 = plot(calib_value,<span class="string">'.-'</span>);
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    grid <span class="string">on</span>
    xlabel(<span class="string">'pairs of antennas'</span>)
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    ylabel([<span class="string">'phase differences between theoretical'</span>,10 ,<span class="string">'and observed values (degrees)'</span>])
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        <span class="keyword">if</span> strcmp(systm,<span class="string">'Helzel'</span>) == 1
            set(h4,<span class="string">'color'</span>,<span class="string">'b'</span>)
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            legend(<span class="string">'Helzel'</span>)
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        <span class="keyword">elseif</span> strcmp(systm,<span class="string">'Flament'</span>) == 1
            set(h4,<span class="string">'color'</span>,<span class="string">'k'</span>)
            legend(<span class="string">'Helzel'</span>,<span class="string">'Flament'</span>,<span class="string">'location'</span>,<span class="string">'southeast'</span>)
        <span class="keyword">end</span>
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    title(site)
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    figure(14)
    hold <span class="string">on</span>
    h5 = plot([1:12],phi_ant(:,sys),<span class="string">'r'</span>);
    grid <span class="string">on</span>
    <span class="keyword">if</span> strcmp(systm,<span class="string">'Helzel'</span>) == 1
        set(h5,<span class="string">'marker'</span>,<span class="string">'o'</span>)
        legend(<span class="string">'Helzel'</span>)
    <span class="keyword">elseif</span> strcmp(systm,<span class="string">'Flament'</span>) == 1
        set(h5,<span class="string">'marker'</span>,<span class="string">'sq'</span>,<span class="string">'markerfacecolor'</span>,<span class="string">'r'</span>)
        legend(<span class="string">'Helzel'</span>,<span class="string">'Flament'</span>,<span class="string">'location'</span>,<span class="string">'southeast'</span>)
    <span class="keyword">end</span>
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    xlabel(<span class="string">'antenna number'</span>)
    ylabel(<span class="string">'calibration phase to be applied (degrees)'</span>)
    title(site)

    <span class="keyword">if</span> strcmp(site,<span class="string">'PAO'</span>) == 1
       <span class="keyword">break</span>
    <span class="keyword">end</span>

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<span class="keyword">end</span>

<span class="comment">% add current calibration phases</span>
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<span class="keyword">if</span> strcmp(site,<span class="string">'PAO'</span>) == 1
    load <span class="string">calibration_pao.wera</span>
    figure(14)
    plot([1:12],calibration_pao(1:12,3),<span class="string">'b.-'</span>)
    legend(<span class="string">'Helzel'</span>,<span class="string">'original calibration'</span>,<span class="string">'location'</span>,<span class="string">'northwest'</span>)
<span class="keyword">elseif</span> strcmp(site,<span class="string">'PAB'</span>) == 1
    load <span class="string">calibration_pab.wera</span>
    figure(14)
    plot([1:12],calibration_pab(1:12,3),<span class="string">'b.-'</span>)
    legend(<span class="string">'Helzel'</span>,<span class="string">'Flament'</span>,<span class="string">'original calibration'</span>,<span class="string">'location'</span>,<span class="string">'southeast'</span>)
<span class="keyword">end</span>






<span class="comment">% save figures</span>
save_flag = 1;

figdir = (<span class="string">'/home/bandma01/Dropbox/UQAR/MEOPAR_Marion/figures/WERAcalibration'</span>);
cd(figdir)

fig_hdl = figure(1);
<span class="keyword">if</span> save_flag
    fname = [<span class="string">'configuration_'</span> site <span class="string">'_calibrations'</span>];
    fig_w = 8;<span class="comment">%cm</span>
    fig_h = 5;<span class="comment">%cm</span>
    set(fig_hdl,<span class="string">'PaperUnits'</span>,<span class="string">'centimeters'</span>)
    set(fig_hdl,<span class="string">'PaperPosition'</span>,[0 0 fig_w fig_h])
    set(fig_hdl, <span class="string">'PaperSize'</span>, [fig_w fig_h]);
    print(fig_hdl,<span class="string">'-dpng'</span>,<span class="string">'-r500'</span>,fname)
    <span class="comment">%crop([fname '.png'])</span>
<span class="keyword">end</span>




