From 92468b4f796f4e8003b5eba5378c6e84e052634b Mon Sep 17 00:00:00 2001
From: Nicola Vigano <nicola.vigano@esrf.fr>
Date: Fri, 10 Jun 2016 19:55:02 +0200
Subject: [PATCH] 6D-Reconstruction-Twins: added masking out what is outside
the parent convex shape for raw images
Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>
---
...t6DCreateProjDataFromTwinnedGrainFwdProj.m | 36 ++++++
.../gt6DSpreadProjectVertices2Det.m | 105 ++++++++++++++++++
2 files changed, 141 insertions(+)
create mode 100644 zUtil_Deformation/gt6DSpreadProjectVertices2Det.m
diff --git a/zUtil_Deformation/gt6DCreateProjDataFromTwinnedGrainFwdProj.m b/zUtil_Deformation/gt6DCreateProjDataFromTwinnedGrainFwdProj.m
index 96470017..4d321c4f 100644
--- a/zUtil_Deformation/gt6DCreateProjDataFromTwinnedGrainFwdProj.m
+++ b/zUtil_Deformation/gt6DCreateProjDataFromTwinnedGrainFwdProj.m
@@ -292,6 +292,9 @@ function [samp_ors, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDat
% Using the same because it gives the same size/uvw-limits
if (ii_g > 1)
blobs(extended_projs(ii_g).shared_refl) = samp_ors(1).proj(conf.det_index).bl(extended_projs(ii_g).shared_refl_pos_in_parent);
+
+ proj_bl_masks = project_masks(samp_ors(ii_g), extended_projs(ii_g), grs(1).fwd_sim(conf.det_index).gv_verts, p, conf);
+ blobs = assign_masks(blobs, proj_bl_masks, ~extended_projs(ii_g).shared_refl);
end
else
fprintf(' - Loading segmented blobs..')
@@ -689,4 +692,37 @@ function blob = load_blob(img_bboxes, img_sizes, stackUSize, stackVSize, p, conf
blob.intensity = blob_int;
end
+function proj_bl_masks = project_masks(refor, eproj, parent_verts, p, conf)
+ sel = eproj.ondet(eproj.included);
+ proj_bl_masks = gt6DSpreadProjectVertices2Det(refor, parent_verts, sel, p, conf.det_index);
+end
+
+function blobs = assign_masks(blobs, proj_mask_blobs, sel)
+ blobs_u_lims = cat(1, blobs(sel).bbuim);
+ blobs_v_lims = cat(1, blobs(sel).bbvim);
+
+ proj_masks_u_lims = cat(1, proj_mask_blobs(sel).bbuim);
+ proj_masks_v_lims = cat(1, proj_mask_blobs(sel).bbvim);
+
+ shifts = [ ...
+ (proj_masks_u_lims(:, 1) - blobs_u_lims(:, 1)), ...
+ (proj_masks_v_lims(:, 1) - blobs_v_lims(:, 1)) ];
+ shifts(:, 3) = 0;
+
+ inds = find(sel);
+ for ii = 1:numel(inds)
+ ii_b = inds(ii);
+
+ mask = uint8(proj_mask_blobs(ii_b).mask);
+ mask = mask(:, :, ones(blobs(ii_b).bbsize(3), 1));
+
+ blobs(ii_b).mask = gtPlaceSubVolume( ...
+ zeros(blobs(ii_b).bbsize, 'uint8'), mask, shifts(ii, :) );
+
+ blobs(ii_b).intm(~blobs(ii_b).mask) = 0;
+ blob_int = gtMathsSumNDVol(blobs(ii_b).intm);
+ blobs(ii_b).intensity = blob_int;
+ end
+end
+
diff --git a/zUtil_Deformation/gt6DSpreadProjectVertices2Det.m b/zUtil_Deformation/gt6DSpreadProjectVertices2Det.m
new file mode 100644
index 00000000..396463d9
--- /dev/null
+++ b/zUtil_Deformation/gt6DSpreadProjectVertices2Det.m
@@ -0,0 +1,105 @@
+ function proj_bls = gt6DSpreadProjectVertices2Det(gr, verts_rec, ondet, parameters, det_ind, verbose)
+% FUNCTION proj_bls = gt6DSpreadProjectVertices2Det(gr, verts_rec, ondet, parameters, det_ind, verbose)
+%
+
+ if (~exist('verbose', 'var') || isempty(verbose))
+ verbose = false;
+ end
+
+ detgeo = parameters.detgeo(det_ind);
+ labgeo = parameters.labgeo;
+ samgeo = parameters.samgeo;
+ recgeo = parameters.recgeo(det_ind);
+
+ omstep = gtGetOmegaStepDeg(parameters, det_ind);
+
+ r_vecs = cat(1, gr.bb_ors(:).R_vector);
+ r_vecs = unique(r_vecs, 'rows');
+
+ if (size(r_vecs, 1) ~= 8)
+ error('gt6DSpreadProjectVertices2Det:wrong_argument', ...
