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. More...

virtual void	reset ()
	Makes sure we will ignore any previous call to set-up() More...

Succeeded	apply (TargetT &data)
	Calls set_up() (if not already done before) and process data in-place. More...

Succeeded	apply (TargetT &out_data, const TargetT &in_data)
	Calls set_up() (if not already done before) and process in_data, putting the result in out_data. More...

bool	parse (std::istream &f)

bool	parse (const char *const filename)

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 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 More...

void	start_timers (bool do_reset=false) const
	start all timers kept by this object More...

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 = "HUToMu"

Protected Member Functions
void	set_defaults () override
	sets default values More...

void	initialise_keymap () override
	Initialise all keywords.

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

Succeeded	virtual_set_up (const TargetT &image) override
	just checks if all variables are set More...

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
	Performs actual operation (in-place)

Protected Member Functions inherited from stir::ParsingObject
virtual void	set_key_values ()
	This will be called before parsing or parameter_info is called. More...

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. More...

Static Public Member Functions inherited from stir::RegisteredObject< Root >
static Root *	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 Root *	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< Root >
typedef Root (	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< Root >
static RegistryType &	registry ()
	Static function returning the registry. More...

Protected Attributes inherited from stir::ParsingObject
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 $a=a1, b=b1$ if $\mathrm{HI} < \mathrm{break}$ , and $a2,b2$ otherwise.

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

Member Function Documentation

◆ 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.

◆ 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.

◆ 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 stir::error(), stir::info(), and stir::round().

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

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

Public Member Functions

Static Public Attributes

Protected Member Functions

Additional Inherited Members

Detailed Description

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

Member Function Documentation

◆ set_defaults()

◆ post_processing()

◆ virtual_set_up()

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