<span class="keyword">for</span> i = 2:12
    fig_hdl = figure(i);
    <span class="keyword">if</span> save_flag
        fname = [<span class="string">'Phases_'</span> site <span class="string">'_pair'</span> num2str(i-1) <span class="string">'-'</span> num2str(i)];
        fig_w = 8;<span class="comment">%cm</span>
        fig_h = 5;<span class="comment">%cm</span>
        set(fig_hdl,<span class="string">'PaperUnits'</span>,<span class="string">'centimeters'</span>)
        set(fig_hdl,<span class="string">'PaperPosition'</span>,[0 0 fig_w fig_h])
        set(fig_hdl, <span class="string">'PaperSize'</span>, [fig_w fig_h]);
        print(fig_hdl,<span class="string">'-dpng'</span>,<span class="string">'-r500'</span>,fname)
        <span class="comment">%         crop([fname '.png'])</span>
    <span class="keyword">end</span>
<span class="keyword">end</span>



fig_hdl = figure(13);
<span class="keyword">if</span> save_flag
    fname = [<span class="string">'PhaseDifference_'</span> site <span class="string">'_calibrations'</span>];
    fig_w = 8;<span class="comment">%cm</span>
    fig_h = 5;<span class="comment">%cm</span>
    set(fig_hdl,<span class="string">'PaperUnits'</span>,<span class="string">'centimeters'</span>)
    set(fig_hdl,<span class="string">'PaperPosition'</span>,[0 0 fig_w fig_h])
    set(fig_hdl, <span class="string">'PaperSize'</span>, [fig_w fig_h]);
    print(fig_hdl,<span class="string">'-dpng'</span>,<span class="string">'-r500'</span>,fname)
    <span class="comment">%         crop([fname '.png'])</span>
<span class="keyword">end</span>

fig_hdl = figure(14);
<span class="keyword">if</span> save_flag
    fname = [<span class="string">'PhaseCalibration_'</span> site];
    fig_w = 8;<span class="comment">%cm</span>
    fig_h = 5;<span class="comment">%cm</span>
    set(fig_hdl,<span class="string">'PaperUnits'</span>,<span class="string">'centimeters'</span>)
    set(fig_hdl,<span class="string">'PaperPosition'</span>,[0 0 fig_w fig_h])
    set(fig_hdl, <span class="string">'PaperSize'</span>, [fig_w fig_h]);
    print(fig_hdl,<span class="string">'-dpng'</span>,<span class="string">'-r500'</span>,fname)
    <span class="comment">%         crop([fname '.png'])</span>
<span class="keyword">end</span>
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</pre><pre class="codeoutput">calibrations started at 29-Oct-2014 17:48:54 and ended at 29-Oct-2014 18:25:54
</pre><img vspace="5" hspace="5" src="WERAcalibration_01.png" alt=""> <img vspace="5" hspace="5" src="WERAcalibration_02.png" alt=""> <img vspace="5" hspace="5" src="WERAcalibration_03.png" alt=""> <img vspace="5" hspace="5" src="WERAcalibration_04.png" alt=""> <img vspace="5" hspace="5" src="WERAcalibration_05.png" alt=""> <img vspace="5" hspace="5" src="WERAcalibration_06.png" alt=""> <img vspace="5" hspace="5" src="WERAcalibration_07.png" alt=""> <img vspace="5" hspace="5" src="WERAcalibration_08.png" alt=""> <img vspace="5" hspace="5" src="WERAcalibration_09.png" alt=""> <img vspace="5" hspace="5" src="WERAcalibration_10.png" alt=""> <img vspace="5" hspace="5" src="WERAcalibration_11.png" alt=""> <img vspace="5" hspace="5" src="WERAcalibration_12.png" alt=""> <img vspace="5" hspace="5" src="WERAcalibration_13.png" alt=""> <img vspace="5" hspace="5" src="WERAcalibration_14.png" alt=""> <p class="footer"><br>
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      Published with MATLAB&reg; 7.14<br></p></div><!--
##### SOURCE BEGIN #####
clear all
close all

