SPM8 r4667

Author: SPMcentral

@gifti/private/base64decode.m

@@ -22,10 +22,6 @@
 
 %   Modified by Guillaume Flandin, May 2008
 
-% check number of input arguments
-%--------------------------------------------------------------------------
-
-error(nargchk(1, 1, nargin));
 
 % Perform the following mapping
 %--------------------------------------------------------------------------

@gifti/private/base64encode.m

@@ -43,8 +43,6 @@
 %   E-mail:      [email protected]
 %   URL:         http://home.online.no/~pjacklam
 
-   % check number of input arguments
-   error(nargchk(1, 2, nargin));
 
    % make sure we have the EOL value
    if nargin < 2

@gifti/private/getdict.m

@@ -4,7 +4,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: getdict.m 2271 2008-09-30 21:19:47Z guillaume $
+% $Id: getdict.m 4613 2012-01-08 12:04:11Z guillaume $
 
 persistent dict;
 if ~isempty(dict)
@@ -15,7 +15,8 @@
 table = {...
     'NIFTI_TYPE_UINT8',   'uint8',   '%d', @uint8, 'uint8'
     'NIFTI_TYPE_INT32',   'int32',   '%d', @int32, 'int32' 
-    'NIFTI_TYPE_FLOAT32', 'float32', '%f', @single, 'single'};
+    'NIFTI_TYPE_FLOAT32', 'float32', '%f', @single, 'single'
+    'NIFTI_TYPE_FLOAT64', 'float64', '%f', @double, 'double'};
 
 for i=1:size(table,1)
     dict.(table{i,1}) = cell2struct({table{i,2:end}},...

@gifti/private/isintent.m

@@ -9,7 +9,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: isintent.m 3999 2010-07-19 10:54:18Z guillaume $
+% $Id: isintent.m 4382 2011-07-06 14:59:41Z guillaume $
 
 a = [];
 b = [];
@@ -51,11 +51,11 @@
             fprintf('Intent %s is ignored.\n',this.data{i}.attributes.Intent);
     end
 end
-[d,i] = unique(a,'first');
+[d,i] = unique(a);
 if length(d) < length(a)
-    %warning('Several fields match intent type. Using first.');
+    warning('Several fields match intent type. Using first.');
     a = a(i);
-    %b = b(i);
+    b = b(i);
 end
 
 function c = cdata

@gifti/private/read_gifti_file.m

@@ -7,7 +7,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: read_gifti_file.m 4013 2010-07-22 17:12:45Z guillaume $
+% $Id: read_gifti_file.m 4613 2012-01-08 12:04:11Z guillaume $
 
 % Import XML-based GIfTI file
 %--------------------------------------------------------------------------
@@ -64,11 +64,26 @@
 
 %==========================================================================
 function s = gifti_LabelTable(t,uid)
-s = struct('name',{}, 'index',[]);
+s = struct('name',{}, 'key',[], 'rgba',[]);
 c = children(t,uid);
 for i=1:length(c)
     a = attributes(t,'get',c(i));
-    s(1).index(i) = str2double(a.val);
+    s(1).rgba(i,1:4) = NaN;
+    for j=1:numel(a)
+        switch lower(a{j}.key)
+            case {'key','index'}
+                s(1).key(i)    = str2double(a{j}.val);
+            case 'red'
+                s(1).rgba(i,1) = str2double(a{j}.val);
+            case 'green'
+                s(1).rgba(i,2) = str2double(a{j}.val);
+            case 'blue'
+                s(1).rgba(i,3) = str2double(a{j}.val);
+            case 'alpha'
+                s(1).rgba(i,4) = str2double(a{j}.val);
+            otherwise
+        end
+    end
     s(1).name{i}  = get(t,children(t,c(i)),'value');
 end
 
@@ -90,10 +105,10 @@
     s(1).attributes = rmfield(s(1).attributes,f);
 end
 s(1).attributes = rmfield(s(1).attributes,'Dimensionality');
-try
+if isfield(s(1).attributes,'ExternalFileName') && ...
+        ~isempty(s(1).attributes.ExternalFileName)
     s(1).attributes.ExternalFileName = fullfile(fileparts(filename),...
         s(1).attributes.ExternalFileName);
-catch
 end
 
 c = children(t,uid);
@@ -149,14 +164,23 @@
         d = typecast(dunzip(sb(base64decode(get(t,children(t,uid),'value')))), tp.cast);
 
