diff --git a/zUtil_Deformation/gt6DCalculateFullSpaceCorners.m b/zUtil_Deformation/gt6DCalculateFullSpaceCorners.m
new file mode 100644
index 0000000000000000000000000000000000000000..f986ac7bb38b8438d437b552b007f938e8220b92
--- /dev/null
+++ b/zUtil_Deformation/gt6DCalculateFullSpaceCorners.m
@@ -0,0 +1,30 @@
+function orients = gt6DCalculateFullSpaceCorners(estim_space_bbox_mm, bbox_size_mm, estim_orient_bbox, bbox_size_rod, refgr, p)
+ 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
+ base_x2 = base_x1 + [0, ii_x2 * bbox_size_mm(2), 0];
+ for ii_x3 = 0:1
+ base_x3 = base_x2 + [0, 0, ii_x3 * bbox_size_mm(3)];
+ for ii_r1 = 0:1
+ base_r1 = estim_orient_bbox(1:3) + [ii_r1 * bbox_size_rod(1), 0, 0];
+ for ii_r2 = 0:1
+ base_r2 = base_r1 + [0, ii_r2 * bbox_size_rod(2), 0];
+ for ii_r3 = 0:1
+ base_r3 = base_r2 + [0, 0, ii_r3 * bbox_size_rod(3)];
+
+% fprintf(' center: %f, %f, %f, r_vec: %f, %f, %f\n', base_x3, base_r3)
+
+ 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);
+ end
+ end
+ end
+ end
+ end
+ end
+
+ orients = gtCalculateGrain_p(orients, p, 'ref_omind', refgr.allblobs.omind);
+ orients = [orients{:}];
+end
\ No newline at end of file
diff --git a/zUtil_Deformation/gt6DCreateProjDataFromExtendedGrain.m b/zUtil_Deformation/gt6DCreateProjDataFromExtendedGrain.m
index fa3ed314a6e88d7edd1043e07633154397ac6377..f815a01273ec63aff10bee8ac4e81762bcf35e90 100644
--- a/zUtil_Deformation/gt6DCreateProjDataFromExtendedGrain.m
+++ b/zUtil_Deformation/gt6DCreateProjDataFromExtendedGrain.m
@@ -13,6 +13,7 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
conf = struct( ...
'verbose', false, ...
'min_eta', 20, ...
+ 'det_index', 1, ...
'ospace_oversize', 1.1, ...
'rspace_oversize', 1.1, ...
'ospace_lims', [], ...
@@ -31,20 +32,10 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
p = gtLoadParameters();
refgr = gr;
- refgr_omind = refgr.allblobs.omind;
- refgr_omind_ind = [ ...
- find(refgr_omind == 1); find(refgr_omind == 2); ...
- find(refgr_omind == 3); find(refgr_omind == 4) ];
-
- 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
+
+ ref_ondet = refgr.proj(conf.det_index).ondet;
+ ref_included = refgr.proj(conf.det_index).included;
+ ref_selected = refgr.proj(conf.det_index).selected;
fwdsim_sel_refl = ref_ondet(ref_included(ref_selected));
fwdsim_sel_refl_logic = false(size(ref_ondet));
@@ -58,12 +49,8 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
used_refl = fwdsim_sel_refl;
end
- vol_half_size = [gr.proj.vol_size_y, gr.proj.vol_size_x, gr.proj.vol_size_z] / 2;
- space_bbox = [ ...
- gr.proj.centerpix - vol_half_size * conf.rspace_oversize, ...
- gr.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);
+ [gr_center_pix, bbox_size_pix, estim_space_bbox_pix] = gt6DMergeRealSpaceVolumes(gr, conf.det_index);
+ gr_center_mm = gtGeoSam2Sam(gr_center_pix, p.recgeo, p.samgeo, false, false);
estim_space_bbox_mm = [ ...
gtGeoSam2Sam(estim_space_bbox_pix(1:3), p.recgeo, p.samgeo, false, false), ...
@@ -71,7 +58,8 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
bbox_size_mm = estim_space_bbox_mm(4:6) - estim_space_bbox_mm(1:3);
if (isempty(conf.ospace_lims))
- sampler = GtOrientationSampling(p, gr, 'verbose', conf.verbose);
+ sampler = GtOrientationSampling(p, gr, ...
+ 'detector_index', conf.det_index, 'verbose', conf.verbose);
r_vecs = sampler.guess_ODF_BB()';
estim_orient_bbox = [min(r_vecs, [], 1), max(r_vecs, [], 1)];
bbox_size_rod = estim_orient_bbox(4:6) - estim_orient_bbox(1:3);
@@ -85,44 +73,17 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
end
bbox_size_rod = estim_orient_bbox(4:6) - estim_orient_bbox(1:3);
+ gr_center_rod = (estim_orient_bbox(4:6) + estim_orient_bbox(1:3)) / 2;
+
bbox_size_deg = 2 * atand(bbox_size_rod);
% Let's now compute the bb on the images, by computing for each corner
% of the space bb, the position on the detector of each corner of the
% orientation bb.
