BiasCorrection.h

/*
 * Developing brain Region Annotation With Expectation-Maximization (Draw-EM)
 *
 * Copyright 2013-2016 Imperial College London
 * Copyright 2013-2016 Daniel Rueckert
 *
 * 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.
 */


#ifndef _MIRTKBIASCORRECTION_H

#define _MIRTKBIASCORRECTION_H

#include "mirtk/Image.h"

#include "mirtk/Resampling.h"

#include "mirtk/Transformation.h"

#include "mirtk/BiasField.h"

namespace mirtk {

class BiasCorrection : public Object
{
    mirtkObjectMacro(BiasCorrection);

protected:

    RealImage *_target;

    RealImage *_reference;

    RealImage *_weights;
    ByteImage *_mask;

    /// Output
    BiasField *_biasfield;

    /// Padding value
    GreyPixel _Padding;

    /// Initial set up for the registration
    virtual void Initialize();

    /// Final set up for the registration
    virtual void Finalize();

public:

    /// Constructor
    BiasCorrection();

    /// Destructor
    virtual ~BiasCorrection();

    /// Sets input for the bias correction filter
    virtual void SetInput (RealImage *, RealImage *);

    /// Sets weights for the bias correction filter
    virtual void SetWeights (RealImage *);

    /// Sets output for the bias correction filter
    virtual void SetOutput(BiasField *);

    virtual void SetMask( ByteImage *);

    /// Runs the bias correction filter
    virtual void Run();

    /// Apply bias correction to _input
    virtual void Apply(RealImage &);

    /// Apply bias correction to any image
    virtual void ApplyToImage(RealImage &);

    /// Apply bias correction to any image including logarithmic transform
    virtual void ApplyToImage(GreyImage &);

    // Access parameters
    virtual void SetPadding(short Padding);
    virtual short GetPadding();

};

inline void BiasCorrection::SetInput(RealImage *target, RealImage *reference)
{
    _target    = target;
    _reference = reference;
}

inline void BiasCorrection::SetWeights(RealImage *weights)
{
    _weights    = weights;
}

inline void BiasCorrection::SetOutput(BiasField *biasfield)
{
    _biasfield = biasfield;
}

inline void BiasCorrection::SetPadding(short Padding)
{
    _Padding = Padding;
}
inline short BiasCorrection::GetPadding(){
    return _Padding;
}

}
#endif