Remove some old versions of the code to load the FVCOM model outputs

utilities/read_netCDF_FVCOM_old.m

-function [varargout]=read_netCDF_FVCOM(varargin)
-% funtion to read underway NetCDF files from discovery
-% possible intputs are
-% all_data = 0 single file or 1 for multiple files
-% directory where the data is stored
-% files = cell array of filenames or if single string then a search pattern
-% i.e. *position-4000.gps
-% varnames in cell array of variables to extract i.e. lat, lon, time
-% they need to be exact matches of variables contained in the netcdf file
-% The options could be (but depend on your model output:
-% Itime, Itime2, Times, h, iint, kh, km, kq, l, lat, latc, lon, lonc,
-% nprocs, nv, partition, q2, q2l, salinity, siglay, siglay_DT,
-% siglay_shift_DT, siglev, siglev_DT, temp, time, u, ua, v, va, wet_cells,
-% wet_cells_prev_ext, wet_cells_prev_int, wet_nodes, wet_nodes_prev_int, x,
-% xc, y, yc, zeta,
-% possible attributes for each variable are:
-% nc{'measureTS'} = ncdouble('time'); %% 2983 elements.
-% nc{'measureTS'}.element_name = ncchar(''measure time'');
-% nc{'measureTS'}.cardinalitymin = nclong(1);
-% nc{'measureTS'}.cardinalitymax = nclong(1);
-% nc{'measureTS'}.comment = ncchar(''time of measure as determined by the GPS'');
-% nc{'measureTS'}.long_name = ncchar(''measure timestamp'');
-% nc{'measureTS'}.units = ncchar(''day since 1899-12-30T00:00:00 UTC'');
-% nc{'measureTS'}.shortunits = ncchar(''days'');
-% nc{'measureTS'}.positive = ncchar(''up'');
-% nc{'measureTS'}.C_format = ncchar(''%14.7f'');
-% nc{'measureTS'}.axis = ncchar(''T'');
-% nc{'measureTS'}.measuretimedata = ncchar(''measureTS'');
-% nc{'measureTS'}.valid_max = ncdouble(100000);
-% nc{'measureTS'}.valid_min = ncdouble(30000);
-% nc{'measureTS'}.precision = nclong(12);
-% nc{'measureTS'}.scale = nclong(7);
-% nc{'measureTS'}.FillValue_ = ncdouble(0);
-% nc{'measureTS'}.missing_value = ncdouble(0);
-% nc{'measureTS'}.scale_factor = ncdouble(1);
-% nc{'measureTS'}.add_offset = ncdouble(0);
-% nc{'measureTS'}.element_version = ncchar(''1.0'');
-% nc{'measureTS'}.valid_range = ncchar(''30000.000000,100000.000000'');
-netcdfpath
-addpath D:\Research\Models\UMASSDvisit\matlab;
-%%
-CD=pwd;
-disp(['Using date conversion of +678942 to go from FVCOM time to matlab time'])
-time_offset = 678942;
-params_opts={'time','data_dir','files','nzopt','trnsopt','varnames','trns_idx','nz_idx'}
-
-disp(['Default values are ...'])
