Romulo:

- Added functionality to generate the BSpline coefficients during the
registration.
- Added new command-line option --CoeffEveryN (requires --coeff and --verbose)
  - see ggo file
- Created new observer class (as specified by ITK) to catch iteration events
triggered by the optmizer

diff --git a/registration/clitkBLUTDIR.ggo b/registration/clitkBLUTDIR.ggo
index 8be34e7b7a9352e406af4040310c2bc29f1d8422..55ac19f54e1075a0d82401f08746c62ab01bd5a6 100755 (executable)
--- a/registration/clitkBLUTDIR.ggo
+++ b/registration/clitkBLUTDIR.ggo
@@ -25,6 +25,7 @@ section "Output"
 
 option "vf"                    -       "Result DVF"                            string          yes
 option "coeff"                 -       "Result coefficient images"             string          no      
+option "coeffEveryN"           -       "Result coefficient images at every N iterations (requires --coeff and --verbose)"              int             no              default="20"
 option "output"                        o       "Deformed target image"                 string          yes
 option "before"                        -       "Difference image before (but after rigid transform)"           string          no
 option "after"                 -       "Difference image after "               string          no

diff --git a/registration/clitkBLUTDIRCommandIterationUpdateDVF.h b/registration/clitkBLUTDIRCommandIterationUpdateDVF.h
new file mode 100644 (file)
index 0000000..7a113e5
--- /dev/null
+++ b/registration/clitkBLUTDIRCommandIterationUpdateDVF.h
@@ -0,0 +1,119 @@
+/*=========================================================================
+Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
+
+Authors belong to:
+- University of LYON              http://www.universite-lyon.fr/
+- Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
+- CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
+
+This software is distributed WITHOUT ANY WARRANTY; without even
+the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+PURPOSE.  See the copyright notices for more information.
+
+It is distributed under dual licence
+
+- BSD        See included LICENSE.txt file
+- CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+======================================================================-====*/
+#ifndef clitkBLUTDIRCommandIterationUpdateDVF_h
+#define clitkBLUTDIRCommandIterationUpdateDVF_h
+
+/* =================================================
+ * @file   clitkBLUTDIRCommandIterationUpdateDVF.h
+ * @author     Romulo Pinho
+ * @date       16/02/2011
+ *
+ * @brief      ITK observer class to respond to iteration events of B-LUT DIR. This
+ * observer is meant to output the DVF of the registration at each iteration.
+ *
+ ===================================================*/
+
+#include "clitkBLUTDIRGenericFilter.h"
+
+namespace clitk
+{
+  template <class FixedImageType, class OptimizerType, class TransformType>
+  class CommandIterationUpdateDVF : public itk::Command
+  {
+    public:
+      typedef  CommandIterationUpdateDVF   Self;
+      typedef  itk::Command             Superclass;
+      typedef  itk::SmartPointer<Self>  Pointer;
+      itkNewMacro( Self );
+    protected:
+      CommandIterationUpdateDVF() : m_Iteration(0) {};
+    public:
+
+      typedef typename FixedImageType::Pointer ImagePointer;
+      typedef typename TransformType::Pointer TransformPointer;
+
+      // Set the fixed image, from the specs of the DVF are obtained.
+      void SetFixedImage(ImagePointer i) { m_FixedImage = i; }
+
+      // Set the transform
+      void SetTransform(TransformPointer t){ m_Transform = t;}
+
+      // Set command line parameters
+      void SetArgsInfo(args_info_clitkBLUTDIR a){m_ArgsInfo=a;}
+
+      // Execute
+      void Execute(itk::Object *object, const itk::EventObject & event)
+      {
+        //Execute( (const itk::Object *)caller, event);
+       if( !(itk::IterationEvent().CheckEvent( &event )) )
+        {
+          std::cout << "CommandIterationUpdateDVF::Execute(): check event failed!\n";
+          return;
+        }
+
+        std::cout << "CommandIterationUpdateDVF::Execute()\n";
+
+        typedef typename OptimizerType::ParametersType ParametersType;
+        OptimizerType* optmizer = dynamic_cast<OptimizerType*>(object); 
+        ParametersType parameters = optmizer->GetCurrentPosition();
+        std::cout << "Iteration " << ++m_Iteration << endl;// << " -> Optimizer parameters: " << parameters << endl;
+
+        //=======================================================
+        // RP: Copy-paste from BLUTDIRGenericFilter::UpdateWithInputImageType()
+        //=======================================================
+        //=======================================================
+        // Get the BSpline coefficient images and write them
+        //=======================================================
+       int niter = m_ArgsInfo.coeffEveryN_arg;
+        if ((m_Iteration % niter == 0) && m_ArgsInfo.coeff_given)
+        {
+          typedef typename TransformType::CoefficientImageType CoefficientImageType;
+          std::vector<typename CoefficientImageType::Pointer> coefficientImages = m_Transform->GetCoefficientImages();
+          typedef itk::ImageFileWriter<CoefficientImageType> CoeffWriterType;
+          typename CoeffWriterType::Pointer coeffWriter = CoeffWriterType::New();
+          unsigned nLabels = m_Transform->GetnLabels();
+
+          std::string fname(m_ArgsInfo.coeff_arg);
+          int dotpos = fname.length() - 1;
+          while (dotpos >= 0 && fname[dotpos] != '.')
+            dotpos--;
+
+          for (unsigned i = 0; i < nLabels; ++i)
+          {
+            std::ostringstream osfname;
+            osfname << fname.substr(0, dotpos) << '_' << i << '_' << m_Iteration << fname.substr(dotpos);
+            coeffWriter->SetInput(coefficientImages[i]);
+            coeffWriter->SetFileName(osfname.str());
+            coeffWriter->Update();
+          }
+        }
+      }
+
+      void Execute(const itk::Object * object, const itk::EventObject & event)
+      {
+        std::cout << "const CommandIterationUpdateDVF::Execute()\n";
+      }
+
+      unsigned int m_Iteration;
+      ImagePointer m_FixedImage;
+      TransformPointer m_Transform;
+      args_info_clitkBLUTDIR m_ArgsInfo;
+  };
+}
+
+#endif // clitkBLUTDIRCommandIterationUpdateDVF_h

