Implementation of OutputFileFormat paradigm using the ITK library for writing. More...

#include "stir/IO/ITKOutputFileFormat.h"

Inheritance diagram for stir::ITKOutputFileFormat:

[legend]

Public Member Functions
	ITKOutputFileFormat (const NumericType &=NumericType::FLOAT, const ByteOrder &=ByteOrder::native)

ByteOrder	set_byte_order (const ByteOrder &, const bool warn=false) override
	set byte order used for output More...

Public Member Functions inherited from stir::RegisteredParsingObject< ITKOutputFileFormat, OutputFileFormat< DiscretisedDensity< 3, float > >, OutputFileFormat< DiscretisedDensity< 3, float > > >
std::string	get_registered_name () const override
	Returns Derived::registered_name.

std::string	parameter_info () override
	Returns a string with all parameters and their values, in a form suitable for parsing again.

Public Member Functions inherited from stir::OutputFileFormat< DiscretisedDensity< 3, float > >
	OutputFileFormat (const NumericType &=NumericType::FLOAT, const ByteOrder &=ByteOrder::native)

Succeeded	write_to_file (std::string &filename, const DiscretisedDensity< 3, float > &data) const
	Write a single image to file. More...

Succeeded	write_to_file (const std::string &filename, const DiscretisedDensity< 3, float > &density) const
	write a single image to file More...

NumericType	get_type_of_numbers () const
	get type used for outputting numbers

ByteOrder	get_byte_order ()
	get byte order used for output

float	get_scale_to_write_data () const
	get scale to write the data More...

virtual NumericType	set_type_of_numbers (const NumericType &, const bool warn=false)
	set type used for outputting numbers More...

virtual void	set_byte_order_and_type_of_numbers (ByteOrder &, NumericType &, const bool warn=false)
	set byte order and data type used for output More...

virtual float	set_scale_to_write_data (const float new_scale_to_write_data, const bool warn=false)
	set scale outputting numbers More...

Public Member Functions inherited from stir::ParsingObject
	ParsingObject (const ParsingObject &)

ParsingObject &	operator= (const ParsingObject &)

void	ask_parameters ()

bool	parse (std::istream &f)

bool	parse (const char *const filename)

Public Attributes
std::string	default_extension
	default extension to use if none present More...

Static Public Attributes
static const char *const	registered_name = "ITK"
	Name which will be used when parsing an OutputFileFormat object.

Protected Member Functions
Succeeded	actual_write_to_file (std::string &output_filename, const DiscretisedDensity< 3, float > &density) const override
	virtual function called by write_to_file() More...

void	set_defaults () override
	Set defaults before parsing.

void	initialise_keymap () override
	Initialise all keywords.

bool	post_processing () override
	This will be called at the end of the parsing. More...

Protected Member Functions inherited from stir::OutputFileFormat< DiscretisedDensity< 3, float > >
void	set_defaults () override
	sets value for output data type More...

void	initialise_keymap () override
	sets keys for output data type for parsing More...

bool	post_processing () override
	Checks if parameters have sensible values after parsing. More...

void	set_key_values () override
	overloaded member for ParsingObject::set_key_values() More...

Additional Inherited Members
Static Public Member Functions inherited from stir::RegisteredParsingObject< ITKOutputFileFormat, OutputFileFormat< DiscretisedDensity< 3, float > >, OutputFileFormat< DiscretisedDensity< 3, float > > >
static OutputFileFormat< DiscretisedDensity< 3, float > > *	read_from_stream (std::istream *)
	Construct a new object (of type Derived) by parsing the istream. More...

Static Public Member Functions inherited from stir::OutputFileFormat< DiscretisedDensity< 3, float > >
static shared_ptr< OutputFileFormat< DiscretisedDensity< 3, float > > >	default_sptr ()
	A function to return a default output file format.

Static Public Member Functions inherited from stir::RegisteredObject< OutputFileFormat< DiscretisedDensity< 3, float > > >
static OutputFileFormat< DiscretisedDensity< 3, float > > *	read_registered_object (std::istream *in, const std::string &registered_name)
	Construct a new object (of a type derived from Root, its actual type determined by the registered_name parameter) by parsing the istream. More...

static OutputFileFormat< DiscretisedDensity< 3, float > > *	ask_type_and_parameters ()
	ask the user for the type, and then calls read_registered_object(0, type) More...

static void	list_registered_names (std::ostream &stream)
	List all possible registered names to the stream. More...

