gtHexagonalUnitCell / gtCubicUnitCell : updated version with fixed crystallographic axes

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

6_rendering/gtCubicUnitCell.m

 function data = gtCubicUnitCell(varargin)
+% GTCUBICUNITCELL  Draws the cubic unit cell with crystallographic axes
+%                      for Euler angles (0,0,0)
+%
+%     data = gtCubicUnitCell(varargin)
+%     --------------------------------
+%     Draws the unit cell using this convention:
+%     Xs // <100> crystallographic axis
+%     Ys // <010> crystallographic axis
+%     Zs // <001> crystallographic axis
+%
+%     Sample axes are Xs,Ys,Zs. Please refer to the
+%     DCTdoc_Crystal_orientation_descriptions.pdf in the DCT_Documentation
+%     folder for the graintracking code.
 
 app.facecolors   = [];
 app.centered     = false;
@@ -10,6 +23,7 @@ app.numbers      = false;
 app.patch        = false;
 app.sampleaxes   = false;
 app.crystaxes    = false;
+app.caxis        = false;
 app.view         = [103 20];
 app.add_vertices = false;
 
@@ -19,10 +33,11 @@ c=1;
 a=1/app.ratio;
 
 % calculation of vertices
-%
-%
+% 
+
 x0 = [0 1 1 0 0]*a;
 y0 = [0 0 1 1 0]*a;
+
 if app.centered
     z0 = repmat(-c/2,1,length(x0));
     z1 = repmat(+c/2,1,length(x0));
@@ -35,6 +50,9 @@ vertices(1,:)=[];
 vertices(5,:)=[];
 
 if app.add_vertices
+    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];
 
@@ -43,20 +61,26 @@ if app.add_vertices
     vertices(end+1,:) = [0 0 (z1(1)-z0(1))/4*3];
 end
 
+caxis(1,:) = [0 0 z0(1)-c/4];
+caxis(2,:) = [0 0 z1(1)+c/4];
+
 faces = {[1 2 6 5]; [2 3 7 6]; [3 4 8 7]; [4 1 5 8];...
          [5 6 7 8]; [1 2 3 4]};
 hkl   = [1 0 0; 0 1 0; -1 0 0; 0 -1 0;...
          0 0 1; 0 0 -1]';
 faces_sides = [1 2 6 5; 2 3 7 6; 3 4 8 7; 4 1 5 8];
 faces_end   = [5 6 7 8; 1 2 3 4]; %
-faceColors = [...
-     1 1 0;...
-     0 0 1;...
-     1 0 0;...
-     0 1 1;...
-     1 0 1;...
+faceColors = [ ...
+     1 1 0; ...
+     0 0 1; ...
+     1 0 0; ...
+     0 1 1; ...
+     1 0 1; ...
      0 1 0];
 
+   
+   
+   
 if ~isempty(app.facecolors)
     faceColors = app.facecolors;
 end
@@ -65,10 +89,10 @@ if size(faceColors,1)==1
 end
 
 % for crystallographic axes and labels
-orig=repmat([0 0 z0(1)],4,1);
-xcrys=[1;0;0;0];
-ycrys=[0;1;0;0];
-zcrys=[z0(1);z0(1);z0(1);z1(1)+0.4];
+orig=repmat([0 0 z0(1)],3,1);
+xcrys=[0.6;0;0];
+ycrys=[0;0.6;0];
+zcrys=[z0(1);z0(1);z0(1)+0.6];
 lcrys={'a [100]';...
        'b [010]';...
        'c [001]'};
@@ -84,9 +108,14 @@ if app.draw
     for ii=1:length(x0)
         plot3([x0(ii) x0(ii)],[y0(ii) y0(ii)],[z0(ii) z1(ii)], 'b-', 'LineWidth', 1)
     end
+    if app.caxis
+        line([0 0],[0 0],[z0(1)-c/4 z1(1)+c/4])
+    end
     % cryst axes
     if app.crystaxes
-        quiver3(orig(:,1),orig(:,2),orig(:,3),xcrys,ycrys,zcrys,0,'k')
+        quiver3(0,0,z0(1),0.6,0,0,0,'k','LineWidth',2)
+        quiver3(0,0,z0(1),0,0.6,0,0,'k','LineWidth',2)
+        quiver3(0,0,z0(1),0,0,0.6,0,'k','LineWidth',2)
         text(xcrys-0.1,ycrys+0.1,zcrys,lcrys,'Color',[0 0 0])
     end
     view(app.view)
@@ -120,17 +149,18 @@ if app.draw
 end
 
