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function bl = gtDefFwdProjGvdm2UVP(grain, selectedph, gv, fedpars, parameters, det_ind, verbose)
if (~exist('det_ind', 'var'))
det_ind = 1;
end
if (~exist('verbose', 'var'))
verbose = true;
end
o = GtConditionalOutput(verbose);
o.fprintf('Forward projection (%s):\n', mfilename)
phstep = gtAcqGetPhiStep(parameters, det_ind);
nbl = gtAcqTotNumberOfImages(parameters, det_ind);
uinds = gv.used_ind;
nv = numel(uinds);
ones_bl = ones(nbl, 1);
detgeo = parameters.detgeo(det_ind);
labgeo = parameters.labgeo;
samgeo = parameters.samgeo;
diff_acq = parameters.diffractometer(det_ind);
diff_ref = parameters.diffractometer(1);
rotcomp = gtMathsRotationMatrixComp(diff_acq.axes_basetilt', 'col');
rotdir = diff_acq.axes_basetilt';
if (~exist('selectedph', 'var') || isempty(selectedph))
lims_basetilt = parameters.acq(det_ind).range_basetilt;
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within_lims = grain.allblobs(det_ind).phi > lims_basetilt(1) & grain.allblobs(det_ind).phi < lims_basetilt(2);
phinds = grain.allblobs(det_ind).phind(within_lims);
phinds_counts = histcounts(phinds, (1:5)-0.5);
[~, phind] = max(phinds_counts);
o.fprintf(' - selected phind: %d (counts: [%s])\n', phind, sprintf(' %d', phinds_counts))
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selectedph = grain.allblobs(det_ind).phind == phind;
end
% we pick the first because they are all the same!
if (strcmpi(fedpars.defmethod, 'rod_rightstretch'))
% In this case, the deformation is relative to [0, 0, 0], so we
% need crystal plane normals
if (isfield(grain.allblobs, 'plcry'))
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pl_orig = grain.allblobs(det_ind).plcry(1, :)';
else
% We bring the plane normals back to the status of pl_cry
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pl_orig = grain.allblobs(det_ind).plorig(1, :);
g = gtMathsRod2OriMat(grain.R_vector);
pl_orig = gtVectorLab2Cryst(pl_orig, g)';
end
else
% Here the deformation is relative to the average oriantion, so we
% need the undeformed sample plane normals
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pl_orig = grain.allblobs(det_ind).plorig(1, :)';
end
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sinths = grain.allblobs(det_ind).sintheta(selectedph);
or_uvpw = grain.allblobs(det_ind).detector.uvpw(selectedph, 1:3);
omega = grain.allblobs(det_ind).omega(selectedph);
phinds = grain.allblobs(det_ind).phind(selectedph);
instr_t = gtGeoDiffractometerTensor(diff_acq, 'sam2lab', ...
'reference_diffractometer', diff_ref, 'angles_rotation', omega);
if (isfield(fedpars, 'detector') ...
&& isfield(fedpars.detector, 'psf') ...
&& ~isempty(fedpars.detector(det_ind).psf))
psf = fedpars.detector(det_ind).psf;
if (~iscell(psf))
psf = { psf };
end
if (numel(psf) == 1)
psf = psf(ones_bl);
end
else
psf = {};
end
if (isfield(fedpars, 'detector') ...
&& isfield(fedpars.detector, 'apply_uv_shift') ...
&& ~isempty(fedpars.detector(det_ind).apply_uv_shift) ...
&& fedpars.detector(det_ind).apply_uv_shift)
uvpw_shifts = [or_uvpw(:, 1:2), round(or_uvpw(:, 3))]';
else
uvpw_shifts = round(or_uvpw)';
end
linear_interp = ~(isfield(fedpars, 'projector') ...
&& isstruct(fedpars.projector) && isfield(fedpars.projector, 'interp') ...
