- filter base (with trial to improve compilation time by explicit template in cxx)

diff --git a/common/clitkImageToImageGenericFilterBase.cxx b/common/clitkImageToImageGenericFilterBase.cxx
new file mode 100644 (file)
index 0000000..fb61bbf
--- /dev/null
+++ b/common/clitkImageToImageGenericFilterBase.cxx
@@ -0,0 +1,297 @@
+/*=========================================================================
+
+  Program:   vv
+  Module:    $RCSfile: clitkImageToImageGenericFilterBase.cxx,v $
+  Language:  C++
+  Date:      $Date: 2010/03/02 13:02:52 $
+  Version:   $Revision: 1.1 $
+  Author :   Joel Schaerer <joel.schaerer@creatis.insa-lyon.fr>
+  David Sarrut <david.sarrut@creatis.insa-lyon.fr>
+
+  Copyright (C) 2008
+  Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+  CREATIS-LRMN http://www.creatis.insa-lyon.fr
+
+  This program is free software: you can redistribute it and/or modify
+  it under the terms of the GNU General Public License as published by
+  the Free Software Foundation, version 3 of the License.
+
+  This program is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  GNU General Public License for more details.
+
+  You should have received a copy of the GNU General Public License
+  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+  =========================================================================*/
+
+#include "clitkImageToImageGenericFilterBase.h"
+#include <itkImage.h>
+
+//--------------------------------------------------------------------
+clitk::ImageToImageGenericFilterBase::~ImageToImageGenericFilterBase() {}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+clitk::ImageToImageGenericFilterBase::ImageToImageGenericFilterBase(std::string n)
+  :mIOVerbose(false) {
+  mFilterName = n;
+  mFailOnImageTypeError = true;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::ImageToImageGenericFilterBase::SetInputFilenames(const std::vector<std::string> & filenames) {
+    mInputFilenames=filenames;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::ImageToImageGenericFilterBase::SetInputFilename(const std::string & filename) {
+  std::vector<std::string> f;
+  f.push_back(filename);
+  SetInputFilenames(f);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::ImageToImageGenericFilterBase::AddInputFilename(const std::string & filename) {
+  mInputFilenames.push_back(filename);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::ImageToImageGenericFilterBase::SetOutputFilename(const std::string & filename) {
+  mOutputFilenames.clear();
+  mOutputFilenames.push_back(filename);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::ImageToImageGenericFilterBase::AddOutputFilename(const std::string & filename)
+{
+  mOutputFilenames.push_back(filename);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::ImageToImageGenericFilterBase::SetOutputFilenames(const std::vector<std::string> & filenames)
+{
+    mOutputFilenames.clear();
+    std::copy(filenames.begin(),filenames.end(),mOutputFilenames.begin());
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+std::string clitk::ImageToImageGenericFilterBase::GetOutputFilename()
+{
+    assert(mOutputFilenames.size() == 1);
+    return mOutputFilenames.front();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::ImageToImageGenericFilterBase::GetInputImageDimensionAndPixelType(unsigned int& dim, \
+        std::string& pixeltype,unsigned int& components)
+{
+  if (mInputFilenames.size())
+    {
+      int comp_temp,dim_temp; //clitkCommonImage takes ints
+      ReadImageDimensionAndPixelType(mInputFilenames[0], dim_temp, pixeltype,comp_temp);
+      components=comp_temp; dim=dim_temp;
+    }
+  else if (mInputVVImages.size())
+    {
+      pixeltype=mInputVVImages[0]->GetScalarTypeAsString();
+      dim=mInputVVImages[0]->GetNumberOfDimensions();
+      components=mInputVVImages[0]->GetNumberOfScalarComponents();
+    }
+  else
+    assert(false); //No input image, shouldn't happen
+  
+  if (mIOVerbose) {
+    std::cout << "Input is " << mDim << "D " << mPixelTypeName << "." << std::endl;
+  }
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+vvImage::Pointer clitk::ImageToImageGenericFilterBase::GetOutputVVImage ()
+{
+    assert(mOutputVVImages.size());
+    return mOutputVVImages[0];
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+std::vector<vvImage::Pointer> clitk::ImageToImageGenericFilterBase::GetOutputVVImages()
+{