 if nargout == 1
-    data.vertices = vertices;
-    data.faces    = faces;
+    data.vertices    = vertices;
+    data.caxis       = caxis;
+    data.faces       = faces;
     data.faces_sides = faces_sides;
     data.faces_end   = faces_end;
-    data.facecolors = faceColors;
-    data.hkl      = hkl;    
-    data.orig     = orig;
-    data.xcrys    = xcrys;
-    data.ycrys    = ycrys;
-    data.zcrys    = zcrys;
-    data.lcrys    = lcrys;
+    data.facecolors  = faceColors;
+    data.hkl         = hkl;    
+    data.orig        = orig;
+    data.xcrys       = xcrys;
+    data.ycrys       = ycrys;
+    data.zcrys       = zcrys;
+    data.lcrys       = lcrys;
     if app.draw
         data.hf   = gcf;
         if app.patch

6_rendering/gtHexagonalUnitCell.m

@@ -5,17 +5,15 @@ function data = gtHexagonalUnitCell(varargin)
 %     data = gtHexagonalUnitCell(varargin)
 %     ------------------------------------
 %     Draws the unit cell using this convention:
-%     Xs // to <2-1-10> or <100> axis (a-axis)
-%     Ys // to 
+%     Xs // to <2-1-10> or <100> crystallographic axis (a-axis)
+%     Ys // to <10-10> or <010> crystallographic axis
+%     Zs // to <0001> or <001> crystallographic axis (c-axis)
 %
-%     Crystallographic axes are Xc, Yc, Zc which corresponds to a,b,c.
-%     For hexagonal unit cells, there are the equivalents axes a1,a2,a3,c in
-%     which a1//a, a2 is a1 rotated 120 deg counterclockwise, a3 is a2 rotated
-%     120 degrees counterclockwise.
 %     Sample axes are Xs,Ys,Zs. Please refer to the
 %     DCTdoc_Crystal_orientation_descriptions.pdf in the DCT_Documentation
 %     folder for the graintracking code.
 %
+%     
 
 app.facecolors   = [];
 app.centered     = false;
@@ -33,15 +31,15 @@ app.add_vertices = false;
 
 app = parse_pv_pairs(app, varargin);
 
-% lattice axes' length; c is normalized to 1
 c=1;
 a=1/app.ratio;
 
-% calculation of vertices
-% first 6 are for 000-1 plane and first is at X=0 and then counterclockwise
+% calculation of vertices: first 6 are for 000-1 plane and first is at X=0
+% then counterclockwise
 v=0:60:360;
 x0 = a*cosd(v);
 y0 = a*sind(v);
+
 if app.centered
     z0 = repmat(-c/2,1,length(x0));
     z1 = repmat(+c/2,1,length(x0));
@@ -117,10 +115,10 @@ if app.draw
     end
     % cryst axes
     if app.crystaxes
-        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,'k')
+        quiver3(0,0,z0(1),1,0,0,0,'k','LineWidth',2)
+        quiver3(0,0,z0(1),-0.5,0.866,0,0,'k','LineWidth',2)
+        quiver3(0,0,z0(1),-0.5,-0.866,0,0,'k','LineWidth',2)
+        quiver3(0,0,z0(1),0,0,1,0,'k','LineWidth',2)
         text(xcrys-0.1,ycrys+0.1,zcrys,lcrys,'Color',[0 0 0])
     end
     view(app.view)