MRImageStore is a version of NDArray that has an orientation matrix. Right now it also has additional data that is unique to nifti. Eventually this class will be forked into a subclass, and this will only have the orientation. More...

#include <mrimage.h>

Inherits npl::NDArrayStore< D, T >, and npl::MRImage.

Public Member Functions
	MRImageStore (std::initializer_list< size_t > a_args)
	Constructor with initializer list. Orientation will be default (direction = identity, spacing = 1, origin = 0). More...

	MRImageStore (const std::vector< size_t > &a_args)
	Constructor with vector. Orientation will be default (direction = identity, spacing = 1, origin = 0). More...

	MRImageStore (size_t len, const size_t *size)
	Constructor with array of length len, Orientation will be default (direction = identity, spacing = 1, origin = 0). More...

	MRImageStore (size_t len, const size_t size, T ptr, const std::function< void(void *)> &deleter)
	Constructor which uses a preexsting array, to graft into the image. No new allocation will be performed, however ownership of the array will be taken, meaning it could be deleted anytime after this constructor completes. More...

	MRImageStore ()
	Default constructor, uses identity for direction matrix, 1 for spacing and 0 for origin. Image size is 0. More...

virtual int	indexToPoint (size_t len, const int64_t xyz, double ras) const
	Converts an index in pixel space to RAS, physical/time coordinates. If len < dimensions, additional dimensions are assumed to be 0. If len > dimensions then additional values are ignored, and only the first DIM values will be transformed and written to ras. More...

virtual int	indexToPoint (size_t len, const double xyz, double ras) const
	Converts an index in pixel space to RAS, physical/time coordinates. If len < dimensions, additional dimensions are assumed to be 0. If len > dimensions then additional values are ignored, and only the first DIM values will be transformed and written to ras. More...

virtual int	pointToIndex (size_t len, const double ras, double xyz) const
	Converts a point in RAS coordinate system to index. If len < dimensions, additional dimensions are assumed to be 0. If len > dimensions then additional values are ignored, and only the first DIM values will be transformed and written to ras. More...

virtual int	pointToIndex (size_t len, const double ras, int64_t index) const
	Converts a point in RAS coordinate system to index. If len < dimensions, additional dimensions are assumed to be 0. If len > dimensions then additional values are ignored, and only the first DIM values will be transformed and written to ras. More...

virtual int	orientVector (size_t len, const double xyz, double ras) const
	Convert a vector in index coordinates to a vector in ras coordinates. Vector is simply multiplied by the internal rotation matrix. More...

virtual int	disOrientVector (size_t len, const double ras, double xyz) const
	Convert a vector in index coordinates to a vector in ras coordinates. Vector is simply multiplied by the internal rotation matrix. More...

virtual bool	pointInsideFOV (size_t len, const double *ras) const
	Returns true if the point is within the field of view of the image. Note, like all coordinates pass to MRImage, if the array given differs from the dimensions of the image, then the result will either pad out zeros and ignore extra values in the input array. More...

virtual bool	indexInsideFOV (size_t len, const double *xyz) const
	Returns true if the constinuous index is within the field of view of the image. Note, like all coordinates pass to MRImage, if the array given differs from the dimensions of the image, then the result will either pad out zeros and ignore extra values in the input array. More...

virtual bool	indexInsideFOV (size_t len, const int64_t *xyz) const
	Returns true if the constinuous index is within the field of view of the image. Note, like all coordinates pass to MRImage, if the array given differs from the dimensions of the image, then the result will either pad out zeros and ignore extra values in the input array. More...

std::string	getUnits (size_t d)
	Returns units of given dimension, note that this is prior to the direction matrix, so if there is oblique orientation you are really looking at a mix of units. More...

int	write (std::string filename, double version) const
	Write out nifti image with the current images data. More...

void	printSelf ()
	Print information about the image. More...

virtual ptr< NDArray >	copy () const
	Performs a deep copy of the entire image and all metadata. More...

virtual ptr< NDArray >	createAnother () const
	Creates an identical array, but does not initialize pixel values. More...

virtual ptr< NDArray >	createAnother (size_t newdims, const size_t *newsize, PixelT newtype) const
	Create a new array that is the same underlying type as this. If this is an image then it will also copy the metdata, but NOT the pixels. More...

virtual ptr< NDArray >	createAnother (PixelT newtype) const
	Create a new array that is the same underlying type as this, but with a different pixel type. More...

virtual ptr< NDArray >	createAnother (size_t newdims, const size_t *newsize) const
	Create a new array that is the same underlying type as this, and same pixel type and orientation as this, but with a different size. More...

virtual ptr< NDArray >	copyCast (size_t newdims, const size_t *newsize, PixelT newtype) const
	Create a new image that is a copy of the input, possibly with new dimensions and pixeltype. The new image will have all overlapping pixels copied from the old image. More...

virtual ptr< NDArray >	copyCast (PixelT newtype) const
	Create a new image that is a copy of the input, with same dimensions but pxiels cast to newtype. The new image will have all overlapping pixels copied from the old image. More...

virtual ptr< NDArray >	copyCast (size_t newdims, const size_t *newsize) const
	Create a new image that is a copy of the input, possibly with new dimensions or size. The new image will have all overlapping pixels copied from the old image. The new image will have the same pixel type as the input image. More...

virtual ptr< NDArray >	extractCast (size_t len, const int64_t index, const size_t size) const
	Create a new array that is a copy of the input, possibly with new dimensions or size. The new array will have all overlapping pixels copied from the old array. The new array will have the same pixel type as the input array. More...

virtual ptr< NDArray >	extractCast (size_t len, const size_t *size) const
	Create a new array that is a copy of the input, possibly with new dimensions or size. The new array will have all overlapping pixels copied from the old array. The new array will have the same pixel type as the input array. Index assumed to be [0,0,...], so the output image will start at the origin of this image. More...

virtual ptr< NDArray >	extractCast (size_t len, const int64_t index, const size_t size, PixelT newtype) const
	Create a new array that is a copy of the input, possibly with new dimensions or size. The new array will have all overlapping pixels copied from the old array. The new array will have the same pixel type as the input array. More...

virtual ptr< NDArray >	extractCast (size_t len, const size_t *size, PixelT newtype) const
	Create a new array that is a copy of the input, possibly with new dimensions or size. The new array will have all overlapping pixels copied from the old array. The new array will have the same pixel type as the input array. Index assumed to be [0,0,...], so the output image will start at the origin of this image. More...

ptr< MRImage >	cloneImage () const
	Create an exact copy of the current image object, and return a pointer to it. More...