&& strcmpi(fedpars.projector.interp, 'nearest'));
num_oversampling = size(gv.d, 3);
gvpow_uinds = gv.pow(1, uinds, :);
% This usually happens for shape functions, where we only have one
% center
element_wise_gcs = size(gv.pcs, 2) ~= 1;
bl = gtFwdSimBlobDefinition('blob_topo', nbl);
for ii_ss = 1:num_oversampling
if (element_wise_gcs)
else
end
if (size(gv.pow, 3) > 1)
gvpow = gvpow_uinds(1, :, ii_ss);
else
gvpow = gvpow_uinds;
end
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gvd = gv.d(:, uinds, ii_ss);
% Deformation tensor (relative to reference state) from its components
defT = gtFedDefTensorFromComps(gvd, fedpars.dcomps, fedpars.defmethod, 0);
%%% Computation of indices
o.fprintf(' - Super sampling %03d/%03d:\n * Computing indices and bbsizes: ', ...
ii_ss, num_oversampling)
t = tic();
uvp = cell(nbl, 1);
uvp_min = zeros(nbl, 3);
uvp_max = zeros(nbl, 3);
valid_voxels = false(nv, nbl);
for ii_b = 1:nbl
num_chars = o.fprintf('%03d/%03d', ii_b, nbl);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Calculate new detector coordinates
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% New deformed plane normals and relative elongations (relative to
% reference state)
% ! use plcry and not plsam to keep omega order below!
[pl_samd, drel] = gtStrainPlaneNormals(pl_orig, defT); % unit column vectors
% The plane normals need to be brought in the Lab reference where the
% beam direction and rotation axis are defined.
% Use the Sample -> Lab orientation transformation assuming omega=0;
% (vector length preserved for free vectors)
pl_samd = gtGeoSam2Lab(pl_samd', instr_t(:, :, ii_b), labgeo, samgeo, true)';
% New sin(theta)
sinth = sinths(ii_b) ./ drel;
% Predict omega angles: 4 for each plane normal
[ph, pllab] = gtFedPredictOmegaMultiple(pl_samd, sinth, ...
labgeo.beamdir', rotdir, rotcomp, phinds(ii_b));
ph = mod(ph + 180, 360) - 180;
valid_voxels(:, ii_b) = ~isnan(ph);
% Delete those where no reflection occurs
if (any(isnan(ph)))
inds_bad = find(isnan(ph));
gvd(:, inds_bad(1:min(10, numel(inds_bad))))
warning('gtFedFwdProjExact:bad_R_vectors', ...
'No diffraction from some elements after deformation (%d over %d) for blob %d.', ...
numel(inds_bad), numel(ph), ii_b)
end
% Diffraction vector
dvec_lab = gtFedPredictDiffVecMultiple(pllab, labgeo.beamdir');
rot_s2l_tot = gtGeoDiffractometerTensor(diff_acq, 'sam2lab', ...
'reference_diffractometer', diff_ref, ...
'angles_rotation', omega(ii_b), ...
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'angles_basetilt', ph);
gvcs_lab = gtGeoSam2Lab(gvpcs, rot_s2l_tot, labgeo, samgeo, ...
false, 'element_wise', element_wise_gcs);
uv_bl = gtFedPredictUVMultiple([], dvec_lab, gvcs_lab', ...
detgeo.detrefpos', detgeo.detnorm', detgeo.Qdet, ...
[detgeo.detrefu, detgeo.detrefv]');
uvp_bl = [uv_bl; ph ./ phstep];
% Transforming into offsets from
uvp_bl = bsxfun(@minus, uvp_bl, uvpw_shifts(:, ii_b));
uvp{ii_b} = uvp_bl;
uvp_min(ii_b, :) = min(uvp{ii_b}, [], 2)';
uvp_max(ii_b, :) = max(uvp{ii_b}, [], 2)';
if (any(uvp_min(ii_b, :) > 0) || any(uvp_max(ii_b, :) < 0))
warning('gtDefFwdProjGvdm2UVP:wrong_result', ...
