diff --git a/zUtil_Fit/gtFITParameters.m b/zUtil_Fit/gtFITParameters.m
index bc54275895a6d4907324f091264c67831c6e2d58..f554e2426d7600fbfc6d092bff870d8f96d0436f 100644
--- a/zUtil_Fit/gtFITParameters.m
+++ b/zUtil_Fit/gtFITParameters.m
@@ -154,7 +154,12 @@ if isempty(par.energy)
end
if isempty(par.labgeoini)
- par.labgeoini = parameters.labgeo;
+ disp('Using initial labgeo parameters from the parameters file.')
+ if (isfield(parameters, 'detgeo'))
+ par.labgeoini = gtGeoConvertDetgeo2LegacyLabgeo(parameters.detgeo, parameters.labgeo);
+ else
+ par.labgeoini = parameters.labgeo;
+ end
end
par.labgeoini.detorig = gtGeoDetOrig(par.labgeoini);
@@ -498,19 +503,19 @@ for ii = 1:length(gr)
end
end
-
% Global
+[detgeo, labgeo] = gtGeoConvertLegacyLabgeo2Detgeo(par.labgeoini);
if any(activeglobal)
- [labgeo, energy] = gtFitUpdateLabgeo(varsopt(1:sum(activeglobal)), ...
- activeglobal, par.iniglobal, par.labgeoini);
+ [labgeo, detgeo, energy] = gtFitUpdateLabgeo(varsopt(1:sum(activeglobal)), ...
+ activeglobal, par.iniglobal, labgeo, detgeo);
+ labgeo = rmfield(labgeo, 'detnorm');
+ labgeo = rmfield(labgeo, 'detorig');
else
- labgeo = par.labgeoini;
energy = par.iniglobal(10);
end
labgeo = rmfield(labgeo,'detnorm');
labgeo = rmfield(labgeo,'detorig');
-
% Drifts
drift = par.drift;
if ~isempty(par.ind.fit_drift_posX); drift.posx = [0, varsopt(par.ind.fit_drift_posX)']; end
@@ -521,8 +526,6 @@ if ~isempty(par.ind.fit_drift_rotY); drift.roty = [0, varsopt(par.ind.fit_drift_
if ~isempty(par.ind.fit_drift_rotZ); drift.rotz = [0, varsopt(par.ind.fit_drift_rotZ)']; end
if ~isempty(par.ind.fit_drift_energy); drift.energy = [0, varsopt(par.ind.fit_drift_energy)']; end
-
-
% Plot strain
meanstrain = mean(grainfit.strain, 2);
@@ -550,6 +553,7 @@ end
% end
% Output structure
+opt.detgeo = detgeo;
opt.labgeo = labgeo;
opt.energy = energy;
opt.grain = grain;
@@ -587,7 +591,6 @@ sfPlotRes(opt)
fprintf('\nTotal elapsed time (sec): %g\n', toc(tStart))
beep, pause(0.5), beep, pause(0.5), beep
-
end % of function
diff --git a/zUtil_Fit/gtFitFwdSimGrains.m b/zUtil_Fit/gtFitFwdSimGrains.m
index 688c872088150e1c0b936bbdc16d4bc3e5320e42..f1eb90f91819b145ef28b7bb631824b4be1a8138 100644
--- a/zUtil_Fit/gtFitFwdSimGrains.m
+++ b/zUtil_Fit/gtFitFwdSimGrains.m
@@ -43,28 +43,23 @@ end
labgeo = parameters.labgeo;
+if (~isfield(labgeo, 'omstep') || isempty(labgeo.omstep))
+ labgeo.omstep = gtGetOmegaStepDeg(parameters);
+end
+if (~isfield(parameters, 'detgeo') || isempty(parameters.detgeo))
+ parameters.detgeo = gtGeoConvertLegacyLabgeo2Detgeo(labgeo);
+end
+detgeo = parameters.detgeo;
samgeo = parameters.samgeo;
cryst = parameters.cryst(grain{1}.phaseid);
energy = parameters.acq.energy;
-omstep = 180/parameters.acq.nproj;
beamdir = labgeo.beamdir';
rotdir = labgeo.rotdir';
-% Scaling for Lab -> Detector transformation (mm -> pixels)
-detscaleu = 1/labgeo.pixelsizeu ;
-detscalev = 1/labgeo.pixelsizev ;
-
% Rotation tensor components
rotcomp = gtMathsRotationMatrixComp(labgeo.rotdir','col');
-% Detector projection matrix
-Qdet = gtFedDetectorProjectionTensor(labgeo.detdiru', labgeo.detdirv', ...
- detscaleu, detscalev);
-
-% Detector normal
-detnorm = cross(labgeo.detdiru, labgeo.detdirv)';
-
% B matrix for transformation from (hkl) to Cartesian Crystal reference
Bmat = gtCrystHKL2CartesianMatrix(cryst.latticepar);
@@ -139,8 +134,8 @@ for ii = 1:length(grain)
gcsam = gcsam(:,ones(1,4*size(plsam,2)));
% Absolute detector coordinates U,V in pixels
- uv = gtFedPredictUVMultiple(rot4, dveclab, gcsam, labgeo.detrefpos', ...
- detnorm, Qdet, [labgeo.detrefu; labgeo.detrefv]);
+ uv = gtFedPredictUVMultiple(rot4, dveclab, gcsam, detgeo.detrefpos', ...
+ detgeo.detnorm, detgeo.Qdet, [detgeo.detrefu; detgeo.detrefv]);
% Absolute coordinates U,V,W (pixel,pixel,image); to account for
@@ -148,7 +143,7 @@ for ii = 1:length(grain)
% to be mod(om,360)/omstep
grain{ii}.fsim.cu = uv(1,:);
grain{ii}.fsim.cv = uv(2,:);
- grain{ii}.fsim.cw = reshape(om4',[],1)'/omstep;
+ grain{ii}.fsim.cw = reshape(om4',[],1)'/labgeo.omstep;
grain{ii}.fsim.omind = reshape(omind4',[],1)';
grain{ii}.fsim.eta = gtGeoEtaFromDiffVec(dveclab', labgeo)';
grain{ii}.fsim.sinth = [sinth, sinth, sinth, sinth];
@@ -252,8 +247,8 @@ for ii = 1:length(grain)
%dveclab4 = gtFedPredictDiffVecMultiple(pllabd4, beamdir);
% Absolute detector coordinates U,V in pixels
- uv = gtFedPredictUVMultiple(rot, dveclab, gcsamd, labgeo.detrefpos', ...
- detnorm, Qdet, [labgeo.detrefu; labgeo.detrefv]);
+ uv = gtFedPredictUVMultiple(rot, dveclab, gcsamd, detgeo.detrefpos', ...