diff --git a/registration/clitkBLUTDIRGenericFilter.cxx b/registration/clitkBLUTDIRGenericFilter.cxx
index c8c42f0f422f039bd30814bac37bcad99a44cd86..dbb38e3f9db84fece8ef41e40563877fa5ea5c3b 100755 (executable)
--- a/registration/clitkBLUTDIRGenericFilter.cxx
+++ b/registration/clitkBLUTDIRGenericFilter.cxx
@@ -28,6 +28,7 @@ It is distributed under dual licence
  ===================================================*/
 
 #include "clitkBLUTDIRGenericFilter.h"
+#include "clitkBLUTDIRCommandIterationUpdateDVF.h"
 
 namespace clitk
 {
@@ -78,7 +79,7 @@ namespace clitk
   {
     InitializeImageType<2>();
     InitializeImageType<3>();
-    m_Verbose=true;
+    m_Verbose=false;
   }
 
   //=========================================================================//
@@ -93,6 +94,8 @@ namespace clitk
     }
 
     if (m_ArgsInfo.output_given) SetOutputFilename(m_ArgsInfo.output_arg);
+    
+    if (m_ArgsInfo.verbose_given) m_Verbose=true;
   }
 
   //=========================================================================//
@@ -273,6 +276,8 @@ namespace clitk
   template<class InputImageType>
     void BLUTDIRGenericFilter::UpdateWithInputImageType()
     {
+      if (m_Verbose) std::cout << "BLUTDIRGenericFilter::UpdateWithInputImageType()" << std::endl;
+      
       //=============================================================================
       //Input
       //=============================================================================
@@ -667,6 +672,17 @@ namespace clitk
         command->SetMaximize(genericMetric->GetMaximize());
         command->SetMetricRegion(metricRegion);
         registration->AddObserver( itk::IterationEvent(), command );
+
+        if (m_ArgsInfo.coeff_given)
+        {
+          std::cout << std::endl << "Output coefficient images every " << m_ArgsInfo.coeffEveryN_arg << " iterations." << std::endl;
+          typedef CommandIterationUpdateDVF<FixedImageType, OptimizerType, TransformType> DVFCommandType;
+          typename DVFCommandType::Pointer observerdvf = DVFCommandType::New();
+          observerdvf->SetFixedImage(fixedImage);
+          observerdvf->SetTransform(transform);
+          observerdvf->SetArgsInfo(m_ArgsInfo);
+          optimizer->AddObserver( itk::IterationEvent(), observerdvf );
+        }
       }