'\nThe average orientation seems to project outside the blob!\n')
end
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o.fprintf(repmat('\b', [1, num_chars]));
end
o.fprintf('Done in %g s\n', toc(t));
o.fprintf(' * Computing max BBox size and feasibilities:\n')
psf_size = zeros(nbl, 2);
if (~isempty(psf))
for ii_b = 1:nbl
psf_size(ii_b, :) = (size(psf{ii_b}) - 1) / 2;
end
end
if (isfield(fedpars, 'detector'))
blob_size_add = fedpars.detector(det_ind).blobsizeadd;
else
blob_size_add = fedpars.blobsizeadd(det_ind, :);
end
blob_size_add = blob_size_add + [max(psf_size, [], 1), 0];
blob_uv_size = max(abs(min(uvp_min(:, 1:2), [], 1)), abs(max(uvp_max(:, 1:2), [], 1)));
blob_uv_size = 2 * (ceil(blob_uv_size) + blob_size_add(1:2)) + 1;
blob_orig_uv_shift = (blob_uv_size - 1) / 2 + 1;
blob_p_sizes = ceil(uvp_max(:, 3)) - floor(uvp_min(:, 3)) + blob_size_add(3) + 1;
blob_orig_p_shifts = 1 - floor(uvp_min(:, 3));
o.fprintf(' Computed Blob UV size: [%d, %d]\n', blob_uv_size);
o.fprintf(' Computed Blob Phi sizes: [%s]\n', sprintf(' %d', blob_p_sizes));
o.fprintf(' Blob size add: [%d, %d, %d] (psf: [%d, %d])\n', ...
blob_size_add, max(psf_size, [], 1));
tmp_bl = gtFwdSimBlobDefinition('blob_topo', nbl);
%%% Blob projection
o.fprintf(' * Projecting volumes: ')
t = tic();
for ii_b = 1:nbl
num_chars = o.fprintf('%03d/%03d', ii_b, nbl);
blob_orig_uvp_shift = [blob_orig_uv_shift, blob_orig_p_shifts(ii_b)]';
blob_uvp_size = [blob_uv_size blob_p_sizes(ii_b)];
% Detector coordinates U,V in blob
uvp_bl = uvp{ii_b} + blob_orig_uvp_shift(:, ones(1, nv));
% Let's now filter valid voxels
uvp_bl = uvp_bl(:, valid_voxels(:, ii_b))';
gvpow_v = reshape(gvpow(valid_voxels(:, ii_b)), [], 1);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Sum intensities
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Distribute value over 8 pixels
if (linear_interp)
[ucbl8, ints8] = gtMathsGetInterpolationIndices(uvp_bl, ...
gvpow_v, fedpars.bltype);
else
ucbl8 = round(uvp_bl);
ints8 = gvpow_v;
end
% Accumulate all intensities in the blob voxel-wise
% 'uvw' needs to be nx3; 'ints' is now 1xnx8
try
tmp_bl(ii_b).intm = accumarray(ucbl8, ints8, blob_uvp_size);
catch mexc
fprintf(['\n\nERROR\nThe error is probably caused by the', ...
' projected intensities falling outside the blob volume.', ...
'\nTry increasing the blob volume padding:', ...
' fedpars.detector(det_ind).blobsizeadd, or FIXING', ...
' YOUR CODE!!\n\n'])
disp('Blob ID:')
disp(ii_b)
disp('Blob size:')
disp(blob_uvp_size)
disp('Min projected U,V,W coordinates:')
fprintf('\t%g\t%g\t%g \t(rounded: %d %d %d )\n', ...
min(uvp_bl, [], 1), min(ucbl8, [], 1))
disp('Max projected U,V,W coordinates:')
fprintf('\t%g\t%g\t%g \t(rounded: %d %d %d )\n', ...
max(uvp_bl, [], 1), max(ucbl8, [], 1))
new_exc = GtFedExceptionFwdProj(mexc, det_ind, [0 0 0]);
throw(new_exc)
end
tmp_bl(ii_b).bbsize = blob_uvp_size;
im_low_lims = uvpw_shifts(1:3, ii_b) - blob_orig_uvp_shift + 1;
tmp_bl(ii_b).bbuim = [im_low_lims(1), im_low_lims(1) + blob_uvp_size(1) - 1];
tmp_bl(ii_b).bbvim = [im_low_lims(2), im_low_lims(2) + blob_uvp_size(2) - 1];
tmp_bl(ii_b).bbpim = [im_low_lims(3), im_low_lims(3) + blob_uvp_size(3) - 1];
o.fprintf(repmat('\b', [1, num_chars]));
end
o.fprintf('Done in %g s\n', toc(t));
if (num_oversampling == 1 || ii_ss == 1)
bl = tmp_bl;
else
o.fprintf(' * Merging super-sampling blobs: ')
t = tic();
tmp_bl_bbs = cat(1, tmp_bl(:).bbuim, tmp_bl(:).bbvim, tmp_bl(:).bbpim);
tmp_bl_bbs = reshape(tmp_bl_bbs, nbl, 3, 2);
bl_bbs = cat(1, bl(:).bbuim, bl(:).bbvim, bl(:).bbpim);
bl_bbs = reshape(bl_bbs, nbl, 3, 2);
should_reallocate = any(any(tmp_bl_bbs ~= bl_bbs, 2), 3);
container_blobs_bb = cat(3, ...
