diff --git a/3_pairmatchingGUI/gtMatchSaveResults.m b/3_pairmatchingGUI/gtMatchSaveResults.m
index 2799ff015e8a8e8480938634e119f8827d53d061..9b0818c950ce65f0bb96663f2371ddacfe43c95d 100644
--- a/3_pairmatchingGUI/gtMatchSaveResults.m
+++ b/3_pairmatchingGUI/gtMatchSaveResults.m
@@ -108,12 +108,12 @@ scattveclab = gtGeoScattVecFromDiffVec(handles.pairsfilt.diffveclab, ...
handles.labgeo.beamdir);
handles.pairsfilt.planenorm = gtGeoLab2Sam(scattveclab,...
- handles.pairsfilt.omegaA, handles.labgeo, samgeo, 1, 1);
+ handles.pairsfilt.omegaA, handles.labgeo, samgeo, true, 'only_rot', true);
% Diffraction vector
handles.pairsfilt.diffvecsam = gtGeoLab2Sam(handles.pairsfilt.diffveclab,...
- handles.pairsfilt.omegaA, handles.labgeo, samgeo, 1, 1);
+ handles.pairsfilt.omegaA, handles.labgeo, samgeo, true, 'only_rot', true);
% Difspot A in Sample reference
@@ -123,7 +123,7 @@ centAlab = gtGeoDet2Lab([handles.pairsfilt.centAU,handles.pairsfilt.centAV],...
handles.labgeo, 0) - handles.pairsfilt.shiftA;
handles.pairsfilt.centsamA = gtGeoLab2Sam(centAlab, handles.pairsfilt.omegaA,...
- handles.labgeo, samgeo, 0, 0);
+ handles.labgeo, samgeo, false);
% Spot B data is not important.
%handles.pairsfilt.centsamB = zeros(length(handles.pairsfilt.indA),3);
diff --git a/7_fed2/gtFedFwdProjExact.m b/7_fed2/gtFedFwdProjExact.m
index 066872fdc0164f11a7dbbc94f0475768e7dc7296..4ae88f7cb90dcc59943659638e42901acbb39442 100755
--- a/7_fed2/gtFedFwdProjExact.m
+++ b/7_fed2/gtFedFwdProjExact.m
@@ -31,7 +31,7 @@ function [gvb, bl] = gtFedFwdProjExact(gv, gvb, bl, fedpars, parameters, det_num
% beam direction and rotation axis are defined.
% Use the Sample -> Lab orientation transformation assuming omega=0;
% (vector length preserved for free vectors)
- plorig = gtGeoSam2Lab(plorig, eye(3), labgeo, samgeo, true, false);
+ plorig = gtGeoSam2Lab(plorig, eye(3), labgeo, samgeo, true);
if (isfield(fedpars, 'detector') ...
&& isfield(fedpars.detector, 'psf') ...
@@ -254,7 +254,7 @@ function [uvw_bl, rot_s2l] = predict_uvw(plsam, gvcs, defT, bl, labgeo, samgeo,
sinth, labgeo.beamdir', labgeo.rotdir', labgeo.rotcomp, bl.omind);
% Delete those where no reflection occurs
- if any(isnan(om));
+ if (any(isnan(om)))
inds_bad = find(isnan(om));
gvd(:, inds_bad(1:10))
error('gtFedFwdProjExact:bad_R_vectors', ...
diff --git a/zUtil_Deformation/gtDefFwdProjGvdm2NW.m b/zUtil_Deformation/gtDefFwdProjGvdm2NW.m
index 1b6735b0a343af63c439fb1a632174bcb01f7661..8e55d979a40f25fe9618524eca2753903c877317 100644
--- a/zUtil_Deformation/gtDefFwdProjGvdm2NW.m
+++ b/zUtil_Deformation/gtDefFwdProjGvdm2NW.m
@@ -67,7 +67,7 @@ function bl = gtDefFwdProjGvdm2NW(grain, ref_sel, gv, fedpars, parameters, eta_s
% beam direction and rotation axis are defined.
% Use the Sample -> Lab orientation transformation assuming omega=0;
% (vector length preserved for free vectors)
- pls_orig = gtGeoSam2Lab(pls_orig, eye(3), labgeo, samgeo, true, false);
+ pls_orig = gtGeoSam2Lab(pls_orig, eye(3), labgeo, samgeo, true);
linear_interp = ~(isfield(fedpars, 'projector') ...
&& strcmpi(fedpars.projector, 'nearest'));
diff --git a/zUtil_Deformation/gtDefFwdProjGvdm2UVW.m b/zUtil_Deformation/gtDefFwdProjGvdm2UVW.m
index 826e1d1ed60d98730d8f1d76faf079919ed7edd7..81f867aa424cdf437dfb1ce35893843f3f077d25 100755
--- a/zUtil_Deformation/gtDefFwdProjGvdm2UVW.m
+++ b/zUtil_Deformation/gtDefFwdProjGvdm2UVW.m
@@ -43,7 +43,7 @@ function bl = gtDefFwdProjGvdm2UVW(grain, ref_sel, gv, fedpars, parameters, det_
% beam direction and rotation axis are defined.
% Use the Sample -> Lab orientation transformation assuming omega=0;
% (vector length preserved for free vectors)
- pls_orig = gtGeoSam2Lab(pls_orig, eye(3), labgeo, samgeo, true, false);
+ pls_orig = gtGeoSam2Lab(pls_orig, eye(3), labgeo, samgeo, true);
if (isfield(fedpars, 'detector') ...
&& isfield(fedpars.detector, 'psf') ...
@@ -137,7 +137,7 @@ function bl = gtDefFwdProjGvdm2UVW(grain, ref_sel, gv, fedpars, parameters, det_
dvec_lab = gtFedPredictDiffVecMultiple(pllab, labgeo.beamdir');
rot_s2l = permute(rot_l2s, [2 1 3]);
- gvcs_lab = gtGeoSam2Lab(gvpcs', rot_s2l, labgeo, samgeo, false, [], element_wise_gcs);
+ gvcs_lab = gtGeoSam2Lab(gvpcs', rot_s2l, labgeo, samgeo, false, 'element_wise', element_wise_gcs);
uvw_bl = gtFedPredictUVWMultiple([], dvec_lab, gvcs_lab', ...
detgeo.detrefpos', detgeo.detnorm', detgeo.Qdet, ...
diff --git a/zUtil_Deformation/gtDefFwdProjGvdm2W.m b/zUtil_Deformation/gtDefFwdProjGvdm2W.m
index fbe3a62957f0d6730be25f63a2ed7fa7b4a9d427..86e763c64ed54d2a748938bd6a89ccfe3453077b 100644
--- a/zUtil_Deformation/gtDefFwdProjGvdm2W.m
+++ b/zUtil_Deformation/gtDefFwdProjGvdm2W.m
@@ -60,7 +60,7 @@ function bl = gtDefFwdProjGvdm2W(grain, ref_sel, gv, fedpars, parameters, det_in
% beam direction and rotation axis are defined.