     case 'ExternalFileBinary'
-        fid = fopen(s.ExternalFileName,'r');
-        if fid == -1
-            error('[GIFTI] Unable to read binary file %s.',s.ExternalFileName);
+        [p,f,e] = fileparts(s.ExternalFileName);
+        if isempty(p)
+            s.ExternalFileName = fullfile(pwd,[f e]);
         end
-        fseek(fid,str2double(s.ExternalFileOffset),0);
-        d = sb(fread(fid,prod(s.Dim),['*' tp.class]));
-        fclose(fid);
-
+        if true
+            fid = fopen(s.ExternalFileName,'r');
+            if fid == -1
+                error('[GIFTI] Unable to read binary file %s.',s.ExternalFileName);
+            end
+            fseek(fid,str2double(s.ExternalFileOffset),0);
+            d = sb(fread(fid,prod(s.Dim),['*' tp.class]));
+            fclose(fid);
+        else
+            d = file_array(s.ExternalFileName, s.Dim, tp.class, ...
+                str2double(s.ExternalFileOffset),1,0,'ro');
+        end
+        
     otherwise
         error('[GIFTI] Unknown data encoding: %s.',s.Encoding);
 end

@gifti/save.m

@@ -2,17 +2,16 @@ function save(this,filename,encoding)
 % Save GIfTI object in a GIfTI format file
 % FORMAT save(this,filename)
 % this      - GIfTI object
-% filename  - name of GIfTI file that will be created
+% filename  - name of GIfTI file to be created [Default: 'untitled.gii']
 % encoding  - optional argument to specify encoding format, among
 %             ASCII, Base64Binary, GZipBase64Binary, ExternalFileBinary,
-%             Collada (.dae), IDTF (.idtf).
+%             Collada (.dae), IDTF (.idtf). [Default: 'GZipBase64Binary']
 %__________________________________________________________________________
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: save.m 4022 2010-07-28 12:50:20Z guillaume $
+% $Id: save.m 4613 2012-01-08 12:04:11Z guillaume $
 
-error(nargchk(1,3,nargin));
 
 % Check filename and file format
 %--------------------------------------------------------------------------
@@ -155,9 +154,15 @@ function save(this,filename,encoding)
     fprintf(fid,'/>\n');
 else
     fprintf(fid,'>\n');
-    for i=1:length(this.label)
-        fprintf(fid,'%s<Label Index="%"><![CDATA[%s]]></Label>\n',o(2),...
-            this.label.index(i), this.label.name{i});
+    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
@@ -172,8 +177,14 @@ function save(this,filename,encoding)
     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},this.data{i}.attributes.(fn{j}),sprintf(oo{j,2}));
+                fn{j},attval,sprintf(oo{j,2}));
     end
     fprintf(fid,'>\n');
 
@@ -223,6 +234,10 @@ function save(this,filename,encoding)
             % 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
@@ -232,7 +247,7 @@ function save(this,filename,encoding)
                 error('Unable to write file %s: permission denied.',extfilename);
             end
             fseek(fide,0,1);
-            fwrite(fide,this.data{i}.data,tp.class);
+            fwrite(fide,dat,tp.class);
             def.offset = ftell(fide);
             fclose(fide);
         otherwise

@meeg/badchannels.m

@@ -5,7 +5,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Stefan Kiebel
-% $Id: badchannels.m 4040 2010-08-20 23:25:46Z vladimir $
+% $Id: badchannels.m 4329 2011-05-19 20:54:36Z christophe $
 
 
 
@@ -18,7 +18,7 @@
 
 if numel(varargin) >= 1  && ~isempty(varargin{1})  
     if ~(all(varargin{1} >= 1) && all(varargin{1} <= nchannels(this)))
-        error('Channel number of out range.');
+        error('Channel number out of range.');
     end
 end
 

@meeg/conditions.m

@@ -5,10 +5,10 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Vladimir Litvak
-% $Id: conditions.m 1373 2008-04-11 14:24:03Z spm $
+% $Id: conditions.m 4310 2011-04-18 16:07:35Z guillaume $
 
 res = getset(this, 'trials', 'label', varargin{:});
 
-if nargin ==1 & ~iscell(res)
+if nargin == 1 && ~iscell(res)
     res = {res};
 end

@meeg/coor2D.m

@@ -5,18 +5,22 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Vladimir Litvak, Laurence Hunt
-% $Id: coor2D.m 3335 2009-08-25 16:37:02Z vladimir $
+% $Id: coor2D.m 4372 2011-06-21 21:26:46Z vladimir $
 
 
 megind = strmatch('MEG', chantype(this));
 eegind = strmatch('EEG', chantype(this), 'exact');
 otherind = setdiff(1:nchannels(this), [megind; eegind]);
 
 if nargin==1 || isempty(ind)
-    if ~isempty(megind)
-        ind = megind;
-    elseif ~isempty(eegind)
-        ind = eegind;
+    if nargin<3 || (size(val, 2)<nchannels(this))
+        if ~isempty(megind)
+            ind = megind;
+        elseif ~isempty(eegind)
+            ind = eegind;
+        else
+            ind = 1:nchannels(this);
+        end
     else
         ind = 1:nchannels(this);
     end

