[1] | 1 | function data = nc_varget(ncfile, varname, varargin ) |
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| 2 | % NC_VARGET: Retrieve data from a netCDF variable. |
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| 3 | % |
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| 4 | % DATA = NC_VARGET(NCFILE,VARNAME) retrieves all the data from the |
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| 5 | % variable VARNAME in the netCDF file NCFILE. |
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| 6 | % |
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| 7 | % DATA = NC_VARGET(NCFILE,VARNAME,START,COUNT) retrieves the contiguous |
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| 8 | % portion of the variable specified by the index vectors START and |
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| 9 | % COUNT. Remember that SNCTOOLS indexing is zero-based, not |
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| 10 | % one-based. Specifying a -1 in COUNT means to retrieve everything |
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| 11 | % along that dimension from the START coordinate. |
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| 12 | % |
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| 13 | % DATA = NC_VARGET(NCFILE,VARNAME,START,COUNT,STRIDE) retrieves |
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| 14 | % a non-contiguous portion of the dataset. The amount of |
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| 15 | % skipping along each dimension is given through the STRIDE vector. |
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| 16 | % |
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| 17 | % NCFILE can also be an OPeNDAP URL if the proper java SNCTOOLS |
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| 18 | % backend is installed. See the README for details. |
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| 19 | % |
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| 20 | % NC_VARGET tries to be intelligent about retrieving the data. |
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| 21 | % Since most general matlab operations are done in double precision, |
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| 22 | % retrieved numeric data will be cast to double precision, while |
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| 23 | % character data remains just character data. |
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| 24 | % |
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| 25 | % Singleton dimensions are removed from the output data. |
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| 26 | % |
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| 27 | % A '_FillValue' attribute is honored by flagging those datums as NaN. |
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| 28 | % A 'missing_value' attribute is honored by flagging those datums as |
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| 29 | % NaN. The exception to this is for NC_CHAR variables, as mixing |
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| 30 | % character data and NaN doesn't really seem to work in matlab. |
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| 31 | % |
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| 32 | % If the named NetCDF variable has valid scale_factor and add_offset |
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| 33 | % attributes, then the data is scaled accordingly. |
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| 34 | % |
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| 35 | % Setting the preference 'PRESERVE_FVD' to true will compel NC_VARGET |
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| 36 | % to preserve the fastest varying dimension. This basically means |
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| 37 | % that NC_VARGET will not transpose the data. This basically flips |
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| 38 | % the order of the dimension IDs from what one would see by using |
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| 39 | % the ncdump C utility. You may get a substantial performance boost from |
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| 40 | % this. |
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| 41 | % |
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| 42 | % EXAMPLE: |
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| 43 | % #1. In this case, the variable in question has rank 2, and has size |
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| 44 | % 500x700. We want to retrieve starting at row 300, column 250. |
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| 45 | % We want 100 contiguous rows, 200 contiguous columns. |
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| 46 | % |
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| 47 | % vardata = nc_varget ( file, variable_name, [300 250], [100 200] ); |
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| 48 | % |
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| 49 | |
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| 50 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 51 | % |
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| 52 | % $Id: nc_varget.m 2681 2009-04-28 14:55:17Z johnevans007 $ |
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| 53 | % $LastChangedDate: 2009-04-28 10:55:17 -0400 (Tue, 28 Apr 2009) $ |
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| 54 | % $LastChangedRevision: 2681 $ |
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| 55 | % $LastChangedBy: johnevans007 $ |
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| 56 | % |
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| 57 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 58 | |
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| 59 | |
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| 60 | |
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| 61 | error(nargchk(2,5,nargin,'struct')); |
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| 62 | error(nargoutchk(0,1,nargout,'struct')); |
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| 63 | |
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| 64 | [start, count, stride] = parse_and_validate_args(ncfile,varname,varargin{:}); |
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| 65 | |
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| 66 | retrieval_method = snc_read_backend(ncfile); |
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| 67 | switch(retrieval_method) |
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| 68 | case 'tmw' |
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| 69 | data = nc_varget_tmw(ncfile,varname,start,count,stride); |
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| 70 | case 'java' |
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| 71 | data = nc_varget_java(ncfile,varname,start,count,stride); |
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| 72 | case 'mexnc' |
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| 73 | data = nc_varget_mexnc(ncfile,varname,start,count,stride); |
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| 74 | end |
