fixed small bugs

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

4_grains/GtThreshold.m

@@ -422,30 +422,26 @@ classdef GtThreshold < handle
 
             if (isfield(obj.param.rec, 'thresholding'))
                 thr_params = obj.param.rec.thresholding;
+
+                def_rec = gtRecDefaultParameters();
+                def_thr = def_rec.thresholding;
+                local_thr(1, :) = fieldnames(thr_params);
+                local_thr(2, :) = struct2cell(thr_params);
+                [thr_params, ~] = parse_pv_pairs(def_thr, local_thr(:));
             else
                 warning('GtThreshold:old_params', ...
                     'Old "rec" parameters. You should produce a new version.')
-                thr_params = struct( ...
-                    'percentile', obj.param.rec.percentile2, ...
-                    'do_morph_recon', obj.param.rec.do_morph_recon, ...
-                    'num_iter', 0, 'iter_factor', 1);
+
+                def_rec = gtRecDefaultParameters();
+                thr_params = def_rec.thresholding;
+                thr_params = parse_pv_pairs(thr_params, ...
+                    {'percentile', obj.param.rec.percentile2, ...
+                    'do_morph_recon', obj.param.rec.do_morph_recon});
             end
 
             if (~isfield(thr_params, 'do_extended'))
                 thr_params.do_extended = false;
             end
-
-            if (~isfield(thr_params, 'percent_of_peak'))
-                thr_params.percent_of_peak = 2.5;
-            end
-
-            if (~isfield(thr_params, 'mask_border_voxels'))
-                thr_params.mask_border_voxels = 5;
-            end
-
-            if (~isfield(thr_params, 'use_levelsets'))
-                thr_params.use_levelsets = false;
-            end
         end
 
         function grain_seg = thresholdAutoSingleGrain(obj, grain_rec)

5_reconstruction/GtAssembleVol3D.m

@@ -72,6 +72,14 @@ classdef GtAssembleVol3D < handle
                 end
             end
 
+            % Coping with older parameters
+            def_rec = gtRecDefaultParameters();
+            def_thr = def_rec.thresholding;
+            local_thr(1, :) = fieldnames(obj.parameters.rec.thresholding);
+            local_thr(2, :) = struct2cell(obj.parameters.rec.thresholding);
+            [def_thr, ~] = parse_pv_pairs(def_thr, local_thr(:));
+            obj.parameters.rec.thresholding = def_thr;
+
             % Array of all the partial phase volumes
             obj.volumes.phases = {};
             % Complete volume: merge of all phases has two fields which really

5_reconstruction/gtRecGrainsDefaultParameters.m

@@ -16,7 +16,7 @@ function par_rec = gtRecGrainsDefaultParameters(algo)
                 'detector_norm', 'l2', ... % Possibilities are: {'l2'} | 'kl' | 'l1'
                 'verbose', false ...
                 );
-        case {'6DL1', '6DTV', '6DTVL1'}
+        case {'6DLS', '6DL1', '6DTV', '6DTVL1'}
             par_rec_opts = struct( ...
                 'ospace_resolution', 0.25, ...
                 'ospace_lims', [], ...

6_rendering/gtRenderGrains.m

@@ -339,7 +339,7 @@ switch (par.patchmode)
             vol_bin = vol_bin | (grains == grainids(ii));
         end
         gauge.delete();
-        
+
         disp('Creating isosurface...')
         vol_smooth = smooth3(vol_bin, 'box', 3);
         isoSurf    = isosurface(vol_smooth, 0.5);
@@ -347,7 +347,7 @@ switch (par.patchmode)
         verts      = get(h.patch, 'vertices');
 
         % Dilation needed before interpolation.
-        grainsRegion = grains .* int16(vol_bin);
+        grainsRegion = int16(grains) .* int16(vol_bin);
         
         % Image Processing Toolbox license test before callling imdilate.
         % This is to avoid crashing when no license is available.