min(bl_bbs(:, :, 1), tmp_bl_bbs(:, :, 1)), ...
max(bl_bbs(:, :, 2), tmp_bl_bbs(:, :, 2)) ...
);
container_blobs_size = container_blobs_bb(:, :, 2) - container_blobs_bb(:, :, 1) + 1;
shift_bls = bl_bbs(:, :, 1) - container_blobs_bb(:, :, 1);
shift_tmp_bls = tmp_bl_bbs(:, :, 1) - container_blobs_bb(:, :, 1);
for ii_b = 1:nbl
if (should_reallocate(ii_b))
new_bl = gtFwdSimBlobDefinition('blob_topo');
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new_bl.intm = zeros(container_blobs_size(ii_b, :), fedpars.bltype);
new_bl.intm = gtPlaceSubVolume(new_bl.intm, bl(ii_b).intm, shift_bls(ii_b, :));
new_bl.intm = gtPlaceSubVolume(new_bl.intm, tmp_bl(ii_b).intm, shift_tmp_bls(ii_b, :), [], 'summed');
new_bl.bbsize = container_blobs_size(ii_b, :);
new_bl.bbuim = reshape(container_blobs_bb(ii_b, 1, :), 1, []);
new_bl.bbvim = reshape(container_blobs_bb(ii_b, 2, :), 1, []);
new_bl.bbpim = reshape(container_blobs_bb(ii_b, 3, :), 1, []);
bl(ii_b) = new_bl;
else
bl(ii_b).intm = bl(ii_b).intm + tmp_bl(ii_b).intm;
end
end
o.fprintf('Done in %g s\n', toc(t));
end
end
if (num_oversampling > 1)
o.fprintf(' - Renormalizing to initial intensity:');
t = tic();
for ii_b = 1:nbl
bl(ii_b).intm = bl(ii_b).intm / num_oversampling;
o.fprintf(repmat('\b', [1, num_chars]));
end
o.fprintf('Done in %g s\n', toc(t));
end
if (~isempty(psf))
o.fprintf(' - Applying PSF:');
t = tic();
for ii_b = 1:nbl
num_chars = o.fprintf('%03d/%03d', ii_b, nbl);
bl(ii_b).intm = convn(bl(ii_b).intm, psf{ii_b}, 'same');
o.fprintf(repmat('\b', [1, num_chars]));
end
o.fprintf('Done in %g s\n', toc(t));
end
o.fprintf(' - Computing boundaries of measured blobs inside blob bounding box..')
t = tic();
for ii_b = 1:nbl
uproj = sum(sum(abs(bl(ii_b).intm), 2), 3);
bl(ii_b).mbbu = [find(uproj, 1, 'first'), find(uproj, 1, 'last')] + bl(ii_b).bbuim(1) - 1;
vproj = sum(sum(abs(bl(ii_b).intm), 1), 3);
bl(ii_b).mbbv = [find(vproj, 1, 'first'), find(vproj, 1, 'last')] + bl(ii_b).bbvim(1) - 1;
pproj = sum(sum(abs(bl(ii_b).intm), 1), 2);
bl(ii_b).mbbp = [find(pproj, 1, 'first'), find(pproj, 1, 'last')] + bl(ii_b).bbpim(1) - 1;
bl(ii_b).mbbsize = [bl(ii_b).mbbu(2) - bl(ii_b).mbbu(1) + 1, ...
bl(ii_b).mbbv(2) - bl(ii_b).mbbv(1) + 1, ...
bl(ii_b).mbbp(2) - bl(ii_b).mbbp(1) + 1 ];
end
o.fprintf('\b\b: Done in %g s\n', toc(t));
for ii_b = 1:nbl
bl(ii_b).intensity = sum(bl(ii_b).intm(:));
end
end