Adds output to SimulateStacksCardiac

- saves transformations
- calculates displacements
- saves info

packages/segmentation/applications/reconstructionCardiac.cc

@@ -175,7 +175,7 @@ int main(int argc, char **argv)
 
   irtkRealImage average;
 
-  string info_filename = "slice_info.tsv";
+  string info_filename = "info.tsv";
   string log_id;
   bool no_log = false;
 
@@ -1308,7 +1308,7 @@ int main(int argc, char **argv)
     if(debug)
     {
       cout<<"SlicesInfoCardiac4D"<<endl;
-      sprintf(buffer,"slice_info_mc%02i.tsv",iter);
+      sprintf(buffer,"info_mc%02i.tsv",iter);
       reconstruction.SlicesInfoCardiac4D( buffer, stack_files );
     }
 

packages/segmentation/applications/simulateStacksCardiac.cc

@@ -445,6 +445,9 @@ int main(int argc, char **argv)
   reconstruction.SetReconstructedCardiacPhase( reconstructedCardPhase );
   reconstruction.SetReconstructedTemporalResolution( rrInterval/numCardPhase );
 
+  //initialise stack factors
+  reconstruction.InitStackFactor(stacks);
+
   //type of recon - default 3D PSF
   if(recon_1d) {
     cout<<"Set1DRecon()" << endl;
@@ -580,6 +583,24 @@ int main(int argc, char **argv)
     }  
   }  
 
+  //Calculate displacements
+  double mean_displacement = reconstruction.CalculateDisplacement();
+  if (debug)
+    cout<<"\tmean displacement = "<<mean_displacement<<" mm."<<endl;
+  double mean__weighted_displacement = reconstruction.CalculateWeightedDisplacement();
+    if (debug)
+      cout<<"\tmean weighted displacement = "<<mean__weighted_displacement<<" mm."<<endl;
+
+  //Save info
+  if (debug)
+    cout<<"Saving Info"<<endl;
+  reconstruction.SlicesInfoCardiac4D( "info.tsv", stack_files );
+
+  //Save transformations
+  if(debug)
+      cout<<"SaveTransformations"<<endl;
+  reconstruction.SaveTransformations();
+
   //Save cine volume
   if(debug)
       cout<<"Saving cine volume."<<endl;

packages/segmentation/include/irtkReconstructionCardiac4D.h

@@ -169,6 +169,9 @@ class irtkReconstructionCardiac4D : public irtkReconstruction
                                double averageValue,
                                bool together=false);
 
+   //Set stack factors
+   void InitStackFactor(vector<irtkRealImage>& stacks);
+
    // Create slices from the stacks and 
    // slice-dependent transformations from stack transformations
    void CreateSlicesAndTransformationsCardiac4D( vector<irtkRealImage>& stacks,

packages/segmentation/src/irtkReconstructionCardiac4D.cc

@@ -354,6 +354,16 @@ void irtkReconstructionCardiac4D::MatchStackIntensitiesWithMasking(vector<irtkRe
 
 }
 
+// -----------------------------------------------------------------------------
+// Initialise Stack Factor
+// -----------------------------------------------------------------------------
+void irtkReconstructionCardiac4D::InitStackFactor(vector<irtkRealImage> &stacks)
+{
+  _stack_factor.clear();
+  for(unsigned int stackIndex=0; stackIndex<stacks.size(); stackIndex++)
+    _stack_factor.push_back(1);
+}
+
 
 // -----------------------------------------------------------------------------
 // Create Slices and Associated Transformations
@@ -409,6 +419,8 @@ void irtkReconstructionCardiac4D::CreateSlicesAndTransformationsCardiac4D( vecto
                     proba.PutPixelSize(attr._dx, attr._dy, thickness[i], attr._dt);
                     _probability_maps.push_back(proba);
                 }
+                //initialise cardiac phase to use for 2D-3D registration
+                _slice_svr_card_index.push_back(0);
             }
             loc_index++;
         }
@@ -1631,6 +1643,11 @@ void irtkReconstructionCardiac4D::SimulateStacksCardiac4D(vector<bool> stack_exc
     //Initialise simlated images
     for (unsigned int inputIndex = 0; inputIndex < _slices.size(); ++inputIndex)    _simulated_slices[inputIndex] = 0;
 
+    //Initialise indicator of images having overlap with volume
+    _slice_inside.clear();
+    for (unsigned int inputIndex = 0; inputIndex < _slices.size(); ++inputIndex)  
+      _slice_inside.push_back(true);
+
     //Simulate images
     cout << "Simulating...";
     cout.flush();