6D-reconstruction: small fixes for sample-shift

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

3_pairmatchingGUI/gtMatchGetSampleShifts.m

@@ -11,32 +11,51 @@ function [shifts_lab, shifts_sam, abspos, relpos] = gtMatchGetSampleShifts(param
     tot_proj = gtAcqTotNumberOfImages(parameters, conf.det_index);
     omstep   = gtGetOmegaStepDeg(parameters, conf.det_index);
     refon    = parameters.acq.refon;
-    ref_grps = tot_proj/refon;
+    ref_grps = tot_proj / refon;
 
-    filename = sprintf('%s/0_rawdata/Orig/%s%04d.edf', parameters.acq.dir, parameters.acq.name, conf.offset_pos);
+    acq_dir = parameters.acq.dir;
+    acq_name = parameters.acq.name;
+    base_dir = fullfile(acq_dir, '0_rawdata', 'Orig');
+
+    filename = sprintf('%s/%s%04d.edf', base_dir, acq_name, conf.offset_pos);
     info     = edf_info(filename);
     offset   = [info.motor.samtx, info.motor.samty, info.motor.samtz];
 
-    shifts_lab  = zeros(tot_proj, 3);
-    shifts_sam  = zeros(tot_proj, 3);
-    refpos      = zeros(ref_grps + 1, 3);
+    % Let's handle some special case
+    if (~exist(filename, 'file'))
+        if (~exist('omega_values', 'var') || isempty(omega_values))
+            omega_values = 0;
+        end
+        shifts_lab = zeros(numel(omega_values, 3));
+        shifts_sam = zeros(numel(omega_values, 3));
+        abspos = zeros(numel(omega_values, 3));
+        relpos = zeros(numel(omega_values, 3));
+        return
+    end
+
+    shifts_lab = zeros(tot_proj, 3);
+    shifts_sam = zeros(tot_proj, 3);
+    abspos = zeros(ref_grps + 1, 3);
+    relpos = zeros(ref_grps + 1, 3);
     rotcomp = gtMathsRotationMatrixComp(parameters.labgeo.rotdir, 'row');
 
     for ii = 1 : ref_grps
-        filename = sprintf('%s/0_rawdata/Orig/%s%04d.edf', parameters.acq.dir, parameters.acq.name, (ii-1) * refon);
+        filename = sprintf('%s/%s%04d.edf', base_dir, acq_name, (ii-1) * refon);
         info = edf_info(filename);
         abspos(ii, :) = [info.motor.samtx, info.motor.samty, info.motor.samtz];
         relpos(ii, :) = abspos(ii, :) - offset;
+
         for jj = 1 : refon
             im_num = (ii - 1) * refon + jj - 1;
             omega = omstep * im_num;
             rottens = gtMathsRotationTensor(omega, rotcomp);
-            shifts_lab(im_num + 1, :) = relpos(ii, :) * rottens * eye(3);
+            shifts_lab(im_num + 1, :) = relpos(ii, :) * rottens;
             shifts_sam(im_num + 1, :) = relpos(ii, :);
         end
     end
+
     % handle 360 degree image after scan
-    filename = sprintf('%s/0_rawdata/Orig/%s%04d.edf', parameters.acq.dir, parameters.acq.name, tot_proj);
+    filename = sprintf('%s/%s%04d.edf', base_dir, acq_name, tot_proj);
     info = edf_info(filename);
     abspos(ref_grps + 1, :) = [info.motor.samtx, info.motor.samty, info.motor.samtz];
     relpos(ref_grps + 1, :) = abspos(ref_grps + 1, :) - offset;

zUtil_Geo/gtGeoProjForReconstruction.m

@@ -72,8 +72,8 @@ function proj_geom = gtGeoProjForReconstruction(projvec_sam, omega, vol_center,.
         ones_omega = ones(length(omega), 1);
     end
 
-    if (~exist('vol_center_shift', 'var'))
-        vol_center_shift = zeros(numel(ones_omega), 3);
+    if (~exist('vol_center_shift', 'var') || isempty(vol_center_shift))
+        vol_center_shift_rec = zeros(numel(ones_omega), 3);
     else
         vol_center_shift_rec = gtGeoSam2Sam(vol_center_shift, samgeo, recgeo, false, false);
     end