This class is used to iterate through an N-Dimensional array. More...

#include <iterators.h>

Public Member Functions
	ChunkIter ()
	Default constructor. Note, this will segfault if you don't use setArray to set the target NDArray/Image. More...

	ChunkIter (std::shared_ptr< NDArray > in)

void	setArray (ptr< NDArray > in)

ChunkIter &	operator++ ()
	Prefix increment operator. More...

ChunkIter &	operator-- ()
	Prefix decrement operator. More...

ChunkIter &	nextChunk ()
	NextChunk. More...

ChunkIter &	prevChunk ()
	Prefix decrement operator. More...

T	operator* () const
	Dereference operator. More...

T	get () const
	Dereference operator. More...

void	set (T v)
	Dereference operator. More...

void	goBegin ()
	Go to beginning of iteration. More...

void	goEnd ()
	Go to end of iteration. More...

bool	isEnd () const
	Are we one past the last element? More...

bool	eof () const
	Are we one past the last element? More...

bool	isBegin () const
	Are we at the first element. More...

bool	operator== (const ChunkIter &other) const
	Whether the position and parent are the same as another. More...

bool	operator!= (const ChunkIter &other) const
	Whether the position and parent are different from another. More...

bool	operator< (const ChunkIter &other) const
	If the parents are different then false, if they are the same, returns whether this iterator is before the other. More...

bool	operator> (const ChunkIter &other) const
	If the parents are different then false, if they are the same, returns whether this iterator is after the other. More...

bool	operator<= (const ChunkIter &other) const
	If the parents are different then false, if they are the same, returns whether this iterator is the same or before the other. More...

bool	operator>= (const ChunkIter &other) const
	If the parents are different then false, if they are the same, returns whether this iterator is the same or after the other. More...

void	setDim (size_t ndim, const size_t *dim)
	Sets the dimensionality of iteration, and the dimensions of the image. More...

bool	isChunkBegin () const
	Returns true when we have reached the end of the chunk. More...

bool	isChunkEnd () const
	Returns true when we have reached the end of the chunk. More...

bool	eoc () const
	Returns true when we have reached the end of the chunk. More...

void	goChunkBegin ()
	Go to the beginning for the current chunk. More...

void	goChunkEnd ()
	Jump to the end of current chunk. More...

void	goIndex (size_t len, int64_t *newpos)
	Jump to the given position, additional values in newpos beyond dim will be ignored. Any values missing due to ndim > len will be treated as zeros. More...

void	goIndex (std::vector< int64_t > newpos)
	Jump to the given position. More...

void	index (size_t len, int64_t *index) const
	Places the first len dimension in the given array. If the number of dimensions exceed the len then the additional dimensions will be ignored, if len exceeds the dimensionality then index[dim...len-1] = 0. In other words index will be completely overwritten in the most sane way possible if the internal dimensions and size index differ. More...

void	index (size_t len, int *index) const
	Places the first len dimension in the given array. If the number of dimensions exceed the len then the additional dimensions will be ignored, if len exceeds the dimensionality then index[dim...len-1] = 0. In other words index will be completely overwritten in the most sane way possible if the internal dimensions and size index differ. More...

void	index (size_t len, double *index) const
	Places the first len dimension in the given array. If the number of dimensions exceed the len then the additional dimensions will be ignored, if len exceeds the dimensionality then index[dim...len-1] = 0. In other words index will be completely overwritten in the most sane way possible if the internal dimensions and size index differ. More...

void	index (std::vector< int64_t > &ind) const
	Places the first len dimension in the given array. If the number of dimensions exceed the len then the additional dimensions will be ignored, if len exceeds the dimensionality then index[dim...len-1] = 0. In other words index will be completely overwritten in the most sane way possible if the internal dimensions and size index differ. More...

void	index (std::vector< int > &ind) const
	Places the first len dimension in the given array. If the number of dimensions exceed the len then the additional dimensions will be ignored, if len exceeds the dimensionality then index[dim...len-1] = 0. In other words index will be completely overwritten in the most sane way possible if the internal dimensions and size index differ. More...

