%======================================================================

%                    H T M L T A B L E . M 

%                    doc: Wed Jun  4 12:58:37 2008

%                    dlm: Wed Nov 18 20:44:02 2009

%                    (c) 2008 M. Visbeck & A.M. Thurnherr

%                    uE-Info: 49 73 NIL 0 0 72 0 2 4 NIL ofnI

%======================================================================

function [] = htmltable(directory, dods)

% function [] = htmltable(directory, dods)

%

% Create HTML Table of LADCP Files in a Directory

%

% Input :  directory  : Either a directory '/home/someone/lookhere/'

%                       Or the 'f' structure from LADCP where

%                       'f.res' will be used.

%      

%          dods       : Structure with DODS info ** OPTIONAL **

%                       dods.cruise - dods address for cruise file

%                       dods.d1     - start of address for cast

%                       dods.d2     - end of address for cast

%                       

% Output : Files created in your directory:

%             index.html  - Start Page with Map

%             index.htm   - Start Page with Map

%             table0.html - Start Page with Map

%             table1.html - Individual Cast Data

%             table2.html - Processing Methods

%             table3.html - Technical

%             table4.html - Plots

%             cruise.ps   - Map of Cruise (filename will vary)

%             cruise.gif  - Map of Cruise (filename will vary)

%

% For DODS addresses, htmltable will insert the cast number to get the

% correct address.

%

% Example: directory = '../ladcp_output/';

%

%          dods.cruise = ['http://kage.ldeo.columbia.edu:81/SOURCES/' ...

%                         '.LDEO/.ClimateGroup/.LADCP/.test/dods'];

%          dods.d1     = ['http://kage.ldeo.columbia.edu:81/SOURCES/' ...

%                         '.LDEO/.ClimateGroup/.LADCP/.test/N+'];

%          dods.d2     = ['+VALUE/dods'];

%

% Modifications by ANT:

%	Jun  4, 2008: - replace all spaces by _ in cruise name

%   Jan  7, 2009: - tightened use of exist()

%	Nov 18, 2009: - replaced "convert" by "pstogif" (syntax is identical)

if nargin < 1, help htmltable, return, end

if nargin == 2 & isstruct(dods)

   DODS = 1;

else

   DODS = 0;

end

disp('HTMLTABLE')

disp(' Surveying Files')

warning off

if isstruct(directory)

   loc = directory.res;

   ii = max(find(loc == '/'));

   loc = loc(1:ii);

else

   loc = directory;

end

d = dir([loc '/*.nc']);

% Ignore Cruise File

count = 0;

bad = [];

for i = 1:length(d)

   f = netcdf([loc '/' d(i).name]);

   % Is this an LADCP File?

   if isempty(f.GEN_Profile_start_decimal_day(:))

      bad = [bad i];

      if ~isempty(f{'cast'}(:))

	 cruise_cast = f{'cast'}(:);

	 cruise_station = f{'station'}(:);

      end

   else

      count = count + 1;

   end

   close(f)

end

d(bad) = [];

if ~exist('cruise_cast','var')

   DODS = 0;

end

if count 

   disp([' Found ' int2str(count) ' Files to Process']);

   for i = 1:length(d)

      disp(['  ' d(i).name]);

   end

else

   error([' Nothing To Do!';])

end

f = netcdf([loc '/' d(1).name]);

name = regexprep(f.cruise_id(:),' ','_');

soft = f.software(:);

time = date;

time(time == '-') = ' ';

if isempty(name)

   name = 'unknown';

end

disp([' Cruise ID: ' name ]);

disp([' Software:  ' soft ]);

disp([' Creating HTML Tables']);

% Header

cr=char(10); % Carriage Return

H0 = ['<TITLE>' name '</TITLE>' cr ...

      '<B>' name '</B>' cr '<BR>' cr ...

      'Created on ' time ' using ' soft cr '<BR>' ...

      '<a href="table0.html"> Cruise Data </a> &nbsp' cr ...

      '<a href="table1.html"> Individual Cast Data </a> &nbsp' cr ...

      '<a href="table2.html"> Processing Methods</a> &nbsp' cr ...

      '<a href="table3.html"> Technical </a> &nbsp' cr ...

      '<a href="table4.html"> Plots </a> &nbsp' cr ...

