Merge pull request #285 from ralfHielscher/develop

merge MTEX 4.5.2 from develop

EBSDAnalysis/@EBSD/KAM.m

@@ -23,8 +23,9 @@
 % Options
 %  threshold - ignore misorientation angles larger then threshold
 %  order     - consider neighbors of order n
+%  max       - take not the mean but the maximum misorientation angle
 %
-% See alo
+% See also
 % grain2d.GOS
 
 % compute adjacent measurements
@@ -76,4 +77,9 @@
 % compute kernel average misorientation
 kam = sparse(Dl(ind),Dr(ind),omega(ind)+0.00001,length(ebsd),length(ebsd));
 kam = kam+kam';
-kam = reshape(full(sum(kam,2)./sum(kam>0,2)),size(ebsd));
+
+if check_option(varargin,'max')
+  kam = reshape(full(max(kam,2)),size(ebsd));
+else
+  kam = reshape(full(sum(kam,2)./sum(kam>0,2)),size(ebsd));
+end

EBSDAnalysis/@EBSD/calcGrains.m

@@ -1,5 +1,5 @@
 function [grains,grainId,mis2mean] = calcGrains(ebsd,varargin)
-% 2d and 3d construction of GrainSets from spatially indexed EBSD data
+% grains reconstruction from 2d EBSD data
 %
 % Syntax
 %   grains = calcGrains(ebsd,'angle',10*degree)
@@ -9,7 +9,7 @@
 %  ebsd   - @EBSD
 %
 % Output
-%  grains  - @Grain2d | @Grain3d
+%  grains  - @grain2d
 %
 % Options
 %  threshold|angle - array of threshold angles per phase of mis/disorientation in radians
@@ -19,7 +19,7 @@
 %  unitcell     - omit voronoi decomposition and treat a unitcell lattice
 %
 % See also
-% GrainSet/GrainSet
+% 
 
 % subdivide the domain into cells according to the measurement locations,
 % i.e. by Voronoi teselation or unit cell
@@ -68,7 +68,7 @@
 for k = 1:numel(doMeanCalc)
 
   qind = subSet(q,d(grainRange(doMeanCalc(k))+1:grainRange(doMeanCalc(k)+1)));
-  mq = mean(qind);
+  mq = mean(qind,'robust');
   meanRotation = setSubSet(meanRotation,doMeanCalc(k),mq);
   GOS(doMeanCalc(k)) = mean(angle(mq,qind));
 

EBSDAnalysis/@EBSD/findByLocation.m

@@ -16,7 +16,7 @@
 %   g = findByLocation(ebsd,p)
 %
 % See also
-% EBSD/findByLocation GrainSet/findByOrientation
+% EBSD/findByLocation grain2d/findByOrientation
 
 if all(isfield(ebsd.prop,{'x','y','z'}))
   x_D = [ebsd.prop.x,ebsd.prop.y,ebsd.prop.z];

EBSDAnalysis/@EBSD/findByOrientation.m

@@ -1,5 +1,5 @@
 function ebsd = findByOrientation(ebsd,q0,epsilon)
-% select grains by orientation
+% select ebsd data by orientation
 %
 % Input
 %  ebsd    - @EBSD
@@ -10,7 +10,7 @@
 %  ebsd - @EBSD
 %
 % See also
-% EBSD/findByLocation GrainSet/findByOrientation
+% EBSD/findByLocation grain2d/findByOrientation
 
 ind  = find(ebsd.orientations,q0,epsilon);
 

EBSDAnalysis/@EBSD/private/gbc_custom.m

@@ -0,0 +1,7 @@
+function criterion = gbc_custom(ori,CS,Dl,Dr,varargin)
+% blue print for a self defined grain boundary criterion
+
+% check whether the two ebsd measurements are seperated by a grain boundary
+custom = get_option(varargin,'custom');
+delta = get_option(varargin,'delta');
+criterion = abs(custom(Dl)-custom(Dr)) < delta;

EBSDAnalysis/@EBSD/private/plotUnitCells.m

@@ -17,9 +17,9 @@
   obj.FaceVertexCData = reshape(d,size(xy,1),[]);
   %if size(d,2) == 3, set(get(ax,'parent'),'renderer','opengl');end
 
-  if check_option(varargin,{'transparent','translucent'})
+  if check_option(varargin,{'transparent','translucent','faceAlpha'})
 
-    s = get_option(varargin,{'transparent','translucent'},1,'double');
+    s = get_option(varargin,{'transparent','translucent','faceAlpha'},1,'double');
 
     if size(d,2) == 3 % rgb
       obj.FaceVertexAlphaData = s.*(1-min(d,[],2));

EBSDAnalysis/@EBSD/subsasgn.m

@@ -35,6 +35,8 @@
       ebsd.id = subsasgn(ebsd.id,s(1),[]);
       ebsd.phaseId = subsasgn(ebsd.phaseId,s(1),[]);      
 
+      ebsd = EBSD(ebsd)
+
     elseif ischar(b)
 
       phId = find(strcmpi(b,ebsd.mineralList),1);