void	index (std::vector< double > &ind) const
	Places the first len dimension in the given array. If the number of dimensions exceed the len then the additional dimensions will be ignored, if len exceeds the dimensionality then index[dim...len-1] = 0. In other words index will be completely overwritten in the most sane way possible if the internal dimensions and size index differ. More...

int64_t	index (size_t dd) const
	Returns the index in the specified dimension. More...

size_t	linIndex () const
	get linear position of current point More...

int64_t	getStride (size_t dd)
	get stride in specified dimension More...

void	setROI (size_t len, const size_t roisize, const int64_t roistart=NULL)
	Sets the region of interest, with lower bound of 0. During iteration or any motion the position will not move outside the specified range. Invalidates position. More...

void	setROI (const std::vector< std::pair< int64_t, int64_t >> &roi)
	Sets the region of interest. During iteration or any motion the position will not move outside the specified range. Extra elements in roi beyond the number of dimensions, are ignored. More...

void	setChunkSize (size_t len, const int64_t *sizes, bool defunity=false)
	Set the sizes of chunks for each dimension. Chunks will end every N steps in each of the provided dimension, with the caveout that 0 indicates no breaks in the given dimension. So size = {0, 2, 2} will cause chunks to after $\{N_x-1, 1, 1\}$ . $\{0,0,0\}$ (the default) indicate * that the entire image will be iterated and only one chunk will be used. Defunity will cause the default to be 1 for non-specified dimensions. More...

void	setChunkSize (size_t len, const size_t *sizes, bool defunity=false)
	Set the sizes of chunks for each dimension. Chunks will end every N steps in each of the provided dimension, with the caveout that 0 indicates no breaks in the given dimension. So size = {0, 2, 2} will cause chunks to after $\{N_x-1, 1, 1\}$ . $\{0,0,0\}$ (the default) indicate * that the entire image will be iterated and only one chunk will be used. Defunity will cause the default to be 1 for non-specified dimensions. More...

void	setLineChunk (size_t dir)
	Sets the chunk sizes so that each chunk is a line in the given dimension. This would be analogous to itk's linear iterator. Usage: More...

void	setOrder (const std::vector< size_t > &order, bool revorder=false)
	Sets the order of iteration from ++/– operators. More...

void	setOrder (std::initializer_list< size_t > order, bool revorder=false)
	Sets the order of iteration from ++/– operators. More...

const std::vector< size_t > &	getOrder () const
	Returns the array giving the order of dimension being traversed. So 3,2,1,0 would mean that the next point in dimension 3 will be next, when wrapping the next point in 2 is visited, when that wraps the next in one and so on. More...

Protected Attributes
size_t	m_linfirst

size_t	m_chunkfirst

bool	m_end

bool	m_chunkend

size_t	m_linpos

std::vector< int64_t >	m_pos

std::vector< std::pair< int64_t, int64_t > >	m_chunk

std::vector< size_t >	m_order

std::vector< std::pair< int64_t, int64_t > >	m_roi

std::vector< int64_t >	m_chunksizes

size_t	m_ndim

std::vector< size_t >	m_dim

std::vector< size_t >	m_strides

Detailed Description

template<typename T = double>
class npl::ChunkIter< T >

This class is used to iterate through an N-Dimensional array.

Unlike NDIter it breaks the NDArray into chunks. Iteration stops at the end of each chunk until nextChunk is called. By default only one chunk is used, equal to the entire image. Use setBreaks() to set the frequency of chunks. The input to setBreaks() is an array of integers, where the next chunk occurs when distbreak == 0, with the special property that break=0 indicates no breaks for the dimension. So for a 3D image, setBreaks({1,0,0}) will stop every time a new x-values is reached. Note that the affects the order of iteration, so x cannot be the fastest iterator. setChunkSize() is an alias for setBreaks. Note that in cases where breaksize != 0, for example image size = 5 and break = 3, chunk sizes will differ during the course of iteration!