- or = {};
- 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
- base_x2 = base_x1 + [0, ii_x2 * bbox_size_mm(2), 0];
- for ii_x3 = 0:1
- base_x3 = base_x2 + [0, 0, ii_x3 * bbox_size_mm(3)];
- for ii_r1 = 0:1
- base_r1 = estim_orient_bbox(1:3) + [ii_r1 * bbox_size_rod(1), 0, 0];
- for ii_r2 = 0:1
- base_r2 = base_r1 + [0, ii_r2 * bbox_size_rod(2), 0];
- for ii_r3 = 0:1
- base_r3 = base_r2 + [0, 0, ii_r3 * bbox_size_rod(3)];
-
-% fprintf(' center: %f, %f, %f, r_vec: %f, %f, %f\n', base_x3, base_r3)
-
- or{end+1} = struct( ...
- 'id', refgr.id, 'phaseid', refgr.phaseid, ...
- 'center', base_x3, 'R_vector', base_r3); %#ok<AGROW>
- end
- end
- end
- end
- end
- end
- or = gtCalculateGrain_p(or, p);
- or = [or{:}];
-
- num_ors = numel(or);
-
- for ii_g = num_ors:-1:1
- or(ii_g) = gtGrainAllblobsFilterOrder(or(ii_g), refgr_omind_ind);
- end
+ ors = gt6DCalculateFullSpaceCorners( ...
+ estim_space_bbox_mm, bbox_size_mm, ...
+ estim_orient_bbox, bbox_size_rod, ...
+ refgr, p);
if (conf.verbose)
fprintf('\n');
@@ -134,11 +95,11 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
fprintf('\n');
end
- or_abs = cat(1, or(:).allblobs);
+ or_abs = cat(1, ors(:).allblobs);
uvw_tab = zeros(numel(used_refl), num_ors, 3);
for ii_g = 1:num_ors
if (isfield(or_abs(1), 'detector'))
- uvw_tab(:, ii_g, :) = or_abs(ii_g).detector(1).uvw(used_refl, :);
+ uvw_tab(:, ii_g, :) = or_abs(ii_g).detector(conf.det_index).uvw(used_refl, :);
else
uvw_tab(:, ii_g, :) = or_abs(ii_g).uvw(used_refl, :);
end
@@ -146,25 +107,13 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
refor = struct( ...
'id', refgr.id, 'phaseid', refgr.phaseid, ...
- 'center', estim_space_bbox_mm(1:3) + bbox_size_mm / 2, ...
- 'R_vector', estim_orient_bbox(1:3) + bbox_size_rod / 2 );
- refor = gtCalculateGrain(refor, p);
- refor = gtGrainAllblobsFilterOrder(refor, refgr_omind_ind);
-
- num_images = gtGetTotNumberOfImages(p);
- refor_ws = refor.allblobs.omega(used_refl) / p.labgeo.omstep;
+ 'center', gr_center_mm, 'R_vector', gr_center_rod );
+ refor = gtCalculateGrain(refor, p, 'ref_omind', refgr.allblobs.omind);
% Let's treat those blobs at the w edge 360->0
% (from the sampled orientations perspective)
- opposite_ws = mod(refor_ws + num_images / 2, num_images);
- gt_ref_int = opposite_ws > num_images / 2;
- lt_ref_int = ~gt_ref_int;
- opposite_ws_repmat = opposite_ws(:, ones(1, size(uvw_tab(:, :, 3), 2)));
-
- uvw_tab(gt_ref_int, :, 3) = uvw_tab(gt_ref_int, :, 3) ...
- - num_images .* (uvw_tab(gt_ref_int, :, 3) > opposite_ws_repmat(gt_ref_int, :));
- uvw_tab(lt_ref_int, :, 3) = uvw_tab(lt_ref_int, :, 3) ...
- + num_images .* (uvw_tab(lt_ref_int, :, 3) < opposite_ws_repmat(lt_ref_int, :));
+ refor_ws = refor.allblobs.omega(used_refl) / gtGetOmegaStepDeg(p, conf.det_index);
+ uvw_tab(:, :, 3) = gtGrainAnglesTabularFix360deg(uvw_tab(:, :, 3), refor_ws, p);
img_bboxes_initial = [
squeeze(floor(min(uvw_tab, [], 2))), ...