      '<a href="../index.html"> Other Cruises </a> &nbsp' cr];

% TABLE 0

H1 = [H0, '<img SRC="' name '.gif" HEIGHT=800 WIDTH=600 ALIGN=center>' cr];

if DODS

   H1 = [H1 '<br><ul><li>' cr...

	 '<a href="' dods.cruise(1:end-4) ...

	 '">Live Access IRI/LDEO Data Server</a><br>'];

else

      H1 = [H1 '<br><ul><li>' cr...

	 'Live Access IRI/LDEO Data Server<br>'];

end

H1 = [H1 '<li>All Cruise Data in one file: ' cr];

H1 = [H1 '<a href="' name '.nc"> NetCDF </a>'];

H1 = [H1 ' <br>' cr '</li><li>' cr];

if DODS

   H1 = [H1 ' <a href="' dods.cruise '"> DODS </a> <br>' cr];   

else

   H1 = [H1 ' DODS <br>' cr];

end

H1 = [H1 '</li><li>' ...

      'One File Per Cast: '];

H1 = [H1 '<a href="' name '_nc.tgz"> NetCDF tarball </a>'];

H1 = [H1 '</li><li>' ];

H1 = [H1 '<a href="' name '_ps.tgz"> PS tarball </a>'];

H1 = [H1 '</li><li>' ];

H1 = [H1 '<a href="' name '_log.tgz"> Logfile tarball </a>'];

H1 = [H1 '</li><li>' ];

H1 = [H1 '<a href="' name '_lad.tgz"> ASCII results tarball </a>'];

H1 = [H1 '</li><li>' ];

H1 = [H1 '<a href="' name '_mat.tgz"> MAT results tarball </a>'];

H1 = [H1 '</li><li>' ];

H1 = [H1 'To unpack tarballs :   tar -xzvf filename.tgz'];

cwd = pwd;

cd(loc)

disp(['  NETCDF tarball']);

system(['tar -czf ' name '_nc.tgz *.nc']); 

disp(['  PostScript tarball']);

system(['tar -czf ' name '_ps.tgz *.ps']); 

disp(['  Logfile tarball']);

system(['tar -czf ' name '_log.tgz *.log']); 

disp(['  ASCII tarball']);

system(['tar -czf ' name '_lad.tgz *.lad']); 

disp(['  Mat-file tarball']);

system(['tar -czf ' name '_mat.tgz *.mat']); 

cd(cwd)

fid = fopen([loc '/table0.html'], 'w');

fwrite(fid, H1);

fclose(fid);

fid = fopen([loc '/index.html'], 'w');

fwrite(fid, H1);

fclose(fid);

fid = fopen([loc '/index.htm'], 'w');

fwrite(fid, H1);

fclose(fid);

disp(['  index.html']);

disp(['  index.htm']);

disp(['  table0.html']);

% TABLE 1

H1 = [H0 '&nbsp ',cr,...

      '<div ALIGN=right><table BORDER COLS=12 WIDTH="100%" NOSAVE >',cr];

H1 = [H1 '<tr align=center>' cr];

H1 = [H1 '<td> Name           </td>' cr];

H1 = [H1 '<td> Year           </td>' cr];

H1 = [H1 '<td> Month          </td>' cr];

H1 = [H1 '<td> Day            </td>' cr];

H1 = [H1 '<td> Lat            </td>' cr];

H1 = [H1 '<td> Lon            </td>' cr];

H1 = [H1 '<td> Max Z          </td>' cr];

H1 = [H1 '<td> Median U Error </td>' cr];

H1 = [H1 '<td> NETCDF File    </td>' cr];

H1 = [H1 '<td> Matlab File    </td>' cr];

H1 = [H1 '<td> Text File      </td>' cr];

H1 = [H1 '<td> DODS           </td>' cr];

for i = 1:length(d)

   f = netcdf([loc '/' d(i).name]);

   warn = f.warnings(:);

   WARN(i) = 0;

   % Are there warnings? If so, we will highlight these

   if length(find(warn == char(10))) > 1

      WARN(i) = 1;

   end

   cruiseid = f{'name'}(:)';

   gtime = f{'date'}(:);

   uerr = f{'uerr'}(:);

   lat = f{'lat'}(:);

   lon = f{'lon'}(:);

   station(i) = f.ladcp_station(:);

   LAT(i) = lat;

   LON(i) = lon;

   maxz = max(f{'z'}(:));

   med_err_vel = median(uerr(~isnan(uerr(:))));

