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Commit fabd60e3 authored by Nicola Vigano's avatar Nicola Vigano
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Revert "add missing file for cluster reconstruction on OAR" 

This reverts commit 4751df8e.
parent f22b4973
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5_reconstruction/gtReconstructGrainTwinClusters.m deleted 100644 → 0
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function gtReconstructGrainTwinClusters(first, last, workingdirectory, phase_id, parameters, varargin)
% gtReconstructGrainOrientation 6D reconstructions on a GPU machine
% gtAstraReconstructGrainTwinClusters(first, last, workingdirectory, phaseID, [parameters], varargin)
% -------------------------------------------------------
cd(workingdirectory);
if (~exist('parameters', 'var') || isempty(parameters))
parameters = gtLoadParameters();
end
parameters.fsim.check_spot = false;
conf = struct( ...
'recompute_osbb', true, ...
'ospace_resolution', [], ...
'ospace_lims', [], ...
'list', []);
[conf, ~] = parse_pv_pairs(conf, varargin);
if (isdeployed)
global GT_DB %#ok<NUSED,TLEV>
global GT_MATLAB_HOME %#ok<NUSED,TLEV>
load('workspaceGlobal.mat');
phase_id = str2double(phase_id);
first = str2double(first);
last = str2double(last);
end
sample = GtSample.loadFromFile;
if isempty(conf.list)
cluster_list = first : last;
else
cluster_list = conf.list;
% in case the code is deployed, we have to convert to strings
if ischar(cluster_list)
cluster_list = sscanf(cluster_list, '%d');
end
end
num_clusters = numel(cluster_list);
for ii_cl = 1 : num_clusters
cluster_id = cluster_list(ii_cl);
grain_ids = sample.phases{phase_id}.clusters(cluster_id).included_ids;
rec_opts = gtReconstruct6DGetParamenters(parameters);
if (isfield(parameters.rec, 'grains') ...
&& isfield(parameters.rec.grains, 'options') ...
&& ~isempty(parameters.rec.grains.options) ...
&& (~isfield(parameters.rec.grains.options, 'use_predicted_scatter_ints') ...
|| isempty(parameters.rec.grains.options.use_predicted_scatter_ints)) )
rec_opts.use_predicted_scatter_ints = true;
end
phase_dir = fullfile(parameters.acq.dir, '4_grains', ...
sprintf('phase_%02d', phase_id));
if (isstruct(grain_ids))
grs = grain_ids.samp_ors;
grains_str_ids = sprintf('_%04d', cat(2, grs.id));
else
grains_str_ids = sprintf('_%04d', grain_ids);
grain_cluster_file = fullfile(phase_dir, ...
sprintf('grain_cluster%s.mat', grains_str_ids));
fprintf('Loading the cluster file..')
grs = load(grain_cluster_file);
grs = grs.samp_ors;
fprintf('\b\b: Done.\n')
end
num_grains = numel(grs);
for ii_g = 1:num_grains
sampler(ii_g) = GtOrientationSampling(parameters, grs(ii_g)); %#ok<AGROW>
if (~isempty(conf.ospace_resolution))
if (numel(conf.ospace_resolution) == 1)
conf.ospace_resolution = conf.ospace_resolution(ones(num_grains, 1));
end
if (isempty(conf.ospace_lims) || (size(conf.ospace_lims, 1) < ii_g))
bb_gvdm = cat(1, grs(ii_g).bb_ors(:).R_vector);
else
diff_r_vecs = tand(conf.ospace_lims(ii_g, :) / 2);
bb_gvdm = [grs(ii_g).R_vector + diff_r_vecs(1:3); grs(ii_g).R_vector + diff_r_vecs(4:6)];
end
sampler(ii_g).make_res_simple_grid('cubic', conf.ospace_resolution(ii_g), bb_gvdm', rec_opts.ospace_oversize);
elseif (conf.recompute_osbb)
sampler(ii_g).make_simple_grid_estim_ODF('cubic', rec_opts.grid_edge, false, rec_opts.ospace_oversize);
