A class in the DataProcessor hierarchy that convert from Hounsfield Units to mu-values. More...

#include "stir/HUToMuImageProcessor.h"

Inheritance diagram for stir::HUToMuImageProcessor< TargetT >:

[legend]

Public Member Functions
	HUToMuImageProcessor ()
	Default constructor.
void	set_slope_filename (const std::string &filename)
	set the JSON filename with the slopes
void	set_manufacturer_name (const std::string &name)
	set the manufacturer name used to select from the JSON entries
void	set_kilovoltage_peak (const float kVp)
	set the CT kVp used to select from the JSON entries
void	set_target_photon_energy (const float gamma_energy)
	set the gamma photon energy (in keV) used to select from the JSON entries
void	apply_scaling_to_HU (TargetT &output_image, const TargetT &input_image) const
	same as apply
void	set_slope (float a1, float a2, float b1, float b2, float breakPoint)
	set the slope without JSON file
Public Member Functions inherited from stir::RegisteredParsingObject< HUToMuImageProcessor< TargetT >, DataProcessor< TargetT >, DataProcessor< TargetT > >
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::DataProcessor< TargetT >
Succeeded	set_up (const TargetT &data)
	Initialises any internal data (if necessary) using data as a template for sizes, sampling distances etc.
virtual void	reset ()
	Makes sure we will ignore any previous call to set-up().
Succeeded	apply (TargetT &data)
	Calls set_up() (if not already done before) and process data in-place.
bool	parse (std::istream &f)
Public Member Functions inherited from stir::ParsingObject
	ParsingObject (const ParsingObject &)
ParsingObject &	operator= (const ParsingObject &)
bool	parse (std::istream &f)
bool	parse (const char *const filename)
void	ask_parameters ()
Public Member Functions inherited from stir::TimedObject
void	reset_timers ()
	reset all timers kept by this object
void	stop_timers () const
	stop all timers kept by this object
void	start_timers (bool do_reset=false) const
	start all timers kept by this object
double	get_CPU_timer_value () const
	get current value of the CPU timer (since first use or last reset)
double	get_wall_clock_timer_value () const
	get current value of the wall-clock timer (since first use or last reset)

Static Public Attributes
static const char *const	registered_name

Protected Member Functions
void	set_defaults () override
	sets default values
void	initialise_keymap () override
	Initialise all keywords.
bool	post_processing () override
	This will be called at the end of the parsing.
Succeeded	virtual_set_up (const TargetT &image) override
	just checks if all variables are set
void	virtual_apply (TargetT &out_density, const TargetT &in_density) const override
	Performs actual operation (virtual_set_up is called before this function).
void	virtual_apply (TargetT &density) const override
virtual void	set_key_values ()
	This will be called before parsing or parameter_info is called.

Additional Inherited Members
Static Public Member Functions inherited from stir::RegisteredParsingObject< HUToMuImageProcessor< TargetT >, DataProcessor< TargetT >, DataProcessor< TargetT > >
static DataProcessor< TargetT > *	read_from_stream (std::istream *)
	Construct a new object (of type Derived) by parsing the istream.
Static Public Member Functions inherited from stir::RegisteredObject< DataProcessor< TargetT > >
static DataProcessor< TargetT > *	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.
static DataProcessor< TargetT > *	ask_type_and_parameters ()
	ask the user for the type, and then calls read_registered_object(0, type)
static void	list_registered_names (std::ostream &stream)
	List all possible registered names to the stream.
Protected Types inherited from stir::RegisteredObject< DataProcessor< TargetT > >
typedef DataProcessor< TargetT > ()	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< DataProcessor< TargetT > >
static RegistryType &	registry ()
	Static function returning the registry.
KeyParser	parser

Detailed Description

template<typename TargetT>
class stir::HUToMuImageProcessor< TargetT >

A class in the DataProcessor hierarchy that convert from Hounsfield Units to mu-values.

This convert HU to mu-values using a piece-wise linear curve. Currently, it supports 2-segment piecewise linear transformations only.

Warning: This does not implement post-filtering to PET resolution, nor resampling to the PET voxel-size.

Parsing from parameter file

The parameters specify a file in JSON format, and the parameters selecting the relevant record.

HUToMu Parameters:=
slope filename := json_filename
; next defaults to GENERIC
manufacturer_name := IN_CAPITALS
; CT tube voltage (defaults to 120)
kilovoltage_peak :=
; gamma energy (defaults to 511 for PET)
target_photon_energy :=
End HUToMu Parameters:=

Format of the slope filename

This file is in JSON format. An example is distributed with STIR. The manufacturer name has to be in capitals. kvp and kev are matched after rounding.

