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classdef Gt6DReconstructionAlgorithmFactory < handle
properties
data_type = 'single';
end
methods (Access = public)
function [algo, blobs] = getBlobReconstructionAlgo(self, bl, selected_bls, sampler, vol_type)
fprintf('Extracting blobs on detector: ')
c = tic();
bl = bl(selected_bls);
fprintf('\b\b (%f s).\n', toc(c));
tot_blobs = numel(bl);
[grains, grains_ss] = sampler.get_orientations();
grains = [grains{:}];
% Array of structures that contain all the info relative to
% each orientation, for each blob
grains_props = Gt6DReconstructionAlgorithmFactory.get_selected_props(grains, selected_bls);
% Tabular of omegas: horizontal direction the n geometries,
% vertical direction the omegas relative to each blob
omega_int_tab = Gt6DReconstructionAlgorithmFactory.getOmegaIntegerTab(grains_props, sampler.parameters);
% [omega_int_tab, omega_int_coeffs] = Gt6DReconstructionAlgorithmFactory.getOmegaIntegersAndCoeffs(grainsProps, sampler.parameters);
[lims, abs_lims, ~, extremesOfBlobs, extremesOmIntTab] ...
= Gt6DReconstructionAlgorithmFactory.getBlobLims(omega_int_tab, bl);
[overflow_b, overflow_o] = Gt6DReconstructionAlgorithmFactory.compute_overflow(omega_int_tab, extremesOfBlobs);
% We have to remove the orientations that don't project to any
% blob
good_or = overflow_o < tot_blobs;
grains_props = grains_props(good_or);
omega_int_tab = omega_int_tab(:, good_or);
if (~isempty(grains_ss))
grains_ss = [grains_ss{:}];
grains_props_ss = Gt6DReconstructionAlgorithmFactory.get_selected_props(grains_ss, selected_bls);
omega_int_tab_ss = Gt6DReconstructionAlgorithmFactory.getOmegaIntegerTab(grains_props_ss, sampler.parameters);
[lims_ss, abs_lims_ss, ~, extremesOfBlobs_ss, extremesOmIntTab_ss] ...
= Gt6DReconstructionAlgorithmFactory.getBlobLims(omega_int_tab_ss, bl);
[overflow_ss_b, overflow_ss_o] = Gt6DReconstructionAlgorithmFactory.compute_overflow(omega_int_tab_ss, extremesOfBlobs_ss);
good_ss_or = overflow_ss_o < tot_blobs;
grains_props_ss = grains_props_ss(good_ss_or);
omega_int_tab_ss = omega_int_tab_ss(:, good_ss_or);
lims_tot = [min(lims(:, 1), lims_ss(:, 1)), max(lims(:, 2), lims_ss(:, 2))];
abs_lims_tot = [min(abs_lims(:, 1), abs_lims_ss(:, 1)), max(abs_lims(:, 2), abs_lims_ss(:, 2))];
extremesOfBlobs_tot = [min(extremesOfBlobs(:, 1), extremesOfBlobs_ss(:, 1)), max(extremesOfBlobs(:, 2), extremesOfBlobs_ss(:, 2))];
extremesOmIntTab_tot = [min(extremesOmIntTab(:, 1), extremesOmIntTab_ss(:, 1)), max(extremesOmIntTab(:, 2), extremesOmIntTab_ss(:, 2))];
else
lims_tot = lims;
abs_lims_tot = abs_lims;
overflow_ss_b = zeros(size(overflow_b));
overflow_ss_o = zeros(size(overflow_o));
extremesOfBlobs_tot = extremesOfBlobs;
extremesOmIntTab_tot = extremesOmIntTab;
end
blobs = cell(1, tot_blobs);
% Let's restrict blobs to the reached regions
for ii = 1:tot_blobs
blob = bl(ii).intm;
blob = blob ./ sum(blob(:));
if (overflow_b(ii) || overflow_ss_b(ii))
warning('Gt6DReconstructionAlgorithmFactory:BlobCreation', ...
