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fcMRI-VAE / CIFTI_read_save /@gifti /save.m
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function save(this,filename,encoding)
% Save GIfTI object in a GIfTI format file
% FORMAT save(this,filename,encoding)
% this - GIfTI object
% filename - name of GIfTI file to be created [Default: 'untitled.gii']
% encoding - optional argument to specify encoding format, among
% ASCII, Base64Binary, GZipBase64Binary, ExternalFileBinary.
% [Default: 'GZipBase64Binary']
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Guillaume Flandin
% $Id: save.m 6516 2015-08-07 17:28:33Z guillaume $
% Check filename
%--------------------------------------------------------------------------
ext = '.gii';
if nargin == 1
filename = 'untitled';
end
[p,f,e] = fileparts(filename);
if ~ismember(lower(e),{ext})
e = ext;
end
filename = fullfile(p,[f e]);
% Open file for writing
%--------------------------------------------------------------------------
fid = fopen(filename,'wt');
if fid == -1
error('Unable to write file %s: permission denied.',filename);
end
% Write file
%--------------------------------------------------------------------------
if nargin < 3, encoding = 'GZipBase64Binary'; end
switch encoding
case {'ASCII','Base64Binary','GZipBase64Binary','ExternalFileBinary'}
otherwise
error('Unknown encoding.');
end
fid = save_gii(fid,this,encoding);
% Close file
%--------------------------------------------------------------------------
fclose(fid);
%==========================================================================
% function fid = save_gii(fid,this,encoding)
%==========================================================================
function fid = save_gii(fid,this,encoding)
% Defaults for DataArray's attributes
%--------------------------------------------------------------------------
[unused,unused,mach] = fopen(fid);
if strncmp('ieee-be',mach,7)
def.Endian = 'BigEndian';
elseif strncmp('ieee-le',mach,7)
def.Endian = 'LittleEndian';
else
error('[GIFTI] Unknown byte order "%s".',mach);
end
def.Encoding = encoding;
def.Intent = 'NIFTI_INTENT_NONE';
def.DataType = 'NIFTI_TYPE_FLOAT32';
def.ExternalFileName = '';
def.ExternalFileOffset = '';
def.offset = 0;
% Edit object DataArray attributes
%--------------------------------------------------------------------------
for i=1:length(this.data)
% Revert the dimension storage
d = this.data{i}.attributes.Dim;
if numel(d) > 1 && d(end) == 1
d = d(1:end-1);
end
this.data{i}.attributes = rmfield(this.data{i}.attributes,'Dim');
this.data{i}.attributes.Dimensionality = num2str(length(d));
for j=1:length(d)
this.data{i}.attributes.(sprintf('Dim%d',j-1)) = num2str(d(j));
end
% Enforce some conventions
this.data{i}.attributes.ArrayIndexingOrder = 'ColumnMajorOrder';
if ~isfield(this.data{i}.attributes,'DataType') || ...
isempty(this.data{i}.attributes.DataType)
warning('DataType set to default: %s', def.DataType);
this.data{i}.attributes.DataType = def.DataType;
end
if ~isfield(this.data{i}.attributes,'Intent') || ...
isempty(this.data{i}.attributes.Intent)
warning('Intent code set to default: %s', def.Intent);
this.data{i}.attributes.Intent = def.Intent;
end
this.data{i}.attributes.Encoding = def.Encoding;
this.data{i}.attributes.Endian = def.Endian;
this.data{i}.attributes.ExternalFileName = def.ExternalFileName;
this.data{i}.attributes.ExternalFileOffset = def.ExternalFileOffset;
switch this.data{i}.attributes.Encoding
case {'ASCII', 'Base64Binary','GZipBase64Binary' }
case 'ExternalFileBinary'
extfilename = this.data{i}.attributes.ExternalFileName;
if isempty(extfilename)
[p,f] = fileparts(fopen(fid));
extfilename = [f '.dat'];
end
[p,f,e] = fileparts(extfilename);
this.data{i}.attributes.ExternalFileName = fullfile(fileparts(fopen(fid)),[f e]);
this.data{i}.attributes.ExternalFileOffset = num2str(def.offset);
otherwise
error('[GIFTI] Unknown data encoding: %s.',this.data{i}.attributes.Encoding);
end
end
% Prolog
%--------------------------------------------------------------------------
fprintf(fid,'<?xml version="1.0" encoding="UTF-8"?>\n');
fprintf(fid,'<!DOCTYPE GIFTI SYSTEM "http://www.nitrc.org/frs/download.php/115/gifti.dtd">\n');
fprintf(fid,'<GIFTI Version="1.0" NumberOfDataArrays="%d">\n',numel(this.data));
o = @(x) blanks(x*3);
% MetaData
%--------------------------------------------------------------------------
fprintf(fid,'%s<MetaData',o(1));
if isempty(this.metadata)
fprintf(fid,'/>\n');
else
fprintf(fid,'>\n');
for i=1:length(this.metadata)
fprintf(fid,'%s<MD>\n',o(2));
fprintf(fid,'%s<Name><![CDATA[%s]]></Name>\n',o(3),...