T &	operator[] (const int64_t *index)

T &	operator[] (const std::vector< int64_t > &index)

T &	operator[] (std::initializer_list< int64_t > index)

T &	operator[] (int64_t pixel)

const T &	operator[] (const int64_t *index) const

const T &	operator[] (const std::vector< int64_t > &index) const

const T &	operator[] (std::initializer_list< int64_t > index) const

const T &	operator[] (int64_t pixel) const

size_t	ndim () const

size_t	bytes () const

size_t	bytesper () const

size_t	elements () const

size_t	dim (size_t dir) const

const size_t *	dim () const

void	resize (const size_t dim[D])
	Changes the dimensions (size) of the image. This does not affect rank/dimensionality. More...

void	resize (std::initializer_list< size_t > dim)
	Changes the dimensions (size) of the image. This does not affect rank/dimensionality. More...

PixelT	type () const
	Return enum PixelT type of pixels. More...

void *	data ()
	Returns a pointer to the data array. Be careful. More...

const void *	data () const
	Returns a pointer to the data array. Be careful. More...

void	graft (const size_t dim[D], T ptr, const std::function< void(void )> &deleter)
	Grafts data of the given dimensions into the image, effectively changing the image size. More...

void	zero ()
	Sets all elements to zero. More...

virtual void *	__getAddr (std::initializer_list< int64_t > index) const

virtual void *	__getAddr (size_t len, const int64_t *index) const

virtual void *	__getAddr (const std::vector< int64_t > &index) const

virtual void *	__getAddr (int64_t i) const

virtual void *	__getAddr (int64_t x, int64_t y, int64_t z, int64_t t) const

virtual int64_t	getLinIndex (std::initializer_list< int64_t > index) const

virtual int64_t	getLinIndex (size_t len, const int64_t *index) const

virtual int64_t	getLinIndex (const std::vector< int64_t > &index) const

virtual int64_t	getLinIndex (int64_t x, int64_t y, int64_t z, int64_t t) const

virtual int64_t	tlen () const
	This function just returns the number of elements in a theoretical fourth dimension (ignoring orgnaization of higher dimensions) More...

bool	floatType () const
	Returns true if the stored type is FLOAT32, FLOAT64, or FLOAT128, ie is a pure float type. More...

bool	complexType () const
	Returns true if the stored type is COMPLEX256, COMPLEX128, or COMPLEX64, ie is a complex floating point type. More...

bool	signedType () const
	Returns true if the stored type is a variant of signed integer . More...

bool	unsignedType () const
	Returns true if the stored type is a variant of unsigned signed integer. More...

ptr< NDArray >	getPtr ()

ptr< const NDArray >	getConstPtr () const

void	orientDefault ()
	Default orientation (dir=ident, space=1 and origin=0), also resizes them. So this could be called without first initializing size. More...

bool	isOriented ()
	Returns true if the image has a valid orientation. More...

void	setOrient (const VectorXd &neworig, const VectorXd &newspace, const MatrixXd &newdir, bool reinit=true, CoordinateT coord=QFORM)
	Update the orientation of the pixels in RAS space. More...

const double &	direction (int64_t row, int64_t col) const
	Returns reference to a value in the direction matrix. Each row indicates the direction of the grid in RAS coordinates. This is the rotation of the Index grid. More...

const double &	invdirection (int64_t row, int64_t col) const
	Returns reference to a value in the inverse direction matrix. Each row indicates the direction of the grid in RAS coordinates. This is the rotation of the Index grid. More...

const MatrixXd &	getDirection () const
	Returns reference to the direction matrix. Each row indicates the direction of the grid in RAS coordinates. This is the rotation of the Index grid. More...

void	setDirection (const MatrixXd &newdir, bool reinit, CoordinateT coord=QFORM)
	Updates orientation information. If reinit is given then it will first set direction to the identity. otherwise old values will be left. After this the first min(DIMENSION,dir.rows()) columns and min(DIMENSION,dir.cols()) columns will be copies into the image direction matrix. More...

double &	origin (int64_t row)
	Returns reference to a value in the origin vector. This is the physical point that corresponds to index 0. More...

const double &	origin (int64_t row) const
	Returns reference to a value in the origin vector. This is the physical point that corresponds to index 0. More...

const VectorXd &	getOrigin () const
	Returns const reference to the origin vector. This is the physical point that corresponds to index 0. More...

void	setOrigin (const VectorXd &neworigin, bool reinit)
	Sets the origin vector. This is the physical point that corresponds to index 0. Note that min(current, new) elements will be copied. More...

double &	spacing (int64_t row)
	Returns reference to a value in the spacing vector. This is the physical distance between adjacent indexes. More...

const double &	spacing (int64_t row) const
	Returns reference to a value in the spacing vector. This is the physical distance between adjacent indexes. More...

const VectorXd &	getSpacing () const
	Returns const reference to the spacing vector. This is the physical distance between adjacent indexes. More...

void	setSpacing (const VectorXd &newspacing, bool reinit)
	Sets the spacing vector. This is the physical point that corresponds to index 0. Note that min(current, new) elements will be copied. More...

