Imported upstream version 8.4290~dfsg.1

neurodebian · Apr 14, 2011 · 0e20250 · 0e20250
1 parent f3a1ee7
commit 0e20250
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diff --git a/@file_array/cat.m b/@file_array/cat.m
@@ -5,7 +5,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 %
-% $Id: cat.m 1143 2008-02-07 19:33:33Z spm $
+% $Id: cat.m 4136 2010-12-09 22:22:28Z guillaume $
 
 
 if dr>32 || dr<0, error('Unknown command option.'); end;
@@ -36,5 +36,5 @@
     error('All matrices on a row in the bracketed expression must have the same number of rows.');
 else
     o = vertcat(tmp{:});
-    o = class(o,'file_array');
+    o = file_array(o);
 end;
diff --git a/@file_array/disp.m b/@file_array/disp.m
@@ -4,7 +4,7 @@ function disp(obj)
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 %
-% $Id: disp.m 1143 2008-02-07 19:33:33Z spm $
+% $Id: disp.m 4136 2010-12-09 22:22:28Z guillaume $
 
 
 if numel(struct(obj))>1,
@@ -19,7 +19,7 @@ function disp(obj)
         fprintf('%d\n',sz(end));
     end;
 else
-    display(mystruct(obj))
+    disp(mystruct(obj))
 end;
 return;
 %=======================================================================

diff --git a/@file_array/file_array.m b/@file_array/file_array.m
@@ -13,7 +13,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 %
-% $Id: file_array.m 1340 2008-04-09 17:11:23Z john $
+% $Id: file_array.m 4136 2010-12-09 22:22:28Z guillaume $
 
 
 if nargin==1
@@ -38,5 +38,5 @@
 if nargin>=7, a = permission(a,varargin{7}); end;
 
 a.pos = ones(size(a.dim));
-a     = class(a,'file_array');
+a     = file_array(a);
 
diff --git a/@file_array/private/datatypes.m b/@file_array/private/datatypes.m
@@ -4,7 +4,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 %
-% $Id: datatypes.m 1143 2008-02-07 19:33:33Z spm $
+% $Id: datatypes.m 4136 2010-12-09 22:22:28Z guillaume $
 
 
 persistent dtype
@@ -24,10 +24,10 @@
         1280,'UINT64'    ,'uint64'  ,@uint64 ,1,8  ,t,t,f
         16  ,'FLOAT32'   ,'float32' ,@single ,1,4  ,f,f,t
         64  ,'FLOAT64'   ,'double'  ,@double ,1,8  ,f,f,t
-        1536,'FLOAT128'  ,'float128',@crash  ,1,16 ,f,f,f
+        1536,'FLOAT128'  ,'float128',@error  ,1,16 ,f,f,f
         32  ,'COMPLEX64' ,'float32' ,@single ,2,4  ,f,f,f
         1792,'COMPLEX128','double'  ,@double ,2,8  ,f,f,f
-        2048,'COMPLEX256','float128',@crash  ,2,16 ,f,f,f
+        2048,'COMPLEX256','float128',@error  ,2,16 ,f,f,f
         128 ,'RGB24'     ,'uint8'   ,@uint8  ,3,1  ,t,t,f};
     dtype = struct(...
         'code'     ,table(:,1),...

diff --git a/@file_array/subsasgn.m b/@file_array/subsasgn.m
@@ -4,7 +4,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 %
-% $Id: subsasgn.m 1355 2008-04-10 10:52:35Z vladimir $
+% $Id: subsasgn.m 4136 2010-12-09 22:22:28Z guillaume $
 
 
 if isempty(subs)
@@ -47,7 +47,7 @@
 end;
 
 dm   = [dm ones(1,16)];
-do   = ones(1,16);
+di   = ones(1,16);
 args = {};
 for i=1:length(subs.subs),
     if ischar(subs.subs{i}),
@@ -56,7 +56,7 @@
     else
         args{i} = int32(subs.subs{i});
     end;
-    do(i) = length(args{i});
+    di(i) = length(args{i});
 end;
 for j=1:length(sobj),
     if strcmp(sobj(j).permission,'ro'),
@@ -69,7 +69,7 @@
     if numel(dat)~=1,
         subfun(sobj,double(dat),args{:});
     else
-        dat1 = double(dat) + zeros(do);
+        dat1 = double(dat) + zeros(di);
         subfun(sobj,dat1,args{:});
     end;
 else

diff --git a/@file_array/subsref.m b/@file_array/subsref.m
@@ -5,7 +5,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 %
-% $Id: subsref.m 3958 2010-06-30 16:24:46Z guillaume $
+% $Id: subsref.m 4136 2010-12-09 22:22:28Z guillaume $
 
 
 if isempty(subs), return; end
@@ -39,7 +39,7 @@
     end
 end
 
-do   = ones(16,1);
+di   = ones(16,1);
 args = cell(1,length(subs.subs));
 for i=1:length(subs.subs)
     if ischar(subs.subs{i})
@@ -58,15 +58,15 @@
     else
         args{i} = subs.subs{i};
     end
-    do(i) = length(args{i});
+    di(i) = length(args{i});
 end
 
