Reads simple VTK files. More...

#include <WReaderVTK.h>

Inheritance diagram for WReaderVTK:

Collaboration diagram for WReaderVTK:

Public Member Functions
	WReaderVTK (std::string fname)
	Constructs and makes a new VTK reader for separate thread start. More...

virtual	~WReaderVTK () throw ()
	Destroys this instance and closes the file. More...

virtual std::shared_ptr< WDataSet >	read ()
	Reads the data file and creates a dataset out of it. More...

Public Member Functions inherited from WReader
	WReader (std::string fname)
	Creates a read object for file reading. More...

OW_API_DEPRECATED void	setFileName (std::string fname)
	Reset the file name and checks if it exists. More...

void	setFilename (std::string fname)
	Reset the file name and checks if it exists. More...

Protected Member Functions
bool	readHeader ()
	Read VTK header from file. More...

std::shared_ptr< WGridRegular3D >	readStructuredPoints ()
	Read VTK Domain specification and create a matching grid. More...

std::shared_ptr< WGridRegular3D >	readRectilinearGrid ()
	Read VTK Domain specification and create a matching grid. More...

std::shared_ptr< WValueSetBase >	readData (std::shared_ptr< WGridRegular3D > const &grid)
	Read domain information for structured points. More...

std::shared_ptr< WValueSetBase >	readScalars (size_t nbScalars, const std::string &name)
	Read VTK SCALARS field. More...

std::shared_ptr< WValueSetBase >	readVectors (size_t nbVectors, const std::string &name)
	Read VTK SCALARS field. More...

std::shared_ptr< WValueSetBase >	readHARDI (std::size_t nbPoints, std::size_t nbGradients, const std::string &)
	Read HARDI data from the file. More...

std::shared_ptr< WValueSetBase >	readTensors (size_t nbTensors, const std::string &name)
	Read VTK TENSORS field. More...

Protected Attributes
std::vector< std::string >	m_header
	VTK header of the read file. More...

std::shared_ptr< std::ifstream >	m_ifs
	Pointer to the input file stream reader. More...

Protected Attributes inherited from WReader
std::string	m_fname
	Absolute path of the file to read from. More...

Private Types
enum	DomainType { STRUCTURED_POINTS , RECTILINEAR_GRID , UNSUPPORTED_DOMAIN }
	The types of domains supported so far. More...

enum	AttributeType { SCALARS , VECTORS , TENSORS , ARRAYS , UNSUPPORTED_ATTRIBUTE }
	The types of attributes supported so far. More...

Private Member Functions
std::string	getLine (const std::string &desc)
	Reads the next line from current position in stream of the fiber VTK file. More...

void	readCoords (std::string const &name, std::size_t dim, std::vector< float > &coords)
	Read the coordinates of the dataset's domain. More...

void	readValuesFromFile (std::vector< float > &values, std::size_t numValues)
	Read values from the file. More...

std::shared_ptr< std::vector< WVector3d > >	readGradients ()
	Read gradients from a gradients file which has the same basename as the data file and ends in .bvec. More...

template<typename T >
T	getLexicalCast (std::string stringValue, const std::string &errMsg) const
	Try to cast from the given string to the template value T. More...

Private Attributes
std::shared_ptr< WDataSet >	m_newDataSet
	reference to the currently loading data set More...

std::shared_ptr< WGridRegular3D >	m_newGrid
	reference to the currently loading grid More...

bool	m_isASCII
	internal flag whether we read ascii or binary More...

DomainType	m_domainType
	The type of domain specified in the file. More...

AttributeType	m_attributeType
	The type of the attributes first read from the file. More...

Friends
class	WReaderVTKTest
	allow member access by the test class More...

Detailed Description

Reads simple VTK files.

For VTK just see http://www.vtk.org. Currently only a subset of the legacy format is supported.