+ detgeo.detnorm, detgeo.Qdet, [detgeo.detrefu; detgeo.detrefv]);
% uv2 = gtFedPredictUVMultiple(rot2, dveclab, gcsamd2, labgeo.detrefpos', ...
% detnorm, Qdet, [labgeo.detrefu; labgeo.detrefv]);
@@ -268,7 +263,7 @@ for ii = 1:length(grain)
% to be mod(om,360)/omstep
grain{ii}.fsim.cu = uv(1,:);
grain{ii}.fsim.cv = uv(2,:);
- grain{ii}.fsim.cw = [om1, om2, om3, om4]/omstep;
+ grain{ii}.fsim.cw = [om1, om2, om3, om4]/labgeo.omstep;
grain{ii}.fsim.omind = reshape(omind',[],1)';
grain{ii}.fsim.eta = gtGeoEtaFromDiffVec(dveclab', labgeo)';
grain{ii}.fsim.sinth = [sinthd1, sinthd2, sinthd3, sinthd4];
@@ -283,8 +278,8 @@ for ii = 1:length(grain)
% Set NaN for spots that fall outside the detector area
if (~offdet)
- offd = (uv(1,:) <= 0.5) | (labgeo.detsizeu+0.5 <= uv(1,:)) | ...
- (uv(2,:) <= 0.5) | (labgeo.detsizev+0.5 <= uv(2,:));
+ offd = (uv(1,:) <= 0.5) | (detgeo.detsizeu+0.5 <= uv(1,:)) | ...
+ (uv(2,:) <= 0.5) | (detgeo.detsizev+0.5 <= uv(2,:));
fn = fieldnames(grain{ii}.fsim);
for jj = 1:length(fn)
diff --git a/zUtil_Fit/gtFitSpotPosDeviations.m b/zUtil_Fit/gtFitSpotPosDeviations.m
index 1438d1a526bbe065bc64cb0e90e69e54e3eb15f6..2f851e0968d92f4ab6136dbf8cf0e5597e9b209c 100644
--- a/zUtil_Fit/gtFitSpotPosDeviations.m
+++ b/zUtil_Fit/gtFitSpotPosDeviations.m
@@ -120,26 +120,18 @@ end
%%% Update labgeo
%%%%%%%%%%%%%%%%%%%%%%%%%
+[labgeo, detgeo] = gtGeoConvertLegacyLabgeo2Detgeo(par.labgeoini);
% Recalculate labgeo
if any(activeglobal)
- [labgeo, energy] = gtFitUpdateLabgeo(newvars(1:sum(activeglobal)), ...
- activeglobal, par.iniglobal, par.labgeoini);
+ [labgeo, detgeo, energy] = gtFitUpdateLabgeo( ...
+ newvars(1:sum(activeglobal)), activeglobal, par.iniglobal, labgeo, detgeo);
else
- labgeo = par.labgeoini;
energy = par.iniglobal(10);
end
% Rotation tensor components
rotcomp = gtMathsRotationMatrixComp(labgeo.rotdir','col');
-% Scaling for Lab -> Detector transformation (mm -> pixels)
-detscaleu = 1/labgeo.pixelsizeu ;
-detscalev = 1/labgeo.pixelsizev ;
-
-% Detector projection matrix
-Qdet = gtFedDetectorProjectionTensor(labgeo.detdiru', labgeo.detdirv', ...
- detscaleu, detscalev);
-
% In case the Sample axes are not aligned with the Lab axes at omega=0,
% the plane normals need to be brought in the Lab reference where the
% beam direction and rotation axis are defined.
@@ -233,8 +225,8 @@ sp.om = sp.om - (ind == 2)*par.numimages + (ind == 3)*par.numimages;
sp.dveclab = gtFedPredictDiffVecMultiple(sp.pl, labgeo.beamdir');
% Absolute detector coordinates U,V in pixels
-uv = gtFedPredictUVMultiple(sp.rot, sp.dveclab, sp.gcenter, labgeo.detrefpos', ...
- labgeo.detnorm', Qdet, [labgeo.detrefu; labgeo.detrefv]);
+uv = gtFedPredictUVMultiple(sp.rot, sp.dveclab, sp.gcenter, detgeo.detrefpos', ...
+ detgeo.detnorm', detgeo.Qdet, [detgeo.detrefu; detgeo.detrefv]);
% Absolute coordinates U,V,W (pixel,pixel,image); to account for
% measurement errors, do not correct for the image number
diff --git a/zUtil_Indexter/gtINDEXDrawGrainUnitCells.m b/zUtil_Indexter/gtINDEXDrawGrainUnitCells.m
index 260fb651aca71d0fb366d290deb96ba0c06b9e4e..eb8829a93cf2a7b1ac737d193be9c82ccdc363be 100644
--- a/zUtil_Indexter/gtINDEXDrawGrainUnitCells.m
+++ b/zUtil_Indexter/gtINDEXDrawGrainUnitCells.m
@@ -59,15 +59,24 @@ sample.rad = parameters.labgeo.samenvrad;
sample.bot = parameters.labgeo.samenvbot;
sample.top = parameters.labgeo.samenvtop;
+labgeo = parameters.labgeo;
+if (~isfield(labgeo, 'omstep') || isempty(labgeo.omstep))
+ labgeo.omstep = gtGetOmegaStepDeg(parameters);
+end
+if (~isfield(parameters, 'detgeo') || isempty(parameters.detgeo))
+ parameters.detgeo = gtGeoConvertLegacyLabgeo2Detgeo(labgeo);
+end
+detgeo = parameters.detgeo;
+
nof_grains = length(grains);
fs = 20;
samradmargin = 0.08;%0.05
samtopmargin = 0.4;%0.2
-pixelsize = (parameters.labgeo.pixelsizeu + parameters.labgeo.pixelsizev)/2;
+pixelsize = (detgeo.pixelsizeu + detgeo.pixelsizev)/2;
-if isfield(parameters.labgeo, 'sourcepoint')
- pixelsize = pixelsize * parameters.labgeo.sourcepoint(1)/(parameters.labgeo.detrefpos(1));
+if (isfield(parameters.labgeo, 'sourcepoint'))
+ pixelsize = pixelsize * parameters.labgeo.sourcepoint(1)/(detgeo.detrefpos(1));
disp('applying projection magnification')
end
diff --git a/zUtil_Indexter/gtINDEXFsimAllGrains.m b/zUtil_Indexter/gtINDEXFsimAllGrains.m
index b3ec142fbb019e45d810a3d74d9d320368b0073b..d7c4bfd84be9fff26eda5ddc4f534ef24d73855a 100644
--- a/zUtil_Indexter/gtINDEXFsimAllGrains.m
+++ b/zUtil_Indexter/gtINDEXFsimAllGrains.m
@@ -15,14 +15,22 @@ function gr = gtINDEXFsimAllGrains(phaseid, fsimID, saveFlag)
load(fullfile('4_grains', sprintf('phase_%02d', phaseid), 'index.mat'), 'grain');
parameters = gtLoadParameters();
+ labgeo = parameters.labgeo;
+ if (~isfield(labgeo, 'omstep') || isempty(labgeo.omstep))
+ labgeo.omstep = gtGetOmegaStepDeg(parameters);
+ end
+ if (~isfield(parameters, 'detgeo') || isempty(parameters.detgeo))
+ parameters.detgeo = gtGeoConvertLegacyLabgeo2Detgeo(labgeo);
+ end
+ detgeo = parameters.detgeo;
grain = gtIndexUpdateGrains(grain, parameters.cryst(phaseid).latticepar);
% add pairs info
grain = gtIndexAddInfo(grain, parameters.acq, parameters.cryst(phaseid), phaseid);
% fsim dct indexed spots
- grain = gtIndexFwdSimPairs(grain, parameters.labgeo, ...
