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,p,ps,f,att - arbitrary metadata structures

%

% Subroutine :  add_struct

% 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: Thu Nov 26 22:01:32 2015

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

%                    uE-Info: 183 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?)

%   Nov     2015: - new coded provided by Diana Cardoso (with support from Eric Firing)

%   Nov 26, 2015: - BUG: code did not work when bottom-track data were missing

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

% check arguments and remove existing NetCDF file with fname(output filename)

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

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

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

%Create a classic format NetCDF file with 8 dimension definitions.

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

mySchema.Name   = '/'; % indicating the full file as opposed to a group

mySchema.Format = 'classic'; %The format of the NetCDF file

%Create Dimensions

mySchema.Dimensions(1).Name   = 'name';

mySchema.Dimensions(1).Length = length(getfield(dr_struct,'name'));

mySchema.Dimensions(2).Name   = 'date';

mySchema.Dimensions(2).Length = 6;

mySchema.Dimensions(3).Name   = 'lat';

mySchema.Dimensions(3).Length = 1;

mySchema.Dimensions(4).Name   = 'lon';

mySchema.Dimensions(4).Length = 1;

if isfield(dr_struct,'z');

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

else

  lz = 0;

end  

mySchema.Dimensions(5).Name   = 'z';

mySchema.Dimensions(5).Length = lz;

if isfield(dr_struct,'tim');

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

else

  ltim = 0;

end  

mySchema.Dimensions(6).Name   = 'tim';

mySchema.Dimensions(6).Length = ltim;

if isfield(dr_struct,'zbot');

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

else

  lbot = 0;

end

mySchema.Dimensions(7).Name   = 'zbot';

mySchema.Dimensions(7).Length = lbot;

if isfield(dr_struct,'z_sadcp');

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

else

  lsadcp = 0;

end

mySchema.Dimensions(8).Name   = 'z_sadcp';

mySchema.Dimensions(8).Length = lsadcp;

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

%Add first 4 variables definitions(name, date, lat, lon) to Variable field

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

mySchema.Variables(1).Name = 'name';

mySchema.Variables(1).Dimensions(1) = mySchema.Dimensions(1);

mySchema.Variables(1).Datatype = 'char';

mySchema.Variables(2).Name = 'date';

mySchema.Variables(2).Dimensions(1) = mySchema.Dimensions(2);

mySchema.Variables(2).Datatype = 'int32';

mySchema.Variables(3).Name = 'lat';

mySchema.Variables(3).Dimensions(1) = mySchema.Dimensions(3);

mySchema.Variables(3).Datatype = 'single';

mySchema.Variables(4).Name = 'lon';

mySchema.Variables(4).Dimensions(1) = mySchema.Dimensions(4);

mySchema.Variables(4).Datatype = 'single';

dr_struct = orderfields(dr_struct) ; %sort dr_struct by fieldnames

fnames = fieldnames(dr_struct);

% find name, date, lat, lon in fnames that have already been added to the 

% NetCDF file and remove from fnames

nn=strncmp('name',fnames,6);   

nda=strncmp('date',fnames,4);

nla=strncmp('lat',fnames,3); 	

nlo=strncmp('lon',fnames,3);

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

fnames(Ktot,:)=[];	

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

%Add the remaining variables definitions from dr_struct to Variable field

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

for n=1:size(fnames,1)

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

    mySchema.Variables(4+n).Name = fnames{n};

    if ~isempty(strfind(fnames{n},'bot'))

        mySchema.Variables(4+n).Dimensions(1) = mySchema.Dimensions(7);

    elseif ~isempty(strfind(fnames{n},'sadcp'))

        mySchema.Variables(4+n).Dimensions(1) = mySchema.Dimensions(8);

    elseif ~isempty(strfind(fnames{n},'tim')) ||  ~isempty(strfind(fnames{n},'ship')) ...

        || ~isempty(strfind(fnames{n},'ctd')) && isempty(strmatch('ctd_t',fnames{n},'exact')) ...