@@ -214,7 +163,7 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
end
sel_reflections = sel_reflections(~inconvenient_etas);
- blobs(1:num_blobs) = gtFwdSimBlobDefinition();
+ blobs = gtFwdSimBlobDefinition('blob', num_blobs);
num_sel_refl = numel(sel_reflections);
for ii_i = 1:num_sel_refl
@@ -223,7 +172,7 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
ii_b = sel_reflections(ii_i);
bb = [img_bboxes(ii_i, 1:2), img_sizes(ii_i, 1:2)];
- blob_vol = gtGetRawRoi(img_bboxes(ii_i, 3), img_bboxes(ii_i, 6), p.acq, bb);
+ blob_vol = gtGetRawRoi(img_bboxes(ii_i, 3), img_bboxes(ii_i, 6), p.acq, bb, conf.det_index);
blob_vol(blob_vol < 0) = 0;
blob_vol(isnan(blob_vol)) = 0;
blob_bb = [img_bboxes(ii_i, 1:3), img_sizes(ii_i, :)];
@@ -298,6 +247,8 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
end
fprintf('Done.\n')
+ proj = gtFwdSimProjDefinition();
+
proj.ondet = ref_ondet;
if (~conf.include_all)
proj.included = ref_included;
@@ -338,8 +289,7 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
spots = permute(cat(3, spots{:}), [1 3 2]);
% These reconstructions usually need some padding
- proj.centerpix = estim_space_bbox_pix(1:3) + bbox_size_pix / 2;
-% proj.centerpix = gtGeoSam2Sam(refor.center, p.samgeo, p.recgeo, false, false);
+ proj.centerpix = gr_center_pix;
proj.bl = blobs;
proj.stack = spots;
% We apply a simple oversize
@@ -348,8 +298,8 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
proj.vol_size_y = vol_size(1);
proj.vol_size_z = vol_size(3);
- refor.proj = proj;
- refor.bb_ors = or;
+ refor.proj(conf.det_index) = proj;
+ refor.bb_ors = ors;
if (conf.save)
fprintf('Saving the extended grain file..')
diff --git a/zUtil_Deformation/gt6DCreateProjDataFromGrainCluster.m b/zUtil_Deformation/gt6DCreateProjDataFromGrainCluster.m
index d261734b3c05f93674d5846fa69d0df4eb2fa08d..1c1054b8b44d15b68489eec5875202e1f7d9afed 100644
--- a/zUtil_Deformation/gt6DCreateProjDataFromGrainCluster.m
+++ b/zUtil_Deformation/gt6DCreateProjDataFromGrainCluster.m
@@ -13,6 +13,8 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
conf = struct( ...
'verbose', false, ...
'min_eta', 15, ...
+ 'det_index', 1, ...
+ 'ospace_oversize', 1.1, ...
'save', false );
conf = parse_pv_pairs(conf, varargin);
@@ -51,96 +53,49 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
refgr = grs(1);
refgr_omind = refgr.allblobs.omind;
- refgr_omind_ind = [ ...
- find(refgr_omind == 1); find(refgr_omind == 2); ...
- find(refgr_omind == 3); find(refgr_omind == 4) ];
for ii_g = num_grains:-1:2
- grs(ii_g) = gtGrainAllblobsFilterOrder(grs(ii_g), refgr_omind_ind);
+ grs(ii_g) = gtGrainAllblobsFilterOrder(grs(ii_g), refgr_omind);
end
- 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
+ ref_ondet = refgr.proj(conf.det_index).ondet;
+ ref_included = refgr.proj(conf.det_index).included;
+ ref_selected = refgr.proj(conf.det_index).selected;
+
fwdsim_sel_refl = ref_ondet(ref_included(ref_selected));
- space_bboxes = zeros(num_grains, 6);
- for ii_g = 1:num_grains
- vol_half_size = [grs(ii_g).proj.vol_size_y, grs(ii_g).proj.vol_size_x, grs(ii_g).proj.vol_size_z] / 2;
- space_bboxes(ii_g, :) = [ ...
- grs(ii_g).proj.centerpix - vol_half_size, ...
- grs(ii_g).proj.centerpix + vol_half_size ];
- end
- estim_space_bbox_pix = [floor(min(space_bboxes(:, 1:3), [], 1)), ceil(max(space_bboxes(:, 4:6), [], 1))];
- bbox_size_pix = estim_space_bbox_pix(4:6) - estim_space_bbox_pix(1:3);
+ % Real-space volume size
+ [gr_center_pix, bbox_size_pix, estim_space_bbox_pix] = gt6DMergeRealSpaceVolumes(grs, conf.det_index);
+ gr_center_mm = gtGeoSam2Sam(gr_center_pix, p.recgeo, p.samgeo, false, false);
estim_space_bbox_mm = [ ...
gtGeoSam2Sam(estim_space_bbox_pix(1:3), p.recgeo, p.samgeo, false, false), ...
gtGeoSam2Sam(estim_space_bbox_pix(4:6), p.recgeo, p.samgeo, false, false) ];
bbox_size_mm = estim_space_bbox_mm(4:6) - estim_space_bbox_mm(1:3);
+ % Orientation-space volume size
for ii_g = num_grains:-1:1
- sampler = GtOrientationSampling(p, grs(ii_g), 'verbose', conf.verbose);
+ sampler = GtOrientationSampling(p, grs(ii_g), ...
