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

%                    M Y C R U I S E . M 

%                    doc: Wed Jun  4 12:22:17 2008

%                    dlm: Wed Jun  4 12:42:33 2008

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

%                    uE-Info: 27 58 NIL 0 0 72 0 2 4 NIL ofnI

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

function [] = cruise(directory, dods)

% function [] = cruise(directory, dods)

%

% Create Cruise netCDF file from cast files.

%

% 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 : cruise.nc : Cruise netCDF file (filename will vary)

%          htmltable is called to create tables.

% Modifications by ANT:

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

if nargin < 1, help cruise, return, end

if nargin < 2, dods = ' '; end

% Interpolation Grids for Cruise netCDF File

GRID.z       = [10:10:6000]';      % Depth (m)

GRID.z_sadcp = [0:10:800]';        % Depth (m)

GRID.zbot    = [0:10:300]';        % Height Above Bottom (m)

GRID.tim     = linspace(0,1,100)'; % Normalized Time

% Attributes will be grouped together by first four letters:

AttVar = {'GEN_'; 'BAR_'; 'INPU'; 'LADC'};

% Main Varables, all others will be grouped by variable length as 'EXTRA'

MainVariables = {'z';'u';'v';'uerr';'lat';'lon';'jul';'maxz'; ...

                 'cast'; 'cast_id'; 'station'};

disp('CRUISE')

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']);

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];

   else

     count = count + 1;

   end

   close(f)

end

d(bad) = [];

%%%

%disp('TESTING - only using first 4 files')

%pause(2)

%d(5:end) = [];

%count = min(count, 4);

%%%

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

ncquiet

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

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

if isempty(name)

   name = 'unknown';

end

close(f);

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

% A : Attributes

% D : Data

% F : Dimensions and lists of Variables

% G : Dimension Lengths 

% H : Variable Type (char, float, etc.)

disp([' Surveying Files For All Possible Dimensions and Variables']);

[F,G,H] = deal([]);

for i = 1:length(d)

   d(i).nc    = d(i).name;

%   disp(['  ' d(i).nc ]);

   d(i).name  = d(i).name(1:end-3); % .nc

   d(i).ps    = dir([d(i).name '*.ps']); % Any Other Plots

   d(i).lad   = [d(i).name '.lad'];

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

   dims = dim(f);

   atts = att(f);

   % Find All Possible Variables (Sorted By Dimension)

   for j = 1:length(dims)

      field = ncnames(dims{j});

      dum = char(ncnames(var(dims{j}))');

      if ~isempty(dum)  

	 for k = 1:size(dum,1)

	    eval(['H.' dum(k,:) ' = datatype(f{''' deblank(dum(k,:)) '''});']);

	 end

	 if ~isfield(F, field)

	    eval(['F.' char(field) ' = dum;']);

	    eval(['G.' char(field) ' = length(f(''' char(field) '''));']);

	 else

	    eval(['G.' char(field) ' = max(G.' char(field) ', ' ...

		  'length(f(''' char(field) ''')));']);	 	 

	    dum = unique(char([cellstr(dum); ...

			       cellstr(eval(['F.' char(field)]))]), 'rows');

	    eval(['F.' char(field) ' = dum;']);

	 end

      end

   end

   % Find Special Global Attributes -> Cast Variables

   for j = 1:length(atts)

      at = char(ncnames(atts{j}));

      if any(strncmp(ncnames(atts{j}), AttVar,4))

	 val = eval(['f.' at '(:);']); 

	 if ischar(val)

	    eval(['F.' at ' = at;'])

	    eval(['H.' at ' = ''char'';']);

	    if ~isfield(G, at)

	       eval(['G.' at ' = length(val);']);

	    else

	       eval(['G.' at ' = max(length(val), G.' at ');']);

	    end

	 elseif numel(val) > 1

	    eval(['F.' at ' = at;']);

	    eval(['H.' at ' = ''float'';'])

	    if ~isfield(G, at)

	       eval(['G.' at ' = length(val);']);

	    else

	       eval(['G.' at ' = max(length(val), G.' at ');']);

	    end

	 else

	    eval(['H.' at ' = ''float'';'])

	    if ~isfield(F, 'cast')

	       eval(['F.cast = at;' ]);

	    else

	       F.cast = unique(char([cellstr(at); cellstr(F.cast)]), 'rows');

