function [] = ladcp2cdf(fname,dr_struct,da,p,ps,f,att);

% function [] = ladcp2cdf(fname,dr_struct,da,p,ps,f,att);

%

% function to save LADCP data into a netcdf file for MatLab version 2012a

%

% input  :	fname		- output filename

%			dr_struct	- main inversion results (velocity profiles)

%			da..att	- arbitrary metadata structures

%

% Created By:   Diana Cardoso, Bedford Institute of Oceangraphy

%               Diana.Cardoso@dfo-mpo.gc.ca

% Description:  Based on LDEO software to Process LADCP, version IX.8,

%               script ladcp2cdf.m version 0.1	last change 08.03.2002. 

%               maintained by A.M. Thurnherr and downloaded from:

%       http://www.ldeo.columbia.edu/cgi-bin/ladcp-cgi-bin/hgwebdir.cgi

%       The function ladcp2cdf was changed to run with the the Matlab

%       version 2012, which now supports netcdf.

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

%                    L A D C P 2 C D F . M 

%                    doc: Thu Aug 15 10:52:55 2013

%                    dlm: Wed Aug 28 12:31:16 2013

%                    (c) 2013 A.M. Thurnherr, from code contributed by D. Cardoso

%                    uE-Info: 99 0 NIL 0 0 72 0 2 8 NIL ofnI

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

% NOTES:

%	- This version creates slightly different files than the original version

%	  created by Visbeck/Krahmann. In the original version, the contents of the

%	  dr structure end up as top-level variables and the contents of

%	  the da, p, ps, f and att structures end of as global attributes. In 

%	  the new version, the latter are saved as sub-structures, with _struct appended

%	  to the internal names to avoid conflicts.

% HISTORY:

%   Aug 15, 2013: - incorporated this code, supplied Diana Cardoso, into IX_10beta

%		  - modified doc in header

%		  - renamded struct variable to dr_struct

%		  - removed 'cd' in and out of results directory (pathnames work just fine)

%		  - delete netcdfile before it is written to (old 'clobber' option)

%		  - removed 'l' suffix from all dims

%		  - replaced yes/no logical vals by true/false

%		  - renamed substructures from st2..st6 to internal names (da,p,ps,f,att)

%   Aug 28, 2013: - incorporated bug fix provided by Diana Cardoso to prevent lat,lon,name and 

%		    date to be stored 2cd in the nc file, which can make the code

%		    bomb if the length of any other var is 6 (or equal to the length of name?)

% check arguments

if nargin<2

  error('need two input arguments')

end

if ~isstruct(dr_struct)

  error('second argument must be a dr structure')

end

netcdfile = deblank(fname); %remove any blanks from string end

if exist(netcdfile,'file')

	delete(netcdfile)

end

%Determine dimensions of variables

lbot = 0;

lz = 0;

ltim = 0;

lsadcp = 0;

if isfield(dr_struct,'z');

  lz = length(getfield(dr_struct,'z'));

end  

if isfield(dr_struct,'tim');

  ltim = length(getfield(dr_struct,'tim'));

end  

if isfield(dr_struct,'zbot');

  lbot = length(getfield(dr_struct,'zbot'));

end  

if isfield(dr_struct,'z_sadcp');

  lsadcp = length(getfield(dr_struct,'z_sadcp'));

end  

% % define dimensions in netcdf file and standard variables

nccreate(netcdfile,'lat','Dimensions',{'lat' 1},'Datatype','single');

nccreate(netcdfile,'lon','Dimensions',{'lon' 1},'Datatype','single');

nccreate(netcdfile,'date','Dimensions',{'date' 6},'Datatype','int32');

nccreate(netcdfile,'name','Dimensions',{'name' length(getfield(dr_struct,'name'))},'Datatype','char');

% store standard variables

ncwrite(netcdfile,'lat',dr_struct.lat);

ncwrite(netcdfile,'lon',dr_struct.lon);

ncwrite(netcdfile,'date',dr_struct.date);

ncwrite(netcdfile,'name',dr_struct.name);

% parse fieldnames, define the proper variable and store it

fnames = fieldnames(dr_struct);

nn=strncmp('name',fnames,6); nla=strncmp('lat',fnames,3); 	% find, name, lat,lon,date from fnames

nlo=strncmp('lon',fnames,3); nda=strncmp('date',fnames,4);

ntot=[nn+nla+nlo+nda]; Ktot = logical(ntot);

fnames(Ktot,:)=[];						% remove , name, lat,lon,date from fnames

for n=1:size(fnames,1)

  dummy = getfield(dr_struct,fnames{n});

  if length(dummy)==lz

    nccreate(netcdfile,fnames{n},'Dimensions',{fnames{n} fix(lz)},'Datatype','single');

    ncwrite(netcdfile,fnames{n},dummy);

  end

  if length(dummy)==ltim

    nccreate(netcdfile,fnames{n},'Dimensions',{fnames{n} fix(ltim)},'Datatype','single');

    ncwrite(netcdfile,fnames{n},dummy);

  end

  if length(dummy)==lbot

    nccreate(netcdfile,fnames{n},'Dimensions',{fnames{n} fix(lbot)},'Datatype','single');

    ncwrite(netcdfile,fnames{n},dummy);

  end

  if length(dummy)==lsadcp

    nccreate(netcdfile,fnames{n},'Dimensions',{fnames{n} fix(lsadcp)},'Datatype','single');

    ncwrite(netcdfile,fnames{n},dummy);

  end

end

add_struct(netcdfile,'da_struct',da)

add_struct(netcdfile,'p_struct',p)

add_struct(netcdfile,'ps_struct',ps)

add_struct(netcdfile,'f_struct',f)

add_struct(netcdfile,'att_struct',att)

end % function

%----------------------------------------------------------------------

function [] = add_struct(ncf,snm,a)

   fnames = fieldnames(a);

   if isstruct(a)

      if ~isstruct(eval(['a.' fnames{1}])) % No SubStructure

	nccreate(ncf,snm,'Datatype','char');

	for n = 1:size(fnames,1)

		dummy = getfield(a,fnames{n});

	    	if size(dummy,1)==1

	       		if isstr(dummy)

                		ncwriteatt(ncf,snm,fnames{n},dummy);

	       		elseif islogical(dummy)

		        	if dummy, dummy='true';

		               	else, 	  dummy='false';

		               	end

				ncwriteatt(ncf,snm,fnames{n},dummy);

			else

		                ncwriteatt(ncf,snm,fnames{n},dummy(:));

			end    

		end

	end % for n

      else % SubStructures -> Variable Attributes

	for n = 1:size(fnames,1)

		atts = eval(['fieldnames(a.' fnames{n} ');']);

	        finfo = ncinfo(ncf);

        	FieldNames = {finfo. Variables.Name};

	        existField=strmatch(fnames{n}, FieldNames);

        	if isempty(existField)

			nccreate(ncf,fnames{n},'Datatype','char');

	        end

		for j = 1:size(atts,1)

			dummy = eval(['a.' fnames{n} '.' atts{j} ';']);

			if size(dummy,1) == 1

				if ischar(dummy)

		                    ncwriteatt(ncf,fnames{n},atts{j},dummy);

                		else

		                    ncwriteatt(ncf,fnames{n},atts{j},dummy(:));

                		end

			end

		end	       

	 end % for n

      end % else (substructures or not)

   else % if issstruct(a)

      disp(' not structure')

   end

end % function