% Use the Sample -> Lab orientation transformation assuming omega=0;
% (vector length preserved for free vectors)
- pls_orig = gtGeoSam2Lab(pls_orig, eye(3), labgeo, samgeo, true, false);
+ pls_orig = gtGeoSam2Lab(pls_orig, eye(3), labgeo, samgeo, true);
linear_interp = ~(isfield(fedpars, 'projector') ...
&& strcmpi(fedpars.projector, 'nearest'));
diff --git a/zUtil_Deformation/gtDefShapeFunctionsCreateNW.m b/zUtil_Deformation/gtDefShapeFunctionsCreateNW.m
index cda6a88b957ef7251f24becaf297132eaf00ab97..87a8ec31f213233869c9e8b4fc1c5faaa28cb957 100644
--- a/zUtil_Deformation/gtDefShapeFunctionsCreateNW.m
+++ b/zUtil_Deformation/gtDefShapeFunctionsCreateNW.m
@@ -45,7 +45,7 @@ function sf = gtDefShapeFunctionsCreateNW(sampler, eta_resoltion, varargin)
g = gtMathsRod2OriMat(ref_gr.R_vector');
pl_cry = gtVectorLab2Cryst(pl_samd, g)';
-% pl_labd = gtGeoSam2Lab(pl_samd, eye(3), self.parameters.labgeo, self.parameters.samgeo, true, false)';
+% pl_labd = gtGeoSam2Lab(pl_samd, eye(3), self.parameters.labgeo, self.parameters.samgeo, true)';
fprintf('Computing bounds of NW shape functions: ')
c = tic();
diff --git a/zUtil_Deformation/gtDefShapeFunctionsCreateW.m b/zUtil_Deformation/gtDefShapeFunctionsCreateW.m
index dad67c497d54511f0f1ce747641e66e6a09f3690..0521e7118057476c1eb331711d8d2f3ba294f9ce 100644
--- a/zUtil_Deformation/gtDefShapeFunctionsCreateW.m
+++ b/zUtil_Deformation/gtDefShapeFunctionsCreateW.m
@@ -20,7 +20,7 @@ function sf = gtDefShapeFunctionsCreateW(sampler)
g = gtMathsRod2OriMat(ref_gr.R_vector');
pl_cry = gtVectorLab2Cryst(pl_samd, g)';
end
-% pl_labd = gtGeoSam2Lab(pl_samd, eye(3), self.parameters.labgeo, self.parameters.samgeo, true, false)';
+% pl_labd = gtGeoSam2Lab(pl_samd, eye(3), self.parameters.labgeo, self.parameters.samgeo, true)';
sub_space_size = sampler.stats.sampling.gaps;
ospace_samp_size = sampler.get_orientation_sampling_size();
diff --git a/zUtil_Deformation/gtDefShapeFunctionsNW2UVW.m b/zUtil_Deformation/gtDefShapeFunctionsNW2UVW.m
index bc94aa3ffe81bb99a563928546ca4a8a080f018b..fef1813f68b6b94029e96bd380f56bca0f934cd9 100644
--- a/zUtil_Deformation/gtDefShapeFunctionsNW2UVW.m
+++ b/zUtil_Deformation/gtDefShapeFunctionsNW2UVW.m
@@ -97,7 +97,7 @@ function sfs_uvw = gtDefShapeFunctionsNW2UVW(sampler, sfs_nw, varargin)
% Calculating all the sample center positions at each omega inside
% the blobs
rot_s2l_all = gtMathsRotationTensor(all_ws, rotcomp_w);
- gclab_v_all = gtGeoSam2Lab(centers, rot_s2l_all, labgeo, samgeo, false, [], false);
+ gclab_v_all = gtGeoSam2Lab(centers, rot_s2l_all, labgeo, samgeo, false, 'element_wise', false);
gclab_v_all = reshape(gclab_v_all', 3, 1, tot_ws, []);
%%% Here we put the scattering vectors and center positions
diff --git a/zUtil_Fit/gtFitFwdSimGrains.m b/zUtil_Fit/gtFitFwdSimGrains.m
index 72181795cd2eff3822d985f4f3e36fb68ea72d88..95db81c3c266a61db00686a50ddb6175a95e5360 100644
--- a/zUtil_Fit/gtFitFwdSimGrains.m
+++ b/zUtil_Fit/gtFitFwdSimGrains.m
@@ -213,10 +213,10 @@ for ii = 1:length(grain)
[plsamd4, gcsamd4, sinthd4] = gtFitApplyDrifts(plsamd, gcsam, dspd, om4, drift, energy);
% Plane normals in Lab at omega positions after drifts
- pllab1 = gtGeoSam2Lab(plsamd1', om1, labgeo, samgeo, 1, 1);
- pllab2 = gtGeoSam2Lab(plsamd2', om2, labgeo, samgeo, 1, 1);
- pllab3 = gtGeoSam2Lab(plsamd3', om3, labgeo, samgeo, 1, 1);
- pllab4 = gtGeoSam2Lab(plsamd4', om4, labgeo, samgeo, 1, 1);
+ pllab1 = gtGeoSam2Lab(plsamd1', om1, labgeo, samgeo, true, 'only_rot', true);
+ pllab2 = gtGeoSam2Lab(plsamd2', om2, labgeo, samgeo, true, 'only_rot', true);
+ pllab3 = gtGeoSam2Lab(plsamd3', om3, labgeo, samgeo, true, 'only_rot', true);
+ pllab4 = gtGeoSam2Lab(plsamd4', om4, labgeo, samgeo, true, 'only_rot', true);
pllab = [pllab1; pllab2; pllab3; pllab4]';
%pllab01 = sam2lab0 * plsamd1;
diff --git a/zUtil_Fit/gtFitSpotPosDeviations.m b/zUtil_Fit/gtFitSpotPosDeviations.m
index 25cd1617e3e1e609b354cd9dd546e8ec33d1a407..b16ccbd45a02c58aec06c21a022369597eb4db04 100644
--- a/zUtil_Fit/gtFitSpotPosDeviations.m
+++ b/zUtil_Fit/gtFitSpotPosDeviations.m
@@ -194,7 +194,7 @@ end
% Plane normal in Lab reference at omega
-sp.pl = gtGeoSam2Lab(sp.pl', sp.om, labgeo, par.samgeo, 1, 1)';
+sp.pl = gtGeoSam2Lab(sp.pl', sp.om, labgeo, par.samgeo, ture, 'only_rot', true)';
% From degrees to images:
sp.om = sp.om/par.omstep;
@@ -276,8 +276,8 @@ error('Function is under development...' )
% The plane normals and grain centers need to be brought in the Lab
% reference where the beam direction and rotation axis are defined.