Order may still be set to decide the order of iteration. The first member of setOrder will be the fastest moving, and the last will be the slowest. Any dimensions not included in the order vector will be slower than the last member of order. Note that order will not necessarily be strictly obeyed when more than one chunk size is > 0. For isntance if setBreaks({1,1,0}), setOrder({0,1,2}) are used, then all of 2 will visited before we iterate in 0 or 1, because otherwise we would be stepping across chunks.

Template Parameters

T

Definition at line 1520 of file iterators.h.

Constructor & Destructor Documentation

template<typename T = double>

npl::ChunkIter< T >::ChunkIter ( )

inline

Default constructor. Note, this will segfault if you don't use setArray to set the target NDArray/Image.

Definition at line 1528 of file iterators.h.

template<typename T = double>

npl::ChunkIter< T >::ChunkIter ( std::shared_ptr< NDArray > in )

inline

Definition at line 1530 of file iterators.h.

Member Function Documentation

bool npl::ChunkSlicer::eoc ( ) const

inlineinherited

Returns true when we have reached the end of the chunk.

Returns: Are we ready for the next chunk?

Definition at line 460 of file slicer.h.

template<typename T = double>

bool npl::ChunkIter< T >::eof ( ) const

inline

Are we one past the last element?

Definition at line 1714 of file iterators.h.

template<typename T = double>

T npl::ChunkIter< T >::get ( ) const

inline

Dereference operator.

Returns: current value

Definition at line 1675 of file iterators.h.

const std::vector<size_t>& npl::ChunkSlicer::getOrder ( ) const

inlineinherited

Returns the array giving the order of dimension being traversed. So 3,2,1,0 would mean that the next point in dimension 3 will be next, when wrapping the next point in 2 is visited, when that wraps the next in one and so on.

Returns: Order of dimensions

Definition at line 784 of file slicer.h.

int64_t npl::ChunkSlicer::getStride ( size_t dd )

inlineinherited

get stride in specified dimension

Returns: returns stride (change in linear index given a position)

Definition at line 655 of file slicer.h.

template<typename T = double>

void npl::ChunkIter< T >::goBegin ( )

inline

Go to beginning of iteration.

Definition at line 1699 of file iterators.h.

void npl::ChunkSlicer::goChunkBegin ( )

inherited

Go to the beginning for the current chunk.

void npl::ChunkSlicer::goChunkEnd ( )

inherited

Jump to the end of current chunk.

template<typename T = double>

void npl::ChunkIter< T >::goEnd ( )

inline

Go to end of iteration.

Definition at line 1704 of file iterators.h.

void npl::ChunkSlicer::goIndex	(	size_t	len,
		int64_t *	newpos
	)

inherited

Jump to the given position, additional values in newpos beyond dim will be ignored. Any values missing due to ndim > len will be treated as zeros.

Parameters

len	length of newpos array
newpos	Position to move to

void npl::ChunkSlicer::goIndex ( std::vector< int64_t > newpos )

inherited

Jump to the given position.

Parameters

newpos location to move to

void npl::ChunkSlicer::index	(	size_t	len,
		int64_t *	index
	)		const

inherited

Places the first len dimension in the given array. If the number of dimensions exceed the len then the additional dimensions will be ignored, if len exceeds the dimensionality then index[dim...len-1] = 0. In other words index will be completely overwritten in the most sane way possible if the internal dimensions and size index differ.

Parameters

len	size of index array
index	output index variable

void npl::ChunkSlicer::index	(	size_t	len,
		int *	index
	)		const

inherited

Places the first len dimension in the given array. If the number of dimensions exceed the len then the additional dimensions will be ignored, if len exceeds the dimensionality then index[dim...len-1] = 0. In other words index will be completely overwritten in the most sane way possible if the internal dimensions and size index differ.

