SPM12 r6685

Author: SPMcentral

@file_array/private/file2mat.c

@@ -1,5 +1,5 @@
 /*
- * $Id: file2mat.c 5446 2013-04-24 16:56:51Z guillaume $
+ * $Id: file2mat.c 6618 2015-12-01 16:25:38Z spm $
  * John Ashburner
  */
 
@@ -625,7 +625,20 @@ 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);
-        map.dtype->func(ndim-1, idim, iptr, idat, odim, mxGetData(plhs[0]));
+#ifdef SPM_WIN32
+        /* 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
+        }
+        __except(GetExceptionCode()==EXCEPTION_IN_PAGE_ERROR ?
+            EXCEPTION_EXECUTE_HANDLER : EXCEPTION_CONTINUE_SEARCH)
+        {
+            mexErrMsgTxt("An exception occured while accessing the data.");
+        }
+#endif
         if (map.swap)
             map.dtype->swap(ocumprod[ndim],mxGetData(plhs[0]));
     }

@file_array/private/file2mat.mexw64

@@ -4,7 +4,7 @@
 % Copyright (C) 2005-2013 Wellcome Trust Centre for Neuroimaging
 
 %
-% $Id: subsasgn.m 6157 2014-09-05 18:17:54Z guillaume $
+% $Id: subsasgn.m 6522 2015-08-14 18:55:42Z john $
 
 
 if isempty(subs), return; end
@@ -145,7 +145,13 @@
 
 %-Convert data into output datatype
 %--------------------------------------------------------------------------
-if dt(ind).isint, dat = round(dat); end
+if dt(ind).isint
+    % Avoid "Warning: Out of range value converted to intmin() or intmax()." 
+    dat = max(dat,dt(ind).min);
+    dat = min(dat,dt(ind).max);
+
+    dat = round(dat);
+end
 
 %ws = warning('off'); % Avoid warning messages in R14 SP3
 dat = feval(dt(ind).conv,dat);

@file_array/private/init.mexw32

@@ -7,10 +7,10 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: fieldnames.m 6345 2015-02-20 12:25:50Z guillaume $
+% $Id: fieldnames.m 6507 2015-07-24 16:48:02Z guillaume $
 
 if numel(this) > 1, warning('Only handle scalar objects yet.'); end
 
-pfn = {'vertices' 'faces' 'normals' 'cdata' 'mat' 'labels' 'indices'};
+pfn = {'vertices','faces','normals','cdata','mat','labels','indices'};
 
-names = pfn(isintent(this,pfn));
+names = unique(pfn(isintent(this,pfn)));

@file_array/private/init.mexw64

@@ -8,7 +8,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: gifti.m 6347 2015-02-24 17:59:16Z guillaume $
+% $Id: gifti.m 6601 2015-11-19 13:55:32Z guillaume $
 
 switch nargin
 
@@ -67,6 +67,9 @@
             elseif strcmpi(e,'.asc') || strcmpi(e,'.srf')
                 this = read_freesurfer_file(varargin{1});
                 this = gifti(this);
+            elseif strcmpi(e,'.vtk')
+                this = mvtk_read(varargin{1});
+                this = gifti(this);
             else
                 this = read_gifti_file(varargin{1},giftistruct);
                 this = class(this,'gifti');

@file_array/subsasgn.m

@@ -8,6 +8,6 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: isfield.m 2076 2008-09-10 12:34:08Z guillaume $
+% $Id: isfield.m 6507 2015-07-24 16:48:02Z guillaume $
 
-tf = ismember(field, fieldnames(this));
+tf = ismember(field, fieldnames(this));

