function H2_week_plots(datafile, h2sciencelist, texname)
%H2_month_plots Creates TimeMon data plots for LHO S5 run
%
% H2_month_plots(datafile, h2sciencelist, texname) reads the
% output datafile created by HTMon_data, the list of H1 science
% segments, creates plots of S5 science segment time data from the 'mean'
% channels ignoring the zeros and known crappy data, and saves the plots as
% PNG and EPS files (FigH1). One set of plots is produced for 
% each week. It saves Tex reference to the eps files in the file texname .
%
% h2sciencelist and h2sciencelist should contain the two dimensional
% matrices titled H2_science_segments and H2_science_segments each of which
% should hold four columns:
%
% Science segment length
% Science segment start GPS time
% Science segment end GPS time
% Science segment serial number
%
% Example: H2_week_plots('HTimeMon_all.mat', 'H2_science_segments.list', 'H2TMon.tex')
%
% See also: HTMon_data, LTMon_plots
%
% Rubab Khan, GECo, Columbia
% https://geco.phys.columbia.edu/~rubab/
% November 29, 2007. 

% Channel names

chandata=[
	'H1:DMT-TIME_EX.mean  ';
	'H1:DMT-TIME_EX.max   ';
	'H1:DMT-TIME_EX.min   ';
    'H1:DMT-TIME_EX.n     ';
	'H1:DMT-TIME_EX.rms   ';
	'H1:DMT-TIME_EY.mean  ';
	'H1:DMT-TIME_EY.max   ';
	'H1:DMT-TIME_EY.min   ';
    'H1:DMT-TIME_EY.n     ';
	'H1:DMT-TIME_EY.rms   ';
	'H2:DMT-TIME_MX.mean  ';
	'H2:DMT-TIME_MX.max   ';
	'H2:DMT-TIME_MX.min   ';
    'H2:DMT-TIME_MX.n     ';
	'H2:DMT-TIME_MX.rms   ';
	'H2:DMT-TIME_MY.mean  ';
	'H2:DMT-TIME_MY.max   ';
	'H2:DMT-TIME_MY.min   ';
    'H2:DMT-TIME_MY.n     ';
	'H2:DMT-TIME_MY.rms   ';
	'H1:DMT-TIME_LVEA.mean';
	'H1:DMT-TIME_LVEA.max ';
	'H1:DMT-TIME_LVEA.min ';
    'H1:DMT-TIME_LVEA.n   ';
	'H1:DMT-TIME_LVEA.rms ';
	'H2:DMT-TIME_LVEA.mean';
	'H2:DMT-TIME_LVEA.max ';
	'H2:DMT-TIME_LVEA.min ';
    'H2:DMT-TIME_LVEA.n   ';
	'H2:DMT-TIME_LVEA.rms '];

channame=[
	'H1:DMT-TIME\_EX.mean  ';
	'H1:DMT-TIME\_EX.max   ';
	'H1:DMT-TIME\_EX.min   ';
    'H1:DMT-TIME\_EX.n     ';
	'H1:DMT-TIME\_EX.rms   ';
	'H1:DMT-TIME\_EY.mean  ';
	'H1:DMT-TIME\_EY.max   ';
	'H1:DMT-TIME\_EY.min   ';
    'H1:DMT-TIME\_EY.n     ';
	'H1:DMT-TIME\_EY.rms   ';
	'H2:DMT-TIME\_MX.mean  ';
	'H2:DMT-TIME\_MX.max   ';
	'H2:DMT-TIME\_MX.min   ';
    'H2:DMT-TIME\_MX.n     ';
	'H2:DMT-TIME\_MX.rms   ';
	'H2:DMT-TIME\_MY.mean  ';
	'H2:DMT-TIME\_MY.max   ';
	'H2:DMT-TIME\_MY.min   ';
    'H2:DMT-TIME\_MY.n     ';
	'H2:DMT-TIME\_MY.rms   ';
	'H1:DMT-TIME\_LVEA.mean';
	'H1:DMT-TIME\_LVEA.max ';
	'H1:DMT-TIME\_LVEA.min ';
    'H1:DMT-TIME\_LVEA.n   ';
	'H1:DMT-TIME\_LVEA.rms ';
	'H2:DMT-TIME\_LVEA.mean';
	'H2:DMT-TIME\_LVEA.max ';
	'H2:DMT-TIME\_LVEA.min ';
    'H2:DMT-TIME\_LVEA.n   ';
	'H2:DMT-TIME\_LVEA.rms '];

