diff --git a/6_rendering/gtHexagonalUnitCell.m b/6_rendering/gtHexagonalUnitCell.m
index 8a4862d7cbc74477737a2742eb31d3eca8d0c271..89260cc469f4f6bb4fb2a1f06f883b80c3b17544 100644
--- a/6_rendering/gtHexagonalUnitCell.m
+++ b/6_rendering/gtHexagonalUnitCell.m
@@ -1,6 +1,18 @@
-function vertices = gtHexagonalUnitCell(a,c,draw)
+function data = gtHexagonalUnitCell(varargin)
-% create a hexagonal grid (radius <r>)
+app.centered = true;
+app.draw = true;
+app.ratio = 1.5857;
+app.ind = 0;
+app.vertices = false;
+app.numbers = false;
+app.patch = false;
+app.axes = false;
+
+app = parse_pv_pairs(app, varargin);
+
+c=1;
+a=1/app.ratio;
% apothem = c2 = r*sqrt(3)/2
cx=a*sqrt(3);
@@ -10,83 +22,111 @@ cv=a*cosd(v);
sv=a*sind(v);
x0 = 0*cx+cv;
y0 = 0*cx+sv;
-z0 = repmat(-c/2,1,length(v));
-z1 = repmat(+c/2,1,length(v));
-
+if app.centered
+ z0 = repmat(-c/2,1,length(v));
+ z1 = repmat(+c/2,1,length(v));
+else
+ z0 = zeros(1,length(v));
+ z1 = repmat(c,1,length(v));
+end
vertices = [[x0;y0;z0],[x0;y0;z1]]';
vertices(7,:)=[];
vertices(end,:)=[];
-if draw
+if app.draw
figure;
line(x0,y0,z0);
line(x0,y0,z1);
-
hold on;
- plot3(x0,y0,z0,'r*')
- plot3(x0(1),y0(1),z0(1),'b*')
- plot3(x0,y0,z1,'r*')
- plot3(x0(1),y0(1),z1(1),'b*')
+ if app.vertices
+ plot3(x0,y0,z0,'.k')
+ plot3(x0(1),y0(1),z0(1),'.b')
+ plot3(x0,y0,z1,'.k')
+ plot3(x0(1),y0(1),z1(1),'.b')
+ end
for ii=1:length(x0)
plot3([x0(ii) x0(ii)],[y0(ii) y0(ii)],[z0(ii) z1(ii)], 'b-', 'LineWidth', 1)
end
- % lab system : x y z vectors
- quiver3(-1,0,0,2,0,0,'r');
- quiver3(0,-1,0,0,2,0,'k');
- quiver3(0,0,-1,0,0,2,'b');
- axis equal;
- xlabel('x (100)')
- ylabel('y (010)')
- zlabel('z (001)')
+ quiver3(0,0,z0(1),1,0,0,0,'k')
+ quiver3(0,0,z0(1),-0.5,0.866,0,0,'k')
+ quiver3(0,0,z0(1),-0.5,-0.866,0,0,'k')
+ quiver3(0,0,z0(1),0,0,1+0.4,0,'k')
+ text(1+0.1,0,z0(1),'a1','Color',[0 0 0])
+ text(-0.5-0.1,0.866+0.1,z0(1),'a2','Color',[0 0 0])
+ text(-0.5-0.1,-0.866-0.1,z0(1),'a3','Color',[0 0 0])
+ text(0,0,z1(1)+0.5,'c','Color',[0 0 0])
+ if app.numbers
+ for ii=1:12
+ text(vertices(ii,1),vertices(ii,2),vertices(ii,3)+0.1,num2str(ii),'Color',[0 0 0])
+ end
+ end
+ view(103,20)
+ if app.axes
+ % lab system : x y z vectors
+ quiver3(-1,0,0,2,0,0,0,'r');
+ quiver3(0,-1,0,0,2,0,0,'k');
+ quiver3(0,0,-1,0,0,2,0,'b');
+ xlabel('x')
+ ylabel('y')
+ zlabel('z')
+ end
+end
+
+% hexagon face directions
+% +yz -yz -xz +xz +xy -xy
+% +x -x -y +y +z -z
+faces_sides = [1 2 8 7; 4 5 11 10; 5 6 12 11; 2 3 9 8; 3 4 10 9; 6 1 7 12];
+faces_end = [1 2 3 4 5 6; 7 8 9 10 11 12]; % -
+hkil = [1 0 -1 0; -1 0 1 0; 0 -1 1 0; 0 1 -1 0; -1 1 0 0; 1 -1 0 0; ...
