Merge pull request #1 from ralfHielscher/master

bug fixes for release 4.0

EBSDAnalysis/@EBSD/plot.m

@@ -91,7 +91,7 @@
 
 datacursormode on;
 
-if isNew, mtexFig.drawNow('position','large',varargin{:}); end
+if isNew, mtexFig.drawNow('figSize',getMTEXpref('figSize'),varargin{:}); end
 mtexFig.keepAspectRatio = false;
 
 end

EBSDAnalysis/@grain2d/plot.m

@@ -101,7 +101,7 @@
 
 datacursormode on;
 
-if isNew, mtexFig.drawNow('position','large',varargin{:}); end
+if isNew, mtexFig.drawNow('figSize',getMTEXpref('figSize'),varargin{:}); end
 mtexFig.keepAspectRatio = false;
 
 end

EBSDAnalysis/@grainBoundary/plot.m

@@ -87,5 +87,5 @@
 axis(mP.ax,'tight'); set(mP.ax,'zlim',[0,1]);
 
 if nargout == 0, clear h; end
-if isNew, mtexFig.drawNow('position','large',varargin{:}); end
+if isNew, mtexFig.drawNow('figSize',getMTEXpref('figSize'),varargin{:}); end
 mtexFig.keepAspectRatio = false;

ODFAnalysis/@ODF/plotIPDF.m

@@ -42,7 +42,7 @@ function plotIPDF(odf,r,varargin)
 
 if isNew % finalize plot
 
-  mtexFig.drawNow('Position','auto',varargin{:});
+  mtexFig.drawNow('figSize',getMTEXpref('figSize'),varargin{:});
   setappdata(gcf,'inversePoleFigureDirection',r);
   setappdata(gcf,'CS',odf.CS);
   setappdata(gcf,'SS',odf.SS);

ODFAnalysis/@ODF/plotODF.m

@@ -69,7 +69,7 @@ function plotODF(odf,varargin)
     setappdata(gcf,'h',h);
   end
 
-  mtexFig.drawNow('Position','auto',varargin{:});
+  mtexFig.drawNow('figSize',getMTEXpref('figSize'),varargin{:});
 
 end
 

ODFAnalysis/@ODF/plotPDF.m

@@ -59,7 +59,7 @@ function plotPDF(odf,h,varargin)
   setappdata(gcf,'h',h);
   set(gcf,'Name',['Pole figures of "',inputname(1),'"']);
 
-  mtexFig.drawNow('Position','auto',varargin{:});
+  mtexFig.drawNow('figSize',getMTEXpref('figSize'),varargin{:});
 end
 
 % -------------- Tooltip function ---------------------------------

PoleFigureAnalysis/@PoleFigure/plot.m

@@ -36,5 +36,5 @@ function plot(pf,varargin)
   setappdata(gcf,'CS',pf.CS);
   set(gcf,'Name',['Pole Figures of Specimen ',inputname(1)]);
   set(gcf,'Tag','pdf');
-  mtexFig.drawNow('Position','auto',varargin{:});
+  mtexFig.drawNow('figSize',getMTEXpref('figSize'),varargin{:});
 end

examples/PoleFigureDemo.m

@@ -29,7 +29,7 @@
 
 close;figure('position',[100 100 900 300])
 plot(pf)
-
+colorbar
 
 %% Extract information from imported pole figure data
 %

examples/SeismicsMultiplot.m

@@ -352,7 +352,7 @@
 
 % add colorbars to all plots
 colorbar
-drawNow(gcm,'position','auto')
+drawNow(gcm,'figSize','large')
 
 %%
 %

examples/geometry_demo.m

@@ -27,8 +27,8 @@
 %%
 % *plotting*
 
-close;figure('position',[43   362   300   300])
-plot([v,w],'FontSize',20)
+close all
+plot([v,w])
 
 %% Rotations
 
@@ -47,10 +47,6 @@
 rot \ v
 rot2 = rot * rot
 
-%%
-% *plotting*
-
-scatter([rot rot2])
 
 %%
 % *Basic Functions*
@@ -69,7 +65,9 @@
 SS = specimenSymmetry ('mmm');
 
 % load from a cif file
-loadCIF('quartz')
+CS = loadCIF('quartz')
+
+
 
 %%
 % *Basic Functions*
@@ -81,8 +79,8 @@
 
 %%
 % *plotting*
-set(gcf,'position',[50,50,400,400]);
-plot(CS,'FontSize',15,'antipodal')
+
+plot(CS)
 
 %%
 %
@@ -104,7 +102,7 @@
 eq(h1,h2)
 angle(h1,h2,'antipodal')
 symmetrise(h)
-plot([h1,h2],'all','labeled')
+plot([h1,h2],'all','labeled','backGroundColor','w')
 