this.metadata(i).name);
fprintf(fid,'%s<Value><![CDATA[%s]]></Value>\n',o(3),...
this.metadata(i).value);
fprintf(fid,'%s</MD>\n',o(2));
end
fprintf(fid,'%s</MetaData>\n',o(1));
end
% LabelTable
%--------------------------------------------------------------------------
fprintf(fid,'%s<LabelTable',o(1));
if isempty(this.label)
fprintf(fid,'/>\n');
else
fprintf(fid,'>\n');
for i=1:length(this.label.name)
if ~all(isnan(this.label.rgba(i,:)))
label_rgba = sprintf(' Red="%f" Green="%f" Blue="%f" Alpha="%f"',...
this.label.rgba(i,:));
else
label_rgba = '';
end
fprintf(fid,'%s<Label Key="%d"%s><![CDATA[%s]]></Label>\n',o(2),...
this.label.key(i), label_rgba, this.label.name{i});
end
fprintf(fid,'%s</LabelTable>\n',o(1));
end
% DataArray
%--------------------------------------------------------------------------
for i=1:length(this.data)
fprintf(fid,'%s<DataArray',o(1));
if def.offset
this.data{i}.attributes.ExternalFileOffset = num2str(def.offset);
end
fn = sort(fieldnames(this.data{i}.attributes));
oo = repmat({o(5) '\n'},length(fn),1); oo{1} = ' '; oo{end} = '';
for j=1:length(fn)
if strcmp(fn{j},'ExternalFileName')
[p,f,e] = fileparts(this.data{i}.attributes.(fn{j}));
attval = [f e];
else
attval = this.data{i}.attributes.(fn{j});
end
fprintf(fid,'%s%s="%s"%s',oo{j,1},...
fn{j},attval,sprintf(oo{j,2}));
end
fprintf(fid,'>\n');
% MetaData
%----------------------------------------------------------------------
fprintf(fid,'%s<MetaData>\n',o(2));
for j=1:length(this.data{i}.metadata)
fprintf(fid,'%s<MD>\n',o(3));
fprintf(fid,'%s<Name><![CDATA[%s]]></Name>\n',o(4),...
this.data{i}.metadata(j).name);
fprintf(fid,'%s<Value><![CDATA[%s]]></Value>\n',o(4),...
this.data{i}.metadata(j).value);
fprintf(fid,'%s</MD>\n',o(3));
end
fprintf(fid,'%s</MetaData>\n',o(2));
% CoordinateSystemTransformMatrix
%----------------------------------------------------------------------
for j=1:length(this.data{i}.space)
fprintf(fid,'%s<CoordinateSystemTransformMatrix>\n',o(2));
fprintf(fid,'%s<DataSpace><![CDATA[%s]]></DataSpace>\n',o(3),...
this.data{i}.space(j).DataSpace);
fprintf(fid,'%s<TransformedSpace><![CDATA[%s]]></TransformedSpace>\n',o(3),...
this.data{i}.space(j).TransformedSpace);
fprintf(fid,'%s<MatrixData>%s</MatrixData>\n',o(3),...
sprintf('%f ',this.data{i}.space(j).MatrixData'));
fprintf(fid,'%s</CoordinateSystemTransformMatrix>\n',o(2));
end
% Data (saved using MATLAB's ColumnMajorOrder)
%----------------------------------------------------------------------
fprintf(fid,'%s<Data>',o(2));
tp = getdict;
try
tp = tp.(this.data{i}.attributes.DataType);
catch
error('[GIFTI] Unknown DataType.');
end
switch this.data{i}.attributes.Encoding
case 'ASCII'
fprintf(fid, [tp.format ' '], this.data{i}.data);
case 'Base64Binary'
fprintf(fid,base64encode(typecast(this.data{i}.data(:),'uint8')));
% uses native machine format
case 'GZipBase64Binary'
fprintf(fid,base64encode(zstream('C',typecast(this.data{i}.data(:),'uint8'))));
% uses native machine format
case 'ExternalFileBinary'
extfilename = this.data{i}.attributes.ExternalFileName;
dat = this.data{i}.data;
if isa(dat,'file_array')
dat = subsref(dat,substruct('()',repmat({':'},1,numel(dat.dim))));
end
if ~def.offset
fide = fopen(extfilename,'w'); % uses native machine format
else
fide = fopen(extfilename,'a'); % uses native machine format
end
if fide == -1
error('Unable to write file %s: permission denied.',extfilename);
end
fseek(fide,0,1);
fwrite(fide,dat,tp.class);
def.offset = ftell(fide);
fclose(fide);
otherwise
error('[GIFTI] Unknown data encoding.');
end
fprintf(fid,'</Data>\n');
fprintf(fid,'%s</DataArray>\n',o(1));
end
fprintf(fid,'</GIFTI>\n');