+    return mOutputVVImages;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::ImageToImageGenericFilterBase::SetInputVVImage (vvImage::Pointer input)
+{
+    mInputVVImages.clear();
+    mInputVVImages.push_back(input);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::ImageToImageGenericFilterBase::AddInputVVImage (vvImage::Pointer input)
+{
+    mInputVVImages.push_back(input);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::ImageToImageGenericFilterBase::SetInputVVImages (std::vector<vvImage::Pointer> input)
+{
+    mInputVVImages=input;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::ImageToImageGenericFilterBase::PrintAvailableImageTypes() {
+  std::cout << GetAvailableImageTypes();
+}
+//--------------------------------------------------------------------
+
+
+
+//--------------------------------------------------------------------
+void clitk::ImageToImageGenericFilterBase::ImageTypeError() {
+  std::cerr << "**Error** The filter <" << mFilterName << "> is not available for " 
+            << mDim << "D images with pixel=" 
+            << mPixelTypeName << " and "
+            << mNbOfComponents << " component." << std::endl;
+  std::cerr << GetAvailableImageTypes();
+  exit(0);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::ImageToImageGenericFilterBase::SetImageTypeError() {
+  std::cerr << "TODO ! " << std::endl;
+  exit(0);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+const std::string & clitk::ImageToImageGenericFilterBase::GetFilterName() { 
+  return mFilterName; 
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::ImageToImageGenericFilterBase::SetFilterName(std::string & n) { 
+  mFilterName = n; 
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::ImageToImageGenericFilterBase::SetIOVerbose(bool b) { 
+  mIOVerbose = b; 
+}
+//--------------------------------------------------------------------
+
+#define DEF_SetNextOutput_And_GetInput(PixelType, Dim) \
+  template \
+void clitk::ImageToImageGenericFilterBase::SetNextOutput<itk::Image<PixelType, Dim> >(itk::Image<PixelType,Dim>::Pointer output); \
+  template \
+   itk::Image<PixelType, Dim>::Pointer clitk::ImageToImageGenericFilterBase::GetInput<itk::Image<PixelType, Dim> >(unsigned int n);
+
+#define DEF_SetNextOutput_And_GetInput_WithCompo(Compo, Dim)   \
+  template \
+  void clitk::ImageToImageGenericFilterBase::SetNextOutput<itk::Image<itk::Vector<float, Compo>, Dim> >(itk::Image<itk::Vector<float, Compo>,Dim>::Pointer output); \
+  template \
+  itk::Image<itk::Vector<float,Compo>, Dim>::Pointer clitk::ImageToImageGenericFilterBase::GetInput<itk::Image<itk::Vector<float, Compo>, Dim> >(unsigned int n);
+
+DEF_SetNextOutput_And_GetInput(char, 2);
+DEF_SetNextOutput_And_GetInput(unsigned char, 2);
+DEF_SetNextOutput_And_GetInput(short, 2);
+DEF_SetNextOutput_And_GetInput(unsigned short, 2);
+DEF_SetNextOutput_And_GetInput(int, 2);
+DEF_SetNextOutput_And_GetInput(float, 2);
+DEF_SetNextOutput_And_GetInput(double, 2);
+
+DEF_SetNextOutput_And_GetInput(char, 3);
+DEF_SetNextOutput_And_GetInput(unsigned char, 3);
+DEF_SetNextOutput_And_GetInput(short, 3);
+DEF_SetNextOutput_And_GetInput(unsigned short, 3);
+DEF_SetNextOutput_And_GetInput(int, 3);
+DEF_SetNextOutput_And_GetInput(float, 3);
+DEF_SetNextOutput_And_GetInput(double, 3);
+
+DEF_SetNextOutput_And_GetInput_WithCompo(2, 2);
+DEF_SetNextOutput_And_GetInput_WithCompo(2, 3);
+DEF_SetNextOutput_And_GetInput_WithCompo(2, 4);
+DEF_SetNextOutput_And_GetInput_WithCompo(3, 2);
+DEF_SetNextOutput_And_GetInput_WithCompo(3, 3);
+DEF_SetNextOutput_And_GetInput_WithCompo(3, 4);
+DEF_SetNextOutput_And_GetInput_WithCompo(4, 2);
+DEF_SetNextOutput_And_GetInput_WithCompo(4, 3);
+DEF_SetNextOutput_And_GetInput_WithCompo(4, 4);
+
+DEF_SetNextOutput_And_GetInput(char, 4);
+DEF_SetNextOutput_And_GetInput(unsigned char, 4);
+DEF_SetNextOutput_And_GetInput(short, 4);
+DEF_SetNextOutput_And_GetInput(unsigned short, 4);
+DEF_SetNextOutput_And_GetInput(int, 4);
+DEF_SetNextOutput_And_GetInput(float, 4);
+DEF_SetNextOutput_And_GetInput(double, 4);
+
+
+//--------------------------------------------------------------------
+template<class ImageType> 
+void clitk::ImageToImageGenericFilterBase::SetNextOutput(typename ImageType::Pointer output) {
+  if (mOutputFilenames.size())
+    {
+      clitk::writeImage<ImageType>(output, mOutputFilenames.front(), mIOVerbose);
+      mOutputFilenames.pop_front();
+    }