EBSDAnalysis/@EBSDsquare/calcGND.m

@@ -1,4 +1,4 @@
-function gnd = calcGND(ebsd,varargin)
+function [gnd,rho] = calcGND(ebsd,varargin)
 % compute the geometrically necessary dislocation
 %
 % Formulae are taken from the paper:

EBSDAnalysis/@grain2d/cat.m

@@ -1,13 +1,13 @@
 function grains = cat(dim,varargin)
-% concatenation of grains from the same GrainSet
+% implements [grain1, grain2]
 %
 % Syntax
 %   g = [grains_1, grains_2, grains_n]
 %   g = [grains('fe') grains('mg')]
 %   g = [grains(1:100) grains(500:end)]
 %
 % See also
-% GrainSet/vertcat
+% grain2d/vertcat
 
 grains = cat@dynProp(1,varargin{:});
 

EBSDAnalysis/@grain2d/findByLocation.m

@@ -16,7 +16,7 @@
 %  hold on, plot(grains(id).boundary,'linecolor','r','lineWidth',2), hold off
 %
 % See also
-% EBSD/findByLocation GrainSet/findByOrientation
+% EBSD/findByLocation grain2d/findByOrientation
 
 poly = grains.poly;
 

EBSDAnalysis/@grain2d/findByOrientation.m

@@ -5,15 +5,15 @@
 %   g = findByOrientation(grains,ori,epsilon);
 %
 % Input
-%  grains - @GrainSet
+%  grains - @grain2d
 %  q0 - @quaternion | @rotation | @orientation 
 %  epsilon - searching radius
 %
 % Output
-%  grains - @GrainSet
+%  grains - @grain2d
 %
 % See also
-% EBSD/findByLocation GrainSet/findByOrientation
+% EBSD/findByLocation grain2d/findByOrientation
 
 ind = find(grains.meanOrientation,q0,epsilon);
 

EBSDAnalysis/@grain2d/neighbors.m

@@ -2,7 +2,7 @@
 % returns the number of neighboring grains
 %
 % Input
-%  grains - @GrainSet
+%  grains - @grain2d
 %
 % Output
 %  counts - number of neighbors per grain

EBSDAnalysis/@grain2d/plot.m

@@ -168,8 +168,8 @@
     obj.Faces(k,1:s(k)) = Faces( cs(k)+1:cs(k+1) );
   end
 
-  if check_option(varargin,{'transparent','translucent'})
-    s = get_option(varargin,{'transparent','translucent'},1,'double');
+  if check_option(varargin,{'transparent','translucent','FaceAlpha'})
+    s = get_option(varargin,{'transparent','translucent','FaceAlpha'},1,'double');
     dg = obj.FaceVertexCData;
     if size(d,2) == 3 % rgb
       obj.FaceVertexAlphaData = s.*(1-min(dg,[],2));

EBSDAnalysis/@grain2d/subSet.m

@@ -2,11 +2,11 @@
 % 
 %
 % Input
-%  grains - @grainSet
+%  grains - @grain2d
 %  ind    - 
 %
 % Ouput
-%  grains - @grainSet
+%  grains - @grain2d
 %
 
 % restrict boundary

EBSDAnalysis/@grain2d/subsref.m

@@ -1,12 +1,16 @@
 function varargout = subsref(grains,s)
-% access subsets of a GrainSet
+% implements grains(1:3)
 %
 % Syntax
-%   grains(1:10)          % the 10 first grains of a GrainSet
-%   grains('Fe')          % only Fe grains
+%   grains(1:10)            % the 10 first grains
+%   grains('Fe')            % only Fe grains
 %   grains( ~grains('fe') ) % all grains but Fe
-%                           logical array with size of the complete
-%                           GrainSet
+%   grains(cond)        
+%
+% Input
+%  grains - @grain2d
+%  cond   - logical array with same size as grains
+%
 
 if strcmp(s(1).type,'()')
 

EBSDAnalysis/@grain2d/text.m

@@ -15,7 +15,8 @@
 
 xy = grains.centroid;
 
-h = optiondraw(text(xy(:,1),xy(:,2),txt),varargin{:});
+h = optiondraw(text(xy(:,1),xy(:,2),txt,...
+  'HorizontalAlignment','center','VerticalAlignment','middle'),varargin{:});
 
 if nargout == 0, clear h; end
 

EBSDAnalysis/@grainBoundary/grainBoundary.m

@@ -92,9 +92,9 @@
       gB.misrotation(isNotBoundary) = ...
         inv(ebsd.rotations(gB.ebsdId(isNotBoundary,2))) ...
         .* ebsd.rotations(gB.ebsdId(isNotBoundary,1));
-      
+
       % compute triple points
-      gB.triplePoints = gB.calcTriplePoints(grainsPhaseId);      
+      gB.triplePoints = gB.calcTriplePoints(grainsPhaseId);
 
     end
 

EBSDAnalysis/@grainBoundary/plot.m

@@ -17,11 +17,118 @@
 %  linecolor
 %
 
-
 % create a new plot
 [mtexFig,isNew] = newMtexFigure(varargin{:});
 mP = newMapPlot('scanUnit',gB.scanUnit,'parent',mtexFig.gca,varargin{:});
 
