remove duplicate function gtTwinTest

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

zUtil_Twins/gtTwinTest.m

-function out = gtTwinTest(phaseid, parameters, grain1, grain2, grain, vol_out, id)
-% out = gtTwinTest(phaseid, parameters, grain1, grain2, grain, vol_out, id)
-% grain1 = grainID for grain 1
-% grain2 = grainID for grain 2
-% grain  = grain structure <cell>
-% vol_out = output from gt_find_grain_boundaries
-
-crystal_system = parameters.cryst(phaseid).crystal_system; 
-spacegroup     = parameters.cryst(phaseid).spacegroup;
-latticepar     = parameters.cryst(phaseid).latticepar;
-
-% find the max grainID
-maxgrain = max(0, grain1);
-maxgrain = max(maxgrain, grain2);
-
-r_vectors = [];
-for ii=1:length(grain)
-    r_vectors(ii, 1) = ii;
-    r_vectors(ii, 2:4) = grain{ii}.R_vector;
-end
-
-% Get symmetry operators
-symm = gtCrystGetSymmetryOperators(crystal_system, spacegroup); 
-
-if grain1==0
-    g1=[];
-    g1equiv=[];
-elseif grain1~=-1 && grain1~=grain2
-    R1 = r_vectors(grain1,2:4);
-    g1 = gtMathsRod2OriMat(R1);
-else
-    out = [];
-    return;
-end
-
-if grain2==0
-    g2 = [];
-elseif grain2~=-1 && grain2~=grain1
-    R2 = r_vectors(grain2,2:4);
-    g2 = gtMathsRod2OriMat(R2);
-else
-    out = [];
-    return;
-end
-
-% this only works for cubic systems until someone works out how to pdo te
-% permutations of the g1 for the hexagonal system
-
-% same calculation but using hexagonal symm operations
-% calculate the misorientation angle and axis between these grains
-% TODO: replace by a MISORIENTATION function
-if ~isempty(g1) && ~isempty(g2)
-    % if we have both grains
-    % Need to search symmetry equivalents for the minimum misorientation
-    rot_offset=[];
-    % warning('g*symm.g maybe should be symm.g*g')
-    for jj=1:length(symm)
-        g1equiv = g1*symm(jj).g3;
-        netg = g1equiv\g2;
-        rot_offset(jj) = acos((trace(netg)-1)/2);
-    end
-
-    dummy = find(rot_offset ==min(rot_offset));
-    g1equiv = g1*symm(dummy).g3;
-    netg = g1equiv\g2;
-
-    misorientation_angle = acosd((trace(netg)-1)/2);
-
-    [eigVec, eigVal]=eig(netg);
-    for p=1:3
-        if isreal(eigVec(:,p))  %find the real eigenvector - should be just one
-            misorientation_axis=eigVec(:,p);
-            eigVal=eigVal(p,p);
-        end
-    end
-end    
-
-
-out.grain1          = grain1;
-out.grain2          = grain2;
-out.grain1_R_vector = r_vectors(grain1,2:4);
-out.grain2_R_vector = r_vectors(grain2,2:4);
-out.mis_angle       = misorientation_angle;
-out.mis_axis        = misorientation_axis';
-
-out.mis_axis_hex    = gtCart2Hex(misorientation_axis', latticepar);
-out.symm            = symm;
-
-
-out.center1         = grain{grain1}.center;
-out.center2         = grain{grain2}.center;
-out.dist_centers    = norm(out.center1-out.center2);
-out.radius1         = min(grain{grain1}.stat.bbxsmean,grain{grain1}.stat.bbysmean);
-out.radius2         = min(grain{grain2}.stat.bbxsmean,grain{grain2}.stat.bbysmean);
-out.distf           = parameters.index.strategy.m.end.distf;
-out.is_inside1      = (out.dist_centers < out.distf*out.radius1);
-out.is_inside2      = (out.dist_centers < out.distf*out.radius2);
-
-
-gtDBConnect();
-[int, x, y] = mym(['select avintint, avbbXsize, avbbYsize from ' parameters.acq.pair_tablename ' where grainID = ',num2str(grain1)]);
-out.avgint1         = mean(int);
-[int, x, y] = mym(['select avintint, avbbXsize, avbbYsize from ' parameters.acq.pair_tablename ' where grainID = ',num2str(grain2)]);
-out.avgint2         = mean(int);
-
-out.ratio1          = out.dist_centers/(out.radius1*out.distf);
-out.ratio2          = out.dist_centers/(out.radius2*out.distf);
-
-out.table           = [out.mis_angle out.mis_axis_hex out.mis_axis out.grain1 out.grain2];
-out.table_header    = 'mis_angle  mis_axis_hex mis_axis grain1 grain2';
-
-if ~isempty(vol_out)
-    %even if we have only one grain, can deal with the boundary plane
-    test = vol_out==id;
-    [x,y,z]=ind2sub(size(test), find(test));
-    [origin, a]=lsplane([x y z]);
-
-
-    gb_normal=a;
-   % gb_normal(3)=-gb_normal(3);
-
-    out.gb_norm = gb_normal';
-    out.gb_centre = origin';
-
-    if ~isempty(g1equiv)
-        plane1=g1equiv\gb_normal;
-    elseif ~isempty(g1)
-        plane1=g1\gb_normal;
-    else
-        plane1=[];
-    end
-
-    if ~isempty(g2)
-        plane2=g2\gb_normal;
-    else
-        plane2=[];
-    end
-
-    if spacegroup==225 || spacegroup==229
-        % if cubic then this is the index plane
-        out.gb_norm_grain1=plane1';
-        out.gb_norm_grain2=plane2';
-
-    elseif spacegroup==167 || spacegroup==663 || spacegroup==194
-        % if hexagonal, keep cartesian vector, but also
-        % convert the cartesian plane normal to hexagonal four index notation
-        % ditto for misorientation axis
-
-        out.gb_norm_grain1=plane1';
-        out.gb_norm_grain2=plane2';
-
-        if ~isempty(plane1)
-            hkl=plane1';
-            hkil = gtCart2Hex(hkl, parameters.cryst(phaseid).latticepar);
-            out.gb_norm_hex_grain1=hkil;
-        else
-            out.gb_norm_hex_grain1=[];
-        end
-        if ~isempty(plane2)
-            hkl=plane2';
-            hkil = gtCart2Hex(hkl, parameters.cryst(phaseid).latticepar);
-            out.gb_norm_hex_grain2=hkil;
-        else
-            out.gb_norm_hex_grain2=[];
-        end
-
-    else
-        disp('crystallography not supported!')
-    end
-end
-
-end
-
-