%cd('/home/bandma01/Documents/WERAs/')
cd('/home/bandma01/hfr-data-processing/calibrations/')

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site = 'PAO';
% site = 'PAB';

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cd(site)

% system
for sys = 1:2
    
    if sys == 1
        systm = 'Helzel';
    elseif sys == 2
        systm = 'Flament';
    end
    
    clear J I E Phase calib_file calib_hr calib_jd calib_min calib_time calib_value
    clear calib_year d data delta_phase_obs delta_phase_th gps_data index_timecalib
    clear theta_pairs 
    
    if strcmp(site,'PAO') == 1
        
        load('HelzelPAO_Track_29-OCT-14 183138.mat')
        
    elseif strcmp(site,'PAB') == 1
        
        if strcmp(systm,'Helzel') == 1
            load('HelzelPAB_Track_30-OCT-14 175446.mat')
        elseif strcmp(systm,'Flament') == 1
            load('FlamentPAB_Track_30-OCT-14 182008.mat')
        end
        
    end
    
    
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    % phases and time of calibration
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    if strcmp(site,'PAO') == 1
        cd('2014302')
    elseif strcmp(site,'PAB') == 1
        cd('2014303')
    end
    
    % list files
    clear d
    d = dir('*.mat');       % returns a structure with name, date, bytes, isdir, datenum
    Nfiles = length(d);     % nombre de fichiers a analyser
    
    
    % look at the names of files and extract information
    for c = 1:Nfiles
        calib_year(c) = str2double(d(c).name(1:4));
        calib_jd(c) = str2double(d(c).name(5:7));
        calib_hr(c) = str2double(d(c).name(8:9));
        calib_min(c) = str2double(d(c).name(10:11));
        
        load(d(c).name,'phase')
        
        Phase(:,c) = phase;
    end
    clear phase
    
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    % for each time stamp (column) compute phase difference between 2
    % consecutive antennas (row)
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    delta_phase_obs = modsym(diff(Phase,1),180);
    
    To = datenum(2014,01,01,0,0,0);
    
    % add 20 sec to center calibration time
    calib_time = To + calib_jd -1 + calib_hr./24 + calib_min/24/60 + 20/24/3600;
    % datevec(calib_time)
    
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        clear calib_year calib_jd calib_hr calib_min
        
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    if strcmp(site,'PAO') == 1 
        % calib time 2min34sec late wrt GPS
        calib_time = calib_time + 2/24/60 + 34/24/3600;
    end
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    disp(['calibrations started at ' datestr(calib_time(1)) ' and ended at ' datestr(calib_time(end))])
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    % separate between calibrations made with Helzel's system and Flament's system
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    % date of new calibration files
    % Helzel 2014-10-30 16:52 to 17:54
    % Flament 2014-10-30 17:55 to 18:20
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    T1 = datenum(2014,10,30,17,55,00);
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        clear J
        if strcmp(systm,'Helzel') == 1
            J = find(calib_time > T1);
        elseif strcmp(systm,'Flament') == 1
            J = find(calib_time < T1);
        end
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        % remove unwanted data to avoid confusion!
%         calib_year(J)=[];
%         calib_jd(J)=[];
%         calib_hr(J)=[];
%         calib_min(J)=[];
        Phase(:,J)=[];
        delta_phase_obs(:,J)=[];
        calib_time(J)=[];
        d(J)=[];
        clear c Nfiles
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    %+++++++++++++++++++++++++++++++++++++++++
    % for each calibration file  (series# 1)
    %+++++++++++++++++++++++++++++++++++++++++
    for calib_file = 1:length(calib_time)
        
        time_calib = calib_time(calib_file);
        
        % find corresponding file in gps data
        clear I
        I = find(data(:,1) > time_calib);
        % take closest point for now
        I = I(1);
        
        % datevec(data(I,1))
        % datevec(time_calib)
        
        index_timecalib(calib_file) = I;
    end
    
    % check
    % datevec(data(index_timecalib,1))
    