 if length(sobj)==1
     t = subfun(sobj,args{:});
 else
     dt  = datatypes;
     dt  = dt([dt.code]==sobj(1).dtype); % assuming identical datatypes
-    t = zeros(do',func2str(dt.conv));
+    t = zeros(di',func2str(dt.conv));
     for j=1:length(sobj)
         ps = [sobj(j).pos ones(1,length(args))];
         dm = [sobj(j).dim ones(1,length(args))];

diff --git a/@gifti/display.m b/@gifti/display.m
@@ -6,7 +6,7 @@ function display(this)
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: display.m 2076 2008-09-10 12:34:08Z guillaume $
+% $Id: display.m 4182 2011-02-01 12:29:09Z guillaume $
 
 display_name = inputname(1);
 if isempty(display_name)
@@ -17,6 +17,9 @@ function display(this)
     eval([display_name ' = struct(this);']);
     eval(['display(' display_name ');']);
 else
+    disp(' ')
+    disp([display_name ' =']);
+    disp(' ');
     eval([display_name ' = this;']);
-    eval(['builtin(''display'',' display_name ');']);
+    eval(['disp(' display_name ');']);
 end
diff --git a/@gifti/private/read_gifti_file.m b/@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 3999 2010-07-19 10:54:18Z guillaume $
+% $Id: read_gifti_file.m 4013 2010-07-22 17:12:45Z guillaume $
 
 % Import XML-based GIfTI file
 %--------------------------------------------------------------------------
@@ -23,7 +23,7 @@
     error('[GIFTI] %s is not a GIFTI 1.0 file.', filename);
 end
 attr = cell2mat(attributes(t,'get',root(t)));
-attr = cell2struct({attr.val},strrep({attr.key},':','_'),2);
+attr = cell2struct({attr.val},strrep({attr.key},':','___'),2);
 if ~all(ismember({'Version','NumberOfDataArrays'},fieldnames(attr)))
     error('[GIFTI] Missing mandatory attributes for GIFTI root element.');
 end

diff --git a/@gifti/save.m b/@gifti/save.m
@@ -10,7 +10,7 @@ function save(this,filename,encoding)
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: save.m 3999 2010-07-19 10:54:18Z guillaume $
+% $Id: save.m 4022 2010-07-28 12:50:20Z guillaume $
 
 error(nargchk(1,3,nargin));
 
@@ -66,9 +66,9 @@ function save(this,filename,encoding)
 % Defaults for DataArray's attributes
 %--------------------------------------------------------------------------
 [unused,unused,mach]   = fopen(fid);
-if ~isempty(strmatch('ieee-be',mach))
+if strncmp('ieee-be',mach,7)
     def.Endian         = 'BigEndian';
-elseif ~isempty(strmatch('ieee-le',mach))
+elseif strncmp('ieee-le',mach,7)
     def.Endian         = 'LittleEndian';
 else
     error('[GIFTI] Unknown byte order "%s".',mach);

diff --git a/@gifti/subsref.m b/@gifti/subsref.m
@@ -4,13 +4,14 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: subsref.m 3999 2010-07-19 10:54:18Z guillaume $
+% $Id: subsref.m 4136 2010-12-09 22:22:28Z guillaume $
 
-if length(this) > 1
+if length(this) > 1 && ~strcmp(subs(1).type,'()')
     warning('Not implemented.');
     for i=1:numel(this)
         varargout{i} = subsref(this(i),subs);
     end
+    return;
 end
 
 switch subs(1).type

diff --git a/@meeg/badchannels.m b/@meeg/badchannels.m
@@ -5,18 +5,19 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Stefan Kiebel
-% $Id: badchannels.m 3942 2010-06-21 14:03:28Z vladimir $
+% $Id: badchannels.m 4040 2010-08-20 23:25:46Z vladimir $
 
 
-if length(varargin) == 2
+
+if length(varargin) == 2 && ~isempty(varargin{1})
     % make sure that the two inputs for set are the same length
     if ~(length(varargin{2}) == 1 | (length(varargin{1}) == length(varargin{2})))
         error('Use either same vector length or scalar for value');
     end
 end
 