channame2=[
	'H1_DMT-TIME\_EX.mean  ';
	'H1_DMT-TIME\_EX.max   ';
	'H1_DMT-TIME\_EX.min   ';
    'H1_DMT-TIME\_EX.n     ';
	'H1_DMT-TIME\_EX.rms   ';
	'H1_DMT-TIME\_EY.mean  ';
	'H1_DMT-TIME\_EY.max   ';
	'H1_DMT-TIME\_EY.min   ';
    'H1_DMT-TIME\_EY.n     ';
	'H1_DMT-TIME\_EY.rms   ';
	'H2_DMT-TIME\_MX.mean  ';
	'H2_DMT-TIME\_MX.max   ';
	'H2_DMT-TIME\_MX.min   ';
    'H2_DMT-TIME\_MX.n     ';
	'H2_DMT-TIME\_MX.rms   ';
	'H2_DMT-TIME\_MY.mean  ';
	'H2_DMT-TIME\_MY.max   ';
	'H2_DMT-TIME\_MY.min   ';
    'H2_DMT-TIME\_MY.n     ';
	'H2_DMT-TIME\_MY.rms   ';
	'H1_DMT-TIME\_LVEA.mean';
	'H1_DMT-TIME\_LVEA.max ';
	'H1_DMT-TIME\_LVEA.min ';
    'H1_DMT-TIME\_LVEA.n   ';
	'H1_DMT-TIME\_LVEA.rms ';
	'H2_DMT-TIME\_LVEA.mean';
	'H2_DMT-TIME\_LVEA.max ';
	'H2_DMT-TIME\_LVEA.min ';
    'H2_DMT-TIME\_LVEA.n   ';
	'H2_DMT-TIME\_LVEA.rms '];

chandata2=[
	'H1_DMT-TIME_EX.mean  ';
	'H1_DMT-TIME_EX.max   ';
	'H1_DMT-TIME_EX.min   ';
    'H1_DMT-TIME_EX.n     ';
	'H1_DMT-TIME_EX.rms   ';
	'H1_DMT-TIME_EY.mean  ';
	'H1_DMT-TIME_EY.max   ';
	'H1_DMT-TIME_EY.min   ';
    'H1_DMT-TIME_EY.n     ';
	'H1_DMT-TIME_EY.rms   ';
	'H2_DMT-TIME_MX.mean  ';
	'H2_DMT-TIME_MX.max   ';
	'H2_DMT-TIME_MX.min   ';
    'H2_DMT-TIME_MX.n     ';
	'H2_DMT-TIME_MX.rms   ';
	'H2_DMT-TIME_MY.mean  ';
	'H2_DMT-TIME_MY.max   ';
	'H2_DMT-TIME_MY.min   ';
    'H2_DMT-TIME_MY.n     ';
	'H2_DMT-TIME_MY.rms   ';
	'H1_DMT-TIME_LVEA.mean';
	'H1_DMT-TIME_LVEA.max ';
	'H1_DMT-TIME_LVEA.min ';
    'H1_DMT-TIME_LVEA.n   ';
	'H1_DMT-TIME_LVEA.rms ';
	'H2_DMT-TIME_LVEA.mean';
	'H2_DMT-TIME_LVEA.max ';
	'H2_DMT-TIME_LVEA.min ';
    'H2_DMT-TIME_LVEA.n   ';
	'H2_DMT-TIME_LVEA.rms '];


chan=cellstr(channame);
load(datafile);               % Load data file produced by HTMon_data
d = H_time';
h = (d-tHStart)/(60*60*24); h = h';   % Time as days
tHEnd = tHStart+tHLength;
r = [];

