ENH - added missing mex files (fieldtrip#2419)

* ENH - added missing mex files

* ENH - updated spm_platform

* ENH - updated large part of spm code to dev-version on github

* ENH - also updated code from lower level folders

* added to-be-ignored word

.codespellrc

@@ -2,7 +2,7 @@
 
 [codespell]
 skip = .git,*.pdf,*.svg,external,src
-ignore-words-list = ans,cfg,siz,pnt,pos,ori,ext,dum,siz,toi,homogenous,whos,nas,ini,lpa,rpa,als,ali,ars,ari,pls,pli,prs,pri,las,lai,ras,rai,lps,lpi,rps,rpi,asl,ail,asr,air,psl,pil,psr,pir,sal,ial,sar,iar,spl,ipl,spr,ipr,sla,ila,sra,ira,slp,ilp,srp,irp,lsa,lia,rsa,ria,lsp,lip,rsp,rip
+ignore-words-list = assignin,ans,cfg,siz,pnt,pos,ori,ext,dum,siz,toi,homogenous,whos,nas,ini,lpa,rpa,als,ali,ars,ari,pls,pli,prs,pri,las,lai,ras,rai,lps,lpi,rps,rpi,asl,ail,asr,air,psl,pil,psr,pir,sal,ial,sar,iar,spl,ipl,spr,ipr,sla,ila,sra,ira,slp,ilp,srp,irp,lsa,lia,rsa,ria,lsp,lip,rsp,rip
 exclude-file = .codespellignorelines
 
 # case sensitive etc as regex

external/spm12/@file_array/Contents.m

@@ -41,10 +41,6 @@
 % size(fa4)
 % size(fa2)
 % length(fa0)
-% _________________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
-
-%
-% $Id: Contents.m 2696 2009-02-05 20:29:48Z guillaume $
-
+%__________________________________________________________________________
 
+% Copyright (C) 2005-2022 Wellcome Centre for Human Neuroimaging

external/spm12/@file_array/cat.m

@@ -1,40 +1,38 @@
 function o = cat(dr,varargin)
 % Concatenate file_array objects.  The result is a non-simple object
 % that can no longer be reshaped.
-% _______________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+%__________________________________________________________________________
 
-%
-% $Id: cat.m 4136 2010-12-09 22:22:28Z guillaume $
+% Copyright (C) 2005-2022 Wellcome Centre for Human Neuroimaging
 
 
-if dr>32 || dr<0, error('Unknown command option.'); end;
+if dr>32 || dr<0, error('Unknown command option.'); end
 dr   = max(round(dr),1);
 d    = ones(nargin-1,16);
 tmp  = {};
 dpos = 0;
-for i=1:nargin-1,
+for i=1:nargin-1
     vi = varargin{i};
     if strcmp(class(vi),'file_array')
         sz                = size(vi);
         d(i,1:length(sz)) = sz;
         svi               = struct(vi);
         svi               = svi(:);
-        for j=1:length(svi(:)),
+        for j=1:length(svi(:))
             if length(svi(j).pos)<dr
                 svi(j).pos((length(svi(j).pos)+1):dr) = 1;
             end
             svi(j).pos(dr)= svi(j).pos(dr) + dpos;
-        end;
+        end
         dpos              = dpos + d(i,dr);
         tmp{i}            = svi;
     else
         error(['Conversion to file_array from ' class(vi) ' is not possible.']);
-    end;
-end;
+    end
+end
 if any(diff(d(:,[1:(dr-1) (dr+1):end]),1,1))
     error('All matrices on a row in the bracketed expression must have the same number of rows.');
 else
     o = vertcat(tmp{:});
     o = file_array(o);
-end;
+end

external/spm12/@file_array/ctranspose.m

@@ -1,9 +1,8 @@
 function varargout = ctranspose(varargin)
 % Transposing not allowed
-% _______________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+%__________________________________________________________________________
+
+% Copyright (C) 2005-2022 Wellcome Centre for Human Neuroimaging
 
-%
-% $Id: ctranspose.m 1143 2008-02-07 19:33:33Z spm $
 
 error('file_array objects can not be transposed.');

external/spm12/@file_array/disp.m

@@ -1,34 +1,31 @@
 function disp(obj)
 % Display a file_array object
-% _______________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+%__________________________________________________________________________
 
-%
-% $Id: disp.m 4136 2010-12-09 22:22:28Z guillaume $
+% Copyright (C) 2005-2022 Wellcome Centre for Human Neuroimaging
 
