Items relating to motion and motion correction

Collaboration diagram for Items relating to motion and motion correction:

Files
file	AbsTimeIntervalFromECAT7ACF.cxx
	Declaration of class stir::AbsTimeIntervalFromECAT7ACF.
file	local_motion_registries.cxx
	registration of parsing objects related to motion
file	MatchTrackerAndScanner.cxx
	Implementation of class stir::MatchTrackerAndScanner.
file	NonRigidObjectTransformationUsingBSplines.cxx
	Implementation of class stir::NonRigidObjectTransformationUsingBSplines.
file	Polaris_MT_File.cxx
	Implementation of class stir::Polaris_MT_File.
file	RigidObject3DMotion.cxx
	Declaration of class stir::RigidObject3DMotion.
file	RigidObject3DMotionFromPolaris.cxx
	Implementation of class stir::RigidObject3DMotionFromPolaris.
file	RigidObject3DTransformation.cxx
	implementation of class RigidObject3DTransformation
file	TimeFrameMotion.cxx
	stir::TimeFrameMotion
file	transform_3d_object.cxx
	Functions to re-interpolate an image or projection data to a new coordinate system.
file	list_polaris_info.cxx
	Utility to list information from a Polaris file.
file	bin_interpolate.h
	Functions to interpolate sinograms.
file	MatchTrackerAndScanner.h
	Definition of class stir::MatchTrackerAndScanner.
file	NonRigidObjectTransformationUsingBSplines.h
	Declaration of class stir::NonRigidObjectTransformationUsingBSplines.
file	ObjectTransformation.h
	Declaration of class stir::ObjectTransformation.
file	Polaris_MT_File.h
	Declaration of class stir::Polaris_MT_File.
file	RigidObject3DMotion.h
	Declaration of class stir::RigidObject3DMotion.
file	RigidObject3DMotionFromPolaris.h
	Declaration of class stir::RigidObject3DMotionFromPolaris.
file	RigidObject3DTransformation.h
	Declaration of class stir::RigidObject3DTransformation.
file	TimeFrameMotion.h
	stir::TimeFrameMotion
file	Transform3DObjectImageProcessor.h
	Declaration of class stir::Transform3DObjectImageProcessor.
file	transform_3d_object.h
	Declaration of functions to re-interpolate an image or projection data to a new coordinate system.
file	transform_3d_object.inl
	Functions to re-interpolate an image.

Classes
class	stir::FindMCNormFactors
	Class to compute 'time-efficiency' factors for motino corrected projection data. More...
class	stir::MyApp
	A class for moving an image according to average motion in the frame. More...
class	stir::MoveImage
	A class for moving an image according to average motion in the frame. More...
class	stir::MoveProjData
	A class for moving projection data according to average motion in the frame. More...
class	stir::ReportMovement
	A class for reporting the movement within the frame w.r.t. to the reference position. More...
class	stir::MatchTrackerAndScanner
	A class for finding the coordinate transformation between tracker and scanner coordinate systems. More...
class	stir::NonRigidObjectTransformationUsingBSplines< num_dimensions, elemT >
	Class to perform non-rigid object transformations in arbitrary dimensions. More...
class	stir::ObjectTransformation< num_dimensions, elemT >
	Base-class for performing (potentially non-rigid) object transformations. More...
class	stir::Polaris_MT_File
	a class for parsing .mt files output by the Polaris software More...
class	stir::RigidObject3DMotion
	Base class for 3D rigid motion. More...
class	stir::RigidObject3DMotionFromPolaris
	A class for handling motion information from the Polaris tracker. More...
class	stir::RigidObject3DTransformation
	Class to perform rigid object transformations in 3 dimensions. More...
class	stir::TimeFrameMotion
	A class for encoding average motion in the frames. More...