% Load the science segments list

load(h2sciencelist);
st1 = H2_science_segments(:,2);
en1 = H2_science_segments(:,3);
M = length(st1);
for j = 1:M
    rr=find(d>=st1(j)&d<=en1(j));
    r = [r rr];
end

fid1 = fopen(texname,'w');
texname_png = (['png_' texname]);
fid2 = fopen(texname_png,'w');  
html_name = 'LHO_H2_Week.html';
fid3 =  fopen(html_name,'w');

fprintf(fid2,'%s\n\n', '% Please use the pdflatex package instead of the conventional latex package to compile documents with png figures.');

fprintf(fid3,'%s\n','<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">');
fprintf(fid3,'%s\n','<html><head>');
fprintf(fid3,'%s%s%s\n','<meta content="text/html; charset=ISO-8859-1" http-equiv="content-type"><title>',html_name,'</title>');
fprintf(fid3,'%s\n','</head>');
fprintf(fid3,'%s\n','<body style="background-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" alink="#ee0000" link="#0000ee" vlink="#551a8b">');
fprintf(fid3,'%s\n','<a style="color: rgb(0, 0, 238);" href="../"><big style="font-weight: bold;"><big>&lt;&lt; Back</big></big></a><br>');
fprintf(fid3,'%s\n','<div style="text-align: center; background-color: rgb(0, 0, 0); color: rgb(255, 255, 255);"><big><big><big><big><span style="font-weight: normal;">LHO 2Km IFO PEM Timing Performance Indicators</span></big></big></big></big>');
fprintf(fid3,'%s\n','<div style="text-align: center;"><span style="color: rgb(255, 255, 255);">(Mean/Std measurements in microseconds)</span></div>');
fprintf(fid3,'%s\n','<table style="width: 100%; text-align: left; color: rgb(255, 255, 255);" border="5" cellpadding="2" cellspacing="2">');
fprintf(fid3,'%s\n','<tbody>');
fprintf(fid3,'%s\n','<tr>');
fprintf(fid3,'%s\n','<td style="text-align: center;" colspan="1" rowspan="2"><span style="font-weight: bold;">Data period</span><br>');
fprintf(fid3,'%s\n','</td>');
fprintf(fid3, '%s\n', '<td style="text-align: center;" colspan="1" rowspan="2"><span style="font-weight: bold;">GPS Start</span><br></td>');
fprintf(fid3, '%s\n', '<td style="text-align: center;" colspan="1" rowspan="2"><span style="font-weight: bold;">GPS End</span><br></td>');
fprintf(fid3,'%s\n','<td style="text-align: center;" colspan="2"><span style="font-weight: bold;">EX-PEM<br></span></td>');
fprintf(fid3,'%s\n','<td style="text-align: center;" colspan="2"><span style="font-weight: bold;">EY-PEM</span></td>');
fprintf(fid3,'%s\n','<td style="text-align: center;" colspan="2"><span style="font-weight: bold;">LVEA</span><span style="font-weight: bold;">-PEM</span></td>');
fprintf(fid3,'%s\n','<td style="text-align: center;" colspan="1" rowspan="2"><span style="font-weight: bold;">Figure</span><span style="font-weight: bold;"><br>');
fprintf(fid3,'%s\n','<a href="../figures/week/H1TMon.tex">tex</a> <a href="../figures/week/png_H1TMon.tex">png_tex</a></span>');
fprintf(fid3,'%s\n','</td>');
fprintf(fid3,'%s\n','</tr>');
fprintf(fid3,'%s\n','<tr>');
fprintf(fid3,'%s\n','<td style="text-align: center; font-weight: bold;">Mean</td>');
fprintf(fid3,'%s\n','<td style="vertical-align: top; text-align: center; font-weight: bold;">Std<br></td>');
fprintf(fid3,'%s\n','<td style="text-align: center; font-weight: bold;">Mean</td>');
fprintf(fid3,'%s\n','<td style="vertical-align: top; text-align: center; font-weight: bold;">Std<br></td>');
fprintf(fid3,'%s\n','<td style="text-align: center; font-weight: bold;">Mean</td>');
fprintf(fid3,'%s\n','<td style="vertical-align: top; text-align: center; font-weight: bold;">Std</td>');
fprintf(fid3,'%s\n','</tr>');

for week = 1:102
    
    disp('************************');
    disp(['week_' num2str(week)]);
    start_day = (week-1)*7;
    end_day = start_day+7;
    start_time = tHStart + start_day*86400;
    end_time = start_time + 7*86400;
   