 %% Orientations
 

geometry/@DelaunaySO3/DelaunaySO3.m

@@ -1,5 +1,10 @@
 classdef (InferiorClasses = {?rotation,?quaternion}) DelaunaySO3 < orientation
-
+% 
+% Syntax
+%   
+%   % define a Delaunay trinangulation from a list of orientations
+%   DSO3 = DelaunaySO3(ori) 
+%
   properties
 
     tetra          % list of vertices of the tetrahegons

geometry/@crystalSymmetry/plotHKL.m

@@ -32,5 +32,5 @@ function plotHKL(s,varargin)
 % postprocess figure
 setappdata(gcf,'CS',s);
 set(gcf,'tag','ipdf');
-mtexFig.drawNow('position','auto',varargin{:});
+mtexFig.drawNow('figSize',getMTEXpref('figSize'),varargin{:});
 

geometry/@orientation/calcODF.m

@@ -1,44 +1,46 @@
 function odf = calcODF(ori,varargin)
-% calculate ODF from individuel orientations via kernel density estimation
+% computes an ODF from individuel orientations
 %
-% *calcODF* is one of the core function of the MTEX toolbox.
-% It estimates an ODF from a set of individual crystal orientations by
-% <EBSD2odf.html kernel density estimation>.
+% The function *calcODF* applies one of the following algorithms to compute
+% an ODF from a list of orientations.
 %
-% The function *calcODF* has several options to control the halfwidth of
-% the kernel functions, the resolution, etc. Most important the estimated
-% ODF is affected by the *halfwidth* of the kernel function.
-%
-% If the halfwidth is large the estimated ODF is smooth whereas a small halfwidth
-% results in a sharp ODF. It depends on your prior information about the
-% ODF to choose this parameter right. Look at this
-% <EBSDSimulation_demo.html description> for exhausive discussion.
+% # direct kernel density estimation 
+% # kernel density estimation via Fourier series
+% # Bingham estimation
 %
 % Syntax
-%   calcODF(ori)
+%
+%   % use kernel density estimation with a 10 degree kernel
+%   odf = calcODF(ori,'halfwidth',10*degree) 
+%
+%   % use a specific kernel
+%   psi = AbelPoissonKernel('halfwidth',10*degree)
+%   odf = calcODF(ori,'kernel',psi) 
+%
+%   % compute the ODF as a Fourier series of order 16
+%   odf = calcODF(ori,'order',16) 
 %
 % Input
 %  ori  - @orientation
-%  ebsd - @EBSD
 %
 % Output
 %  odf - @ODF
 %
 % Options
-%  HALFWIDTH        - halfwidth of the kernel function
-%  RESOLUTION       - resolution of the grid where the ODF is approximated
-%  KERNEL           - kernel function (default -- de la Valee Poussin kernel)
-%  L/HARMONICDEGREE - (if Fourier) order up to which Fourier coefficients are calculated
+%  halfwidth  - halfwidth of the kernel function
+%  resolution - resolution of the grid where the ODF is approximated
+%  kernel     - kernel function (default -- de la Valee Poussin kernel)
+%  order      - order up to which Fourier coefficients are calculated
 %
 % Flags
-%  SILENT           - no output
-%  EXACT            - no approximation to a corser grid
-%  FOURIER          - force Fourier method
-%  BINGHAM          - model bingham odf
+%  silent           - no output
+%  exact            - no approximation to a corser grid
+%  Fourier          - force Fourier method
+%  Bingham          - model bingham odf
 %  noFourier        - no Fourier method
 %
 % See also
-% ebsd_demo EBSD2odf EBSDSimulation_demo loadEBSD ODF/calcEBSD EBSD/calcKernel kernel/kernel
+% orientation/calcFourierODF orientation/calcKernelODF orientation/calcBinghamODF ebsd_demo EBSD2odf EBSDSimulation_demo 
 
 % Bingham ODF estimation
 if check_option(varargin,'bingham')  

geometry/@orientation/plotIPDF.m

@@ -70,7 +70,7 @@ function plotIPDF(o,varargin)
 end
 
 if isNew
-  mtexFig.drawNow('Position','auto',varargin{:});
+  mtexFig.drawNow('figSize',getMTEXpref('figSize'),varargin{:});
 end
 
 % --------------- Tooltip function ------------------

geometry/@orientation/plotODF.m

@@ -108,6 +108,6 @@ function plotODF(o,varargin)
     setappdata(gcf,'h',h);
   end
 
-  mtexFig.drawNow('Position','auto',varargin{:});
+  mtexFig.drawNow('figSize',getMTEXpref('figSize'),varargin{:});
 end
 

geometry/@orientation/plotPDF.m

@@ -86,7 +86,7 @@ function plotPDF(o,h,varargin)
 
 end
 
-if isNew, mtexFig.drawNow('Position','auto',varargin{:}); end
+if isNew, mtexFig.drawNow('figSize',getMTEXpref('figSize'),varargin{:}); end
 
 % ----------- Tooltip function ------------------------
 function txt = tooltip(varargin)

geometry/@sphericalRegion/sphericalRegion.m

@@ -54,10 +54,10 @@
         sR.N = [sR.N,vector3d('theta',90*degree,'rho',[90*degree+minRho,maxRho-90*degree])];
         sR.alpha = [sR.alpha,0,0];
       end
-
+
+      if check_option(varargin,{'complete','3d'}), sR = sphericalRegion; end
       if check_option(varargin,'upper'), sR = sR.restrict2Upper; end
       if check_option(varargin,'lower'), sR = sR.restrict2Lower; end
-      if check_option(varargin,{'complete','3d'}), sR = sphericalRegion; end
 
     end
 

geometry/@symmetry/plot.m

@@ -57,7 +57,7 @@ function plot(s,varargin)
   set(ax,'xlim',1.1*get(ax,'xlim'));
   set(ax,'ylim',1.1*get(ax,'ylim'));  
 end
-mtexFig.drawNow('position','auto',varargin{:});
+mtexFig.drawNow('figSize',getMTEXpref('figSize'),varargin{:});
 
 hold off
 

geometry/@tensor/plot.m

@@ -108,7 +108,17 @@ function plot(T,varargin)
       end
     end
 
-    [vp,vs1,vs2,pp,ps1,ps2] = velocity(T,S2); %#ok<ASGLU>
+    if isfield(T.opt,'density')
+      rho = T.opt.density;
+    elseif check_option(varargin,'density')
+      rho = get_option(varargin,'density',1);
+    else
+      error(['No density given! For computing wave velocities '...
+        'the material density has to be specified. ' ...
+        'Please use the option ..''density'',value.. to do this.']);
+    end
+
+    [vp,vs1,vs2,pp,ps1,ps2] = velocity(T,S2,rho); %#ok<ASGLU>
     d = eval(get_option(varargin,'velocity','pp','char'));
 
   otherwise
@@ -149,6 +159,6 @@ function plot(T,varargin)
 
 set(gcf,'tag','tensor');
 
-if isNew, mtexFig.drawNow('position','auto',varargin{:}); end
+if isNew, mtexFig.drawNow('figSize',getMTEXpref('figSize'),varargin{:}); end
 
 %plot(S2,'data',d,'antipodal','smooth',varargin{:});

geometry/@tensor/plotS2Grid.m

@@ -0,0 +1,9 @@
+function S2G = plotS2Grid(T,varargin)
+% define a plotting grid suitable for tensor plots
+
+if iseven(T.rank)
+  varargin = [varargin,'antipodal'];
+end
+
+sR = fundamentalSector(T.CS,varargin{:});
+S2G = plotS2Grid(sR,varargin{:});

geometry/@tensor/quiverGrid.m

@@ -0,0 +1,6 @@
+function S2G = quiverGrid(T,varargin)
+
+if iseven(T.rank), varargin = [varargin,'antipodal']; end 
+sR = fundamentalSector(T.CS,varargin{:});
+S2G = equispacedS2Grid('resolution',10*degree,'no_center','antipodal',varargin{:});
+S2G = S2G(sR.checkInside(S2G));

geometry/@tensor/velocity.m

@@ -63,6 +63,6 @@
 
 end
 
-pp = vector3d(pp);
-ps1 = vector3d(ps1);
-ps2 = vector3d(ps2);
+pp = vector3d(pp,'antipodal');
+ps1 = vector3d(ps1,'antipodal');
+ps2 = vector3d(ps2,'antipodal');

geometry/@vector3d/quiver.m

@@ -27,7 +27,7 @@ function quiver(v, d, varargin )
 
   % make the quiver plot
 
-  mhs = get_option(varargin,'MaxHeadSize',0.9);
+  mhs = get_option(varargin,'MaxHeadSize',0.9*d.antipodal);
   arrowSize = get_option(varargin,'arrowSize',0.03);
 
   proj = sP(j).proj;

geometry/@vector3d/scatter.m

@@ -133,7 +133,7 @@
 
   if isappdata(sP(1).parent,'mtexFig')
     mtexFig = getappdata(sP(1).parent,'mtexFig');
-    mtexFig.drawNow('Position','auto',varargin{:});
+    mtexFig.drawNow('figSize',getMTEXpref('figSize'),varargin{:});
   end
 end
 

geometry/@vector3d/subsref.m

@@ -7,7 +7,12 @@
     v.x = subsref(v.x,s(1));
     v.y = subsref(v.y,s(1));
     v.z = subsref(v.z,s(1));
-
+
+    if v.isOption('plot')
+      v.opt = rmfield(v.opt,{'theta','rho','plot','resolution'});
+    end
+
+
     if numel(s)>1
       [varargout{1:nargout}] = builtin('subsref',v,s(2:end));
     else

geometry/@vector3d/vector3d.m

@@ -17,16 +17,21 @@
 
     function v = vector3d(x,y,z,varargin)
       % Constructor
-      % Syntax
-      %  v = vector3d(1,2,3)
       %
+      % Syntax
+      %   v = vector3d(x,y,z)
       %
+      % Input
       %  x,y,z - cart. coordinates
-      %  v     - @vector3d
-      %  empty -> vector3d(0,0,0)
+      %
+      % Flags
+      %   antipodal - consider vector as an axis and not as an direction
+      %
+      % See also
+      % AxialDirectional
 
       if nargin == 0
-      elseif nargin ==1
+      elseif nargin <= 2
         if isa(x,'vector3d') % copy-constructor
           [v.x,v.y,v.z] = double(x);
           v.antipodal = x.antipodal;