else
bb_gvdm = cat(1, grs(ii_g).bb_ors(:).R_vector);
sampler(ii_g).make_even_simple_grid('cubic', rec_opts.grid_edge, bb_gvdm', rec_opts.ospace_oversize)
end
if (rec_opts.ospace_super_sampling > 1)
sampler(ii_g).make_supersampling_simple_grid([1 2 3], rec_opts.ospace_super_sampling);
end
end
algo = gtReconstruct6DLaunchAlgorithm(sampler, rec_opts, parameters);
vols = algo.getCurrentSolution();
ranges = zeros(num_grains, 2);
ranges(1, 1) = 1;
for ii_g = 2:num_grains
ranges(ii_g, 1) = ranges(ii_g-1) + sampler(ii_g-1).get_total_num_orientations();
end
ranges(1:end-1, 2) = ranges(2:end, 1) - 1;
ranges(end, 2) = numel(vols);
for ii_g = num_grains:-1:1
or_sizes = sampler(ii_g).get_orientation_sampling_size();
gr_vols = vols(ranges(ii_g, 1):ranges(ii_g, 2));
[avg_R_vecs, avg_R_vecs_int, stddev_R_vecs] = sampler(ii_g).getAverageOrientations(gr_vols);
avg_R_vec = sampler(ii_g).getAverageOrientation(gr_vols);
s_g_odf = reshape(sampler(ii_g).getODF(gr_vols), or_sizes{1});
[kam, gam(ii_g)] = gtDefComputeKernelAverageMisorientation(avg_R_vecs, avg_R_vecs_int);
[igm, gos(ii_g)] = gtDefComputeIntraGranularMisorientation(avg_R_vecs, avg_R_vecs_int, 'R_vector', grs(ii_g).R_vector);
% Restoring initial volume size (depending on the rounding)
if (rec_opts.volume_downscaling > 1)
avg_R_vecs_int = gtMathsUpsampleVolume(avg_R_vecs_int, rec_opts.volume_downscaling);
avg_R_vecs = gtMathsUpsampleVolume(avg_R_vecs, rec_opts.volume_downscaling);
stddev_R_vecs = gtMathsUpsampleVolume(stddev_R_vecs, rec_opts.volume_downscaling);
kam = gtMathsUpsampleVolume(kam, rec_opts.volume_downscaling);
igm = gtMathsUpsampleVolume(igm, rec_opts.volume_downscaling);
end
vol_size = size(avg_R_vecs_int);
shift = gtFwdSimComputeVolumeShifts(grs(ii_g).proj, parameters, vol_size);
ODF6D(ii_g) = struct( ...
'voxels_avg_R_vectors', {avg_R_vecs}, ...
'intensity', {avg_R_vecs_int}, ...
'shift', {shift}, ...
'R_vectors', {sampler(ii_g).get_R_vectors()}, ...
'voxels_stddev_R_vectors', {stddev_R_vecs}, ...
'single_grain_ODF', {s_g_odf}, ...
'single_grain_avg_R_vector', {avg_R_vec}, ...
'kernel_average_misorientation', {kam}, ...
'intra_granular_misorientation', {igm} );
end
cluster_rec_file = fullfile(phase_dir, ...
sprintf('grain_cluster_details%s.mat', grains_str_ids));
% Saving and cleaning at the same time
if (exist(cluster_rec_file, 'file'))
cl_rec = load(cluster_rec_file);
cl_rec.ODF6D = ODF6D;
else
cl_rec = struct('ODF6D', ODF6D); %#ok<NASGU>
end
save(cluster_rec_file, '-struct', 'cl_rec', '-v7.3');
if (algo.verbose)
clear('ODF6D')
[proj_blobs, proj_spots] = algo.getProjectionOfCurrentSolution();
% Restoring initial volume size (depending on the rounding)
if (rec_opts.volume_downscaling > 1)
fprintf('Expanding volumes..')
c = tic();
vols = gtMathsUpsampleVolume(vols, rec_opts.volume_downscaling);
fprintf('\b\b: Done (%f seconds).\n', toc(c))
end
for ii_g = num_grains:-1:1
gr_vols = vols(ranges(ii_g, 1):ranges(ii_g, 2));
ODF6D(ii_g) = struct( ...
'orientation_volumes', {gr_vols}, ...
'fwd_projected_blobs', {proj_blobs}, ...
'fwd_projected_spots', {proj_spots}, ...
'grain_average_misorientation', {gam(ii_g)}, ...
'grain_orientation_spread', {gos(ii_g)}, ...
'compute_statistics', {algo.get_statistics()} );
end
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
end
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