-if numel(varargin) >= 1    
-    if ~(varargin{1} >= 1 & varargin{1} <= nchannels(this))
+if numel(varargin) >= 1  && ~isempty(varargin{1})  
+    if ~(all(varargin{1} >= 1) && all(varargin{1} <= nchannels(this)))
         error('Channel number of out range.');
     end
 end

diff --git a/@meeg/clone.m b/@meeg/clone.m
@@ -11,7 +11,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Stefan Kiebel, Vladimir Litvak
-% $Id: clone.m 3807 2010-04-06 19:29:08Z vladimir $
+% $Id: clone.m 4207 2011-02-22 10:48:36Z christophe $
 
 if nargin < 4
     reset = 0;
@@ -32,11 +32,26 @@
 if isempty(pth)
     pth = this.path;
 end
-newFileName = [fullfile(pth,fname),ext];
+newFileName = [fullfile(pth,fname),'.dat'];
 % copy the file_array
 d = this.data.y; % 
 d.fname = newFileName;
-d.dim = dim; 
+dim_o = d.dim;
+
+% This takes care of an issue specific to data files with a scaling factor
+% which are not officially supported in SPM8 (float without scaling).
+% Also assuming scaling is the *same* for all channels...
+if dim(1)>dim_o(1) && length(d.scl_slope)>1
+    % adding channel to montage and scl_slope defined for old montage
+    %       -> need to increase size of scl_slope
+    v_slope = mode(d.scl_slope);
+    if length(v_slope)>1
+        warning(['Trying to guess the scaling factor for new channels.',...
+            ' This factor might be wrong now.']);        
+    end
+    d.scl_slope = [d.scl_slope' ones(1,dim(1)-dim_o(1))*v_slope]';
+end
+d.dim = dim;
 
 % physically initialise file
 if length(dim) == 3

diff --git a/@meeg/frequencies.m b/@meeg/frequencies.m
@@ -5,7 +5,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Stefan Kiebel
-% $Id: frequencies.m 3579 2009-11-18 16:21:55Z vladimir $
+% $Id: frequencies.m 4015 2010-07-23 16:35:03Z vladimir $
 
 if nargin < 3
     if strncmpi(transformtype(this), 'TF',2)
@@ -34,7 +34,11 @@
           error('Wrong frequency axis or indices'); 
     end
 
-    this.transform.frequencies(ind) = f;
+    if length(ind) == size(this.data.y, 2)
+        this.transform.frequencies = f;
+    else
+        this.transform.frequencies(ind) = f;
+    end
 
     res = this;    
 end
diff --git a/@meeg/private/checkmeeg.m b/@meeg/private/checkmeeg.m
@@ -9,7 +9,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Vladimir Litvak
-% $Id: checkmeeg.m 3978 2010-07-08 14:26:39Z vladimir $
+% $Id: checkmeeg.m 4207 2011-02-22 10:48:36Z christophe $
 
 if nargin==1
     option = 'basic';
@@ -64,10 +64,24 @@
     end
 
     for k = 1:Ntrials
-        if isnumeric(meegstruct.trials(k).label)
-            meegstruct.trials(k).label = num2str(meegstruct.trials(k).label);
+
+        label = meegstruct.trials(k).label;
+
+        if iscell(label) && numel(label) == 1
+            label = label{1};
         end
 
+        if isnumeric(label)
+            label = num2str(label);
+        end
+
+        if isa(label, 'char')
+           meegstruct.trials(k).label = label;
+        else
+           meegstruct.trials(k).label = 'Unknown';
+           disp('checkmeeg: some trial labels were not strings, changing back to ''Unknown''');
+        end                        
+
         if  length(meegstruct.trials(k).bad)>1 || ~ismember(meegstruct.trials(k).bad, [0, 1])
             disp(['checkmeeg: illegal value for bad flag in trial ' num2str(k) ', setting to zero.']);
             meegstruct.trials(k).bad = 0;
@@ -135,6 +149,11 @@
     else
         [meegstruct.channels(find(cellfun('isempty', {meegstruct.channels.bad}))).bad] = deal(0);
     end
+
+    for i = 1:Nchannels
+        meegstruct.channels(i).bad = double(~~meegstruct.channels(i).bad);
+    end            
+
     if ~isfield(meegstruct.channels, 'type')
         disp('checkmeeg: no channel type, assigning default');
         [meegstruct.channels.type] = deal('Other');
@@ -199,12 +218,20 @@
     end
 
     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);
+        if ~strcmp([yfname yext],[dfname dext])
+            meegstruct.data.fnamedat = [yfname yext];
+        end
+        % save original file_array scale & offset, just in case
+        sav_sc = meegstruct.data.y.scl_slope;
+        sav_os = meegstruct.data.y.offset;
         try
             % Try reading data, i.e. check if it's a "good" filearray
             meegstruct.data.y(1, 1, 1);
         catch
-            % save original file_array scale, just in case
-            sav_sc = meegstruct.data.y.scl_slope;
             meegstruct.data.y = [];
         end
     end
@@ -235,9 +262,14 @@
                 error('Unknown transform type');
         end
         % and restore original file_array scale, if available (exist) & useful (~=[])
-        if exist('sav_sc','var') && ~isempty(sav_sc)
+        if exist('sav_sc','var') && ~isempty(sav_sc) && ...
+                   size(meegstruct.data.y, 1) == length(sav_sc)            
             meegstruct.data.y.scl_slope = sav_sc;
         end
+        % and restore original file_array offset, if available (exist) & useful (~=0)
+        if exist('sav_os','var') && sav_os
+            meegstruct.data.y.offset = sav_os;
+        end
 
     end