SPM12 r7487

spm · Nov 14, 2018 · 50b4fd3 · 50b4fd3
1 parent 0f9eada
commit 50b4fd3
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diff --git a/@file_array/private/file2mat.c b/@file_array/private/file2mat.c
@@ -1,5 +1,5 @@
 /*
- * $Id: file2mat.c 6988 2017-01-16 12:38:29Z guillaume $
+ * $Id: file2mat.c 7353 2018-06-19 10:39:55Z guillaume $
  * John Ashburner
  */
 
@@ -26,8 +26,10 @@ Memory mapping is used by this module. For more information on this, see:
 HANDLE hFile, hMapping;
 typedef char *caddr_t;
 #if defined _FILE_OFFSET_BITS && _FILE_OFFSET_BITS == 64
+#ifdef _MSC_VER_
 #define stat _stati64
 #define fstat _fstati64
+#endif
 #define open _open
 #define close _close
 #if defined _MSC_VER
@@ -625,13 +627,13 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
     if (map.dtype->channels == 1)
     {
         plhs[0] = mxCreateNumericArray(ndim,odim,map.dtype->clss,mxREAL);
-#ifdef SPM_WIN32
+#ifdef _MSC_VER_
         /* https://msdn.microsoft.com/en-us/library/windows/desktop/aa366801.aspx */
         __try
         {
 #endif
             map.dtype->func(ndim-1, idim, iptr, idat, odim, mxGetData(plhs[0]));
-#ifdef SPM_WIN32
+#ifdef _MSC_VER_
         }
         __except(GetExceptionCode()==EXCEPTION_IN_PAGE_ERROR ?
             EXCEPTION_EXECUTE_HANDLER : EXCEPTION_CONTINUE_SEARCH)

diff --git a/@file_array/private/file2mat.mexw32 b/@file_array/private/file2mat.mexw32
diff --git a/@file_array/private/file2mat.mexw64 b/@file_array/private/file2mat.mexw64
diff --git a/@file_array/private/init.mexw32 b/@file_array/private/init.mexw32
diff --git a/@file_array/private/init.mexw64 b/@file_array/private/init.mexw64
diff --git a/@file_array/private/mat2file.mexw32 b/@file_array/private/mat2file.mexw32
diff --git a/@file_array/private/mat2file.mexw64 b/@file_array/private/mat2file.mexw64
diff --git a/@file_array/size.m b/@file_array/size.m
@@ -4,7 +4,7 @@
 % Copyright (C) 2005-2017-2012 Wellcome Trust Centre for Neuroimaging
 
 %
-% $Id: size.m 7147 2017-08-03 14:07:01Z spm $
+% $Id: size.m 7440 2018-10-10 17:28:26Z john $
 
 
 sa  = struct(a);
@@ -35,9 +35,8 @@
 d   = d(1:lim);
 
 if nargin > 1
-    if varargin{1} <= length(d)
-        d = d(varargin{1});
-    else
-        d = 1;
-    end
+    d_tmp  = d;
+    d      = ones(size(varargin{1}));
+    msk    = varargin{1}<=length(d_tmp);
+    d(msk) = d_tmp(varargin{1}(msk));
 end
diff --git a/@file_array/subsref.m b/@file_array/subsref.m
@@ -5,7 +5,7 @@
 % Copyright (C) 2005-2017 Wellcome Trust Centre for Neuroimaging
 
 %
-% $Id: subsref.m 7209 2017-11-10 15:33:10Z guillaume $
+% $Id: subsref.m 7439 2018-10-10 17:19:31Z john $
 
 
 if isempty(subs), return; end

diff --git a/@gifti/Contents.m b/@gifti/Contents.m
@@ -6,23 +6,27 @@
 %                      http://nifti.nimh.nih.gov/
 %
 % This MATLAB class is part of SPM:
-%                  http://www.fil.ion.ucl.ac.uk/spm/
+%                  https://www.fil.ion.ucl.ac.uk/spm/
 %
 % It relies on external libraries:
 %   Base64, by Peter J. Acklam:
 %      http://home.online.no/~pjacklam/
 %   miniz, by Rich Geldreich:
-%      http://code.google.com/p/miniz/
-%   XMLTree, by Guillaume Flandin:
-%      http://www.artefact.tk/software/matlab/xml/
+%      https://github.com/richgel999/miniz
+%   dzip, by Michael Kleder:
+%      https://www.mathworks.com/matlabcentral/fileexchange/8899
+%   XMLTree, mVTK and JSONio, by Guillaume Flandin:
+%      https://www.artefact.tk/software/matlab/xml/
+%      https://www.artefact.tk/software/matlab/mvtk/
+%      https://www.artefact.tk/software/matlab/jsonio/
 %__________________________________________________________________________
-% Copyright (C) 2008-2015 Wellcome Trust Centre for Neuroimaging
+% Copyright (C) 2008-2018 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: Contents.m 6404 2015-04-13 14:29:53Z guillaume $
+% $Id: Contents.m 7379 2018-07-25 09:11:24Z guillaume $
 