Functions
std::ostream &	stir::operator<< (std::ostream &out, const RigidObject3DTransformation &rigid_object_transformation)
	Output to (text) stream.
std::istream &	stir::operator>> (std::istream &, RigidObject3DTransformation &rigid_object_transformation)
	Input from (text) stream.
RigidObject3DTransformation	stir::compose (const RigidObject3DTransformation &apply_last, const RigidObject3DTransformation &apply_first)
	Composition of 2 transformations.
template<class ObjectTransformationT, class PushInterpolatorT>
Succeeded	stir::transform_3d_object_push_interpolation (DiscretisedDensity< 3, float > &out_density, const DiscretisedDensity< 3, float > &in_density, const ObjectTransformationT &transformation_in_to_out, const PushInterpolatorT &interpolator, const bool do_jacobian)
	transform image data
template<class ObjectTransformationT, class PullInterpolatorT>
Succeeded	stir::transform_3d_object_pull_interpolation (DiscretisedDensity< 3, float > &out_density, const DiscretisedDensity< 3, float > &in_density, const ObjectTransformationT &transformation_out_to_in, const PullInterpolatorT &interpolator, const bool do_jacobian)
	transform image data
Succeeded	stir::transform_3d_object (DiscretisedDensity< 3, float > &out_density, const DiscretisedDensity< 3, float > &in_density, const RigidObject3DTransformation &transformation_in_to_out)
	transform image data
Succeeded	stir::transform_3d_object (ProjData &out_proj_data, const ProjData &in_proj_data, const RigidObject3DTransformation &object_transformation)
	transform projection data
Succeeded	stir::transpose_of_transform_3d_object (DiscretisedDensity< 3, float > &out_density, const DiscretisedDensity< 3, float > &in_density, const RigidObject3DTransformation &transformation_in_to_out)
	transform image data using transposed matrix
Succeeded	stir::transform_3d_object (ProjData &out_proj_data, const ProjData &in_proj_data, const RigidObject3DTransformation &rigid_object_transformation, const int min_in_segment_num_to_process, const int max_in_segment_num_to_process)
	transform projection data

Detailed Description

Function Documentation

operator<<()

std::ostream & stir::operator<<	(	std::ostream &	out,
		const RigidObject3DTransformation &	rigid_object_transformation )

Output to (text) stream.

Will be written as

{ quaternion, translation } 

References stir::RigidObject3DTransformation::get_quaternion(), and stir::RigidObject3DTransformation::get_translation().

operator>>()

std::istream & stir::operator>>	(	std::istream &	,
		RigidObject3DTransformation &	rigid_object_transformation )

Input from (text) stream.

Should have format

{ quaternion, translation } 

compose()

RigidObject3DTransformation stir::compose	(	const RigidObject3DTransformation &	apply_last,
		const RigidObject3DTransformation &	apply_first )

Composition of 2 transformations.

This provides a way to perform 2 transformations after eachother. The following code will work

RigidObject3DTransformation tf_1,tf_2; // initialise somehow
const RigidObject3DTransformation tf_2_1 = compose(tf_2,tf_1));
  const CartesianCoordinate3D<float> point(1.F,-5.F,2.F);
  assert(norm(tf_2.transform_point(tf_1.transform_point(point)) -
              tf_2_ 1.transform_point(point))
         < .01);

Referenced by stir::RigidObject3DMotion::get_motion_in_scanner_coords_rel_time(), stir::LmToProjDataWithMC::process_new_time_event(), and stir::RigidObject3DTransformationTests::run_tests().

transform_3d_object_push_interpolation()

template<class ObjectTransformationT, class PushInterpolatorT>

Succeeded stir::transform_3d_object_push_interpolation ( DiscretisedDensity< 3, float > & out_density, const DiscretisedDensity< 3, float > & in_density, const ObjectTransformationT & transformation_in_to_out, const PushInterpolatorT & interpolator, const bool do_jacobian )

inline

transform image data

the interpolator has to push values from the input into the output image

Warning

transformation_in_to_out has to transform from in to out

See also

PushTransposeLinearInterpolator for an example interpolator.

Developer's note

This function is inline to avoid template instantiation problems.

References stir::VectorWithOffset< T >::get_max_index(), stir::VectorWithOffset< T >::get_min_index(), stir::DiscretisedDensity< num_dimensions, elemT >::get_origin(), stir::VoxelsOnCartesianGrid< elemT >::get_voxel_size(), and transform_3d_object_push_interpolation().