+ grain = gtIndexFwdSimPairs(grain, detgeo, labgeo, ...
parameters.samgeo, [], parameters.cryst(phaseid).latticepar, ...
- gtGetOmegaStepDeg(parameters), parameters.acq.energy);
+ parameters.acq.energy);
% load DB and update dct grains
difspotIDs = gtIndexAllGrainValues(grain, 'difspotID', [], [], [], false);
diff --git a/zUtil_Indexter/gtINDEXMatchGrains_2.m b/zUtil_Indexter/gtINDEXMatchGrains_2.m
index f14678987fa77afd78b683c2dc8ef92af1f8d092..0d39bb682786bef554980d05c3ed24d27c10bad0 100644
--- a/zUtil_Indexter/gtINDEXMatchGrains_2.m
+++ b/zUtil_Indexter/gtINDEXMatchGrains_2.m
@@ -130,10 +130,18 @@ nof_grains2 = length(grain2);
out.odisp('Loading crystallographic info from parameters.mat ...')
parameters = gtLoadParameters();
+labgeo = parameters.labgeo;
+if (~isfield(labgeo, 'omstep') || isempty(labgeo.omstep))
+ labgeo.omstep = gtGetOmegaStepDeg(parameters);
+end
+if (~isfield(parameters, 'detgeo') || isempty(parameters.detgeo))
+ parameters.detgeo = gtGeoConvertLegacyLabgeo2Detgeo(labgeo);
+end
+detgeo = parameters.detgeo;
cryst = parameters.cryst(ph1);
-if ~exist('px1','var') || isempty(px1)
- px1 = (parameters.labgeo.pixelsizeu+parameters.labgeo.pixelsizev)/2;
+if (~exist('px1', 'var') || isempty(px1))
+ px1 = (detgeo.pixelsizeu + detgeo.pixelsizev) / 2;
disp(['pixelsize loaded from parameters: ' num2str(px1)])
end
if (~exist('px2', 'var') || isempty(px2))
diff --git a/zUtil_Indexter/gtIndexAddInfo.m b/zUtil_Indexter/gtIndexAddInfo.m
index 61bf573b7c70f7e138a424c38772d6a17053b684..06c73c62254aaa93e02e30d624fa9b6f32489686 100644
--- a/zUtil_Indexter/gtIndexAddInfo.m
+++ b/zUtil_Indexter/gtIndexAddInfo.m
@@ -152,19 +152,22 @@ grain = gtIndexUniqueReflections(grain, parameters.cryst(phaseid).dspacing,...
% Forward simulation
disp('Forward simulating reflections...')
-omstep = 180/parameters.acq.nproj;
labgeo = parameters.labgeo;
-labgeo.detorig = gtGeoDetOrig(labgeo);
-labgeo.detnorm = cross(labgeo.detdiru, labgeo.detdirv);
+if (~isfield(labgeo, 'omstep') || isempty(labgeo.omstep))
+ labgeo.omstep = gtGetOmegaStepDeg(parameters);
+end
+if (~isfield(parameters, 'detgeo') || isempty(parameters.detgeo))
+ parameters.detgeo = gtGeoConvertLegacyLabgeo2Detgeo(labgeo);
+end
+detgeo = parameters.detgeo;
% Fwd simulate pairs
-grain = gtIndexFwdSimPairs(grain, labgeo, parameters.samgeo,...
- [], parameters.cryst(phaseid).latticepar, omstep, parameters.acq.energy);
+grain = gtIndexFwdSimPairs(grain, detgeo, labgeo, parameters.samgeo,...
+ [], parameters.cryst(phaseid).latticepar, parameters.acq.energy);
% Fwd simulate individual spots
grain = gtFitFwdSimGrains(grain, parameters, 0, 0, []);
toc
-
-end % of function
\ No newline at end of file
+end
\ No newline at end of file
diff --git a/zUtil_Indexter/gtIndexApplyDrifts.m b/zUtil_Indexter/gtIndexApplyDrifts.m
index 6adee79a1dcdd8d8e55346ed182f0a9eb2aca68b..9424cc850a8a7c8a7a4da590bd8dd94bd345b4f4 100644
--- a/zUtil_Indexter/gtIndexApplyDrifts.m
+++ b/zUtil_Indexter/gtIndexApplyDrifts.m
@@ -1,5 +1,5 @@
-function fsim = gtIndexApplyDrifts(pl, dsp, gc, om, drift, labgeo, ...
- samgeo, rotcomp, Qdet, omstep, energy)
+function fsim = gtIndexApplyDrifts(pl, dsp, gc, om, drift, detgeo, labgeo, ...
+ samgeo, rotcomp, energy)
% pl - plane normals before drifts
% sinth - sin(theta) in deformed state
% om - omega-s to interpolate the rotational drift
@@ -37,7 +37,8 @@ function fsim = gtIndexApplyDrifts(pl, dsp, gc, om, drift, labgeo, ...
% Get fwd simulated data for the observed reflections
fsim = gtIndexFwdSim(om, gcd, ...
- sinthd, om4, pllab4, rot4, omind4, labgeo, samgeo, Qdet, omstep);
+ sinthd, om4, pllab4, rot4, omind4, ...
