/usr/include/CiftiLib/Cifti/VolumeSpace.h is in libcifti-dev 1.5.1-1build1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 | #ifndef __VOLUME_SPACE_H__
#define __VOLUME_SPACE_H__
/*LICENSE_START*/
/*
* Copyright (c) 2014, Washington University School of Medicine
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification,
* are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
* THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
* FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
* EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include "Common/Vector3D.h"
#include "Common/XmlAdapter.h"
#include "stdint.h"
#include <vector>
namespace cifti
{
class VolumeSpace
{
int64_t m_dims[3];
std::vector<std::vector<float> > m_sform, m_inverse;
void computeInverse();
public:
enum OrientTypes
{
LEFT_TO_RIGHT = 0,
RIGHT_TO_LEFT = 4,
POSTERIOR_TO_ANTERIOR = 1,
ANTERIOR_TO_POSTERIOR = 5,
INFERIOR_TO_SUPERIOR = 2,
SUPERIOR_TO_INFERIOR = 6
};
VolumeSpace();
VolumeSpace(const int64_t dims[3], const std::vector<std::vector<float> >& sform);
VolumeSpace(const int64_t dims[3], const float sform[12]);
void setSpace(const int64_t dims[3], const std::vector<std::vector<float> >& sform);
void setSpace(const int64_t dims[3], const float sform[12]);
const int64_t* getDims() const { return m_dims; }
const std::vector<std::vector<float> >& getSform() const { return m_sform; }
void getSpacingVectors(Vector3D& iStep, Vector3D& jStep, Vector3D& kStep, Vector3D& origin) const;
bool matchesVolumeSpace(const VolumeSpace& right) const;//allows slight mismatches
bool operator==(const VolumeSpace& right) const;//requires that it be exact
bool operator!=(const VolumeSpace& right) const { return !(*this == right); }
///returns true if volume space is not skew, and each axis and index is separate
bool isPlumb() const;
///returns orientation, spacing, and center (spacing/center can be negative, spacing/center is LPI rearranged to ijk (first dimension uses first element), will assert false if isOblique is true)
void getOrientAndSpacingForPlumb(OrientTypes* orientOut, float* spacingOut, float* originOut) const;
///get just orientation, even for non-plumb volumes
void getOrientation(OrientTypes orientOut[3]) const;
///returns coordinate triplet of an index triplet
template <typename T>
inline void indexToSpace(const T* indexIn, float* coordOut) const
{ indexToSpace<T>(indexIn[0], indexIn[1], indexIn[2], coordOut[0], coordOut[1], coordOut[2]); }
///returns coordinate triplet of three indices
template <typename T>
inline void indexToSpace(const T& indexIn1, const T& indexIn2, const T& indexIn3, float* coordOut) const
{ indexToSpace<T>(indexIn1, indexIn2, indexIn3, coordOut[0], coordOut[1], coordOut[2]); }
///returns three coordinates of an index triplet
template <typename T>
inline void indexToSpace(const T* indexIn, float& coordOut1, float& coordOut2, float& coordOut3) const
{ indexToSpace<T>(indexIn[0], indexIn[1], indexIn[2], coordOut1, coordOut2, coordOut3); }
///returns three coordinates of three indices
template <typename T>
void indexToSpace(const T& indexIn1, const T& indexIn2, const T& indexIn3, float& coordOut1, float& coordOut2, float& coordOut3) const;
///returns floating point index triplet of a given coordinate triplet
inline void spaceToIndex(const float* coordIn, float* indexOut) const { spaceToIndex(coordIn[0], coordIn[1], coordIn[2], indexOut[0], indexOut[1], indexOut[2]); }
///returns floating point index triplet of three given coordinates
inline void spaceToIndex(const float& coordIn1, const float& coordIn2, const float& coordIn3, float* indexOut) const { spaceToIndex(coordIn1, coordIn2, coordIn3, indexOut[0], indexOut[1], indexOut[2]); }
///returns three floating point indexes of a given coordinate triplet
inline void spaceToIndex(const float* coordIn, float& indexOut1, float& indexOut2, float& indexOut3) const { spaceToIndex(coordIn[0], coordIn[1], coordIn[2], indexOut1, indexOut2, indexOut3); }
///returns three floating point indexes of three given coordinates
void spaceToIndex(const float& coordIn1, const float& coordIn2, const float& coordIn3, float& indexOut1, float& indexOut2, float& indexOut3) const;
///returns integer index triplet of voxel whose center is closest to the coordinate triplet
inline void enclosingVoxel(const float* coordIn, int64_t* indexOut) const { enclosingVoxel(coordIn[0], coordIn[1], coordIn[2], indexOut[0], indexOut[1], indexOut[2]); }
///returns integer index triplet of voxel whose center is closest to the three coordinates
inline void enclosingVoxel(const float& coordIn1, const float& coordIn2, const float& coordIn3, int64_t* indexOut) const { enclosingVoxel(coordIn1, coordIn2, coordIn3, indexOut[0], indexOut[1], indexOut[2]); }
///returns integer indexes of voxel whose center is closest to the coordinate triplet
inline void enclosingVoxel(const float* coordIn, int64_t& indexOut1, int64_t& indexOut2, int64_t& indexOut3) const { enclosingVoxel(coordIn[0], coordIn[1], coordIn[2], indexOut1, indexOut2, indexOut3); }
///returns integer indexes of voxel whose center is closest to the three coordinates
void enclosingVoxel(const float& coordIn1, const float& coordIn2, const float& coordIn3, int64_t& indexOut1, int64_t& indexOut2, int64_t& indexOut3) const;
template <typename T>
inline bool indexValid(const T* indexIn) const
{
return indexValid(indexIn[0], indexIn[1], indexIn[2]);//implicit cast to int64_t
}
///checks if an index is within array dimensions
inline bool indexValid(const int64_t& indexIn1, const int64_t& indexIn2, const int64_t& indexIn3) const
{
if (indexIn1 < 0 || indexIn1 >= m_dims[0]) return false;
if (indexIn2 < 0 || indexIn2 >= m_dims[1]) return false;
if (indexIn3 < 0 || indexIn3 >= m_dims[2]) return false;
return true;
}
inline int64_t getIndex(const int64_t& indexIn1, const int64_t& indexIn2, const int64_t& indexIn3) const
{
return indexIn1 + m_dims[0] * (indexIn2 + m_dims[1] * indexIn3);
}
template <typename T>
inline int64_t getIndex(const T* indexIn) const
{
return getIndex(indexIn[0], indexIn[1], indexIn[2]);//implicit cast to int64_t
}
void readCiftiXML1(XmlReader& xml);//xml functions
void readCiftiXML2(XmlReader& xml);
void writeCiftiXML1(XmlWriter& xml) const;
void writeCiftiXML2(XmlWriter& xml) const;
};
template <typename T>
void VolumeSpace::indexToSpace(const T& indexIn1, const T& indexIn2, const T& indexIn3, float& coordOut1, float& coordOut2, float& coordOut3) const
{
coordOut1 = indexIn1 * m_sform[0][0] + indexIn2 * m_sform[0][1] + indexIn3 * m_sform[0][2] + m_sform[0][3];
coordOut2 = indexIn1 * m_sform[1][0] + indexIn2 * m_sform[1][1] + indexIn3 * m_sform[1][2] + m_sform[1][3];
coordOut3 = indexIn1 * m_sform[2][0] + indexIn2 * m_sform[2][1] + indexIn3 * m_sform[2][2] + m_sform[2][3];
}
}
#endif //__VOLUME_SPACE_H__
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