gtReconstructTestCase.m

function [result_viewer, result, post_result, algo] = gtReconstructTestCase(test_data, det_index, do_plot, single_orientation)

    if (~exist('det_index', 'var') || isempty(det_index))
        det_index = 1;
    end
    if (~exist('do_plot', 'var') || isempty(do_plot))
        do_plot = false;
    end
    if (~exist('single_orientation', 'var') || isempty(single_orientation))
        single_orientation = false;
    end

    rec_opts = gtReconstruct6DGetParamenters(test_data.parameters);

    if (~isfield(test_data, 'gv'))
        test_data.gv.dm = gtDefDmvol2Gvdm(test_data.dmvol);
    end
    gvdm = test_data.gv.dm(:, test_data.gv.used_ind);
%     gvcs = test_data.gv.cs(:, test_data.gv.used_ind);
%     if (~isfield(test_data, 'intvol'))
%         size_int_vol = [ ...
%             size(test_data.dmvol, 1), ...
%             size(test_data.dmvol, 2), ...
%             size(test_data.dmvol, 3) ];
%         test_data.intvol = ones(size_int_vol, 'like', test_data.dmvol);
%     end
%     gvpow = test_data.intvol(test_data.gv.used_ind);

    cryst = test_data.parameters.cryst(test_data.grain.phaseid);
    symm = gtCrystGetSymmetryOperators(cryst.crystal_system, cryst.spacegroup);
    gtGetMaxDisorientation(gvdm, symm, 'diameter_average');
    gtGetMaxDisorientation(gvdm, symm, 'diameter_zero');

    if (do_plot)
        f = figure();
        ax = axes('parent', f);
        hold(ax, 'on')
        scatter3(ax, gvdm(1, 1:10:end)', gvdm(2, 1:10:end)', gvdm(3, 1:10:end)', 20);
    end

    sampler = GtOrientationSampling(test_data.parameters, test_data.grain, 'detector_index', det_index(1));

    if (do_plot)
        % Testing ability of GtOrientationSampling to detect the correct
        % orientation-space boundingbox
        sampler.make_grid_resolution(rec_opts.ospace_resolution, rec_opts.max_grid_edge_points);

        scatter3(ax, sampler.R_vectors(:, 1), sampler.R_vectors(:, 2), sampler.R_vectors(:, 3), 20, 'r');
        drawnow();

        sampler = GtOrientationSampling(test_data.parameters, test_data.grain, 'detector_index', det_index(1));
    end

    gvdm_lims = [min(gvdm, [], 2), max(gvdm, [], 2)];
    gvdm_lims(:, 1) = gvdm_lims(:, 1) - tand(rec_opts.ospace_resolution / 4);
    gvdm_lims(:, 2) = gvdm_lims(:, 2) + tand(rec_opts.ospace_resolution / 4);
    if ((numel(det_index) == 1) && strcmpi(test_data.parameters.acq(det_index).type, 'topotomo'))
        gvdm_lims(3, :) = [-1, 1] * tand(rec_opts.ospace_resolution / 4);
    end

    for ii_d = 1:numel(det_index)
        % Using the optimal orientation-space boundingbox
        if (single_orientation)
            sampler.make_undeformed_sampling('det_ind', det_index(ii_d));
        else
            sampler.make_grid_resolution(rec_opts.ospace_resolution, ...
                rec_opts.max_grid_edge_points, gvdm_lims, ...
                'oversize', 1, 'det_ind', det_index(ii_d));
        end

        if (rec_opts.ospace_super_sampling > 1)
            sampler.make_supersampling_simple_grid([1 2 3], rec_opts.ospace_super_sampling, det_index(ii_d));
        end
    end

    if (do_plot)
%         ospace_bb = [min(gvdm, [], 2) - 0.002, max(gvdm, [], 2) + 0.002];
%         sampler.make_grid('cubic', 3, ospace_bb, rec_opts.ospace_oversize);

        scatter3(ax, sampler.R_vectors(:, 1), sampler.R_vectors(:, 2), sampler.R_vectors(:, 3), 20, 'g');
        hold(ax, 'off')
        drawnow();
    end

    algo = gtReconstruct6DLaunchAlgorithm(sampler, rec_opts, ...
        test_data.parameters, 'det_index', det_index);

    vols = algo.getCurrentSolution();

    or_sizes = sampler.get_orientation_sampling_size();

    [avg_R_vecs, avg_R_vecs_int, stddev_R_vecs] = sampler.getAverageOrientations(vols);
    avg_R_vec = sampler.getAverageOrientation(vols);
    s_g_odf = reshape(sampler.getODF(vols), or_sizes);

    vol_size = size(avg_R_vecs_int);
    shift = gtFwdSimComputeVolumeShifts(test_data.grain.proj, test_data.parameters, vol_size, det_index(1));

    [kam, gam] = gtDefComputeKernelAverageMisorientation(avg_R_vecs, avg_R_vecs_int);
    [igm, gos] = gtDefComputeIntraGranularMisorientation(avg_R_vecs, avg_R_vecs_int, 'R_vector', test_data.grain.R_vector);

    % Restoring initial volume size (depending on the rounding)
    if (rec_opts.volume_downscaling > 1)
        fprintf('Expanding volumes..')
        c = tic();
        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);

        vols = gtMathsUpsampleVolume(vols, rec_opts.volume_downscaling);
        fprintf('\b\b: Done (%f seconds).\n', toc(c))
    end

    result = gt6DAssembleResult(test_data, sampler.get_orientations(), vols, det_index);

    result.ODF6D = struct( ...
        'voxels_avg_R_vectors', {avg_R_vecs}, ...
        'intensity', {avg_R_vecs_int}, ...
        'shift', {shift}, ...
        'R_vectors', {sampler.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} );

    t = GtThreshold(test_data.parameters);
    t.param.rec.thresholding.do_region_prop = false;
    gr_rec = struct('vol', avg_R_vecs_int, 'shift', shift);
    result.SEG = t.thresholdAutoSingleGrain(gr_rec);

    post_result = gt6DPostProcessOrientationSpread(test_data, result, true);

    [proj_blobs, proj_spots] = algo.getProjectionOfCurrentSolution();

    post_result.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()} );

    result_viewer = GtOrientationResultView(test_data, result, post_result);
end