diff --git a/6_rendering/gtAaxisCmap.m b/6_rendering/gtAaxisCmap.m
index 4621c8e8c16689872a8efe7db792d3cd84e32f3e..0a820f2d88480cee2065a52f40ddf856ab0ed192 100644
--- a/6_rendering/gtAaxisCmap.m
+++ b/6_rendering/gtAaxisCmap.m
@@ -16,6 +16,8 @@ function [a_axis, a_axismap] = gtAaxisCmap(phaseid, reflection)
% r_vectors -> a-axis -> phi/psi -> hsl -> rgb colormap
% use psi to give brightness; phi to give colour
%
+% Version 003 19-10-2012 by YGuilhem
+% Factorized using gtVectorOrientationColor
%
% Version 002 28-06-2012 by LNervo
% Update to version 2 of parameters; cleaning formatting
@@ -55,10 +57,9 @@ normalised_hkls = all_hkls./(repmat(tmp,1,3));
all_hkls = [];
all_hkls = all_hkils;
-
for i=1:size(r_vectors,1)
- g = Rod2g(r_vectors(i,2:4));
- all_normals = (g * normalised_hkls')';
+ crys2sam = Rod2g(r_vectors(i,2:4));
+ all_normals = (crys2sam * normalised_hkls')';
a_axis(i,1)=r_vectors(i,1);
if all_normals(6,1)>=0
a_axis(i,2)=all_normals(6,1);
@@ -71,46 +72,18 @@ for i=1:size(r_vectors,1)
end
end
+save('a_axis.mat', 'a_axis'); % list of the a axis
-save a_axis a_axis % list of the a axis
-
-
-psi=acosd(a_axis(:,4));
-phi=atan2(a_axis(:,3), a_axis(:,2));
-
-
-
-%get everything in degrees, and on the right interval
-phi=phi*180/pi;
-% %want all psi between 0 and 90
-% psi(find(psi>90))=180-psi(find(psi>90));
-% %if we change psi, should also change phi
-% phi(find(psi>90))=phi(find(psi>90))+180;
+% Get the orientation color defined by HSL color code, translated to RGB
+rgb = gtVectorOrientationColor(a_axis(:, 2:4));
-dummy=find(psi>90);
-psi(dummy)=180-psi(dummy);
-%if we change psi, should also change phi
-phi(dummy)=phi(dummy)+180;
-
-phi(find(phi<0))=phi(find(phi<0))+360;
-phi(find(phi>360))=phi(find(phi>360))-360;
-
-%use hsl2rgb.m
-%hue
-h=phi/360;
-%saturation
-s=ones(size(h));
-%lightness (white //z, black in x-y plane)
-l=0.9-(0.8*(psi/90));
-
-rgb=hsl2rgb([h s l]);
-
-%add black background
-a_axismap=zeros(size(rgb, 1)+1, 3);
-a_axismap(2:end, :)=rgb;
+% Add black background and expand list length of max(grainid)+1
+a_axismap = zeros(max(a_axis(:, 1))+1, 3);
+for i=1:length(a_axis)
+ a_axismap(a_axis(i,1)+1, :) = rgb(i, :);
+end
-%save the a-axis colourmap
-save a_axismap a_axismap
+% Save the a-axis colourmap
+save('a_axismap.mat', 'a_axismap');
end % end of function
-
diff --git a/6_rendering/gtCaxisCmap.m b/6_rendering/gtCaxisCmap.m
index 69d2b08d67bf652c1faa6b6d8850111f4bc135c1..c5a46977fe103068bffaf99e5d2f53ffe5d26d05 100644
--- a/6_rendering/gtCaxisCmap.m
+++ b/6_rendering/gtCaxisCmap.m
@@ -16,6 +16,8 @@ function [c_axis, c_axismap] = gtCaxisCmap(phaseid, reflection)
% r_vectors -> c-axis -> phi/psi -> hsl -> rgb colormap
% use psi to give brightness; phi to give colour
%
+% Version 003 19-10-2012 by YGuilhem
+% Factorized using gtVectorOrientationColor
%
% Version 002 28-06-2012 by LNervo
% Update to version 2 of parameters; cleaning formatting
@@ -55,11 +57,9 @@ normalised_hkls = all_hkls./(repmat(tmp,1,3));
all_hkls = [];
all_hkls = all_hkils;
-