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| 75 | |
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| 76 | return |
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| 77 | |
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| 78 | |
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| 79 | |
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| 80 | |
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| 81 | |
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| 82 | |
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| 83 | |
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| 84 | |
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| 85 | |
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| 86 | |
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| 87 | |
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| 88 | %---------------------------------------------------------------------- |
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| 89 | function values = nc_varget_mexnc(ncfile,varname,start,count,stride) |
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| 90 | |
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| 91 | |
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| 92 | |
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| 93 | [ncid,status]=mexnc('open',ncfile,'NOWRITE'); |
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| 94 | if status ~= 0 |
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| 95 | ncerr = mexnc('strerror', status); |
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| 96 | error ( 'SNCTOOLS:NC_VARGET:MEXNC:OPEN', ncerr ); |
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| 97 | end |
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| 98 | |
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| 99 | |
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| 100 | [varid, status]=mexnc('inq_varid',ncid,varname); |
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| 101 | if status ~= 0 |
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| 102 | ncerr = mexnc('strerror', status); |
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| 103 | mexnc('close',ncid); |
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| 104 | error ( 'SNCTOOLS:NC_VARGET:MEXNC:INQ_VARID', ncerr ); |
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| 105 | end |
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| 106 | |
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| 107 | [dud,var_type,nvdims,dimids,dud,status]=mexnc('inq_var',ncid,varid); |
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| 108 | if status ~= 0 |
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| 109 | mexnc('close',ncid); |
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| 110 | error ( 'SNCTOOLS:NC_VARGET:MEXNC:INQ_VAR', mexnc('strerror',status) ); |
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| 111 | end |
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| 112 | |
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| 113 | |
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| 114 | % mexnc does not preserve the fastest varying dimension. If we want this, |
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| 115 | % then we flip the indices. |
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| 116 | preserve_fvd = getpref('SNCTOOLS','PRESERVE_FVD',false); |
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| 117 | if preserve_fvd |
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| 118 | start = fliplr(start); |
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| 119 | count = fliplr(count); |
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| 120 | stride = fliplr(stride); |
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| 121 | end |
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| 122 | |
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| 123 | |
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| 124 | % |
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| 125 | % Check that the start, count, stride parameters have appropriate lengths. |
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| 126 | % Otherwise we get confusing error messages later on. |
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| 127 | validate_index_vectors(start,count,stride,nvdims); |
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| 128 | |
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| 129 | % |
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| 130 | % What mexnc operation will we use? |
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| 131 | [funcstr_family, funcstr] = determine_funcstr ( var_type, nvdims, start, count, stride ); |
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| 132 | |
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| 133 | |
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| 134 | the_var_size = determine_varsize_mex ( ncid, dimids, nvdims ); |
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| 135 | |
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| 136 | % |
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| 137 | % If the user had set non-positive numbers in "count", then we replace them |
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| 138 | % with what we need to get the rest of the variable. |
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| 139 | negs = find(count<0); |
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| 140 | count(negs) = the_var_size(negs) - start(negs); |
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| 141 | |
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| 142 | |
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| 143 | |
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| 144 | % |
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| 145 | % At long last, retrieve the data. |
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| 146 | switch funcstr_family |
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| 147 | case 'get_var' |
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| 148 | [values, status] = mexnc ( funcstr, ncid, varid ); |
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| 149 | |
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| 150 | case 'get_var1' |
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| 151 | [values, status] = mexnc ( funcstr, ncid, varid, 0 ); |
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| 152 | |
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| 153 | case 'get_vara' |
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| 154 | [values, status] = mexnc ( funcstr, ncid, varid, start, count ); |
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| 155 | |
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| 156 | |
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| 157 | case 'get_vars' |
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| 158 | [values, status] = mexnc ( funcstr, ncid, varid, start, count, stride ); |
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| 159 | |
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| 160 | otherwise |