-var_in_list = {'all_data','netfile_dir','files','nz','trnsxy','varnames','trns_idx','nz_idx'};
-all_data = 1;
-netfile_dir = 'D:\research\Data\ICON\underway\netcdf';
-files = '*.nc';
-nz=0;nz_idx=-1;
-trnsxy=0;trns_idx=-1;
-varnames={'time','lat','lon','h',};
-for aa=1:2:nargin
-    res=strmatch(varargin(aa),params_opts)
-    if ~isempty(res),
-        eval([var_in_list{res},' = varargin{aa+1};'])
-        disp([params_opts{res}])
-    end
-    %     eval([var_in_list{aa},' = varargin{aa};'])
-end
-if nz==0
-    nz_idx=-1;
-end
-if trnsxy==0;
-    trns_idx=-1;
-end
-
-nvarnames = length(varnames);
-for nn=1:nvarnames
-    data{nn} = [];
-end
-%%
-cd (netfile_dir)
-filen = dir(files);
-for ff=1:length(filen)
-    file_netcdf{ff} = filen(ff).name;
-end
-%     filen(1).name = files;
-%     file_netcdf{1} = files;
-% Extract time range for all available files
-files_to_read = [];times=[];
-for ff=1:length(filen)
-    nc = netcdf(file_netcdf{ff}, 'nowrite');
-
-    gatts = att(nc); % this are the general file attributes
-    vars = var(nc);
-    for ii = 1 : length(vars)
-        output = name(vars{ii});
-        to_show{ii}=output;
-        switch output
-            case 'Itime'
-                [start_d(1),end_d(1)] = deal(vars{ii}(1)+time_offset,vars{ii}(end)+time_offset)
-                [start_d(2),end_d(2)] = deal(vars{ii+1}(1),vars{ii+1}(end))
-                var_time{ff} = (vars{ii}(:)+time_offset)+(vars{ii+1}(:)./(24*600*6000));
-        end
-    end
-    start_date=sum(start_d.*[1 1/(24*60*60)]);
-    end_date = sum(end_d.*[1 1/(24*60*60)]);
-    disp(['Start and end of file, ', datestr(start_date),' ',datestr(end_date)])
-    files_to_read(ff)=ff;
-    times(ff,:) = [start_date ,end_date];
-    close(nc)
-end
-disp(['Possible variables to extract are: '])
-for ii = 1 : length(to_show)
-    fprintf('%s, ',to_show{ii})
-end
-
-
-if (length(all_data)==2)
-    req_st = datenum(all_data{1},'dd/mm/yy HH:MM:SS');
-    req_end = datenum(all_data{2},'dd/mm/yy HH:MM:SS');
-    files_to_read(:)=NaN;
-    sel1 = find(req_st > times(:,1) & req_st < times(:,2));
-    sel2 = find(req_end > times(:,1) & req_end < times(:,2));
-    sel=[sel1,sel2];
-    sel(find(~diff(sel)))=[];
-    files_to_read(sel)=1;
-    if (req_end > times(end,2));files_to_read(end)=1;end
-end
-file_netcdf(isnan(files_to_read))=[];
-var_time(isnan(files_to_read))=[];
-time_idx = find(req_st <= var_time{1} &   var_time{1} <= req_end );
-
-clear vars
-for ff=1:length(file_netcdf)
-    cdfid = ncmex('OPEN',file_netcdf{ff},'NOWRITE')
-    if cdfid ==-1
-        disp(['NetCDF file ', file_netcdf{ff},' not found'])
-        return
-    else
-        disp(['NetCDF file ', file_netcdf{ff},' opened successfully.'])
-    end
-    [ndims, nvars, natts, recdim, status] = ncmex('INQUIRE', cdfid);
-    nombre={};dim={};
-    for aa=1:nvars
-        [nombre{aa}, datatype, ndims(aa), dim{aa}, natts, status] = ncmex('VARINQ', cdfid, aa-1);
-    end
-    for aa=1:length(varnames)
-        TF = strcmpi(varnames{aa},nombre);varidx(aa) = find(TF)-1;TF = sum(TF);
-        dimens=ndims(aa);
-        if TF;
-            disp(['Variable ',varnames{aa},' found in file'])
-        else
-            disp(['Variable ',varnames{aa},' NOT found in file Stopping. Check variable names.'])