	    end

	 end

      end

   end

   close(f);

end

% Add Interpolation Grids 

field = fieldnames(GRID);

for i = 1:length(field)

   eval(['G.' field{i} ' = length(GRID.' field{i} ');']);

end

% Merge Dimensions of Length 1 -> 'cast'

field = fieldnames(G);

dd = [];

for i = 1:length(field)

   if eval(['G.' field{i} ' == 1']) % Dimension Length = 1

      dd = [dd i];

   end

end

if ~isempty(dd)

   ff = field(dd);

   if isfield(F, 'cast')

      dd = cellstr(F.cast);

   else

      dd = [];

   end

   for i = 1:length(ff)

      dd = [dd; cellstr(eval(['F.' ff{i}]))];

   end

   for i = 1:length(ff)

      eval(['F = rmfield(F, ''' ff{i} ''');']);

      eval(['G = rmfield(G, ''' ff{i} ''');']);

   end

   F.cast = char(dd);

   G.cast = 1;

end

dd = fieldnames(G);

disp([' Found ' int2str(length(dd)) ' Dimensions'])

%for i = 1:length(dd)

%   disp(['  ' dd{i}]);

%end

dd = fieldnames(H);

disp([' Found ' int2str(length(dd)) ' Variables'])

%for i = 1:length(dd)

%   disp(['  ' dd{i}]);

%end

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

% Create Dummy Arrays For Every Cast %

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

disp(' Creating Dummy Arrays For Every Cast');

d1 = length(d);

dims = fieldnames(F);

for i = 1:length(dims)

   if isfield(GRID, dims{i})

      d2 = length(eval(['GRID.' dims{i} ]));

   else

      d2 = eval(['G.' dims{i}]);

   end

   vars = eval(['F.' dims{i}]);

   if ~isempty(vars)

      for j = 1:size(vars,1)

	 if eval(['strcmp(H.' vars(j,:) ', ''char'')'])

	    eval(['D.' vars(j,:) '= repmat('' '', d1, d2);']);	    

	 else

	    eval(['D.' vars(j,:) '= repmat(nan, d1, d2);']);

	 end

      end

   else

      eval(['F = rmfield(F, ''' vars{i} ''');']);

   end

end

field = fieldnames(GRID);

for i = 1:length(field)

   eval(['D.' field{i} '=GRID.' field{i} ';']);

end

D.cast = [1:length(d)]';

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

% Load Cast Data %

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

disp(' Loading Cast Data');

for i = 1:length(d)

   fprintf(['  ' d(i).nc]);

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

   dims = ncnames(dim(f));

   vars = ncnames(var(f));

   atts = ncnames(att(f));

   D.lat(i,1) = f.lat(:);

   D.lon(i,1) = f.lon(:);

   D.maxz(i,1) = max(f{'z'}(:));

   % Global Attributes -> Variables

   for j = 1:length(atts)

      if any(strncmp(atts{j}, {'GEN_'; 'BAR_'; 'INPU'; 'LADC'},4))

	 nam = atts{j};

	 val = eval(['f.' nam '(:)']);

	 eval(['D.' nam '(i,1:length(val)) = val;']);

      end      

   end 

   % Catalog Variables

   D.cast_id(i,1:length(f{'name'}(:))) = f{'name'}(:)';

   D.station(i,1) = f.ladcp_station(:);

   start = julian(2000,1,1,0);

   D.date(i,:) = f{'date'}(:)';

   D.jul(i,1)  = julian(D.date(i,:)) - start;

   % Additional Variables

   for j = 1:length(dims)

     dd = dims{j};

     if isfield(F, dd)

       v = cellstr(eval(['F.' dd]));

       for k = 1:length(v)

	 vv = v{k};

