MRImage can basically be used like an NDArray, with the addition of orientation related additions. More...

#include <mrimage.h>

Inherited by npl::MRImageStore< 3, double > [virtual], npl::MRImageStore< 4, double > [virtual], npl::MRImageStore< 5, double > [virtual], and npl::MRImageStore< D, T > [virtual].

Public Member Functions
	MRImage ()

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 int	indexToPoint (size_t len, const int64_t xyz, double ras) const =0

virtual int	indexToPoint (size_t len, const double xyz, double ras) const =0
	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 =0
	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 =0
	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 =0
	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 =0
	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 =0
	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 =0
	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 =0
	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	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...

virtual int	write (std::string filename, double version=1) const =0
	Write the image to a nifti file. More...

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

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

virtual ptr< MRImage >	cloneImage () const =0
	Create a copy of this image. This is identical to copy() but will return a pointer to an image rather than an NDArray. More...

virtual ptr< NDArray >	copy () const =0
	Performs a deep copy of the entire image and all metadata. More...

virtual ptr< NDArray >	createAnother () const =0
	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 =0
	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 =0
	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 =0
	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 =0
	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 =0
	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 =0
	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 =0
	extracts a region of this image. Zeros in the size variable indicate dimension to be removed. More...

virtual ptr< NDArray >	extractCast (size_t len, const size_t *size) const =0
	extracts a region of this image. Zeros in the size variable indicate dimension to be removed. More...

virtual ptr< NDArray >	extractCast (size_t len, const int64_t index, const size_t size, PixelT newtype) const =0
	extracts a region of this image. Zeros in the size variable indicate dimension to be removed. More...

virtual ptr< NDArray >	extractCast (size_t len, const size_t *size, PixelT newtype) const =0
	extracts a region of this image. Zeros in the size variable indicate dimension to be removed. 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)

virtual size_t	ndim () const =0

virtual size_t	bytes () const =0

virtual size_t	bytesper () const =0

virtual size_t	elements () const =0

virtual size_t	dim (size_t dir) const =0

virtual const size_t *	dim () const =0

virtual PixelT	type () const =0
	Return enum PixelT type of pixels. 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...

virtual void *	data ()=0

virtual const void *	data () const =0

virtual void	zero ()=0
	Sets all elements to zero. More...

virtual void *	__getAddr (std::initializer_list< int64_t > index) const =0

virtual void *	__getAddr (size_t len, const int64_t *index) const =0

virtual void *	__getAddr (const std::vector< int64_t > &index) const =0

virtual void *	__getAddr (int64_t i) const =0

virtual void *	__getAddr (int64_t x, int64_t y, int64_t z, int64_t t) const =0

virtual int64_t	getLinIndex (std::initializer_list< int64_t > index) const =0

virtual int64_t	getLinIndex (size_t len, const int64_t *index) const =0

virtual int64_t	getLinIndex (const std::vector< int64_t > &index) const =0

virtual int64_t	getLinIndex (int64_t x, int64_t y, int64_t z, int64_t t) const =0

virtual int64_t	tlen () const =0
	This function just returns the number of elements in a theoretical fourth dimension (ignoring orgnaization of higher dimensions) More...

Public Attributes
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
virtual int	writeNifti1Image (gzFile file) const =0

virtual int	writeNifti2Image (gzFile file) const =0

Protected Attributes
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...

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...

Friends
ptr< MRImage >	readNiftiImage (gzFile file, bool verbose)

Detailed Description

MRImage can basically be used like an NDArray, with the addition of orientation related additions.

Definition at line 123 of file mrimage.h.

Constructor & Destructor Documentation

npl::MRImage::MRImage ( )

inline

Definition at line 126 of file mrimage.h.

Member Function Documentation

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

pure virtualinherited

Implemented in npl::NDArrayStore< D, T >, npl::NDArrayStore< D, double >, npl::NDArrayStore< 1, double >, npl::NDArrayStore< 2, double >, and npl::NDArrayStore< 3, double >.

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

pure virtualinherited

Implemented in npl::NDArrayStore< D, T >, npl::NDArrayStore< D, double >, npl::NDArrayStore< 1, double >, npl::NDArrayStore< 2, double >, and npl::NDArrayStore< 3, double >.

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

pure virtualinherited

Implemented in npl::NDArrayStore< D, T >, npl::NDArrayStore< D, double >, npl::NDArrayStore< 1, double >, npl::NDArrayStore< 2, double >, and npl::NDArrayStore< 3, double >.

virtual void* npl::NDArray::__getAddr ( int64_t i ) const

pure virtualinherited

Implemented in npl::NDArrayStore< D, T >, npl::NDArrayStore< D, double >, npl::NDArrayStore< 1, double >, npl::NDArrayStore< 2, double >, and npl::NDArrayStore< 3, double >.