 
-if numel(struct(obj))>1,
+if numel(struct(obj))>1
     fprintf('       %s object: ', class(obj));
     sz = size(obj);
-    if length(sz)>4,
+    if length(sz)>4
         fprintf('%d-D\n',length(sz));
     else
-        for i=1:(length(sz)-1),
+        for i=1:(length(sz)-1)
             fprintf('%d-by-',sz(i));
-        end;
+        end
         fprintf('%d\n',sz(end));
-    end;
+    end
 else
     disp(mystruct(obj))
-end;
-return;
-%=======================================================================
+end
 
-%=======================================================================
+
+%==========================================================================
+% function t = mystruct(obj)
+%==========================================================================
 function t = mystruct(obj)
 fn = fieldnames(obj);
 for i=1:length(fn)
     t.(fn{i}) = subsref(obj,struct('type','.','subs',fn{i}));
-end;
-return;
-%=======================================================================
+end

external/spm12/@file_array/display.m

@@ -1,10 +1,8 @@
 function display(obj)
 % Display a file_array object
-% _______________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+%__________________________________________________________________________
 
-%
-% $Id: display.m 1143 2008-02-07 19:33:33Z spm $
+% Copyright (C) 2005-2022 Wellcome Centre for Human Neuroimaging
 
 
 disp(' ');

external/spm12/@file_array/double.m

@@ -2,11 +2,9 @@
 % Convert to double precision
 % FORMAT double(fa)
 % fa - a file_array
-% _______________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+%__________________________________________________________________________
 
-%
-% $Id: double.m 1143 2008-02-07 19:33:33Z spm $
+% Copyright (C) 2005-2022 Wellcome Centre for Human Neuroimaging
 
-out = double(numeric(fa));
 
+out = double(full(fa));

external/spm12/@file_array/end.m

@@ -1,17 +1,16 @@
 function en = end(a,k,n)
 % Overloaded end function for file_array objects.
-% _______________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+%__________________________________________________________________________
+
+% Copyright (C) 2005-2022 Wellcome Centre for Human Neuroimaging
 
-%
-% $Id: end.m 1143 2008-02-07 19:33:33Z spm $
 
 dim = size(a);
 if k>length(dim)
     en = 1;
 else
-    if n<length(dim),
+    if n<length(dim)
     dim = [dim(1:(n-1)) prod(dim(n:end))];
-    end;
+    end
     en = dim(k);
-end;
+end

external/spm12/@file_array/fieldnames.m

@@ -1,10 +1,9 @@
 function t = fieldnames(obj)
 % Fieldnames of a file-array object
-% _______________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+%__________________________________________________________________________
+
+% Copyright (C) 2005-2022 Wellcome Centre for Human Neuroimaging
 
-%
-% $Id: fieldnames.m 1143 2008-02-07 19:33:33Z spm $
 
 t = {...
     'fname'

external/spm12/@file_array/file_array.m

@@ -9,34 +9,31 @@
 % scl_slope  - scalefactor (default = 1)
 % scl_inter  - DC offset, such that dat = raw*scale + inter (default = 0)
 % permission - Write permission, either 'rw' or 'ro' (default = 'rw')
-% _______________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+%__________________________________________________________________________
 
-%
-% $Id: file_array.m 4136 2010-12-09 22:22:28Z guillaume $
+% Copyright (C) 2005-2022 Wellcome Centre for Human Neuroimaging
 
 
 if nargin==1
-    if isstruct(varargin{1}),
+    if isstruct(varargin{1})
         a = class(varargin{1},'file_array');
         return;
-    elseif isa(varargin{1},'file_array'),
+    elseif isa(varargin{1},'file_array')
         a = varargin{1};
         return;
-    end;
-end;
+    end
+end
 a = struct('fname','','dim',[0 0],'dtype',2,...
            'be',0,'offset',0,'pos',[],'scl_slope',[],'scl_inter',[], 'permission','rw');
 %a = class(a,'file_array');
 
-if nargin>=1, a =     fname(a,varargin{1}); end;
-if nargin>=2, a =       dim(a,varargin{2}); end;
-if nargin>=3, a =     dtype(a,varargin{3}); end;
-if nargin>=4, a =    offset(a,varargin{4}); end;
-if nargin>=5, a = scl_slope(a,varargin{5}); end;
-if nargin>=6, a = scl_inter(a,varargin{6}); end;
-if nargin>=7, a = permission(a,varargin{7}); end;
+if nargin>=1, a =     fname(a,varargin{1}); end
+if nargin>=2, a =       dim(a,varargin{2}); end
+if nargin>=3, a =     dtype(a,varargin{3}); end
+if nargin>=4, a =    offset(a,varargin{4}); end
+if nargin>=5, a = scl_slope(a,varargin{5}); end
+if nargin>=6, a = scl_inter(a,varargin{6}); end
+if nargin>=7, a = permission(a,varargin{7}); end
 
 a.pos = ones(size(a.dim));
 a     = file_array(a);
-

external/spm12/@file_array/horzcat.m

@@ -1,11 +1,8 @@
 function o = horzcat(varargin)
 % Horizontal concatenation of file_array objects
-% _______________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+%__________________________________________________________________________
 