@meeg/private/checkmeeg.m

@@ -9,7 +9,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Vladimir Litvak
-% $Id: checkmeeg.m 4207 2011-02-22 10:48:36Z christophe $
+% $Id: checkmeeg.m 4437 2011-08-23 13:09:24Z vladimir $
 
 if nargin==1
     option = 'basic';
@@ -191,6 +191,12 @@
     end
 end
 
+if isfield(meegstruct, 'path')
+    filepath = meegstruct.path;
+else
+    filepath = pwd;
+end
+
 if ~isfield(meegstruct, 'data') && (Nsamples~=0)
     disp('checkmeeg: no data field');
     return;
@@ -201,7 +207,9 @@
         disp('checkmeeg: data file name missing');
         return;
     else
-        [junk, fnamedat, ext] = fileparts(meegstruct.data.fnamedat);
+        fname = meegstruct.data.fnamedat;
+        if ~ispc, fname = strrep(fname,'\',filesep); end
+        [junk, fnamedat, ext] = fileparts(fname);
         if isempty(ext)
             meegstruct.data.fnamedat = [fnamedat '.dat'];
         else
@@ -220,11 +228,19 @@
     if isa(meegstruct.data.y, 'file_array')
         % catching up (unlikely case) where filearray.fname is
         % different from data.fnamedat -> set data.fnamedat
-        [junk, yfname, yext] = fileparts(meegstruct.data.y.fname);
-        [junk, dfname, dext] = fileparts(meegstruct.data.fnamedat);
+        fname = meegstruct.data.y.fname;
+        if ~ispc, fname = strrep(fname,'\',filesep); end
+        [junk, yfname, yext] = fileparts(fname);
+        
+        fnamedat = meegstruct.data.fnamedat;
+        if ~ispc, fnamedat = strrep(fnamedat,'\',filesep); end
+        [junk, dfname, dext] = fileparts(fnamedat);
         if ~strcmp([yfname yext],[dfname dext])
             meegstruct.data.fnamedat = [yfname yext];
         end
+        
+        meegstruct.data.y.fname = fullfile(filepath, [yfname yext]);
+        
         % save original file_array scale & offset, just in case
         sav_sc = meegstruct.data.y.scl_slope;
         sav_os = meegstruct.data.y.offset;
@@ -236,14 +252,15 @@
         end
     end
 
+    if isa(meegstruct.data.y, 'file_array')
+        fn = meegstruct.data.y.fname;
+        if ~ispc, fn = strrep(fn,'\',filesep); end
+    else
+        fn = '';
+    end
     if ~isa(meegstruct.data.y, 'file_array') ...
-            || isempty(fileparts(meegstruct.data.y.fname)) ...
+            || isempty(fileparts(fn)) ...
             || ~exist(meegstruct.data.y.fname, 'file')
-        if isfield(meegstruct, 'path')
-            filepath = meegstruct.path;
-        else
-            filepath = pwd;
-        end
         switch(meegstruct.transform.ID)
             case 'time'
                 meegstruct.data.y = file_array(fullfile(filepath, meegstruct.data.fnamedat), ...
@@ -318,15 +335,19 @@
 end
 
 try
-    [pdat, fdat] = fileparts(meegstruct.data.y.fname);
+    fname = meegstruct.data.y.fname;
+    if ~ispc, fname = strrep(fname,'\',filesep); end
+    [pdat, fdat] = fileparts(fname);
 catch
     fdat = 'spm8';
 end
 
 if ~isfield(meegstruct, 'fname')
     meegstruct.fname = [fdat '.mat'];
 else
-    [p, f] = fileparts(meegstruct.fname);
+    fname = meegstruct.fname;
+    if ~ispc, fname = strrep(fname,'\',filesep); end
+    [p, f] = fileparts(fname);
     if isempty(f)
         f = fdat;
     end
@@ -335,7 +356,9 @@
 
 if ~isfield(meegstruct, 'path')
     try
-        meegstruct.path = fileparts(meegstruct.data.y.fname);
+        fname = meegstruct.data.y.fname;
+        if ~ispc, fname = strrep(fname,'\',filesep); end
+        meegstruct.path = fileparts(fname);
     catch
         meegstruct.path = pwd;
     end
@@ -440,7 +463,7 @@
 
 % Allow DCM on a pure LFP dataset
 if strcmp(option, 'dcm') && isempty([eegind(:); megind(:)])...
-        && ~isempty(lfpind)&& strcmp(meegstruct.transform.ID, 'time')
+        && ~isempty(lfpind) && ismember(meegstruct.transform.ID, {'time', 'TF'})
     result = 1;
     return;
 end