virtual bool	matchingOrient (ptr< const MRImage > other, bool checkdim, bool checksize, double tol=0.01) const
	Returns true of the other image has matching orientation as this. If checksize = true, then it will also check the size of the two images and return true if both orientation and size match, and false if they don't. More...

virtual bool	isIsotropic (bool only3d=true, double tol=0.01) const
	Returns true if the image is isotropic (same spacing in all dimensions). This can be looseened to checking only the first 3 dims with only3d = true. Tolerence in the absolute maximum difference between the first dim and any other dim. More...

ptr< MRImage >	getPtr ()
	Returns a pointer to self. More...

ptr< const MRImage >	getConstPtr () const
	Returns a constant pointer to self. More...

virtual void	copyMetadata (ptr< const MRImage > src)
	Copies metadata from another image. This includes slice timing, anything read from nifti files, spacing, orientation etc, but NOT pixel data, size, and dimensionality. More...

void	updateSliceTiming (double duration, int start, int end, SliceOrderT order)

Public Attributes
T *	_m_data

size_t	_m_stride [D]

size_t	_m_dim [D]

int	m_freqdim

int	m_phasedim

int	m_slicedim

CoordinateT	m_coordinate

double	m_slice_duration

int	m_slice_start

int	m_slice_end

SliceOrderT	m_slice_order

std::map< int64_t, double >	m_slice_timing

Protected Member Functions
int	writeNifti1Image (gzFile file) const

int	writeNifti2Image (gzFile file) const

int	writeNifti1Header (gzFile file) const

int	writeNifti2Header (gzFile file) const

int	writeJSON (gzFile file) const

void	updateStrides ()

virtual int	writePixels (gzFile file) const

virtual int	writeCSV (gzFile file) const

Protected Attributes
std::string	m_units [D]
	Vector of units for each dimension. More...

std::function< void(void *)>	m_freefunc
	The function which should be called when deleting data. By default this will just be delete[], but if data is grafted or if. More...

MatrixXd	m_direction
	Direction Matrix. Each row indicates the direction of the grid in RAS coordinates. This is the rotation of the Index grid. Note that you should not set this directly,. More...

MatrixXd	m_inv_direction
	Inverse of Direction Matrix. More...

VectorXd	m_spacing
	Spacing vector. Indicates distance between adjacent pixels in each dimension. Note that you should not set this directly, use setSpacing() instead because it will update the affine Matrix. More...

VectorXd	m_origin
	Origin vector. Indicates the RAS coordinates of index [0,0,0,..] Note that you should not set this directly, use setOrigin() instead because it will update the affine Matrix. More...

Detailed Description

template<size_t D, typename T>
class npl::MRImageStore< D, T >

MRImageStore is a version of NDArray that has an orientation matrix. Right now it also has additional data that is unique to nifti. Eventually this class will be forked into a subclass, and this will only have the orientation.

Template Parameters

D	Number of dimensions
T	Pixel type

Definition at line 748 of file mrimage.h.

Constructor & Destructor Documentation

template<size_t D, typename T>

npl::MRImageStore< D, T >::MRImageStore ( std::initializer_list< size_t > a_args )

Constructor with initializer list. Orientation will be default (direction = identity, spacing = 1, origin = 0).

Parameters

a_args dimensions of input, the length of this initializer list may not be fully used if a_args is longer than D. If it is shorter then D then additional dimensions are left as size 1.

template<size_t D, typename T>

npl::MRImageStore< D, T >::MRImageStore ( const std::vector< size_t > & a_args )

Constructor with vector. Orientation will be default (direction = identity, spacing = 1, origin = 0).

Parameters

a_args dimensions of input, the length of this initializer list may not be fully used if a_args is longer than D. If it is shorter then D then additional dimensions are left as size 1.

template<size_t D, typename T>

npl::MRImageStore< D, T >::MRImageStore	(	size_t	len,
		const size_t *	size
	)

Constructor with array of length len, Orientation will be default (direction = identity, spacing = 1, origin = 0).

Parameters

len	Length of array 'size'
size	dimensions of input, the length of this initializer list may not be fully used if a_args is longer than D. If it is shorter then D then additional dimensions are left as size 1.

template<size_t D, typename T>

npl::MRImageStore< D, T >::MRImageStore	(	size_t	len,
		const size_t *	size,
		T *	ptr,
		const std::function< void(void *)> &	deleter
	)

Constructor which uses a preexsting array, to graft into the image. No new allocation will be performed, however ownership of the array will be taken, meaning it could be deleted anytime after this constructor completes.

Parameters

len	Length of array 'size'
size	dimensions of input, the length of this initializer list may not be fully used if a_args is longer than D. If it is shorter then D then additional dimensions are left as size 1.
ptr	Pointer to data array, should be allocated with new, and size should be exactly sizeof(T)size[0]size[1]...size[len-1]
deleter	Function to use to delete (free) ptr

template<size_t D, typename T>

npl::MRImageStore< D, T >::MRImageStore ( )

Default constructor, uses identity for direction matrix, 1 for spacing and 0 for origin. Image size is 0.

Member Function Documentation

template<size_t D, typename T>

virtual void* npl::NDArrayStore< D, T >::__getAddr ( std::initializer_list< int64_t > index ) const

inlinevirtualinherited

Implements npl::NDArray.

Definition at line 765 of file ndarray.h.

template<size_t D, typename T>

virtual void* npl::NDArrayStore< D, T >::__getAddr	(	size_t	len,
		const int64_t *	index
	)		const

inlinevirtualinherited

Implements npl::NDArray.

Definition at line 770 of file ndarray.h.

template<size_t D, typename T>

virtual void* npl::NDArrayStore< D, T >::__getAddr ( const std::vector< int64_t > & index ) const

inlinevirtualinherited

Implements npl::NDArray.

Definition at line 775 of file ndarray.h.

template<size_t D, typename T>

virtual void* npl::NDArrayStore< D, T >::__getAddr ( int64_t i ) const

inlinevirtualinherited

Implements npl::NDArray.