%(Should be done the other way, in the Sample ref., as that's faster)
- pllab = gtGeoSam2Lab(pld', om, labgeo, samgeo, 1, 1)';
- gclab = gtGeoSam2Lab(gcd', om, labgeo, samgeo, 0, 0)';
+ pllab = gtGeoSam2Lab(pld', om, labgeo, samgeo, true, 'only_rot', true)';
+ gclab = gtGeoSam2Lab(gcd', om, labgeo, samgeo, false)';
% Check if all reflections occur
%if any(isnan(omp))
@@ -286,7 +286,7 @@ error('Function is under development...' )
% Diffraction vector
dveclab = gtFedPredictDiffVecMultiple(pllab, labgeo.beamdir');
- %dvecsam = gtGeoLab2Sam(dveclab', omp, labgeo, samgeo, 1, 1)';
+ %dvecsam = gtGeoLab2Sam(dveclab', omp, labgeo, samgeo, true, 'only_rot', true)';
% Absolute detector coordinates U,V in pixels
uv = gtFedPredictUVMultiple([], dveclab, gclab, labgeo.detrefpos', ...
diff --git a/zUtil_ForwardSim/gtForwardSimulate_v2.m b/zUtil_ForwardSim/gtForwardSimulate_v2.m
index 0de4c59831d1c25007268f6dadf6cbad86f1266d..b15023b66c195c4f9968a8c0d3c36b7a721391f1 100644
--- a/zUtil_ForwardSim/gtForwardSimulate_v2.m
+++ b/zUtil_ForwardSim/gtForwardSimulate_v2.m
@@ -851,7 +851,7 @@ function proj_bls = predict_spot_masks_from_indexed(gr, grain_INDX, ...
segmentedSpots(det_index).CentroidX(difspotID_INDXTR), ...
segmentedSpots(det_index).CentroidY(difspotID_INDXTR)];
projvecs = gtGeoDet2Lab(projvecs, detgeo, false);
- projvecs = gtGeoLab2Sam(projvecs, Ws, labgeo, samgeo, 0, 0) - gr_center;
+ projvecs = gtGeoLab2Sam(projvecs, Ws, labgeo, samgeo, false) - gr_center;
verts_rec = gtFwdSimComputeCircumscribingPolyhedron(gr.center, ...
projvecs, Ws, BBs, parameters, det_index, 'convhull');
diff --git a/zUtil_ForwardSim/gtFwdSimComputeCircumscribingPolyhedron.m b/zUtil_ForwardSim/gtFwdSimComputeCircumscribingPolyhedron.m
index e6945b228f3f27f341de42810a6523866a70a01a..5229bac3b028bd5a1114b3a790380d24a523b7c7 100644
--- a/zUtil_ForwardSim/gtFwdSimComputeCircumscribingPolyhedron.m
+++ b/zUtil_ForwardSim/gtFwdSimComputeCircumscribingPolyhedron.m
@@ -45,10 +45,10 @@ function verts = gtFwdSimComputeCircumscribingPolyhedron(gr_center, projvecs, om
cbr_pos_lab = gtGeoDet2Lab([(bb(:, 1) + bb(:, 3)), (bb(:, 2) + bb(:, 4))], detgeo, false);
% positions in the reconstruction coordinates
- ctl_pos_rec = gtGeoLab2Sam(ctl_pos_lab, rot_s2l_w, labgeo, recgeo, 0, 0);
- ctr_pos_rec = gtGeoLab2Sam(ctr_pos_lab, rot_s2l_w, labgeo, recgeo, 0, 0);
- cbl_pos_rec = gtGeoLab2Sam(cbl_pos_lab, rot_s2l_w, labgeo, recgeo, 0, 0);
- cbr_pos_rec = gtGeoLab2Sam(cbr_pos_lab, rot_s2l_w, labgeo, recgeo, 0, 0);
+ ctl_pos_rec = gtGeoLab2Sam(ctl_pos_lab, rot_s2l_w, labgeo, recgeo, false);
+ ctr_pos_rec = gtGeoLab2Sam(ctr_pos_lab, rot_s2l_w, labgeo, recgeo, false);
+ cbl_pos_rec = gtGeoLab2Sam(cbl_pos_lab, rot_s2l_w, labgeo, recgeo, false);
+ cbr_pos_rec = gtGeoLab2Sam(cbr_pos_lab, rot_s2l_w, labgeo, recgeo, false);
projvecs_rec = gtGeoSam2Sam(projvecs, samgeo, recgeo, true);
projvecs_rec = gtMathsNormalizeVectorsList(projvecs_rec);
diff --git a/zUtil_Geo/gtGeoDiffVecInSample.m b/zUtil_Geo/gtGeoDiffVecInSample.m
index da1bdd4dc55e34941347c4e9777ca5d8a4c18e0c..ddf96b67a7f77ab6867240db3cc73f508db508bb 100644
--- a/zUtil_Geo/gtGeoDiffVecInSample.m
+++ b/zUtil_Geo/gtGeoDiffVecInSample.m
@@ -48,7 +48,7 @@ function [diffvec, samAXYZ, theta] = gtGeoDiffVecInSample(detAUV, omega, samBXYZ
labA = gtGeoDet2Lab(detAUV, detgeo, 0);
% Coordinate transformation from Lab to Sample
- samAXYZ = gtGeoLab2Sam(labA, omega, labgeo, samgeo, 0, 0);
+ samAXYZ = gtGeoLab2Sam(labA, omega, labgeo, samgeo, false);
% Diffraction vectors from points samXYZ to point samA:
diffvec = samAXYZ - samBXYZ(ones(size(samAXYZ, 1), 1), :);
@@ -65,7 +65,7 @@ function [diffvec, samAXYZ, theta] = gtGeoDiffVecInSample(detAUV, omega, samBXYZ
% Coordinate transformation from Lab to Sample for beam direction
% (free vector)
beamdirlab = labgeo.beamdir(ones(length(omega), 1), :);
- beamdirsam = gtGeoLab2Sam(beamdirlab, omega, labgeo, samgeo, 1, 1);
+ beamdirsam = gtGeoLab2Sam(beamdirlab, omega, labgeo, samgeo, true, 'only_rot', true);
% Use the dot products of beamdir and diffvec to get theta
theta = 0.5 * acosd( sum(beamdirsam.*diffvec, 2) );
diff --git a/zUtil_Geo/gtGeoDiffVecInSamplePair.m b/zUtil_Geo/gtGeoDiffVecInSamplePair.m
index 7e242210af6691c146ebed83376e4f900ec1bdd6..a367e5ae6b7c457263ac313fbd2ea9b0e82d1e27 100644
--- a/zUtil_Geo/gtGeoDiffVecInSamplePair.m
+++ b/zUtil_Geo/gtGeoDiffVecInSamplePair.m
@@ -73,11 +73,11 @@ function [diffvec, samA, theta] = gtGeoDiffVecInSamplePair(detUVA, detUVB, ...