+  if (mInputVVImages.size()) //We assume that if a vv image is set as input, we want one as the output
+    mOutputVVImages.push_back(vvImageFromITK<ImageType::ImageDimension,typename ImageType::PixelType>(output));
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ImageType> 
+typename ImageType::Pointer clitk::ImageToImageGenericFilterBase::GetInput(unsigned int n) {
+  if (mInputFilenames.size() > n) {
+    return clitk::readImage<ImageType>(mInputFilenames[n], mIOVerbose);
+  }
+  else if (mInputVVImages.size() > n)
+    return typename ImageType::Pointer(const_cast<ImageType*>(vvImageToITK<ImageType>(mInputVVImages[n]).GetPointer()));
+  else
+    {
+      assert(false); //No input, this shouldn't happen
+      return typename ImageType::Pointer(NULL);
+    }
+}
+//--------------------------------------------------------------------
+
+
+

diff --git a/common/clitkImageToImageGenericFilterBase.h b/common/clitkImageToImageGenericFilterBase.h
new file mode 100644 (file)
index 0000000..007f40b
--- /dev/null
+++ b/common/clitkImageToImageGenericFilterBase.h
@@ -0,0 +1,132 @@
+/*=========================================================================
+
+  Program:   clitk
+  Module:    $RCSfile: clitkImageToImageGenericFilterBase.h,v $
+  Language:  C++
+  Date:      $Date: 2010/03/02 13:02:52 $
+  Version:   $Revision: 1.1 $
+  Author :   Joel Schaerer <joel.schaerer@creatis.insa-lyon.fr>
+             David Sarrut <david.sarrut@creatis.insa-lyon.fr>
+
+  Copyright (C) 2008
+  Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+  CREATIS-LRMN http://www.creatis.insa-lyon.fr
+
+  This program is free software: you can redistribute it and/or modify
+  it under the terms of the GNU General Public License as published by
+  the Free Software Foundation, version 3 of the License.
+
+  This program is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  GNU General Public License for more details.
+
+  You should have received a copy of the GNU General Public License
+  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+  =========================================================================*/
+
+#ifndef CLITKIMAGETOIMAGEGENERICFILTERBASE_H
+#define CLITKIMAGETOIMAGEGENERICFILTERBASE_H
+
+// clitk include
+#include "clitkCommon.h"
+#include "clitkImageCommon.h"
+#include "clitkCommonGenericFilter.h"
+
+// itk include
+#include <itkImage.h>
+
+// vv include
+#include "vvImage.h"
+#include "vvFromITK.h"
+#include "vvToITK.h"
+
+namespace clitk {
+  
+  //--------------------------------------------------------------------
+  class ImageToImageGenericFilterBase: public itk::Object {
+    
+  public: 
+    // constructor - destructor
+    ImageToImageGenericFilterBase(std::string filterName);
+    virtual ~ImageToImageGenericFilterBase();
+
+    // Types
+    typedef ImageToImageGenericFilterBase Self;
+    typedef Object                        Superclass;
+    typedef itk::SmartPointer<Self>       Pointer;
+    typedef itk::SmartPointer<const Self> ConstPointer;
+
+    // Filters information
+    const std::string & GetFilterName();
+    void SetFilterName(std::string & n);
+
+    // Generic IO
+    /// Returns the dimension and pixel type of the *first* input
+    void GetInputImageDimensionAndPixelType(unsigned int& dim, std::string& pixeltype,
+                                            unsigned int & components);
+
+    // File IO
+    void SetInputFilename(const std::string & filename);
+    void AddInputFilename(const std::string & filename);
+    void SetInputFilenames(const std::vector<std::string> & filenames);
+    void SetOutputFilename(const std::string & filename);
+    void AddOutputFilename(const std::string & filename);
+    void SetOutputFilenames(const std::vector<std::string> & filenames);
+    std::string GetOutputFilename();
+    void SetIOVerbose(bool b);
+
+    // VVImage IO
+    void SetInputVVImage (vvImage::Pointer input);
+    void SetInputVVImages (std::vector<vvImage::Pointer> input);
+    void AddInputVVImage (vvImage::Pointer input);
+    vvImage::Pointer GetOutputVVImage ();
+    std::vector<vvImage::Pointer> GetOutputVVImages ();
+
+    // Information on available image types
+    void PrintAvailableImageTypes();
+    virtual std::string GetAvailableImageTypes() = 0;
+
+    virtual bool CheckImageType(unsigned int dim,unsigned int ncomp, std::string pixeltype) = 0;
+    virtual bool CheckImageType() = 0;
+
+    // Main function to call for using the filter. 