+ detgeo, labgeo, samgeo);
end
diff --git a/zUtil_Indexter/gtIndexDifSpots_2.m b/zUtil_Indexter/gtIndexDifSpots_2.m
index 467ce8940a921f42a8efb4f4dd4d591b53532bcc..05c942214b8af85560b16ebf484b59158052a06c 100644
--- a/zUtil_Indexter/gtIndexDifSpots_2.m
+++ b/zUtil_Indexter/gtIndexDifSpots_2.m
@@ -30,145 +30,153 @@ function [gid, conf, sp] = gtIndexDifSpots_2(grain, sp, parameters, fsimID, lim)
% conf = <double> list of conflicts
% sp = <struct> updated sp info (like difspot table)
+ %%%%%%%%%%%%%%%%%%
+ % Prepare input
+ %%%%%%%%%%%%%%%%%%
-%%%%%%%%%%%%%%%%%%
-% Prepare input
-%%%%%%%%%%%%%%%%%%
-
-if ~exist('grain','var') || isempty(grain)
- gtError('gtIndexDifspots:missingArgument','Argument ''grain'' must be given...Quitting')
-end
-if ~exist('sp','var') || isempty(sp)
- gtError('gtIndexDifspots:missingArgument','Argument ''sp'' must be given...Quitting')
-end
-if ~exist('parameters','var') || isempty(parameters)
- gtError('gtIndexDifspots:missingArgument','Argument ''parameters'' must be given...Quitting')
-end
-if ~exist('lim','var') || isempty(lim)
- gtError('gtIndexDifspots:missingArgument','Argument ''lim'' must be given...Quitting')
-end
-
-if ~exist('fsimID','var') || isempty(fsimID)
- fsimID = 1;
-end
+ if (~exist('grain', 'var') || isempty(grain))
+ gtError('gtIndexDifspots:missingArgument', ...
+ 'Argument ''grain'' must be given...Quitting')
+ end
+ if (~exist('sp', 'var') || isempty(sp))
+ gtError('gtIndexDifspots:missingArgument', ...
+ 'Argument ''sp'' must be given...Quitting')
+ end
+ if (~exist('parameters', 'var') || isempty(parameters))
+ gtError('gtIndexDifspots:missingArgument', ...
+ 'Argument ''parameters'' must be given...Quitting')
+ end
+ if (~exist('lim', 'var') || isempty(lim))
+ gtError('gtIndexDifspots:missingArgument', ...
+ 'Argument ''lim'' must be given...Quitting')
+ end
-omstep = 180/parameters.acq.nproj;
+ if (~exist('fsimID', 'var') || isempty(fsimID))
+ fsimID = 1;
+ end
-% Get spot and pair data
-if all(isfield(sp, {'difspotID','CentroidX','CentroidY','CentroidImage'}))
+ labgeo = parameters.labgeo;
+ if (~isfield(labgeo, 'omstep') || isempty(labgeo.omstep))
+ labgeo.omstep = gtGetOmegaStepDeg(parameters);
+ end
+ if (~isfield(parameters, 'detgeo') || isempty(parameters.detgeo))
+ parameters.detgeo = gtGeoConvertLegacyLabgeo2Detgeo(labgeo);
+ end
+ detgeo = parameters.detgeo;
- sp.uvw = [sp.CentroidX sp.CentroidY sp.CentroidImage];
- sp.om = sp.CentroidImage * omstep;
- sp.id = sp.difspotID;
+ % Get spot and pair data
+ if all(isfield(sp, {'difspotID', 'CentroidX', 'CentroidY', 'CentroidImage'}))
- pairsinfo = true;
-elseif all(isfield(sp, {'difspotidA','difspotidB','omega','omegaB',...
- 'eta','etaB','theta','grainID',...
- 'samcentXA','samcentYA','samcentZA',...
- 'samcentXB','samcentYB','samcentZB'}))
+ sp.uvw = [sp.CentroidX sp.CentroidY sp.CentroidImage];
+ sp.om = sp.CentroidImage * labgeo.omstep;
+ sp.id = sp.difspotID;
- sp.eta = [sp.eta, sp.etaB];
- sp.id = [sp.difspotidA, sp.difspotidB];
- sp.om = [sp.omega, sp.omegaB];
- sp.uvw(:,3) = sp.om / omstep;
+ pairsinfo = true;
+ elseif all(isfield(sp, {'difspotidA', 'difspotidB', 'omega', 'omegaB', ...
+ 'eta', 'etaB', 'theta', 'grainID', ...
+ 'samcentXA', 'samcentYA', 'samcentZA', ...
+ 'samcentXB', 'samcentYB', 'samcentZB'}))
- xyzA = [sp.samcentXA sp.samcentYA sp.samcentZA];
- xyzB = [sp.samcentXB sp.samcentYB sp.samcentZB];
- xyz = [xyzA; xyzB];
+ sp.eta = [sp.eta, sp.etaB];
+ sp.id = [sp.difspotidA, sp.difspotidB];
+ sp.om = [sp.omega, sp.omegaB];
+ sp.uvw(:, 3) = sp.om / labgeo.omstep;
- uvwLab = gtGeoSam2Lab(xyz, sp.om, parameters.labgeo, parameters.samgeo, 0, false);
- sp.uvw(:,1:2) = gtGeoLab2Det(uvwLab, parameters.labgeo, 0);
+ xyzA = [sp.samcentXA sp.samcentYA sp.samcentZA];
+ xyzB = [sp.samcentXB sp.samcentYB sp.samcentZB];
+ xyz = [xyzA; xyzB];
- pairsinfo = true;
-% check if it is by chance a taper scan, so then it contains those fields
-elseif all(isfield(sp, {'spot3d_id','fc','sc','omega'}) & ~isfield(sp, 'cu'))
+ uvwLab = gtGeoSam2Lab(xyz, sp.om, labgeo, parameters.samgeo, 0, false);
+ sp.uvw(:, 1:2) = gtGeoLab2Det(uvwLab, detgeo, 0);
- sp.uvw = [sp.fc sp.sc sp.omega / omstep];
- sp.om = sp.omega;
- sp.id = sp.spot3d_id;
+ pairsinfo = true;
+ % check if it is by chance a taper scan, so then it contains those fields
+ elseif all(isfield(sp, {'spot3d_id', 'fc', 'sc', 'omega'}) & ~isfield(sp, 'cu'))
- pairsinfo = false;
-else
- gtError('gtIndexDifspots:wrong_input','Wrong input for ''sp''... Quitting!')
-end
+ sp.uvw = [sp.fc sp.sc sp.omega / labgeo.omstep];
+ sp.om = sp.omega;
+ sp.id = sp.spot3d_id;
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Vectorise fwd simulated grain spots
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-uvw = gtIndexAllGrainValues(grain, 'fsim', 'uvw', fsimID, [], false);
-uvw = [uvw{:}];
-gr.u = uvw(1,:);
-gr.v = uvw(2,:);
-gr.w = uvw(3,:);
-
-gr.om = gtIndexAllGrainValues(grain, 'fsim', 'om', fsimID, [], false);
-gr.om = [gr.om{:}];
-gr.id =[];
-for ii=1:length(grain)
- gr.id = [gr.id; grain{ii}.id(ones(1,length(grain{ii}.fsim(fsimID).om)))'];
-end
-gr.id = gr.id';
+ pairsinfo = false;
+ else
+ gtError('gtIndexDifspots:wrong_input', 'Wrong input for ''sp''... Quitting!')