+ 'detector_index', conf.det_index, 'verbose', conf.verbose);
odfw_R_vectors{ii_g} = sampler.guess_ODF_BB()';
end
r_vecs = cat(1, odfw_R_vectors{:});
estim_orient_bbox = [min(r_vecs, [], 1), max(r_vecs, [], 1)];
bbox_size_rod = estim_orient_bbox(4:6) - estim_orient_bbox(1:3);
- % oversizing the orienation a bit
- delta_bbox_size_rod = bbox_size_rod * 0.05;
+ % oversizing the orienation BB a bit
+ delta_bbox_size_rod = bbox_size_rod * (conf.ospace_oversize - 1) / 2;
estim_orient_bbox = estim_orient_bbox + [-delta_bbox_size_rod, delta_bbox_size_rod];
bbox_size_rod = estim_orient_bbox(4:6) - estim_orient_bbox(1:3);
- bbox_size_deg = 2 * atand(bbox_size_rod);
-
- % Let's now compute the bb on the images, by computing for each corner
- % of the space bb, the position on the detector of each corner of the
- % orientation bb.
- or = {};
- 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
- base_x2 = base_x1 + [0, ii_x2 * bbox_size_mm(2), 0];
- for ii_x3 = 0:1
- base_x3 = base_x2 + [0, 0, ii_x3 * bbox_size_mm(3)];
- for ii_r1 = 0:1
- base_r1 = estim_orient_bbox(1:3) + [ii_r1 * bbox_size_rod(1), 0, 0];
- for ii_r2 = 0:1
- base_r2 = base_r1 + [0, ii_r2 * bbox_size_rod(2), 0];
- for ii_r3 = 0:1
- base_r3 = base_r2 + [0, 0, ii_r3 * bbox_size_rod(3)];
-
-% fprintf(' center: %f, %f, %f, r_vec: %f, %f, %f\n', base_x3, base_r3)
-
- or{end+1} = struct( ...
- 'id', refgr.id, 'phaseid', refgr.phaseid, ...
- 'center', base_x3, 'R_vector', base_r3); %#ok<AGROW>
- end
- end
- end
- end
- end
- end
- or = gtCalculateGrain_p(or, p);
- or = [or{:}];
-
- num_ors = numel(or);
+ gr_center_rod = (estim_orient_bbox(4:6) + estim_orient_bbox(1:3)) / 2;
- for ii_g = num_ors:-1:1
- or(ii_g) = gtGrainAllblobsFilterOrder(or(ii_g), refgr_omind_ind);
- end
+ bbox_size_deg = 2 * atand(bbox_size_rod);
if (conf.verbose)
f = figure();
ax = axes('parent', f);
hold(ax, 'on');
- gt6DPlotOrientationBBox(ax, cat(1, or(:).R_vector));
+ gt6DPlotOrientationBBox(ax, [estim_orient_bbox(1:3); estim_orient_bbox(4:6)]);
for ii_g = 1:num_grains
scatter3(ax, grs(ii_g).R_vector(1), grs(ii_g).R_vector(2), grs(ii_g).R_vector(3), 30);
end
@@ -157,37 +112,30 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
fprintf('\n');
end
- or_abs = cat(1, or(:).allblobs);
+ % Let's now compute the bb on the images, by computing for each corner
+ % of the space bb, the position on the detector of each corner of the
+ % orientation bb.
+ ors = gt6DCalculateFullSpaceCorners( ...
+ estim_space_bbox_mm, bbox_size_mm, ...
+ estim_orient_bbox, bbox_size_rod, ...
+ refgr, p);
+
+ or_abs = cat(1, ors(:).allblobs);
+ num_ors = numel(ors);
uvw_tab = zeros(numel(fwdsim_sel_refl), num_ors, 3);
for ii_g = 1:num_ors
- if (isfield(or_abs(1), 'detector'))
- uvw_tab(:, ii_g, :) = or_abs(ii_g).detector(1).uvw(fwdsim_sel_refl, :);
- else
- uvw_tab(:, ii_g, :) = or_abs(ii_g).uvw(fwdsim_sel_refl, :);
- end
+ uvw_tab(:, ii_g, :) = or_abs(ii_g).detector(conf.det_index).uvw(fwdsim_sel_refl, :);
end
refor = struct( ...
'id', refgr.id, 'phaseid', refgr.phaseid, 'gids', grs_list, ...
- 'center', estim_space_bbox_mm(1:3) + bbox_size_mm / 2, ...