-% GIfTI file format for MATLAB (The Mathworks, Inc.).
-% Copyright (C) 2008-2015 Wellcome Trust Centre for Neuroimaging
+% GIfTI library for MATLAB
+% Copyright (C) 2008-2018 Wellcome Trust Centre for Neuroimaging
 %
 % This program is free software; you can redistribute it and/or
 % modify it under the terms of the GNU General Public License
@@ -36,4 +40,4 @@
 % 
 % You should have received a copy of the GNU General Public License
 % along with this program; if not, write to the Free Software
-% Foundation Inc, 59 Temple Pl. - Suite 330, Boston, MA 02111-1307, USA.
+% Foundation Inc, 59 Temple Pl. - Suite 330, Boston, MA 02111-1307, USA.
diff --git a/@gifti/export.m b/@gifti/export.m
@@ -8,12 +8,17 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: export.m 6401 2015-04-09 17:21:33Z guillaume $
-
-if numel(this) > 1, warning('Only handle scalar objects yet.'); end
+% $Id: export.m 7383 2018-07-31 10:53:37Z guillaume $
 
 if nargin <= 1, target = 'MATLAB'; end
 
+if numel(this) > 1
+    for i=1:numel(this)
+        s(i) = export(this(i),target);
+    end
+    return;
+end
+
 switch lower(target)
     case 'matlab'
         s = struct(this);

diff --git a/@gifti/gifti.m b/@gifti/gifti.m
@@ -8,7 +8,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: gifti.m 7037 2017-03-15 11:45:13Z guillaume $
+% $Id: gifti.m 7471 2018-11-02 11:14:39Z guillaume $
 
 switch nargin
 
@@ -41,7 +41,7 @@
         elseif ishandle(varargin{1})
             this = struct('vertices',get(varargin{1},'Vertices'), ...
                           'faces',   get(varargin{1},'Faces'));
-            if ~isempty(get(varargin{1},'FaceVertexCData'));
+            if ~isempty(get(varargin{1},'FaceVertexCData'))
                   this.cdata = get(varargin{1},'FaceVertexCData');
             end
             this = gifti(this);
@@ -76,7 +76,9 @@
                 catch
                     error('[GIFTI] Loading of file %s failed.', varargin{1});
                 end
-            elseif strcmpi(e,'.asc') || strcmpi(e,'.srf')
+            elseif ismember(lower(e),{'.asc','.srf','.mgh','.mgz','.pial',...
+                    '.white','.inflated','.nofix','.orig','.smoothwm',...
+                    '.sphere','.reg','.surf','.curv','.area','.sulc'})
                 this = read_freesurfer_file(varargin{1});
                 this = gifti(this);
             elseif strcmpi(e,'.vtk')
@@ -85,6 +87,15 @@
             elseif strcmpi(e,'.obj')
                 this = obj_read(varargin{1});
                 this = gifti(this);
+            elseif strcmpi(e,'.ply')
+                this = ply_read(varargin{1});
+                this = gifti(this);
+            elseif strcmpi(e,'.stl')
+                this = stl_read(varargin{1});
+                this = gifti(this);
+            elseif strcmpi(e,'.mz3')
+                this = mz3_read(varargin{1});
+                this = gifti(this);
             else
                 this = read_gifti_file(varargin{1},giftistruct);
                 this = class(this,'gifti');

diff --git a/@gifti/plot.m b/@gifti/plot.m
@@ -4,7 +4,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: plot.m 5888 2014-02-19 19:54:12Z guillaume $
+% $Id: plot.m 7381 2018-07-25 10:27:54Z guillaume $
 
 % if ishandle(varargin{1})
 %     h = figure(varargin{1});
@@ -14,9 +14,9 @@
 %     %axis off;
 %     %camlight;
 %     %camlight(-80,-10);
-%     %lighting phong;
+%     %lighting gouraud;
 % end
-% cameramenu;
+% cameratoolbar;
 
 
 cdata = [];
@@ -55,12 +55,10 @@
     set(hp,'FaceVertexCData',cdata(:,indc), 'FaceColor','interp')
 end
 
-axes(ax);
-camlight;
-camlight(-80,-10);
-lighting phong;
-axes(ax);
-cameramenu;
+camlight(ax);
+camlight(ax,-80,-10);
+lighting(ax,'gouraud');
+cameratoolbar(h);
 
 if nargout
     varargout{1} = hp;

diff --git a/@gifti/private/getdict.m b/@gifti/private/getdict.m
@@ -4,7 +4,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: getdict.m 4505 2011-09-30 11:45:58Z guillaume $
+% $Id: getdict.m 7379 2018-07-25 09:11:24Z guillaume $
 
 persistent dict;
 if ~isempty(dict)
@@ -13,8 +13,12 @@
 end
 
 table = {...
-    'NIFTI_TYPE_UINT8',   'uint8',   '%d', @uint8, 'uint8'
-    'NIFTI_TYPE_INT32',   'int32',   '%d', @int32, 'int32' 
+    'NIFTI_TYPE_UINT8',   'uint8',   '%d', @uint8,  'uint8'
+    'NIFTI_TYPE_INT8',    'int8',    '%d', @int8,   'int8'
+    'NIFTI_TYPE_UINT16',  'uint16',  '%d', @uint16, 'uint16'
+    'NIFTI_TYPE_INT16',   'int16',   '%d', @int16,  'int16'
+    'NIFTI_TYPE_UINT32',  'uint32',  '%d', @uint32, 'uint32' 
+    'NIFTI_TYPE_INT32',   'int32',   '%d', @int32,  'int32' 
     'NIFTI_TYPE_FLOAT32', 'float32', '%f', @single, 'single'
     'NIFTI_TYPE_FLOAT64', 'float64', '%f', @double, 'double'};