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Commit d2fb04cf authored by Nicola Vigano's avatar Nicola Vigano Committed by Nicola Vigano
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6D-Reconstruction/multi-region: hopefuly fixed new num_interp behavior 


Signed-off-by: default avatarNicola Vigano <vigano@yoda.esrf.fr>
parent d116f730
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zUtil_Deformation/Gt6DReconstructionAlgorithmFactory.m
+ 173
− 33
View file @ d2fb04cf
......@@ -64,13 +64,13 @@ classdef Gt6DReconstructionAlgorithmFactory < handle
end
function [algo, blobs] = get6DAlgorithmMultiRegion(self, sampler, num_interp, varargin)
num_grains = numel(sampler);
num_regions = numel(sampler);
% Build Empty volumes
ref_gr = sampler(1).get_reference_grain();
volume_size = self.get_volume_size(ref_gr);
for ii_o_reg = 1:num_grains
for ii_o_reg = 1:num_regions
gr = sampler(ii_o_reg).get_reference_grain();
fprintf('%d) Grainid %d:\n', ii_o_reg, gr.id)
shape_funcs = self.get_shape_functions(sampler);
......@@ -86,52 +86,192 @@ classdef Gt6DReconstructionAlgorithmFactory < handle
geometries = cat(1, algo_params(:).geometries);
geometries_ss = cat(1, algo_params(:).geometries_ss);
offsets = algo_params(1).offsets;
offsets_ss = algo_params(1).offsets_ss;
% This vector will tell us where we will find in the blobs, the
% ones that were selected among the included, because the
% information we have in the twins about the spots that
% coincide are about the included and not the selected
included_pos_in_selected = zeros(size(proj.included));
included_pos_in_selected(proj.selected) = 1:numel(find(proj.selected));
included_pos_in_selected = zeros(size(ref_gr.proj(self.det_index).included));
included_pos_in_selected(proj.selected) = 1:numel(find(ref_gr.proj(self.det_index).selected));
num_parent_blobs = numel(algo_params(1).blobs);
% We should first go through all the shared blobs in each
% orientation and extend them if needed, and then extend the
% positions pointed by the orientations in the shared blobs
all_shared_blobs = find(ref_gr.proj(self.det_index).shared_bls_twins);
% First entry (in the third dimension) contains the final size
shared_blobs_w_lims = zeros(num_parent_blobs, 2, num_regions+1);
shared_blobs_w_lims(all_shared_blobs, :, 1) = algo_params(1).blobs_w_lims(all_shared_blobs, :);
shared_blobs_w_lims(all_shared_blobs, :, 2) = algo_params(1).blobs_w_lims(all_shared_blobs, :);
% The reference num_interps
shared_blobs_w_interp = zeros(num_parent_blobs, 1);
shared_blobs_w_interp(all_shared_blobs) = algo_params(1).blobs_w_interp(all_shared_blobs);
% Same as above, but rescaled with num_interp
rescaled_shared_blobs_w_lims(all_shared_blobs, :, 2) = zeros(num_parent_blobs, 2, num_regions+1);
rescaled_shared_blobs_w_lims(all_shared_blobs, :, 2) = shared_blobs_w_lims(all_shared_blobs, :, 2) ./ shared_blobs_w_interp(all_shared_blobs, [1 1]);
for ii_o_reg = 2:num_regions
curr_or = sampler(ii_o_reg).get_reference_grain();
curr_sel = sampler(ii_o_reg).selected;
% This contains the position of the shared blobs in
% parent's numbering
shared_pos = curr_or.proj(self.det_index).shared_bls_parent(curr_sel);
% This indicates the ones that are actually shared among
% the twin's blobs
shared = shared_pos > 0;
if (any(shared_blobs_w_interp(shared_pos(shared)) ~= algo_params(ii_o_reg).blobs_w_interp(shared)))
warning('Gt6DReconstructionAlgorithmFactory:wrong_interpolation', ...
['For some reason, the num_interp used for the ' ...