   H1 = [H1 '<tr align=center>' cr];

   if WARN(i)

      H1 = [H1 '<td> <font color="red">' cruiseid '</font></td>' cr];      

   else

      H1 = [H1 '<td>' cruiseid                     '</td>' cr];

   end

   H1 = [H1 '<td>' num2str(gtime(1))            '</td>' cr];

   H1 = [H1 '<td>' num2str(gtime(2))            '</td>' cr];

   H1 = [H1 '<td>' num2str(gtime(3))            '</td>' cr];   

   H1 = [H1 '<td>' num3str(lat, 0,2,'0')        '</td>' cr];

   H1 = [H1 '<td>' num3str(lon, 0,2,'0')        '</td>' cr];

   H1 = [H1 '<td>' num2str(maxz)                '</td>' cr];

   H1 = [H1 '<td>' num3str(med_err_vel,0,3,'0') '</td>' cr];   

   H1 = [H1 '<td> <a href="' d(i).name    '"> nc </td>' cr];

   mat = [d(i).name(1:end-2) 'mat'];

   if exist([loc '/' mat],'file')

      H1 = [H1 '<td> <a href="' mat '"> mat </td>' cr];

   else

      H1 = [H1 '<td> mat </td>' cr];

   end

   lad = [d(i).name(1:end-2) 'lad'];

   if exist([loc '/' lad],'file')

      H1 = [H1 '<td> <a href="' lad '"> lad </td>' cr];

   else

      H1 = [H1 '<td> lad </td>' cr];

   end

   if DODS

      cast = cruise_cast(find(cruise_station == station(i)));

      H1 = [H1 '<td> <a href="' dods.d1 int2str(cast) dods.d2 ...

	    '"> dods </a> <td>' cr];      

   else

      H1 = [H1 '<td> dods <td>' cr];

   end

   close(f)

end

H1 = strrep(H1, '<td></td>', '<td>&nbsp </td>'); % Pad Empty Cells

fid = fopen([loc '/table1.html'], 'w');

fwrite(fid, H1);

fclose(fid);

disp(['  table1.html']);

% TABLE 2 - Processing Data

empty = '<td>&nbsp </td>';

H1 = [H0 '&nbsp ',cr,...

      '<div ALIGN=right><table BORDER COLS=6 WIDTH="100%" NOSAVE >', cr];

H1 = [H1 '<tr align=center>' cr];

H1 = [H1 '<td> Name </td>' cr];

H1 = [H1 '<td> Bar Ref </td>' cr];

H1 = [H1 '<td> Depth Source </td>' cr];

H1 = [H1 '<td> Sound Speed </td>' cr];

H1 = [H1 '<td> Percent 3-Beam </td>' cr];

H1 = [H1 '<td> Log </td>' cr];

for i = 1:length(d)

   H1 = [H1 '<tr align=center>' cr];

   f = netcdf([loc '/' d(i).name]);

   cruiseid = f{'name'}(:)';

   if WARN(i)

      H1 = [H1 '<td> <font color="red">' cruiseid '</font></td>' cr];      

   else

      H1 = [H1 '<td>' cruiseid                     '</td>' cr];

   end

   dum = f.BAR_ref_descr(:);

   if ~isempty(dum)

      H1 = [H1 '<td>' dum '</td>' cr];

   else

      H1 = [H1 empty];

   end

   dum = f.GEN_Depth_source(:);

   if ~isempty(dum)

      H1 = [H1 '<td>' dum '</td>' cr];

   else

      H1 = [H1 empty];

   end

   dum = f.GEN_Sound_sp_calc(:);

   if ~isempty(dum)

      H1 = [H1 '<td>' dum '</td>' cr];

   else

      H1 = [H1 empty];

   end

   dum = f.GEN_Percent_3beam(:);

   if ~isempty(dum)

      H1 = [H1 '<td>' num2str(dum) '</td>' cr];

   else

      H1 = [H1 empty];

   end

   H1 = [H1 '<td> <a href="' d(i).name(1:end-2) 'log"> log </td>' cr];

   close(f)

end

H1 = strrep(H1, '<td></td>', '<td>&nbsp </td>'); % Pad Empty Cells

fid = fopen([loc '/table2.html'], 'w');

fwrite(fid, H1);

fclose(fid);

disp(['  table2.html']);

% TABLE 3 - LADCP Technical Data

H1 = [H0 '&nbsp',cr,...

