moves mex files and adapt installation

extern/nfft/.gitignore

@@ -0,0 +1 @@
+*.mex*

extern/nfft_openMP/.gitignore

@@ -0,0 +1 @@
+*.mex*

extern/nfft_openMP/readme.md

@@ -0,0 +1,13 @@
+
+1. Download the FFTW
+
+2. Download the NFFT
+
+3. in a terminal do
+./bootstrap
+./configure --with-matlab=MATLAB_DIR --enable-nfsoft --enable-nfsft --enable-openmp --enable-portable-binary 
+make
+
+4. copy the following files into this directory
+nfft/matlab/nfsoft/nfsoftmex.mex* 
+nfft/matlab/nfsoft/nfsftmex.mex* 

geometry/@quaternion/Euler.m

@@ -110,11 +110,7 @@
 elseif check_option(varargin,'nfft')
 
   alpha = fft_rho(alpha);
-  if getMTEXpref('nfft_bug')
-    beta  = fft_theta(-beta);
-  else
-    beta  = fft_theta(beta);
-  end
+  beta  = fft_theta(beta);
   gamma = fft_rho(gamma);
   varargout{1} = 2*pi*[alpha(:),beta(:),gamma(:)].';
 

mex/.gitignore

@@ -0,0 +1 @@
+*.mex*

c/mex/mex_install.m → mex/mex_install.m

@@ -2,18 +2,9 @@ function mex_install(mtexpath,varargin)
 % compiles all mex files for use with MTEX
 
 if nargin == 0, mtexpath = mtex_path;end
-mexpath = fullfile(mtexpath,'c','mex');
+mexpath = fullfile(mtexpath,'mex');
 mexfile = @(file)fullfile(mexpath,file);
 
-% check whether to set largeArrayDims option
-if nargin <= 2 && newer_version(7.3)
-  if strfind(computer,'64')
-    varargin = {'-largeArrayDims'};
-  else
-    varargin = {'-compatibleArrayDims'};
-  end
-end
-
 places = strcat({'S1Grid','S2Grid','SO3Grid'}, '_*.c');
 
 % compile all the files
@@ -22,9 +13,9 @@ function mex_install(mtexpath,varargin)
   files = {files.name};
   for f = 1:length(files)
     if exist(mexfile(files{f}),'file')
-      disp(['... compile ',files{f}]);
+      disp(['... compiling ',files{f}]);
       try
-        mex(varargin{:},'-outdir',mexfile(getMTEXpref('architecture')),mexfile(files{f}));
+        mex('-largeArrayDims',mexfile(files{f}));
       catch %#ok<CTCH>
         disp(['Compiling ' mexfile(files{f}) ' failed!']);
       end      

startup_mtex.m

@@ -6,7 +6,6 @@ function startup_mtex(varargin)
 % mtex_settings.m in this directory.
 %
 
-
 % this is a bugfix for MATLAB having very high cpu load on idle
 if isunix && ~ismac
   try
@@ -16,7 +15,6 @@ function startup_mtex(varargin)
   end
 end
 
-
 % Check MATLAB version
 % --------------------
 lasterr('') %#ok<LERR> %reset all errors
@@ -153,7 +151,7 @@ function do_install(local_path)
 % set MTEX search path
 function setMTEXPath(local_path)
 
-exclPath = {'c','data','help','templates'};
+exclPath = {'c','data','help','templates','nfft'};
 
 if ~MATLABverLessThan('8.1')
   exclPath = [exclPath,'8.4'];

tools/misc_tools/check_installation.m

@@ -1,164 +1,77 @@
 function check_installation
 % check whether all binaries are working properly
 
