Color maps : fixing bugs for c-axis and IPF maps.

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

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@629 4c865b51-4357-4376-afb4-474e03ccb993

6_rendering/gtCaxisCmap.m

-function c_axismap = gtCaxisCmap(phaseid)
+function c_axismap = gtCaxisCmap(phaseid, bodge)
 % GTCAXISCMAP  Make a colourmap according to c-axis orientation
-%     c_axismap = gtCaxisCmap(phaseid)
+%     c_axismap = gtCaxisCmap(phaseid, bodge)
 %     --------------------------------
 %     Loads parameters.mat and 4_grains/phase_##/r_vectors.mat
-%     Saves c_axis.map and c_axismap.mat
+%     Saves c_axis.mat, map.mat and c_axismap.mat
 %
 %     INPUT:
 %       phaseid   = phase number <int> {1}
 %
 %     OUTPUT:
-%       c_axismap = c_axis colourmpa calculated from r_vectors list as produced by gtReadGrains
+%       c_axismap = c_axis colourmap calculated from r_vectors list as produced by gtReadGrains
 %
 %     r_vectors -> c-axis -> phi/psi -> hsl -> rgb colormap
 %     use psi to give brightness; phi to give colour
@@ -20,6 +20,9 @@ function c_axismap = gtCaxisCmap(phaseid)
 if ~exist('phaseid','var') || isempty(phaseid)
     phaseid = 1;
 end
+if ~exist('bodge','var') || isempty(bodge)
+    bodge = 0;
+end
 
 parameters = [];
 r_vectors  = [];
@@ -54,6 +57,10 @@ all_hkls = all_hkils;
 
 for i=1:size(r_vectors,1)
     g = Rod2g(r_vectors(i,2:4));
+    
+    disp([num2str(bodge) ' degrees bodge here!'])
+    g=[cosd(bodge) sind(bodge) 0; -sind(bodge) cosd(bodge) 0; 0 0 1]*g;
+    
     all_normals = (g * normalised_hkls')';
     c_axis(i,1)=r_vectors(i,1);
     if all_normals(2,3)>=0
@@ -108,4 +115,7 @@ end
 %save the caxis colourmap
 save('c_axismap.mat','c_axismap');
 
+map = gtIVPhexCmap(r_vectors,bodge);
+sa('map.mat','map');
+
 end % end of function
\ No newline at end of file

6_rendering/gtIVPhexCmap.m

-function cmap = gtIVPhexCmap(r_vectors)
-% map = gtIVPhexCmap(r_vectors)
+function cmap = gtIVPhexCmap(r_vectors, bodge)
+% map = gtIVPhexCmap(r_vectors, bodge)
+
+if ~exist('bodge','var') || isempty(bodge)
+    bodge = 0; % degrees
+end
+
 cmap = [];
 RD=[0 0 1];
 
@@ -7,12 +12,12 @@ RD=[0 0 1];
 % six fold rotation around z
 for i=1:6
     a=(i-1)*60;
-    sym(i).g3 = [...
+    symm(i).g3 = [...
         cosd(a) sind(a) 0;...
         -sind(a) cosd(a) 0;...
         0 0 1];
     % include the mirror
-    sym(i+6).g3=[1 0 0; 0 -1 0; 0 0 1]*sym(i).g3;
+    symm(i+6).g3=[1 0 0; 0 -1 0; 0 0 1]*symm(i).g3;
 end
 
 map = zeros(length(r_vectors+1),3);
@@ -20,18 +25,22 @@ map = zeros(length(r_vectors+1),3);
 for i=1:length(r_vectors)
     
     g=Rod2g(r_vectors(i, 2:4));
+
+    disp([num2str(bodge) ' degrees bodge here!'])
+    g=[cosd(bodge) sind(bodge) 0; -sind(bodge) cosd(bodge) 0; 0 0 1]*g;
     
     % RD in cryst axes
     RDc = g*RD';
     % all equivilents by sym
     RDc_sym=[];
     for jj=1:12
-        RDc_sym(jj, :)=(sym(jj).g3*RDc)';
+        RDc_sym(jj, :)=(symm(jj).g3*RDc)';
     end
     RDc_sym=[RDc_sym; -RDc_sym];
     
     RDc_psi=acosd(RDc_sym(:,3));
     RDc_phi=rad2deg(atan2(RDc_sym(:,2), RDc_sym(:,1)));
+
     
     % pick equiv that is in out triangle
     ndx=find(RDc_psi<90 & RDc_phi>=60 & RDc_phi<90);

6_rendering/gtMakePoleFigure2.m

-function gtMakePoleFigure2(poles, weights)
-
-% as for gtMakePoleFigure...  however, given poles, gtMakePoleFigure uses a
-% search radius to find all poles close to each data point on the pole
-% figure, thus doing some inherent smoothing.  This is also slow for large
-% numbers of poles.  If the data going in does not require smoothing
-% (remains to be seen!) maybe can construct the pole figue data in a faster
-% way.
-
-%at the mo this is quick (~10x cf gtMakePoleFigure) but not clever enough
-%because the sampling areas get too small near the pole, and thus noise
-% here overpowers the signal.  Needs something cleverer...  Triangle mesh
-% from isosurface on a sphere?
-
-
-%step size in pole figure
-inc=0.02;
-
-%change this if you want a 360deg or 90deg view
-phimax=pi/2;
-%phimax=2*pi;
-psimax=pi/2;
-phi_range=0:inc:(phimax-inc);
-psi_range=0:inc:(psimax-inc);
-
-
-%before building figure, take only those poles that fall in the range 0-phimax,
-%0-psimax (allowing for seach radius)
-if phimax==pi/2
-   %for a 90 degree section of the pole figure
-   poles=poles(find(poles(:,1)>0 & poles(:,2)>0 & poles(:,3)>0),:);
-elseif phimax==2*pi
-    %for 360 pole figure - reduce only using psi
-   poles=poles(find(poles(:,3)>cos(psimax)-sin(searchR)),:);
-else
-    disp('dont know how take a subset of the poles input')
-end
-
-
-
-%preallocate density
-density=zeros(length(phi_range), length(psi_range));
-
-%calc phi and psi for all poles
-psi=acos(poles(:,3));
-phi=atan2(poles(:,2), poles(:,1));
-
-for i=1:length(phi_range)
-    i
-    for j=1:length(psi_range)
-        dum=find(phi>=phi_range(i) & phi<phi_range(i)+inc & psi>=psi_range(j) & psi<psi_range(j)+inc);
-        density(i, j)=sum(weights(dum));     
-    end
-end
-
-%normalise density values
-%needs to be wrt random population, and account for the search area
-%increment size as function of psi:
-inc_area=inc*[-cos(psi_range+inc)+cos(psi_range)];
-inc_area=repmat(inc_area, length(phi_range), 1);
-density2=density./inc_area;
-
-%total density/total area
-total_density=sum(density(:));
-total_area=sum(inc_area(:));
-
-
-density2=10*density2/max(density2(:));
-
-keyboard
-phi=0:inc:phimax; %around z-axis
-psi=0:inc:psimax; %away from z axis
-%radius distorted for stereographic proj
-r=tan((psi_range+(inc/2))/2);
-[phi,r]=meshgrid((phi_range+(inc/2)),r);
-[x,y]=pol2cart(phi,r);
-
-figure
-surf(x,y,density2')
-hold on
-shading('interp')
-axis equal