      '<div ALIGN=right><table BORDER COLS=11 WIDTH="100%" NOSAVE >', cr];

H1 = [H1 '<tr align=center>' cr];

H1 = [H1 '<td> Name </td>' cr];

H1 = [H1 '<td> LADCP Up Hard Type </td>' cr];

H1 = [H1 '<td> LADCP Up Hard SN </td>' cr];

H1 = [H1 '<td> LADCP Up Hard Conf Single Ping Acc </td>' cr];

H1 = [H1 '<td> LADCP Up Conf Bin Len </td>' cr];

H1 = [H1 '<td> LADCP Up Conf Number Pings </td>' cr];

H1 = [H1 '<td> LADCP Dn Hard Type </td>' cr];

H1 = [H1 '<td> LADCP Dn Hard SN </td>' cr];

H1 = [H1 '<td> LADCP Dn Hard Conf Single Ping Acc </td>' cr];

H1 = [H1 '<td> LADCP Dn Conf Bin Len </td>' cr];

H1 = [H1 '<td> LADCP Dn Conf Number Pings </td>' cr];

for i = 1:length(d)

   f = netcdf([loc '/' d(i).name]);

   H1 = [H1 '<tr align=center>' cr];

   cruiseid = f{'name'}(:)';

   if WARN(i)

      H1 = [H1 '<td> <font color="red">' cruiseid '</font></td>' cr];      

   else

      H1 = [H1 '<td>' cruiseid                     '</td>' cr];

   end

   dum = f.LADCP_up_hard_type(:);

   if ~isempty(dum)

      H1 = [H1 '<td>' dum '</td>' cr];

   else

      H1 = [H1 empty];

   end

   dum = f.LADCP_up_hard_SN(:);

   if ~isempty(dum)

      H1 = [H1 '<td>' num2str(dum) '</td>' cr];

   else

      H1 = [H1 empty];

   end

   dum = f.LADCP_up_conf_single_ping_acc(:);

   if ~isempty(dum)

      H1 = [H1 '<td>' num3str(dum,1,3,'0') '</td>' cr];

   else

      H1 = [H1 empty];

   end

    dum = f.LADCP_up_conf_bin_len_m(:);

   if ~isempty(dum)

      H1 = [H1 '<td>' num2str(dum) '</td>' cr];

   else

      H1 = [H1 empty];

   end

   dum = f.LADCP_up_conf_number_pings(:);

   if ~isempty(dum)

      H1 = [H1 '<td>' num2str(dum) '</td>' cr];

   else

      H1 = [H1 empty];

   end

   dum = f.LADCP_dn_hard_type(:);

   if ~isempty(dum)

      H1 = [H1 '<td>' dum '</td>' cr];

   else

      H1 = [H1 empty];

   end

   dum = f.LADCP_dn_hard_SN(:);

   if ~isempty(dum)

      H1 = [H1 '<td>' num2str(dum) '</td>' cr];

   else

      H1 = [H1 empty];

   end

   dum = f.LADCP_dn_conf_single_ping_acc(:);

   if ~isempty(dum)

      H1 = [H1 '<td>' num3str(dum,1,3,'0') '</td>' cr];

   else

      H1 = [H1 empty];

   end

   dum = f.LADCP_dn_conf_bin_len_m(:);

   if ~isempty(dum)

      H1 = [H1 '<td>' num2str(dum) '</td>' cr];

   else

      H1 = [H1 empty];

   end

   dum = f.LADCP_dn_conf_number_pings(:);

   if ~isempty(dum)

      H1 = [H1 '<td>' num2str(dum) '</td>' cr];

   else

      H1 = [H1 empty];

   end

   close(f)

end

H1 = strrep(H1, '<td></td>', '<td>&nbsp </td>'); % Pad Empty Cells

fid = fopen([loc '/table3.html'], 'w');

fwrite(fid, H1);

fclose(fid);

disp(['  table3.html']);

% TABLE 4 - Plots

H1 = [H0 '&nbsp ',cr,...