'main orientation-space region and the region ' ...
'n.%d, are different.\nThe ' ...
'reconstruction will not be correct!!'], ii_o_reg)
end
offsets = algo_params(1).offsets;
offsets_ss = algo_params(1).offsets_ss;
base_offset_shift = numel(algo_params(1).blobs);
for ii_g = 2:num_grains
temp_gr = sampler(ii_g).get_reference_grain();
shared = temp_gr.proj.shared_parent(sampler(ii_g).selected) > 0;
shared_pos = temp_gr.proj.shared_parent(sampler(ii_g).selected);
shared_blobs_w_lims(all_shared_blobs, :, ii_o_reg+1) = algo_params(ii_o_reg).blobs_w_lims(shared, :);
rescaled_shared_blobs_w_lims(all_shared_blobs, :, ii_o_reg+1) = algo_params(ii_o_reg).blobs_w_lims(shared, :) ./ shared_blobs_w_interp(shared_pos(shared), [1 1]);
% Shifting projection to the concatenated blobs, unless that
% blob was shared between parent and twin
if (~isempty(geometries_ss))
orient_offsets_ss = algo_params(ii_g).offsets_ss;
for ii_o = 1:numel(orient_offsets_ss)
for ii_ss = 1:numel(orient_offsets_ss{ii_o})
to_be_summed = ~shared(orient_offsets{ii_o}{ii_ss}.blob_offsets);
shared_blobs_w_lims(all_shared_blobs, :, 1) = [ ...
min(shared_blobs_w_lims(all_shared_blobs, 1), algo_params(ii_o_reg).blobs_w_lims(shared, 1)), ...
max(shared_blobs_w_lims(all_shared_blobs, 2), algo_params(ii_o_reg).blobs_w_lims(shared, 2)) ];
end
orient_offsets_ss{ii_o}{ii_ss}.blob_offsets(to_be_summed) ...
= orient_offsets_ss{ii_o}{ii_ss}.blob_offsets(to_be_summed) + base_offset_shift;
rescaled_shared_blobs_w_lims(all_shared_blobs, :, 1) = shared_blobs_w_lims(all_shared_blobs, :, 1) ./ shared_blobs_w_interp(all_shared_blobs, [1 1]);
to_be_changed = any(rescaled_shared_blobs_w_lims(all_shared_blobs, :, 1) ~= rescaled_shared_blobs_w_lims(all_shared_blobs, :, 2), 2);
rescaled_shared_blobs_sizes = rescaled_shared_blobs_w_lims(all_shared_blobs, 2, 1) - rescaled_shared_blobs_w_lims(all_shared_blobs, 1, 1) + 1;
% And now let's extend those blobs that need it!
for ii_b = 1:numel(all_shared_blobs)
% if they changed, let's enlarge them
if (to_be_changed(ii_b))
proj_shift = rescaled_shared_blobs_w_lims(all_shared_blobs(ii_b), 1, 2) ...
- rescaled_shared_blobs_w_lims(all_shared_blobs(ii_b), 1, 1);
curr_blob_size = size(blobs{all_shared_blobs(ii_b)});
new_size = [curr_blob_size(1), rescaled_shared_blobs_sizes(ii_b), curr_blob_size(3)];
% Creating the new blob
new_blob = zeros(new_size, 'like', blobs{all_shared_blobs(ii_b)});
new_blob = gtPlaceSubVolume(new_blob, blobs{all_shared_blobs(ii_b)}, [0, proj_shift, 0]);
blobs{all_shared_blobs(ii_b)} = new_blob;
% Fixing the shift in parent's projection
if (~isempty(geometries_ss))
for ii_o = 1:numel(offsets_ss)
for ii_ss = 1:numel(offsets_ss{ii_o})
inds_of_shared_blobs = offsets_ss{ii_o}{ii_ss}.blob_offsets == all_shared_blobs(ii_b);
offsets_ss{ii_o}{ii_ss}.proj_offsets(inds_of_shared_blobs) ...
