MeanShift.h

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

#define _MIRTKMEANSHIFT_H
// queue::push/pop

#include "mirtk/GenericImage.h"
#include "mirtk/Image.h"
#include "mirtk/Dilation.h"
#include "mirtk/Erosion.h"
#include "mirtk/Point.h"
#include "mirtk/GaussianBlurring.h"
#include <algorithm>
#include <queue>

using namespace std;
namespace mirtk {

class MeanShift
{

    int _nBins;
    int _padding;
    GreyImage _image;
    queue<Point> _q;
    GreyImage _map, _orig_image;
    GreyImage *_brain;
    GreyImage *_output;
    GreyPixel _imin, _imax;
    double _limit1, _limit2, _limit, _treshold;
    double _bin_width;
    double * _density;
    int _clusterSize;
public:
    double _bg,_wm,_gm,_split1,_split2;


public:

    MeanShift(GreyImage& image, int padding = -1, int nBins = 256);
    ~MeanShift();
    void SetOutput( GreyImage *_output);
    double ValueToBin(double value);
    double BinToValue(int bin);
    void AddPoint(int x, int y, int z);
    void AddPoint(int x, int y, int z, int label);
    double msh(double y, double h);
    double findMax(double tr1, double tr2);
    double findMin(double tr1, double tr2);
    double findGMvar();
    double split(double pos1, double pos2, double bw, double h1, double h2);
    double GenerateDensity(double cut_off=0.02);
    void Grow(int x, int y, int z, int label);
    int Lcc(int label, bool add_second = false);
    int LccS(int label, double treshold = 0.5);
    void RemoveBackground();
    void RegionGrowing();
    void FindWMGMmeans();
    void Write(char *output_name);
    void WriteMap(char *output_name);
    void SetTreshold();
    void SetTreshold(double treshold);

    RealImage ReturnMask();
};

}

#endif