-% check tmp dir
-if strfind(getMTEXpref('tempdir',tempdir),' ')
-  hline()
-  disp('Warning: The path MTEX uses for temporary files');
-  disp(['  tempdir = ''' getMTEXpref('tempdir') '''']);
-  disp('contains white spaces!');
-  disp(['Please change this in your <a href="matlab:edit mtex_settings.m">' ...
-    'mtex_settings.m</a>!']);
+% check nfft
+if ~check_nfft
+
+  rmpath([mtex_path filesep 'extern' filesep 'nfft_openMP'])
+  addpath([mtex_path filesep 'extern' filesep 'nfft'])
+
   hline()
-end
-
-% check binaries
-check_binaries;
-
-% check mex binaries
-check_mex;
+  if check_nfft
+
+    disp(' ');
+    disp('  MTEX: Error running NFFT with openmp - I''m going to use it without openmp!');
+
+  else
 
-% check for nfft bug
-setMTEXpref('nfft_bug',0);
-try
-  setMTEXpref('nfft_bug',~checkNfftBug);
-catch
+    disp(' ');
+    disp('  MTEX: Error running NFFT!');
+    disp('   ');
+    disp('  The original error message was:');
+    e = lasterror;
+    disp(['  ' e.message]);
 
+    disp(' ');
+    disp('  Try to compile the binaries or contact author for help!');
+
+  end
+  hline()
 end
-
+
+% check mex 
+check_mex;
 
 end
 
-% ------------ check for binaries --------------------------
-function check_binaries
 
-% check binaries do exist
-fast_check_binaries;
+% -------- check nfft
 
-[th,rh] = polar(equispacedS2Grid('points',10));
-
-th = fft_theta(th);
-rh = fft_rho(rh);
-
-gh = [reshape(rh,1,[]);reshape(th,1,[])];
-r = [reshape(rh,1,[]);reshape(th,1,[])];
-
-c = ones(size(th));
-
-Al = ones(size(th));
-setpref('mtex','binaries',false);
+function e = check_nfft
 
+e = 0;
 try
-
-  f = call_extern('odf2pf','EXTERN',gh,r,c,Al);
-  assert(any(f));
-
-  setpref('mtex','binaries',true);
-
-catch %#ok<*CTCH>
+  % check NFSFT
+  f = @(x) x.theta;
+  sF = S2FunHarmonic.quadrature(f,'bandwidth',12);
+  assert(abs(f(xvector) - sF.eval(xvector))<1e-5);
 
-  if ismac && strcmp(getMTEXpref('architecture'),'maci') % maybe it is a 64 bit mac
-    try
-      setMTEXpref('architecture','maci64');
-      f = call_extern('odf2pf','EXTERN',gh,r,c,Al);
-      assert(any(f));
-      setpref('mtex','binaries',true);
-      return
-    catch
-      setMTEXpref('architecture','maci');
-    end
-  end
-
-  hline()
-  disp('  MTEX binary check failed!');
-  disp(' ');
-  disp('  The original error message was:');
-  e = lasterror; %#ok<*LERR>
-  disp(['  ',e.message]);
-
-  disp(' ');
-  disp('  Check the following options:');
-  disp(['  * ' doclink('compilation','Compile') ' the binaries yourself.']);
-  disp('  * Ask the maintainer for help!');
-  hline()
+  % check NFSOFT
+  ori = orientation.rand(100,crystalSymmetry);
+  odf = calcODF(ori,'Fourier','bandwidth',12);
+  odf.eval(ori);
+  e = 1;
 end
-
 end
 
-function fast_check_binaries
-
-if ispc, mtex_ext = '.exe';else mtex_ext = '';end
-binariespath = fullfile(mtex_path,'c','bin',getMTEXpref('architecture'));
-binaries = {'pf2odf','pdf2pf','odf2pf','odf2fc','fc2odf'};
-
-% check for existence
-for k=1:numel(binaries)
-  prg = fullfile(binariespath,binaries{k});
-  if ~exist([prg mtex_ext],'file'),
-    warning(['missing binary ' binaries{k} mtex_ext])
-    return; 
-  end
-end
-
-end
-
-%    ----------- check mex files ---------------------------
+% ----------- check mex files ---------------------------
 function check_mex
 