'Blob: %03d --> Some orientations (%d, ss %d) will be missing', ...
ii, overflow_b(ii), overflow_ss_b(ii) )
end
blobs{ii} = blob(:, :, lims_tot(ii, 1):lims_tot(ii, 2));
blobs{ii} = permute(blobs{ii}, [1 3 2]);
blobs{ii} = cast(blobs{ii}, self.data_type);
fprintf(' - ExremesBlobs %4d:%4d, ExtremesProjs %4d:%4d, Lims %3d:%3d, Size 1:%d, ', ...
extremesOfBlobs_tot(ii, :), extremesOmIntTab_tot(ii, :), lims_tot(ii, :), size(blobs{ii}, 3))
intensExcl = sum(sum(sum(blob(:, :, [1:(lims_tot(ii, 1)-1), (lims_tot(ii, 2)+1):end]))));
intensBlob = sum(sum(sum(blobs{ii})));
fprintf('Blob: %03d -> Intensities: included %f, excluded %f\n', ...
ii, intensBlob, intensExcl);
end
[geometries, offsets] = Gt6DReconstructionAlgorithmFactory.makeBlobGeometries(grains_props, omega_int_tab, abs_lims_tot);
if (~isempty(grains_ss))
[geometries_ss, offsets_ss] = Gt6DReconstructionAlgorithmFactory.makeBlobGeometries(grains_props_ss, omega_int_tab_ss, abs_lims_tot);
else
geometries_ss = {};
offsets_ss = {};
end
% Build Empty volumes
blob_size = size(bl(1).intm);
volume_size = Gt6DReconstructionAlgorithmFactory.getVolSize(blob_size, vol_type);
num_geoms = numel(geometries);
zero_volumes = arrayfun(@(x){zeros(volume_size, self.data_type)}, 1:num_geoms);
algo = Gt6DBlobReconstructor(zero_volumes, blobs, ...
'geometries', geometries, ...
'offsets', offsets, ...
'ss_geometries', geometries_ss, ...
'ss_offsets', offsets_ss, ...
'ss_coeffs', sampler.get_ss_coeffs() );
end
function [algo, blobs] = getSubBlobReconstructionAlgo(self, bl, selected_bls, sampler, vol_type, num_interp)
fprintf('Extracting blobs on detector: ')
c = tic();
bl = bl(selected_bls);
fprintf('\b\b (%f s).\n', toc(c));
tot_blobs = numel(bl);
[grains, grains_ss] = sampler.get_orientations();
grains = [grains{:}];
% Array of structures that contain all the info relative to
% each orientation, for each blob
grains_props = Gt6DReconstructionAlgorithmFactory.get_selected_props(grains, selected_bls);
omega_int_tab = Gt6DReconstructionAlgorithmFactory.getOmegaIntegerTab(grains_props, sampler.parameters);
[sub_blob_slices, proj_coeffs] = self.getSubBlobSlices(bl, num_interp);
blobs = cell(size(sub_blob_slices));
[slice_lims, lims, abs_lims, ~, extremesOfBlobs, extremesOmIntTab] = ...
Gt6DReconstructionAlgorithmFactory.getSubBlobLims(omega_int_tab, bl, num_interp);
[overflow_b, overflow_o] = Gt6DReconstructionAlgorithmFactory.compute_overflow(omega_int_tab, extremesOfBlobs);
% We have to remove the orientations that don't project to any
% blob
class(grains_props)
size(grains_props)
good_or = overflow_o < tot_blobs;
grains_props = grains_props(good_or);
omega_int_tab = omega_int_tab(:, good_or);
if (~isempty(grains_ss))
grains_ss = [grains_ss{:}];
grains_props_ss = Gt6DReconstructionAlgorithmFactory.get_selected_props(grains_ss, selected_bls);
omega_int_tab_ss = Gt6DReconstructionAlgorithmFactory.getOmegaIntegerTab(grains_props_ss, sampler.parameters);
[slice_lims_ss, lims_ss, abs_lims_ss, ~, extremesOfBlobs_ss, extremesOmIntTab_ss] ...