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| 161 | error ( 'SNCTOOLS:NC_VARGET:unhandledType', ... |
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| 162 | 'Unhandled function string type ''%s''\n', funcstr_family ); |
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| 163 | |
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| 164 | end |
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| 165 | |
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| 166 | if ( status ~= 0 ) |
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| 167 | mexnc('close',ncid); |
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| 168 | ncerr = mexnc('strerror', status); |
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| 169 | eid = sprintf ( 'SNCTOOLS:nc_varget:%s', funcstr ); |
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| 170 | error ( eid, ncerr ); |
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| 171 | end |
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| 172 | |
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| 173 | |
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| 174 | |
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| 175 | |
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| 176 | % |
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| 177 | % If it's a 1D vector, make it a column vector. |
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| 178 | % Otherwise permute the data |
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| 179 | % to make up for the row-major-order-vs-column-major-order issue. |
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| 180 | if length(the_var_size) == 1 |
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| 181 | values = values(:); |
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| 182 | else |
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| 183 | % Ok it's not a 1D vector. If we are not preserving the fastest |
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| 184 | % varying dimension, we should permute the data. |
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| 185 | if ~getpref('SNCTOOLS','PRESERVE_FVD',false) |
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| 186 | pv = fliplr ( 1:length(the_var_size) ); |
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| 187 | values = permute(values,pv); |
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| 188 | end |
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| 189 | end |
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| 190 | |
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| 191 | |
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| 192 | values = handle_fill_value_mex ( ncid, varid, var_type, values ); |
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| 193 | values = handle_mex_missing_value ( ncid, varid, var_type, values ); |
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| 194 | values = handle_scaling_mex ( ncid, varid, values ); |
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| 195 | |
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| 196 | |
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| 197 | % |
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| 198 | % remove any singleton dimensions. |
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| 199 | values = squeeze ( values ); |
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| 200 | |
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| 201 | |
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| 202 | mexnc('close',ncid); |
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| 203 | |
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| 204 | |
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| 205 | return |
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| 206 | |
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| 207 | |
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| 208 | |
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| 209 | |
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| 210 | |
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| 211 | |
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| 212 | |
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| 213 | |
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| 214 | |
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| 215 | |
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| 216 | |
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| 217 | |
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| 218 | |
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| 219 | |
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| 220 | |
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| 221 | |
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| 222 | |
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| 223 | %-------------------------------------------------------------------------- |
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| 224 | function [start, count, stride] = parse_and_validate_args(ncfile,varname,varargin) |
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| 225 | |
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| 226 | % |
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| 227 | % Set up default outputs. |
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| 228 | start = []; |
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| 229 | count = []; |
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| 230 | stride = []; |
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| 231 | |
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| 232 | |
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| 233 | switch nargin |
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| 234 | case 4 |
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| 235 | start = varargin{1}; |
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| 236 | count = varargin{2}; |
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| 237 | |
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| 238 | case 5 |
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| 239 | start = varargin{1}; |
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| 240 | count = varargin{2}; |
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| 241 | stride = varargin{3}; |
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| 242 | |
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| 243 | end |
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| 244 | |
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| 245 | |
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| 246 | |
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| 247 | % |
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| 248 | % Error checking on the inputs. |
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| 249 | if ~ischar(ncfile) |
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| 250 | error ( 'SNCTOOLS:NC_VARGET:badInput', 'the filename must be character.' ); |
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| 251 | end |
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| 252 | if ~ischar(varname) |