	 %clearline

	 %fprintf(['  ' d(i).nc ' : ' dd ' : ' vv ])

	 if any(strcmp(vv, vars)) & ~strcmp(vv,dd) % Found a Variable

	   if isfield(GRID, dd)  % We need to Interpolate

	     oldgrid = eval(['f{''' dd '''}(:)']);

	     switch dd

	      case 'zbot'

	       oldgrid = eval(['f.GEN_Ocean_depth_m(:)']) - oldgrid;

	      case 'tim'

	       oldgrid = (oldgrid - oldgrid(1)) / (oldgrid(end)-oldgrid(1));

	     end

	     olddata = eval(['f{''' vv '''}(:)']);

	     newgrid = eval(['GRID.' dd]);

	     eval(['D.' vv '(i,:) = interp1q(oldgrid, olddata, newgrid);']);

	   else % Just Store the Data

	     data = eval(['f{''' vv '''}(:)']);

	     ii = length(data);

	     eval(['D.' vv '(i,1:ii) = data;']);

	   end

	 end

	 if any(strcmp(vv, vars)) % Variable or Dimension

           % Store Attributes

	   aa = eval(['ncnames(att(f{''' vv '''}));']);   

	   for t = 1:length(aa)

	     a = aa{t};

	     eval(['A.' vv '.' a ' = f{''' vv '''}.' a '(:);']);

	   end

	   % Non-char Variables : Add missing_value Tag

	   if eval(['~strcmp(H.' vv ', ''char'') & ~strcmp(vv,dd)']) 

	      eval(['A.' vv '.missing_value = nan;']);

	   end

	 end

       end

%     end

     %%%  

     elseif isfield(H,dd)

        % Store Attributes

	aa = eval(['ncnames(att(f{''' dd '''}));']);   

	for t = 1:length(aa)

	   a = aa{t};

	   eval(['A.' dd '.' a ' = f{''' dd '''}.' a '(:);']);

	end

        % Non-char Variables : Add missing_value Tag

	if eval(['~strcmp(H.' dd ', ''char'')']) 

	   eval(['A.' dd '.missing_value = nan;']);

	end

     end

     %%%

   end

   close(f)

   clearline

   fprintf(['  ' d(i).nc '\n']);

end

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

% Add Attributes For Variables Created Here %

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

F = rmfield(F, 'name'); %

G = rmfield(G, 'name'); % For Ingrid Compatability

H = rmfield(H, 'name'); % We have renamed 'name' to 'cast_id'

A = rmfield(A, 'name'); %

F.cast     = char([cellstr(F.cast); cellstr({'jul';'maxz';'station'})]);

F.cast_id  = 'cast_id';

G.cast     = size(D.cast,1);

G.cast_id  = size(D.cast_id,2);

H.cast     = 'float';

H.cast_id  = 'char';

H.jul      = 'float';

H.maxz     = 'float';

H.station  = 'float';

A.cast.long_name    = 'Cast';

A.cast_id.long_name = 'Cast ID';

A.jul.long_name     = 'Date';

A.jul.units         = 'Days Since 2000-01-01';

A.maxz.long_name    = 'Maximum Depth';	

A.maxz.units        = 'Meters';

A.station.long_name = 'Station Number';

% Limits for Ingrid Plot

fac = 0.1;

lon = D.lon;

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

lonmin = floor(min(lon));

lonmax = ceil(max(lon));

lonmin = lonmin - fac*(lonmax-lonmin);

lonmax = lonmax + fac*(lonmax-lonmin);

latmin = floor(min(D.lat));

latmax = ceil(max(D.lat));

latmin = latmin - fac*(latmax-latmin);

latmax = latmax + fac*(latmax-latmin);

A.lon.scale_min = lonmin;

A.lon.scale_max = lonmax;

A.lat.scale_min = latmin;

A.lat.scale_max = latmax;

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

% Create Cruise netCDF File %

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

disp(' Creating Cruise NetCDF matlab');

eval([' save ',loc '/' name ' A D F G H ']);

disp(' Creating Cruise NetCDF File');

f = netcdf([loc '/' name '.nc'], 'clobber');

% Dimensions

disp(' Saving Dimensions');

FF = fieldnames(F);

for i = 1:length(FF) 

   dd = FF{i};

   DD = dd;

   % Convert BLAH_blah to BLAH.blah if BLAH is in AttVar

   % This is done to create subgroups for Ingrid

   if any(strncmp(DD, AttVar,4))

      ii = min(find(DD == '_'));

      if ~isempty(ii)

	 DD(ii) = '.';

      end

   end

   SKIP = 0;

   if eval(['strcmp(H.' dd ', ''char'')'])

      DD = [DD '_char'];

      SKIP = 1;

   elseif eval(['numel(D.' dd ') ~= length(D.' dd ')'])

      DD = [DD '_num'];      