= Gt6DReconstructionAlgorithmFactory.getSubBlobLims(omega_int_tab_ss, bl, num_interp);
[overflow_ss_b, overflow_ss_o] = Gt6DReconstructionAlgorithmFactory.compute_overflow(omega_int_tab_ss, extremesOfBlobs_ss);
good_ss_or = overflow_ss_o < tot_blobs;
grains_props_ss = grains_props_ss(good_ss_or);
omega_int_tab_ss = omega_int_tab_ss(:, good_ss_or);
lims_tot = [min(lims(:, 1), lims_ss(:, 1)), max(lims(:, 2), lims_ss(:, 2))];
abs_lims_tot = [min(abs_lims(:, 1), abs_lims_ss(:, 1)), max(abs_lims(:, 2), abs_lims_ss(:, 2))];
slice_lims_tot = [min(slice_lims(:, 1), slice_lims_ss(:, 1)), max(slice_lims(:, 2), slice_lims_ss(:, 2))];
extremesOfBlobs_tot = [min(extremesOfBlobs(:, 1), extremesOfBlobs_ss(:, 1)), max(extremesOfBlobs(:, 2), extremesOfBlobs_ss(:, 2))];
extremesOmIntTab_tot = [min(extremesOmIntTab(:, 1), extremesOmIntTab_ss(:, 1)), max(extremesOmIntTab(:, 2), extremesOmIntTab_ss(:, 2))];
else
lims_tot = lims;
abs_lims_tot = abs_lims;
slice_lims_tot = slice_lims;
overflow_ss_b = zeros(size(overflow_b));
overflow_ss_o = zeros(size(overflow_o));
extremesOfBlobs_tot = extremesOfBlobs;
extremesOmIntTab_tot = extremesOmIntTab;
end
% Let's restrict blobs to the reached regions
for ii = 1:tot_blobs
if (overflow_b(ii) || overflow_ss_b(ii))
warning('Gt6DReconstructionAlgorithmFactory:BlobCreation', ...
'Blob: %03d --> Some orientations (%d, ss %d) will be missing', ...
ii, overflow_b(ii), overflow_ss_b(ii) )
end
if (slice_lims_tot(ii, 2) > size(sub_blob_slices{ii}, 3))
depth_blob = size(bl(ii).intm, 3);
fprintf('\n AHIA! numInterp: %d, lims: %d:%d, blob size: 1:%d, virtual slices 1:%d\n\n', ...
num_interp, lims_tot(ii, :), depth_blob, depth_blob + mod(num_interp - mod(depth_blob, num_interp), num_interp) + 1)
end
fprintf(' - ExremesBlobs %4d:%4d, ExtremesProjs %4d:%4d, Lims %3d:%3d, SliceLims %d:%d, Size 1:%d, ', ...
extremesOfBlobs_tot(ii, :), extremesOmIntTab_tot(ii, :), lims_tot(ii, :), slice_lims_tot(ii, :), size(sub_blob_slices{ii}, 3))
blobs{ii} = sub_blob_slices{ii}(:, :, slice_lims_tot(ii, 1):slice_lims_tot(ii, 2));
blobs{ii} = permute(blobs{ii}, [1 3 2]);
intensIncl = sum(sum(sum(blobs{ii}, 2)));
intensExcl = sum(sum(sum(sub_blob_slices{ii}(:, :, [1:(slice_lims_tot(ii, 1)-1), (slice_lims_tot(ii, 2)+1):end]), 2)));
fprintf('Blob: %03d -> Intensities: included %f, excluded %f\n', ...
ii, intensIncl, intensExcl);
end
[geometries, offsets] = Gt6DReconstructionAlgorithmFactory.makeSubBlobGeometries( ...
grains_props, proj_coeffs, extremesOfBlobs_tot, omega_int_tab, abs_lims_tot, slice_lims_tot);
if (~isempty(grains_ss))
[geometries_ss, offsets_ss] = Gt6DReconstructionAlgorithmFactory.makeSubBlobGeometries( ...
grains_props_ss, proj_coeffs, extremesOfBlobs_tot, omega_int_tab_ss, abs_lims_tot, slice_lims_tot);
else
geometries_ss = {};
offsets_ss = {};
end
% Build Empty volumes
blob_size = size(bl(1).intm);
volume_size = Gt6DReconstructionAlgorithmFactory.getVolSize(blob_size, vol_type);
num_geoms = numel(geometries);
zero_volumes = arrayfun(@(x){zeros(volume_size, self.data_type)}, 1:num_geoms);
algo = Gt6DBlobReconstructor(zero_volumes, blobs, ...
'geometries', geometries, ...
'offsets', offsets, ...
