NiftyRegistration.h

Go to the documentation of this file.

/*
SyneRBI Synergistic Image Reconstruction Framework (SIRF)
Copyright 2017 - 2020 University College London
 
This is software developed for the Collaborative Computational
Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR)
(http://www.ccpsynerbi.ac.uk/).
 
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
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.
 
*/
 
#pragma once
 
#include "sirf/Reg/NiftiBasedRegistration.h"
 
namespace sirf {
 
template<class dataType> class NiftiImageData3D;
 
template<class dataType>
class NiftyRegistration : public NiftiBasedRegistration<dataType>
{
public:
 
    NiftyRegistration();
 
    virtual ~NiftyRegistration() {}
 
    void set_parameter_file(const std::string &parameter_filename) { _parameter_filename = parameter_filename; }
 
    void set_parameter(const std::string &par, const std::string &arg1 = "", const std::string &arg2 = "");
 
    void set_reference_mask(const std::shared_ptr<const ImageData> reference_mask_sptr) { _reference_mask_sptr = reference_mask_sptr; }
 
    void set_floating_mask(const std::shared_ptr<const ImageData> floating_mask_sptr)   {  _floating_mask_sptr = floating_mask_sptr;  }
 
protected:
 
    virtual void parse_parameter_file() = 0;
 
    void set_up_inputs();
 
    virtual void set_parameters() = 0;
 
    std::vector<std::string> _extra_params;
 
    std::string _parameter_filename;
 
    std::shared_ptr<const ImageData> _floating_mask_sptr;
    std::shared_ptr<const ImageData> _reference_mask_sptr;
 
    std::shared_ptr<const NiftiImageData3D<dataType> > _floating_mask_nifti_sptr;
    std::shared_ptr<const NiftiImageData3D<dataType> > _reference_mask_nifti_sptr;
};
}