Formats read: Original ASCII and BINARY. The xml format is not supported. Grids read are: STRUCTURED_POINTS, RECTILINEAR_GRID is interpreted as a grid with equal spacing per coordinate axis Data types read: SCALARS, VECTORS, TENSORS

Endianess is kept as on the platform, so for intel hosts, most files, which are typically stored in little endian, are not readable if they are binary files.

Definition at line 56 of file WReaderVTK.h.

Member Enumeration Documentation

◆ AttributeType

enum WReaderVTK::AttributeType

private

The types of attributes supported so far.

Enumerator
SCALARS	scalar data
VECTORS	vector data
TENSORS	tensor data
ARRAYS	array data
UNSUPPORTED_ATTRIBUTE	anything else

Definition at line 181 of file WReaderVTK.h.

◆ DomainType

enum WReaderVTK::DomainType

private

The types of domains supported so far.

Enumerator
STRUCTURED_POINTS	structured points
RECTILINEAR_GRID	rectilinear grid
UNSUPPORTED_DOMAIN	anything else

Definition at line 168 of file WReaderVTK.h.

Constructor & Destructor Documentation

◆ WReaderVTK()

WReaderVTK::WReaderVTK ( std::string fname )

explicit

Constructs and makes a new VTK reader for separate thread start.

Parameters

fname File name where to read data from

Exceptions

WDHNoSuchFile

Definition at line 49 of file WReaderVTK.cpp.

◆ ~WReaderVTK()

WReaderVTK::~WReaderVTK	(	)
throw	(
	)

virtual

Destroys this instance and closes the file.

Definition at line 54 of file WReaderVTK.cpp.

Member Function Documentation

◆ getLexicalCast()

template<typename T >

T WReaderVTK::getLexicalCast	(	std::string	stringValue,
		const std::string &	errMsg
	)		const

inlineprivate

Try to cast from the given string to the template value T.

If the cast fails a WDHParseError is thrown.

Exceptions

WDHParseError

Parameters

stringValue	The string to cast from
errMsg	Error message incase the cast fails

Returns: The casted value from the given string.

Definition at line 266 of file WReaderVTK.h.

References WReader::m_fname.

◆ getLine()

std::string WReaderVTK::getLine ( const std::string & desc )

private

Reads the next line from current position in stream of the fiber VTK file.

Parameters

desc	In case of trouble while reading, this gives information in the error message about what was tried to read

Exceptions

WDHIOFailure,WDHParseError

Returns: Next line as string.

Definition at line 545 of file WReaderVTK.cpp.

References WReader::m_fname, and m_ifs.

Referenced by readCoords(), readData(), readHARDI(), readHeader(), readRectilinearGrid(), readScalars(), readStructuredPoints(), readTensors(), readValuesFromFile(), and readVectors().

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◆ read()

std::shared_ptr< WDataSet > WReaderVTK::read ( )

virtual

Reads the data file and creates a dataset out of it.

Returns: Reference to the dataset.

Definition at line 58 of file WReaderVTK.cpp.

References ARRAYS, wlog::error(), m_attributeType, m_domainType, WReader::m_fname, m_ifs, readData(), readGradients(), readHeader(), readRectilinearGrid(), readStructuredPoints(), RECTILINEAR_GRID, SCALARS, STRUCTURED_POINTS, TENSORS, and VECTORS.

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◆ readCoords()

void WReaderVTK::readCoords	(	std::string const &	name,
		std::size_t	dim,
		std::vector< float > &	coords
	)

private

Read the coordinates of the dataset's domain.

Parameters

name	The name to look for in the first line.
dim	The number of coordinates.
coords	The resulting vector of coordinates.

Definition at line 316 of file WReaderVTK.cpp.

References getLine(), readValuesFromFile(), string_utils::tokenize(), and string_utils::toLower().

Referenced by readRectilinearGrid().

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◆ readData()

std::shared_ptr< WValueSetBase > WReaderVTK::readData ( std::shared_ptr< WGridRegular3D > const & grid )

protected

Read domain information for structured points.