Definition at line 780 of file ndarray.h.

template<size_t D, typename T>

virtual void* npl::NDArrayStore< D, T >::__getAddr	(	int64_t	x,
		int64_t	y,
		int64_t	z,
		int64_t	t
	)		const

inlinevirtualinherited

Implements npl::NDArray.

Definition at line 784 of file ndarray.h.

template<size_t D, typename T>

size_t npl::NDArrayStore< D, T >::bytes ( ) const

virtualinherited

Implements npl::NDArray.

template<size_t D, typename T>

size_t npl::NDArrayStore< D, T >::bytesper ( ) const

virtualinherited

Implements npl::NDArray.

template<size_t D, typename T>

ptr<MRImage> npl::MRImageStore< D, T >::cloneImage ( ) const

virtual

Create an exact copy of the current image object, and return a pointer to it.

Returns: Pointer to exact duplicate of current image.

Implements npl::MRImage.

bool npl::NDArray::complexType ( ) const

inlineinherited

Returns true if the stored type is COMPLEX256, COMPLEX128, or COMPLEX64, ie is a complex floating point type.

Returns: True if the number can be represented by a complex<long double>

Definition at line 203 of file ndarray.h.

template<size_t D, typename T>

virtual ptr<NDArray> npl::MRImageStore< D, T >::copy ( ) const

virtual

Performs a deep copy of the entire image and all metadata.

Returns: Copied image.

Implements npl::MRImage.

template<size_t D, typename T>

virtual ptr<NDArray> npl::MRImageStore< D, T >::copyCast	(	size_t	newdims,
		const size_t *	newsize,
		PixelT	newtype
	)		const

virtual

Create a new image that is a copy of the input, possibly with new dimensions and pixeltype. The new image will have all overlapping pixels copied from the old image.

Parameters

newdims	Number of dimensions in output image
newsize	Size of output image
newtype	Type of pixels in output image

Returns: Image with overlapping sections cast and copied from 'in'

Implements npl::MRImage.

template<size_t D, typename T>

virtual ptr<NDArray> npl::MRImageStore< D, T >::copyCast ( PixelT newtype ) const

virtual

Create a new image that is a copy of the input, with same dimensions but pxiels cast to newtype. The new image will have all overlapping pixels copied from the old image.

Parameters

newtype Type of pixels in output image

Returns: Image with overlapping sections cast and copied from 'in'

Implements npl::MRImage.

template<size_t D, typename T>

virtual ptr<NDArray> npl::MRImageStore< D, T >::copyCast	(	size_t	newdims,
		const size_t *	newsize
	)		const

virtual

Create a new image that is a copy of the input, possibly with new dimensions or size. The new image will have all overlapping pixels copied from the old image. The new image will have the same pixel type as the input image.

Parameters

newdims	Number of dimensions in output image
newsize	Size of output image

Returns: Image with overlapping sections cast and copied from 'in'

Implements npl::MRImage.

virtual void npl::MRImage::copyMetadata ( ptr< const MRImage > src )

virtualinherited

Copies metadata from another image. This includes slice timing, anything read from nifti files, spacing, orientation etc, but NOT pixel data, size, and dimensionality.

Parameters

src	Other image to copy from

template<size_t D, typename T>

virtual ptr<NDArray> npl::MRImageStore< D, T >::createAnother ( ) const

virtual

Creates an identical array, but does not initialize pixel values.

Returns: New array.

Implements npl::MRImage.

template<size_t D, typename T>

virtual ptr<NDArray> npl::MRImageStore< D, T >::createAnother	(	size_t	newdims,
		const size_t *	newsize,
		PixelT	newtype
	)		const

virtual

Create a new array that is the same underlying type as this. If this is an image then it will also copy the metdata, but NOT the pixels.

Parameters

newdims	Number of dimensions in copied output
newsize	Size of output, this array should be of size newdims
newtype	Type of pixels in output array

Returns: Image with identical orientation but different size and pixeltype

Implements npl::MRImage.

template<size_t D, typename T>

virtual ptr<NDArray> npl::MRImageStore< D, T >::createAnother ( PixelT newtype ) const

virtual

Create a new array that is the same underlying type as this, but with a different pixel type.

Parameters

newtype Type of pixels in output array

Returns: Image with identical orientation and size but different pixel type

Implements npl::MRImage.

template<size_t D, typename T>

virtual ptr<NDArray> npl::MRImageStore< D, T >::createAnother	(	size_t	newdims,
		const size_t *	newsize
	)		const

virtual

Create a new array that is the same underlying type as this, and same pixel type and orientation as this, but with a different size.

Parameters

newdims	Number of dimensions in output array
newsize	Input array of length newdims that gives the size of output array,

Returns: Image with identical orientation and pixel type but different size from this

Implements npl::MRImage.

template<size_t D, typename T>

void* npl::NDArrayStore< D, T >::data ( )

inlinevirtualinherited

Returns a pointer to the data array. Be careful.

Returns: Pointer to data

Implements npl::NDArray.

Definition at line 559 of file ndarray.h.

template<size_t D, typename T>

const void* npl::NDArrayStore< D, T >::data ( ) const

inlinevirtualinherited

Returns a pointer to the data array. Be careful.

Returns: Pointer to data

Implements npl::NDArray.

Definition at line 566 of file ndarray.h.

template<size_t D, typename T>

size_t npl::NDArrayStore< D, T >::dim ( size_t dir ) const

virtualinherited

Implements npl::NDArray.

template<size_t D, typename T>

const size_t* npl::NDArrayStore< D, T >::dim ( ) const

virtualinherited

Implements npl::NDArray.

const double& npl::MRImage::direction	(	int64_t	row,
		int64_t	col
	)		const

inherited

Returns reference to a value in the direction matrix. Each row indicates the direction of the grid in RAS coordinates. This is the rotation of the Index grid.