- 'R_vector', estim_orient_bbox(1:3) + bbox_size_rod / 2 );
- refor = gtCalculateGrain(refor, p);
- refor = gtGrainAllblobsFilterOrder(refor, refgr_omind_ind);
-
- num_images = gtGetTotNumberOfImages(p);
- refor_ws = refor.allblobs.omega(fwdsim_sel_refl) / p.labgeo.omstep;
+ 'center', gr_center_mm, 'R_vector', gr_center_rod );
+ refor = gtCalculateGrain(refor, p, 'ref_omind', refgr_omind);
% Let's treat those blobs at the w edge 360->0
% (from the sampled orientations perspective)
- opposite_ws = mod(refor_ws + num_images / 2, num_images);
- gt_ref_int = opposite_ws > num_images / 2;
- lt_ref_int = ~gt_ref_int;
- opposite_ws_repmat = opposite_ws(:, ones(1, size(uvw_tab(:, :, 3), 2)));
-
- uvw_tab(gt_ref_int, :, 3) = uvw_tab(gt_ref_int, :, 3) ...
- - num_images .* (uvw_tab(gt_ref_int, :, 3) > opposite_ws_repmat(gt_ref_int, :));
- uvw_tab(lt_ref_int, :, 3) = uvw_tab(lt_ref_int, :, 3) ...
- + num_images .* (uvw_tab(lt_ref_int, :, 3) < opposite_ws_repmat(lt_ref_int, :));
+ refor_ws = refor.allblobs.omega(fwdsim_sel_refl) / gtGetOmegaStepDeg(p, conf.det_index);
+ uvw_tab(:, :, 3) = gtGrainAnglesTabularFix360deg(uvw_tab(:, :, 3), refor_ws, p);
img_bboxes = [
squeeze(floor(min(uvw_tab, [], 2))), ...
@@ -222,7 +170,7 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
fprintf('Loading raw images: ')
num_blobs = numel(ref_included);
- blobs(1:num_blobs) = gtFwdSimBlobDefinition();
+ blobs = gtFwdSimBlobDefinition('blob', num_blobs);
sel_reflections = find(ref_selected);
sel_reflections = sel_reflections(~inconvenient_etas);
@@ -234,7 +182,7 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
ii_b = sel_reflections(ii_i);
bb = [img_bboxes(ii_i, 1:2), img_sizes(ii_i, 1:2)];
- blob_vol = gtGetRawRoi(img_bboxes(ii_i, 3), img_bboxes(ii_i, 6), p.acq, bb);
+ blob_vol = gtGetRawRoi(img_bboxes(ii_i, 3), img_bboxes(ii_i, 6), p.acq, bb, conf.det_index);
blob_vol(blob_vol < 0) = 0;
blob_bb = [img_bboxes(ii_i, 1:3), img_sizes(ii_i, :)];
@@ -318,7 +266,9 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
spots = arrayfun(@(x){sum(x.intm, 3)}, blobs);
spots = permute(cat(3, spots{:}), [1 3 2]);
- proj.centerpix = estim_space_bbox_pix(1:3) + bbox_size_pix / 2;
+ proj = gtFwdSimProjDefinition();
+
+ proj.centerpix = gr_center_pix;
proj.bl = blobs;
proj.stack = spots;
vol_size = bbox_size_pix + mean(bbox_size_pix) * 0.3;
@@ -333,8 +283,8 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
finally_selected(sel_reflections) = true;
proj.selected = finally_selected;
- refor.proj = proj;
- refor.bb_ors = or;
+ refor.proj(conf.det_index) = proj;
+ refor.bb_ors = ors;
if (conf.save)
fprintf('Saving the cluster file..')
diff --git a/zUtil_Deformation/gt6DCreateProjDataFromTwinnedGrainFwdProj.m b/zUtil_Deformation/gt6DCreateProjDataFromTwinnedGrainFwdProj.m
index c15470ce73ec6dd0eafeb54a8ad073d2dc2c4377..4d447226f998815c6f272149e9464e7695d448d2 100644
--- a/zUtil_Deformation/gt6DCreateProjDataFromTwinnedGrainFwdProj.m
+++ b/zUtil_Deformation/gt6DCreateProjDataFromTwinnedGrainFwdProj.m
@@ -14,9 +14,10 @@ function [samp_ors, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDat
conf = struct( ...
'verbose', false, ...
- 'det_ind', 1, ...
+ 'det_index', 1, ...
'min_eta', 15, ...
'rspace_oversize', 1.1, ...
+ 'ospace_oversize', 1.1, ...
'check_spots', false, ...
'stack_oversize', 1.4, ...
