Save a set of strings into NetCDF in MATLAB

Question

I have a list of strings that I want to save into a netCDF using MATLAB. However, I'm having trouble creating the file.

method_ID is a char array like this:

'55-059-0019-88101-1'
'55-059-0019-88101-1'
'55-059-0019-88101-1'
'55-059-0019-88101-1'
'55-059-0019-88101-1'
'55-059-0019-88101-1'
'55-059-0019-88101-1'
'55-059-0019-88101-1'
'55-059-0019-88101-1'
'55-059-0019-88101-1'

I tried to do the following, but it saves the strings out as one long string instead of 10 strings.

filename = ['PM25_24hr_',num2str(years(y)),'_EPA_AQS.nc'];
ncfilename = ['/data3/jg3223/PM25/netCDF/',filename]; 

method_ID = char(data_PM25{:,1});

% Create the file, overwriting if already exists (Clobber) and
% 64-bit offset (Allow easier creation of files and variables which are larger
% than two gigabytes.)
mode = bitor(netcdf.getConstant('CLOBBER'),netcdf.getConstant('64BIT_OFFSET'));
ncid = netcdf.create(ncfilename,mode);

% Define (file) global attributes
globalVarId=netcdf.getConstant('GLOBAL');
netcdf.putAtt(ncid,globalVarId,'name','PM25_24hr_AQS');

[a,b] = size(method_ID);
IDDimId = netcdf.defDim(ncid,'method_ID',a*b); % I know this size is wrong, but using `length(method_ID)` runs a size error later on

% Define variables, starting with coordinate variables,
% with appropriate names, types, and dimensions
IDVarId = netcdf.defVar(ncid,'method_ID','char',IDDimId);

% Exit the "define mode", i.e., structure creation mode
netcdf.endDef(ncid);

method ID
netcdf.putVar(ncid,IDVarId,method_ID);

% Close the netCDF file
netcdf.close(ncid);

Packard CPW · Accepted Answer · 2018-08-04 04:25:38Z

You should define two dimensions, if you are using "classic strings".

Strings can be stored using netCDF in two flavors, "classic strings" and "arrays of strings" (https://www.unidata.ucar.edu/software/netcdf/netcdf-4/newdocs/netcdf-c/Strings.html). "Classic strings" do not require netCDF version 4.0+ and following answer is based on this.

%% Solution using classic string (without NETCDF-4)

ncfilename ='./AQS.nc';
uint_method=uint8('55-059-0019-88101-1');
method_ID = char(repmat(uint_method,10,1));
[a,b] = size(method_ID);  %a=10, b=19

mode = bitor(netcdf.getConstant('CLOBBER'),netcdf.getConstant('64BIT_OFFSET'));
ncid = netcdf.create(ncfilename,mode);

globalVarId=netcdf.getConstant('GLOBAL');
netcdf.putAtt(ncid,globalVarId,'name','PM25_24hr_AQS');

%IDDimId = netcdf.defDim(ncid,'method_ID',a*b);
% IDDimId = netcdf.defDim(ncid,'method_ID',length(method_ID)); % ERROR: input elements does not match the variable size
% IDVarId = netcdf.defVar(ncid,'method_ID','char',IDDimId);

IDDim1 = netcdf.defDim(ncid,'charlen',b);
IDDim2 = netcdf.defDim(ncid,'methods',a);
IDVarId = netcdf.defVar(ncid,'method_ID','char',[IDDim1 IDDim2]);

netcdf.endDef(ncid);
netcdf.putVar(ncid,IDVarId,method_ID'); %transpose
netcdf.close(ncid);

You will get:

$ ncdump AQS.nc 
netcdf AQS {
dimensions:
    charlen = 19 ;
    methods = 10 ;
variables:
    char method_ID(methods, charlen) ;

// global attributes:
        :name = "PM25_24hr_AQS" ;
data:

 method_ID =
  "55-059-0019-88101-1",
  "55-059-0019-88101-1",
  "55-059-0019-88101-1",
  "55-059-0019-88101-1",
  "55-059-0019-88101-1",
  "55-059-0019-88101-1",
  "55-059-0019-88101-1",
  "55-059-0019-88101-1",
  "55-059-0019-88101-1",
  "55-059-0019-88101-1" ;
}

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