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| 253 | error ( 'SNCTOOLS:NC_VARGET:badInput', 'the variable name must be character.' ); |
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| 254 | end |
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| 255 | |
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| 256 | if ~isnumeric ( start ) |
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| 257 | error ( 'SNCTOOLS:NC_VARGET:badInput', 'the ''start'' argument must be numeric.' ); |
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| 258 | end |
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| 259 | if ~isnumeric ( count ) |
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| 260 | error ( 'SNCTOOLS:NC_VARGET:badInput', 'the ''count'' argument must be numeric.' ); |
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| 261 | end |
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| 262 | if ~isnumeric ( stride ) |
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| 263 | error ( 'SNCTOOLS:NC_VARGET:badInput', 'the ''stride'' argument must be numeric.' ); |
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| 264 | end |
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| 265 | |
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| 266 | |
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| 267 | return |
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| 268 | |
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| 269 | |
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| 270 | |
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| 271 | |
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| 272 | |
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| 273 | |
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| 274 | |
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| 275 | |
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| 276 | |
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| 277 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 278 | % |
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| 279 | % DETERMINE_FUNCSTR |
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| 280 | % Determines if we are to use, say, 'get_var1_text', or 'get_vars_double', |
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| 281 | % or whatever. |
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| 282 | % |
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| 283 | function [prefix,funcstr] = determine_funcstr ( var_type, nvdims, start, count, stride ) |
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| 284 | |
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| 285 | % |
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| 286 | % Determine if we are retriving a single value, the whole variable, a |
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| 287 | % contiguous portion, or a strided portion. |
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| 288 | if nvdims == 0 |
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| 289 | |
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| 290 | % |
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| 291 | % It is a singleton variable. |
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| 292 | prefix = 'get_var1'; |
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| 293 | |
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| 294 | elseif isempty(start) |
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| 295 | |
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| 296 | % |
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| 297 | % retrieving the entire variable. |
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| 298 | prefix = 'get_var'; |
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| 299 | |
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| 300 | elseif ~isempty(start) && ~isempty(count) && isempty(stride) |
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| 301 | |
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| 302 | % |
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| 303 | % retrieving a contiguous portion |
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| 304 | prefix = 'get_vara'; |
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| 305 | |
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| 306 | elseif ~isempty(start) && ~isempty(count) && ~isempty(stride) |
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| 307 | |
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| 308 | % |
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| 309 | % retrieving a contiguous portion |
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| 310 | prefix = 'get_vars'; |
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| 311 | |
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| 312 | else |
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| 313 | error ( 'SNCTOOLS:NC_VARGET:FUNCSTR', 'Could not determine funcstr prefix.' ); |
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| 314 | end |
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| 315 | |
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| 316 | |
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| 317 | |
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| 318 | switch ( var_type ) |
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| 319 | case nc_char |
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| 320 | funcstr = [prefix '_text']; |
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| 321 | |
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| 322 | case { nc_double, nc_float, nc_int, nc_short, nc_byte } |
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| 323 | funcstr = [prefix '_double']; |
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| 324 | |
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| 325 | otherwise |
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| 326 | error ( 'SNCTOOLS:NC_VARGET:badDatatype', ... |
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| 327 | 'Unhandled datatype %d.', var_type ); |
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| 328 | |
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| 329 | end |
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| 330 | return |
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| 331 | |
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| 332 | |
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| 333 | |
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| 334 | |
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| 335 | |
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| 336 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 337 | % |
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| 338 | % HANDLE_MEX_FILL_VALUE |
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| 339 | % If there is a fill value, then replace such values with NaN. |
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| 340 | % |
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| 341 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 342 | function values = handle_fill_value_mex ( ncid, varid, var_type, values ) |
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| 343 | |