= offsets_ss{ii_o}{ii_ss}.proj_offsets(inds_of_shared_blobs) + proj_shift;
end
end
else
for ii_o = 1:numel(offsets)
inds_of_shared_blobs = offsets{ii_o}.blob_offsets == all_shared_blobs(ii_b);
orient_offsets_ss{ii_o}{ii_ss}.blob_offsets(~to_be_summed) ...
= included_pos_in_selected(shared_pos(orient_offsets_ss{ii_o}{ii_ss}.blob_offsets(~to_be_summed)));
offsets{ii_o}.blob_offsets(inds_of_shared_blobs) ...
= offsets{ii_o}.blob_offsets(inds_of_shared_blobs) + proj_shift;
end
end
offsets_ss = cat(1, offsets_ss, orient_offsets_ss);
else
orient_offsets = algo_params(ii_g).offsets;
for ii_o = 1:numel(orient_offsets)
to_be_summed = ~shared(orient_offsets{ii_o}.blob_offsets);
end
end
orient_offsets{ii_o}.blob_offsets(to_be_summed) ...
= orient_offsets{ii_o}.blob_offsets(to_be_summed) + base_offset_shift;
base_offset_shift = num_parent_blobs;
for ii_o_reg = 2:num_regions
curr_or = sampler(ii_o_reg).get_reference_grain();
curr_sel = sampler(ii_o_reg).selected;
% This contains the position of the shared blobs in
% parent's numbering
shared_pos = curr_or.proj(self.det_index).shared_bls_parent(curr_sel);
% This indicates the ones that are actually shared among
% the twin's blobs
shared = shared_pos > 0;
proj_shifts = rescaled_shared_blobs_w_lims(shared_pos(shared), 1, ii_o_reg+1) ...
- rescaled_shared_blobs_w_lims(shared_pos(shared), 1, 1);
blobs_with_proj_to_be_shifted = find(proj_shifts > 0);
orient_offsets{ii_o}.blob_offsets(~to_be_summed) ...
= included_pos_in_selected(shared_pos(orient_offsets{ii_o}.blob_offsets(~to_be_summed)));
% Shifting projection to the concatenated blobs, unless that
% blob was shared between parent and twin
if (~isempty(geometries_ss))
proj_coeffs_ss = algo_params(ii_o_reg).offsets_ss;
for ii_o = 1:numel(proj_coeffs_ss)
for ii_ss = 1:numel(proj_coeffs_ss{ii_o})
% Indices of the blobs, that we project to, in
% curr_or
inds_of_blobs = proj_coeffs_ss{ii_o}{ii_ss}.blob_offsets;
% to_be_summed contains the indices to the
% blobs belonging only to the current region
% identified by temp_gr
to_be_summed = ~shared(inds_of_blobs);
% The indices of the given blobs belonging to
% the current orientation will be shifted by
% the number of blobs accumulated already
inds_of_blobs(to_be_summed) ...
= inds_of_blobs(to_be_summed) + base_offset_shift;
% Treating the shared blobs
inds_of_blobs(~to_be_summed) ...
= included_pos_in_selected(shared_pos(inds_of_blobs(~to_be_summed)));
proj_coeffs_ss{ii_o}{ii_ss}.blob_offsets = inds_of_blobs;
% And now taking care of the positions inside
% those blobs
for ii_b = 1:numel(blobs_with_proj_to_be_shifted)
inds_of_shared_blobs = inds_of_blobs == shared_pos(shared(blobs_with_proj_to_be_shifted(ii_b)));
proj_coeffs_ss{ii_o}{ii_ss}.proj_offsets(inds_of_shared_blobs) = ...
proj_coeffs_ss{ii_o}{ii_ss}.proj_offsets(inds_of_shared_blobs) + proj_shifts(blobs_with_proj_to_be_shifted(ii_b));
end
end
end
offsets_ss = cat(1, offsets_ss, proj_coeffs_ss);
else
proj_coeffs = algo_params(ii_o_reg).offsets;
for ii_o = 1:numel(proj_coeffs)
% Indices of the blobs, that we project to, in
% curr_or
inds_of_blobs = proj_coeffs{ii_o}.blob_offsets;
% to_be_summed contains the indices to the
% blobs belonging only to the current region
% identified by temp_gr
to_be_summed = ~shared(inds_of_blobs);
% The indices of the given blobs belonging to
% the current orientation will be shifted by
% the number of blobs accumulated already
inds_of_blobs(to_be_summed) ...