'ss_geometries', geometries_ss, ...
'ss_offsets', offsets_ss, ...
'ss_coeffs', sampler.get_ss_coeffs() );
end
end
methods (Access = protected)
function [subBlobSlices, projCoeffs] = getSubBlobSlices(self, blobs, numInterp)
subBlobSlices = cell(size(blobs));
subBlobCoeffs = cell(size(blobs));
projCoeffs = cell(size(blobs));
blocky_groups = false;
fprintf('Creating sub-blob volumes: ')
c = tic();
for ii = 1:numel(subBlobSlices)
num_chars = fprintf('%03d/%03d', ii, numel(subBlobSlices));
[blobSize(1), blobSize(2), blobSize(3)] = size(blobs(ii).intm);
% Number of interpolated slices should be at least enough
% to accomodate all the slices of the blob
numSlices = ceil((blobSize(3) -1) / numInterp) +1;
covered_slices_size = (numSlices-1) * numInterp + 1;
% num_chars = num_chars + fprintf(' Blob size %d, numSlices %d, convertedSliceSize %d', ...
% blobSize(3), numSlices, covered_slices_size);
subBlobSlices{ii} = zeros(blobSize(1), blobSize(2), numSlices, self.data_type);
for n = numSlices:-1:1
coeffs = abs( (numInterp * (n-1) +1) - (1:covered_slices_size));
coeffs = 1 - coeffs / numInterp;
% these will be the blob slices that relate to the
% given ii interpolated slice
if (blocky_groups)
goodCoeffs = find(coeffs >= 0.5);
else
goodCoeffs = find(coeffs > 0);
end
% The corresponding coefficients
coeffs = coeffs(goodCoeffs);
if (blocky_groups)
coeffs(1:end) = 1;
if (mod(numInterp, 2) == 0)
coeffs(1) = 0.5;
coeffs(end) = 0.5;
end
end
safe_coeffs_pos = goodCoeffs <= blobSize(3);
safe_good_coeffs = goodCoeffs(safe_coeffs_pos);
safe_coeffs = coeffs(safe_coeffs_pos);
% Let's build the interpolated slices
blob = blobs(ii).intm;
blob = blob ./ sum(blob(:));
for w = 1:numel(safe_coeffs)
subBlobSlices{ii}(:, :, n) = ...
subBlobSlices{ii}(:, :, n) + safe_coeffs(w) .* blob(:, :, safe_good_coeffs(w));
end
% Save the metadata
subBlobCoeffs{ii}(n) = struct('indexes', goodCoeffs, 'coeffs', coeffs);
end
% Perpare next metadata structure
projCoeffs{ii} = struct( ...
'slices', arrayfun(@(x){[]}, 1:covered_slices_size), ...
'coeffs', arrayfun(@(x){[]}, 1:covered_slices_size) );
fprintf(repmat('\b', [1 num_chars]));
end
fprintf('\b\b (%f s), transforming coeffs..', toc(c));
c = tic();
% Let's transform the coeffs to something that is easy to
% assign for projections:
% Per each blob we want to easily find out what the projections
% project to. The metadata from subBlobCoeffs is the other way
% around.
for ii = 1:numel(subBlobSlices)
numSlices = numel(subBlobCoeffs{ii});
for n = numSlices:-1:1
indexes = subBlobCoeffs{ii}(n).indexes;
coeffs = subBlobCoeffs{ii}(n).coeffs;
for m = numel(indexes):-1:1
projCoeffs{ii}(indexes(m)).slices = ...
[ projCoeffs{ii}(indexes(m)).slices, n ];
projCoeffs{ii}(indexes(m)).coeffs = ...