'save', false );
@@ -106,9 +107,13 @@ function [samp_ors, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDat
end
refgr = grs(1);
- grs(2:end) = reorder_reflections(grs(2:end), refgr);
- refgr_proj = refgr.proj(conf.det_ind);
+ refgr_omind = refgr.allblobs.omind;
+ for ii_g = 2:numel(grs)
+ grs(ii_g) = gtGrainAllblobsFilterOrder(grs(ii_g), refgr_omind); %#ok<AGROW>
+ end
+
+ refgr_proj = refgr.proj(conf.det_index);
ref_ondet = refgr_proj.ondet;
ref_included = refgr_proj.included;
@@ -162,7 +167,6 @@ function [samp_ors, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDat
if (conf.verbose)
vis_sel = ref_ondet(ref_included);
-% vis_sel = ref_ondet;
fprintf('%02d) w1 %6.2f, w2 %6.2f, n1 %6.2f, n2 %6.2f, w_inds (%d<->%d), hkls [%2d %2d %2d]<->[%2d %2d %2d] <- diff: %7.2f (!! %d, L %g) [bad n1 %d n2 %d]\n', ...
[(1:numel(vis_sel))', ...
grs(1).allblobs.omega(vis_sel), ...
@@ -181,62 +185,57 @@ function [samp_ors, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDat
]');
end
- 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 ];
- 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);
+ [gr_center_pix, bbox_size_pix, estim_space_bbox_pix] = gt6DMergeRealSpaceVolumes(grs, conf.det_index, conf.rspace_oversize);
+ gr_center_mm = gtGeoSam2Sam(gr_center_pix, p.recgeo, p.samgeo, false, false);
estim_space_bbox_mm = [ ...
gtGeoSam2Sam(estim_space_bbox_pix(1:3), p.recgeo, p.samgeo, false, false), ...
gtGeoSam2Sam(estim_space_bbox_pix(4:6), p.recgeo, p.samgeo, false, false) ];
bbox_size_mm = estim_space_bbox_mm(4:6) - estim_space_bbox_mm(1:3);
+ if (conf.verbose)
+ fprintf('\n');
+ fprintf('Estimated spatial voxel BBox: [%3d, %3d, %3d] -> [%3d, %3d, %3d]\n', estim_space_bbox_pix);
+ fprintf(' BBox size: %3d, %3d, %3d (%f, %f, %f mm)\n', bbox_size_pix, bbox_size_mm);
+ end
+
img_sizes = zeros(num_grains, 2);
for ii_g = num_grains:-1:1
- sampler = GtOrientationSampling(p, grs(ii_g), 'verbose', conf.verbose);
+ sampler = GtOrientationSampling(p, grs(ii_g), ...
+ 'detector_index', conf.det_index, 'verbose', conf.verbose);
r_vecs = sampler.guess_ODF_BB()';
estim_orient_bbox = [min(r_vecs, [], 1), max(r_vecs, [], 1)];
bbox_size_rod = estim_orient_bbox(4:6) - estim_orient_bbox(1:3);
% oversizing the orienation a bit
- delta_bbox_size_rod = bbox_size_rod * 0.05;
+ delta_bbox_size_rod = bbox_size_rod * (conf.ospace_oversize - 1) / 2;
estim_orient_bbox = estim_orient_bbox + [-delta_bbox_size_rod, delta_bbox_size_rod];
bbox_size_rod = estim_orient_bbox(4:6) - estim_orient_bbox(1:3);
bbox_size_deg = 2 * atand(bbox_size_rod);
if (conf.verbose)
- fprintf('\n');
- fprintf('Estimated spatial voxel BBox: [%3d, %3d, %3d] -> [%3d, %3d, %3d]\n', estim_space_bbox_pix);
- fprintf(' BBox size: %3d, %3d, %3d (%f, %f, %f mm)\n', bbox_size_pix, bbox_size_mm);
-
- fprintf(' Estimated orientation BBox: [%3.3f, %3.3f, %3.3f] -> [%3.3f, %3.3f, %3.3f]\n', estim_orient_bbox);
- fprintf(' BBox size: %3.3f, %3.3f, %3.3f (deg)\n', bbox_size_deg);
+ fprintf('%d) Estimated orientation BBox: [%3.3f, %3.3f, %3.3f] -> [%3.3f, %3.3f, %3.3f]\n', ii_g, estim_orient_bbox);
+ fprintf(' BBox size: %3.3f, %3.3f, %3.3f (deg)\n', bbox_size_deg);
fprintf('\n');
end
refor = struct( ...
'id', grs(ii_g).id, 'phaseid', grs(ii_g).phaseid, ...
- 'center', estim_space_bbox_mm(1:3) + bbox_size_mm / 2, ...
- 'R_vector', grs(ii_g).R_vector );
- refor = gtCalculateGrain(refor, p);
+ 'center', gr_center_mm, 'R_vector', grs(ii_g).R_vector );
+ refor = gtCalculateGrain(refor, p, 'ref_omind', refgr_omind);
- refor.bb_ors = get_6D_space_corners(estim_space_bbox_mm, ...