% Coordinate transformation from Lab to Sample (free vector)
omega = (omegaA + omegaB) / 2;
- diffvec = gtGeoLab2Sam(dveclab, omega, labgeo, samgeo, 1, 1);
+ diffvec = gtGeoLab2Sam(dveclab, omega, labgeo, samgeo, true, 'only_rot', true);
if (nargout > 1)
% Coordinate transformation from Lab to Sample
- samA = gtGeoLab2Sam(labA, omegaA, labgeo, samgeo, 0, 0);
+ samA = gtGeoLab2Sam(labA, omegaA, labgeo, samgeo, false);
if (nargout == 3)
% Use the dot products of beamdir and diffvec to get theta
diff --git a/zUtil_Geo/gtGeoDiffractometerAlignPllab.m b/zUtil_Geo/gtGeoDiffractometerAlignPllab.m
new file mode 100644
index 0000000000000000000000000000000000000000..67eb4f377d0eb0c14672dbc2dbdb9074caf72c1a
--- /dev/null
+++ b/zUtil_Geo/gtGeoDiffractometerAlignPllab.m
@@ -0,0 +1,24 @@
+function [tilts, feasible] = gtGeoDiffractometerAlignPllab(diff, gr, pl_ind, lims)
+ num_sample_tilts = size(diff.axes_sam_tilt, 1);
+ if (~exist('pl_ind', 'var') || isempty(pl_ind))
+ pl_ind = 1:numel(gr.allblobs.omega);
+ end
+ pl_sam = permute(gr.allblobs.pl(pl_ind, :), [2 3 1]);
+ pl_sam(4, 1, :) = 1;
+
+ if (~exist('lims', 'var') || isempty(lims))
+ lims = [10, 20];
+ end
+
+ rot_ax = find(diff.axes_rotation);
+ other_axes = gtMathsCross(diff.axes_sam_tilt, diff.axes_rotation);
+ [ind_axes, ~] = find(other_axes);
+ for ii = num_sample_tilts:-1:1
+ tilts(ii, :) = atan2d(pl_sam(ind_axes(ii), 1, :), pl_sam(rot_ax, 1, :)); %#ok<FNDSB>
+ t = gtMathsRotationTranslationTensor(diff.axes_sam_tilt(ii, :), tilts(ii, :), diff.origin_sam_tilt, true);
+ pl_sam = gtMathsMatrixProduct(t, pl_sam);
+ end
+
+ feasible = all(bsxfun(@le, abs(tilts), lims'), 1);
+end
+
diff --git a/zUtil_Geo/gtGeoDiffractometerDefinition.m b/zUtil_Geo/gtGeoDiffractometerDefinition.m
new file mode 100644
index 0000000000000000000000000000000000000000..01a72ded64bf4106cfd65029b838e5721200910e
--- /dev/null
+++ b/zUtil_Geo/gtGeoDiffractometerDefinition.m
@@ -0,0 +1,27 @@
+function diff = gtGeoDiffractometerDefinition(types)
+ diff = struct( ...
+ 'axes_basetilt', {zeros(1, 3)}, ...
+ 'axes_rotation', {zeros(1, 3)}, ...
+ 'axes_sam_tilt', {zeros(0, 3)}, ... % They are applied in reverse order (last->first) for SAM->LAB transformations in gtGeoDiffractometerTensor
+ 'origin_basetilt', {zeros(1, 3)}, ...
+ 'origin_rotation', {zeros(1, 3)}, ...
+ 'origin_sam_tilt', {zeros(0, 3)} );
+
+ if (iscell(types))
+ diff(2:numel(types)) = diff;
+ for ii = 1:numel(types)
+ diff(ii) = gtAcqDiffractometerDefinition(types{ii});
+ end
+ else
+ switch (lower(types))
+ case 'esrf_id11'
+ diff.axes_basetilt = [0, 1, 0];
+ diff.axes_rotation = [0, 0, 1];
+ diff.axes_sam_tilt = [0, 1, 0; 1, 0, 0];
+ diff.origin_sam_tilt = [0, 0, 0; 0, 0, 0];
+ otherwise
+ error('gtAcqDiffractometerDefinition:wrong_argument', ...
+ 'Unknown diffractometer: %s', types)
+ end
+ end
+end
diff --git a/zUtil_Geo/gtGeoDiffractometerTensor.m b/zUtil_Geo/gtGeoDiffractometerTensor.m
new file mode 100644
index 0000000000000000000000000000000000000000..729dfc468752e3e94548d2ca287c0b8bb7935144
--- /dev/null
+++ b/zUtil_Geo/gtGeoDiffractometerTensor.m
@@ -0,0 +1,69 @@
+function [t, t_sam, t_rot, t_base] = gtGeoDiffractometerTensor(diff, type, freevec, varargin)
+ conf = struct( ...
+ 'angles_basetilt', 0, ...
+ 'angles_rotation', 0, ...
+ 'angles_sam_tilt', zeros(0, 1) );
+ conf = parse_pv_pairs(conf, varargin);
+
+ num_rotations = numel(conf.angles_rotation);
+ num_basetilts = numel(conf.angles_basetilt);
+ if (num_basetilts > 1 && num_rotations > 1 && num_basetilts ~= num_rotations)
+ error('gtGeoDiffractometerTensor:wrong_argument', ...
+ 'Only one direction allowed for scanning at a time')
+ end
+
+ % Whether we do a SAM->LAB or a LAB->SAM tensor
+ is_sam2lab = strcmpi(type, 'sam2lab');
+
+ % Building sample tilt components
+ if (iscell(conf.angles_sam_tilt))
+ error('gtGeoDiffractometerTensor:not_implemented', 'multiple_sample tilts not implemented yet')
+ elseif (isempty(conf.angles_sam_tilt) || isempty(diff.axes_sam_tilt))
+ t_sam = eye(4);
+ else
+ t_sam = eye(4);
+ if (is_sam2lab)
+ axes_order = size(diff.axes_sam_tilt, 1):-1:1;
+ else
+ axes_order = 1:size(diff.axes_sam_tilt, 1);
+ end
+
+ for ii = axes_order
+ sam_tilt_ii = build_tensor(diff.axes_sam_tilt(ii, :), ...
+ conf.angles_sam_tilt(ii), diff.origin_sam_tilt(ii, :), ...
+ is_sam2lab, freevec);
+ t_sam = sam_tilt_ii * t_sam;
+ end
+ end
+
+ % Building rotation components
+ if (isempty(conf.angles_rotation))
+ t_rot = eye(4);
+ else
+ t_rot = build_tensor(diff.axes_rotation, conf.angles_rotation, ...
+ diff.origin_rotation, is_sam2lab, freevec);
+ end
+
+ % Building base tilt components
+ if (isempty(conf.angles_basetilt))
+ t_base = eye(4);
+ else
+ t_base = build_tensor(diff.axes_basetilt, conf.angles_basetilt, ...