[ projCoeffs{ii}(indexes(m)).coeffs, coeffs(m) ];
end
end
end
fprintf('\b\b (%f s).\n', toc(c));
end
end
methods (Access = protected, Static)
function grains_props = get_selected_props(grains, blobs_on_det)
% grains_props = [grains(:).allblobs];
for ii = numel(grains):-1:1
all_props = grains(ii).allblobs;
grains_props(ii) = Gt6DReconstructionAlgorithmFactory.selectBlobsFromGrain(...
all_props, blobs_on_det);
end
end
function allblobs = selectBlobsFromGrain(allblobs, blobs_on_det)
names = fieldnames(allblobs);
for ii = 1:numel(names)
name = names{ii};
if (strcmpi(name, 'srot'))
allblobs.(name) = allblobs.(name)(:, :, blobs_on_det);
else
allblobs.(name) = allblobs.(name)(blobs_on_det, :);
end
end
end
function volume_size = getVolSize(blob_size, vol_type)
% volume_size = floor(sqrt(blob_size(1:2) * blob_size(1:2)') /2)+1;
volume_size = [blob_size(1), blob_size(1:2)];
% volume_size = volume_size * 0.7;
volume_size = volume_size * 0.8;
% volume_size = volume_size * 1.2;
volume_size = volume_size - mod(volume_size, 8);
switch (vol_type)
case '3D'
% volume_size = [volume_size, volume_size, volume_size];
case '2D'
% volume_size = [volume_size, volume_size, 8];
volume_size(3) = 8;
otherwise
error('Gt6DReconstructionAlgorithmFactory:getVolSize:wrong_argument', ...
'Volume type should be either "2D" or "3D"')
end
end
function omegaIntegerTab = getOmegaIntegerTab(grainsProps, parameters)
omega_step = 180 / parameters.acq.nproj;
% Tabular of omegas: horizontal direction the n geometries,
% vertical direction the omegas relative to each blob
omegaTab = [grainsProps(:).omega];
omegaSlicesTab = omegaTab / omega_step;
% Images numbers
omegaIntegerTab = round(omegaSlicesTab);
end
function [overflow_b, overflow_o] = compute_overflow(omegaIntegerTab, extremesOfBlobs)
num_orient = size(omegaIntegerTab, 2);
ones_orient = ones(1, num_orient);
lower_lims = omegaIntegerTab < extremesOfBlobs(:, 1 .* ones_orient);
upper_lims = omegaIntegerTab > extremesOfBlobs(:, 2 .* ones_orient);
overflow_b = sum(lower_lims, 2) + sum(upper_lims, 2);
overflow_o = sum(lower_lims, 1) + sum(upper_lims, 1);
end
function [lims, absLims, overflow, extremesOfBlobs, extremesOmIntTab] = getBlobLims(omegaIntegerTab, bl)
% Let's add extreme values
extremesOmIntTab = [ ...
min(omegaIntegerTab, [], 2), ...
max(omegaIntegerTab, [], 2) ];
extremesOfBlobs = vertcat( bl(:).bbwim );
% Blob limits in the full omega stack
absLims = [ ...
max([extremesOmIntTab(:, 1), extremesOfBlobs(:, 1)], [], 2), ...
min([extremesOmIntTab(:, 2), extremesOfBlobs(:, 2)], [], 2) ];
% blob limits in its volume size
lims = absLims - extremesOfBlobs(:, [1 1]) + 1;
overflow = ...
(extremesOmIntTab(:, 1) < extremesOfBlobs(:, 1)) ...
| (extremesOmIntTab(:, 2) > extremesOfBlobs(:, 2));
end
function [sliceLims, lims, absLims, overflow, extremesOfBlobs, extremesOmIntTab] = getSubBlobLims(omegaIntegerTab, bl, numInterp)
[~, ~, ~, extremesOfBlobs, extremesOmIntTab] = Gt6DReconstructionAlgorithmFactory.getBlobLims(omegaIntegerTab, bl);
blobs_sizes = extremesOfBlobs(:, 2) - extremesOfBlobs(:, 1) +1;
extremesOfBlobs(:, 2) = extremesOfBlobs(:, 1) + (blobs_sizes-1) ...
+ mod(numInterp - mod((blobs_sizes-1), numInterp), numInterp);
% Blob limits in the full omega stack
absLims = [ ...
max([extremesOmIntTab(:, 1), extremesOfBlobs(:, 1)], [], 2), ...
min([extremesOmIntTab(:, 2), extremesOfBlobs(:, 2)], [], 2) ];
% blob limits in its volume size
lims = absLims - extremesOfBlobs(:, [1 1]) + 1;
sliceLims = (lims -1) / numInterp;
sliceLims = [floor(sliceLims(:, 1)), ceil(sliceLims(:, 2))] + 1;
overflow = ...