{"scale": {
  "MANUFACTURER": {
    "type": "bilinear",
    "transform": [
      {
        "kvp": 120,
        "kev": 75,
        "a1": 0.16,
        "b1": 1.66e-4,
        "a2": 0.16,
        "b2": 1.48e-4,
        "break": 0
      },
      # more entries like the above
    ]
  }
}
}

This implements the following transformation for every voxel in the image:

$\‍[ \mu = a + b * \mathrm{HU} \‍]$

with if $\mathrm{HI} < \mathrm{break}$ , and $a2,b2$ otherwise.

When adding your own entries, you want avoid a discontinuity at the break point.

Constructor & Destructor Documentation

◆ HUToMuImageProcessor()

template<typename TargetT>

stir::HUToMuImageProcessor< TargetT >::HUToMuImageProcessor ( )

Default constructor.

References HUToMuImageProcessor(), and set_defaults().

Referenced by HUToMuImageProcessor().

Member Function Documentation

◆ set_slope_filename()

template<typename TargetT>

void stir::HUToMuImageProcessor< TargetT >::set_slope_filename ( const std::string & filename )

set the JSON filename with the slopes

References set_slope_filename().

Referenced by set_slope_filename().

◆ set_manufacturer_name()

template<typename TargetT>

void stir::HUToMuImageProcessor< TargetT >::set_manufacturer_name ( const std::string & name )

set the manufacturer name used to select from the JSON entries

References set_manufacturer_name().

Referenced by set_manufacturer_name().

◆ set_kilovoltage_peak()

template<typename TargetT>

void stir::HUToMuImageProcessor< TargetT >::set_kilovoltage_peak ( const float kVp )

set the CT kVp used to select from the JSON entries

References set_kilovoltage_peak().

Referenced by set_kilovoltage_peak().

◆ set_target_photon_energy()

template<typename TargetT>

void stir::HUToMuImageProcessor< TargetT >::set_target_photon_energy ( const float gamma_energy )

set the gamma photon energy (in keV) used to select from the JSON entries

References set_target_photon_energy().

Referenced by set_target_photon_energy().

◆ apply_scaling_to_HU()

template<typename TargetT>

void stir::HUToMuImageProcessor< TargetT >::apply_scaling_to_HU	(	TargetT &	output_image,
		const TargetT &	input_image ) const

same as apply

References apply_scaling_to_HU().

Referenced by apply_scaling_to_HU(), and virtual_apply().

◆ set_slope()

template<typename TargetT>

void stir::HUToMuImageProcessor< TargetT >::set_slope	(	float	a1,
		float	a2,
		float	b1,
		float	b2,
		float	breakPoint )

set the slope without JSON file

References set_slope().

Referenced by set_slope().

◆ set_defaults()

template<typename TargetT>

void stir::HUToMuImageProcessor< TargetT >::set_defaults ( )

overrideprotectedvirtual

sets default values

Sets manufacturer_name to "GENERIC", kilovoltage_peak to 120.F, target_photon_energy to 511.F

Reimplemented from stir::ParsingObject.

References set_defaults(), and stir::ParsingObject::set_defaults().

Referenced by HUToMuImageProcessor(), and set_defaults().

◆ initialise_keymap()

template<typename TargetT>

void stir::HUToMuImageProcessor< TargetT >::initialise_keymap ( )

overrideprotectedvirtual

Initialise all keywords.

Reimplemented from stir::ParsingObject.

References initialise_keymap(), and stir::ParsingObject::initialise_keymap().

Referenced by initialise_keymap().

◆ post_processing()

template<typename TargetT>

bool stir::HUToMuImageProcessor< TargetT >::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.

References post_processing(), and stir::ParsingObject::post_processing().

Referenced by post_processing().

◆ virtual_set_up()

template<typename TargetT>

Succeeded stir::HUToMuImageProcessor< TargetT >::virtual_set_up ( const TargetT & image )

overrideprotectedvirtual

just checks if all variables are set

Todo: could get manufacturer name, kVp from the image later on, when these become available

Implements stir::DataProcessor< TargetT >.

References virtual_set_up().

Referenced by virtual_set_up().

◆ virtual_apply()

template<typename TargetT>

void stir::HUToMuImageProcessor< TargetT >::virtual_apply	(	TargetT &	data,
		const TargetT &	in_data ) const

overrideprotectedvirtual

Performs actual operation (virtual_set_up is called before this function).

Implements stir::DataProcessor< TargetT >.

References apply_scaling_to_HU(), and virtual_apply().

Referenced by virtual_apply().

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

/home/kris/devel/STIRdistrib/STIR/src/include/stir/HUToMuImageProcessor.h
/home/kris/devel/STIRdistrib/STIR/src/buildblock/HUToMuImageProcessor.cxx

Public Member Functions

Static Public Attributes

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ HUToMuImageProcessor()

Member Function Documentation

◆ set_slope_filename()

◆ set_manufacturer_name()

◆ set_kilovoltage_peak()

◆ set_target_photon_energy()

◆ apply_scaling_to_HU()

◆ set_slope()

◆ set_defaults()

◆ initialise_keymap()

◆ post_processing()

◆ virtual_set_up()

◆ virtual_apply()