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

pure virtualinherited

Implemented in npl::NDArrayStore< D, T >, npl::NDArrayStore< D, double >, npl::NDArrayStore< 1, double >, npl::NDArrayStore< 2, double >, and npl::NDArrayStore< 3, double >.

virtual size_t npl::NDArray::bytes ( ) const

pure virtualinherited

Implemented in npl::NDArrayStore< D, T >, npl::NDArrayStore< D, double >, npl::NDArrayStore< 1, double >, npl::NDArrayStore< 2, double >, and npl::NDArrayStore< 3, double >.

virtual size_t npl::NDArray::bytesper ( ) const

pure virtualinherited

Implemented in npl::NDArrayStore< D, T >, npl::NDArrayStore< D, double >, npl::NDArrayStore< 1, double >, npl::NDArrayStore< 2, double >, and npl::NDArrayStore< 3, double >.

virtual ptr<MRImage> npl::MRImage::cloneImage ( ) const

pure virtual

Create a copy of this image. This is identical to copy() but will return a pointer to an image rather than an NDArray.

Returns: Pointer to deep-copied image.

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

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.

virtual ptr<NDArray> npl::MRImage::copy ( ) const

pure virtual

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

Returns: Copied image (as NDarray pointer)

Implements npl::NDArray.

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

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

pure 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::NDArray.

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

virtual ptr<NDArray> npl::MRImage::copyCast ( PixelT newtype ) const

pure 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::NDArray.

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

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

pure 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::NDArray.

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

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

virtual

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

virtual ptr<NDArray> npl::MRImage::createAnother ( ) const

pure virtual

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

Returns: New array.

Implements npl::NDArray.

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

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

pure 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::NDArray.

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

virtual ptr<NDArray> npl::MRImage::createAnother ( PixelT newtype ) const

pure 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::NDArray.

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

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

pure 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::NDArray.

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

virtual void* npl::NDArray::data ( )

pure virtualinherited

Implemented in npl::NDArrayStore< D, T >, npl::NDArrayStore< D, double >, npl::NDArrayStore< 1, double >, npl::NDArrayStore< 2, double >, and npl::NDArrayStore< 3, double >.

virtual const void* npl::NDArray::data ( ) const

pure virtualinherited

Implemented in npl::NDArrayStore< D, T >, npl::NDArrayStore< D, double >, npl::NDArrayStore< 1, double >, npl::NDArrayStore< 2, double >, and npl::NDArrayStore< 3, double >.

virtual size_t npl::NDArray::dim ( size_t dir ) const

pure virtualinherited

Implemented in npl::NDArrayStore< D, T >, npl::NDArrayStore< D, double >, npl::NDArrayStore< 1, double >, npl::NDArrayStore< 2, double >, and npl::NDArrayStore< 3, double >.

virtual const size_t* npl::NDArray::dim ( ) const

pure virtualinherited

Implemented in npl::NDArrayStore< D, T >, npl::NDArrayStore< D, double >, npl::NDArrayStore< 1, double >, npl::NDArrayStore< 2, double >, and npl::NDArrayStore< 3, double >.

const double& npl::MRImage::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.

Parameters

row	Row to access
col	Column to access

Returns: Element in direction matrix

virtual int npl::MRImage::disOrientVector	(	size_t	len,
		const double *	ras,
		double *	xyz
	)		const

pure 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

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

virtual size_t npl::NDArray::elements ( ) const

pure virtualinherited

Implemented in npl::NDArrayStore< D, T >, npl::NDArrayStore< D, double >, npl::NDArrayStore< 1, double >, npl::NDArrayStore< 2, double >, and npl::NDArrayStore< 3, double >.

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

pure virtual

extracts a region of this image. Zeros in the size variable indicate dimension to be removed.

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::NDArray.

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

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

pure virtual

extracts a region of this image. Zeros in the size variable indicate dimension to be removed.

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::NDArray.

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

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

pure virtual

extracts a region of this image. Zeros in the size variable indicate dimension to be removed.

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::NDArray.

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

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

pure virtual

extracts a region of this image. Zeros in the size variable indicate dimension to be removed.

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::NDArray.

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

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

inline

Returns a constant pointer to self.

Returns: this

Definition at line 490 of file mrimage.h.

const MatrixXd& npl::MRImage::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.

Returns: Direction matrix

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

pure virtualinherited

Implemented in npl::NDArrayStore< D, T >, npl::NDArrayStore< D, double >, npl::NDArrayStore< 1, double >, npl::NDArrayStore< 2, double >, and npl::NDArrayStore< 3, double >.

virtual int64_t npl::NDArray::getLinIndex	(	size_t	len,
		const int64_t *	index
	)		const

pure virtualinherited

Implemented in npl::NDArrayStore< D, T >, npl::NDArrayStore< D, double >, npl::NDArrayStore< 1, double >, npl::NDArrayStore< 2, double >, and npl::NDArrayStore< 3, double >.

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

pure virtualinherited

Implemented in npl::NDArrayStore< D, T >, npl::NDArrayStore< D, double >, npl::NDArrayStore< 1, double >, npl::NDArrayStore< 2, double >, and npl::NDArrayStore< 3, double >.

virtual int64_t npl::NDArray::getLinIndex	(	int64_t	x,
		int64_t	y,
		int64_t	z,
		int64_t	t
	)		const

pure virtualinherited

Implemented in npl::NDArrayStore< D, T >, npl::NDArrayStore< D, double >, npl::NDArrayStore< 1, double >, npl::NDArrayStore< 2, double >, and npl::NDArrayStore< 3, double >.

