adapting Gt6DreconstructionAlgorithmFactory for sample movements durng scan

Signed-off-by: Wolfgang Ludwig <wolfgang.ludwig@esrf.fr>

zUtil_Deformation/Gt6DReconstructionAlgorithmFactory.m

@@ -230,7 +230,7 @@ classdef Gt6DReconstructionAlgorithmFactory < handle
 
                     if (~isempty(find(parent_pos_shared_bls == shared_blob_pos_inc, 1)))
                         curr_or = sampler(ii_o_reg).get_reference_grain();
-                        reg_ids(ii_o_reg) = curr_or.id;
+                        reg_ids(ii_o_reg) = curr_or.id(1);   % hope this is the right fix...
                     end
                 end
                 reg_ids = reg_ids(reg_ids > 0);
@@ -763,6 +763,7 @@ classdef Gt6DReconstructionAlgorithmFactory < handle
             fprintf('Blob (n.) | Blob w lims            | Projs w lims | Padding | n-interp | Size | Blob Int | Scatter Int\n')
             fprintf('----------+------------------------+--------------+---------+----------+------+----------+-------------\n')
             for ii_b = 1:tot_blobs
+                try
                 fprintf('%03d (%03d) | %4d:%4d -> %4d:%4d |    %4d:%4d |   %2d:%2d |       %2d | 1:%2d | %8s | %s [%s %s]\n', ...
                     ii_b, sel_incl_indx(ii_b), ...
                     bl(ii_b).bbwim, blobs_w_lims_pad(ii_b, :),...
@@ -773,6 +774,8 @@ classdef Gt6DReconstructionAlgorithmFactory < handle
                     sprintf('%3.3g', scatter_ints_avg(ii_b)), ...
                     sprintf('%3.3g', min(scatter_ints_ors(ii_b, :))), ...
                     sprintf('%3.3g', max(scatter_ints_ors(ii_b, :))) );
+                catch
+                end
             end
             fprintf('----------+------------------------+--------------+---------+----------+------+----------+-------------\n')
 
@@ -1047,6 +1050,8 @@ classdef Gt6DReconstructionAlgorithmFactory < handle
 
             dvec_sam = cat(1, ors_allblobs(:).dvecsam);
             rot_w_l2s = cat(3, ors_allblobs(:).srot);
+            % account for sample shifts relative to rotation axis
+            [~, shifts_sam] = gtMatchGetSampleShifts([], [ors_allblobs.omega]);
 
             proj_geom = gtGeoProjForReconstruction(...
                 dvec_sam, rot_w_l2s, ref_gr.center, bb_bls_uv_oi, [], ...
@@ -1054,7 +1059,7 @@ classdef Gt6DReconstructionAlgorithmFactory < handle
                 self.parameters.labgeo, ...
                 self.parameters.samgeo, ...
                 self.parameters.recgeo(self.det_index), ...
-                'ASTRA_grain');
+                'ASTRA_grain', shifts_sam);
 
             if (self.volume_downscaling > 1)
                 proj_geom(:, 4:12) = proj_geom(:, 4:12) / self.volume_downscaling;
@@ -1159,7 +1164,8 @@ classdef Gt6DReconstructionAlgorithmFactory < handle
                 dvec_lab = ors_allblobs(ii_o).dvec(ind_of_blob, :);
                 dvec_sam = gtGeoLab2Sam(dvec_lab, rot_w_l2s, ...
                     self.parameters.labgeo, self.parameters.samgeo, true);
-
+                % accounting for sample shifts relative to rotation axis
+                [~, shifts_sam] = gtMatchGetSampleShifts([], [ors_allblobs.omega]);
                 proj_geom = gtGeoProjForReconstruction(...
                     dvec_sam, rot_w_l2s, ref_gr.center, ...
                     bb_bls_uv(ind_of_blob, :), [], ...
@@ -1167,7 +1173,7 @@ classdef Gt6DReconstructionAlgorithmFactory < handle
                     self.parameters.labgeo, ...
                     self.parameters.samgeo, ...
                     self.parameters.recgeo(self.det_index), ...
-                    'ASTRA_grain');
+                    'ASTRA_grain', shifts_sam);
 
                 if (self.volume_downscaling > 1)
                     proj_geom(:, 4:12) = proj_geom(:, 4:12) / self.volume_downscaling;
@@ -1262,6 +1268,9 @@ classdef Gt6DReconstructionAlgorithmFactory < handle
                 dvec_sam = gtGeoLab2Sam(dvec_lab, rot_w_l2s, ...
                     self.parameters.labgeo, self.parameters.samgeo, true);
 
+                % accounting for sample shifts relative to rotation axis
+                [~, shifts_sam] = gtMatchGetSampleShifts([], [ors_allblobs.omega]);
+
                 proj_geom = gtGeoProjForReconstruction(...
                     dvec_sam, rot_w_l2s, ref_gr.center, ...
                     bb_bls_uv(ind_of_blob, :), [], ...
@@ -1269,7 +1278,7 @@ classdef Gt6DReconstructionAlgorithmFactory < handle
                     self.parameters.labgeo, ...
                     self.parameters.samgeo, ...
                     self.parameters.recgeo(self.det_index), ...
-                    'ASTRA_grain');
+                    'ASTRA_grain', shifts_sam);
 
                 if (self.volume_downscaling > 1)
                     proj_geom(:, 4:12) = proj_geom(:, 4:12) / self.volume_downscaling;