A class for finding the coordinate transformation between tracker and scanner coordinate systems. More...

#include "stir_experimental/motion/MatchTrackerAndScanner.h"

Inheritance diagram for stir::MatchTrackerAndScanner:

Public Member Functions
	MatchTrackerAndScanner (const char *const par_filename)

Succeeded	run ()
	finds the match when all parameters have been set More...

const TimeFrameDefinitions &	get_time_frame_defs () const

double	get_frame_start_time (unsigned frame_num) const

double	get_frame_end_time (unsigned frame_num) const

const std::string &	get_image_filename_prefix () const

const RigidObject3DMotion &	get_motion () const

const RigidObject3DTransformation &	get_transformation_from_scanner_coords () const

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

ParsingObject &	operator= (const ParsingObject &)

void	ask_parameters ()

virtual std::string	parameter_info ()

bool	parse (std::istream &f)

bool	parse (const char *const filename)

Protected Member Functions
void	set_defaults () override
	parsing functions

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::ParsingObject
virtual void	set_key_values ()
	This will be called before parsing or parameter_info is called. More...

Protected Attributes
TimeFrameDefinitions	frame_defs

int	scan_start_time_secs_since_1970_UTC

double	_current_frame_end_time

double	_current_frame_start_time

std::string	frame_definition_filename
	parsing variables

double	scan_start_time

std::string	_image_filename_prefix

float	relative_threshold

Protected Attributes inherited from stir::ParsingObject
KeyParser	parser

Detailed Description

A class for finding the coordinate transformation between tracker and scanner coordinate systems.

Input data

You need to have performed a scan where the '0' marker of the tracker is filled with some radioactive material, and the marker is then moved to various stationary positions inside the scanner, while performing a (list-mode) scan, while the tracker is running. Remember: discrete movements.

Then you need to make a frame-definition file where all non-stationary parts are skipped. Then you sort the list mode data into sinograms, and reconstruct images (preferably with large zoom) for each of these discrete positions.

What does it do?

This implements Horn's method, as discussed in detail in Roger Fulton's thesis. Briefly:

for each time frame, we find the centre of gravity (after applying a threshold) in the image as the location of the point source.
for each tracker-sample in the time frame, we find where the tracker says that the 0 marker moved to.
All the data for all time frames is then put through RigidObject3DTransformation::find_closest_transformation to find a least-squares fit between the 2 sets of coordinates.
The class writes various diagnostics to stdout, including the value of the fit.

Note that if you have movement within a time frame, the diagnostics will tell you, but your fit will be wrong.

Example par file

  MoveImage Parameters:=
  ; see TimeFrameDefinitions
  time frame_definition filename := frame_definition_filename

  ; next parameter is optional (and not normally necessary)
  ; it can be used if the frame definitions are relative to another scan as what
  ; is used to for the rigid object motion (i.e. currently the list mode data used
  ;  for the Polaris synchronisation)
  ; scan_start_time_secs_since_1970_UTC


  ; specify motion, see stir::RigidObject3DMotion
  Rigid Object 3D Motion Type := type

  ; optional field to determine relative threshold to apply to
  ; the image before taking the centre of gravity
  ; it is relative to the maximum in each image (i.e. .5 would be at half the maximum)
  ; default is .1
  relative threshold := .2
  ; prefix for finding the images
  ; filenames will be constructed by appending _f#g1d0b0 (and the extension .hv)
  image_filename_prefix :=
  END :=

Warning: Currently the motion object needs to be defined using a transformation_from_scanner_coords file. However, the value of the transformation is completely ignored by the current class.

Member Function Documentation

◆ run()

Succeeded stir::MatchTrackerAndScanner::run ( )

finds the match when all parameters have been set

will store the transformation as part of this object, but also write it to stdout

References stir::error(), stir::find_centre_of_gravity_in_mm(), stir::DiscretisedDensityOnCartesianGrid< num_dimensions, elemT >::get_grid_spacing(), stir::indices_at_maximum(), stir::read_from_file(), stir::square(), stir::threshold_lower(), and stir::warning().

◆ post_processing()

bool stir::MatchTrackerAndScanner::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 stir::warning().

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

/home/sirfuser/devel/STIRdistrib/STIR/src/include/stir_experimental/motion/MatchTrackerAndScanner.h
/home/sirfuser/devel/STIRdistrib/STIR/src/experimental/motion/MatchTrackerAndScanner.cxx

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Function Documentation

◆ run()

◆ post_processing()