Referenced by transform_3d_object_push_interpolation(), and transpose_of_transform_3d_object().

transform_3d_object_pull_interpolation()

template<class ObjectTransformationT, class PullInterpolatorT>

Succeeded stir::transform_3d_object_pull_interpolation ( DiscretisedDensity< 3, float > & out_density, const DiscretisedDensity< 3, float > & in_density, const ObjectTransformationT & transformation_out_to_in, const PullInterpolatorT & interpolator, const bool do_jacobian )

inline

transform image data

the interpolator has to pull values from the input into the output image

Warning

transformation_out_to_in has to transform from out to in

See also

PullLinearInterpolator for an example interpolator.

Developer's note

This function is inline to avoid template instantiation problems.

References stir::VectorWithOffset< T >::get_max_index(), stir::VectorWithOffset< T >::get_min_index(), stir::DiscretisedDensity< num_dimensions, elemT >::get_origin(), stir::VoxelsOnCartesianGrid< elemT >::get_voxel_size(), and transform_3d_object_pull_interpolation().

Referenced by transform_3d_object(), and transform_3d_object_pull_interpolation().

transform_3d_object() [1/3]

Succeeded stir::transform_3d_object	(	DiscretisedDensity< 3, float > &	out_density,
		const DiscretisedDensity< 3, float > &	in_density,
		const RigidObject3DTransformation &	transformation_in_to_out )

transform image data

Currently only supports VoxelOnCartesianGrid image. Uses (tri)linear interpolation.

Todo

cannot use ObjectTransformation yet as it needs the inverse transformation

References stir::RigidObject3DTransformation::inverse(), transform_3d_object(), and transform_3d_object_pull_interpolation().

Referenced by transform_3d_object(), transform_3d_object(), and transform_3d_object().

transform_3d_object() [2/3]

Succeeded stir::transform_3d_object	(	ProjData &	out_proj_data,
		const ProjData &	in_proj_data,
		const RigidObject3DTransformation &	object_transformation )

transform projection data

Currently only supports non-arccorrected data.

Uses all available input segments

References stir::DataWithProjDataInfo::get_max_segment_num(), stir::DataWithProjDataInfo::get_min_segment_num(), and transform_3d_object().

transpose_of_transform_3d_object()

Succeeded stir::transpose_of_transform_3d_object	(	DiscretisedDensity< 3, float > &	out_density,
		const DiscretisedDensity< 3, float > &	in_density,
		const RigidObject3DTransformation &	transformation_in_to_out )

transform image data using transposed matrix

Implements the transpose (not the inverse) of transform_3d_object(DiscretisedDensity<3,float>&, const DiscretisedDensity<3,float>&,const RigidObject3DTransformation&)

Todo

cannot use ObjectTransformation yet as it needs the inverse transformation

References stir::RigidObject3DTransformation::inverse(), transform_3d_object_push_interpolation(), and transpose_of_transform_3d_object().

Referenced by transpose_of_transform_3d_object().

transform_3d_object() [3/3]

Succeeded stir::transform_3d_object	(	ProjData &	out_proj_data,
		const ProjData &	in_proj_data,
		const RigidObject3DTransformation &	rigid_object_transformation,
		const int	min_in_segment_num_to_process,
		const int	max_in_segment_num_to_process )

transform projection data

Currently only supports non-arccorrected data.

References stir::Bin::axial_pos_num(), stir::Bin::get_bin_value(), stir::ProjData::get_empty_segment_by_view(), stir::DataWithProjDataInfo::get_max_segment_num(), stir::DataWithProjDataInfo::get_max_tangential_pos_num(), stir::DataWithProjDataInfo::get_max_view_num(), stir::DataWithProjDataInfo::get_min_segment_num(), stir::DataWithProjDataInfo::get_min_tangential_pos_num(), stir::DataWithProjDataInfo::get_min_view_num(), stir::DataWithProjDataInfo::get_proj_data_info_sptr(), stir::ProjData::get_segment_by_view(), info(), stir::RigidObject3DTransformation::inverse(), stir::SegmentIndices::segment_num(), stir::ProjData::set_segment(), stir::Bin::tangential_pos_num(), transform_3d_object(), stir::RigidObject3DTransformation::transform_bin(), stir::ViewgramIndices::view_num(), and warning().