Grain segmentation: added logic that uses the reconstruction std-dev to reduce artifacts

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

4_grains/GtThreshold.m

@@ -292,6 +292,25 @@ classdef GtThreshold < handle
             if (is_6D)
                 grain_out.vol = grain_rec.ODF6D.intensity;
                 grain_out.shift = grain_rec.ODF6D.shift;
+
+                par_thr = obj.getThrParams();
+                if (par_thr.weight_by_stddev ...
+                        && isfield(grain_rec.ODF6D, 'voxels_stddev_R_vectors'))
+                    % Let's use the std-dev info about the reconstruction to
+                    % make the segmentation better
+                    valid_inds =  grain_out.vol > 0;
+
+                    stddev_vol = smooth3(grain_rec.ODF6D.voxels_stddev_R_vectors);
+                    stddev_valid = stddev_vol(valid_inds);
+
+                    vol_valid =  grain_out.vol(valid_inds);
+
+                    stddev_rescale = max(stddev_valid(:)) - stddev_valid;
+                    stddev_rescale = (stddev_rescale - min(stddev_rescale(:))) ...
+                        ./ (max(stddev_rescale(:)) - min(stddev_rescale(:)));
+
+                     grain_out.vol(valid_inds) = vol_valid .* stddev_rescale;
+                end
             else
                 grain_out.vol = grain_rec.VOL3D.intensity;
                 grain_out.shift = grain_rec.VOL3D.shift;
@@ -369,6 +388,10 @@ classdef GtThreshold < handle
             if (~isfield(thr_params, 'percent_of_peak'))
                 thr_params.percent_of_peak = 2.5;
             end
+
+            if (~isfield(thr_params, 'weight_by_stddev'))
+                thr_params.weight_by_stddev = true;
+            end
         end
 
         function grain_seg = thresholdAutoSingleGrain(obj, grain_rec)

5_reconstruction/gtRecDefaultParameters.m

@@ -21,5 +21,6 @@ function par_rec = gtRecDefaultParameters(varargin)
     % Grain segmentation related values
     par_rec.thresholding = struct( ...
         'percentile', 20, 'do_morph_recon', true, ...
-        'percent_of_peak', 2.5, 'num_iter', 0, 'iter_factor', 1);
+        'percent_of_peak', 2.5, 'num_iter', 0, 'iter_factor', 1, ...
+        'weight_by_stddev', true);
 end