fixed small format and function call issues

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

2_difspot/gtSegmentationBlob2SpotTable.m

@@ -121,15 +121,15 @@ sfDoInsert(spot, difspot_table)
 % Write edf file on disk
 if (writeedfs)
     
-    if ismember(seg.difspotmask, {'none', 'blob2D', 'blob2Dsoft'})
+    if (ismember(seg.difspotmask, {'none', 'blob2D', 'blob2Dsoft'}))
         % create summed image
         im = sum(blob.rawgreyvol, 3);
     end
     
     % Check minimum area condition
-    if ~isempty(thr_area)
+    if (~isempty(thr_area))
         mask2D = blob2D > 0 ;
-        if sum(mask2D(:)) < thr_area
+        if (sum(mask2D(:)) < thr_area)
             % we don't write this spot,so  quit
             return
         end
@@ -164,7 +164,7 @@ if (writeedfs)
             lower_thresh = min(im(im > 0));
             
             % Apply soft threshold
-            im = gtSoftThreshold(im, lower_thresh);
+            im = gtSoftThreshold2(im, lower_thresh);
             
         case {'blob3D', 'blob3Dsoft'}
             % The segmented blob volume is simply summed through the omega
@@ -183,7 +183,7 @@ end % end if writeedfs
 
 end % end of function
 
-%%
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%% Sub-functions
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

5_reconstruction/GtAssembleVol3D.m

@@ -550,8 +550,7 @@ classdef GtAssembleVol3D < handle
 
             % Sample translation
             sample_shift = obj.localPar.sample_shift;
-            sample_shift_size = size(sample_shift);
-            if (isempty(sample_shift) || (sample_shift_size(2) < 3))
+            if (isempty(sample_shift) || (size(sample_shift, 2) < 3))
                 sample_shift = [0, 0, 0];
             end
 
@@ -608,7 +607,7 @@ classdef GtAssembleVol3D < handle
                             crop_bb = seg_bb;
                             crop_bb(1:3) = crop_bb(1:3) - cl_rec.ODF6D.shift + 1;
                             int_vol = gtCrop(int_vol, crop_bb) .* logical(seg_vol);
-                            int_vol = int_vol * numel(find(seg_vol)) / sum(int_vol(:));
+%                             int_vol = int_vol * numel(find(seg_vol)) / sum(int_vol(:));
 
                             p_gids = gtPlaceSubVolume( p_gids, seg_vol, ...
                                 seg_bb(1:3) + sample_shift, ...