-            ncmex('CLOSE',cdfid)
-            return
-        end
-        [dud, dud, dimens, vardims, dud, status] = ncmex('varinq', cdfid, varidx(aa));
-
-
-        switch dimens
-            case 1
-                x_dimid = vardims(dimens)
-
-                [dud, x_length, status] = ncmex('diminq', cdfid, x_dimid);
-                eval(['[',varnames{aa},', status] = ncmex(''VARGET'', cdfid, varidx(aa), [0], [-1],''autoscale'');'])
-            case 2
-                z_dimid = vardims(dimens-1)
-                x_dimid = vardims(dimens)
-
-                [dud, z_length, status] = ncmex('diminq', cdfid, z_dimid);
-                [dud, x_length, status] = ncmex('diminq', cdfid, x_dimid);
-                eval(['[',varnames{aa},', status] = ncmex(''VARGET'', cdfid, varidx(aa), [0 0], [-1 -1],''autoscale'');'])
-            case 3
-                z_dimid = vardims(dimens-1)
-                x_dimid = vardims(dimens)
-                t_dimid = vardims(dimens-2)
-
-                [dud, z_length, status] = ncmex('diminq', cdfid, z_dimid);
-                [dud, x_length, status] = ncmex('diminq', cdfid, x_dimid);
-                [dud, t_length, status] = ncmex('diminq', cdfid, t_dimid);
-                eval(['[',varnames{aa},', status] = ncmex(''VARGET'', cdfid, varidx(aa), [time_idx(1)-1 nz 0], [length(time_idx) length(nz_idx)*sign(nz_idx(1)) -1],''autoscale'');'])
-                if trnsxy
-
-                    eval([varnames{aa},' = squeeze(',varnames{aa},'(trns_idx, : ,:));'])
-                end
-        end
-        eval(['data(aa) = {[data{aa};',varnames{aa},']};'])
-        eval(['clear ',varnames{aa}])
-
-    end
-    ncmex('CLOSE',cdfid)
-end
-cd(CD)
-varargout{1} = data;
-    ncmex('CLOSE',cdfid)
-return
-%
-% pcolor(zero_to_nan(squeeze(value(:,:,1,1)))'),colorbar
-%
-%
-% ncmex('CLOSE',cdfid)
-%
-% [value, status] = ncmex('VARGET', cdfid, varid, [0 0 0], [londimid latdimid depdimid])
-%  [value, status] = ncmex('VARGET', cdfid, varid, [0 0 0], [-1 -1 -1])
-%
-%
-%   status = ncmex('VARPUT1', cdfid, varid, coords, value, autoscale)
-%   [value, status] = ncmex('VARGET1', cdfid, varid, coords, autoscale)
-%   status = ncmex('VARPUT', cdfid, varid, start, count, value, autoscale)
-%   [value, status] = ncmex('VARGET', cdfid, varid, start, count, autoscale)
-%   status = ncmex('VARPUTG', cdfid, varid, start, count, stride, [], value, autoscale)
-%   [value, status] = ncmex('VARGETG', cdfid, varid, start, count, stride, [], autoscale)
-%   status = ncmex('VARRENAME', cdfid, varid, 'name')
-%
-%   status = ncmex('ATTPUT', cdfid, varid, 'name', datatype, len, value)
-%   [datatype, len, status] = ncmex('ATTINQ', cdfid, varid, 'name')
-%   [value, status] = ncmex('ATTGET', cdfid, varid, 'name')
-%   status = ncmex('ATTCOPY', incdf, invar, 'name', outcdf, outvar)
-%   ['name', status] = ncmex('ATTNAME', cdfid, varid, attnum)
-%   status = ncmex('ATTRENAME', cdfid, varid, 'name', 'newname')
-%   status = ncmex('ATTDEL', cdfid, varid, 'name')
-%
-%   status = ncmex('RECPUT', cdfid, recnum, [data], autoscale, recdim)
-%   [[data], status] = ncmex('RECGET', cdfid, recnum, autoscale, recdim)
-%   [[recvarids], [recsizes], status] = ncmex('RECINQ', cdfid, recdim)
-%
-%   len = ncmex('TYPELEN', datatype)
-%   old_fillmode = ncmex('SETFILL', cdfid, fillmode)
-%
-%   old_ncopts = ncmex('SETOPTS', ncopts)
-%   ncerr = ncmex('ERR')
-%   code = ncmex('PARAMETER', 'NC_...')
-%
-%   Notes:
-%    1. The rcode is always zero.
-%    2. The dimid can be number or name.
-%    3. The varid can be number or name.
-%    4. The attname can be name or number.
-%    5. The operation and parameter names are not case-sensitive.
-%    6. The cmode defaults to 'NC_NOCLOBBER'.
-%    7. The mode defaults to 'NC_NOWRITE'.
-%    8. The value -1 determines length automatically.
-%    9. The operation names can prepend 'nc'.
-%   10. The parameter names can drop 'NC_' prefix.
-%   11. Dimensions: Matlab (i, j, ...) <==> [..., j, i] NetCDF.
-%   12. Indices and identifiers are zero-based.
-%   13. One-dimensional arrays are returned as column-vectors.