more consistent handling of minimum spot size

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

3_pairmatchingGUI/gtMatchGetSampleShifts.m

@@ -4,10 +4,33 @@ function [shifts_lab, shifts_sam, abspos, relpos] = gtMatchGetSampleShifts(param
     conf = struct('display', false, 'offset_pos', 0, 'det_index', 1);
     conf = parse_pv_pairs(conf, varargin);
 
+    tot_proj = gtAcqTotNumberOfImages(parameters, conf.det_index);
+    omstep   = gtAcqGetOmegaStep(parameters, conf.det_index);
+    refon    = parameters.acq.refon;
+    ref_grps = tot_proj / refon;
+
+    acq_dir = parameters.acq.dir;
+    acq_name = parameters.acq.name;
+    base_dir = fullfile(acq_dir, '0_rawdata', 'Orig');
+
     if (~exist('parameters', 'var') || isempty(parameters))
         parameters = gtLoadParameters();
     end
-
+    if isfield(parameters.acq,'shifts_sam')
+        if (exist('omega_values', 'var') && ~isempty(omega_values))
+            % set NaN entries in omega to 0;
+            nans = isnan(omega_values);
+            omega_values(nans) = 0;
+            % transform into image_numbers
+            im_num = round(omega_values / omstep) + 1;
+            shifts_lab = parameters.acq.shifts_lab(im_num, :);
+            shifts_sam = parameters.acq.shifts_sam(im_num, :);
+        else
+            shifts_lab = parameters.acq.shifts_lab;
+            shifts_sam = parameters.acq.shifts_sam;
+        end
+        return
+    end
     tot_proj = gtAcqTotNumberOfImages(parameters, conf.det_index);
     omstep   = gtAcqGetOmegaStep(parameters, conf.det_index);
     refon    = parameters.acq.refon;

zUtil_ForwardSim/gtFwdSimFindCandidates.m

@@ -13,7 +13,11 @@ function [candidateIDs, cands_info] = gtFwdSimFindCandidates(spot_props, gr, spo
     if (~exist('det_index', 'var') || isempty(det_ind))
         det_ind = 1;
     end
-
+    if isfield(parameters.fsim, 'allowed_dist')
+        allowed_dist = parameters.fsim.allowed_dist;
+    else
+        allowed_dist = 5;
+    end
     spots_info = segmentedSpots(det_ind);
 
     uvw = gr.allblobs(det_ind).detector.uvw(spot_index, :);
@@ -23,8 +27,8 @@ function [candidateIDs, cands_info] = gtFwdSimFindCandidates(spot_props, gr, spo
     dist_v_pix = abs(spots_info.BoundingBoxYorigin + spots_info.BoundingBoxYsize / 2 - uvw(2));
     dist_w_im = abs(spots_info.CentroidImage - uvw(3));
 
-    dist_u_ok = dist_u_pix < (spots_info.BoundingBoxXsize - spot_props.XsizeAvg / 2) / 2;
-    dist_v_ok = dist_v_pix < (spots_info.BoundingBoxYsize - spot_props.YsizeAvg / 2) / 2;
+    dist_u_ok = dist_u_pix < max(allowed_dist, (spots_info.BoundingBoxXsize + spot_props.XsizeMin / 2) / 2);
+    dist_v_ok = dist_v_pix < max(allowed_dist, (spots_info.BoundingBoxYsize + spot_props.YsizeMin / 2) / 2);
 
     dist_w_ok = dist_w_im <=  spot_props.max_w_offset_im;
 

zUtil_ForwardSim/gtFwdSimGetDiffspotsCommonProperties.m

@@ -31,16 +31,17 @@ function spotsProps = gtFwdSimGetDiffspotsCommonProperties(grain, parameters, de
     spotsProps.Ysize = grain.stat.bbysmean; % average Y Size of difspots
 
     % define theshold values which will be used during the database search later
-    % - limit to 5 pixels minimum width
-    spotsProps.XsizeMin = max(5, spotsProps.Xsize - fsim.bbsize_factor * grain.stat.bbxsstd);
+    segMinX = parameters.seg.minblobsize(1);
+    segMinY = parameters.seg.minblobsize(2);
+    spotsProps.XsizeMin = max(segMinX, spotsProps.Xsize - fsim.bbsize_factor * grain.stat.bbxsstd);
     spotsProps.XsizeMax = spotsProps.Xsize + fsim.bbsize_factor * grain.stat.bbxsstd;
-    spotsProps.YsizeMin = max(5, spotsProps.Ysize - fsim.bbsize_factor * grain.stat.bbysstd);
+    spotsProps.YsizeMin = max(segMinY, spotsProps.Ysize - fsim.bbsize_factor * grain.stat.bbysstd);
     spotsProps.YsizeMax = spotsProps.Ysize + fsim.bbsize_factor * grain.stat.bbysstd;
 
     % allow for a lateral deviation of spot postions based on grain orientation statics
     % dif_props.Offset = fsim.Rdist_factor * gr.stat.Rdiststd * norm(detrefpos_pix)
     % !!! detrefpos is not necessarily the distance; depends on definition by user
-    spotsProps.Offset = fsim.Rdist_factor * deg2rad(grain.stat.dangstd) * norm(detrefpos_pix);
+    spotsProps.Offset = fsim.Rdist_factor * deg2rad(grain.stat.dangstd) * norm(detrefpos_pix)
 
     grainBBox = [max(grain.bbxs), max(grain.bbys)];
     % take the biggest spot and add a relative extra margin (multiplicative factor oversize)