Some header formatting and drawing improving... try to compare gtPlotHexagon...

Some header formatting and drawing improving... try to compare gtPlotHexagon and gtHexagonalUnitCell

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@964 4c865b51-4357-4376-afb4-474e03ccb993

6_rendering/gtHexagonalUnitCell.m

-function vertices = hexagon(a,c,draw)
+function vertices = gtHexagonalUnitCell(a,c,draw)
 
 % create a hexagonal grid (radius <r>)
 
@@ -21,10 +21,19 @@ if 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*')
+    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)')
@@ -80,4 +89,4 @@ end
 %     'linestyle','none',...
 %     'color',[1,0,0]);
 
-end
+end
\ No newline at end of file

6_rendering/gtPlotHexagon.m

-
-function 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
-
-%as in gtShowSampleSurface
-%Deal 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.
+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
+%
+%     as in gtShowSampleSurface
+%     Deal 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.
 
 
 if ~exist('cmap', 'var')
@@ -22,43 +22,43 @@ end
 
 
 % patch object hexagonal prism
-%12 corners
-%[u v x 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];
+% 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
 
-%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);
+% 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);
 
-id=figure;
+hf=figure;
 
-%apply the R-vector
+% apply the R-vector
 for i=1:length(grains)
 
-    grain=grains(i);
-    R=r_vectors(find(r_vectors(:,1)==grain),2:4);
-    g=Rod2g(R);
-    corners3a=(g*corners3')';
+    grainID = grains(i);
+    R = r_vectors(find(r_vectors(:,1)==grainID),2:4);
+    g = Rod2g(R);
+    corners3a = (g*corners3')';
 
-    %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)]; 
+    % 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)]; 
     
-    %do the rotate to follow the the section plane
+    % 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
+    % write these corners into the correct format for patch
 
-    %corners3a is "vertices"
+    % 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;...
@@ -68,28 +68,29 @@ for i=1:length(grains)
         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)
-    %reference background like the section plane
+    % reference hex
+    % 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)));
     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)
-    %including the rotation for sectioning
-    patch('Vertices', corners3b, 'Faces', hex_faces, 'FaceColor', cmap(grain+1,:), 'FaceAlpha', 1)
-    patch('Vertices', corners3b, 'Faces', rec_faces, 'FaceColor', cmap(grain+1,:), 'FaceAlpha', 1)
-
-    set(get(get(id, 'CurrentAxes'), 'Title'), 'String', sprintf('grain %d unit cell', grain))
-    set(get(get(id, 'CurrentAxes'), 'xLabel'),'String', 'x axis')
-    set(get(get(id, 'CurrentAxes'), 'yLabel'),'String', 'y axis')
-    set(get(get(id, 'CurrentAxes'), 'zLabel'),'String', 'z axis')
-    set(get(id, 'CurrentAxes'), 'zdir','reverse')
-    set(get(id, 'CurrentAxes'), 'xdir','reverse')
-    %need to mirror twice to stay consistant with tomo
-    set(get(id, 'CurrentAxes'), 'view', [90 0])
+    % including the rotation for sectioning
+    patch('Vertices', corners3b, 'Faces', hex_faces, 'FaceColor', cmap(grainID+1,:), 'FaceAlpha', 1)
+    patch('Vertices', corners3b, 'Faces', rec_faces, 'FaceColor', cmap(grainID+1,:), 'FaceAlpha', 1)
+
+    set(get(get(hf, 'CurrentAxes'), 'Title'), 'String', sprintf('grain %d unit cell', grainID))
+    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 vis3d
 end
 

6_rendering/gtShowSampleSurface.m

 function gtShowSampleSurface(vol, angle, depth_orig, cmap, r_vectors, grains)
-%rotate volume by angle, remove layer depth pixels thick from surface
-%use volume with surface added (surface label is 800, grains 1-700)
-%show what's left
-%highlight grains of interest
-%show trace of basal planes on section, display inclination, using
-%gtPlotHexagon to display crystallographic orientation.
-
-%rotation convention for section: starting from 12-6 o'clock on grain map // y, angle
-%is measured clockwise.  Hence, first cut of interest is around 13.1
-%degrees.  Depth is removed from the left of the sample, after rotation
-
-%Deal 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.
+%     gtShowSampleSurface(vol, angle, depth_orig, cmap, r_vectors, grains)
+%     --------------------------------------------------------------------
+%     rotate volume by angle, remove layer depth pixels thick from surface
+%     use volume with surface added (surface label is 800, grains 1-700)
+%     show what's left
+%     highlight grains of interest
+%     show trace of basal planes on section, display inclination, using
+%     gtPlotHexagon to display crystallographic orientation.
+%
+%     rotation convention for section: starting from 12-6 o'clock on grain map // y, angle
+%     is measured clockwise.  Hence, first cut of interest is around 13.1
+%     degrees.  Depth is removed from the left of the sample, after rotation
+%
+%     Deal 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.
 
 vol=imrotate(vol, angle, 'nearest', 'crop');
 

zUtil_Drawing/gtSampleGeometry.m

@@ -20,17 +20,17 @@ color = [0.501960813999176 0.501960813999176 0.501960813999176];
 
 % Create axes
 set(gca,'ZMinorTick','on')
-             set(gca,'ZColor',color);
-             set(gca,'YMinorTick','on');
-             set(gca,'YColor',color);
-             set(gca,'XMinorTick','on');
-             set(gca,'XColor',color);
-             set(gca,'FontSize',12);
-             set(gca,'Visible','on');
-             set(gca,'Box','on');
-             set(gca,'XGrid','on');
-             set(gca,'YGrid','on');
-             set(gca,'ZGrid','on');
+set(gca,'ZColor',color);
+set(gca,'YMinorTick','on');
+set(gca,'YColor',color);
+set(gca,'XMinorTick','on');
+set(gca,'XColor',color);
+set(gca,'FontSize',12);
+set(gca,'Visible','on');
+set(gca,'Box','on');
+set(gca,'XGrid','on');
+set(gca,'YGrid','on');
+set(gca,'ZGrid','on');
 % Create xlabel
 xlabel('X','Color',color);
 % Create ylabel