Protected Types inherited from stir::RegisteredObject< OutputFileFormat< DiscretisedDensity< 3, float > > >
typedef OutputFileFormat< DiscretisedDensity< 3, float > > (	RootFactory) (std::istream *)
	The type of a root factory is a function, taking an istream* as argument, and returning a Root*.

typedef FactoryRegistry< std::string, RootFactory, interfile_less >	RegistryType
	The type of the registry.

Static Protected Member Functions inherited from stir::RegisteredObject< OutputFileFormat< DiscretisedDensity< 3, float > > >
static RegistryType &	registry ()
	Static function returning the registry. More...

Protected Attributes inherited from stir::OutputFileFormat< DiscretisedDensity< 3, float > >
NumericType	type_of_numbers
	type used for outputting numbers

ByteOrder	file_byte_order
	byte order used for output

float	scale_to_write_data
	scale to write the data More...

Protected Attributes inherited from stir::ParsingObject
KeyParser	parser

Detailed Description

Implementation of OutputFileFormat paradigm using the ITK library for writing.

ITK (http://www.itk.org) has its own registry of file formats, so the current class provides an interface to that code. We translate the STIR data to ITK and then use its writing code. This translation is currently incomplete however.

ITK chooses the file format based on the extension of the filename. This is currently different from STIR. Therefore, this class can be used to write Nifti (.nii), Teem (.nhdr), MetaIO (.mhdr), etc.

In this class, we provide a default extension that will be appended if a filename without extension is used.

Parameters

ITK Output File Format Parameters:=
  default extension:= .nhdr ; current default value
End ITK Output File Format Parameters:=

Member Function Documentation

◆ set_byte_order()

ByteOrder stir::ITKOutputFileFormat::set_byte_order	(	const ByteOrder &	,
		const bool	warn = `false`
	)

overridevirtual

set byte order used for output

Returns type actually used. Calls warning() with some text if the requested type is not supported.

Default implementation accepts any byte order.

Reimplemented from stir::OutputFileFormat< DiscretisedDensity< 3, float > >.

◆ actual_write_to_file()

Succeeded stir::ITKOutputFileFormat::actual_write_to_file	(	std::string &	filename,
		const DiscretisedDensity< 3, float > &	density
	)		const

overrideprotectedvirtual

virtual function called by write_to_file()

This function has to be overloaded by the derived class.

The reason we do not simply make write_to_file() virtual is that we have 2 versions of write_to_file. C++ rules are such that overloading the virtual function in a derived class means that the other version gets hidden. Having the non-virtual write_to_file() call the virtual actual_write_to_file() solves this problem.

Implements stir::OutputFileFormat< DiscretisedDensity< 3, float > >.

References stir::add_extension(), stir::Array< num_dimensions, elemT >::begin_all_const(), stir::DiscretisedDensity< num_dimensions, elemT >::get_LPS_coordinates_for_indices(), stir::Array< num_dimensions, elemT >::get_regular_range(), stir::VoxelsOnCartesianGrid< elemT >::get_voxel_size(), stir::VoxelsOnCartesianGrid< elemT >::get_x_size(), stir::norm(), and stir::warning().

◆ post_processing()

bool stir::ITKOutputFileFormat::post_processing ( )

overrideprotectedvirtual

This will be called at the end of the parsing.

Returns: false if everything OK, true if not

Reimplemented from stir::ParsingObject.

Member Data Documentation

◆ default_extension

std::string stir::ITKOutputFileFormat::default_extension

default extension to use if none present

This will determine the file format used if passing a filename without extension.

Referenced by stir::TestBSplineTransformation::run_transformation().

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

/home/sirfuser/devel/STIRdistrib/STIR/src/include/stir/IO/ITKOutputFileFormat.h
/home/sirfuser/devel/STIRdistrib/STIR/src/IO/ITKOutputFileFormat.cxx

Public Member Functions

Public Attributes

Static Public Attributes

Protected Member Functions