+ 0 0 0 -1; 0 0 0 1]'; % column vectors
+
+if app.draw && app.patch
+ if app.ind >=1 && app.ind <=6
+ patch('Vertices', vertices, 'Faces', faces_sides(app.ind,:), ...
+ 'FaceVertexCData', repmat([0 0.8 0],length(app.ind),1), 'FaceColor', 'flat');
+ elseif app.ind==7 || app.ind==8
+ patch('Vertices', vertices, 'Faces', faces_end(app.ind-6,:), ...
+ 'FaceVertexCData', repmat([0 0.8 0],length(app.ind-6),1), 'FaceColor', 'flat');
+ elseif app.ind==0
+ patch('Vertices', vertices, 'Faces', faces_sides, ...
+ 'FaceVertexCData', repmat([0 0.8 0],6,1), 'FaceColor', 'flat');
+ patch('Vertices', vertices, 'Faces', faces_end, ...
+ 'FaceVertexCData', repmat([0 0.8 0],2,1), 'FaceColor', 'flat');
+ end
end
-%
-%
-% % hexagon made of hexagons
-% figure;
-% axis equal;
-% for f=[1,2] % we test <f>!
-% for a=0:60:360
-% line(f*cx*cosd(a)+cv,f*cx*sind(a)+sv);
-% end
-% if f==2
-% for a=30:60:360
-% line(c2*cx*cosd(a)+cv,c2*cx*sind(a)+sv);
-% end
-% end
-% end
-%
-% xy=unique([x,y],'rows')
-%
-% x=xy(:,1);
-% y=xy(:,2);
-% xx=[];
-% yy=[];
-% for i=1:3
-% p=convhull(x,y);
-% xx=[xx;x(p)]; % quick and dirty!
-% yy=[yy;y(p)];
-% x(p)=[];
-% y(p)=[];
-% end
-% at=atan2(xx,yy);
-% [ax,ax]=sort(at);
-% xx=xx(ax);
-% yy=yy(ax);
-% line(xx,yy,...
-% 'marker','s',...
-% 'color',[0,0,0]);
-% % test some data points
-% px=20*rand(500,1)-10;
-% py=20*rand(500,1)-10;
-% line(px,py,...
-% 'marker','.',...
-% 'markersize',4,...
-% 'linestyle','none');
-% ix=inpolygon(px,py,xx,yy);
-% line(px(ix),py(ix),...
-% 'marker','.',...
-% 'linestyle','none',...