    % isolate gps calibration data
    gps_data = data(index_timecalib,:); % time lat lon
    
    figure(1)
    hold on
    h1=plot(gps_data(:,2),gps_data(:,3),'.');
    grid on
        if strcmp(systm,'Helzel') == 1
            set(h1,'marker','.','color','b')
        elseif strcmp(systm,'Flament') == 1
            set(h1,'marker','x','color','k')
        end
        
    % load antenna coordinates
    cd ..
    load([site '_Rx_coords.mat'])
    
    hold on
    plot(lon,lat,'x')
    grid on
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    legend('gps','antennas','location','southeast')
    xlabel('longitude')
    ylabel('latitude')
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    title(['site = ' site ])
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    % compute theoretical phase values
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    % wavelength
    lambda = 3E8/16.15E6;
    
    
    % initialize variables
    theta_pairs = nan(11,length(gps_data));
    
    % for each gps point
    for pt = 1:length(gps_data)
        
        % compute distance between GPS and antennas
        for ant = 1:12
            clear E W
            [E,W] = lonlat2km(gps_data(pt,2),gps_data(pt,3),lon(ant),lat(ant));
            ddist = sqrt(E.^2+W.^2);
            r(ant) = ddist*1000;    %meters
        end
        
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        % for each pair of antennas
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        for p = 1:11
            
            %delta_r
            delta_r(p) = r(p+1) - r(p);
            
            % theoretical phase
            delta_phase_th(p,pt) = modsym((delta_r(p)*360./lambda),180);
            
            
            % position of middle of pairs
            clear lon_mid lat_mid
            lon_mid = (lon(p+1)+lon(p))/2;
            lat_mid = (lat(p+1)+lat(p))/2;
            
            % distance between middle of pair and one of the antenna in the pair
            %         clear E W
            %         [E,W] = lonlat2km(lon_mid,lat_mid,lon(p),lat(p));
            %         ddist = sqrt(E.^2+W.^2);
            %         a(p) = ddist*1000;    %meters
            
            % distance between middle of pair and GPS pt
            clear ddsit phasAng
            [ddist,phasAng] = sw_dist([gps_data(pt,3) lat_mid],[gps_data(pt,2) lon_mid],'km');
            r_mid(p) = ddist*1000;    %meters
            zeta(p) = phasAng;
            
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            % distance between pair of antennas
            clear ddsit phasAng
            [ddist,phasAng] = sw_dist([lat(p) lat(p+1)],[lon(p) lon(p+1)],'km');
            phi(p) = phasAng;
            
            
            % azimuth
            theta_pairs(p,pt) = modsym(zeta(p)-phi(p)+90,180);
            %rad2deg(theta_pairs)
        end
    end
    
    
    
    % for each pair of antenna
    for p = 1:11
        figure(p+1)
        h2=plot(theta_pairs(p,:),delta_phase_th(p,:),'x');
        hold on
        h3=plot(theta_pairs(p,:),-delta_phase_obs(p,:),'or');
        grid on
        xlabel('incidence (degrees)')
        ylabel('phase difference (degrees)')
        legend('theoretical','observed','location','best')
        if strcmp(systm,'Helzel') == 1
            set(h2,'color','b')
            set(h3,'color','r','marker','o')
        elseif strcmp(systm,'Flament') == 1
            set(h2,'color','k','marker','*')
            set(h3,'color','r','marker','sq','markerfacecolor','r')
        end
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        title([site ' - antennas ' num2str(p) '-' num2str(p+1)])
       
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        % compute calibration value for antennas pairs
        calib_value(p) = nanmean(modsym(-delta_phase_obs(p,:)-delta_phase_th(p,:),180),2);