+ diff.origin_basetilt, is_sam2lab, freevec);
+ end
+
+ if (is_sam2lab)
+ t = gtMathsMatrixProduct(t_base, gtMathsMatrixProduct(t_rot, t_sam));
+ else
+ t = gtMathsMatrixProduct(t_sam, gtMathsMatrixProduct(t_rot, t_base));
+ end
+end
+
+function t = build_tensor(t_axis, t_angles, t_orig, is_sam2lab, freevec)
+ if (is_sam2lab)
+ t = gtMathsRotationTranslationTensor(t_axis, t_angles, t_orig, freevec);
+ else
+ t = gtMathsRotationTranslationTensor(t_axis, -t_angles, t_orig, freevec);
+ end
+end
+
diff --git a/zUtil_Geo/gtGeoLab2Sam.m b/zUtil_Geo/gtGeoLab2Sam.m
index 3b82fa6fd16b2629a413b1980586f4631b31f669..e238754ff3198e413ca2d7ad2e6c3ee1d133d6f6 100644
--- a/zUtil_Geo/gtGeoLab2Sam.m
+++ b/zUtil_Geo/gtGeoLab2Sam.m
@@ -1,9 +1,10 @@
-function [samXYZ, lab2sam] = gtGeoLab2Sam(labXYZ, omega, labgeo, samgeo, ...
- freevec, rot_flag, element_wise)
+function [samXYZ, lab2sam, rottensors] = gtGeoLab2Sam(labXYZ, omega, labgeo, samgeo, freevec, varargin)
% GTGEOLAB2SAM LAB -> SAMPLE reference coordinate transformation
%
-% [samXYZ, lab2sam] = gtGeoLab2Sam(labXYZ, omega, labgeo, ...
-% samgeo, freevec, rot_flag)
+% [samXYZ, lab2sam] = gtGeoLab2Sam(labXYZ, omega, labgeo, samgeo, varargin)
+%
+% conf = struct('only_rot', false, 'element_wise', true, ...
+% 'diffractometer', [], 'phi', 0, 'omega', 0, 'alpha', 0, 'beta', 0);
%
% ----------------------------------------------------------------------
%
@@ -21,7 +22,8 @@ function [samXYZ, lab2sam] = gtGeoLab2Sam(labXYZ, omega, labgeo, samgeo, ...
% samgeo.voxsize - [x,y,z] voxel sizes in lab units
% freevec - 0 for fixed vectors (e.g. location);
% 1 for free vectors (e.g. orientation/direction)
-% rot_flag - if true, only applies rotation so the norm of the
+% (Optional)
+% only_rot - if true, only applies rotation so the norm of the
% input vectors will be unchanged;
% i.e. no scaling applied according to the
% voxel sizes (only works if 'samgeo.lab2sam' is undefined)
@@ -36,13 +38,16 @@ function [samXYZ, lab2sam] = gtGeoLab2Sam(labXYZ, omega, labgeo, samgeo, ...
% lab vectors.
%
-if (~exist('rot_flag', 'var') || isempty(rot_flag))
- rot_flag = false;
-end
+conf = struct('only_rot', false, 'element_wise', true, ...
+ 'diffractometer', [], 'phi', 0, 'omega', 0, 'alpha', 0, 'beta', 0);
+conf = parse_pv_pairs(conf, varargin);
-if (~exist('element_wise', 'var') || isempty(element_wise))
- element_wise = true;
-end
+[size_omega(1), size_omega(2), size_omega(3)] = size(omega);
+
+use_instr_tensor_4x4 = all(size_omega(1:2) == 4);
+use_instr_tensor_3x3 = all(size_omega(1:2) == 3);
+
+use_diffractometer = ~isempty(conf.diffractometer) || use_instr_tensor_4x4;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Change of reference from Lab to Sample
@@ -53,7 +58,7 @@ end
% Therefore needs calculation of the inverse, and not only transpose.
if (~isfield(samgeo,'lab2sam') || (isfield(samgeo,'lab2sam') && isempty(samgeo.lab2sam)))
- if (rot_flag)
+ if (conf.only_rot)
% Keep norm of input vectors -> keep unit lengths in the rows of
% the transformation matrix
sam2lab = [samgeo.dirx; samgeo.diry; samgeo.dirz];
@@ -66,8 +71,8 @@ if (~isfield(samgeo,'lab2sam') || (isfield(samgeo,'lab2sam') && isempty(samgeo.l
lab2sam = inv(sam2lab);
-elseif (rot_flag)
- error('Transformation matrix already defined. Set ''rot_flag'' to false.')
+elseif (conf.only_rot)
+ error('Transformation matrix already defined. Set ''only_rot'' to false.')
else
lab2sam = samgeo.lab2sam;
end
@@ -76,47 +81,74 @@ end
%%% Rotation in Lab
%%%%%%%%%%%%%%%%%%%%%
-ones_in = ones(size(labXYZ, 1), 1);
+if (use_diffractometer)
+ if (use_instr_tensor_4x4)
+ rottensors = omega;
+ else
+ rottensors = gtGeoDiffractometerTensor(conf.diffractometer, 'sam2lab', freevec, ...
+ 'angles_basetilt', conf.basetilt, ...
+ 'angles_rotation', conf.omega, ...
+ 'angles_sam_tilt', conf.sample_tilts );
+ end
+ if (conf.element_wise)
+ labXYZ = permute(labXYZ, [2 3 1]);
+ labXYZ(4, 1, :) = 1;
+ else
+ labXYZ = labXYZ';
+ labXYZ(4, :) = 1;
+ end
-[size_omega(1), size_omega(2), size_omega(3)] = size(omega);
-% Tensor which rotates with omega from Lab back to Sample:
-if (all(size_omega(1:2) == [3 3]))
- % This means that the rotation tensors were passed already!
- if (size_omega(3) == 1)
- rottensors = omega(:, :, ones_in);
+ labXYZ_rot = gtMathsMatrixProduct(rottensors, labXYZ);
+
+ if (conf.element_wise)
+ labXYZ_rot = labXYZ_rot(1:3, 1, :);
+ labXYZ_rot = permute(labXYZ_rot, [3 1 2]);
else
- rottensors = omega;
+ labXYZ_rot = permute(labXYZ_rot, [2 3 1]);
+ labXYZ_rot = labXYZ_rot(:, 1:3);
end
else
- rotcomp = gtMathsRotationMatrixComp(labgeo.rotdir', 'col');
- rottensors = gtMathsRotationTensor(omega, rotcomp);
-end
+ ones_in = ones(size(labXYZ, 1), 1);
+
+ % Tensor which rotates with omega from Lab back to Sample:
+ if (use_instr_tensor_3x3)
+ % This means that the rotation tensors were passed already!