    fprintf(fid3,'%s\n','<tr>');
    fprintf(fid3,'%s%d%s\n','<td style="text-align: center;">Week ', week, '<br>');
    fprintf(fid3,'%s\n','</td>');
    fprintf(fid3,'%s%d%s\n','<td style="text-align: center;">',start_time,'</td>');
    fprintf(fid3,'%s%d%s\n','<td style="text-align: center;">',end_time,'</td>');

    clf;

    figure(1)
    
    i=2;
    n = 5*i+1;      % First of every five channels: the mean channels
    a = [h H2MX_mean];
    g = a(r,1); j = a(r,2); bb = [g j];
    i=find(g>=start_day&g<end_day);
    g = bb(i,1); j = bb(i,2); b = [g j];
    i=find(j~=0&(abs(j))<1e-4);                % Disregard zeros and crappy data  
    if ~isempty(i)
        subplot (3,3,1)     % Create time series plots
        plot(b(i,1),(b(i,2)*1000000),'b.');
        grid; ylabel('\Deltat[\mus]'); xlabel(['t[day] from ' num2str(tHStart)])
        title(chan(n));
        subplot (3,3,2)     % Create histogram plots
        hist((b(i,2)*1000000),50)
        Mean = mean(b(i,2)*1000000); Std = std(b(i,2)*1000000);
        legend(['mean = ' num2str(Mean) ', std = ' num2str(Std)]);        
        grid; xlabel('\Deltat[\mus]'); ylabel('N.events')
        title(chan(n));
        subplot (3,3,3)     % Create normal fit plots
        normplot(b(i,2)*1000000)
        xlabel('\Deltat[\mus]');
        title(chan(n));
        fprintf(fid3,'%s%f%s\n','<td style="text-align: center;">',Mean,'</td>');
        fprintf(fid3,'%s%f%s\n','<td style="text-align: center;">',Std,'</td>');
    else
        fprintf(fid3,'%s\n','<td style="text-align: center;">Processing</td>');
        fprintf(fid3,'%s\n','<td style="text-align: center;">Processing</td>');
    end
    
    % Repeat the steps for all channels

    i=3;
    n = 5*i+1;
    a = [h H2MY_mean];
    g = a(r,1); j = a(r,2); bb = [g j];
    i=find(g>=start_day&g<end_day);
    g = bb(i,1); j = bb(i,2); b = [g j];
    i=find(j~=0&(abs(j))<1e-4);                % Disregard zeros and crappy data   
    if ~isempty(i)
        subplot (3,3,4)     % Create time series plots
        plot(b(i,1),(b(i,2)*1000000),'b.');
        grid; ylabel('\Deltat[\mus]'); xlabel(['t[day] from ' num2str(tHStart)])
        title(chan(n));
        subplot (3,3,5)     % Create histogram plots
        hist((b(i,2)*1000000),50)
        Mean = mean(b(i,2)*1000000); Std = std(b(i,2)*1000000);
        legend(['mean = ' num2str(Mean) ', std = ' num2str(Std)]);        
        grid; xlabel('\Deltat[\mus]'); ylabel('N.events')
        title(chan(n));
        subplot (3,3,6)     % Create normal fit plots
        normplot(b(i,2)*1000000)
        xlabel('\Deltat[\mus]');
        title(chan(n));
        fprintf(fid3,'%s%f%s\n','<td style="text-align: center;">',Mean,'</td>');
        fprintf(fid3,'%s%f%s\n','<td style="text-align: center;">',Std,'</td>');
    else
        fprintf(fid3,'%s\n','<td style="text-align: center;">Processing</td>');
        fprintf(fid3,'%s\n','<td style="text-align: center;">Processing</td>');
    end
    