+ refor.bb_ors = gt6DCalculateFullSpaceCorners(estim_space_bbox_mm, ...
bbox_size_mm, estim_orient_bbox, bbox_size_rod, refgr, p);
- img_sizes(ii_g, :) = [size(grs(ii_g).proj.stack, 1), size(grs(ii_g).proj.stack, 3), ];
+ img_sizes(ii_g, :) = [ ...
+ size(grs(ii_g).proj(conf.det_index).stack, 1), ...
+ size(grs(ii_g).proj(conf.det_index).stack, 3), ];
samp_ors(ii_g) = refor;
end
- samp_ors = reorder_reflections(samp_ors, refgr);
[stackUSize, stackVSize] = get_stack_UV_size(cat(1, img_sizes), p, conf);
@@ -245,13 +244,16 @@ function [samp_ors, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDat
bool_ref_sel = false(size(refgr.allblobs.omega));
bool_ref_sel(ref_ondet(ref_included(ref_selected))) = true;
+ % At the moment we only support the configuration: parent + twins
+ refl_matches = gt6DGetMatchingReflections(refgr, grs(2:end), 2);
+
for ii_g = 1:num_grains
fprintf('Loading raw images for grain %d: ', ii_g)
if (ii_g > 1)
twingr = grs(ii_g);
- twingr_proj = twingr.proj(conf.det_ind);
+ twingr_proj = twingr.proj(conf.det_index);
twin_ondet = twingr_proj.ondet;
twin_inc = twingr_proj.included;
@@ -268,17 +270,7 @@ function [samp_ors, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDat
% twin, and were included for the parent
bool_test_inc = bool_ref_inc & bool_twin_ondet;
- inc_ref_omegas = samp_ors(1).allblobs.omega(bool_test_inc);
- inc_ref_Lfac = samp_ors(1).allblobs.lorentzfac(bool_test_inc);
- inc_ref_etas = samp_ors(1).allblobs.eta(bool_test_inc);
-
- inc_twin_omegas = samp_ors(ii_g).allblobs.omega(bool_test_inc);
- inc_twin_etas = samp_ors(ii_g).allblobs.eta(bool_test_inc);
-
- w_diff = abs(mod(inc_ref_omegas - inc_twin_omegas + 180, 360) - 180);
- n_diff = abs(mod(inc_ref_etas - inc_twin_etas + 180, 360) - 180);
-
- test_shared = (w_diff < inc_ref_Lfac) & (n_diff < 5);
+ test_shared = refl_matches(bool_test_inc, ii_g-1);
% let's add the shared as included
shared_parent = false(size(refgr.allblobs.omega));
@@ -338,7 +330,9 @@ function [samp_ors, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDat
spots = arrayfun(@(x){sum(x.intm, 3)}, blobs);
spots = permute(cat(3, spots{:}), [1 3 2]);
- proj.centerpix = estim_space_bbox_pix(1:3) + bbox_size_pix / 2;
+ proj = gtFwdSimProjDefinition();
+
+ proj.centerpix = gr_center_pix;
proj.bl = blobs;
proj.stack = spots;
vol_size = bbox_size_pix + mean(bbox_size_pix) * 0.3;
@@ -354,15 +348,15 @@ function [samp_ors, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDat
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;
+ samp_ors(1).proj(conf.det_index).shared_bls_twins(shared_parent_pos) = true;
else
proj.shared_bls_twins = false(num_blobs, 1);
end
- samp_ors(ii_g).proj(conf.det_ind) = proj;
+ samp_ors(ii_g).proj(conf.det_index) = proj;
if (conf.check_spots && ii_g > 1)
- samp_ors(ii_g).proj.selected = gtGuiGrainMontage(samp_ors(ii_g), [], true);
+ samp_ors(ii_g).proj.selected = gtGuiGrainMontage(samp_ors(ii_g), [], true, conf.det_index);
end
end
@@ -397,49 +391,6 @@ function [samp_ors, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDat
end
end
-function orients = get_6D_space_corners(estim_space_bbox_mm, bbox_size_mm, estim_orient_bbox, bbox_size_rod, refgr, p)
- 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
- base_x2 = base_x1 + [0, ii_x2 * bbox_size_mm(2), 0];
- for ii_x3 = 0:1
- base_x3 = base_x2 + [0, 0, ii_x3 * bbox_size_mm(3)];
- for ii_r1 = 0:1
- base_r1 = estim_orient_bbox(1:3) + [ii_r1 * bbox_size_rod(1), 0, 0];
- for ii_r2 = 0:1
- base_r2 = base_r1 + [0, ii_r2 * bbox_size_rod(2), 0];
- for ii_r3 = 0:1
- base_r3 = base_r2 + [0, 0, ii_r3 * bbox_size_rod(3)];
-
-% fprintf(' center: %f, %f, %f, r_vec: %f, %f, %f\n', base_x3, base_r3)
-
- 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);
- end
- end
- end
- end
- end
- end
- orients = gtCalculateGrain_p(orients, p);
- orients = [orients{:}];
-
- orients = reorder_reflections(orients, refgr);
-end
-
-function orients = reorder_reflections(orients, refgr)
- refgr_omind = refgr.allblobs.omind;
- refgr_omind_ind = [ ...