-% 'color',[1,0,0]);
+
+vertices(end+1,:) = [0 0 z0(1)];
+vertices(end+1,:) = [0 0 z1(1)];
+
+vertices(end+1,:) = [0 0 (z1(1)-z0(1))/3];
+vertices(end+1,:) = [0 0 (z1(1)-z0(1))/3*2];
+
+vertices(end+1,:) = [0 0 (z1(1)-z0(1))/4];
+vertices(end+1,:) = [0 0 (z1(1)-z0(1))/4*2];
+vertices(end+1,:) = [0 0 (z1(1)-z0(1))/4*3];
+
+if app.draw
+ axis equal
+ set(gca,'Visible','off')
+ if app.numbers
+ for ii=13:14
+ text(vertices(ii,1),vertices(ii,2),vertices(ii,3)+0.1,num2str(ii),'Color',[0 0 0])
+ end
+ end
+ if app.vertices
+ for ii=13:length(vertices)
+ plot3(vertices(ii,1),vertices(ii,2),vertices(ii,3),'.k')
+ end
+ end
end
+if nargout == 1
+ data.vertices = vertices;
+ data.faces_sides = faces_sides;
+ data.faces_end = faces_end;
+ data.hkil = hkil;
+ data.hf = gcf;
+end
+
+end % end of function
diff --git a/6_rendering/gtPlotHexagon.m b/6_rendering/gtPlotHexagon.m
index afea72947095cc7ea86ec5b766aecfdfc6f9a444..cc9636e110100a2ad7fc67bbbd0ad14a59e5bb86 100644
--- a/6_rendering/gtPlotHexagon.m
+++ b/6_rendering/gtPlotHexagon.m
@@ -1,45 +1,43 @@
function hf = gtPlotHexagon(grains, r_vectors, angle, cmap)
% hf = gtPlotHexagon(grains, r_vectors, angle, cmap)
% --------------------------------------------------
-% make a figure containing subplots of the unit cells of the selected grains
-% angle is the angle of the section plane, defined as in
-% gtShowSampleSurface
-% can pass in a colormap as well, so colours match the section
+% Makes a figure containing subplots of the unit cells of the selected grains
%
-% as in gtShowSampleSurface
-% Deal with coordinate systems. R-vector orientation data in the instrument
+% INPUT:
+% grains = IDs of grains of interest <double 1xN>
+% r_vectors = orientations for all the grains <double Nx4>
+% angle = rotation around z-axis to visualize orientations from the
+% section plane as defined in gtShowSampleSurface
+% cmap = colour map for all the grains (rgb) <double N+1x3>
+%
+% OUTPUT:
+% hf = figure handle
+%
+% Deals with coordinate systems. R-vector orientation data in the instrument
% system: x//beam, z upwards, y towards door.
% In the reconstructed tomography/grain map data, z is downwards, y//x
% instruments, x//y instrument.
-% Finally present all information in the frame of the tomo data.
+%
+% Reference hexagon coordinates see gtHexagonalUnitCell
-if ~exist('cmap', 'var')
+if ~exist('angle','var') || isempty(angle)
+ angle = 0;
+end
+if ~exist('cmap', 'var') || isempty(cmap)
%if no colourmap passed in, use red
- cmap=zeros(size(r_vectors, 1), 3);
- cmap(:,1)=1;
+ cmap = zeros(size(r_vectors, 1), 3);
+ cmap(:,1) = 1;
end
% patch object hexagonal prism
-% 12 corners
-% [u v t w]
-corners4=[ 2 -1 -1 3;...
- -1 2 -1 3;...
- -1 -1 2 3;...
- 1 1 -2 3;...
- 1 -2 1 3;...
- -2 1 1 3];
-corners4=[corners4; corners4];
-corners4(7:12, 4)=-3;%lower corners
+data = gtHexagonalUnitCell('ratio',2,'draw',false);
+corners3 = data.vertices(1:12,:);
+rec_faces = data.faces_sides;
+hex_faces = data.faces_end;
-% turn these into 3 index coords
-corners3(:,3) = corners4(:,4);
-corners3(:,1) = (corners4(:,1)-corners4(:,3))*cosd(30);
-corners3(:,2) = corners4(:,2)-((corners4(:,1)+corners4(:,3))*sind(30));
-corners3 = corners3./repmat(sqrt(sum((corners3.*corners3),2)), 1,3);
-
-hf=figure;
+hf=figure();
% apply the R-vector
for i=1:length(grains)
@@ -51,28 +49,17 @@ for i=1:length(grains)
% allow for the two coordinate systems. Transform from instrument to
% reconstructed tomo coordinates: x-->y y-->x z-->-z
- %corners3a=[corners3a(:,2) corners3a(:,1) -corners3a(:,3)];
+% corners3a=[corners3a(:,2) corners3a(:,1) -corners3a(:,3)];
% do the rotate to follow the section plane
corners3b = ([cosd(angle) sind(angle) 0; -sind(angle) cosd(angle) 0;0 0 1]*corners3a')';
- % write these corners into the correct format for patch
-
- % corners3a is "vertices"
- hex_faces=[1 4 2 6 3 5; 7 11 9 12 8 10];
- rec_faces=[1 7 10 4;...