        
         % compute calibration value for each antenna
        phi_ant(p+1,sys) = sum(calib_value);
        
    end
    
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    P = ones(16,3);
    P(13:16,:) = 0;
    P(1:12,3) = phi_ant(:,1);
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    % save file (we only keep results from Helzel
    if strcmp(site,'PAO') == 1
        dlmwrite('calibration_pao_29OCT2014.wera',P,'delimiter','\t','precision','%.7f')
    elseif strcmp(site,'PAB') == 1
        dlmwrite('calibration_pab_30OCT2014.wera',P,'delimiter','\t','precision','%.7f')
    end
    
    
    figure(13)
    hold on
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    h4 = plot(calib_value,'.-');
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    grid on
    xlabel('pairs of antennas')
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    ylabel(['phase differences between theoretical',10 ,'and observed values (degrees)'])
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        if strcmp(systm,'Helzel') == 1
            set(h4,'color','b')
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            legend('Helzel')
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        elseif strcmp(systm,'Flament') == 1
            set(h4,'color','k')
            legend('Helzel','Flament','location','southeast')
        end
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    title(site)
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    figure(14)
    hold on
    h5 = plot([1:12],phi_ant(:,sys),'r');
    grid on
    if strcmp(systm,'Helzel') == 1
        set(h5,'marker','o')
        legend('Helzel')
    elseif strcmp(systm,'Flament') == 1
        set(h5,'marker','sq','markerfacecolor','r')
        legend('Helzel','Flament','location','southeast')
    end
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    xlabel('antenna number')
    ylabel('calibration phase to be applied (degrees)')
    title(site)
    
    if strcmp(site,'PAO') == 1
       break
    end

end

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% add current calibration phases
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if strcmp(site,'PAO') == 1
    load calibration_pao.wera
    figure(14)
    plot([1:12],calibration_pao(1:12,3),'b.-')
    legend('Helzel','original calibration','location','northwest')
elseif strcmp(site,'PAB') == 1
    load calibration_pab.wera
    figure(14)
    plot([1:12],calibration_pab(1:12,3),'b.-')
    legend('Helzel','Flament','original calibration','location','southeast')
end

    




% save figures
save_flag = 1;

figdir = ('/home/bandma01/Dropbox/UQAR/MEOPAR_Marion/figures/WERAcalibration');
cd(figdir)

fig_hdl = figure(1);
if save_flag
    fname = ['configuration_' site '_calibrations'];
    fig_w = 8;%cm
    fig_h = 5;%cm
    set(fig_hdl,'PaperUnits','centimeters')
    set(fig_hdl,'PaperPosition',[0 0 fig_w fig_h])
    set(fig_hdl, 'PaperSize', [fig_w fig_h]);
    print(fig_hdl,'-dpng','-r500',fname)
    %crop([fname '.png'])
end




for i = 2:12
    fig_hdl = figure(i);
    if save_flag
        fname = ['Phases_' site '_pair' num2str(i-1) '-' num2str(i)];
        fig_w = 8;%cm
        fig_h = 5;%cm
        set(fig_hdl,'PaperUnits','centimeters')
        set(fig_hdl,'PaperPosition',[0 0 fig_w fig_h])
        set(fig_hdl, 'PaperSize', [fig_w fig_h]);
        print(fig_hdl,'-dpng','-r500',fname)
        %         crop([fname '.png'])
    end
end



fig_hdl = figure(13);
if save_flag
    fname = ['PhaseDifference_' site '_calibrations'];
    fig_w = 8;%cm
    fig_h = 5;%cm
    set(fig_hdl,'PaperUnits','centimeters')
    set(fig_hdl,'PaperPosition',[0 0 fig_w fig_h])
    set(fig_hdl, 'PaperSize', [fig_w fig_h]);
    print(fig_hdl,'-dpng','-r500',fname)
    %         crop([fname '.png'])
end

fig_hdl = figure(14);
if save_flag
    fname = ['PhaseCalibration_' site];
    fig_w = 8;%cm
    fig_h = 5;%cm
    set(fig_hdl,'PaperUnits','centimeters')
    set(fig_hdl,'PaperPosition',[0 0 fig_w fig_h])
    set(fig_hdl, 'PaperSize', [fig_w fig_h]);
    print(fig_hdl,'-dpng','-r500',fname)
    %         crop([fname '.png'])
end
##### SOURCE END #####
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