+if get_option(varargin,'linewidth',0) > 3 || check_option(varargin,'smooth')
+  plotOrdered(gB,varargin{:});
+else
+  plotSimple(gB,varargin{:});
+end
+
+% if no DisplayName is set remove patch from legend
+if ~check_option(varargin,'DisplayName')
+  set(get(get(h,'Annotation'),'LegendInformation'),'IconDisplayStyle','off');
+else
+  legend('-DynamicLegend','location','NorthEast');
+end
+
+try axis(mP.ax,'tight'); end
+mP.micronBar.setOnTop
+
+if nargout == 0, clear h; end
+if isNew, mtexFig.drawNow('figSize',getMTEXpref('figSize'),varargin{:}); end
+mtexFig.keepAspectRatio = false;
+
+function plotOrdered(gB,varargin)
+
+% add a nan vertex at the end - patch should not close the faces
+V = [gB.V;nan(1,2)];
+
+% extract the edges
+F = gB.F;
+
+% detect where the edges are not consistent
+breaks = F(2:end,1) ~= F(1:end-1,2);
+
+% generate a new list of edges
+% which has a nan pointer at every point of inconsistency
+% first a full list of nan pointers
+FF = size(V,1) * ones(size(F,1) + sum(breaks),2);
+
+% insert the edges at the right positions
+newpos = (1:length(breaks)+1).' + cumsum([0;breaks]);
+FF(newpos,:) = F;
+
+% remove duplicated
+F = reshape(FF.',[],1);
+dF = [true;diff(F)~=0];
+F = F(dF);
+
+% extract x and y values
+x = V(F,1).';
+y = V(F,2).';
+
+% color given by second argument
+if nargin > 1 && isnumeric(varargin{1}) && ...
+    (size(varargin{1},1) == length(gB) || size(varargin{1},2) == length(gB))
+
+  if size(varargin{1},1) ~= length(gB), varargin{1} = varargin{1}.'; end
+  data = reshape(varargin{1},length(gB),[]);
+
+  alpha = 0.01;
+
+  % for colorizing the segments with different colors we have to make a lot
+  % of efford
+  % 1. colors are asigned to vertices in Matlab not to edges
+  % 2. therefore we replace every vertex by two vertices 
+  x = repelem(x,1,2);
+  x(1) = []; x(end)=[];
+  xx = x;
+  x(2:2:end-1) = (1-alpha)*xx(2:2:end-1) + alpha*xx(1:2:end-2);
+  x(3:2:end-1) = (1-alpha)*xx(3:2:end-1) + alpha*xx(4:2:end);
+  x(end+1) = NaN;
+
+  y = repelem(y,1,2);
+  y(1) = []; y(end)=[];
+  yy = y;
+  y(2:2:end-1) = (1-alpha)*yy(2:2:end-1) + alpha*yy(1:2:end-2);
+  y(3:2:end-1) = (1-alpha)*yy(3:2:end-1) + alpha*yy(4:2:end);
+  y(end+1) = NaN;
+
+  % align the data
+  data = repelem(data,2,1);
+  color = nan(length(y),size(data,2));
+  color(~isnan(y),:) = data;
+
+  % plot the line
+  p = patch('XData',x(:),'YData',y(:),'FaceVertexCData',color,...
+    'faceColor','none','hitTest','off','parent',...
+    mP.ax,'EdgeColor','interp');
+
+  % this makes the line connectors more nice
+try
+  pause(0.01)
+  e = p.Edge;
+  e.LineJoin = 'round';
+end
+
+else % color given directly
+
+  color = get_option(varargin,{'linecolor','edgecolor','facecolor'},'k');
+
+  %p = patch(x,y,'r','faceColor','none','hitTest','off','parent',mP.ax,'EdgeColor',color);
+  p = line(x,y,'hitTest','off','parent',mP.ax,'color',color,'lineJoin','round');
+
+end
+
+h = optiondraw(p,varargin{:});
+
+end
+
+
+function plotSimple(gB,varargin)
 obj.Faces    = gB.F;
 obj.Vertices = gB.V;
 obj.parent = mP.ax;
@@ -52,17 +159,6 @@
 
 h = optiondraw(patch(obj),varargin{:});
 
-% if no DisplayName is set remove patch from legend
-if ~check_option(varargin,'DisplayName')
-  set(get(get(h,'Annotation'),'LegendInformation'),'IconDisplayStyle','off');
-else
-  legend('-DynamicLegend','location','NorthEast');
 end
 
-
-try axis(mP.ax,'tight'); end
-mP.micronBar.setOnTop
-
-if nargout == 0, clear h; end
-if isNew, mtexFig.drawNow('figSize',getMTEXpref('figSize'),varargin{:}); end
-mtexFig.keepAspectRatio = false;
+end