+ end
-disp(['current pixelsizeu: ' num2str(parameters.labgeo.pixelsizeu)])
-disp(['current pixelsizev: ' num2str(parameters.labgeo.pixelsizev)])
-disp(['omega step: ' num2str(omstep)])
+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ % Vectorise fwd simulated grain spots
+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+ uvw = gtIndexAllGrainValues(grain, 'fsim', 'uvw', fsimID, [], false);
+ uvw = [uvw{:}];
+ gr.u = uvw(1, :);
+ gr.v = uvw(2, :);
+ gr.w = uvw(3, :);
+
+ gr.om = gtIndexAllGrainValues(grain, 'fsim', 'om', fsimID, [], false);
+ gr.om = [gr.om{:}];
+ gr.id =[];
+ for ii=1:length(grain)
+ gr.id = [gr.id; grain{ii}.id(ones(1, length(grain{ii}.fsim(fsimID).om)))'];
+ end
+ gr.id = gr.id';
-% pixelsize of fsim detector
-if (pairsinfo)
- lim.u = lim.u / parameters.labgeo.pixelsizeu; % pixels
- lim.v = lim.v / parameters.labgeo.pixelsizev; % pixels
- lim.w = lim.w / omstep; % image number
-end
+ disp(['current pixelsizeu: ' num2str(detgeo.pixelsizeu)])
+ disp(['current pixelsizev: ' num2str(detgeo.pixelsizev)])
+ disp(['omega step: ' num2str(labgeo.omstep)])
-print_structure(lim , 'lim')
+ % pixelsize of fsim detector
+ if (pairsinfo)
+ lim.u = lim.u / detgeo.pixelsizeu; % pixels
+ lim.v = lim.v / detgeo.pixelsizev; % pixels
+ lim.w = lim.w / labgeo.omstep; % image number
+ end
+ print_structure(lim, 'lim')
-%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Loop to find grain ID-s
-%%%%%%%%%%%%%%%%%%%%%%%%%%
+ %%%%%%%%%%%%%%%%%%%%%%%%%%
+ % Loop to find grain ID-s
+ %%%%%%%%%%%%%%%%%%%%%%%%%%
-gid = zeros(1,length(sp.uvw));
-conf = zeros(1,length(sp.uvw));
-ok = false(length(gr.id),3);
+ gid = zeros(1, length(sp.uvw));
+ conf = zeros(1, length(sp.uvw));
+ ok = false(length(gr.id), 3);
-gauge = GtGauge(length(sp.uvw), 'Processing spots: ');
+ gauge = GtGauge(length(sp.uvw), 'Processing spots: ');
-%tic
+ %tic
-% Loop through spots - could be a parallel parfor loop
-for ii = 1:length(sp.uvw)
- gauge.incrementAndDisplay(100);
+ % Loop through spots - could be a parallel parfor loop
+ for ii = 1:length(sp.uvw)
+ gauge.incrementAndDisplay(100);
- % Check if position is within limits
- ok(:,1) = abs(gr.u - sp.uvw(ii,1)) < lim.u;
- ok(:,2) = abs(gr.v - sp.uvw(ii,2)) < lim.v;
- ok(:,3) = abs(gr.w - sp.uvw(ii,3)) < lim.w;
+ % Check if position is within limits
+ ok(:, 1) = abs(gr.u - sp.uvw(ii, 1)) < lim.u;
+ ok(:, 2) = abs(gr.v - sp.uvw(ii, 2)) < lim.v;
+ ok(:, 3) = abs(gr.w - sp.uvw(ii, 3)) < lim.w;
- oks = all(ok, 2);
- sumoks = sum(oks);
+ oks = all(ok, 2);
+ sumoks = sum(oks);
- % Check metadata, if exactly one candidate grain found
- if sumoks == 1
+ % Check metadata, if exactly one candidate grain found
+ if (sumoks == 1)
- idg = gr.id(find(oks,1,'first'));
- ids = gtIndexAllGrainValues(grain, 'id', [], [], []);
- ind = find(ids == idg);
+ idg = gr.id(find(oks, 1, 'first'));
+ ids = gtIndexAllGrainValues(grain, 'id', [], [], []);
+ ind = find(ids == idg);
- gid(ii) = idg;
+ gid(ii) = idg;
- elseif sumoks > 1
- % spot in conflict
- conf(ii) = sum(oks);
+ elseif (sumoks > 1)
+ % spot in conflict
+ conf(ii) = sum(oks);
+ end
end
-end
-gauge.delete();
+ gauge.delete();
-%toc;
-disp(' ')
-fprintf('No. of spots analysed : %d\n', length(gid));
-fprintf('No. of spots indexed : %d\n', sum(gid>0));
-fprintf('No. of spots in conflict: %d\n', sum(conf));
-
-end % end of function
+ %toc;
+ disp(' ')
+ fprintf('No. of spots analysed : %d\n', length(gid));
+ fprintf('No. of spots indexed : %d\n', sum(gid>0));
+ fprintf('No. of spots in conflict: %d\n', sum(conf));
+end
diff --git a/zUtil_Indexter/gtIndexFwdSim.m b/zUtil_Indexter/gtIndexFwdSim.m
index 8f67fbf5705ec5ef5b0e215d96a9b8e9f55786bd..4a35a068b586706cdf7f633a22791dff7dbb9375 100644
--- a/zUtil_Indexter/gtIndexFwdSim.m
+++ b/zUtil_Indexter/gtIndexFwdSim.m
@@ -1,18 +1,18 @@
-function fwdSim = gtIndexFwdSim(om_mes, gcsam, sinth, om4, pllab4, rot4, ...
- omind4, labgeo, samgeo, Qdet, omstep)
+function fwdSim = gtIndexFwdSim(om_mes, gcsam, ~, om4, pllab4, rot4, ...
+ omind4, detgeo, labgeo, samgeo)
% fwdSim = gtIndexFwdSim(om_mes, gcsam, sinth, om4, pllab4, rot4, ...
-% omind4, labgeo, samgeo, Qdet, omstep)
+% omind4, detgeo, labgeo, samgeo, omstep)
% -------------------------------------------------------------------
% Provides the fwd simulation data for a given omega index set.