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| 344 | % |
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| 345 | % Handle the fill value, if any. Change those values into NaN. |
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| 346 | [dud, dud, status] = mexnc('INQ_ATT', ncid, varid, '_FillValue' ); |
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| 347 | if ( status == 0 ) |
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| 348 | |
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| 349 | switch ( var_type ) |
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| 350 | case nc_char |
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| 351 | % |
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| 352 | % For now, do nothing. Does a fill value even make sense with char data? |
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| 353 | % If it does, please tell me so. |
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| 354 | |
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| 355 | case { nc_double, nc_float, nc_int, nc_short, nc_byte } |
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| 356 | [fill_value, status] = mexnc ( 'get_att_double', ncid, varid, '_FillValue' ); |
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| 357 | values(values==fill_value) = NaN; |
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| 358 | |
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| 359 | otherwise |
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| 360 | mexnc('close',ncid); |
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| 361 | error ( 'SNCTOOLS:nc_varget:mexnc:unhandledFillValueDatatype', ... |
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| 362 | 'Unhandled datatype %d.', var_type ); |
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| 363 | end |
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| 364 | |
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| 365 | if ( status ~= 0 ) |
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| 366 | mexnc('close',ncid); |
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| 367 | ncerr = mexnc ( 'strerror', status ); |
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| 368 | error ( 'SNCTOOLS:NC_VARGET:MEXNC:GET_ATT', ncerr ); |
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| 369 | end |
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| 370 | |
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| 371 | |
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| 372 | |
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| 373 | end |
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| 374 | |
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| 375 | return |
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| 376 | |
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| 377 | |
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| 378 | |
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| 379 | |
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| 380 | %-------------------------------------------------------------------------- |
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| 381 | function values = handle_mex_missing_value ( ncid, varid, var_type, values ) |
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| 382 | % HANDLE_MEX_MISSING_VALUE |
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| 383 | % If there is a missing value, then replace such values with NaN. |
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| 384 | |
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| 385 | % |
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| 386 | % If there is a fill value attribute, then that had precedence. Do nothing. |
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| 387 | [dud, dud, status] = mexnc('INQ_ATT', ncid, varid, '_FillValue' ); |
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| 388 | if status == 0 |
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| 389 | return |
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| 390 | end |
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| 391 | |
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| 392 | % |
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| 393 | % Handle the missing value, if any. Change those values into NaN. |
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| 394 | [dud, dud, status] = mexnc('INQ_ATT', ncid, varid, 'missing_value' ); |
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| 395 | if ( status == 0 ) |
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| 396 | |
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| 397 | switch ( var_type ) |
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| 398 | case nc_char |
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| 399 | % |
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| 400 | % For now, do nothing. Does a fill value even make sense with char data? |
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| 401 | % If it does, please tell me so. |
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| 402 | |
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| 403 | case { nc_double, nc_float, nc_int, nc_short, nc_byte } |
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| 404 | [fill_value, status] = mexnc ( 'get_att_double', ncid, varid, 'missing_value' ); |
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| 405 | values(values==fill_value) = NaN; |
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| 406 | |
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| 407 | otherwise |
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| 408 | mexnc('close',ncid); |
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| 409 | error ( 'SNCTOOLS:nc_varget:mexnc:unhandledDatatype', ... |
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| 410 | 'Unhandled datatype %d.', var_type ); |
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| 411 | |
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| 412 | end |
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| 413 | |
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| 414 | if ( status ~= 0 ) |
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| 415 | mexnc('close',ncid); |
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| 416 | ncerr = mexnc ( 'strerror', status ); |
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| 417 | error ( 'SNCTOOLS:NC_VARGET:MEXNC:GET_ATT', ncerr ); |
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| 418 | end |
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| 419 | |
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| 420 | |
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| 421 | end |
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| 422 | |
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| 423 | return |
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| 424 | |
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| 425 | |
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| 426 | |
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| 427 | |
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| 428 | |