- find(refgr_omind == 1); find(refgr_omind == 2); ...
- find(refgr_omind == 3); find(refgr_omind == 4) ];
-
- for ii_g = 1:numel(orients)
- orients(ii_g) = gtGrainAllblobsFilterOrder(orients(ii_g), refgr_omind_ind);
- end
-end
-
function [u_size, v_size] = get_stack_UV_size(img_sizes, p, conf)
max_img_sizes = [max(img_sizes(:, 1)), max(img_sizes(:, 2))];
@@ -496,4 +447,3 @@ end
-
diff --git a/zUtil_Deformation/gt6DGetMatchingReflections.m b/zUtil_Deformation/gt6DGetMatchingReflections.m
new file mode 100644
index 0000000000000000000000000000000000000000..f756d2deb9c7d4a039ee7f102a9b9fbef3dc32f3
--- /dev/null
+++ b/zUtil_Deformation/gt6DGetMatchingReflections.m
@@ -0,0 +1,28 @@
+function match = gt6DGetMatchingReflections(ref_or, ors, angular_toll)
+
+ if (~exist('angular_toll', 'var') || isempty(angular_toll))
+ angular_toll = 1; % degrees
+ end
+
+ ref_ws = ref_or.allblobs.omega;
+ ref_ns = ref_or.allblobs.eta;
+ ref_Lfactors = ref_or.allblobs.lorentzfac;
+
+ w_toll = angular_toll * ref_Lfactors;
+ n_toll = angular_toll;
+
+ ors_allblobs = [ors(:).allblobs];
+ ors_ws = cat(2, ors_allblobs(:).omega);
+ ors_ns = cat(2, ors_allblobs(:).eta);
+
+ ones_num_ors = ones(numel(ors), 1);
+ ref_ws = ref_ws(:, ones_num_ors);
+ ref_ns = ref_ns(:, ones_num_ors);
+
+ w_toll = w_toll(:, ones_num_ors);
+
+ w_diff = abs(mod(ref_ws - ors_ws + 180, 360) - 180);
+ n_diff = abs(mod(ref_ns - ors_ns + 180, 360) - 180);
+
+ match = (w_diff < w_toll) & (n_diff < n_toll);
+end
diff --git a/zUtil_Deformation/gt6DMergeRealSpaceVolumes.m b/zUtil_Deformation/gt6DMergeRealSpaceVolumes.m
new file mode 100644
index 0000000000000000000000000000000000000000..36e824630748d3ed57c20768e227ac006abb59b6
--- /dev/null
+++ b/zUtil_Deformation/gt6DMergeRealSpaceVolumes.m
@@ -0,0 +1,39 @@
+function [gr_center_pix, vol_size_pix, bbox_pix] = gt6DMergeRealSpaceVolumes(grs, det_index, oversize)
+% num_ors = numel(grs);
+% vol_sizes = zeros(num_ors, 3);
+% vol_centers = zeros(num_ors, 3);
+% for ii = 1:num_ors
+% vol_sizes(ii, :) = [ ...
+% grs(ii).proj(det_index).vol_size_y, ...
+% grs(ii).proj(det_index).vol_size_x, ...
+% grs(ii).proj(det_index).vol_size_z ];
+% vol_centers(ii, :) = grs(ii).proj(det_index).centerpix;
+% end
+
+ projs = arrayfun(@(x){x.proj(det_index)}, grs);
+ projs = [projs{:}];
+
+ vol_sizes = [cat(1, projs.vol_size_y), cat(1, projs.vol_size_x), cat(1, projs.vol_size_z)];
+ vol_centers = cat(1, projs.centerpix);
+
+ vol_half_sizes = vol_sizes / 2;
+
+ min_corners = vol_centers - vol_half_sizes;
+ max_corners = vol_centers + vol_half_sizes;
+
+ full_vol_min_corners = min(min_corners, [], 1);
+ full_vol_max_corners = max(max_corners, [], 1);
+
+ gr_center_pix = (full_vol_max_corners + full_vol_min_corners) / 2;
+
+ vol_size_pix = full_vol_max_corners - full_vol_min_corners;
+
+ if (exist('oversize', 'var'))
+ vol_size_pix = vol_size_pix * oversize;
+ end
+
+ vol_size_pix = ceil(vol_size_pix);
+
+ vol_half_size_pix = vol_size_pix / 2;
+ bbox_pix = [gr_center_pix - vol_half_size_pix, gr_center_pix + vol_half_size_pix];
+end