Parameters

len	size of index
index	output index variable

void npl::ChunkSlicer::index	(	size_t	len,
		double *	index
	)		const

inherited

Places the first len dimension in the given array. If the number of dimensions exceed the len then the additional dimensions will be ignored, if len exceeds the dimensionality then index[dim...len-1] = 0. In other words index will be completely overwritten in the most sane way possible if the internal dimensions and size index differ.

Parameters

len	size of index
index	output index variable

void npl::ChunkSlicer::index ( std::vector< int64_t > & ind ) const

inlineinherited

Places the first len dimension in the given array. If the number of dimensions exceed the len then the additional dimensions will be ignored, if len exceeds the dimensionality then index[dim...len-1] = 0. In other words index will be completely overwritten in the most sane way possible if the internal dimensions and size index differ.

Parameters

ind	output index variable

Definition at line 596 of file slicer.h.

void npl::ChunkSlicer::index ( std::vector< int > & ind ) const

inlineinherited

Places the first len dimension in the given array. If the number of dimensions exceed the len then the additional dimensions will be ignored, if len exceeds the dimensionality then index[dim...len-1] = 0. In other words index will be completely overwritten in the most sane way possible if the internal dimensions and size index differ.

Parameters

ind	output index variable

Definition at line 610 of file slicer.h.

void npl::ChunkSlicer::index ( std::vector< double > & ind ) const

inlineinherited

Places the first len dimension in the given array. If the number of dimensions exceed the len then the additional dimensions will be ignored, if len exceeds the dimensionality then index[dim...len-1] = 0. In other words index will be completely overwritten in the most sane way possible if the internal dimensions and size index differ.

Parameters

ind	output index variable

Definition at line 624 of file slicer.h.

int64_t npl::ChunkSlicer::index ( size_t dd ) const

inlineinherited

Returns the index in the specified dimension.

Parameters

dd	Dimension of image to sample index of

Definition at line 634 of file slicer.h.

template<typename T = double>

bool npl::ChunkIter< T >::isBegin ( ) const

inline

Are we at the first element.

Definition at line 1719 of file iterators.h.

bool npl::ChunkSlicer::isChunkBegin ( ) const

inlineinherited

Returns true when we have reached the end of the chunk.

Returns: Are we ready for the next chunk?

Definition at line 446 of file slicer.h.

bool npl::ChunkSlicer::isChunkEnd ( ) const

inlineinherited

Returns true when we have reached the end of the chunk.

Returns: Are we ready for the next chunk?

Definition at line 453 of file slicer.h.

template<typename T = double>

bool npl::ChunkIter< T >::isEnd ( ) const

inline

Are we one past the last element?

Definition at line 1709 of file iterators.h.

size_t npl::ChunkSlicer::linIndex ( ) const

inlineinherited

get linear position of current point

Returns: returns linear index

Definition at line 645 of file slicer.h.

template<typename T = double>

ChunkIter& npl::ChunkIter< T >::nextChunk ( )

inline

NextChunk.

Returns: new value

Definition at line 1640 of file iterators.h.

template<typename T = double>

bool npl::ChunkIter< T >::operator!= ( const ChunkIter< T > & other ) const

inline

Whether the position and parent are different from another.

Parameters

other

Returns

Definition at line 1740 of file iterators.h.

template<typename T = double>

T npl::ChunkIter< T >::operator* ( ) const

inline

Dereference operator.

Returns: current value

Definition at line 1662 of file iterators.h.

template<typename T = double>

ChunkIter& npl::ChunkIter< T >::operator++ ( )

inline

Prefix increment operator.

Returns: new value

Definition at line 1618 of file iterators.h.

template<typename T = double>

ChunkIter& npl::ChunkIter< T >::operator-- ( )

inline

Prefix decrement operator.

Returns: new value

Definition at line 1629 of file iterators.h.

template<typename T = double>

bool npl::ChunkIter< T >::operator< ( const ChunkIter< T > & other ) const

inline

If the parents are different then false, if they are the same, returns whether this iterator is before the other.