Parameters

row	Row to access
col	Column to access

Returns: Element in direction matrix

template<size_t D, typename T>

virtual int npl::MRImageStore< D, T >::disOrientVector	(	size_t	len,
		const double *	ras,
		double *	xyz
	)		const

virtual

Convert a vector in index coordinates to a vector in ras coordinates. Vector is simply multiplied by the internal rotation matrix.

Parameters

len	Length of input vector (may be different than dimension - extra values will be ignored, missing values will be assumed zero)
ras	Input vector in physical space.
xyz	Output vector in index space ijk. This is the product of the input vector and inverse rotation matrix

Returns: Success

Implements npl::MRImage.

template<size_t D, typename T>

size_t npl::NDArrayStore< D, T >::elements ( ) const

virtualinherited

Implements npl::NDArray.

template<size_t D, typename T>

virtual ptr<NDArray> npl::MRImageStore< D, T >::extractCast	(	size_t	len,
		const int64_t *	index,
		const size_t *	size
	)		const

virtual

Create a new array that is a copy of the input, possibly with new dimensions or size. The new array will have all overlapping pixels copied from the old array. The new array will have the same pixel type as the input array.

Parameters

len	Length of index/newsize arrays
index	Index to start copying from.
size	Size of output image. Note length 0 dimensions will be removed, while length 1 dimensions will be left.

Returns: Image with overlapping sections cast and copied from 'in'

Implements npl::MRImage.

template<size_t D, typename T>

virtual ptr<NDArray> npl::MRImageStore< D, T >::extractCast	(	size_t	len,
		const size_t *	size
	)		const

virtual

Create a new array that is a copy of the input, possibly with new dimensions or size. The new array will have all overlapping pixels copied from the old array. The new array will have the same pixel type as the input array. Index assumed to be [0,0,...], so the output image will start at the origin of this image.

Parameters

len	Length of index/size arrays
size	Size of output image. Note length 0 dimensions will be removed, while length 1 dimensions will be left.

Returns: Image with overlapping sections cast and copied from 'in'

Implements npl::MRImage.

template<size_t D, typename T>

virtual ptr<NDArray> npl::MRImageStore< D, T >::extractCast	(	size_t	len,
		const int64_t *	index,
		const size_t *	size,
		PixelT	newtype
	)		const

virtual

Create a new array that is a copy of the input, possibly with new dimensions or size. The new array will have all overlapping pixels copied from the old array. The new array will have the same pixel type as the input array.

Parameters

len	Length of index/size arrays
index	Index to start copying from.
size	Size of output image. Note length 0 dimensions will be removed, while length 1 dimensions will be left.
newtype	Pixel type of output image.

Returns: Image with overlapping sections cast and copied from 'in'

Implements npl::MRImage.

template<size_t D, typename T>

virtual ptr<NDArray> npl::MRImageStore< D, T >::extractCast	(	size_t	len,
		const size_t *	size,
		PixelT	newtype
	)		const

virtual

Create a new array that is a copy of the input, possibly with new dimensions or size. The new array will have all overlapping pixels copied from the old array. The new array will have the same pixel type as the input array. Index assumed to be [0,0,...], so the output image will start at the origin of this image.

Parameters

len	Length of index/size arrays
size	Size of output image. Note length 0 dimensions will be removed, while length 1 dimensions will be left.
newtype	Pixel type of output image.

Returns: Image with overlapping sections cast and copied from 'in'

Implements npl::MRImage.

bool npl::NDArray::floatType ( ) const

inlineinherited

Returns true if the stored type is FLOAT32, FLOAT64, or FLOAT128, ie is a pure float type.

Returns: True if the number can be represented by a long double

Definition at line 193 of file ndarray.h.

ptr<const NDArray> npl::NDArray::getConstPtr ( ) const

inlineinherited

Definition at line 231 of file ndarray.h.

ptr<const MRImage> npl::MRImage::getConstPtr ( ) const

inlineinherited

Returns a constant pointer to self.

Returns: this

Definition at line 490 of file mrimage.h.

const MatrixXd& npl::MRImage::getDirection ( ) const

inherited

Returns reference to the direction matrix. Each row indicates the direction of the grid in RAS coordinates. This is the rotation of the Index grid.

Returns: Direction matrix

template<size_t D, typename T>

virtual int64_t npl::NDArrayStore< D, T >::getLinIndex ( std::initializer_list< int64_t > index ) const

virtualinherited

Implements npl::NDArray.

template<size_t D, typename T>

virtual int64_t npl::NDArrayStore< D, T >::getLinIndex	(	size_t	len,
		const int64_t *	index
	)		const

virtualinherited

Implements npl::NDArray.

template<size_t D, typename T>

virtual int64_t npl::NDArrayStore< D, T >::getLinIndex ( const std::vector< int64_t > & index ) const

virtualinherited

Implements npl::NDArray.

template<size_t D, typename T>

virtual int64_t npl::NDArrayStore< D, T >::getLinIndex	(	int64_t	x,
		int64_t	y,
		int64_t	z,
		int64_t	t
	)		const

virtualinherited

Implements npl::NDArray.

const VectorXd& npl::MRImage::getOrigin ( ) const

inherited

Returns const reference to the origin vector. This is the physical point that corresponds to index 0.

Returns: Origin vector

ptr<NDArray> npl::NDArray::getPtr ( )

inlineinherited

Definition at line 227 of file ndarray.h.

ptr<MRImage> npl::MRImage::getPtr ( )

inlineinherited

Returns a pointer to self.

Returns: this

Definition at line 481 of file mrimage.h.

const VectorXd& npl::MRImage::getSpacing ( ) const

inherited

Returns const reference to the spacing vector. This is the physical distance between adjacent indexes.

Returns: Spacing vector

template<size_t D, typename T>

std::string npl::MRImageStore< D, T >::getUnits ( size_t d )

inline

Returns units of given dimension, note that this is prior to the direction matrix, so if there is oblique orientation you are really looking at a mix of units.