-%
-% $Id: horzcat.m 1143 2008-02-07 19:33:33Z spm $
+% Copyright (C) 2005-2022 Wellcome Centre for Human Neuroimaging
 
-o    = cat(2,varargin{:});
-return;
 
+o = cat(2,varargin{:});

external/spm12/@file_array/initialise.m

@@ -4,10 +4,8 @@ function initialise(fa)
 % This creates a file on disk with the appropriate size by explicitly
 % writing data to prevent a sparse file.
 %__________________________________________________________________________
-% Copyright (C) 2013 Wellcome Trust Centre for Neuroimaging
 
-%
-% $Id: initialise.m 5458 2013-05-01 14:32:23Z guillaume $
+% Copyright (C) 2005-2022 Wellcome Centre for Human Neuroimaging
 
 
 % first approach

external/spm12/@file_array/isnan.m

@@ -1,21 +1,19 @@
 function out = isnan(fa)
-% Convert to numeric form
+% Logical array containing true where the elements of file_array are NaN's
 % FORMAT isnan(fa)
 % fa - a file_array
-% _______________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+%__________________________________________________________________________
+
+% Copyright (C) 2005-2022 Wellcome Centre for Human Neuroimaging
 
-%
-% $Id: isnan.m 1301 2008-04-03 13:21:44Z john $
 
 bs  = 10240;
 m   = size(fa);
 fa  = reshape(fa,prod(m),1);
 n   = prod(m);
 out = false(m);
-for i=1:ceil(n/bs),
+for i=1:ceil(n/bs)
     ii      = ((((i-1)*bs)+1):min((i*bs),n))';
     tmp     = subsref(fa,struct('type','()','subs',{{ii}}));
     out(ii) = isnan(tmp);
 end
-

external/spm12/@file_array/length.m

@@ -1,11 +1,8 @@
 function l = length(x)
 % Overloaded length function for file_array objects
-% _______________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+%__________________________________________________________________________
 
-%
-% $Id: length.m 1143 2008-02-07 19:33:33Z spm $
+% Copyright (C) 2005-2022 Wellcome Centre for Human Neuroimaging
 
 
 l = max(size(x));
-

external/spm12/@file_array/loadobj.m

@@ -1,14 +1,13 @@
 function b = loadobj(a)
 % loadobj for file_array class
-% _______________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+%__________________________________________________________________________
+
+% Copyright (C) 2005-2022 Wellcome Centre for Human Neuroimaging
 
-%
-% $Id: loadobj.m 1544 2008-05-06 10:34:36Z guillaume $
 
 if isa(a,'file_array')
     b = a;
 else
     a = permission(a, 'rw');
     b = file_array(a);
-end
+end

external/spm12/@file_array/ndims.m

@@ -1,12 +1,9 @@
 function out = ndims(fa)
 % Number of dimensions
-%_______________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+%__________________________________________________________________________
 
-%
-% $Id: ndims.m 1143 2008-02-07 19:33:33Z spm $
+% Copyright (C) 2005-2022 Wellcome Centre for Human Neuroimaging
 
 
 out = size(fa);
 out = length(out);
-

external/spm12/@file_array/numel.m

@@ -1,10 +1,8 @@
 function t = numel(obj)
 % Number of simple file arrays involved.
-% _______________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+%__________________________________________________________________________
 
-%
-% $Id: numel.m 1143 2008-02-07 19:33:33Z spm $
+% Copyright (C) 2005-2022 Wellcome Centre for Human Neuroimaging
 
 
 % Should be this, but it causes problems when accessing

external/spm12/@file_array/numeric.m

@@ -2,13 +2,9 @@
 % Convert to numeric form
 % FORMAT numeric(fa)
 % fa - a file_array
-% _______________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+%__________________________________________________________________________
 
-%
-% $Id: numeric.m 1143 2008-02-07 19:33:33Z spm $
+% Copyright (C) 2005-2022 Wellcome Centre for Human Neuroimaging
 
 
-[vo{1:ndims(fa)}] = deal(':');
-out = subsref(fa,struct('type','()','subs',{vo}));
-
+out = full(fa);

external/spm12/@file_array/permute.m

@@ -1,10 +1,8 @@
 function varargout = permute(varargin)
-% Can not be permuted.
-% _______________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+% file_array objects can not be permuted
+%__________________________________________________________________________
 
-%
-% $Id: permute.m 1143 2008-02-07 19:33:33Z spm $
+% Copyright (C) 2005-2022 Wellcome Centre for Human Neuroimaging
 
 
 error('file_array objects can not be permuted.');