Parameters

other

Returns

Definition at line 1753 of file iterators.h.

template<typename T = double>

bool npl::ChunkIter< T >::operator<= ( const ChunkIter< T > & other ) const

inline

If the parents are different then false, if they are the same, returns whether this iterator is the same or before the other.

Parameters

other

Returns

Definition at line 1795 of file iterators.h.

template<typename T = double>

bool npl::ChunkIter< T >::operator== ( const ChunkIter< T > & other ) const

inline

Whether the position and parent are the same as another.

Parameters

other

Returns

Definition at line 1728 of file iterators.h.

template<typename T = double>

bool npl::ChunkIter< T >::operator> ( const ChunkIter< T > & other ) const

inline

If the parents are different then false, if they are the same, returns whether this iterator is after the other.

Parameters

other

Returns

Definition at line 1774 of file iterators.h.

template<typename T = double>

bool npl::ChunkIter< T >::operator>= ( const ChunkIter< T > & other ) const

inline

If the parents are different then false, if they are the same, returns whether this iterator is the same or after the other.

Parameters

other

Returns

Definition at line 1814 of file iterators.h.

template<typename T = double>

ChunkIter& npl::ChunkIter< T >::prevChunk ( )

inline

Prefix decrement operator.

Returns: new value

Definition at line 1651 of file iterators.h.

template<typename T = double>

void npl::ChunkIter< T >::set ( T v )

inline

Dereference operator.

Returns: current value

Definition at line 1688 of file iterators.h.

template<typename T = double>

void npl::ChunkIter< T >::setArray ( ptr< NDArray > in )

inline

Definition at line 1535 of file iterators.h.

void npl::ChunkSlicer::setChunkSize	(	size_t	len,
		const int64_t *	sizes,
		bool	defunity = `false`
	)

inherited

Set the sizes of chunks for each dimension. Chunks will end every N steps in each of the provided dimension, with the caveout that 0 indicates no breaks in the given dimension. So size = {0, 2, 2} will cause chunks to after $\{N_x-1, 1, 1\}$ . $\{0,0,0\}$ (the default) indicate * that the entire image will be iterated and only one chunk will be used. Defunity will cause the default to be 1 for non-specified dimensions.

Parameters

len	Length of sizes array
sizes	Size of chunk in each dimension. If you multiply together the elements of sizes that is the MAXIMUM number of iterations between chunks. Note however that there could be less if we are at the edge.
defunity	Sets the default to unity rather than 0. Thus unreferenced dimensions will be broken up at each step; so {0,1} for a 4D image will be effectively {0,1,1,1} instead of {0,1,0,0}. This is convenient, for instance, if you want to split up based on volumes, {0,0,0} would stop at the end of each volume, whereas the default would be to treat the entire ND-image as a chunk.

void npl::ChunkSlicer::setChunkSize	(	size_t	len,
		const size_t *	sizes,
		bool	defunity = `false`
	)

inherited

Set the sizes of chunks for each dimension. Chunks will end every N steps in each of the provided dimension, with the caveout that 0 indicates no breaks in the given dimension. So size = {0, 2, 2} will cause chunks to after $\{N_x-1, 1, 1\}$ . $\{0,0,0\}$ (the default) indicate * that the entire image will be iterated and only one chunk will be used. Defunity will cause the default to be 1 for non-specified dimensions.

Parameters

len	Length of sizes array
sizes	Size of chunk in each dimension. If you multiply together the elements of sizes that is the MAXIMUM number of iterations between chunks. Note however that there could be less if we are at the edge.
defunity	Sets the default to unity rather than 0. Thus unreferenced dimensions will be broken up at each step; so {0,1} for a 4D image will be effectively {0,1,1,1} instead of {0,1,0,0}. This is convenient, for instance, if you want to split up based on volumes, {0,0,0} would stop at the end of each volume, whereas the default would be to treat the entire ND-image as a chunk.

void npl::ChunkSlicer::setDim	(	size_t	ndim,
		const size_t *	dim
	)

inherited

Sets the dimensionality of iteration, and the dimensions of the image.