% /mntdirect/_data_id19_graintracking/DCT_Analysis/RD4_15N_taper_/workspace/grid/
-% peaks_t100_s_cleaned_smalls.flt.new
+% peaks_t100_s_cleaned_smalls.flt.new
% Absolute differences
-dom = om4 - om_mes([1 1 1 1],:);
+dom = om4 - om_mes([1 1 1 1], :);
-% Find the indices with the smallest absolute difference; consider
+% Find the indices with the smallest absolute difference; consider
% errors and periodicity of 360deg in omega
-[~, ind] = min( abs( [dom; dom - 360; dom + 360] ) , [], 1);
+[~, ind] = min( abs( [dom; dom - 360; dom + 360] ), [], 1);
% Predicted omega is 360deg more
omhigh = ( (5 <= ind) & (ind <= 8) );
@@ -26,33 +26,33 @@ ind(omlow) = ind(omlow) - 8;
% Get final omega angles (can be <0) using the corresponding linear
% indices of omind4
-linind = ind + (0:length(ind)-1)*4;
+linind = ind + (0:length(ind)-1) * 4;
fwdSim.om = om4(linind);
-fwdSim.om(omhigh) = fwdSim.om(omhigh) - 360;
-fwdSim.om(omlow) = fwdSim.om(omlow) + 360;
+fwdSim.om(omhigh) = fwdSim.om(omhigh) - 360;
+fwdSim.om(omlow) = fwdSim.om(omlow) + 360;
-% Omega index
+% Omega index
fwdSim.omind = omind4(linind);
% Omegas in a column vector
-ind1 = (ind==1);
-ind2 = (ind==2);
-ind3 = (ind==3);
-ind4 = (ind==4);
+ind1 = (ind == 1);
+ind2 = (ind == 2);
+ind3 = (ind == 3);
+ind4 = (ind == 4);
% Extract the correct pllab vectors according to omind
fwdSim.pllab = zeros(3, length(ind));
-fwdSim.pllab(:,ind1) = pllab4(:,ind1,1);
-fwdSim.pllab(:,ind2) = pllab4(:,ind2,2);
-fwdSim.pllab(:,ind3) = pllab4(:,ind3,3);
-fwdSim.pllab(:,ind4) = pllab4(:,ind4,4);
+fwdSim.pllab(:, ind1) = pllab4(:, ind1, 1);
+fwdSim.pllab(:, ind2) = pllab4(:, ind2, 2);
+fwdSim.pllab(:, ind3) = pllab4(:, ind3, 3);
+fwdSim.pllab(:, ind4) = pllab4(:, ind4, 4);
% Extract the correct rotation matrices according to omind
fwdSim.rot = zeros(3, 3, length(ind));
-fwdSim.rot(:,:,ind1) = rot4(:,:,ind1,1);
-fwdSim.rot(:,:,ind2) = rot4(:,:,ind2,2);
-fwdSim.rot(:,:,ind3) = rot4(:,:,ind3,3);
-fwdSim.rot(:,:,ind4) = rot4(:,:,ind4,4);
+fwdSim.rot(:, :, ind1) = rot4(:, :, ind1, 1);
+fwdSim.rot(:, :, ind2) = rot4(:, :, ind2, 2);
+fwdSim.rot(:, :, ind3) = rot4(:, :, ind3, 3);
+fwdSim.rot(:, :, ind4) = rot4(:, :, ind4, 4);
% Diffraction vector
@@ -60,25 +60,25 @@ fwdSim.dveclab = gtFedPredictDiffVecMultiple(fwdSim.pllab, labgeo.beamdir');
fwdSim.dvecsam = gtGeoLab2Sam(fwdSim.dveclab', fwdSim.om, labgeo, samgeo, 1, 1)';
% Make sure grain center is extended
-gcsam = gcsam(:,ones(size(fwdSim.dveclab,2),1));
+gcsam = gcsam(:, ones(size(fwdSim.dveclab, 2), 1));
-% Absolute detector coordinates U,V in pixels
-uv = gtFedPredictUVMultiple(fwdSim.rot, fwdSim.dveclab, gcsam, labgeo.detrefpos', ...
- labgeo.detnorm', Qdet, [labgeo.detrefu; labgeo.detrefv]);
+% Absolute detector coordinates U, V in pixels
+uv = gtFedPredictUVMultiple(fwdSim.rot, fwdSim.dveclab, gcsam, detgeo.detrefpos', ...
+ detgeo.detnorm', detgeo.Qdet, [detgeo.detrefu; detgeo.detrefv]);
-is_nan = isnan(uv(1,:));
+is_nan = isnan(uv(1, :));
-keep = (uv(1,:) >= 1) & (labgeo.detsizeu >= uv(1,:)) & ...
- (uv(2,:) >= 1) & (labgeo.detsizev >= uv(2,:));
-% Absolute coordinates U,V,W (pixel,pixel,image); to account for
+keep = (uv(1, :) >= 1) & (detgeo.detsizeu >= uv(1, :)) & ...
+ (uv(2, :) >= 1) & (detgeo.detsizev >= uv(2, :));
+% Absolute coordinates U, V, W (pixel, pixel, image); to account for
% measurement errors, do not correct for the image number
-% to be mod(om,360)/omstep
+% to be mod(om, 360)/omstep
index_original = ismember(om_mes, fwdSim.om);
-fwdSim.uvw = [uv; fwdSim.om/omstep];
-fwdSim.uvw_nan = [uv(:,is_nan); fwdSim.om(is_nan)/omstep];
+fwdSim.uvw = [uv; fwdSim.om/labgeo.omstep];
+fwdSim.uvw_nan = [uv(:, is_nan); fwdSim.om(is_nan)/labgeo.omstep];
fwdSim.keep = keep;
fwdSim.is_nan = is_nan;
-fwdSim.image = mod(fwdSim.om,360)/omstep;
+fwdSim.image = mod(fwdSim.om, 360)/labgeo.omstep;
end % end of function
diff --git a/zUtil_Indexter/gtIndexFwdSimGrains.m b/zUtil_Indexter/gtIndexFwdSimGrains.m
index f79c9255df6460d2c7e89e7ba352c31bafd0c287..5b29a3b346f229f9092d99eed0237c5ec77fb240 100644
--- a/zUtil_Indexter/gtIndexFwdSimGrains.m
+++ b/zUtil_Indexter/gtIndexFwdSimGrains.m
@@ -74,12 +74,13 @@ else
end
labgeo = parameters.labgeo;
-if ~isfield(labgeo,'detorig')
- labgeo.detorig = gtGeoDetOrig(labgeo);
+if (~isfield(labgeo, 'omstep') || isempty(labgeo.omstep))
+ labgeo.omstep = gtGetOmegaStepDeg(parameters);
end
-if ~isfield(labgeo,'detnorm')
- labgeo.detnorm = cross(labgeo.detdiru,labgeo.detidirv);
+if (~isfield(parameters, 'detgeo') || isempty(parameters.detgeo))
+ parameters.detgeo = gtGeoConvertLegacyLabgeo2Detgeo(labgeo);
end
+detgeo = parameters.detgeo;
energy = parameters.acq.energy;
samgeo = parameters.samgeo;
@@ -104,14 +105,8 @@ end
cryst.usedfamsp = ismember(cryst.thetatypesp, cryst.used_thetatype);
-% Scaling for Lab -> Detector transformation (mm -> pixels)
-detscaleu = 1/labgeo.pixelsizeu;
-detscalev = 1/labgeo.pixelsizev;
% Rotation tensor components
rotcomp = gtMathsRotationMatrixComp(labgeo.rotdir', 'col');
-% Detector projection matrix
-Qdet = gtFedDetectorProjectionTensor(labgeo.detdiru',labgeo.detdirv',...