Parameters

d Dimension

Returns: String describing units.

Definition at line 950 of file mrimage.h.

template<size_t D, typename T>

void npl::NDArrayStore< D, T >::graft	(	const size_t	dim[D],
		T *	ptr,
		const std::function< void(void *)> &	deleter
	)

inherited

Grafts data of the given dimensions into the image, effectively changing the image size.

Parameters

dim	Dimensions of image
ptr	Pointer to data which we will take control of
deleter	Function which can be called on ptr to delete it.

template<size_t D, typename T>

virtual bool npl::MRImageStore< D, T >::indexInsideFOV	(	size_t	len,
		const double *	xyz
	)		const

virtual

Returns true if the constinuous index is within the field of view of the image. Note, like all coordinates pass to MRImage, if the array given differs from the dimensions of the image, then the result will either pad out zeros and ignore extra values in the input array.

Parameters

len	Length of xyz array
xyz	Array of continouos indices

Returns: Whether the index would round to a voxel inside the image.

Implements npl::MRImage.

template<size_t D, typename T>

virtual bool npl::MRImageStore< D, T >::indexInsideFOV	(	size_t	len,
		const int64_t *	xyz
	)		const

virtual

Returns true if the constinuous index is within the field of view of the image. Note, like all coordinates pass to MRImage, if the array given differs from the dimensions of the image, then the result will either pad out zeros and ignore extra values in the input array.

Parameters

len	Length of xyz array
xyz	Array of indices

Returns: Whether the index is inside the image

Implements npl::MRImage.

template<size_t D, typename T>

virtual int npl::MRImageStore< D, T >::indexToPoint	(	size_t	len,
		const int64_t *	xyz,
		double *	ras
	)		const

virtual

Converts an index in pixel space to RAS, physical/time coordinates. If len < dimensions, additional dimensions are assumed to be 0. If len > dimensions then additional values are ignored, and only the first DIM values will be transformed and written to ras.

Parameters

len	Length of xyz/ras arrays.
xyz	Array in xyz... coordinates (maybe as long as you want).
ras	Corresponding coordinate

Returns: 0

Implements npl::MRImage.

template<size_t D, typename T>

virtual int npl::MRImageStore< D, T >::indexToPoint	(	size_t	len,
		const double *	xyz,
		double *	ras
	)		const

virtual

Converts an index in pixel space to RAS, physical/time coordinates. If len < dimensions, additional dimensions are assumed to be 0. If len > dimensions then additional values are ignored, and only the first DIM values will be transformed and written to ras.

Parameters

len	Length of xyz/ras arrays.
xyz	Array in xyz... coordinates (maybe as long as you want).
ras	Corresponding coordinate

Returns: 0

Implements npl::MRImage.

const double& npl::MRImage::invdirection	(	int64_t	row,
		int64_t	col
	)		const

inherited

Returns reference to a value in the inverse direction matrix. Each row indicates the direction of the grid in RAS coordinates. This is the rotation of the Index grid.

Parameters

row	Row to access
col	Column to access

Returns: Element in direction matrix

virtual bool npl::MRImage::isIsotropic	(	bool	only3d = `true`,
		double	tol = `0.01`
	)		const

virtualinherited

Returns true if the image is isotropic (same spacing in all dimensions). This can be looseened to checking only the first 3 dims with only3d = true. Tolerence in the absolute maximum difference between the first dim and any other dim.

Parameters

only3d	Only check spacing in the first 3 dimensions (default)
tol	Tolerence in the absolute maximum difference between the first dim and any other dim.

Returns: True if the image is roughly isotropic

bool npl::MRImage::isOriented ( )

inlineinherited

Returns true if the image has a valid orientation.

Returns: True if the image has a valid orientation

Definition at line 145 of file mrimage.h.

virtual bool npl::MRImage::matchingOrient	(	ptr< const MRImage >	other,
		bool	checkdim,
		bool	checksize,
		double	tol = `0.01`
	)		const

virtualinherited

Returns true of the other image has matching orientation as this. If checksize = true, then it will also check the size of the two images and return true if both orientation and size match, and false if they don't.

Parameters

other	MRimage to compare.
checkdim	Whether to enforce identical dimensionality. If this is false then the first min(D1,D2) dimensions will be checked, if this is true then mismatched dimensionality will cause this to return a false
checksize	Whether to enforce identical size as well as orientation
tol	tolerance for differences in orientation. Because the orientation matrix must undergo floating operationt to convert from Quaternions there are likely to be (small) errors.

Returns: True if the two images have matching orientation information.

template<size_t D, typename T>

size_t npl::NDArrayStore< D, T >::ndim ( ) const

virtualinherited

Implements npl::NDArray.

template<size_t D, typename T>

T& npl::NDArrayStore< D, T >::operator[] ( const int64_t * index )

inherited

template<size_t D, typename T>

T& npl::NDArrayStore< D, T >::operator[] ( const std::vector< int64_t > & index )

inherited

template<size_t D, typename T>

T& npl::NDArrayStore< D, T >::operator[] ( std::initializer_list< int64_t > index )

inherited

template<size_t D, typename T>

T& npl::NDArrayStore< D, T >::operator[] ( int64_t pixel )

inherited

template<size_t D, typename T>

const T& npl::NDArrayStore< D, T >::operator[] ( const int64_t * index ) const

inherited

template<size_t D, typename T>

const T& npl::NDArrayStore< D, T >::operator[] ( const std::vector< int64_t > & index ) const

inherited

template<size_t D, typename T>

const T& npl::NDArrayStore< D, T >::operator[] ( std::initializer_list< int64_t > index ) const

inherited

template<size_t D, typename T>

const T& npl::NDArrayStore< D, T >::operator[] ( int64_t pixel ) const

inherited

void npl::MRImage::orientDefault ( )

inherited

Default orientation (dir=ident, space=1 and origin=0), also resizes them. So this could be called without first initializing size.

template<size_t D, typename T>

virtual int npl::MRImageStore< D, T >::orientVector	(	size_t	len,
		const double *	xyz,
		double *	ras
	)		const

virtual

Convert a vector in index coordinates to a vector in ras coordinates. Vector is simply multiplied by the internal rotation matrix.

