add fallback solution to gtThresholdGrain3D

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@654 4c865b51-4357-4376-afb4-474e03ccb993

5_reconstruction/gtRecDefaultParameters.m

@@ -2,6 +2,7 @@ function rec = gtRecDefaultParameters()
 
 rec.method         = '2DFBP'; % can be '3DART' or '2DFBP'
 rec.list           = [];
+rec.percentile1    = 25; 
 rec.percentile2    = 20;
 rec.do_morph_recon = true;
 rec.absinterval    = 10;

5_reconstruction/gtSetupForwardSimulation.m

@@ -36,7 +36,7 @@ ngrains = length(grain);
 %create / reset sample.mat spot2grain.mat
 filename = fullfile(parameters.acq.dir, '4_grains', 'sample.mat');
 if exist(filename, 'file') && (nof_phases > 1)
-    sample = GtSample.loadFromFile(filetable, filename);     % do not create from scratch - we want to keep information related to other phases
+    sample = GtSample.loadFromFile(filename);     % do not create from scratch - we want to keep information related to other phases
 else
     sample = GtSample(nof_phases);
     sample.fileTable = sprintf('%s_filetable',parameters.acq.name);

5_reconstruction/gtThresholdGrain3D.m

@@ -32,11 +32,22 @@ background = mean2(vol(centerx, centery, centerz)) / 10;
 % Small performance boost
 indexes = vol > background;
 % define threshold as percentile/100 x standard dev below the mean, excluding low (10 percentile background) values
-threshold_val = mean( vol(indexes) ) ...
-                - (rec.percentile2/100) * std( vol(indexes) );
+stdvol  = std( vol(indexes) );
+meanvol = mean( vol(indexes) );
+
+if stdvol > meanvol
+    threshold_val = rec.percentile1/100 * meanvol;
+else    
+    threshold_val = meanvol - rec.percentile2/100 * stdvol;
+end
 
 segvol = vol > threshold_val;
 
+% while any(size(segvol) == size(vol))
+%     threshold_val = threshold_val + 0.1    
+%     segvol = vol > threshold_val;
+% end
+
 % morphological reconstruction removes not connected areas
 if (rec.do_morph_recon)
     try
@@ -56,7 +67,7 @@ if isempty(regprop)
     segbb       = [];
     grain.seg   = [];
     grain.Area  = [];
-    grain.segbb = [];
+    grain.segbb = [];    
 else
     segbb = regprop.BoundingBox([2 1 3 5 4 6]);
     

zUtil_Parameters/build_list_v2.m

@@ -756,7 +756,7 @@ list.rec{2,1} = 'list';                                list.rec{2,2} = 'list of
 list.rec{3,1} = 'percentile2';                         list.rec{3,2} = 'Adaptive threshold: percentile/100 * std below grain average value';
                                                        list.rec{3,3} = 'double'; % scalar
                                                        list.rec{3,4} = 2;
-list.rec{4,1} = 'do_morph_recon';                         list.rec{4,2} = 'Perform morphological reconstruction during segmentation';
+list.rec{4,1} = 'do_morph_recon';                      list.rec{4,2} = 'Perform morphological reconstruction during segmentation';
                                                        list.rec{4,3} = 'logical';
                                                        list.rec{4,4} = 2;
 list.rec{5,1} = 'absinterval';                         list.rec{5,2} = 'Interval between radiographs used for reconstruction of absorption scan';
@@ -768,7 +768,11 @@ list.rec{6,1} = 'abs_num_iter';                        list.rec{6,2} = 'Number o
 list.rec{7,1} = 'num_iter';                            list.rec{7,2} = 'Number of iterations used in SIRT reconstruction of grain volumes';
                                                        list.rec{7,3} = 'double'; % scalar
                                                        list.rec{7,4} = 2;
-% list.rec{8,1}  = 'select_projections_auto';               list.rec{8,2} = 'select projecions automatically';
+list.rec{8,1} = 'percentile1';                         list.rec{8,2} = 'Alternative adaptive threshold: percentile/100 * mean below grain average value';
+                                                       list.rec{8,3} = 'double'; % scalar
+                                                       list.rec{8,4} = 2;
+                                                       
+%list.rec{8,1}  = 'select_projections_auto';             list.rec{8,2} = 'select projecions automatically';
 %                                                        list.rec{8,3} = 'logical';
 %                                                        list.rec{8,4} = 2;
 % list.rec{9,1}  = 'use_extspots';                          list.rec{9,2} = 'Use extension spots';