minor fixes

Signed-off-by: Wolfgang Ludwig <wolfgang.ludwig@esrf.fr>

1_preprocessing/gtPreprocessing.m

@@ -200,8 +200,9 @@ else
     if strcmpi(check,'y')
         parameters.acq.rotu = gtFindRotationAxis(parameters.acq, bbdir);
         parameters.acq.rotx = parameters.acq.rotu;
-        parameters.detgeo.detrefpos(2) = -(parameters.acq.rotu - parameters.acq.xdet / 2 - 0.5) * parameters.detgeo.pixelsizeu;
-        parameters.detgeo.detrefpos(3) =  0;  % Here we define the LabZ = 0 position as the center of the detector
+        %Calculate detrefpos later using gtGeoDetRefPos
+        %parameters.detgeo.detrefpos(2) = -(parameters.acq.rotu - parameters.acq.xdet / 2 - 0.5) * parameters.detgeo.pixelsizeu;
+        %parameters.detgeo.detrefpos(3) =  0;
     end
     save(parameters_name,'parameters');
 
@@ -215,7 +216,7 @@ else
     if strcmpi(check,'y')
         parameters.acq.bb  = gtFindSampleEdges(parameters.acq,parameters.prep,bbdir);
         parameters.prep.bbox = parameters.acq.bb+[-parameters.prep.margin 0 2*parameters.prep.margin 0];
-        
+
         % define the sample envelope - assume centred on direct beam
         labgeo_tmp = gtGeoSamEnvFromAcq(parameters.labgeo, parameters.acq);
         parameters.labgeo.samenvtop = labgeo_tmp.samenvtop;
@@ -225,6 +226,10 @@ else
     save(parameters_name,'parameters');
 end % end no_direct_beam case
 
+% Update Detector reference position
+parameters.detgeo = gtGeoDetDefaultParameters(parameters.acq);
+save(parameters_name,'parameters');
+
 if isempty(parameters.acq.maxradius)
     check='y';
 else

5_reconstruction/gtReconstructGrains.m

-function gtReconstructGrains(first, last, workingdirectory, phaseID, parameters, varargin)
+function varargout = gtReconstructGrains(first, last, workingdirectory, phaseID, parameters, varargin)
 % GTRECONSTRUCTGRAINS  Launch a series of 3D ART (ASTRA) reconstruction on a GPU machine
 %     gtReconstructGrains(first, last, workingdirectory, phaseID, [parameters], [varargin])
 %     --------------------------------------------------------------------------------------------------
@@ -14,6 +14,7 @@ function gtReconstructGrains(first, last, workingdirectory, phaseID, parameters,
 %       parameters       = <struct>  {parameters.mat}
 %       varargin         =           parameters.rec
 %           example: 'list', [1, 3, 4:10]
+%           'display', true
 %     Version 001 
 
     if (~gtCheckGpu())
@@ -45,7 +46,7 @@ function gtReconstructGrains(first, last, workingdirectory, phaseID, parameters,
         rec_gr = parameters.rec;
         rec_gr.algorithm = 'SIRT';
     end
-
+    rec_gr.display = false;
     if (~isempty(varargin))
         rec_gr = parse_pv_pairs(rec_gr, varargin);
         parameters.rec.grains = rec_gr;
@@ -91,9 +92,9 @@ function gtReconstructGrains(first, last, workingdirectory, phaseID, parameters,
 
         switch(upper(rec_gr.algorithm))
             case {'SIRT', '3DTV'}
-                gtAstraReconstructGrain(gr_id, phaseID, parameters);
+                rec_vol = gtAstraReconstructGrain(gr_id, phaseID, parameters);
             case {'6DL1', '6DLS', '6DTV', '6DTVL1'}
-                gtReconstructGrainOrientation(gr_id, phaseID, parameters);
+                rec_vol = gtReconstructGrainOrientation(gr_id, phaseID, parameters);
         end
         if (~isdeployed)
             try
@@ -102,9 +103,14 @@ function gtReconstructGrains(first, last, workingdirectory, phaseID, parameters,
             catch
                 sprintf('Segmentation of grain %d failed - check reconstruction!', gr_id)
             end
+            if rec_gr.display
+                GtVolView(rec_vol.intensity)
+            end
         end
     end
     fprintf('Done (in %f seconds).\n', toc(c))
-
+    if nargout > 0
+        varargout{1} = rec_vol;
+    end
     cd(currentDir);
 end