SPM8 r3408

Author: SPMcentral

@file_array/private/file2mat.mexa64

@@ -8,7 +8,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: export.m 3081 2009-04-22 20:15:38Z guillaume $
+% $Id: export.m 3332 2009-08-25 13:50:08Z guillaume $
 
 if numel(this) > 1, warning('Only handle scalar objects yet.'); end
 
@@ -20,7 +20,7 @@
 
     case 'patch'
         if isfield(this,'vertices')
-            s.vertices = subsref(this, substruct('.', 'vertices'));
+            s.vertices = double(subsref(this, substruct('.', 'vertices')));
         end
         if isfield(this,'faces')
             s.faces = subsref(this, substruct('.', 'faces'));

@file_array/private/file2mat.mexglx

@@ -4,32 +4,60 @@ function save(this,filename,encoding)
 % this      - GIfTI object
 % filename  - name of GIfTI file that will be created
 % encoding  - optional argument to specify encoding format, among
-%             ASCII, Base64Binary, GZipBase64Binary, ExternalFileBinary
+%             ASCII, Base64Binary, GZipBase64Binary, ExternalFileBinary,
+%             Collada (.dae)
 %__________________________________________________________________________
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: save.m 2076 2008-09-10 12:34:08Z guillaume $
+% $Id: save.m 3290 2009-07-27 18:11:52Z guillaume $
 
 error(nargchk(1,3,nargin));
 
-% Open file for writing
+% Check filename and file format
 %--------------------------------------------------------------------------
+ext = '.gii';
 if nargin == 1
     filename = 'untitled.gii';
 else
+    if nargin == 3 && strcmpi(encoding,'collada')
+        ext = '.dae';
+    end
     [p,f,e] = fileparts(filename);
-    if ~ismember(lower(e),{'.gii'})
-        e = '.gii';
+    if ~ismember(lower(e),{ext})
+        e = ext;
     end
     filename = fullfile(p,[f e]);
 end
 
+% Open file for writing
+%--------------------------------------------------------------------------
 fid = fopen(filename,'wt');
 if fid == -1
     error('Unable to write file %s: permission denied.',filename);
 end
 
+% Write file
+%--------------------------------------------------------------------------
+switch ext
+    case '.gii'
+        if nargin < 3, encoding = 'GZipBase64Binary'; end
+        fid = save_gii(fid,this,encoding);
+    case '.dae'
+        fid = save_dae(fid,this);
+    otherwise
+        error('Unknown file format.');
+end
+
+% 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);
@@ -40,11 +68,7 @@ function save(this,filename,encoding)
 else
     error('[GIFTI] Unknown byte order "%s".',mach);
 end
-if nargin > 2
-    def.Encoding       = encoding;
-else
-    def.Encoding       = 'GZipBase64Binary';
-end
+def.Encoding       = encoding;
 def.Intent             = 'NIFTI_INTENT_NONE';
 def.DataType           = 'NIFTI_TYPE_FLOAT32';
 def.ExternalFileName   = '';
@@ -214,4 +238,144 @@ function save(this,filename,encoding)
 end
 