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

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

Returns: Origin vector

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

inline

Returns a pointer to self.

Returns: this

Definition at line 481 of file mrimage.h.

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

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

Returns: Spacing vector

virtual bool npl::MRImage::indexInsideFOV	(	size_t	len,
		const double *	xyz
	)		const

pure 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.

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

virtual bool npl::MRImage::indexInsideFOV	(	size_t	len,
		const int64_t *	xyz
	)		const

pure 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

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

virtual int npl::MRImage::indexToPoint	(	size_t	len,
		const int64_t *	xyz,
		double *	ras
	)		const

pure virtual

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

virtual int npl::MRImage::indexToPoint	(	size_t	len,
		const double *	xyz,
		double *	ras
	)		const

pure 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

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

const double& npl::MRImage::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.

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

virtual

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 ( )

inline

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

virtual

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.

virtual size_t npl::NDArray::ndim ( ) const

pure virtualinherited

Implemented in npl::NDArrayStore< D, T >, npl::NDArrayStore< D, double >, npl::NDArrayStore< 1, double >, npl::NDArrayStore< 2, double >, and npl::NDArrayStore< 3, double >.

void npl::MRImage::orientDefault ( )

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

virtual int npl::MRImage::orientVector	(	size_t	len,
		const double *	xyz,
		double *	ras
	)		const

pure 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

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

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

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

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

virtual bool npl::MRImage::pointInsideFOV	(	size_t	len,
		const double *	ras
	)		const

pure 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.

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

virtual int npl::MRImage::pointToIndex	(	size_t	len,
		const double *	ras,
		double *	xyz
	)		const

pure 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

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

virtual int npl::MRImage::pointToIndex	(	size_t	len,
		const double *	ras,
		int64_t *	index
	)		const

pure 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

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

void npl::MRImage::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.

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`
	)

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
	)

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
	)

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 )

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

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

virtual int64_t npl::NDArray::tlen ( ) const

pure virtualinherited

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

Implemented in npl::NDArrayStore< D, T >, npl::NDArrayStore< D, double >, npl::NDArrayStore< 1, double >, npl::NDArrayStore< 2, double >, and npl::NDArrayStore< 3, double >.

virtual PixelT npl::NDArray::type ( ) const

pure virtualinherited

Return enum PixelT type of pixels.

Returns: Type of values stored

Implemented in npl::NDArrayStore< D, T >, npl::NDArrayStore< D, double >, npl::NDArrayStore< 1, double >, npl::NDArrayStore< 2, double >, and npl::NDArrayStore< 3, double >.

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
	)

virtual int npl::MRImage::write	(	std::string	filename,
		double	version = `1`
	)		const

pure virtual

Write the image to a nifti file.

Parameters

filename	Filename
version	Version of nifti to use

Returns: 0 if successful

Implements npl::NDArray.

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

virtual int npl::MRImage::writeNifti1Image ( gzFile file ) const

protectedpure virtual

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

virtual int npl::MRImage::writeNifti2Image ( gzFile file ) const

protectedpure virtual

Implemented in npl::MRImageStore< D, T >, npl::MRImageStore< 3, double >, npl::MRImageStore< 4, double >, and npl::MRImageStore< 5, double >.

virtual void npl::NDArray::zero ( )

pure virtualinherited

Sets all elements to zero.

Implemented in npl::NDArrayStore< D, T >, npl::NDArrayStore< D, double >, npl::NDArrayStore< 1, double >, npl::NDArrayStore< 2, double >, and npl::NDArrayStore< 3, double >.

Friends And Related Function Documentation

ptr<MRImage> readNiftiImage	(	gzFile	file,
		bool	verbose
	)

friend

Member Data Documentation

CoordinateT npl::MRImage::m_coordinate

Definition at line 675 of file mrimage.h.

MatrixXd npl::MRImage::m_direction

protected

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

Definition at line 672 of file mrimage.h.

MatrixXd npl::MRImage::m_inv_direction

protected

Inverse of Direction Matrix.

Definition at line 719 of file mrimage.h.

VectorXd npl::MRImage::m_origin

protected

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

Definition at line 673 of file mrimage.h.

double npl::MRImage::m_slice_duration

Definition at line 685 of file mrimage.h.

int npl::MRImage::m_slice_end

Definition at line 687 of file mrimage.h.

SliceOrderT npl::MRImage::m_slice_order

Definition at line 700 of file mrimage.h.

int npl::MRImage::m_slice_start

Definition at line 686 of file mrimage.h.

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

Definition at line 703 of file mrimage.h.

int npl::MRImage::m_slicedim

Definition at line 674 of file mrimage.h.

VectorXd npl::MRImage::m_spacing

protected

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.

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

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation