Merge remote-tracking branch 'origin/develop'

EBSDAnalysis/@EBSD/calcTensor.m

@@ -38,9 +38,10 @@
 
 % initialize avarage tensors
 TVoigt = T{1};
-TVoigt.M = zeros(repmat(3,1,TVoigt.rank));
 TVoigt.CS = specimenSymmetry;
-TReuss = TVoigt;
+TReuss = inv(TVoigt);
+TVoigt.M = zeros(repmat(3,1,TVoigt.rank));
+TReuss.M = zeros(repmat(3,1,TReuss.rank));
 
 % get phases and populate tensors
 phases = unique(ebsd.phaseId)';

EBSDAnalysis/@EBSD/plot.m

@@ -79,7 +79,12 @@
 
   h = plotUnitCells([ebsd.prop.x(:), ebsd.prop.y(:)],...
     property, ebsd.unitCell, 'parent', mP.ax, varargin{:});
-
+
+elseif nargin>1 && isa(varargin{1},'crystalShape')
+
+  cS = varargin{1};
+  plot(ebsd.prop.x,ebsd.prop.y,zUpDown * cS.diameter,ebsd.orientations * cS,varargin{2:end});
+
 else % phase plot
 
   for k=1:numel(ebsd.phaseMap)

EBSDAnalysis/@EBSD/subsasgn.m

@@ -35,7 +35,7 @@
       ebsd.id = subsasgn(ebsd.id,s(1),[]);
       ebsd.phaseId = subsasgn(ebsd.phaseId,s(1),[]);      
 
-      ebsd = EBSD(ebsd)
+      ebsd = EBSD(ebsd);
 
     elseif ischar(b)
 

EBSDAnalysis/@EBSDsquare/smooth.m

@@ -102,5 +102,8 @@
 
 % store to EBSD variable
 ebsd.rotations = rot;
+
+% set nan rotations to not indexed
+ebsd.phaseId(isnan(rot(:))) = 1;
 
 end

EBSDAnalysis/@grain2d/area.m

@@ -5,7 +5,7 @@
 %  grains - @grain2d
 %
 % Output
-%  A  - list of areas
+%  A  - list of areas (in measurement units)
 %
 
 A = zeros(length(grains.poly),1);

EBSDAnalysis/@grain2d/diameter.m

@@ -1,5 +1,5 @@
 function [d] = diameter(grains)
-% diameter of a grain 
+% diameter of a grain in measurement units
 % longest distance between any two vertices of the grain boundary
 
 % do extract this as it is much faster

EBSDAnalysis/@grain2d/equivalentPerimeter.m

@@ -11,8 +11,7 @@
 % Input
 %  grains - @grain2d
 %
-% Output
-%  p   - perimeter
+% Output (in measurement units)
 %
 % See also
 % grain2d/deltaarea grain2d/paris grain2d/equivalentRadius

EBSDAnalysis/@grain2d/equivalentRadius.m

@@ -11,7 +11,7 @@
 %  grains - @grain2d
 %
 % Output
-%  r  - radius
+%  r  - radius (in measurement units)
 %
 % See also
 % grain2d/deltaarea grain2d/equivalentPerimeter grain2d/paris

EBSDAnalysis/@grain2d/grain2d.m

@@ -121,6 +121,7 @@
 
     function grains = set.V(grains,V)
       grains.boundary.V = V;
+      grains.innerBoundary.V = V;
 
       % update V in triple points
       tP = grains.triplePoints;

EBSDAnalysis/@grain2d/hist.m

@@ -1,34 +1,59 @@
-function hist(grains,varargin)
+function [binId, cumArea] = hist(grains,varargin)
+% plot a grain size histogram
 %
+% Syntax
+%   hist(grains)
+%   hist(grains,n) % specify the number of bins
 %
+%   % use an arbitrary property for the histogramm
+%   hist(grains,grains.equivalentRadius) 
+%
+%   binId = hist(grains) % returns the bin for each grain
+%    
+% Input
+%   grains - @grain2d
+%   n      - number of bins, default ist 15
+%   
 
 [mtexFig,isNew] = newMtexFigure(varargin{:});
 mtexFig.keepAspectRatio = false;
 
-if nargin>1 && isnumeric(varargin{1})
+% exract area and maybe an aditional property
+area = grains.area;
+if nargin>1 && isnumeric(varargin{1}) && length(varargin{1}) == length(grains)
+  prop = varargin{1};
+  varargin(1) = [];
+else
+  prop = area;
+end
+
+if ~isempty(varargin) && isnumeric(varargin{1})
   nbins = varargin{1};
 else
   nbins = 15;
 end
 
-area = grains.area;
 idList = grains.indexedPhasesId;
 
-bins = linspace(0,max(area)+eps,nbins);
+bins = linspace(0,max(prop)+eps,nbins);
 
 cumArea = zeros(numel(bins)-1,numel(idList));
+binId = zeros(length(grains),1);
 
+% loop through all phases
 for id = 1:numel(idList)
 
-  phaseArea = area(grains.phaseId==idList(id));
+  phaseId = grains.phaseId==idList(id);
+  phaseArea = area(phaseId);
+  phaseProp = prop(phaseId);
 
   % find for each area the binId
-  [tmp,binId] = histc(phaseArea,bins);
-
-  % compute the sum of areas belonging to the same bin
+  [~,binIdLocal] = histc(phaseProp,bins);
+  binId(phaseId) = binIdLocal;
 
+  % compute the sum of areas belonging to the same bin
   for i = 1:numel(bins)-1
-    cumArea(i,id) = sum(phaseArea(binId == i)) ./ sum(area);
+    cumArea(i,id) = sum(phaseArea(binIdLocal == i)) ./ sum(area);
   end
 
 end
@@ -46,3 +71,5 @@ function hist(grains,varargin)
 legend(min{:})
 
 if isNew, mtexFig.drawNow(varargin{:});end
+
+if nargout == 0, clear binId; end

EBSDAnalysis/@grain2d/perimeter.m

@@ -11,7 +11,7 @@
 %  grains - @grain2d
 %
 % Output
-%  peri - perimeter
+%  peri - perimeter (in measurement units)
 %
 % See also
 % grain2d/equivalentPerimeter

EBSDAnalysis/@grain2d/plot.m

@@ -10,6 +10,10 @@
 %
 %  PatchProperty - see documentation of patch objects for manipulating the
 %                 apperance, e.g. 'EdgeColor'
+% Options
+%  noBoundary  - do not plot boundaries 
+%  displayName - name used in legend
+%
 % See also
 % EBSD/plot grainBoundary/plot
 
@@ -36,6 +40,12 @@
   disp('  plot(oM)')
 end
 
+plotBoundary = true;
+% allow to plot grain faces only without boundaries
+if check_option(varargin,'noBoundary')
+plotBoundary = false;
+end
+
 % numerical data are given
 if nargin>1 && isnumeric(varargin{1})
 
@@ -46,6 +56,16 @@
 
   % plot polygons
   h = plotFaces(grains.poly,grains.V,property,'parent', mP.ax,varargin{:});
+
+elseif nargin>1 && isa(varargin{1},'crystalShape')
+
+  scaling = sqrt(grains.area);
+  xy = [grains.centroid,scaling*zUpDown];
+
+  h = plot(xy + scaling .* (rotate(varargin{1},grains.meanOrientation)),...
+    'parent', mP.ax,varargin{:});
+
+  plotBoundary = false;
 
 elseif check_option(varargin,'FaceColor')
 
@@ -83,11 +103,13 @@
 end
 
 % we have to plot grain boundary individually
-hold on
-hh = plot(grains.boundary,varargin{:});
-set(get(get(hh,'Annotation'),'LegendInformation'),'IconDisplayStyle','off');
-hold off
-
+if plotBoundary
+  hold on
+  hh = plot(grains.boundary,varargin{:});
+  set(get(get(hh,'Annotation'),'LegendInformation'),'IconDisplayStyle','off');
+  hold off
+end
+
 if check_option(varargin,'DisplayName') 
   legend('-DynamicLegend','location','NorthEast');
 end

EBSDAnalysis/@grain2d/smooth.m

@@ -1,11 +1,22 @@
 function grains = smooth(grains,iter,varargin)
-% constraint laplacian smoothing of grains
+% constraint laplacian smoothing of grain boundaries 
+% and inner boundaries.
 %
+% Input
+%  grains - @grain2d
+%  iter   - number of iterations (optional, default: 1)
+%
+% Output
+%  grains - @grain2d
+%
+% Options
+%  'gauss','exp','umbrella' or 'rate' - interpoaltion methods (default: 'rate')
+%  second_order, S2 - second order smoothing
 
 if nargin < 2 || isempty(iter), iter = 1; end
 
 % compute incidence matrix vertices - faces
-I_VF = grains.boundary.I_VF;
+I_VF = [grains.boundary.I_VF,grains.innerBoundary.I_VF];
 
 % compute vertice adjacency matrix
 A_V = I_VF * I_VF';

EBSDAnalysis/EBSDSmoothing/EBSDFilter.m

@@ -1,6 +1,7 @@
 classdef EBSDFilter < handle
 % abstract class for denoising EBSD data
-
+%
+
   methods (Abstract = true)
     q = smooth(q,varargin)
   end