Parameters

len	Length of input vector (may be different than dimension - extra values will be ignored, missing values will be assumed zero)
xyz	Input vector in index space ijk....
ras	Output vector in physical space. This is the product of the input vector and rotation matrix

Returns: Success

Implements npl::MRImage.

double& npl::MRImage::origin ( int64_t row )

inherited

Returns reference to a value in the origin vector. This is the physical point that corresponds to index 0.

Parameters

row	Row to access

Returns: Element in origin vector

const double& npl::MRImage::origin ( int64_t row ) const

inherited

Returns reference to a value in the origin vector. This is the physical point that corresponds to index 0.

Parameters

row	Row to access

Returns: Element in origin vector

template<size_t D, typename T>

virtual bool npl::MRImageStore< D, T >::pointInsideFOV	(	size_t	len,
		const double *	ras
	)		const

virtual

Returns true if the point is within the field of view of the image. Note, like all coordinates pass to MRImage, if the array given differs from the dimensions of the image, then the result will either pad out zeros and ignore extra values in the input array.

Parameters

len	Length of RAS array
ras	Array of Right-handed coordinates Right+, Anterior+, Superior+

Returns: Whether the point would round to a voxel inside the image.

Implements npl::MRImage.

template<size_t D, typename T>

virtual int npl::MRImageStore< D, T >::pointToIndex	(	size_t	len,
		const double *	ras,
		double *	xyz
	)		const

virtual

Converts a point in RAS coordinate system to index. If len < dimensions, additional dimensions are assumed to be 0. If len > dimensions then additional values are ignored, and only the first DIM values will be transformed and written to ras.

Parameters

len	Length of xyz/ras arrays.
ras	Array in RAS... coordinates (may be as long as you want).
xyz	Corresponding coordinate

Returns: 0

Implements npl::MRImage.

template<size_t D, typename T>

virtual int npl::MRImageStore< D, T >::pointToIndex	(	size_t	len,
		const double *	ras,
		int64_t *	index
	)		const

virtual

Converts a point in RAS coordinate system to index. If len < dimensions, additional dimensions are assumed to be 0. If len > dimensions then additional values are ignored, and only the first DIM values will be transformed and written to ras.

Parameters

len	Length of xyz/ras arrays.
ras	Array in RAS... coordinates (may be as long as you want).
index	Corresponding coordinate, rounded to nearest integer

Returns: 0

Implements npl::MRImage.

template<size_t D, typename T>

void npl::MRImageStore< D, T >::printSelf ( )

Print information about the image.

template<size_t D, typename T>

void npl::NDArrayStore< D, T >::resize ( const size_t dim[D] )

inherited

Changes the dimensions (size) of the image. This does not affect rank/dimensionality.

Parameters

dim New size

template<size_t D, typename T>

void npl::NDArrayStore< D, T >::resize ( std::initializer_list< size_t > dim )

inherited

Changes the dimensions (size) of the image. This does not affect rank/dimensionality.

Parameters

dim New size

void npl::MRImage::setDirection	(	const MatrixXd &	newdir,
		bool	reinit,
		CoordinateT	coord = `QFORM`
	)

inherited

Updates orientation information. If reinit is given then it will first set direction to the identity. otherwise old values will be left. After this the first min(DIMENSION,dir.rows()) columns and min(DIMENSION,dir.cols()) columns will be copies into the image direction matrix.

Parameters

newdir	Input direction/rotation
reinit	Whether to reset everything to Identity/0 before applying. You may want to do this if theinput matrices/vectors differ in dimension from this image.
coord	coordinate system this refers to. Eventually this might include more advanced options (scanner,anat etc). For now it is just QFORM or SFORM

void npl::MRImage::setOrient	(	const VectorXd &	neworig,
		const VectorXd &	newspace,
		const MatrixXd &	newdir,
		bool	reinit = `true`,
		CoordinateT	coord = `QFORM`
	)

inherited

Update the orientation of the pixels in RAS space.

Parameters

neworig	New Origin.
newspace	New Spacing.
newdir	New Direction
reinit	Whether to reset everything to Identity/0 before applying. You may want to do this if theinput matrices/vectors differ in dimension from this image.
coord	coordinate system this refers to. Eventually this might include more advanced options (scanner,anat etc). For now it is just QFORM or SFORM

void npl::MRImage::setOrigin	(	const VectorXd &	neworigin,
		bool	reinit
	)

inherited

Sets the origin vector. This is the physical point that corresponds to index 0. Note that min(current, new) elements will be copied.

Parameters

neworigin	the new origin vector to copy.
reinit	Whether to reset everything to Identity/0 before applying. You may want to do this if theinput matrices/vectors differ in dimension from this image.

void npl::MRImage::setSpacing	(	const VectorXd &	newspacing,
		bool	reinit
	)

inherited

Sets the spacing vector. This is the physical point that corresponds to index 0. Note that min(current, new) elements will be copied.

Parameters

newspacing	the new spacing vector to copy.
reinit	Set the whole vector to 1s first. This might be useful if you are setting fewer elements than dimensions

bool npl::NDArray::signedType ( ) const

inlineinherited

Returns true if the stored type is a variant of signed integer .

Returns: True if the number can be represented by an int64_t

Definition at line 212 of file ndarray.h.

double& npl::MRImage::spacing ( int64_t row )

inherited

Returns reference to a value in the spacing vector. This is the physical distance between adjacent indexes.