- detscaleu,detscalev);
% B matrix for transformation from (hkl) to Cartesian Crystal reference
Bmat = gtCrystHKL2CartesianMatrix(cryst.latticepar);
@@ -129,7 +124,7 @@ Rvec = gtIndexAllGrainValues(grain, 'R_vector', [], 1, 1:3);
cry2sam = gtFedRod2RotTensor(Rvec');
% calc radius of u, v coordinate
-getradius = @(u,v) sqrt((u - labgeo.detrefu).^2 + (v - labgeo.detrefv).^2);
+getradius = @(u, v) sqrt((u - detgeo.detrefu).^2 + (v - detgeo.detrefv).^2);
% loop through grains
for ii = 1:length(grain)
diff --git a/zUtil_Indexter/gtIndexFwdSimLimits.m b/zUtil_Indexter/gtIndexFwdSimLimits.m
index 6e0364e3a00d916c74f09745b7b6b96aa937febd..efdc13ecb0d11bea5e3fddb7d8a16f05af827d61 100644
--- a/zUtil_Indexter/gtIndexFwdSimLimits.m
+++ b/zUtil_Indexter/gtIndexFwdSimLimits.m
@@ -15,56 +15,62 @@ function lim = gtIndexFwdSimLimits(grain, parameters, pairinfo)
% .v = <double> Limits in mm for V coordinate
% .w = <double> Limits in degrees for omega coordinate
-omstep = 180/parameters.acq.nproj;
+ labgeo = parameters.labgeo;
+ if (~isfield(labgeo, 'omstep') || isempty(labgeo.omstep))
+ labgeo.omstep = gtGetOmegaStepDeg(parameters);
+ end
+ if (~isfield(parameters, 'detgeo') || isempty(parameters.detgeo))
+ parameters.detgeo = gtGeoConvertLegacyLabgeo2Detgeo(labgeo);
+ end
+ detgeo = parameters.detgeo;
-if pairinfo
- uvwA_sim = gtIndexAllGrainValues(grain,'fsimA','uvw',[],[],false); uvwA_sim = [uvwA_sim{:}];
- uvwB_sim = gtIndexAllGrainValues(grain,'fsimB','uvw',[],[],false); uvwB_sim = [uvwB_sim{:}];
- uvwA_exp = gtIndexAllGrainValues(grain,'uvwA',[],[],[],false); uvwA_exp = [uvwA_exp{:}];
- uvwB_exp = gtIndexAllGrainValues(grain,'uvwB',[],[],[],false); uvwB_exp = [uvwB_exp{:}];
-
- uvw_sim = [uvwA_sim, uvwB_sim];
- uvw_exp = [uvwA_exp, uvwB_exp];
-
- % Deviations between fwd simulation and measured spot positions
- du = uvw_sim(1,:) - uvw_exp(1,:);
- dv = uvw_sim(2,:) - uvw_exp(2,:);
- dw = uvw_sim(3,:) - uvw_exp(3,:);
+ if pairinfo
+ uvwA_sim = gtIndexAllGrainValues(grain, 'fsimA', 'uvw', [], [], false); uvwA_sim = [uvwA_sim{:}];
+ uvwB_sim = gtIndexAllGrainValues(grain, 'fsimB', 'uvw', [], [], false); uvwB_sim = [uvwB_sim{:}];
+ uvwA_exp = gtIndexAllGrainValues(grain, 'uvwA', [], [], [], false); uvwA_exp = [uvwA_exp{:}];
+ uvwB_exp = gtIndexAllGrainValues(grain, 'uvwB', [], [], [], false); uvwB_exp = [uvwB_exp{:}];
- lim.u = mean(du) + 3*std(du); % pixel
- lim.v = mean(dv) + 3*std(dv); % pixel
- lim.w = mean(dw) + 3*std(dw); % images
-
- % convert to mm and degrees
- lim.u = lim.u*parameters.labgeo.pixelsizeu; % mm
- lim.v = lim.v*parameters.labgeo.pixelsizev; % mm
- lim.w = lim.w*omstep; % omega [degrees]
-else
- % fsim only indexed peaks
+ uvw_sim = [uvwA_sim, uvwB_sim];
+ uvw_exp = [uvwA_exp, uvwB_exp];
-% uvw = gtIndexAllGrainValues(grain,'fsimU','uvw',[],[],false); uvw = [uvw{:}];
-% ind = find(isnan(uvw(3,:)));
-% % experimental positions
-% fc = gtIndexAllGrainValues(grain,'fc',[],[],[],false); fc = [fc{:}];
-% sc = gtIndexAllGrainValues(grain,'sc',[],[],[],false); sc = [sc{:}];
-% omega = gtIndexAllGrainValues(grain,'omega',[],[],[],false); omega = [omega{:}];
-%
-% uvw(:,ind) = [];
-%
-% fc(ind) = [];
-% sc(ind) = [];
-% omega(ind) = [];
-%
-% cent = [fc; sc];
-% centim = omega/omstep;
-
- lim.u = 2; % pixel
- lim.v = 2; % pixel
- lim.w = 5; % image number
-end
+ % Deviations between fwd simulation and measured spot positions
+ du = uvw_sim(1, :) - uvw_exp(1, :);
+ dv = uvw_sim(2, :) - uvw_exp(2, :);
+ dw = uvw_sim(3, :) - uvw_exp(3, :);
+
+ lim.u = mean(du) + 3*std(du); % pixel
+ lim.v = mean(dv) + 3*std(dv); % pixel
+ lim.w = mean(dw) + 3*std(dw); % images
-disp(['current pixelsizeu: ' num2str(parameters.labgeo.pixelsizeu)])
-disp(['current pixelsizev: ' num2str(parameters.labgeo.pixelsizev)])
-disp(['omega step: ' num2str(omstep)])
+ % convert to mm and degrees
+ lim.u = lim.u * detgeo.pixelsizeu; % mm
+ lim.v = lim.v * detgeo.pixelsizev; % mm
+ lim.w = lim.w * labgeo.omstep; % omega [degrees]
+ else
+ % fsim only indexed peaks
-end % end of function
+% uvw = gtIndexAllGrainValues(grain, 'fsimU', 'uvw', [], [], false); uvw = [uvw{:}];
+% ind = find(isnan(uvw(3, :)));
+% % experimental positions
+% fc = gtIndexAllGrainValues(grain, 'fc', [], [], [], false); fc = [fc{:}];
+% sc = gtIndexAllGrainValues(grain, 'sc', [], [], [], false); sc = [sc{:}];
+% omega = gtIndexAllGrainValues(grain, 'omega', [], [], [], false); omega = [omega{:}];
+%
+% uvw(:, ind) = [];
+%
+% fc(ind) = [];
+% sc(ind) = [];
+% omega(ind) = [];
+%
+% cent = [fc; sc];
+% centim = omega/labgeo.omstep;
+
+ lim.u = 2; % pixel
+ lim.v = 2; % pixel
+ lim.w = 5; % image number
+ end
+
+ disp(['current pixelsizeu: ' num2str(detgeo.pixelsizeu)])
+ disp(['current pixelsizev: ' num2str(detgeo.pixelsizev)])
+ disp(['omega step: ' num2str(labgeo.omstep)])
+end
diff --git a/zUtil_Indexter/gtIndexFwdSimPairs.m b/zUtil_Indexter/gtIndexFwdSimPairs.m
index 371d99f80cbdb6f9eb28bae6a958173be70c7002..288fc7c32ef426677139e100f2673036b4dab128 100644
--- a/zUtil_Indexter/gtIndexFwdSimPairs.m
+++ b/zUtil_Indexter/gtIndexFwdSimPairs.m
@@ -1,18 +1,18 @@
-function grain = gtIndexFwdSimPairs(grain, labgeo, samgeo, drift, ...