-% set mex/directory
-mexpath = fullfile(mtex_path,'c','mex',getMTEXpref('architecture'));
-addpath(mexpath,0);
-
 % check for mex files
-if fast_check_mex(mexpath), return;end
+if fast_check_mex, return;end
 
 hline('-');
 disp('Checking mex files failed!');
 
-% check old mex version
-if exist(fullfile(mexpath,'v7.1'),'dir')
-
-  % change path
-  rmpath(mexpath);
-  addpath(fullfile(mexpath,'v7.1'));
-  disp('> Trying now with older version.');
-  if fast_check_mex(mexpath)
-    disp('> Hurray - everythink works!')
-    disp(' ');
-    try
-      copyfile(fullfile(mexpath,'v7.1','*.*'),mexpath,'f');
-      % restore path
-      rmpath(fullfile(mexpath,'v7.1'));
-      addpath(mexpath);
-    catch
-      hline()
-      disp('> Error while copying!')
-      disp('> You should copy');
-      disp(['  ' fullfile(mexpath,'v7.1')]);
-      disp(' to ');
-      disp(['  ', mexpath]);
-      disp('> before starting the next session');
-      hline()
-      disp(' ');
-    end
-    return
-  else
-    disp('> Checking old mex files failed!');
-    % restore path
-    rmpath(fullfile(mexpath,'v7.1'));
-    addpath(mexpath);
-  end
-end
-
 disp('> Trying now to recompile mex files.');
 opwd = pwd;
-cd(fullfile(mtex_path,'c','mex'));
+cd(fullfile(mtex_path,'mex'));
 mex_install(mtex_path,false);
 cd(opwd);
 
-if ~fast_check_mex(mexpath)
-  %   disp('> Hurray - everythink works!')
-  % else
+if fast_check_mex
+  disp('> Hurray - everythink works!')
+else
   hline()
   disp('  MTEX: Couldn''t get the mex files working!');
   disp('   ');
@@ -175,16 +88,17 @@
 
 % ----------------------------------------------------------------------
 
-function e = fast_check_mex(mexpath)
+function e = fast_check_mex
 
 e = false;
+mexpath = [mtex_path filesep 'mex'];
 
-% check for existence
+% check for existence of the files
 mex = {'quaternion_*','S1Grid_*','S2Grid_*','SO3Grid_*'};
 for k=1:numel(mex)
-  cfile = dir(fullfile(mexpath,'..', [mex{k} '.c']));
+  cfile = dir(fullfile(mexpath, [mex{k} '.c']));
   for c=1:numel(cfile)
-    [a,cname] = fileparts(cfile(c).name);
+    [~,cname] = fileparts(cfile(c).name);
     mexfile = fullfile(mexpath, [cname,'.' mexext]);
     if ~exist(mexfile,'file')
        warning(['missing mex-file ' [cname,'.' mexext]])
@@ -203,51 +117,6 @@
 
 end
 
-% --------------------------------------------------------------
-
-function out = checkNfftBug
-
-  % set bandwidth
-  L = 2;
-
-  % set an orientation
-  q = axis2quat(xvector+yvector,25*degree);
-
-  % set a direction
-  h = vector3d(1,2,3);
-
-  % convert to export parameters
-  g = Euler(q,'nfft');
-
-  % set parameters
-  c = 1;
-  A = ones(1,L+1);
-
-  % run NFSOFT
-  D = call_extern('odf2fc','EXTERN',g,c,A); % conjugate(D)
-
-  % extract result
-  D = complex(D(1:2:end),D(2:2:end));
-
-  l = 1;
-
-  % rotate spherical harmonics manualy
-  Y = sphericalY(l,h).'; % -> Y
-  gY = sphericalY(l,q*h).'; % -> rotated Y
-
-  % rotate spherical harmonics by matrix D
-  D3 = reshape(D(2:10),3,3);
-
-  TY = D3 * Y;
-
-  % check whether spherical Y are rotated correctly by D
-  out = sqrt(norm(TY - gY)) < 0.001;
-
-end
-
-
-% -----------------------------------------------------------------------
-
 
 function hline(st)