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Slepi/Code/Utilities/spm12/spm_read_netcdf.m
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spm_read_netcdf.m
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function cdf = spm_read_netcdf(fname)
% Read the header information from a NetCDF file into a data structure.
% FORMAT cdf = spm_read_netcdf(fname)
% fname - name of NetCDF file
% cdf - data structure
%
% See: http://www.unidata.ucar.edu/packages/netcdf/
% _________________________________________________________________________
% Copyright (C) 1999-2011 Wellcome Trust Centre for Neuroimaging
% John Ashburner
% $Id: spm_read_netcdf.m 4182 2011-02-01 12:29:09Z guillaume $
dsiz = [1 1 2 4 4 8];
fp=fopen(fname,'r','ieee-be');
if fp==-1
cdf = [];
return;
end
% Return null if not a CDF file.
%--------------------------------------------------------------------------
mgc = fread(fp,4,'uchar')';
if ~all(['CDF' 1] == mgc)
cdf = [];
fclose(fp);
if all(mgc==[137,72,68,70])
fprintf(['"%s" appears to be based around HDF.\n',...
'This is a newer version of MINC that SPM can not yet read.\n'],...
fname);
end
return;
end
% I've no idea what this is for
numrecs = fread(fp,1,'uint32');
cdf = struct('numrecs', numrecs,...
'dim_array', [], ...
'gatt_array', [], ...
'var_array', []);
dt = fread(fp,1,'uint32');
if dt == 10
% Dimensions
nelem = fread(fp,1,'uint32');
for j=1:nelem
str = readname(fp);
dim_length = fread(fp,1,'uint32');
cdf.dim_array(j).name = str;
cdf.dim_array(j).dim_length = dim_length;
end
dt = fread(fp,1,'uint32');
end
while ~dt, dt = fread(fp,1,'uint32'); end
if dt == 12
% Attributes
nelem = fread(fp,1,'uint32');
for j=1:nelem
str = readname(fp);
nc_type = fread(fp,1,'uint32');
nnelem = fread(fp,1,'uint32');
val = fread(fp,nnelem,dtypestr(nc_type));
if nc_type == 2, val = deblank([val' ' ']); end
padding= fread(fp,...
ceil(nnelem*dsiz(nc_type)/4)*4-nnelem*dsiz(nc_type),'uchar');
cdf.gatt_array(j).name = str;
cdf.gatt_array(j).nc_type = nc_type;
cdf.gatt_array(j).val = val;
end
dt = fread(fp,1,'uint32');
end
while ~dt, dt = fread(fp,1,'uint32'); end
if dt == 11
% Variables
nelem = fread(fp,1,'uint32');
for j=1:nelem
str = readname(fp);
nnelem = fread(fp,1,'uint32');
val = fread(fp,nnelem,'uint32');
cdf.var_array(j).name = str;
cdf.var_array(j).dimid = val+1;
cdf.var_array(j).nc_type = 0;
cdf.var_array(j).vsize = 0;
cdf.var_array(j).begin = 0;
dt0 = fread(fp,1,'uint32');
if dt0 == 12
nelem0 = fread(fp,1,'uint32');
for jj=1:nelem0
str = readname(fp);
nc_type= fread(fp,1,'uint32');
nnelem = fread(fp,1,'uint32');
val = fread(fp,nnelem,dtypestr(nc_type));
if nc_type == 2, val = deblank([val' ' ']); end
padding= fread(fp,...
ceil(nnelem*dsiz(nc_type)/4)*4-nnelem*dsiz(nc_type),'uchar');
cdf.var_array(j).vatt_array(jj).name = str;
cdf.var_array(j).vatt_array(jj).nc_type = nc_type;
cdf.var_array(j).vatt_array(jj).val = val;
end
dt0 = fread(fp,1,'uint32');
end
cdf.var_array(j).nc_type = dt0;
cdf.var_array(j).vsize = fread(fp,1,'uint32');
cdf.var_array(j).begin = fread(fp,1,'uint32');
end
dt = fread(fp,1,'uint32');
end
fclose(fp);
%==========================================================================
% function str = dtypestr(i)
%==========================================================================
function str = dtypestr(i)
% Returns a string appropriate for reading or writing the CDF data-type.
types = char('uint8','uint8','int16','int32','float32','float64');
str = deblank(types(i,:));
%==========================================================================
% function name = readname(fp)
%==========================================================================
function name = readname(fp)
% Extracts a name from a CDF file pointed to at the right location by fp.
stlen = fread(fp,1,'uint32');
name = deblank([fread(fp,stlen,'uchar')' ' ']);
padding = fread(fp,ceil(stlen/4)*4-stlen,'uchar');
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