mrimage_utils.h

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/******************************************************************************
 * Copyright 2014 Micah C Chambers (micahc.vt@gmail.com)
 *
 * NPL is free software: you can redistribute it and/or modify it under the
 * terms of the BSD 2-Clause License available in LICENSE or at
 * http://opensource.org/licenses/BSD-2-Clause
 *
 * @file mrimage_utils.h
 * @brief This file contains common functions which are useful for image
 * processing. Note that ndarray_utils.h has utilities which are more general
 * whereas this file contains functions which are specifically for image
 * processing.
 ******************************************************************************/

#ifndef MRIMAGE_UTILS_H
#define MRIMAGE_UTILS_H

#include "ndarray.h"
#include "mrimage.h"
#include "basic_functions.h"
#include "npltypes.h"

#include <string>
#include <iostream>
#include <iomanip>
#include <cassert>
#include <memory>

namespace npl {

using std::vector;

std::ostream& operator<<(std::ostream &out, const MRImage& img);

/*****************************************************************************
 * Kernel Functions
 ****************************************************************************/

void gaussianSmooth1D(ptr<MRImage> inout, size_t dim, double stddev);


/******************************************************
 * Resample Image Functions
 ******************************************************/

ptr<MRImage> smoothDownsample(ptr<const MRImage> in,
            double sigma, double spacing = -1);

ptr<MRImage> resample(ptr<const MRImage> in, double* spacing,
        double(*window)(double, double) = hannWindow);

/******************************************************
 * FFT Tools
 *****************************************************/
ptr<MRImage> shiftImage(ptr<MRImage> in, size_t len, double* vect);

void writeComplex(std::string basename, ptr<const MRImage> in,
        bool absPhase = false);

ptr<MRImage> fft_forward(ptr<const MRImage> in,
        const std::vector<size_t>& in_osize);

ptr<MRImage> fft_backward(ptr<const MRImage> in,
        const std::vector<size_t>& in_osize);

int rotateImageShearKern(ptr<MRImage> inout, double rx, double ry, double rz,
        double(*kern)(double,double) = npl::lanczosKern);

int rotateImageShearFFT(ptr<MRImage> inout, double rx, double ry, double rz,
        double(*window)(double,double) = npl::sincWindow);

ptr<MRImage> rigidTransform(ptr<MRImage> in, double rx, double ry, double rz,
        double sx, double sy, double sz);

ptr<MRImage> diffOfGauss(ptr<const MRImage> in, double sd1, double sd2);

double overlapRatio(ptr<const MRImage> a, ptr<const MRImage> b);

ptr<MRImage> resampleNN(ptr<const MRImage> in, ptr<const MRImage> atlas,
        PixelT type = UNKNOWN_TYPE);


ptr<MRImage> resampleNN(ptr<const MRImage> in, double* newspace,
        PixelT type = UNKNOWN_TYPE);

ptr<MRImage> randImage(PixelT type, double mean, double sd,
        size_t x, size_t y, size_t z, size_t t);

} // npl
#endif  //MRIMAGE_UTILS_H