    i=5;
    n = 5*i+1;
    a = [h H2LV_mean];
    g = a(r,1); j = a(r,2); bb = [g j];
    i=find(g>=start_day&g<end_day);
    g = bb(i,1); j = bb(i,2); b = [g j];
    i=find(j~=0&(abs(j))<1e-4);                % Disregard zeros and crappy data
    if ~isempty(i)
        subplot (3,3,7)     % Create time series plots
        plot(b(i,1),(b(i,2)*1000000),'b.');
        grid; ylabel('\Deltat[\mus]'); xlabel(['t[day] from ' num2str(tHStart)])
        title(chan(n));
        subplot (3,3,8)     % Create histogram plots
        hist((b(i,2)*1000000),50)
        Mean = mean(b(i,2)*1000000); Std = std(b(i,2)*1000000);
        legend(['mean = ' num2str(Mean) ', std = ' num2str(Std)]);        
        grid; xlabel('\Deltat[\mus]'); ylabel('N.events')
        title(chan(n));
        subplot (3,3,9)     % Create normal fit plots
        normplot(b(i,2)*1000000)
        xlabel('\Deltat[\mus]');
        title(chan(n));
        fprintf(fid3,'%s%f%s\n','<td style="text-align: center;">',Mean,'</td>');
        fprintf(fid3,'%s%f%s\n','<td style="text-align: center;">',Std,'</td>');
    else
        fprintf(fid3,'%s\n','<td style="text-align: center;">Processing</td>');
        fprintf(fid3,'%s\n','<td style="text-align: center;">Processing</td>');
    end

    figure_title = sprintf('GPS Start Time: %d and GPS Stop Time: %d', start_time, end_time);
    suptitle(figure_title);

    FigH2.png = sprintf('%s',[strcat(chandata2(11,:)) '_' strcat(chandata2(16,:)) '_and_' strcat(chandata2(26,:)) '_week_' num2str(week) '.png']);
    FigH2.eps = sprintf('%s',[strcat(chandata2(11,:)) '_' strcat(chandata2(16,:)) '_and_' strcat(chandata2(26,:)) '_week_' num2str(week) '.eps']);

    set(figure(1),'PaperOrientation','portrait');
    set(figure(1),'PaperPosition',[0.25 0.25 10.5 8]);
    print(figure(1),'-dpng',FigH2.png);

    set(figure(1),'PaperOrientation','landscape');
    set(figure(1),'PaperPosition',[0.25 0.25 10.5 8]);
    print(figure(1),'-depsc2',FigH2.eps);

    abc = sprintf('\\begin{figure}[!t]\n\\includegraphics[angle=0,width=180mm]{%s}\n\\caption{Time series of channels %s, %s and %s for GPS time %s to %s}\n\\label{fig:%s}\n\\end{figure}\n\n',...
    FigH2.eps,strcat(channame2(11,:)),strcat(channame2(16,:)),strcat(channame2(26,:)),num2str(start_time),num2str(end_time),FigH2.eps);

    fprintf(fid1,'%s',abc);

    abc_png = sprintf('\\begin{figure}[!t]\n\\includegraphics[angle=90,width=180mm]{%s}\n\\caption{Time series of channels %s, %s and %s for GPS time %s to %s}\n\\label{fig:%s}\n\\end{figure}\n\n',...
    FigH2.png,strcat(channame2(11,:)),strcat(channame2(16,:)),strcat(channame2(26,:)),num2str(start_time),num2str(end_time),FigH2.png);

    fprintf(fid2,'%s',abc_png);    

    fprintf(fid3,'%s\n','<td style="text-align: center;">');
    fprintf(fid3,'%s%s%s\n','<a href="../figures/week/', FigH2.png, '">png</a>');
    fprintf(fid3,'%s%s%s\n','<a href="../figures/week/', FigH2.eps, '">eps</a>');
    fprintf(fid3,'%s\n','</td>');
    fprintf(fid3,'%s\n','</tr>');
    fprintf(fid3,'%s\n','');   
        
    disp('************************');
        
end

fprintf(fid3,'%s\n','</tbody>');
fprintf(fid3,'%s\n','</table>');
fprintf(fid3,'%s\n','</div>');
fprintf(fid3,'%s\n','<br>');
fprintf(fid3,'%s\n','<a style="color: rgb(0, 0, 238);" href="../"><big style="font-weight: bold;"><big>&lt;&lt; Back</big></big></a>');
fprintf(fid3,'%s\n','</body></html>');

fclose(fid1);
fclose(fid2);
fclose(fid3);