for i=1:size(r_vectors,1)
- g = Rod2g(r_vectors(i,2:4));
-
- all_normals = (g * normalised_hkls')';
+ crys2sam = Rod2g(r_vectors(i,2:4));
+ all_normals = (crys2sam * normalised_hkls')';
c_axis(i,1)=r_vectors(i,1);
if all_normals(2,3)>=0
c_axis(i,2)=all_normals(2,1);
@@ -72,45 +72,18 @@ for i=1:size(r_vectors,1)
end
end
-
save('c_axis.mat','c_axis'); % list of the c axis
+% Get the orientation color defined by HSL color code, translated to RGB
+rgb = gtVectorOrientationColor(c_axis(:, 2:4));
-psi=acosd(c_axis(:,4));
-phi=atan2(c_axis(:,3), c_axis(:,2));
-% phi=atan2(c_axis(:,2), c_axis(:,3));
-%get everything in degrees, and on the right interval
-phi=phi*180/pi;
-% %want all psi between 0 and 90
-% psi(find(psi>90))=180-psi(find(psi>90));
-% %if we change psi, should also change phi
-% phi(find(psi>90))=phi(find(psi>90))+180;
-
-dummy=find(psi>90);
-psi(dummy)=180-psi(dummy);
-%if we change psi, should also change phi
-phi(dummy)=phi(dummy)+180;
-
-phi(find(phi<0))=phi(find(phi<0))+360;
-phi(find(phi>360))=phi(find(phi>360))-360;
-
-%use hsl2rgb.m
-%hue
-h=phi/360;
-%saturation
-s=ones(size(h));
-%lightness (white //z, black in x-y plane)
-l=0.9-(0.8*(psi/90));
-
-rgb=hsl2rgb([h s l]);
-
-%add black background and expand list length of max(grainid)+1
-c_axismap=zeros(max(c_axis(:,1))+1, 3);
+% Add black background and expand list length of max(grainid)+1
+c_axismap = zeros(max(c_axis(:, 1))+1, 3);
for i=1:length(c_axis)
- c_axismap(c_axis(i,1)+1, :)=rgb(i,:);
+ c_axismap(c_axis(i,1)+1, :) = rgb(i, :);
end
-%save the c-axis colourmap
+% Save the c-axis colourmap
save('c_axismap.mat','c_axismap');
end % end of function
diff --git a/zUtil_Analysis/gtAnalyseCrackPlane.m b/zUtil_Analysis/gtAnalyseCrackPlane.m
index cfb91ca6af8499a4ce518e4d66ea9ffbc9621bbf..5866c39b0e623755427a0ffaf61175dce233d1d5 100644
--- a/zUtil_Analysis/gtAnalyseCrackPlane.m
+++ b/zUtil_Analysis/gtAnalyseCrackPlane.m
@@ -1,11 +1,8 @@
-function [data, vol, map, surface_view]=gtAnalyseCrackPlane(crack);
-
+function [data, vol, map, surface_view] = gtAnalyseCrackPlane(crack)
%returns the crack plane data as a list [x y z nx ny nz]
%also returns a labelled volume and tle corresponding colourmap
%surface_view is a top down image
-
-
%read the x,y,z points of the crack
[y,x,z]=ind2sub(size(crack),find(crack)); %voxels of crack
@@ -13,80 +10,54 @@ boxsize=5;
%data out =[x y z nx ny nz]
data=zeros(length(find(crack)), 6);
-
for i=1:length(x)
-
- xx=x(i); yy=y(i); zz=z(i);
-
-
-dummy=find(x>xx-boxsize & x<xx+boxsize & y>yy-boxsize & y<yy+boxsize & z>zz-boxsize & z<zz+boxsize);
-
-if length(dummy)>3
-
-%this is right in tomography coordinates (ie as in volview, x l->r, y
-%top->bot, z up->down)
-
- [origin, a]=lsplane([x(dummy) y(dummy) z(dummy)]);
-
-%convert to instrument coordinates to agree with gtCaxisCmap conventions
-a=a([2 1 3]);
-a(3)=-a(3);
+ xx=x(i); yy=y(i); zz=z(i);
+ dummy=find(x>xx-boxsize & x<xx+boxsize & y>yy-boxsize & y<yy+boxsize & z>zz-boxsize & z<zz+boxsize);
-data(i, :)=[xx yy zz a(1) a(2) a(3)];