- 4 2 8 10;...
- 2 6 12 8;...
- 6 3 9 12;...
- 3 5 11 9;...
- 5 1 7 11];
-
subplot(1, length(grains), i);
% reference hex
- % patch('Vertices', corners3, 'Faces', hex_faces, 'FaceColor', 'b', 'FaceAlpha', 0.4)
- % patch('Vertices', corners3, 'Faces', rec_faces, 'FaceColor', 'b', 'FaceAlpha', 0.4)
+ patch('Vertices', corners3, 'Faces', hex_faces, 'FaceColor', 'b', 'FaceAlpha', 0.4)
+ patch('Vertices', corners3, 'Faces', rec_faces, 'FaceColor', 'b', 'FaceAlpha', 0.4)
% reference background like the section plane
- xpos=min(mean(corners3b([1 4 2 6 3 5], 1)), mean(corners3b([7 11 9 12 8 10], 1)));
+ xpos=min(mean(corners3b(hex_faces(1,:), 1)), mean(corners3b(hex_faces(2,:), 1)));
section_plane_vertices=[xpos 1 1; xpos 1 -1; xpos -1 1; xpos -1 -1];
section_plane_face=[1 2 4 3];
patch('Vertices', section_plane_vertices, 'Faces', section_plane_face, 'FaceColor', 'k', 'FaceAlpha', 0.4)
@@ -84,19 +71,13 @@ for i=1:length(grains)
set(get(get(hf, 'CurrentAxes'), 'xLabel'),'String', 'x axis')
set(get(get(hf, 'CurrentAxes'), 'yLabel'),'String', 'y axis')
set(get(get(hf, 'CurrentAxes'), 'zLabel'),'String', 'z axis')
- %set(get(hf, 'CurrentAxes'), 'zdir','reverse')
- %set(get(hf, 'CurrentAxes'), 'xdir','reverse')
% need to mirror twice to stay consistant with tomo
set(get(hf, 'CurrentAxes'), 'view', [90 0])
axis tight
axis equal
+ axis square
axis vis3d
end
-
-
-
-
-
-
+end % end of function
diff --git a/zUtil_Drawing/gtDrawGrainUnitCells.m b/zUtil_Drawing/gtDrawGrainUnitCells.m
index 248deafb7884230664c58f2ed4c3b926310e1f4b..1d0c88eac76316ba82e16768e20dd834753336ec 100644
--- a/zUtil_Drawing/gtDrawGrainUnitCells.m
+++ b/zUtil_Drawing/gtDrawGrainUnitCells.m
@@ -124,14 +124,11 @@ elseif strcmpi(app.type, 'hexagonal')
c = app.latticepar(3);
maxx = max(a,c);
% normalize the biggest axis to 1
- vertices = gtHexagonalUnitCell(a/maxx,c/maxx,false);
- % hexagon face directions
- % +yz -yz -xz +xz +xy -xy
- % +x -x -y +y +z -z
- faces_sides = [1 2 8 7; 4 5 11 10; 5 6 12 11; 2 3 9 8; 3 4 10 9; 6 1 7 12];
- faces_end = [1 2 3 4 5 6; 7 8 9 10 11 12];
- hkl = [1 0 -1 0; -1 0 -1 0; 0 -1 1 0; 0 1 -1 0; -1 1 0 0; 1 -1 0 0; ...
- 0 0 0 1; 0 0 0 -1]'; % column vectors
+ data = gtHexagonalUnitCell('ratio',c/a,'draw',false);
+ vertices = data.vertices(1:12,:);
+ faces_sides = data.faces_sides;
+ faces_end = data.faces_end;
+ hkl = data.hkil;
end
[Bmat, Amat] = gtCrystHKL2CartesianMatrix(app.latticepar);