Makefile

@@ -1,66 +1,7 @@
-# Makefile of the MTEX toolbox
-#
-#--------------- begin editable section -------------------------------
-#
-# here comes your operating system
-# glnx86  - 32 bit Linux
-# glnxa64 - 64 bit Linux
-# maci    - 32 bit Mac OSX
-# maci64  - 64 bit Mac OSX
-# win32   - 32 bit Windows
-# win64   - 64 bit Windows
-#
-TARGET= glnxa64
-#
-# please correct the following installation directories:
-#
-# path to FFTW, i.e. to libfftw3.a
-FFTW_LIB_PATH = /usr/lib/x86_64-linux-gnu/
-# path to FFTW header file, i.e., to fftw3.h
-FFTW_H_PATH = /usr/include/
-#
-# path to NFFT, i.e. to libnfft3.a
-NFFT_LIB_PATH = /usr/local/lib
-# path the NFFT header file, i.e., to nfft.h
-NFFT_H_PATH = /usr/local/include/
-#
-# matlab path
-MATLABPATH = /opt/matlab
-#
-# compiler flags
-CFLAGS= -c -O3 -Wall -fomit-frame-pointer -fstrict-aliasing -ffast-math -mfpmath=sse,387 -mieee-fp -m3dnow -mmmx -msse -msse2
-LDFLAGS= -lm #-lpthread
-# MEX flags
-# for 32 bit systems set
-#MEXFLAGS=-$(TARGET) -compatibleArrayDims
-# for 64 bit systems set
-MEXFLAGS=-$(TARGET) -largeArrayDims
-#
-#--------------- end editable section ---------------------------------
-#
-# local directories
-BPATH = c/bin/$(TARGET)/
-SUBDIRS = c/kernel.dir c/test.dir c/mex.dir
-
-
-# top-level rule, to compile everything.
-all: $(SUBDIRS)
-
-
-# descent into subdirectories
-%.dir:
-	$(MAKE) -e CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" NFFT_LIB_PATH=$(NFFT_LIB_PATH) NFFT_H_PATH=$(NFFT_H_PATH) FFTW_LIB_PATH=$(FFTW_LIB_PATH) FFTW_H_PATH=$(FFTW_H_PATH) MATLABPATH=$(MATLABPATH) MEXFLAGS="$(MEXFLAGS)" TARGET="$(TARGET)" -C $*
-	$(MAKE) TARGET="$(TARGET)" install -C $*
-
-
-# rule for cleaning re-compilable files.
-clean:
-# rm -f c/bin/*
-	find . -name '*~' -or -name '*.log' -or -name '.directory' -or -name '*.o' -or -name '*.mex*' | xargs /bin/rm -rf
 
 
 # rule for making release
-RNAME = mtex-4.5.2
+RNAME = mtex-5.0.0
 RDIR = ../releases
 release:
 	rm -rf $(RDIR)/$(RNAME)*
@@ -69,26 +10,10 @@ release:
 	chmod -R a+rX $(RDIR)/$(RNAME)
 	rm -rf $(RDIR)/$(RNAME)/.git
 	rm -rf $(RDIR)/$(RNAME)/.git*
-  #rm -rf $(RDIR)/$(RNAME)/doc/html/helpsearch/*
+	rm -rf $(RDIR)/$(RNAME)/doc/html/helpsearch*
 	find $(RDIR)/$(RNAME) -name '*~' -or -name '*.log' -or -name '*.o' -or -name '*.orig' -or -name '.directory' -or -name '*.mat' | xargs /bin/rm -rf
 	rm -f $(RDIR)/$(RNAME)/c/nsoft/test_nfsoft_adjoint
 	rm -rf $(RDIR)/$(RNAME)/help/html
 	rm -rf $(RDIR)/$(RNAME).zip
 
 	cd $(RDIR); zip -rq  $(RNAME).zip $(RNAME)
-
-windows-binaries:
-	rm -rf ../../mtex-win.tar.gz
-	tar -czvf mtex-win.tar.gz ./c/bin/win32/*.exe `find . -name '*.mexw32'`
-
-linux-binaries:
-	rm -rf ../../mtex-linux.tar.gz
-	tar -czvf ../../mtex-linux.tar.gz ./c/bin/glnx86/* `find . -name '*.mexglx'`
-
-mac-binaries:
-	rm -rf ../../mtex-mac.tar.gz
-	tar -czvf ../../mtex-mac.tar.gz ./c/bin/maci/* `find . -name '*.mexmaci'`
-
-mac64-binaries:
-	rm -rf ../../mtex-mac64.tar.gz
-	tar -czvf ../../mtex-mac64.tar.gz ./c/bin/maci64(* `find . -name '*.mexmaci'`

ODFAnalysis/@BinghamComponent/calcPDF.m

@@ -29,12 +29,8 @@
     c = (A1 .*  A2) * component.kappa;
 
     bc = sqrt(b.^2 + c.^2);
-    if isfinite(C)
-      Z = Z + reshape(exp(a) ./ C .* besseli(0,bc),size(Z));
-    else
-      Z = Z + reshape(call_extern('evalmhyper','INTERN',d,'EXTERN',component.kappa,a,bc),size(Z));
-    end
-
+    Z = Z + reshape(exp(a) ./ C .* besseli(0,bc),size(Z));
+
   end
 end