= inds_of_blobs(to_be_summed) + base_offset_shift;
% Treating the shared blobs
inds_of_blobs(~to_be_summed) ...
= included_pos_in_selected(shared_pos(inds_of_blobs(~to_be_summed)));
proj_coeffs{ii_o}.blob_offsets = inds_of_blobs;
% And now taking care of the positions inside
% those blobs
for ii_b = 1:numel(blobs_with_proj_to_be_shifted)
inds_of_shared_blobs = inds_of_blobs == shared_pos(shared(blobs_with_proj_to_be_shifted(ii_b)));
proj_coeffs{ii_o}.proj_offsets(inds_of_shared_blobs) = ...
proj_coeffs{ii_o}.proj_offsets(inds_of_shared_blobs) + proj_shifts(blobs_with_proj_to_be_shifted(ii_b));
end
end
offsets = cat(1, offsets, orient_offsets);
offsets = cat(1, offsets, proj_coeffs);
end
base_offset_shift = base_offset_shift + numel(algo_params(ii_g).blobs);
base_offset_shift = base_offset_shift + numel(algo_params(ii_o_reg).blobs);
end
algo = Gt6DBlobReconstructor(volume_size, blobs, ...
......
zUtil_Deformation/gt6DCreateProjDataFromTwinnedGrainFwdProj.m
+ 33
− 31
View file @ d2fb04cf
......@@ -14,6 +14,7 @@ function [samp_ors, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDat
conf = struct( ...
'verbose', false, ...
'det_ind', 1, ...
'min_eta', 15, ...
'rspace_oversize', 1.1, ...
'check_spots', false, ...
......@@ -25,8 +26,8 @@ function [samp_ors, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDat
symm = gtCrystGetSymmetryOperators(p.cryst(phase_id).crystal_system);
if (numel(parent_id) > 1)
error('gt6DCreateProjDataFromTwinnedGrainTheoFwdProj:wrong_argument', ...
'Only one grain should be passed')
error('gt6DCreateProjDataFromTwinnedGrainFwdProj:wrong_argument', ...
'Only one grain should be passed as parent')
end
if (~isstruct(parent_id))
grs(1) = gtLoadGrain(phase_id, parent_id);
......@@ -107,15 +108,11 @@ function [samp_ors, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDat
refgr = grs(1);
grs(2:end) = reorder_reflections(grs(2:end), refgr);
if (isfield(refgr.proj, 'ondet'))
ref_ondet = refgr.proj.ondet;
ref_included = refgr.proj.included;
ref_selected = refgr.proj.selected;
else
ref_ondet = refgr.ondet;
ref_included = refgr.included;
ref_selected = refgr.selected;
end
refgr_proj = refgr.proj(conf.det_ind);
ref_ondet = refgr_proj.ondet;
ref_included = refgr_proj.included;
ref_selected = refgr_proj.selected;
if (conf.verbose && false)
try
......@@ -184,10 +181,14 @@ function [samp_ors, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDat
]');
end
vol_half_size = [refgr.proj.vol_size_y, refgr.proj.vol_size_x, refgr.proj.vol_size_z] / 2;
vol_size = [ ...
refgr_proj.vol_size_y, ...
refgr_proj.vol_size_x, ...
refgr_proj.vol_size_z ];
vol_half_size = vol_size / 2;
space_bbox = [ ...
refgr.proj.centerpix - vol_half_size * conf.rspace_oversize, ...