@gifti/fieldnames.m

@@ -0,0 +1,165 @@
+function M = mvtk_read(filename)
+% Read VTK formatted data from disk
+% FORMAT M = mvtk_read(filename)
+%
+% filename - VTK-formatted file name
+% M        - data structure
+%__________________________________________________________________________
+% 
+% VTK File Formats Specifications:
+% http://www.vtk.org/VTK/img/file-formats.pdf
+% 
+% Requirements: zstream, base64decode
+%__________________________________________________________________________
+% Copyright (C) 2015 Wellcome Trust Centre for Neuroimaging
+
+% Guillaume Flandin
+% $Id: mvtk_read.m 6601 2015-11-19 13:55:32Z guillaume $
+
+
+[pth,name,ext] = fileparts(filename);
+switch ext
+    case '.vtk'
+        M = mvtk_read_legacy(filename);
+    case {'.vti','.vtp','.vtr','.vts','.vtu'}
+        % Serial vtkImageData (structured)
+        % Serial vtkPolyData (unstructured)
+        % Serial vtkRectilinearGrid (structured)
+        % Serial vtkStructuredGrid (structured)
+        % Serial vtkUnstructuredGrid (unstructured)
+        M = mvtk_read_xml(filename);
+    otherwise
+        error('Unknown file format.');
+end
+
+%==========================================================================
+% function M = mvtk_read_legacy(filename)
+%==========================================================================
+function M = mvtk_read_legacy(filename)
+
+fid = fopen(filename,'rt');
+if fid == -1
+    error('Cannot open %s.',filename);
+end
+
+%- Part 1: file version and identifier
+% # vtk DataFile Version 2.0
+l = fgetl(fid);
+if ~ischar(l), error('VTK file incomplete.'); end
+if ~strncmpi(l,'# vtk DataFile Version',22)
+    error('This is not a VTK formatted file.');
+end
+
+%- Part 2: header
+l = fgetl(fid);
+if ~ischar(l), error('VTK file incomplete.'); end
+
+%- Part 3: file format
+format = fgetl(fid);
+if ~ismember(format,{'ASCII','BINARY'})
+    error('Unknown file format.');
+end
+
+%- Part 4: dataset structure
+data_attributes = false;
+l = fgetl(fid);
+if ~ischar(l), error('VTK file incomplete.'); end
+[D,l] = strtok(l);
+if ~strcmp(D,'DATASET'), error('Invalid VTK file.'); end
+F = strtok(l(2:end));
+switch F
+    case 'STRUCTURED_POINTS'
+        warning('Unsupported dataset format.');
+        l = fgetl(fid);
+        DIM = sscanf(l,'DIMENSIONS %d %d %d');
+        l = fgetl(fid);
+        ORIGIN = sscanf(l,'ORIGIN %f %f %f');
+        l = fgetl(fid);
+        SPACING = sscanf(l,'SPACING %f %f %f');
+    case 'STRUCTURED_GRID'
+        warning('Unsupported dataset format.');
+        l = fgetl(fid);
+        DIM = sscanf(l,'DIMENSIONS %d %d %d');
+        l = fgetl(fid);
+        % assume float and n = prod(DIM)
+        PTS = textscan(fid,'%f %f %f\n',prod(DIM),'CollectOutput',true);
+        PTS = PTS{1};
+    case 'RECTILINEAR_GRID'
+        warning('Unsupported dataset format.');
+        l = fgetl(fid);
+        DIM = sscanf(l,'DIMENSIONS %d %d %d');
+        l = fgetl(fid);
+        XCOORDS = textscan(fid,'%f',DIM(1),'CollectOutput',true);
+        XCOORDS = XCOORDS{1};
+        l = fgetl(fid);
+        YCOORDS = textscan(fid,'%f',DIM(2),'CollectOutput',true);
+        YCOORDS = YCOORDS{1};
+        l = fgetl(fid);
+        ZCOORDS = textscan(fid,'%f',DIM(3),'CollectOutput',true);
+        ZCOORDS = ZCOORDS{1};
+    case 'POLYDATA'
+        while true
+            l = fgetl(fid);
+            if ~ischar(l), break; end
+            [D,l] = strtok(l);
+            switch D
+                case 'POINTS'
+                    [N,l] = strtok(l(2:end)); % l still contains dataType
+                    N = str2double(N);
+                    M.vertices = textscan(fid,'%f %f %f\n',N,'CollectOutput',true);
+                    M.vertices = M.vertices{1};
+                case 'POLYGONS'
+                    [N,l] = strtok(l(2:end));
+                    N = str2double(N);
+                    S = strtok(l);
+                    S = str2double(S);
+                    if 4*N ~= S, error('Unsupported dataset format.'); end
+                    M.faces = textscan(fid,'3 %d %d %d\n',N,'CollectOutput',true);
+                    M.faces = M.faces{1} + 1;
+                case {'VERTICES','LINES','TRIANGLE_STRIPS'}
+                    error('Unsupported data type.');
+                case {'POINT_DATA','CELL_DATA'}
+                    data_attributes = true;
+                    [N,l] = strtok(l(2:end));
+                    N = str2double(N);
+                    break;
+                otherwise
+                    error('Invalid VTK file.');
+            end
+        end
+    case {'UNSTRUCTURED_GRID','FIELD'}
+        error('Unsupported data type.');
+    otherwise
+        error('Invalid VTK file.');
+end
+
+%- Part 5: dataset attributes (POINT_DATA and CELL_DATA)
+if data_attributes
+    %l = fgetl(fid); % {POINT_DATA,CELL_DATA} N
+    l = fgetl(fid); % SCALARS dataName dataType numComp
+    [P,l] = strtok(l);
+    [S,l] = strtok(l(2:end));
+    [S,l] = strtok(l(2:end));
+    S = strtok(l(2:end)); S = str2double(S);
+    l = fgetl(fid); % LOOKUP_TABLE default
+    fmt = repmat('%f ',1,S);
+    fmt = [fmt(1:end-1) '\n'];
+    M.cdata = textscan(fid,fmt,N,'CollectOutput',true);
+    M.cdata = M.cdata{1};
+end
+
+fclose(fid);
+
+%==========================================================================
+% function M = mvtk_read_xml(filename)
+%==========================================================================
+function M = mvtk_read_xml(filename)
+
+try
+    X = xmltree(filename);
+catch
+    error('Cannot parse file %s.',filename);
+end
+
+warning('Unsupported file format.');
+M = struct([]);