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| 429 | |
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| 430 | %-------------------------------------------------------------------------- |
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| 431 | function values = handle_scaling_mex ( ncid, varid, values ) |
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| 432 | % HANDLE_MEX_SCALING |
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| 433 | % If there is a scale factor and/or add_offset attribute, convert the data |
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| 434 | % to double precision and apply the scaling. |
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| 435 | |
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| 436 | have_scale = false; |
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| 437 | have_addoffset = false; |
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| 438 | [dud, dud, status] = mexnc('INQ_ATT', ncid, varid, 'scale_factor' ); |
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| 439 | if ( status == 0 ) |
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| 440 | have_scale = true; |
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| 441 | end |
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| 442 | [dud, dud, status] = mexnc('INQ_ATT', ncid, varid, 'add_offset' ); |
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| 443 | if ( status == 0 ) |
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| 444 | have_addoffset = true; |
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| 445 | end |
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| 446 | |
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| 447 | % |
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| 448 | % Return early if we don't have either one. |
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| 449 | if ~(have_scale || have_addoffset) |
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| 450 | return; |
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| 451 | end |
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| 452 | |
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| 453 | scale_factor = 1.0; |
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| 454 | add_offset = 0.0; |
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| 455 | |
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| 456 | if have_scale |
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| 457 | [scale_factor, status] = mexnc ( 'get_att_double', ncid, varid, 'scale_factor' ); |
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| 458 | if ( status ~= 0 ) |
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| 459 | mexnc('close',ncid); |
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| 460 | ncerr = mexnc('strerror', status); |
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| 461 | error ( 'SNCTOOLS:NC_VARGET:MEXNC:GET_ATT_DOUBLE', ncerr ); |
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| 462 | end |
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| 463 | end |
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| 464 | |
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| 465 | if have_addoffset |
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| 466 | [add_offset, status] = mexnc ( 'get_att_double', ncid, varid, 'add_offset' ); |
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| 467 | if ( status ~= 0 ) |
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| 468 | mexnc('close',ncid); |
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| 469 | ncerr = mexnc('strerror', status); |
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| 470 | error ( 'SNCTOOLS:NC_VARGET:MEXNC:GET_ATT_DOUBLE', ncerr ); |
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| 471 | end |
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| 472 | end |
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| 473 | |
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| 474 | values = double(values) * scale_factor + add_offset; |
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| 475 | |
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| 476 | return |
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| 477 | |
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| 478 | |
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| 479 | |
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| 480 | |
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| 481 | |
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| 482 | |
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| 483 | |
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| 484 | |
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| 485 | %----------------------------------------------------------------------- |
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| 486 | function the_var_size = determine_varsize_mex ( ncid, dimids, nvdims ) |
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| 487 | % DETERMINE_VARSIZE_MEX: Need to figure out just how big the variable is. |
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| 488 | % |
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| 489 | % VAR_SIZE = DETERMINE_VARSIZE_MEX(NCID,DIMIDS,NVDIMS); |
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| 490 | |
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| 491 | % |
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| 492 | % If not a singleton, we need to figure out how big the variable is. |
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| 493 | if nvdims == 0 |
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| 494 | the_var_size = 1; |
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| 495 | else |
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| 496 | the_var_size = zeros(1,nvdims); |
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| 497 | for j=1:nvdims, |
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| 498 | dimid = dimids(j); |
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| 499 | [dim_size,status]=mexnc('inq_dimlen', ncid, dimid); |
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| 500 | if ( status ~= 0 ) |
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| 501 | ncerr = mexnc ( 'strerror', status ); |
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| 502 | mexnc('close',ncid); |
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| 503 | error ( 'SNCTOOLS:NC_VARGET:MEXNC:INQ_DIM_LEN', ncerr ); |
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| 504 | end |
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| 505 | the_var_size(j)=dim_size; |
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| 506 | end |
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| 507 | end |
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| 508 | |
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| 509 | return |
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| 510 | |
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| 511 | |
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| 512 | |
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| 513 | |
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