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function this = read_gifti_file_standalone(filename, this) |
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try |
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fid = fopen(filename,'rt'); |
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xmlstr = fread(fid,'*char')'; |
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fclose(fid); |
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t = xml_parser(xmlstr); |
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catch |
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error('[GIFTI] Loading of XML file |
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end |
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if ~strcmp(xml_get(t,xml_root(t),'name'),'GIFTI') |
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error('[GIFTI] %s is not a GIFTI 1.0 file.', filename); |
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end |
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attr = cell2mat(xml_attributes(t,'get',xml_root(t))); |
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attr = cell2struct({attr.val},strrep({attr.key},':','___'),2); |
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if ~all(ismember({'Version','NumberOfDataArrays'},fieldnames(attr))) |
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error('[GIFTI] Missing mandatory attributes for GIFTI root element.'); |
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end |
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if str2double(attr.Version) ~= 1 |
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warning('[GIFTI] Unknown specification version of GIFTI file (%s).',attr.Version); |
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end |
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nbData = str2double(attr.NumberOfDataArrays); |
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uid = xml_children(t,xml_root(t)); |
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for i=1:length(uid) |
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switch xml_get(t,uid(i),'name') |
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case 'MetaData' |
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this.metadata = gifti_MetaData(t,uid(i)); |
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case 'LabelTable' |
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this.label = gifti_LabelTable(t,uid(i)); |
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case 'DataArray' |
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this.data{end+1} = gifti_DataArray(t,uid(i),filename); |
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otherwise |
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warning('[GIFTI] Unknown element "%s": ignored.',xml_get(t,uid(i),'name')); |
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end |
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end |
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if nbData ~= length(this.data) |
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warning('[GIFTI] Mismatch between expected and effective number of datasets.'); |
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end |
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function s = gifti_MetaData(t,uid) |
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s = struct('name',{}, 'value',{}); |
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c = xml_children(t,uid); |
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for i=1:length(c) |
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for j=xml_children(t,c(i)) |
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s(i).(lower(xml_get(t,j,'name'))) = xml_get(t,xml_children(t,j),'value'); |
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end |
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end |
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function s = gifti_LabelTable(t,uid) |
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s = struct('name',{}, 'key',[], 'rgba',[]); |
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c = xml_children(t,uid); |
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for i=1:length(c) |
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a = xml_attributes(t,'get',c(i)); |
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s(1).rgba(i,1:4) = NaN; |
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for j=1:numel(a) |
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switch lower(a{j}.key) |
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case {'key','index'} |
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s(1).key(i) = str2double(a{j}.val); |
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case 'red' |
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s(1).rgba(i,1) = str2double(a{j}.val); |
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case 'green' |
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s(1).rgba(i,2) = str2double(a{j}.val); |
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case 'blue' |
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s(1).rgba(i,3) = str2double(a{j}.val); |
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case 'alpha' |
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s(1).rgba(i,4) = str2double(a{j}.val); |
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otherwise |
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end |
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end |
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s(1).name{i} = xml_get(t,xml_children(t,c(i)),'value'); |
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end |
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function s = gifti_DataArray(t,uid,filename) |
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s = struct(... |
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'attributes', {}, ... |
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'data', {}, ... |
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'metadata', struct([]), ... |
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'space', {} ... |
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); |
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attr = cell2mat(xml_attributes(t,'get',uid)); |
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s(1).attributes = cell2struct({attr.val},{attr.key},2); |
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s(1).attributes.Dim = []; |
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for i=1:str2double(s(1).attributes.Dimensionality) |
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f = sprintf('Dim%d',i-1); |
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s(1).attributes.Dim(i) = str2double(s(1).attributes.(f)); |
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s(1).attributes = rmfield(s(1).attributes,f); |
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end |
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s(1).attributes = rmfield(s(1).attributes,'Dimensionality'); |
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if isfield(s(1).attributes,'ExternalFileName') && ... |
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~isempty(s(1).attributes.ExternalFileName) |
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s(1).attributes.ExternalFileName = fullfile(fileparts(filename),... |
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s(1).attributes.ExternalFileName); |
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end |
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c = xml_children(t,uid); |
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for i=1:length(c) |
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switch xml_get(t,c(i),'name') |
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case 'MetaData' |
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s(1).metadata = gifti_MetaData(t,c(i)); |