- latticepar, omstep, energy)
-% GTINDEXFWDSIMPAIRS Forward simulates spot positions on the detector
+function grain = gtIndexFwdSimPairs(grain, detgeo, labgeo, samgeo, drift, ...
+ latticepar, energy)
+% GTINDEXFWDSIMPAIRS Forward simulates spot positions on the detector
% for all spots indexed as Friedel pairs.
-%
-% grain = gtIndexFwdSimPairs(grain, labgeo, samgeo, drift, latticepar, omstep, energy)
+%
+% grain = gtIndexFwdSimPairs(grain, detgeo, labgeo, samgeo, drift, latticepar, energy)
% ------------------------------------------------------------------------------------
%
% INPUT:
% grain = <cell> all the grains as in index.mat
+% detgeo = <struct> as in parameters.detgeo
% labgeo = <struct> as in parameters.labgeo
% samgeo = <struct> as in parameters.samgeo
% drift = <double> sample drifts; if empty, no drifts are considered
% latticepar = <double> lattice parameters (1x6)
-% omstep = <double> omega rotational stepping (degrees/image)
% energy = <double> beam energy in keV
%
% OUTPUT:
@@ -28,23 +28,11 @@ function grain = gtIndexFwdSimPairs(grain, labgeo, samgeo, drift, ...
% Prepare input
%%%%%%%%%%%%%%%%%%%
-% B matrix for transformation from (hkl) to Cartesian Crystal reference
+% B matrix for transformation from (hkl) to Cartesian Crystal reference
Bmat = gtCrystHKL2CartesianMatrix(latticepar);
-% Scaling for Lab -> Detector transformation (mm -> pixels)
-detscaleu = 1/labgeo.pixelsizeu ;
-detscalev = 1/labgeo.pixelsizev ;
-
-
-labgeo.detorig = gtGeoDetOrig(labgeo);
-labgeo.detnorm = cross(labgeo.detdiru, labgeo.detdirv);
-
% Rotation tensor components
-rotcomp = gtMathsRotationMatrixComp(labgeo.rotdir','col');
-
-% Detector projection matrix
-Qdet = gtFedDetectorProjectionTensor(labgeo.detdiru', labgeo.detdirv', ...
- detscaleu, detscalev);
+rotcomp = gtMathsRotationMatrixComp(labgeo.rotdir', 'col');
% Rotation tensor describing crystal orientation; calculate all grains
% at once for speed-up.
@@ -101,15 +89,15 @@ for ii = 1:length(grain)
if isfield(grain{ii}, 'omegaA')
grain{ii}.fsimA = gtIndexApplyDrifts(pl_samd, dsp_d, grain{ii}.center',...
- grain{ii}.omegaA, drift, labgeo, samgeo, rotcomp, Qdet, omstep, energy);
+ grain{ii}.omegaA, drift, detgeo, labgeo, samgeo, rotcomp, energy);
end
if isfield(grain{ii}, 'omegaB')
grain{ii}.fsimB = gtIndexApplyDrifts(pl_samd, dsp_d, grain{ii}.center',...
- grain{ii}.omegaB, drift, labgeo, samgeo, rotcomp, Qdet, omstep, energy);
+ grain{ii}.omegaB, drift, detgeo, labgeo, samgeo, rotcomp, energy);
end
if isfield(grain{ii}, 'omega') && ~isfield(grain{ii}, 'omegaA') && ~isfield(grain{ii}, 'omegaB')
grain{ii}.fsimU = gtIndexApplyDrifts(pl_samd, dsp_d, grain{ii}.center',...
- grain{ii}.omega, drift, labgeo, samgeo, rotcomp, Qdet, omstep, energy);
+ grain{ii}.omega, drift, detgeo, labgeo, samgeo, rotcomp, energy);
end
else
@@ -146,15 +134,15 @@ for ii = 1:length(grain)
% or the one corrected for the pair).
if isfield(grain{ii}, 'omegaA')
grain{ii}.fsimA = gtIndexFwdSim(grain{ii}.omegaA, grain{ii}.center', ...
- sinth_d, om4, pl_lab4, rot4, omind4, labgeo, samgeo, Qdet, omstep);
+ sinth_d, om4, pl_lab4, rot4, omind4, detgeo, labgeo, samgeo);
end
if isfield(grain{ii}, 'omegaB')
grain{ii}.fsimB = gtIndexFwdSim(grain{ii}.omegaB, grain{ii}.center', ...
- sinth_d, om4, pl_lab4, rot4, omind4, labgeo, samgeo, Qdet, omstep);
+ sinth_d, om4, pl_lab4, rot4, omind4, detgeo, labgeo, samgeo);
end
if isfield(grain{ii}, 'omega') && ~isfield(grain{ii}, 'omegaA') && ~isfield(grain{ii}, 'omegaB')
grain{ii}.fsimU = gtIndexFwdSim(grain{ii}.omega, grain{ii}.center', ...
- sinth_d, om4, pl_lab4, rot4, omind4, labgeo, samgeo, Qdet, omstep);
+ sinth_d, om4, pl_lab4, rot4, omind4, detgeo, labgeo, samgeo);
end
end
end