Parameters

row	Row to access

Returns: Element in spacing vector

const double& npl::MRImage::spacing ( int64_t row ) const

inherited

Returns reference to a value in the spacing vector. This is the physical distance between adjacent indexes.

Parameters

row	Row to access

Returns: Element in spacing vector

template<size_t D, typename T>

virtual int64_t npl::NDArrayStore< D, T >::tlen ( ) const

inlinevirtualinherited

This function just returns the number of elements in a theoretical fourth dimension (ignoring orgnaization of higher dimensions)

Returns: number of elements in the 4th or greater dimensions

Implements npl::NDArray.

Definition at line 800 of file ndarray.h.

template<size_t D, typename T>

PixelT npl::NDArrayStore< D, T >::type ( ) const

virtualinherited

Return enum PixelT type of pixels.

Returns: Type of values stored

Implements npl::NDArray.

bool npl::NDArray::unsignedType ( ) const

inlineinherited

Returns true if the stored type is a variant of unsigned signed integer.

Returns: True if the number can be represented by an size_t

Definition at line 222 of file ndarray.h.

void npl::MRImage::updateSliceTiming	(	double	duration,
		int	start,
		int	end,
		SliceOrderT	order
	)

inherited

template<size_t D, typename T>

void npl::NDArrayStore< D, T >::updateStrides ( )

protectedinherited

template<size_t D, typename T>

int npl::MRImageStore< D, T >::write	(	std::string	filename,
		double	version
	)		const

virtual

Write out nifti image with the current images data.

Parameters

filename
version	> 2 or < 2 to indicate whether to use nifti version 2 or nifti version 1.

Returns: Success if 0

Implements npl::MRImage.

template<size_t D, typename T>

virtual int npl::NDArrayStore< D, T >::writeCSV ( gzFile file ) const

protectedvirtualinherited

template<size_t D, typename T>

int npl::MRImageStore< D, T >::writeJSON ( gzFile file ) const

protectedvirtual

Reimplemented from npl::NDArrayStore< D, T >.

template<size_t D, typename T>

int npl::MRImageStore< D, T >::writeNifti1Header ( gzFile file ) const

protectedvirtual

Reimplemented from npl::NDArrayStore< D, T >.

template<size_t D, typename T>

int npl::MRImageStore< D, T >::writeNifti1Image ( gzFile file ) const

protectedvirtual

Implements npl::MRImage.

template<size_t D, typename T>

int npl::MRImageStore< D, T >::writeNifti2Header ( gzFile file ) const

protectedvirtual

Reimplemented from npl::NDArrayStore< D, T >.

template<size_t D, typename T>

int npl::MRImageStore< D, T >::writeNifti2Image ( gzFile file ) const

protectedvirtual

Implements npl::MRImage.

template<size_t D, typename T>

virtual int npl::NDArrayStore< D, T >::writePixels ( gzFile file ) const

protectedvirtualinherited

template<size_t D, typename T>

void npl::NDArrayStore< D, T >::zero ( )

virtualinherited

Sets all elements to zero.

Implements npl::NDArray.

Member Data Documentation

template<size_t D, typename T>

T* npl::NDArrayStore< D, T >::_m_data

inherited

Definition at line 805 of file ndarray.h.

template<size_t D, typename T>

size_t npl::NDArrayStore< D, T >::_m_dim[D]

inherited

Definition at line 809 of file ndarray.h.

template<size_t D, typename T>

size_t npl::NDArrayStore< D, T >::_m_stride[D]

inherited

Definition at line 808 of file ndarray.h.

CoordinateT npl::MRImage::m_coordinate

inherited

Definition at line 675 of file mrimage.h.

MatrixXd npl::MRImage::m_direction

protectedinherited

Direction Matrix. Each row indicates the direction of the grid in RAS coordinates. This is the rotation of the Index grid. Note that you should not set this directly,.

Definition at line 714 of file mrimage.h.

std::function<void(void*)> npl::NDArray::m_freefunc

protectedinherited

The function which should be called when deleting data. By default this will just be delete[], but if data is grafted or if.

Definition at line 435 of file ndarray.h.

int npl::MRImage::m_freqdim

inherited

Definition at line 672 of file mrimage.h.

MatrixXd npl::MRImage::m_inv_direction

protectedinherited

Inverse of Direction Matrix.

Definition at line 719 of file mrimage.h.

VectorXd npl::MRImage::m_origin

protectedinherited

Origin vector. Indicates the RAS coordinates of index [0,0,0,..] Note that you should not set this directly, use setOrigin() instead because it will update the affine Matrix.

Definition at line 733 of file mrimage.h.

int npl::MRImage::m_phasedim

inherited

Definition at line 673 of file mrimage.h.

double npl::MRImage::m_slice_duration

inherited

Definition at line 685 of file mrimage.h.

int npl::MRImage::m_slice_end

inherited

Definition at line 687 of file mrimage.h.

SliceOrderT npl::MRImage::m_slice_order

inherited

Definition at line 700 of file mrimage.h.

int npl::MRImage::m_slice_start

inherited

Definition at line 686 of file mrimage.h.

std::map<int64_t,double> npl::MRImage::m_slice_timing

inherited

Definition at line 703 of file mrimage.h.

int npl::MRImage::m_slicedim

inherited

Definition at line 674 of file mrimage.h.

VectorXd npl::MRImage::m_spacing

protectedinherited

Spacing vector. Indicates distance between adjacent pixels in each dimension. Note that you should not set this directly, use setSpacing() instead because it will update the affine Matrix.

Definition at line 726 of file mrimage.h.

template<size_t D, typename T>

std::string npl::MRImageStore< D, T >::m_units[D]

protected

Vector of units for each dimension.

Definition at line 1146 of file mrimage.h.

The documentation for this class was generated from the following file:

/home/micahc/coding/npl/lib/mrimage.h

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

template<size_t D, typename T> class npl::MRImageStore< D, T >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<size_t D, typename T>
class npl::MRImageStore< D, T >