Random fixes from segmentation and assembling

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

4_grains/GtThreshold.m

@@ -223,7 +223,7 @@ classdef GtThreshold < handle
                         tmp_seg = obj.thresholdAutoSingleGrainSimpleSearch(cl_sub_recs(ii_g), 0.02);
 
                         tmp_seg.seg = gtPlaceSubVolume( ...
-                            zeros(cl_seg.segbb(4:6), 'like', cl_seg(1).seg), ...
+                            zeros(cl_seg(1).segbb(4:6), 'like', cl_seg(1).seg), ...
                             tmp_seg.seg, ...
                             tmp_seg.segbb(1:3) - cl_seg(1).segbb(1:3) );
                         tmp_seg.segbb = cl_seg(1).segbb;
@@ -365,6 +365,10 @@ classdef GtThreshold < handle
             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
         end
 
         function grain_seg = thresholdAutoSingleGrain(obj, grain_rec)
@@ -467,7 +471,7 @@ classdef GtThreshold < handle
             centery = round(seed(2) - size(vol, 2) * peak_region_fact) : round(seed(2) + size(vol, 2) * peak_region_fact);
             centerz = round(seed(3) - size(vol, 3) * peak_region_fact) : round(seed(3) + size(vol, 3) * peak_region_fact);
 
-            threshold_val = gtImgMeanValue(vol(centerx, centery, centerz)) / 2.5
+            threshold_val = gtImgMeanValue(vol(centerx, centery, centerz)) / par_thr.percent_of_peak
 
             grain_seg = obj.segmentAndDoMorph(grain_rec, threshold_val, ...
                 par_thr.do_morph_recon, seed);

5_reconstruction/GtAssembleVol3D.m

@@ -544,7 +544,7 @@ classdef GtAssembleVol3D < handle
             % Sample translation
             sample_shift = obj.localPar.sample_shift;
             sample_shift_size = size(sample_shift);
-            if sample_shift_size(2)<3
+            if (isempty(sample_shift) || (sample_shift_size(2) < 3))
                 sample_shift = [0, 0, 0];
             end
 

5_reconstruction/GtGuiThresholdVolume.m

@@ -18,19 +18,21 @@ classdef GtGuiThresholdVolume < GtGuiThresholdGrain
                 filter, 'Select file...', ...
                 fullfile('5_reconstruction', 'volume_mask.mat'));
 
-            thr = GtThreshold();
-            if (exist('morpho_seed', 'var'))
-                seg_struct = thr.volumeThreshold(obj.conf.vol, threshold, morpho_seed);
-            else
-                seg_struct = thr.volumeThreshold(obj.conf.vol, threshold);
-            end
-            seg_struct.vol = zeros(size(obj.conf.vol), 'like', seg_struct.seg);
-            seg_struct.vol = gtPlaceSubVolume(seg_struct.vol, seg_struct.seg, seg_struct.segbb(1:3));
+            if (~isempty(filename) && filename)
+                thr = GtThreshold();
+                if (exist('morpho_seed', 'var'))
+                    seg_struct = thr.volumeThreshold(obj.conf.vol, threshold, morpho_seed);
+                else
+                    seg_struct = thr.volumeThreshold(obj.conf.vol, threshold);
+                end
+                seg_struct.vol = zeros(size(obj.conf.vol), 'like', seg_struct.seg);
+                seg_struct.vol = gtPlaceSubVolume(seg_struct.vol, seg_struct.seg, seg_struct.segbb(1:3));
 
-            if (filerIndex == 1)
-                save(fullfile(pathname, filename), '-struct', 'seg_struct', '-v7.3');
-            else
-                edf_write(seg_struct.vol, fullfile(pathname, filename));
+                if (filerIndex == 1)
+                    save(fullfile(pathname, filename), '-struct', 'seg_struct', '-v7.3');
+                else
+                    edf_write(seg_struct.vol, fullfile(pathname, filename));
+                end
             end
         end
     end

5_reconstruction/gtRecDefaultParameters.m

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