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function vols = gtReconstructGrainCluster(grain_ids, phase_id, parameters, varargin)
% gtReconstructGrainOrientation 6D reconstructions on a GPU machine
% gtAstraReconstructGrain(grainIDs, phaseID, [parameters])
% -------------------------------------------------------
if (~exist('parameters', 'var') || isempty(parameters))
parameters = gtLoadParameters();
end
parameters.fsim.check_spot = false;
rec = parameters.rec;
if (isfield(rec, 'grains'))
num_iter = rec.grains.num_iter;
algorithm = rec.grains.algorithm;
else
num_iter = rec.num_iter;
algorithm = '6DL1';
end
if (isfield(rec, 'grains') && isfield(rec.grains, 'options') ...
&& ~isempty(rec.grains.options))
grid_edge = rec.grains.options.grid_edge;
num_interp = rec.grains.options.num_interp;
lambda = rec.grains.options.lambda;
ss_grid_edge = rec.grains.options.super_sampling;
else
warning('gtReconstructGrainOrientation:wrong_parameters', ...
'The rec.grains structure doesn''t seem to be valid. Falling back to defaults')
grid_edge = 7;
num_interp = 1;
lambda = 1e-3;
ss_grid_edge = 1;
end
phase_dir = fullfile(parameters.acq.dir, '4_grains', ...
sprintf('phase_%02d', phase_id));
grains_str_ids = sprintf('_%04d', grain_ids);
grain_cluster_file = fullfile(phase_dir, ...
sprintf('grain_cluster%s.mat', grains_str_ids));
if (~exist(grain_cluster_file, 'file'))
grs = [];
for ii_g = numel(grain_ids):-1:1
grain_id = grain_ids(ii_g);
grs(ii_g) = gtForwardSimulate_v2(grain_id, grain_id, ...
pwd, phase_id, 'save_grain', false, 'display_figure', false);
end
[proj, gr, bb_ors] = gt6DCreateProjDataFromGrainCluster(grs, phase_id, varargin);
gr.proj = proj;
gr.bb_ors = bb_ors;
fprintf('Saving the cluster file..')
save(grain_cluster_file, '-struct', 'gr', '-v7.3');
fprintf('\b\b: Done.\n')
else
gr = load(grain_cluster_file);
bb_ors = gr.bb_ors;
end
bb_gvdm = cat(1, bb_ors(:).R_vector)';
sampler = GtOrientationSampling(parameters, gr);
sampler.make_simple_grid('cubic', grid_edge, bb_gvdm, 1);
if (ss_grid_edge > 1)
sampler.make_supersampling_simple_grid([1 2 3], ss_grid_edge);
end
rec_factory = Gt6DReconstructionAlgorithmFactory(parameters);
[algo, good_or] = rec_factory.getSubBlobReconstructionAlgo(sampler, num_interp);
algo.verbose = true;
mem_cons = [ ...
algo.get_peak_memory_consumption(algorithm), ...
algo.get_memory_consumption_volumes(), ...
algo.get_memory_consumption_blobs(), ...
algo.get_memory_consumption_sinograms(), ...
algo.get_memory_consumption_astra() ];
fprintf(['Estimated memory consumption: %d MB (Volumes %d MB, Blobs %d MB, Sinograms %d MB)'...
' of which ASTRA''s copies: %d MB\n'], ...
round(mem_cons / (2^20)))
switch (upper(algorithm))
case '6DL1'
algo.cp_ls(30); % To get close to the feasible region
algo.cp_l1(num_iter, lambda);
case '6DLS'
algo.cp_ls(num_iter);
case '6DTV'
algo.cp_ls(30); % To get close to the feasible region
algo.cp_tv(num_iter);
case '6DTVL1'
algo.cp_ls(30); % To get close to the feasible region
algo.cp_tvl1(num_iter, lambda);
otherwise
error('gtReconstructGrainOrientation:wrong_parameter', ...
'Unknown 6D algorithm: "%s"', algorithm)
end
vols = algo.getCurrentSolution();
[avg_R_vecs, avg_R_vecs_int] = sampler.getAverageOrientations(vols, good_or);
avg_R_vec = sampler.getAverageOrientation(vols, good_or);
s_g_odf = reshape(sampler.getODF(vols, good_or), grid_edge([1 1 1]));
vol_size = size(avg_R_vecs_int);
shift = gtFwdSimComputeVolumeShifts(gr.proj, parameters, vol_size);
[kam, gam] = gtDefComputeKernelAverageMisorientation(avg_R_vecs, avg_R_vecs_int);
[igm, gos] = gtDefComputeIntraGranularMisorientation(avg_R_vecs, avg_R_vecs_int, 'R_vector', gr.R_vector);
ODF6D = struct( ...
'voxels_avg_R_vectors', {avg_R_vecs}, ...
'intensity', {avg_R_vecs_int}, ...
'shift', {shift}, ...
'R_vectors', {sampler.get_R_vectors()}, ...
'single_grain_ODF', {s_g_odf}, ...
'single_grain_avg_R_vector', {avg_R_vec}, ...
'kernel_average_misorientation', {kam}, ...
'intra_granular_misorientation', {igm} ); %#ok<NASGU>
grain_details_file = fullfile(phase_dir, ...
sprintf('grain_cluster_details%s.mat', grains_str_ids));
save(grain_details_file, 'ODF6D', '-v7.3');
if (algo.verbose)
[proj_blobs, proj_spots] = algo.getProjectionOfCurrentSolution();
ODF6D = struct( ...
'orientation_volumes', {vols}, ...
'fwd_projected_blobs', {proj_blobs}, ...
'fwd_projected_spots', {proj_spots}, ...
'grain_average_misorientation', {gam}, ...
'grain_orientation_spread', {gos}, ...
'compute_statistics', {algo.get_statistics()} ); %#ok<NASGU>
grain_full_details_file = fullfile(phase_dir, ...
sprintf('grain_cluster_full_details%s.mat', grains_str_ids));
save(grain_full_details_file, 'ODF6D', '-v7.3');
end
end