refgr.proj.centerpix + vol_half_size * conf.rspace_oversize ];
refgr_proj.centerpix - vol_half_size * conf.rspace_oversize, ...
refgr_proj.centerpix + vol_half_size * conf.rspace_oversize ];
estim_space_bbox_pix = [floor(space_bbox(1:3)), ceil(space_bbox(4:6))];
bbox_size_pix = estim_space_bbox_pix(4:6) - estim_space_bbox_pix(1:3);
......@@ -250,15 +251,11 @@ function [samp_ors, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDat
if (ii_g > 1)
twingr = grs(ii_g);
if (isfield(twingr.proj, 'ondet'))
twin_ondet = twingr.proj.ondet;
twin_inc = twingr.proj.included;
twin_sel = twingr.proj.selected;
else
twin_ondet = twingr.ondet;
twin_inc = twingr.included;
twin_sel = twingr.selected;
end
twingr_proj = twingr.proj(conf.det_ind);
twin_ondet = twingr_proj.ondet;
twin_inc = twingr_proj.included;
twin_sel = twingr_proj.selected;
bool_twin_ondet = false(size(refgr.allblobs.omega));
bool_twin_ondet(twin_ondet) = true;
......@@ -316,16 +313,17 @@ function [samp_ors, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDat
local_selected = ref_selected;
end
num_blobs = numel(local_included);
if (ii_g == 1)
blobs = grs(ii_g).proj.bl;
else
blobs = gtFwdSimBlobDefinition();
blobs = gtFwdSimBlobDefinition('blob', num_blobs);
blobs(~shared_parent) = grs(ii_g).proj.bl(~shared_parent_inc_redundant);
% Using the same because it gives the same size/uvw-limits
blobs(shared_parent) = samp_ors(1).proj.bl(shared_parent_pos);
end
num_blobs = numel(local_included);
for ii_b = 1:num_blobs
num_chars = fprintf('%02d/%02d', ii_b, num_blobs);
......@@ -353,11 +351,15 @@ function [samp_ors, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDat
proj.selected = local_selected;
if (ii_g > 1)
proj.shared_parent = zeros(size(shared_parent));
proj.shared_parent(shared_parent) = find(shared_parent_pos);
proj.shared_bls_parent = zeros(size(shared_parent));
proj.shared_bls_parent(shared_parent) = find(shared_parent_pos);
samp_ors(ii_g).proj(conf.det_ind).shared_bls_twins(shared_parent_pos) = true;
else
proj.shared_bls_twins = false(num_blobs, 1);
end
samp_ors(ii_g).proj = proj;
samp_ors(ii_g).proj(conf.det_ind) = proj;
if (conf.check_spots && ii_g > 1)
samp_ors(ii_g).proj.selected = gtGuiGrainMontage(samp_ors(ii_g), [], true);
......@@ -396,7 +398,7 @@ function [samp_ors, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDat
end
function orients = get_6D_space_corners(estim_space_bbox_mm, bbox_size_mm, estim_orient_bbox, bbox_size_rod, refgr, p)
orients = {};
orients = cell(2, 2, 2, 2, 2, 2);
for ii_x1 = 0:1
base_x1 = estim_space_bbox_mm(1:3) + [ii_x1 * bbox_size_mm(1), 0, 0];
for ii_x2 = 0:1
......@@ -412,9 +414,9 @@ function orients = get_6D_space_corners(estim_space_bbox_mm, bbox_size_mm, estim
% fprintf(' center: %f, %f, %f, r_vec: %f, %f, %f\n', base_x3, base_r3)
orients{end+1} = struct( ...
orients{ii_r3+1, ii_r2+1, ii_r1+1, ii_x3+1, ii_x2+1, ii_x1+1} = struct( ...
'id', refgr.id, 'phaseid', refgr.phaseid, ...
'center', base_x3, 'R_vector', base_r3); %#ok<AGROW>
'center', base_x3, 'R_vector', base_r3);
end
end
end
......
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