+ if (size_omega(3) == 1)
+ rottensors = omega(:, :, ones_in);
+ else
+ rottensors = omega;
+ end
+ else
+ rotcomp = gtMathsRotationMatrixComp(labgeo.rotdir', 'col');
+ rottensors = gtMathsRotationTensor(omega, rotcomp);
+ end
-if (~freevec)
- % Vectors relative to rotation axis position
- labXYZ = labXYZ - labgeo.rotpos(ones_in, :);
-end
+ if (~freevec)
+ % Vectors relative to rotation axis position
+ labXYZ = labXYZ - labgeo.rotpos(ones_in, :);
+ end
-rottensors_t = reshape(rottensors, 3, []);
+ rottensors_t = reshape(rottensors, 3, []);
-if (element_wise)
- % Multiply element-wise to avoid loop (applying rottensors to labXYZ)
- labXYZ_t = [labXYZ, labXYZ, labXYZ]';
- labXYZ_t = reshape(labXYZ_t, 3, []);
- pro = labXYZ_t .* rottensors_t;
+ if (conf.element_wise)
+ % Multiply element-wise to avoid loop (applying rottensors to labXYZ)
+ labXYZ_t = [labXYZ, labXYZ, labXYZ]';
+ labXYZ_t = reshape(labXYZ_t, 3, []);
+ pro = labXYZ_t .* rottensors_t;
- % Sum, reshape, transpose to get rotated vector
- labXYZ_rot = reshape(sum(pro, 1), 3, [])';
-else
- % output wll be groupped by (all rotations per center) x number centers
- labXYZ_rot = labXYZ * rottensors_t;
- labXYZ_rot = reshape(labXYZ_rot', 3, [])';
-end
+ % Sum, reshape, transpose to get rotated vector
+ labXYZ_rot = reshape(sum(pro, 1), 3, [])';
+ else
+ % output wll be groupped by (all rotations per center) x number centers
+ labXYZ_rot = labXYZ * rottensors_t;
+ labXYZ_rot = reshape(labXYZ_rot', 3, [])';
+ end
-if (~freevec)
- ones_out = ones(size(labXYZ_rot, 1), 1);
- % Set offset back to get rotated vector
- labXYZ_rot = labXYZ_rot + labgeo.rotpos(ones_out, :) - samgeo.orig(ones_out, :);
+ if (~freevec)
+ ones_out = ones(size(labXYZ_rot, 1), 1);
+ % Set offset back to get rotated vector
+ labXYZ_rot = labXYZ_rot + labgeo.rotpos(ones_out, :) - samgeo.orig(ones_out, :);
+ end
end
samXYZ = labXYZ_rot * lab2sam;
diff --git a/zUtil_Geo/gtGeoProjForReconstruction.m b/zUtil_Geo/gtGeoProjForReconstruction.m
index 7584c2140e53bb3b0f05efcbf6363d3519625a42..a5d3853ef2445e97b47b049d1fe223328a6887e2 100644
--- a/zUtil_Geo/gtGeoProjForReconstruction.m
+++ b/zUtil_Geo/gtGeoProjForReconstruction.m
@@ -79,18 +79,18 @@ function proj_geom = gtGeoProjForReconstruction(projvec_sam, omega, vol_center,.
% Bounding box center X,Y,Z coordinates in LAB and REC reference
bbcent_lab = gtGeoDet2Lab(bbcent_det, detgeo, 0);
- bbcent_rec = gtGeoLab2Sam(bbcent_lab, rot_omega, labgeo, recgeo, 0, 0);
+ bbcent_rec = gtGeoLab2Sam(bbcent_lab, rot_omega, labgeo, recgeo, false);
% Detector orientation vectors in REC reference
detdiru = detgeo.detdiru ./ sqrt(sum(detgeo.detdiru .^ 2)) * detgeo.pixelsizeu;
detdirv = detgeo.detdirv ./ sqrt(sum(detgeo.detdirv .^ 2)) * detgeo.pixelsizev;
- detdiru_rec = gtGeoLab2Sam(detdiru(ones_omega, :), rot_omega, labgeo, recgeo, true, false);
- detdirv_rec = gtGeoLab2Sam(detdirv(ones_omega, :), rot_omega, labgeo, recgeo, true, false);
+ detdiru_rec = gtGeoLab2Sam(detdiru(ones_omega, :), rot_omega, labgeo, recgeo, true);
+ detdirv_rec = gtGeoLab2Sam(detdirv(ones_omega, :), rot_omega, labgeo, recgeo, true);
if (strcmpi(rectype, 'ASTRA_absorption'))
projvec_lab = labgeo.beamdir(ones_omega, :);
- projvec_rec = gtGeoLab2Sam(projvec_lab, rot_omega, labgeo, recgeo, true, false);
+ projvec_rec = gtGeoLab2Sam(projvec_lab, rot_omega, labgeo, recgeo, true);
else
% Normalised projection vector in REC reference
projvec_rec = gtGeoSam2Sam(projvec_sam, samgeo, recgeo, true, false);
diff --git a/zUtil_Geo/gtGeoSam2Lab.m b/zUtil_Geo/gtGeoSam2Lab.m
index 6605fea299c5f1dd2c800ca2e87c12cabc675854..b6da8499aede0191c128755a89d287d5e7aaf5b3 100644
--- a/zUtil_Geo/gtGeoSam2Lab.m
+++ b/zUtil_Geo/gtGeoSam2Lab.m
@@ -1,9 +1,10 @@
-function [labXYZ, sam2lab] = gtGeoSam2Lab(samXYZ, omega, labgeo, samgeo, ...
- freevec, rot_flag, element_wise)
+function [labXYZ, sam2lab, rottensors] = gtGeoSam2Lab(samXYZ, omega, labgeo, samgeo, freevec, varargin)
% GTGEOSAM2LAB SAMPLE -> LAB reference coordinate transformation.
%
-% [labXYZ, sam2lab] = gtGeoSam2Lab(samXYZ, om, labgeo, samgeo, ...
-% freevec, rot_flag)
+% [labXYZ, sam2lab] = gtGeoSam2Lab(samXYZ, om, labgeo, samgeo, freevec, varargin)
+%
+% conf = struct('only_rot', false, 'element_wise', true, ...
+% 'diffractometer', [], 'phi', 0, 'omega', 0, 'alpha', 0, 'beta', 0);
%
% -----------------------------------------------------------------------
%
@@ -21,7 +22,8 @@ function [labXYZ, sam2lab] = gtGeoSam2Lab(samXYZ, omega, labgeo, samgeo, ...
% samgeo.voxsize - [x,y,z] voxel sizes in lab units
% freevec - 0 for fixed vectors (e.g. location);
% 1 for free vectors (e.g. orientation)
-% rot_flag - if true, only applies rotation and the norm of the
+% (optional)
+% only_rot - if true, only applies rotation and the norm of the
% input vectors will be unchanged; i.e. no scaling
% applied according to the voxel sizes (only works if
% 'samgeo.sam2lab' is undefined)
@@ -36,13 +38,16 @@ function [labXYZ, sam2lab] = gtGeoSam2Lab(samXYZ, omega, labgeo, samgeo, ...
% lab vectors.
