Changes spatial drift correction

registers reference volume to reconstructed volume by default, with optional flag to swap target and source for registration
jfpva · Nov 23, 2017 · 80498e9 · 80498e9
1 parent 87a7e1c
commit 80498e9
Show file tree

Hide file tree

Showing 2 changed files with 34 additions and 14 deletions.
diff --git a/packages/segmentation/applications/reconstructionCardiac.cc b/packages/segmentation/applications/reconstructionCardiac.cc
@@ -65,6 +65,7 @@ void usage()
   cerr << "\t-no_robust_statistics      Switch off robust statistics."<<endl;
   cerr << "\t-exclude_slices_only       Do not exclude individual voxels."<<endl;
   cerr << "\t-ref_vol                   Reference volume for adjustment of spatial position of reconstructed volume."<<endl;
+  cerr << "\t-rreg_recon_to_ref         Register reconstructed volume to reference volume [Default: recon to ref]"<<endl;
   cerr << "\t-ref_transformations [folder]  Reference slice-to-volume transformation folder."<<endl;
   cerr << "\t-log_prefix [prefix]       Prefix for the log file."<<endl;
   cerr << "\t-info [filename]           Filename for slice information in tab-sparated columns."<<endl;
@@ -108,6 +109,7 @@ int main(int argc, char **argv)
   char * ref_vol_name = NULL;
   bool have_ref_vol = false;
   irtkRigidTransformation transformation_recon_to_ref; 
+  bool rreg_recon_to_ref = false;
   /// Slice stacks
   vector<irtkRealImage> stacks;
   vector<string> stack_files;
@@ -760,6 +762,14 @@ int main(int argc, char **argv)
       ok = true;
     }
 
+    //Register reconstructed volume to reference volume
+    if ((ok == false) && (strcmp(argv[1], "-rreg_recon_to_ref") == 0)){
+      argc--;
+      argv++;
+      rreg_recon_to_ref = true;
+      ok = true;
+    }
+
     //Read transformations from this folder
     if ((ok == false) && (strcmp(argv[1], "-ref_transformations") == 0)){
       argc--;
@@ -1325,12 +1335,28 @@ int main(int argc, char **argv)
     // Calculate Displacements
     if(have_ref_vol){
 
-      // Estimate Transformation to Align Reconsctructed Volume with Reference Volume
+      // Change logging 
       if ( ! no_log ) {
         cerr.rdbuf(file_e.rdbuf());
         cout.rdbuf (file.rdbuf());
       }
-      reconstruction.VolumeToVolumeRegistration(ref_vol,reconstructed,transformation_recon_to_ref);
+
+      // Get Current Reconstructed Volume
+      reconstructed=reconstruction.GetReconstructedCardiac4D();
+      reconstructed=reconstruction.StaticMaskVolume4D(reconstructed,-1);
+
+      // Invert to get recon to ref transformation
+      if(rreg_recon_to_ref) {
+        reconstruction.VolumeToVolumeRegistration(ref_vol,reconstructed,transformation_recon_to_ref);
+      }
+      else {
+        reconstruction.VolumeToVolumeRegistration(reconstructed,ref_vol,transformation_recon_to_ref);
+        irtkMatrix m = transformation_recon_to_ref.GetMatrix();
+        m.Invert();  // Invert to get recon to ref transformation
+        transformation_recon_to_ref.PutMatrix(m);
+      }
+
+      // Change logging 
       if ( ! no_log ) {
         cout.rdbuf (strm_buffer);
         cerr.rdbuf (strm_buffer_e);

diff --git a/packages/segmentation/src/irtkReconstructionCardiac4D.cc b/packages/segmentation/src/irtkReconstructionCardiac4D.cc
@@ -1982,20 +1982,14 @@ void irtkReconstructionCardiac4D::VolumeToVolumeRegistration(irtkGreyImage targe
 
   // Initialise registration
   irtkImageRigidRegistrationWithPadding registration;
-
-  // Get target min and max values
-  irtkGreyPixel smin, smax;
-  target.GetMinMax(&smin, &smax);
 
   // Register source volume to target volume
-  if (smax > -1) {
-      registration.SetInput(&target,&source);
-      registration.SetOutput(&rigidTransf);
-      registration.GuessParameter();
-      registration.SetTargetPadding(-1);
-      registration.Run();
-  }
-
+  registration.SetInput(&target,&source);
+  registration.SetOutput(&rigidTransf);
+  registration.GuessParameter();
+  registration.SetTargetPadding(-1);
+  registration.Run();
+
 }