Parameters

grid	The grid constructed from the domain information.

Returns: The value set containing the values read from the file or an invalid pointer if anything went wrong.

Definition at line 493 of file WReaderVTK.cpp.

References ARRAYS, getLine(), m_attributeType, readHARDI(), readScalars(), readTensors(), readVectors(), SCALARS, TENSORS, string_utils::tokenize(), string_utils::toUpper(), and VECTORS.

Referenced by read().

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◆ readGradients()

std::shared_ptr< std::vector< WVector3d > > WReaderVTK::readGradients ( )

private

Read gradients from a gradients file which has the same basename as the data file and ends in .bvec.

Returns: A pointer to a vector of gradients.

Definition at line 134 of file WReaderVTK.cpp.

References WReader::m_fname.

Referenced by read().

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◆ readHARDI()

std::shared_ptr< WValueSetBase > WReaderVTK::readHARDI	(	std::size_t	nbPoints,
		std::size_t	nbGradients,
		const std::string &
	)

protected

Read HARDI data from the file.

Parameters

nbPoints	The number of voxels.
nbGradients	The number of gradients for this HARDI dataset.

Returns: The data read as a value set of floats.

Definition at line 463 of file WReaderVTK.cpp.

References getLine(), m_ifs, readValuesFromFile(), string_utils::tokenize(), and string_utils::toUpper().

Referenced by readData().

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◆ readHeader()

bool WReaderVTK::readHeader ( )

protected

Read VTK header from file.

Sets the m_isASCII member accordingly.

Returns: true, if the header was valid

Definition at line 186 of file WReaderVTK.cpp.

References wlog::error(), getLine(), m_domainType, WReader::m_fname, m_header, m_isASCII, RECTILINEAR_GRID, STRUCTURED_POINTS, and wlog::warn().

Referenced by read().

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◆ readRectilinearGrid()

std::shared_ptr< WGridRegular3D > WReaderVTK::readRectilinearGrid ( )

protected

Read VTK Domain specification and create a matching grid.

Returns: The constructed grid or an invalid pointer if any problem occurred.

Definition at line 289 of file WReaderVTK.cpp.

References getLine(), readCoords(), string_utils::tokenize(), string_utils::toLower(), and wlog::warn().

Referenced by read().

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◆ readScalars()

std::shared_ptr< WValueSetBase > WReaderVTK::readScalars	(	size_t	nbScalars,
		const std::string &	name
	)

protected

Read VTK SCALARS field.

Postcondition: the data set pointer is set to the data set constructed of the current grid and the read scalar values

Parameters

nbScalars	the number of scalars to read
name	the name of the data set that may be overwritten by information in the scalars line

Returns: The resulting value set.

Definition at line 368 of file WReaderVTK.cpp.

References getLine(), m_ifs, readValuesFromFile(), string_utils::tokenize(), and string_utils::toUpper().

Referenced by readData().

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◆ readStructuredPoints()

std::shared_ptr< WGridRegular3D > WReaderVTK::readStructuredPoints ( )

protected

Read VTK Domain specification and create a matching grid.

Returns: The constructed grid or an invalid pointer if any problem occurred.

Definition at line 245 of file WReaderVTK.cpp.

References getLine(), string_utils::tokenize(), string_utils::toLower(), and WGridTransformOrthoTemplate< T >::translate().

Referenced by read().

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◆ readTensors()

std::shared_ptr< WValueSetBase > WReaderVTK::readTensors	(	size_t	nbTensors,
		const std::string &	name
	)

protected

Read VTK TENSORS field.

Postcondition: the data set pointer is set to the data set constructed of the current grid and the read tensor values

Parameters

nbTensors	the number of tensors to read
name	the name of the data set that may be overwritten by information in the tensors line

Returns: The resulting value set.

Definition at line 418 of file WReaderVTK.cpp.

References ARRAYS, getLine(), m_attributeType, m_ifs, readValuesFromFile(), string_utils::tokenize(), and string_utils::toUpper().