      '<div ALIGN=right><table BORDER COLS=11 WIDTH="100%" NOSAVE >', cr];

H1 = [H1 '<tr align=center>' cr];

H1 = [H1 '<td> Name                     </td>' cr]; %  Name

H1 = [H1 '<td> Summary                  </td>' cr]; %  1

H1 = [H1 '<td> Engineering Data         </td>' cr]; %  2

H1 = [H1 '<td> Data Quality             </td>' cr]; %  3

H1 = [H1 '<td> Depth                    </td>' cr]; %  4

H1 = [H1 '<td> Heading Corrections      </td>' cr]; %  5

H1 = [H1 '<td> Up/Down Differences      </td>' cr]; %  6

H1 = [H1 '<td> CTD Position             </td>' cr]; %  7

H1 = [H1 '<td> Shear                    </td>' cr]; %  8

H1 = [H1 '<td> SADCP U, V               </td>' cr]; %  9

H1 = [H1 '<td> U, V Offsets, Tilt Error </td>' cr]; % 10

for i = 1:length(d)

   H1 = [H1 '<tr align=center>' cr];

   f = netcdf([loc '/' d(i).name]);

   cruiseid = f{'name'}(:)';

   if WARN(i)

      H1 = [H1 '<td> <font color="red">' cruiseid '</font></td>' cr];      

   else

      H1 = [H1 '<td>' cruiseid                     '</td>' cr];

   end

   for j = 1:10

      ps = char([d(i).name(1:end-3) '_' int2str(j) '.ps']);

      if exist([loc '/' ps],'file')

	 H1 = [H1 '<td><a href=' ps '> PS ' int2str(j) '</a></td>' cr];

      else

	 H1 = [H1 '<td> PS ' int2str(j) '</td>' cr];

      end

   end

   close(f)

end

fid = fopen([loc '/table4.html'], 'w');

fwrite(fid, H1);

fclose(fid);

disp(['  table4.html']);

% Map of Casts

disp([' Creating Map of Casts']);

load topo.mat

figure

clf

orient tall

if abs(median(LON)) > 90

   LON(LON < 0) = LON(LON < 0) + 360;

end

lonmin = floor(min(LON));

lonmax = ceil(max(LON));

latmin = floor(min(LAT));

latmax = ceil(max(LAT));

n = length(d);

col = hsv(n);

dx = .02 * (lonmax-lonmin);

dy = .02 * (latmax-latmin);

lon = LON;

lat = LAT;

topo_2 = [topo topo];

topo_x = -359.5:359.5;

topo_y = -89.5:89.5;

axes('pos', [.1 .7 .8 .2])

pcolor(topo_x, topo_y, topo_2)

shading flat

colormap(topomap1)

brighten(.8);

hold on

plot([lonmin lonmax lonmax lonmin lonmin lonmax], ...

     [latmin latmin latmax latmax latmin latmin], '-r', 'linewidth', 3)

title(name, 'fontsize', 20)

axes('pos', [.1 .1 .8 .5])

pcolor(topo_x, topo_y, topo_2)

shading interp

colormap(topomap1)

brighten(.8);

hold on

for i = 1:n

   if station(i) == 1 | station(i) == max(station)

      plot(lon(i), lat(i), '.', 'markersize', 30, 'color', col(i,:))

      text(lon(i)+dx, lat(i)+dy, int2str(station(i)), 'color', [0 0 0])

   else

      plot(lon(i), lat(i), '.', 'markersize', 20, 'color', col(i,:))      

      if mod(station(i),10) == 0

	 text(lon(i)+dx, lat(i)+dy, int2str(station(i)), 'color', [0 0 0])

      end

   end

end

% Put Text Labels On Top

htext = findall(gca, 'type', 'text');

ltext = findall(gca, 'type', 'line');

child = get(gca, 'children');

set(gca, 'children', [htext; ltext; setxor([htext; ltext], child)]);

axis([lonmin lonmax latmin latmax])

ylabel('Latitude [^oN]', 'fontsize', 12)

xlabel('Longitude [^oE]', 'fontsize', 12)

drawnow

eval(['print -dpsc ' loc '/' name '.ps']);

disp(['  ' name '.ps']);

s = system(['pstogif -density 150 ' loc '/' name '.ps ' loc '/' name '.gif']);

if s

   disp([' Unable to create ' name '.gif']);

else

   disp(['  ' name '.gif']);

end

cwd = pwd;

cd(directory);

loc = pwd;

disp([' View HTML Table at:'])

disp(['  file://' loc '/table0.html']);

cd(cwd);