Invalidates position and ROI.

Parameters

ndim	Number of dimension
dim	Dimensions (size)

void npl::ChunkSlicer::setLineChunk ( size_t dir )

inherited

Sets the chunk sizes so that each chunk is a line in the given dimension. This would be analogous to itk's linear iterator. Usage:

it.setLineChunk(0); while(!it.isEnd()) { while(!it.isChunkEnd()) {

++it; } it.nextChunk(); }

Parameters

dir	Dimension to travel linearly along

void npl::ChunkSlicer::setOrder	(	const std::vector< size_t > &	order,
		bool	revorder = `false`
	)

inherited

Sets the order of iteration from ++/– operators.

Parameters

order	vector of priorities, with first element being the fastest iteration and last the slowest. All other dimensions not used will be slower than the last
revorder	Reverse order, in which case the first element of order will have the slowest iteration, and dimensions not specified in order will be faster than those included.

void npl::ChunkSlicer::setOrder	(	std::initializer_list< size_t >	order,
		bool	revorder = `false`
	)

inherited

Sets the order of iteration from ++/– operators.

Parameters

order	vector of priorities, with first element being the fastest iteration and last the slowest. All other dimensions not used will be slower than the last
revorder	Reverse order, in which case the first element of order will have the slowest iteration, and dimensions not specified in order will be faster than those included.

void npl::ChunkSlicer::setROI	(	size_t	len,
		const size_t *	roisize,
		const int64_t *	roistart = `NULL`
	)

inherited

Sets the region of interest, with lower bound of 0. During iteration or any motion the position will not move outside the specified range. Invalidates position.

Invalidates position

Parameters

len	length of roi array
roistart	lower bound of ROI
roisize	Size of ROI (which runs in the block from: [0 to roisize[0]-1,0. to roisize[1]-1, etc]

void npl::ChunkSlicer::setROI ( const std::vector< std::pair< int64_t, int64_t >> & roi )

inherited

Sets the region of interest. During iteration or any motion the position will not move outside the specified range. Extra elements in roi beyond the number of dimensions, are ignored.

Parameters

roi	pair of [min,max] values in the desired hypercube

Member Data Documentation

std::vector<std::pair<int64_t,int64_t> > npl::ChunkSlicer::m_chunk

protectedinherited

Definition at line 803 of file slicer.h.

bool npl::ChunkSlicer::m_chunkend

protectedinherited

Definition at line 798 of file slicer.h.

size_t npl::ChunkSlicer::m_chunkfirst

protectedinherited

Definition at line 796 of file slicer.h.

std::vector<int64_t> npl::ChunkSlicer::m_chunksizes

protectedinherited

Definition at line 808 of file slicer.h.

std::vector<size_t> npl::ChunkSlicer::m_dim

protectedinherited

Definition at line 811 of file slicer.h.

bool npl::ChunkSlicer::m_end

protectedinherited

Definition at line 797 of file slicer.h.

size_t npl::ChunkSlicer::m_linfirst

protectedinherited

Definition at line 784 of file slicer.h.

size_t npl::ChunkSlicer::m_linpos

protectedinherited

Definition at line 801 of file slicer.h.

size_t npl::ChunkSlicer::m_ndim

protectedinherited

Definition at line 810 of file slicer.h.

std::vector<size_t> npl::ChunkSlicer::m_order

protectedinherited

Definition at line 806 of file slicer.h.

std::vector<int64_t> npl::ChunkSlicer::m_pos

protectedinherited

Definition at line 802 of file slicer.h.

std::vector<std::pair<int64_t,int64_t> > npl::ChunkSlicer::m_roi

protectedinherited

Definition at line 807 of file slicer.h.

std::vector<size_t> npl::ChunkSlicer::m_strides

protectedinherited

Definition at line 812 of file slicer.h.

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

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

Public Member Functions

Protected Attributes

Detailed Description

template<typename T = double> class npl::ChunkIter< T >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<typename T = double>
class npl::ChunkIter< T >