 fprintf(fid,'</GIFTI>\n');
-fclose(fid);
+
+%==========================================================================
+% function fid = save_dae(fid,this)
+%==========================================================================
+function fid = save_dae(fid,this)
+
+o = inline('blanks(x*3)');
+
+% Split the mesh into connected components
+%--------------------------------------------------------------------------
+s = struct(this);
+try
+    C = spm_mesh_label(s.faces);
+    d = [];
+    for i=1:numel(unique(C))
+        d(i).faces    = s.faces(C==i,:);
+        u             = unique(d(i).faces);
+        d(i).vertices = s.vertices(u,:);
+        a             = 1:max(d(i).faces(:));
+        a(u)          = 1:size(d(i).vertices,1);
+        %a = sparse(1,double(u),1:1:size(d(i).vertices,1));
+        d(i).faces    = a(d(i).faces);
+    end
+    s = d;
+end
+    
+% Prolog & root of the Collada XML file
+%--------------------------------------------------------------------------
+fprintf(fid,'<?xml version="1.0"?>\n');
+fprintf(fid,'<COLLADA xmlns="http://www.collada.org/2008/03/COLLADASchema" version="1.5.0">\n');
+
+% Assets
+%--------------------------------------------------------------------------
+fprintf(fid,'%s<asset>\n',o(1));
+fprintf(fid,'%s<contributor>\n',o(2));
+fprintf(fid,'%s<author_website>%s</author_website>\n',o(3),...
+    'http://www.fil.ion.ucl.ac.uk/spm/');
+fprintf(fid,'%s<authoring_tool>%s</authoring_tool>\n',o(3),spm('Ver'));
+fprintf(fid,'%s</contributor>\n',o(2));
+fprintf(fid,'%s<created>%s</created>\n',o(2),datestr(now,'yyyy-mm-ddTHH:MM:SSZ'));
+fprintf(fid,'%s<modified>%s</modified>\n',o(2),datestr(now,'yyyy-mm-ddTHH:MM:SSZ'));
+fprintf(fid,'%s<unit name="millimeter" meter="0.001"/>\n',o(2));
+fprintf(fid,'%s<up_axis>Z_UP</up_axis>\n',o(2));
+fprintf(fid,'%s</asset>\n',o(1));
+
+% Image, Materials, Effects
+%--------------------------------------------------------------------------
+%fprintf(fid,'%s<library_images/>\n',o(1));
+
+fprintf(fid,'%s<library_materials>\n',o(1));
+for i=1:numel(s)
+    fprintf(fid,'%s<material id="material%d" name="material%d">\n',o(2),i,i);
+    fprintf(fid,'%s<instance_effect url="#material%d-effect"/>\n',o(3),i);
+    fprintf(fid,'%s</material>\n',o(2));
+end
+fprintf(fid,'%s</library_materials>\n',o(1));
+
+fprintf(fid,'%s<library_effects>\n',o(1));
+for i=1:numel(s)
+    fprintf(fid,'%s<effect id="material%d-effect" name="material%d-effect">\n',o(2),i,i);
+    fprintf(fid,'%s<profile_COMMON>\n',o(3));
+    fprintf(fid,'%s<technique sid="COMMON">\n',o(4));
+    fprintf(fid,'%s<lambert>\n',o(5));
+    fprintf(fid,'%s<emission>\n',o(6));
+    fprintf(fid,'%s<color>%f %f %f %d</color>\n',o(7),[0 0 0 1]);
+    fprintf(fid,'%s</emission>\n',o(6));
+    fprintf(fid,'%s<ambient>\n',o(6));
+    fprintf(fid,'%s<color>%f %f %f %d</color>\n',o(7),[0 0 0 1]);
+    fprintf(fid,'%s</ambient>\n',o(6));
+    fprintf(fid,'%s<diffuse>\n',o(6));
+    fprintf(fid,'%s<color>%f %f %f %d</color>\n',o(7),[0.5 0.5 0.5 1]);
+    fprintf(fid,'%s</diffuse>\n',o(6));
+    fprintf(fid,'%s<transparent>\n',o(6));
+    fprintf(fid,'%s<color>%d %d %d %d</color>\n',o(7),[1 1 1 1]);
+    fprintf(fid,'%s</transparent>\n',o(6));
+    fprintf(fid,'%s<transparency>\n',o(6));
+    fprintf(fid,'%s<float>%f</float>\n',o(7),0);
+    fprintf(fid,'%s</transparency>\n',o(6));
+    fprintf(fid,'%s</lambert>\n',o(5));
+    fprintf(fid,'%s</technique>\n',o(4));
+    fprintf(fid,'%s</profile_COMMON>\n',o(3));
+    fprintf(fid,'%s</effect>\n',o(2));
+end
+fprintf(fid,'%s</library_effects>\n',o(1));
+
+% Geometry
+%--------------------------------------------------------------------------
+fprintf(fid,'%s<library_geometries>\n',o(1));
+for i=1:numel(s)
+    fprintf(fid,'%s<geometry id="shape%d" name="shape%d">\n',o(2),i,i);
+    fprintf(fid,'%s<mesh>\n',o(3));
+    fprintf(fid,'%s<source id="shape%d-positions">\n',o(4),i);
+    fprintf(fid,'%s<float_array id="shape%d-positions-array" count="%d">',o(5),i,numel(s(i).vertices));
+    fprintf(fid,'%f ',repmat(s(i).vertices',1,[]));
+    fprintf(fid,'</float_array>\n');
+    fprintf(fid,'%s<technique_common>\n',o(5));
+    fprintf(fid,'%s<accessor count="%d" offset="0" source="#shape%d-positions-array" stride="3">\n',o(6),size(s(i).vertices,1),i);
+    fprintf(fid,'%s<param name="X" type="float" />\n',o(7));
+    fprintf(fid,'%s<param name="Y" type="float" />\n',o(7));
+    fprintf(fid,'%s<param name="Z" type="float" />\n',o(7));
+    fprintf(fid,'%s</accessor>\n',o(6));
+    fprintf(fid,'%s</technique_common>\n',o(5));
+    fprintf(fid,'%s</source>\n',o(4));
+    fprintf(fid,'%s<vertices id="shape%d-vertices">\n',o(4),i);
+    fprintf(fid,'%s<input semantic="POSITION" source="#shape%d-positions"/>\n',o(5),i);
+    fprintf(fid,'%s</vertices>\n',o(4));
+    fprintf(fid,'%s<triangles material="material%d" count="%d">\n',o(4),i,size(s(i).faces,1));
+    fprintf(fid,'%s<input semantic="VERTEX" source="#shape%d-vertices" offset="0"/>\n',o(5),i);
+    fprintf(fid,'%s<p>',o(5));
+    fprintf(fid,'%d ',repmat(s(i).faces',1,[])-1);
+    fprintf(fid,'</p>\n');
+    fprintf(fid,'%s</triangles>\n',o(4));
+    fprintf(fid,'%s</mesh>\n',o(3));
+    fprintf(fid,'%s</geometry>\n',o(2));
+end
+fprintf(fid,'%s</library_geometries>\n',o(1));
+
+% Scene
+%--------------------------------------------------------------------------
+fprintf(fid,'%s<library_visual_scenes>\n',o(1));
+fprintf(fid,'%s<visual_scene id="VisualSceneNode" name="SceneNode">\n',o(2));
+for i=1:numel(s)
+    fprintf(fid,'%s<node id="node%d">\n',o(3),i);
+    fprintf(fid,'%s<instance_geometry url="#shape%d">\n',o(4),i);
+    fprintf(fid,'%s<bind_material>\n',o(5));
+    fprintf(fid,'%s<technique_common>\n',o(6));
+    fprintf(fid,'%s<instance_material symbol="material%d" target="#material%d"/>\n',o(7),i,i);
+    fprintf(fid,'%s</technique_common>\n',o(6));
+    fprintf(fid,'%s</bind_material>\n',o(5));
+    fprintf(fid,'%s</instance_geometry>\n',o(4));
+    fprintf(fid,'%s</node>\n',o(3));
+end
+fprintf(fid,'%s</visual_scene>\n',o(2));
+fprintf(fid,'%s</library_visual_scenes>\n',o(1));
+fprintf(fid,'%s<scene>\n',o(1));
+fprintf(fid,'%s<instance_visual_scene url="#VisualSceneNode" />\n',o(2));
+fprintf(fid,'%s</scene>\n',o(1));
+
+% End of XML
+%--------------------------------------------------------------------------
+fprintf(fid,'</COLLADA>\n');