      SKIP = 1;

   end

   eval(['f(''' DD ''') = G.' dd ';']);

   if ~SKIP

      eval(['f{''' DD '''} = ncfloat(''' DD ''');']);

   end

   if eval(['numel(D.' dd ') == length(D.' dd ')'])

      eval(['f{''' DD '''}(:) = D.' dd ';']);      

   else

% Fixes ingrid problem      

%      eval(['f{''' DD '''}(:) = [1:G.' dd '];']);

   end

   % Dimension Attributes

   if isfield(A, dd)

      aa = eval(['fieldnames(A.' dd ')']);

      for j = 1:length(aa)

	 at = aa{j};

	 eval(['f{''' DD '''}.' at '=A.' dd '.' at ';']);

      end

   end

   %disp(['  ' DD]);

end

% Variables

disp(' Saving Variables');

FF = fieldnames(F);

for i = 1:length(FF) 

   dd = FF{i};

   DD = dd;

   if eval(['strcmp(H.' dd ', ''char'')'])

      DD = [DD '_char'];

   elseif eval(['numel(D.' dd ') ~= length(D.' dd ')'])

      DD = [DD '_num'];      

   end

   if any(strncmp(DD, AttVar,4))

      ii = min(find(DD == '_'));

      if ~isempty(ii)

	 DD(ii) = '.';

      end

   end

   V = eval(['F.' dd]);

   for j = 1:size(V,1)

      vv = char(cellstr(V(j,:)));

      VV = vv;

      % What Kind of Variable?

      % Main: z,u,v, etc.

      % Extra: u_do, range, nvel, etc.

      % Attribute Derived: GEN_Depth_source, BAR_ref_descr, etc.

      if ~strcmp(DD, vv) % Variable, Not a Dimension

         % Attribute Derived

	 if any(strncmp(VV, AttVar,4))

	    ii = min(find(VV == '_'));

	    if ~isempty(ii)

	       VV(ii) = '.';

	    end

         % Extra

	 elseif ~any(strcmp(VV, MainVariables))

	    switch dd

	     case 'z'

	      VV = ['EXTRA.PROFILE.' VV];

	     case 'tim'

	      VV = ['EXTRA.TIMESERIES.' VV];

	     case 'zbot'

	      VV = ['EXTRA.BOTTOM.' VV];

	     case 'z_sadcp'

	      VV = ['EXTRA.SADCP.' VV];

	    end

	 end 

	 if ~strcmp(vv, 'cast') & ~strcmp(dd, 'cast')

	    if eval(['strcmp(H.' vv ', ''char'')'])

	       eval(['f{''' VV '''} = ncchar(''cast'', ''' DD ''');']);

	    else

	       eval(['f{''' VV '''} = ncfloat(''cast'', ''' DD ''');']);

	    end

	    eval(['f{''' VV '''}(:,:) = D.' vv ';']);

	 else

	    if eval(['strcmp(H.' vv ', ''char'')'])

	       eval(['f{''' VV '''} = ncchar(''cast'');']);

	    else

	       eval(['f{''' VV '''} = ncfloat(''cast'');']);	    

	    end

	    eval(['f{''' VV '''}(:) = D.' vv ';']);

	 end

         % Variable Attributes

	 if isfield(A, vv)

	    aa = eval(['fieldnames(A.' vv ')']);

	    for k = 1:length(aa)

	       at = aa{k};

	       eval(['f{''' VV '''}.' at '=A.' vv '.' at ';']);

	    end

	 end

      else

      end

      %disp(['  ' VV]);

   end

end

% Global Attributes

f.EXTRA.description            = 'More Data';

f.EXTRA.PROFILE.description    = 'PROFILES';

f.EXTRA.TIMESERIES.description = 'TIMESERIES';

f.EXTRA.BOTTOM.description     = 'BOTTOM';

f.BAR.description              = 'Barotropic Data';

f.GEN.description              = 'General Processing Parameters';

f.INPUT.description            = 'Available Inputs';

f.LADCP.description            = 'LADCP Technical Data';

close(f);

% Create TAR Files for .nc, .lad, .ps files

disp(' Finished')

htmltable(directory, dods)

function [] = clearline()

fprintf(repmat('\b',1,80));

fprintf(repmat(' ' ,1,80));

fprintf(repmat('\b',1,80));