+    virtual bool Update() = 0;
+
+  protected:  
+    /// Call this function to dispatch an output towards the correct sink
+    template<class ImageType> 
+    void SetNextOutput(typename ImageType::Pointer output);
+
+    /// Call this function to get the nth itk input image, regardless of input source
+    template<class ImageType> 
+    typename ImageType::Pointer GetInput(unsigned int n);
+
+    std::vector<std::string> mInputFilenames;
+    std::list<std::string> mOutputFilenames;
+
+    bool mIOVerbose;
+    unsigned int mDim;
+    std::string mPixelTypeName;
+    unsigned int mNbOfComponents;
+    std::string mFilterName;
+
+    std::vector<vvImage::Pointer> mInputVVImages;
+    std::vector<vvImage::Pointer> mOutputVVImages;
+
+    void ImageTypeError();
+    void SetImageTypeError();
+    bool mFailOnImageTypeError;
+
+  }; // end class clitk::ImageToImageGenericFilter
+
+#define ADD_VEC_IMAGE_TYPE(DIM, COMP, PT) this->mImageTypesManager.template AddNewDimensionAndPixelType<DIM,COMP, PT>();
+#define ADD_IMAGE_TYPE(DIM, PT) this->mImageTypesManager.template AddNewDimensionAndPixelType<DIM, PT>();
+
+#include "clitkImageToImageGenericFilterBase.txx"
+
+} // end namespace
+
+#endif /* end #define CLITKIMAGETOIMAGEGENERICFILTERBASE_H */
+

diff --git a/common/clitkImageToImageGenericFilterBase.txx b/common/clitkImageToImageGenericFilterBase.txx
new file mode 100644 (file)
index 0000000..d37635e
--- /dev/null
+++ b/common/clitkImageToImageGenericFilterBase.txx
@@ -0,0 +1,59 @@
+/*=========================================================================
+
+  Program:   vv
+  Module:    $RCSfile: clitkImageToImageGenericFilterBase.txx,v $
+  Language:  C++
+  Date:      $Date: 2010/03/02 13:02:52 $
+  Version:   $Revision: 1.1 $
+  Author :   Joel Schaerer <joel.schaerer@creatis.insa-lyon.fr>
+  David Sarrut <david.sarrut@creatis.insa-lyon.fr>
+
+  Copyright (C) 2008
+  Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+  CREATIS-LRMN http://www.creatis.insa-lyon.fr
+
+  This program is free software: you can redistribute it and/or modify
+  it under the terms of the GNU General Public License as published by
+  the Free Software Foundation, version 3 of the License.
+
+  This program is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  GNU General Public License for more details.
+
+  You should have received a copy of the GNU General Public License
+  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+  =========================================================================*/
+
+// //--------------------------------------------------------------------
+// template<class ImageType> 
+// void clitk::ImageToImageGenericFilterBase::SetNextOutput(typename ImageType::Pointer output) {
+//   if (mOutputFilenames.size())
+//     {
+//       clitk::writeImage<ImageType>(output, mOutputFilenames.front(), mIOVerbose);
+//       mOutputFilenames.pop_front();
+//     }
+//   if (mInputVVImages.size()) //We assume that if a vv image is set as input, we want one as the output
+//     mOutputVVImages.push_back(vvImageFromITK<ImageType::ImageDimension,typename ImageType::PixelType>(output));
+// }
+// //--------------------------------------------------------------------
+
+
+// //--------------------------------------------------------------------
+// template<class ImageType> 
+// typename ImageType::Pointer clitk::ImageToImageGenericFilterBase::GetInput(unsigned int n) {
+//   if (mInputFilenames.size() > n) {
+//     return clitk::readImage<ImageType>(mInputFilenames[n], mIOVerbose);
+//   }
+//   else if (mInputVVImages.size() > n)
+//     return typename ImageType::Pointer(const_cast<ImageType*>(vvImageToITK<ImageType>(mInputVVImages[n]).GetPointer()));
+//   else
+//     {
+//       assert(false); //No input, this shouldn't happen
+//       return typename ImageType::Pointer(NULL);
+//     }
+// }
+// //--------------------------------------------------------------------
+
+