        && isempty(strmatch('ctd_s',fnames{n}))

        mySchema.Variables(4+n).Dimensions(1) = mySchema.Dimensions(6);

    elseif ~isempty(strfind(fnames{n},'vel')) ||  ~isempty(strfind(fnames{n},'shear')) ...

        || ~isempty(strfind(fnames{n},'ctd_')) || ~isempty(strfind(fnames{n},'uerr')) ...

        ||  ~isempty(strfind(fnames{n},'range'))  || ~isempty(strfind(fnames{n},'ts')) ...

        || ~isempty(strmatch('p',fnames{n},'exact')) || ~isempty(strmatch('u',fnames{n},'exact')) ...

        || ~isempty(strmatch('v',fnames{n},'exact'))|| ~isempty(strmatch('z',fnames{n},'exact')) ...

        || ~isempty(strfind(fnames{n},'u_')) || ~isempty(strfind(fnames{n},'v_'));

        mySchema.Variables(4+n).Dimensions(1) = mySchema.Dimensions(5);

    else

        mySchema.Variables(4+n).Dimensions.Name = fnames{n};

        mySchema.Variables(4+n).Dimensions.Length = length(dummy);

    end 

    if strncmp(fnames{n},'tim',4)==1 ||  ~isempty(strfind(fnames{n},'vbar')) ||  ~isempty(strfind(fnames{n},'ubar'))

        mySchema.Variables(4+n).Datatype = 'double';

    elseif strncmp(fnames{n},'nvel',4)==1 

        mySchema.Variables(4+n).Datatype = 'int16';

    else

        mySchema.Variables(4+n).Datatype = 'single'; 

    end   

%    disp(sprintf('%d: %s %d',n,mySchema.Variables(4+n).Dimensions.Name,mySchema.Variables(4+n).Dimensions.Length));

end

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

%Add the attributes definitions from dr_struct to the Variable field

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

ncwriteschema(fname, mySchema);

ncwriteatt(fname,'name','long_name',att.name.long_name);

ncwriteatt(fname,'date','long_name',att.date.long_name);

ncwriteatt(fname,'date','units',att.date.units);

ncwriteatt(fname,'lat','long_name',att.lat.long_name);

ncwriteatt(fname,'lat','units',att.lat.units);

ncwriteatt(fname,'lon','long_name',att.lon.long_name);

ncwriteatt(fname,'lon','units',att.lon.units);

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

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

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

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

for n=1:size(fnames,1)

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

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

    if isfield(att,fnames{n});

        ncwriteatt(fname,fnames{n},'long_name',att.(fnames{n}).long_name);

        if isfield(att.(fnames{n}),'units');

             ncwriteatt(fname,fnames{n},'units',att.(fnames{n}).units);

        end

    end

end

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

%Add the attributes definitions from da, p, f, ps mat structures to

%Attributes field using subroutine add_struct

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

% remove duplicate fields from mat structures

ps = rmfield(ps,'outlier');

p = rmfield(p,'checkpoints');

f = rmfield(f,'ctd_time_base');

f = rmfield(f,'nav_time_base');

% combine all mat structures and sort fieldnames

names = [fieldnames(da); fieldnames(p)];

struct1 = cell2struct([struct2cell(da); struct2cell(p)], names, 1);

names = [fieldnames(struct1); fieldnames(ps)];

struct2 = cell2struct([struct2cell(struct1); struct2cell(ps)], names, 1);

names = [fieldnames(struct2); fieldnames(f)];

struct3 = cell2struct([struct2cell(struct2); struct2cell(f)], names, 1);

structsorted = orderfields(struct3) ;

% add attributes to netcdf from the p, ps, da and f structures

% the slash indicates a global variable, if you change it the value in the 

% structures will be placed in the Variables field of the netcdf 

add_struct(fname,'/',structsorted); 

end % function

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