SPMRegistration.h

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/*
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"
#include <MatlabEngine.hpp>

namespace sirf {

template<class dataType> class AffineTransformation;

template<class dataType> class SPMRegistration : public NiftiBasedRegistration<dataType>
{
public:

    virtual ~SPMRegistration();

    void process();

    void set_working_folder(const std::string &working_folder);

    void set_working_folder_file_overwrite(const bool working_folder_overwrite) { _working_folder_overwrite = working_folder_overwrite; }

    void set_delete_temp_files(const bool delete_temp_files) { _delete_temp_files = delete_temp_files; }

    virtual const std::shared_ptr<const ImageData> get_output_sptr(const unsigned idx = 0) const;

    virtual const std::shared_ptr<const AffineTransformation<float> > get_transformation_matrix_forward_sptr(const unsigned idx = 0) const { return _TMs_fwd.at(idx); }

    virtual const std::shared_ptr<const AffineTransformation<float> > get_transformation_matrix_inverse_sptr(const unsigned idx = 0) const { return _TMs_inv.at(idx); }

    virtual const std::shared_ptr<const Transformation<dataType> > get_deformation_field_forward_sptr(const unsigned idx = 0) const;

    virtual const std::shared_ptr<const Transformation<dataType> > get_deformation_field_inverse_sptr(const unsigned idx = 0) const;

protected:

    virtual void parse_parameter_file() {}

    virtual void check_parameters() const;

    virtual void set_parameters() {}

    std::string _working_folder = "";
    bool _working_folder_overwrite = false;
    bool _delete_temp_files = false;

    std::vector<std::shared_ptr<AffineTransformation<float> > > _TMs_fwd;
    std::vector<std::shared_ptr<AffineTransformation<float> > > _TMs_inv;
    std::unique_ptr<matlab::engine::MATLABEngine> _matlab_uptr;

    std::vector<std::string> _filenames_to_delete;
    std::vector<std::string> _folders_to_delete;
    std::vector<std::string> _resliced_filenames;

};
}