itkPSMCommandLineClass.h

/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/

#ifndef ____itkPSMCommandLineClass__h
#define ____itkPSMCommandLineClass__h

#include <iostream>
#include <string>
#include <sstream>
#include "itkImage.h"
#include "itkPSMProcrustesRegistration.h"
#include "itkImageFileReader.h"
#include "itkPSMEntropyModelFilter.h"
#include "itkPSMProject.h"
#include "itkPSMProjectReader.h"
#include "itkPSMParticleSystem.h"
#include "itkCommand.h"

namespace itk
{
template <unsigned int VDimension>
class ITK_EXPORT PSMCommandLineClass : public DataObject
{
  public:
    typedef PSMCommandLineClass  Self;
    typedef DataObject Superclass;
    typedef SmartPointer<Self>   Pointer;
    typedef SmartPointer<const Self>  ConstPointer;
  
    itkNewMacro(Self);
  
    itkTypeMacro(PSMCommandLineClass, DataObject);
  
    typedef typename itk::Image<float, VDimension> ImageType;

    typedef PSMEntropyModelFilter<typename PSMCommandLineClass::ImageType>
      EntropyModelFilterType;

    typedef PSMProcrustesRegistration<VDimension> ProcrustesRegistrationType;

    typedef PSMProjectReader ProjectReaderType;

    typedef PSMProject ProjectType;


    void ReadProjectFile(const char *fn);
    
    void ReadDistanceTransforms(std::string input_path_prefix);


    void ReadCuttingPlanes();
    
    void ReadModelPointFiles();
    
    void SetPSMFilterParameters();

    void WriteOutputs(std::string output_path);

    void Run(const char *fname, std::string input_path_prefix, std::string output_path);

    PSMCommandLineClass();
    virtual ~PSMCommandLineClass() {};
  
    itkGetObjectMacro(PSMFilter, EntropyModelFilterType);

    itkGetMacro(ReportInterval,unsigned int);
    itkSetMacro(ReportInterval,unsigned int);
    
  protected:
    void IterateCallback(itk::Object *, const itk::EventObject &);
  
  private:
    PSMCommandLineClass(const Self&); //purposely not implemented
    void operator=(const Self&);      //purposely not implemented

    std::string m_ProjectFileName;

    typename EntropyModelFilterType::Pointer m_PSMFilter;

    typename ProcrustesRegistrationType::Pointer m_ProcrustesRegistration;

    typename ProjectReaderType::Pointer m_ProjectReader;

    typename ProjectType::Pointer m_Project;

    int m_ProcrustesCounter;

    std::vector<unsigned int> m_ProcrustesInterval;

    typename itk::MemberCommand<PSMCommandLineClass>::Pointer m_IterateCmd;

    unsigned int m_ReportInterval;
};
} // end namespace

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkPSMCommandLineClass.hxx"
#endif

#endif