Twin variants and forward simulation code : not ready but running..... not finished!!!

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

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@965 4c865b51-4357-4376-afb4-474e03ccb993

zUtil_Cryst/gtCrystHKL2CartesianMatrix.m

@@ -49,7 +49,7 @@ crossa2a3 = [a2(2)*a3(3)-a2(3)*a3(2); a2(3)*a3(1)-a2(1)*a3(3); a2(1)*a3(2)-a2(2)
 avol = a1*crossa2a3;
 
 % for output
-Amat=[a1 a2 a3];
+Amat=[a1' a2' a3'];
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %% Reciprocal lattice vectors in the Cartesian basis
@@ -66,4 +66,4 @@ b3 = [a1(2)*a2(3)-a1(3)*a2(2); a1(3)*a2(1)-a1(1)*a2(3); a1(1)*a2(2)-a1(2)*a2(1)]
 Bmat = [b1 b2 b3];
 
 
-end % of function
\ No newline at end of file
+end % of function

zUtil_Twins/gtTwinCalculateVariants.m

-function grain = gtCalculateTwinVariants(grain, parameters, variant, varargin)
-% GTCALCULATETWINVARIANTS  Calulate diffraction vectors and detector intersection points
+function grain = gtTwinCalculateVariants(grain, parameters, varargin)
+% GTTWINCALCULATEVARIANTS  Calulate diffraction vectors and detector intersection points
 %
-%     grain = gtCalculateTwinVariants(grain, parameters, variant, varargin)
+%     grain = gtTwinCalculateVariants(grain, parameters, varargin)
 %     ---------------------------------------------------------------------
 %     Input and output arguments description, variable type (in <>) and default value (in {}) are written below.
 %
@@ -25,37 +25,36 @@ function grain = gtCalculateTwinVariants(grain, parameters, variant, varargin)
 %     OUTPUT:
 %       grain = grain of interest (<struct>)
 %               added fields:
-%                - twins.allblobs{variant}
+%                - g_twins(variant).allblobs
 
 
 if ~exist('parameters','var') || isempty(parameters)
     parameters = load('parameters.mat');
     parameters = parameters.parameters;
 end
-if ~exist('variant','var') || isempty(variant)
-    variant = 1;
-end
 
 
 %% set default values for optional arguments
-app.color = 0;
-app.showfigure = 0;
-app.axis = 0;
+app.color = false;
+app.showfigure = false;
+app.axis = false;
 app.Markersize = 15;
 app.Grayscale = [-300 500];
 app.overlay = zeros(parameters.acq.ydet, parameters.acq.xdet);
-app.usestrain = 0;
+app.usestrain = false;
 app = parse_pv_pairs(app,varargin);
 
 
 % If strain data is not available, disable strain
-if ~isfield(grain,'strain') || ~isfield(grain.strain,'strainT') || ...
-   isnan(grain.strain.strainT(1,1))
-    app.usestrain = 0;
+if ( ~isfield(grain,'strain') || ...
+     ~isfield(grain.strain,'strainT') || ...
+     isnan(grain.strain.strainT(1,1)) )
+   
+    app.usestrain = false;
+else
+    app.usestrain = true;
 end
 
-% Rodrigues vector (grain orientation)
-% Rvec = grain.R_vector;
 
 %disp(['grain.center: ' num2str(grain.center)]);
 
@@ -101,22 +100,23 @@ for ii = 1:size(hklsp,2)
     pl_cry(ii, :) = gtCrystHKL2Cartesian(hklsp(:, ii), Bmat)';
 end
 
+
+
+for kkk = 1 : length(grain.g_twins)
 % Coordinate transformation matrix from CRYSTAL to SAMPLE
-% cry2sam = Rod2g(Rvec);  
 
+% Rodrigues vector (grain orientation)
+if ~isfield(grain.g_twins(kkk),'R_vector')
+    Rvec = gtMathsRotMat2Rod(grain.g_twins(kkk).g);
+    grain.g_twins(kkk).R_vector = Rvec;
+end
 
-% [g, g_twins] = gtTwinOrientations(Rvec)
-cry2sam = grain.g_twins(variant).g;
+cry2sam = grain.g_twins(kkk).g;
 
-% pl_sam = [];
-% % Plane normals in SAMPLE coordinates
-% for jj =1 : size(cry2sam,2)
+pl_sam = (cry2sam*pl_cry')';
 
-pl_sam = (cry2sam*pl_cry')';   
-% pl_sam = [pl_sam; pl_sam_tmp];
-% end
 
-%% Initialse output variables
+%% Initialyze output variables
 allblobs.pl    = [];
 allblobs.pllab = [];
 allblobs.hkl   = [];
@@ -385,8 +385,10 @@ if app.showfigure
 end % showfigure
 
 
-grain.twins.allblobs{variant} = allblobs;
+grain.g_twins(kkk).allblobs = allblobs;
 
 end
 
+end % end of function
+
 

zUtil_Twins/gtTwinOrientations.m

@@ -70,6 +70,7 @@ elseif spacegroup==194 % hexagonal case
         cry2twin = gtMathsRotationTensor(twin_angle, rotcomp);
         
         g_twins(ii).g = cry2sam*cry2twin;
+        g_twins(ii).R_vector = gtMathsRotMat2Rod( g_twins(ii).g );
         
     end