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case 'CoordinateSystemTransformMatrix' |
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s(1).space(end+1) = gifti_Space(t,c(i)); |
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case 'Data' |
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s(1).data = gifti_Data(t,c(i),s(1).attributes); |
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otherwise |
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error('[GIFTI] Unknown DataArray element "%s".',xml_get(t,c(i),'name')); |
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end |
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end |
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function s = gifti_Space(t,uid) |
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s = struct('DataSpace','', 'TransformedSpace','', 'MatrixData',[]); |
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for i=xml_children(t,uid) |
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s.(xml_get(t,i,'name')) = xml_get(t,xml_children(t,i),'value'); |
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end |
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s.MatrixData = reshape(str2num(s.MatrixData),4,4)'; |
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%========================================================================== |
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function d = gifti_Data(t,uid,s) |
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tp = getdict; |
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try |
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tp = tp.(s.DataType); |
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catch |
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error('[GIFTI] Unknown DataType.'); |
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end |
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[unused,unused,mach] = fopen(1); |
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sb = @(x) x; |
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try |
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if (strcmp(s.Endian,'LittleEndian') && ~isempty(strmatch('ieee-be',mach))) ... |
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|| (strcmp(s.Endian,'BigEndian') && ~isempty(strmatch('ieee-le',mach))) |
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sb = @swapbyte; |
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end |
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catch |
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% Byte Order can be absent if encoding is ASCII, assume native otherwise |
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end |
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switch s.Encoding |
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case 'ASCII' |
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d = feval(tp.conv,sscanf(xml_get(t,xml_children(t,uid),'value'),tp.format)); |
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case 'Base64Binary' |
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d = typecast(sb(base64decode(xml_get(t,xml_children(t,uid),'value'))), tp.cast); |
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case 'GZipBase64Binary' |
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d = typecast(zstream('D',sb(base64decode(xml_get(t,xml_children(t,uid),'value')))), tp.cast); |
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case 'ExternalFileBinary' |
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[p,f,e] = fileparts(s.ExternalFileName); |
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if isempty(p) |
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s.ExternalFileName = fullfile(pwd,[f e]); |
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end |
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if true |
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fid = fopen(s.ExternalFileName,'r'); |
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if fid == -1 |
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error('[GIFTI] Unable to read binary file |
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end |
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fseek(fid,str2double(s.ExternalFileOffset),0); |
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d = sb(fread(fid,prod(s.Dim),['*' tp.class])); |
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fclose(fid); |
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else |
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d = file_array(s.ExternalFileName, s.Dim, tp.class, ... |
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str2double(s.ExternalFileOffset),1,0,'rw'); |
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end |
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otherwise |
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error('[GIFTI] Unknown data encoding: %s.',s.Encoding); |
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end |
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if length(s.Dim) == 1, s.Dim(end+1) = 1; end |
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switch s.ArrayIndexingOrder |
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case 'RowMajorOrder' |
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d = permute(reshape(d,fliplr(s.Dim)),length(s.Dim):-1:1); |
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case 'ColumnMajorOrder' |
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d = reshape(d,s.Dim); |
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otherwise |
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error('[GIFTI] Unknown array indexing order.'); |
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end |
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function uid = xml_root(tree) |
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uid = 1; |
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for i=1:length(tree) |
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if strcmp(xml_get(tree,i,'type'),'element') |
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uid = i; |
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break |
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end |
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end |
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function child = xml_children(tree,uid) |
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if strcmp(tree{uid}.type,'element') |
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child = tree{uid}.contents; |
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else |
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child = []; |
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end |
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function value = xml_get(tree,uid,parameter) |
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if isempty(uid), value = {}; return; end |
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try |
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value = tree{uid}.(parameter); |
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catch |
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error(sprintf('[XML] Parameter %s not found.',parameter)); |
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end |
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function varargout = xml_attributes(tree,method,uid) |
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if ~strcmpi(method,'get'), error('[XML] Unknown attributes method.'); end |
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if isempty(tree{uid}.attributes) |
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varargout{1} = {}; |
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else |
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varargout{1} = tree{uid}.attributes; |
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end |
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