+ if length(dummy)>3
+ %this is right in tomography coordinates (ie as in volview, x l->r, y
+ %top->bot, z up->down)
+ [origin, a]=lsplane([x(dummy) y(dummy) z(dummy)]);
-if mod(i, 1000)==0
- 100*i/length(x)
-end
+ %convert to instrument coordinates to agree with gtCaxisCmap conventions
+ a=a([2 1 3]);
+ a(3)=-a(3);
-end
+ data(i, :)=[xx yy zz a(1) a(2) a(3)];
+ if mod(i, 1000)==0
+ 100*i/length(x)
+ end
+ end
end
%cut the empty bits of data
-data(find(data(:,1)==0), :)=[];
+data(find(data(:,1)==0), :)=[];
%now produce a labelled volume, and the corresponding colormap
%volume
vol=zeros(size(crack));
for i=1:length(data)
- vol(data(i,2), data(i,1), data(i,3))=i;
+ vol(data(i,2), data(i,1), data(i,3))=i;
end
-%colormap
-%as in gtCaxisCmap
-psi=acosd(data(:,6));
-phi=atan2(data(:,5), data(:,4));
-%get everything in degrees, and on the right interval
-phi=phi*180/pi;
-dummy=find(psi>90);
-psi(dummy)=180-psi(dummy);
-phi(dummy)=phi(dummy)+180;
-phi(find(phi<0))=phi(find(phi<0))+360;
-phi(find(phi>360))=phi(find(phi>360))-360;
+% Colormap
+rgb = gtVectorOrientationColor(data(:, 4:6));
-%hue
-h=phi/360;
-%saturation
-s=ones(size(h));
-%lightness (white //z, black in x-y plane)
-l=0.9-(0.8*(psi/90));
-rgb=hsl2rgb([h s l]);
%add black background
map=zeros(size(data,1)+1, 3);
map(2:end, :)=rgb; %ie rgb plus zero background
-
%read out "bird's eye" view of coloured crack;
surface_view=zeros(size(crack, 1), size(crack, 2));
for y=1:size(crack, 1)
for x=1:size(crack, 2)
-a=squeeze(vol(y,x,:));
-a=a(find(a, 1, 'first'));
-if ~isempty(a)
- surface_view(y,x)=a;
-end
+ a=squeeze(vol(y,x,:));
+ a=a(find(a, 1, 'first'));
+ if ~isempty(a)
+ surface_view(y,x)=a;
+ end
end
end
-
-
+end % end of function
diff --git a/zUtil_Imaging/gtVectorOrientationColor.m b/zUtil_Imaging/gtVectorOrientationColor.m
new file mode 100644
index 0000000000000000000000000000000000000000..cf6909401683ee80fcbd3b325e3d747e759bab08
--- /dev/null
+++ b/zUtil_Imaging/gtVectorOrientationColor.m
@@ -0,0 +1,35 @@
+function rgb = gtVectorOrientationColor(vectors)
+% GTVECTORORIENTATIONCOLOR Convert a list of unit vectors into RGB color values
+%
+% rgb = gtVectorOrientationColor(vectors)
+% -------------------------------------------------------------------------
+% The output RGB color values describe roientation with HSL code which use:
+% - psi to give brightness
+% - phi to give color
+%
+% INPUT:
+% vectors = <double> M row vectors (Mx3 matrix)
+%
+% OUTPUT:
+% rgb = <double> Red-Green-Blue color values
+%
+% Version 001 16-10-2012 by YGuilhem
+
+ psi = acos(vectors(:, 3));
+ phi = atan2(vectors(:, 2), vectors(:, 1));
+
+ % Get everything in the right interval
+ dummy = find(psi > pi/2);
+ psi(dummy) = pi - psi(dummy);
+
+ % If we change psi, should also change phi
+ phi(dummy) = phi(dummy) + pi;
+ phi = mod(phi, pi);
+
+ h = phi/pi; % Hue
+ s = ones(size(h)); % Saturation
+ l = 0.9 - (0.8*(psi/(pi/2))); % Lightness (white //z, black in x-y plane)
+
+ rgb = hsl2rgb([h s l]); % Turn HSL into RGB
+
+end % end of function