%
-if (~exist('rot_flag', 'var') || isempty(rot_flag))
- rot_flag = false;
-end
+conf = struct('only_rot', false, 'element_wise', true, ...
+ 'diffractometer', [], 'basetilt', [], 'omega', [], 'sample_tilts', []);
+conf = parse_pv_pairs(conf, varargin);
-if (~exist('element_wise', 'var') || isempty(element_wise))
- element_wise = true;
-end
+[size_omega(1), size_omega(2), size_omega(3)] = size(omega);
+
+use_instr_tensor_4x4 = all(size_omega(1:2) == 4);
+use_instr_tensor_3x3 = all(size_omega(1:2) == 3);
+
+use_diffractometer = ~isempty(conf.diffractometer) || use_instr_tensor_4x4;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Change of reference from Sample to Lab
@@ -52,7 +57,7 @@ end
% (Lab is an orthonormal basis by definition.)
if (~isfield(samgeo,'sam2lab') || (isfield(samgeo,'sam2lab') && isempty(samgeo.sam2lab)))
- if (rot_flag)
+ if (conf.only_rot)
% Keep norm of input vectors -> keep unit lengths in the rows of
% the transformation matrix
sam2lab = [samgeo.dirx; samgeo.diry; samgeo.dirz];
@@ -63,8 +68,8 @@ if (~isfield(samgeo,'sam2lab') || (isfield(samgeo,'sam2lab') && isempty(samgeo.s
samgeo.dirz * samgeo.voxsize(3) ];
end
-elseif (rot_flag)
- error('Transformation matrix already defined. Set ''rot_flag'' to false.')
+elseif (conf.only_rot)
+ error('Transformation matrix already defined. Set ''only_rot'' to false.')
else
sam2lab = samgeo.sam2lab;
end
@@ -73,51 +78,79 @@ end
%%% Rotation in Lab
%%%%%%%%%%%%%%%%%%%%%
-ones_in = ones(size(samXYZ, 1), 1);
+% Vectors in Lab reference at the origin before rotation
+labXYZprerot = samXYZ * sam2lab;
-[size_omega(1), size_omega(2), size_omega(3)] = size(omega);
-% Tensor which rotates with omega from Sample to Lab
-if (all(size_omega(1:2) == [3 3]))
- % This means that the rotation tensors were passed already!
- if (size_omega(3) == 1)
- rottensors = omega(:, :, ones_in);
- else
+if (use_diffractometer)
+ if (use_instr_tensor_4x4)
rottensors = omega;
+ else
+ rottensors = gtGeoDiffractometerTensor(conf.diffractometer, 'sam2lab', freevec, ...
+ 'angles_basetilt', conf.basetilt, ...
+ 'angles_rotation', conf.omega, ...
+ 'angles_sam_tilt', conf.sample_tilts );
+ end
+ if (conf.element_wise)
+ labXYZprerot = permute(labXYZprerot, [2 3 1]);
+ labXYZprerot(4, 1, :) = 1;
+ else
+ labXYZprerot = labXYZprerot';
+ labXYZprerot(4, :) = 1;
+ end
+
+ labXYZ = gtMathsMatrixProduct(rottensors, labXYZprerot);
+
+ if (conf.element_wise)
+ labXYZ = labXYZ(1:3, 1, :);
+ labXYZ = permute(labXYZ, [3 1 2]);
+ else
+ labXYZ = labXYZ(1:3, :, :);
+ labXYZ = reshape(labXYZ, 3, []);
+ labXYZ = permute(labXYZ, [2 3 1]);
end
else
- rotcomp = gtMathsRotationMatrixComp(labgeo.rotdir', 'col');
- rottensors = gtMathsRotationTensor(-omega, rotcomp);
-end
+ ones_in = ones(size(samXYZ, 1), 1);
-% Vectors in Lab reference at the origin before rotation
-labXYZprerot = samXYZ * sam2lab;
+ % Tensor which rotates with omega from Sample to Lab
+ if (use_instr_tensor_3x3)
+ % This means that the rotation tensors were passed already!
+ if (size_omega(3) == 1)
+ rottensors = omega(:, :, ones_in);
+ else
+ rottensors = omega;
+ end
+ else
+ rotcomp = gtMathsRotationMatrixComp(labgeo.rotdir', 'col');
+ rottensors = gtMathsRotationTensor(-omega, rotcomp);
+ end
-if (~freevec)
- % Vectors relative to rot. axis position in Lab reference
- vv = samgeo.orig - labgeo.rotpos;
- labXYZprerot = labXYZprerot + vv(ones_in,:);
-end
+ if (~freevec)
+ % Vectors relative to rot. axis position in Lab reference
+ vv = samgeo.orig - labgeo.rotpos;
+ labXYZprerot = labXYZprerot + vv(ones_in,:);
+ end
-rottensors_t = reshape(rottensors, 3, []);
+ rottensors_t = reshape(rottensors, 3, []);
-if (element_wise)
- % Multiply element-wise to avoid loop
- labXYZprerot_t = [labXYZprerot, labXYZprerot, labXYZprerot]';
- labXYZprerot_t = reshape(labXYZprerot_t, 3, []);
- pro = labXYZprerot_t .* rottensors_t;
+ if (conf.element_wise)
+ % Multiply element-wise to avoid loop
+ labXYZprerot_t = [labXYZprerot, labXYZprerot, labXYZprerot]';
+ labXYZprerot_t = reshape(labXYZprerot_t, 3, []);
+ pro = labXYZprerot_t .* rottensors_t;
- % Sum, reshape, transpose
- labXYZ = reshape(sum(pro, 1), 3, [])';
-else
- % output wll be groupped by (all rotations per center) x number centers
- labXYZ = labXYZprerot * rottensors_t;
- labXYZ = reshape(labXYZ', 3, [])';
-end
+ % Sum, reshape, transpose
+ labXYZ = reshape(sum(pro, 1), 3, [])';
+ else
+ % output wll be groupped by (all rotations per center) x number centers
+ labXYZ = labXYZprerot * rottensors_t;
+ labXYZ = reshape(labXYZ', 3, [])';
+ end
-if (~freevec)
- ones_out = ones(size(labXYZ, 1), 1);
- % Set offset back
- labXYZ = labXYZ + labgeo.rotpos(ones_out, :);
+ if (~freevec)
+ ones_out = ones(size(labXYZ, 1), 1);
+ % Set offset back
+ labXYZ = labXYZ + labgeo.rotpos(ones_out, :);
+ end
end
end % of function
diff --git a/zUtil_Geo/gtGeoSamEnvInSampleRef.m b/zUtil_Geo/gtGeoSamEnvInSampleRef.m
index afa6ca8e65e5d6bb252a15a13636b9b9c5e77d92..0031c8e8c96f380d6f30edfce1ce7da0390a88f1 100644
--- a/zUtil_Geo/gtGeoSamEnvInSampleRef.m
+++ b/zUtil_Geo/gtGeoSamEnvInSampleRef.m
@@ -1,5 +1,5 @@
-function samenv = gtGeoSamEnvInSampleRef(labgeo,samgeo)
-% samenv = gtSampleVolInSampleRef(labgeo,samgeo)
+function samenv = gtGeoSamEnvInSampleRef(labgeo, samgeo)
+% samenv = gtSampleVolInSampleRef(labgeo, samgeo)
% ----------------------------------------------
% Returns the coordinates of the irradiated sample volume in the Sample
% reference.