Referenced by readData().

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◆ readValuesFromFile()

void WReaderVTK::readValuesFromFile	(	std::vector< float > &	values,
		std::size_t	numValues
	)

private

Read values from the file.

The m_isASCII flag must be initialized accordingly.

Parameters

values	The values read from the file.
numValues	The number of values to read.

Definition at line 328 of file WReaderVTK.cpp.

References wlog::debug(), getLine(), m_ifs, m_isASCII, and string_utils::tokenize().

Referenced by readCoords(), readHARDI(), readScalars(), readTensors(), and readVectors().

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◆ readVectors()

std::shared_ptr< WValueSetBase > WReaderVTK::readVectors	(	size_t	nbVectors,
		const std::string &	name
	)

protected

Read VTK SCALARS field.

Postcondition: the data set pointer is set to the data set constructed of the current grid and the read vector values

Parameters

nbVectors	the number of vectors to read
name	the name of the data set that may be overwritten by information in the vectors line

Returns: The resulting value set.

Definition at line 388 of file WReaderVTK.cpp.

References getLine(), m_ifs, readValuesFromFile(), string_utils::tokenize(), and string_utils::toUpper().

Referenced by readData().

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Friends And Related Function Documentation

◆ WReaderVTKTest

friend class WReaderVTKTest

friend

allow member access by the test class

Definition at line 59 of file WReaderVTK.h.

Member Data Documentation

◆ m_attributeType

AttributeType WReaderVTK::m_attributeType

private

The type of the attributes first read from the file.

Definition at line 263 of file WReaderVTK.h.

Referenced by read(), readData(), and readTensors().

◆ m_domainType

DomainType WReaderVTK::m_domainType

private

The type of domain specified in the file.

Definition at line 260 of file WReaderVTK.h.

Referenced by read(), and readHeader().

◆ m_header

std::vector< std::string > WReaderVTK::m_header

protected

VTK header of the read file.

Definition at line 162 of file WReaderVTK.h.

Referenced by readHeader().

◆ m_ifs

std::shared_ptr< std::ifstream > WReaderVTK::m_ifs

protected

Pointer to the input file stream reader.

Definition at line 164 of file WReaderVTK.h.

Referenced by getLine(), read(), readHARDI(), readScalars(), readTensors(), readValuesFromFile(), and readVectors().

◆ m_isASCII

bool WReaderVTK::m_isASCII

private

internal flag whether we read ascii or binary

Definition at line 257 of file WReaderVTK.h.

Referenced by readHeader(), and readValuesFromFile().

◆ m_newDataSet

std::shared_ptr< WDataSet > WReaderVTK::m_newDataSet

private

reference to the currently loading data set

Definition at line 247 of file WReaderVTK.h.

◆ m_newGrid

std::shared_ptr< WGridRegular3D > WReaderVTK::m_newGrid

private

reference to the currently loading grid

Definition at line 252 of file WReaderVTK.h.

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

Public Member Functions

Protected Member Functions

Protected Attributes

Private Types

Private Member Functions

Private Attributes

Friends

Detailed Description

Member Enumeration Documentation

◆ AttributeType

◆ DomainType

Constructor & Destructor Documentation

◆ WReaderVTK()

◆ ~WReaderVTK()

Member Function Documentation

◆ getLexicalCast()

◆ getLine()

◆ read()

◆ readCoords()

◆ readData()

◆ readGradients()

◆ readHARDI()

◆ readHeader()

◆ readRectilinearGrid()

◆ readScalars()

◆ readStructuredPoints()

◆ readTensors()

◆ readValuesFromFile()

◆ readVectors()

Friends And Related Function Documentation

◆ WReaderVTKTest

Member Data Documentation

◆ m_attributeType

◆ m_domainType

◆ m_header

◆ m_ifs

◆ m_isASCII

◆ m_newDataSet

◆ m_newGrid