+ 'Incoming bb orientations have %d unique orietations (8 were expected)', ...
+ size(r_vecs, 1))
+ end
+
+ ors = cell(8, 1);
+ for ii_o = 1:8
+ ors{ii_o} = struct('id', gr.id, 'phaseid', gr.phaseid, ...
+ 'center', gr.center, 'R_vector', r_vecs(ii_o, :));
+ end
+ ors = gtCalculateGrain_p(ors, parameters, 'ref_omind', gr.allblobs.omind);
+ ors = [ors{:}];
+
+ num_blobs = numel(ondet);
+ proj_bls = gtFwdSimBlobDefinition('blob', num_blobs);
+
+ dvecs_lab = zeros(num_blobs, 3, 8);
+ omegas = zeros(num_blobs, 8);
+ rot_l2s = zeros(3, 3, num_blobs, 8);
+
+ for ii_o = 1:8
+ dvecs_lab(:, :, ii_o) = ors(ii_o).allblobs.dvec(ondet, :);
+ omegas(:, ii_o) = ors(ii_o).allblobs.omega(ondet);
+ rot_l2s(:, :, :, ii_o) = ors(ii_o).allblobs.srot(:, :, ondet);
+ end
+ rot_s2l = permute(rot_l2s, [2 1 3 4]);
+
+ if (verbose)
+ uv = gr.allblobs.detector(det_ind).uvw(ondet, 1:2);
+ end
+
+ ones_verts = ones(size(verts_rec, 1), 1);
+ gc_sam = gr.center(ones_verts, :);
+
+ verts_sam = repmat(gtGeoSam2Sam(verts_rec, recgeo, samgeo, false) + gc_sam, [8, 1]);
+
+ % Now we project the vertices to the spots and take the convex hull
+ for ii_b = 1:num_blobs
+ rot_s2l_w = rot_s2l(:, :, ii_b .* ones_verts, :);
+ rot_s2l_w = reshape(rot_s2l_w, 3, 3, []);
+ verts_lab = gtGeoSam2Lab(verts_sam, rot_s2l_w, labgeo, samgeo, false);
+ dvec_vers = dvecs_lab(ii_b .* ones_verts, :, :);
+ dvec_vers = reshape(permute(dvec_vers, [1 3 2]), [], 3);
+
+ verts_det_pos = gtFedPredictUVMultiple([], dvec_vers', verts_lab', ...
+ detgeo.detrefpos', detgeo.detnorm', detgeo.Qdet, ...
+ [detgeo.detrefu, detgeo.detrefv]')';
+
+ if (verbose)
+ f = figure();
+ ax = axes('parent', f);
+ hold(ax, 'on')
+ scatter(ax, verts_det_pos(:, 1), verts_det_pos(:, 2));
+ scatter(ax, uv(ii_b, 1), uv(ii_b, 2), 30, 'r');
+ hold(ax, 'off')
+ end
+
+ verts_idxs = convhull(verts_det_pos);
+ verts_det_pos = verts_det_pos(verts_idxs, :);
+
+ bb_2d = [floor(min(verts_det_pos, [], 1)), ceil(max(verts_det_pos, [], 1))];
+ bb_2d = [bb_2d(1:2), (bb_2d(3:4) - bb_2d(1:2) + 1)];
+
+ mask = zeros(bb_2d(3:4));
+ verts_mask_pos = round(verts_det_pos) - bb_2d(ones(numel(verts_idxs), 1), 1:2) + 1;
+ verts_mask_indx = verts_mask_pos(:, 1) + bb_2d(3) * (verts_mask_pos(:, 2) - 1);
+ mask(verts_mask_indx) = 1;
+ mask = bwconvhull(mask);
+
+ proj_bls(ii_b).bbuim = [bb_2d(1), (bb_2d(1) + bb_2d(3) - 1)];
+ proj_bls(ii_b).bbvim = [bb_2d(2), (bb_2d(2) + bb_2d(4) - 1)];
+ proj_bls(ii_b).bbwim = [ ...
+ floor(min(omegas(ii_b, :)) / omstep), ...
+ ceil(max(omegas(ii_b, :)) / omstep) ];
+ proj_bls(ii_b).bbsize = [bb_2d(3:4), 1];
+ proj_bls(ii_b).mask = mask;
+
+ if (verbose)
+ f = figure();
+ ax = axes('parent', f);
+ imshow(mask, 'parent', ax)
+
+ pause
+ end
+ end
+ end
--
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