@@ -17,19 +17,18 @@ function samenv = gtGeoSamEnvInSampleRef(labgeo,samgeo)
% size of the three)
% samenv.axis = <double> rotation axis direction
-% Envelope top and bottom point in Lab
-toppoint = labgeo.rotpos + labgeo.rotdir*labgeo.samenvtop;
-botpoint = labgeo.rotpos + labgeo.rotdir*labgeo.samenvbot;
+ % Envelope top and bottom point in Lab
+ toppoint = labgeo.rotpos + labgeo.rotdir * labgeo.samenvtop;
+ botpoint = labgeo.rotpos + labgeo.rotdir * labgeo.samenvbot;
-% Envelope top and bottom point in Sample
-samenv.top = gtGeoLab2Sam(toppoint,0,labgeo,samgeo,0,0);
-samenv.bot = gtGeoLab2Sam(botpoint,0,labgeo,samgeo,0,0);
+ % Envelope top and bottom point in Sample
+ samenv.top = gtGeoLab2Sam(toppoint, 0, labgeo, samgeo, false);
+ samenv.bot = gtGeoLab2Sam(botpoint, 0, labgeo, samgeo, false);
-% Radius
-samenv.rad = labgeo.samenvrad/max(samgeo.voxsize);
+ % Radius
+ samenv.rad = labgeo.samenvrad / max(samgeo.voxsize);
-% Normalised rotation axis direction
-samenv.axis = gtGeoLab2Sam(labgeo.rotdir,0,labgeo,samgeo,1,1);
-samenv.axis = samenv.axis/sqrt(sum(samenv.axis.*samenv.axis,2));
-
-end % end of function
+ % Normalised rotation axis direction
+ samenv.axis = gtGeoLab2Sam(labgeo.rotdir, 0, labgeo, samgeo, true, 'only_rot', true);
+ samenv.axis = samenv.axis / sqrt(sum(samenv.axis .* samenv.axis, 2));
+end
diff --git a/zUtil_Indexter/gtIndexDifSpots_2.m b/zUtil_Indexter/gtIndexDifSpots_2.m
index 05c942214b8af85560b16ebf484b59158052a06c..9b4349fbd57afc3ba9a4983b56b848d1c8cfe525 100644
--- a/zUtil_Indexter/gtIndexDifSpots_2.m
+++ b/zUtil_Indexter/gtIndexDifSpots_2.m
@@ -86,7 +86,7 @@ function [gid, conf, sp] = gtIndexDifSpots_2(grain, sp, parameters, fsimID, lim)
xyzB = [sp.samcentXB sp.samcentYB sp.samcentZB];
xyz = [xyzA; xyzB];
- uvwLab = gtGeoSam2Lab(xyz, sp.om, labgeo, parameters.samgeo, 0, false);
+ uvwLab = gtGeoSam2Lab(xyz, sp.om, labgeo, parameters.samgeo, false);
sp.uvw(:, 1:2) = gtGeoLab2Det(uvwLab, detgeo, 0);
pairsinfo = true;
diff --git a/zUtil_Indexter/gtIndexFwdSim.m b/zUtil_Indexter/gtIndexFwdSim.m
index 4a35a068b586706cdf7f633a22791dff7dbb9375..cf807a93e3191fde7c70ba8bfa735fcb444a6e51 100644
--- a/zUtil_Indexter/gtIndexFwdSim.m
+++ b/zUtil_Indexter/gtIndexFwdSim.m
@@ -57,7 +57,7 @@ fwdSim.rot(:, :, ind4) = rot4(:, :, ind4, 4);
% Diffraction vector
fwdSim.dveclab = gtFedPredictDiffVecMultiple(fwdSim.pllab, labgeo.beamdir');
-fwdSim.dvecsam = gtGeoLab2Sam(fwdSim.dveclab', fwdSim.om, labgeo, samgeo, 1, 1)';
+fwdSim.dvecsam = gtGeoLab2Sam(fwdSim.dveclab', fwdSim.om, labgeo, samgeo, true, 'only_rot', true)';
% Make sure grain center is extended
gcsam = gcsam(:, ones(size(fwdSim.dveclab, 2), 1));
diff --git a/zUtil_Indexter/gtIndexFwdSimGrains.m b/zUtil_Indexter/gtIndexFwdSimGrains.m
index 6c58738539bf96bf3cd7a617354989e3638e4c4e..88a2d48fe847bdc0710aaf337b3a3b9197cc95e7 100644
--- a/zUtil_Indexter/gtIndexFwdSimGrains.m
+++ b/zUtil_Indexter/gtIndexFwdSimGrains.m
@@ -215,7 +215,7 @@ for ii = 1:length(grain)
% Diffraction vectors in Lab and Sample
dveclab = gtFedPredictDiffVecMultiple(pllab4, labgeo.beamdir');
- dvecsam = gtGeoLab2Sam(dveclab', om, labgeo, samgeo, 1, 1)';
+ dvecsam = gtGeoLab2Sam(dveclab', om, labgeo, samgeo, true, 'only_rot', true)';
% Extend grain center
gc_sam = grain{ii}.center';
diff --git a/zUtil_Maths/gtMathsRotationTranslationTensor.m b/zUtil_Maths/gtMathsRotationTranslationTensor.m
new file mode 100644
index 0000000000000000000000000000000000000000..fd424e937af551a350fee18e528df64f28677f9f
--- /dev/null
+++ b/zUtil_Maths/gtMathsRotationTranslationTensor.m
@@ -0,0 +1,22 @@
+function t = gtMathsRotationTranslationTensor(t_axis, t_angles, t_orig, freevec)
+% function t = gtMathsRotationTranslationTensor(t_axis, t_angles, t_orig, freevec)
+%
+% It returns a <4 x 4 x n> stack of rotation + translation tensors
+
+ rot_comp = gtMathsRotationMatrixComp(t_axis', 'col');
+ t = eye(4);
+ t = repmat(t, 1, 1, numel(t_angles));
+ t(1:3, 1:3, :) = gtMathsRotationTensor(t_angles, rot_comp);
+
+ t_tr_pre = eye(4);
+ if (~freevec)
+ t_tr_pre(:, 4) = [-t_orig'; 1];
+ end
+
+ t_tr_post = eye(4);
+ if (~freevec)
+ t_tr_post(:, 4) = [t_orig'; 1];
+ end
+
+ t = gtMathsMatrixProduct(t_tr_post, gtMathsMatrixProduct(t, t_tr_pre));
+end