Topotomo import: added simple background removal and projection geometry...

Topotomo import: added simple background removal and projection geometry construction for 3D reconstruction/projection

Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>

4_grains/gtGrainImportTopotomoScan.m

@@ -35,6 +35,11 @@ function gr = gtGrainImportTopotomoScan(gr, p, det_ind, data_type)
             filen_name = fullfile(base_dir, [base_name, sprintf('%04d.edf', (ii_b - 1) * nph + ii_p)]);
             b_vol(:, :, ii_p) = edf_read(filen_name, [], 'nodisp', info);
         end
+
+        bck_grnd = median(b_vol(:,:,[1:5, end-5:end]), 3);
+        b_vol = bsxfun(@minus, b_vol, bck_grnd);
+        b_vol(b_vol < 0) = 0;
+
         bl(ii_b).intm = b_vol;
         bl(ii_b).mask = true(b_size);
         bl(ii_b).bbuim = roi_u;
@@ -87,12 +92,15 @@ function gr = gtGrainImportTopotomoScan(gr, p, det_ind, data_type)
     proj.included = (1:nbl)';
     proj.selected = true(size(proj.ondet));
 
-%     sel = proj.ondet(proj.included(proj.selected));
-%     dvecsam = gr.allblobs(det_ind).dvecsam(sel, :);
-%     rot_s2l = gr.allblobs(det_ind).rot_s2l(:, :, sel);
-%     proj.geom = gtGeoProjForReconstruction(dvecsam, ...
-%         rot_s2l, gr.center, bbpos_det_grain, [], ...
-%         p.detgeo(det_ind), labgeo, samgeo, p.recgeo(det_ind), 'ASTRA_grain');
+    sel = proj.ondet(proj.included(proj.selected));
+    dvecsam = gr.allblobs(det_ind).dvecsam(sel, :);
+    rot_l2s = gr.allblobs(det_ind).rot_l2s(:, :, sel);
+    bb_blobs_pos = [1, 1, p.detgeo(det_ind).detsizeu, p.detgeo(det_ind).detsizev];
+    bb_blobs_pos = bb_blobs_pos(ones(1, nbl), :);
+
+    proj.geom = gtGeoProjForReconstruction(dvecsam, ...
+        rot_l2s, gr.center, bb_blobs_pos, [], ...
+        p.detgeo(det_ind), p.labgeo, p.samgeo, p.recgeo(1), 'ASTRA_grain');
 
     fprintf('\b\b: Done in %g seconds.\n', toc(c))