NiftyResample.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 <nifti1_io.h>
#include <string>
#include <vector>
#include <iostream>
#include "sirf/Reg/Resample.h"
#include "sirf/iUtilities/iutilities.h"
 
namespace NiftyMoMo {
class BSplineTransformation;
}
 
namespace sirf {
 
namespace detail {
template<class dataType>
class ComplexNiftiImageData
{
public:
    ComplexNiftiImageData() {}
    virtual ~ComplexNiftiImageData() {}
    bool is_complex() const { return _imag_sptr != nullptr; }
    const std::shared_ptr<const NiftiImageData<dataType> > real() const { return _real_sptr; }
    std::shared_ptr<NiftiImageData<dataType> > &real() { return _real_sptr; }
    const std::shared_ptr<const NiftiImageData<dataType> > imag() const { return _imag_sptr; }
    std::shared_ptr<NiftiImageData<dataType> > &imag() { return _imag_sptr; }
    size_t size() const { return is_complex() ? 2 : 1; }
    const std::shared_ptr<const NiftiImageData<dataType> > at(const unsigned idx) const { check_bounds(idx); return idx == 0 ? real() : imag(); }
    std::shared_ptr<NiftiImageData<dataType> > at(const unsigned idx) { check_bounds(idx); return idx == 0 ? real() : imag(); }
 
private:
    void check_bounds(const unsigned idx) const
    {
        if (idx > 1)
            throw std::runtime_error("ComplexNiftiImageData::at(): Exceeds index range");
        if (idx == 1 && !is_complex())
            throw std::runtime_error("ComplexNiftiImageData::at(): Trying to access imaginary part of non-complex image");
    }
    std::shared_ptr<NiftiImageData<dataType> > _real_sptr;
    std::shared_ptr<NiftiImageData<dataType> > _imag_sptr;
};
}
 
template<class dataType>
class NiftyResampler : public Resampler<dataType>
{
public:
 
    NiftyResampler() {}
 
    virtual ~NiftyResampler() {}
 
    virtual void process();
 
    virtual std::shared_ptr<ImageData> forward(const std::shared_ptr<const ImageData> input_sptr);
 
    virtual void forward(std::shared_ptr<ImageData> output_sptr, const std::shared_ptr<const ImageData> input_sptr);
 
    virtual std::shared_ptr<ImageData> adjoint(const std::shared_ptr<const ImageData> input_sptr);
 
    virtual void adjoint(std::shared_ptr<ImageData> output_sptr, const std::shared_ptr<const ImageData> input_sptr);
 
    std::shared_ptr<const ImageData> reference_image_sptr() const
    {
        return this->_reference_image_sptr;
    }
 
    virtual float norm(int num_iter, int verb) const;
 
protected:
 
    virtual void set_up();
 
    virtual void set_up_forward();
 
    virtual void set_up_adjoint();
 
    void set_up_input_images();
 
    detail::ComplexNiftiImageData<dataType> _reference_image_niftis;
    detail::ComplexNiftiImageData<dataType> _floating_image_niftis;
    detail::ComplexNiftiImageData<dataType> _output_image_forward_niftis;
    detail::ComplexNiftiImageData<dataType> _output_image_adjoint_niftis;
 
    std::shared_ptr<NiftiImageData3DDeformation<dataType> > _deformation_sptr;
    std::shared_ptr<NiftyMoMo::BSplineTransformation> _adjoint_transformer_sptr;
    std::shared_ptr<NiftiImageData<dataType> > _adjoint_input_weights_sptr;
    std::shared_ptr<NiftiImageData<dataType> > _adjoint_output_weights_sptr;
};
}