(extremesOmIntTab(:, 1) < extremesOfBlobs(:, 1)) ...
| (extremesOmIntTab(:, 2) > extremesOfBlobs(:, 2));
end
function [omega_int_tab, omega_int_coeffs] = getOmegaIntegersAndCoeffs(grainsProps, parameters)
omega_step = 180 / parameters.acq.nproj;
% Tabular of omegas: horizontal direction the n geometries,
% vertical direction the omegas relative to each blob
omega_tab = [grainsProps(:).omega];
omega_slices_tab = omega_tab / omega_step;
% Images numbers
omega_int_tab(:, :, 1) = floor(omega_slices_tab);
omega_int_coeffs(:, :, 1) = 1 - (omega_slices_tab - omega_integer_min_tab);
omega_int_tab(:, :, 2) = ceil(omega_slices_tab);
omega_int_coeffs(:, :, 2) = 1 - omega_int_coeffs(:, :, 1);
end
function [geometries, offsets] = makeBlobGeometries(grains_props, omega_int_tab, abs_lims)
% ASTRA Geometry
geometries = {grains_props(:).proj_geom};
num_geoms = numel(geometries);
offsets = cell(1, num_geoms);
% Compute Offsets
rescaled_omegas = omega_int_tab - repmat(abs_lims(:, 1), [1 num_geoms]) + 1;
exceding_omegas = omega_int_tab - repmat(abs_lims(:, 2), [1 num_geoms]);
% Assign offsets
for ii = 1:num_geoms
valid_proj_dirs = ...
(rescaled_omegas(:, ii) >= 1) ...
& (exceding_omegas(:, ii) < 1);
if (all(~valid_proj_dirs))
warning('Geometry:wrong_orientation', ...
'This orientation is useless! %d', ii)
end
offsets{ii} = struct('blob_offsets', find(valid_proj_dirs), ...
'proj_offsets', rescaled_omegas(valid_proj_dirs, ii), ...
'proj_coeffs', ones(numel(find(valid_proj_dirs)), 1), ...
'sino_offsets', 1:numel(find(valid_proj_dirs)) );
geometries{ii} = double(geometries{ii}(valid_proj_dirs, :));
end
end
function [geometries, offsets] = makeSubBlobGeometries( ...
grains_props, proj_coeffs, extremesOfBlobs, omega_int_tab, abs_lims, slice_lims)
% ASTRA Geometry
geometries = {grains_props(:).proj_geom};
num_geoms = numel(geometries);
% extremesOfBlobs = vertcat( bl(:).bbwim );
slice_pos_in_blob = omega_int_tab - repmat(extremesOfBlobs(:, 1), [1 num_geoms]) + 1;
% Assign offsets
offsets = cell(1, num_geoms);
for ii = 1:num_geoms
valid_proj_dirs = ...
(omega_int_tab(:, ii) >= abs_lims(:, 1)) ...
& (omega_int_tab(:, ii) <= abs_lims(:, 2));
if (all(~valid_proj_dirs))
warning('Geometry:wrong_orientation', ...
'This orientation is useless! %d', ii)
end
offsets{ii}.('sino_offsets') = [];
offsets{ii}.('blob_offsets') = [];
offsets{ii}.('proj_offsets') = [];
offsets{ii}.('proj_coeffs') = [];
valid_proj_indxes = find(valid_proj_dirs)';
for jj = 1:numel(valid_proj_indxes)
n = valid_proj_indxes(jj);
slices = [proj_coeffs{n}(slice_pos_in_blob(n, ii)).slices];
coeffs = [proj_coeffs{n}(slice_pos_in_blob(n, ii)).coeffs];
slices = slices - slice_lims(n, 1) +1;
offsets{ii}.('sino_offsets') = [offsets{ii}.('sino_offsets'), jj(1, ones(numel(slices), 1))];
offsets{ii}.('blob_offsets') = [offsets{ii}.('blob_offsets'), n(1, ones(numel(slices), 1))];
offsets{ii}.('proj_offsets') = [offsets{ii}.('proj_offsets'), slices];
offsets{ii}.('proj_coeffs') = [offsets{ii}.('proj_coeffs'), coeffs];
end
geometries{ii} = double(geometries{ii}(valid_proj_dirs, :));
end
end
end
end