@file_array/private/file2mat.mexmaci

@@ -11,7 +11,11 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Vladimir Litvak
-% $Id: check.m 2720 2009-02-09 19:50:46Z vladimir $
+% $Id: check.m 3196 2009-06-11 12:54:47Z vladimir $
+
+if nargin == 1
+    option = 'basic';
+end
 
 [ok, this] = checkmeeg(struct(this), option);
 

@file_array/private/file2mat.mexmaci64

@@ -1,15 +1,21 @@
-function new = clone(this, fnamedat, dim)
+function new = clone(this, fnamedat, dim, reset)
 % Creates a copy of the object with a new, empty data file,
 % possibly changing dimensions
-% FORMAT new = clone(this, fnamedat, dim)
+% FORMAT new = clone(this, fnamedat, dim, reset)
+% reset - 0 (default) do not reset channel or trial info unless dimensions
+%          change, 1 - reset channels only, 2 - trials only, 3 both
 % Note that when fnamedat comes with a path, the cloned meeg object uses
 % it. Otherwise, its path is by definition that of the meeg object to be
 % cloned.
 % _________________________________________________________________________
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Stefan Kiebel, Vladimir Litvak
-% $Id: clone.m 2476 2008-11-18 12:58:57Z christophe $
+% $Id: clone.m 3350 2009-09-03 13:19:20Z vladimir $
+
+if nargin < 4
+    reset = 0;
+end
 
 if nargin < 3
     if ~strcmp(transformtype(this), 'TF')
@@ -39,6 +45,10 @@
     d(end, end, end, end) = 0;
     nsampl = dim(3);
     ntrial = dim(4);
+    
+    if ~strncmpi(transformtype(new), 'TF',2)
+        new = transformtype(new, 'TF');
+    end        
 else
    error('Dimensions different from 3 or 4 are not supported.');
 end
@@ -52,14 +62,14 @@
 new.path = pth;
 
 % ensure consistency 
-if dim(1) ~= nchannels(this)
+if (dim(1) ~= nchannels(this)) || ismember(reset, [1 3])
     new.channels = [];
     for i = 1:dim(1)
         new.channels(i).label = ['Ch' num2str(i)];
     end
 end
 
-if ntrial ~= ntrials(this)
+if ntrial ~= ntrials(this) || ismember(reset, [2 3])
     new.trials = repmat(struct('label', 'Undefined'), 1, ntrial);
 end
 

@file_array/private/file2mat.mexw32

@@ -6,7 +6,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Vladimir Litvak
-% $Id: condlist.m 3046 2009-04-02 14:28:31Z vladimir $
+% $Id: condlist.m 3254 2009-07-07 15:18:54Z vladimir $
 
 res = getset(this, 'trials', 'label');
 if ~iscell(res)
@@ -23,7 +23,7 @@
 
     if numel(res)>1 && isfield(this.other, 'condlist') &&...
             iscell(this.other.condlist) && ~isempty(this.other.condlist)
-        [sel1, sel2] = spm_match_str(this.other.condlist, res);
+        [sel1, sel2] = match_str(this.other.condlist, res);
         res = res([sel2(:)' setdiff(1:numel(res), sel2)]);
     end
 else