Uses of Interface
edu.stanford.rsl.apps.gui.Citeable

Packages that use Citeable

Package	Description
edu.stanford.rsl.apps	This package contains all applications that are delivered with CONRAD.
edu.stanford.rsl.apps.gui	Contains classes for the graphical user interface of CONRAD.
edu.stanford.rsl.conrad.cuda	Contains classes for hardware-accelerated projection and volume handling using CUDA.
edu.stanford.rsl.conrad.filtering	Contains classes for filtering of image data.
edu.stanford.rsl.conrad.filtering.multiprojection	Contains classes for filtering of image data accessing multiple images at a time.
edu.stanford.rsl.conrad.filtering.multiprojection.anisotropic	Contains classes for anisotropic filtering of image data.
edu.stanford.rsl.conrad.filtering.redundancy	Contains classes for redundancy weighting of image data for filtered backprojection.
edu.stanford.rsl.conrad.geometry.splines	Contains classes to model splines.
edu.stanford.rsl.conrad.io	Contains classes for input and output of data.
edu.stanford.rsl.conrad.metric	Contains classes to measure image quality.
edu.stanford.rsl.conrad.opencl	Contains classes to use OpenCL.
edu.stanford.rsl.conrad.phantom	Contains classes to model different numerical phantoms.
edu.stanford.rsl.conrad.phantom.electrondensity	Contains classes to model the electron density phantom.
edu.stanford.rsl.conrad.phantom.forbild	Contains classes to parse the Forbild phantoms.
edu.stanford.rsl.conrad.phantom.renderer	Contains classes to render the phantoms.
edu.stanford.rsl.conrad.phantom.workers	Contains classes that model the worker threads of the phantom renderers.
edu.stanford.rsl.conrad.phantom.xcat	Contains classes to create a phantom that is similar to NCAT.
edu.stanford.rsl.conrad.pipeline	Contains classes to enable pipeline processing.
edu.stanford.rsl.conrad.reconstruction	Contains classes to implement different reconstruction algorithms.
edu.stanford.rsl.conrad.reconstruction.iterative	Contains classes to implement different iterative reconstruction algorithms.
edu.stanford.rsl.tutorial.motionEstimation	This package contains a motion estimator.
edu.stanford.rsl.tutorial.truncation	This package contains truncation experiments.

Uses of Citeable in edu.stanford.rsl.apps

Classes in edu.stanford.rsl.apps that implement Citeable

Modifier and Type	Class and Description
class	TestJang Generate random integers in a certain range.

Uses of Citeable in edu.stanford.rsl.apps.gui

Constructors in edu.stanford.rsl.apps.gui with parameters of type Citeable

Constructor and Description
GUICompatibleObjectVisualizationPanel(GUIConfigurable config, Citeable citation)

Uses of Citeable in edu.stanford.rsl.conrad.cuda

Classes in edu.stanford.rsl.conrad.cuda that implement Citeable

Modifier and Type	Class and Description
class	CUDABackProjector
class	CUDACompensatedBackProjector This is the existing CUDABackProjector with added motion compensation.
class	CUDAForwardProjector Forward projection expects input of a volumetric phantom scaled to mass density.
class	CUDAForwardProjectorWithMotion Forward projection expects input of a volumetric phantom scaled to mass density.

Uses of Citeable in edu.stanford.rsl.conrad.filtering

Classes in edu.stanford.rsl.conrad.filtering that implement Citeable

Modifier and Type	Class and Description
class	AbsoluteValueTool
class	ApplyHounsfieldScaling This Class can be used to apply a previously learned Hounsfield scaling to an existing reconstruction.
class	ApplyLambdaWeightingTool This class applies the beam hardening correction after Joseph & Spittal in projection domain.
class	AtractResidual2D Filters all projections of a stack with the 2D residual kernel of the ATRACT reconstruction
class	BilateralFilteringTool
class	CosineWeightingTool Filtering tool to apply cosine weights.
class	DynamicDensityOptimizationScatterCorrectionTool
class	ExtremeValueTruncationFilter This filter thresholds the values in imageProcessors.
class	FastRadialSymmetryTool Tool to apply a Fast Radial Symmetry Transform on slices
class	FiducialMarkerDetectionTool
class	Filtering2DTool Filtering tool to apply a 2D filter.
class	HilbertFilteringTool Tool to apply a 1-D Hilbert filter.
class	HorizontalFlippingTool
class	HoughFilteringTool Tool to apply a Hough filter for circles with fixed dimension.
class	ImageConstantMathFilter
class	ImageFilteringTool Abstract class to describe the blue print of an ImageFilteringTool.
class	ImageJParallelTool Filtering tool to apply an arbitrary ImageJ operation in parallel.
class	ImageMathFilter
class	IndividualImageFilteringTool
class	KinectBasedDetectorSaturationCorrectionTool
class	LaplaceFilteringTool
class	LogPoissonNoiseFilteringTool Applies Poisson noise to the input image as it would happen in the physical process (based on a monochromatic x-ray source).
class	MeanFilteringTool
class	MeanMarkerBasedProjectionShiftingTool
class	MeanMarkerBasedProjectionShiftingToolForXCAT
class	MedianFilteringTool Implements a simple median filter based on sorting of all values in the kernel.
class	NonLinearGainCorrectionTool
class	NumericalDerivativeComputationTool Tool to compute first derivate numerically.
class	NumericalLinewiseAntiderivativeFilteringTool Tool to compute the antiderivative of the projection line-wise.
class	PoissonNoiseFilteringTool Applies Poisson noise to the input image.
class	PrimaryModulationScatterCorrectionTool
class	RampFilteringTool Class to apply a ramp filter to an image before 3D reconstruction.
class	Rotate90DegreeLeftTool
class	ThinPlateSplinesBasedProjectionWarpingTool
class	ThinPlateSplinesBasedProjectionWarpingToolForXCAT
class	TruncationCorrectionTool Class implements a simple truncation correction algorithm after Ohnesorge, Flohr, Schwarz, Heiken, and Bae "Efficient correction for CT image artifacts caused by objects extending outside the scan field of view" Med.
class	VolumeAttenuationFactorCorrectionTool This Class implements the first step of the beam hardening correction after Joseph & Spittal.

Uses of Citeable in edu.stanford.rsl.conrad.filtering.multiprojection

Classes in edu.stanford.rsl.conrad.filtering.multiprojection that implement Citeable

Modifier and Type	Class and Description
class	BilateralFilter3D
class	BlockWiseMultiProjectionFilter Class for simplified parallelization of MultiProjectionFilters.
class	BlockWiseStructureTensor
class	DiaphragmTrackingTool This tool can be used to track a diaphragm in the projection data.
class	IdentityTransformFilter Class to test the BlockWiseMultiProjectionFilter.
class	IterativeReconstructionFilter
class	Lambda3DDerivativeFilter Class for the computation of a derivative along the source trajectory.
class	MultiProjectionFilter Abstract class to handle multi projection filter.
class	ProjectionSortingFilter
class	Triangulation This class triangulates the 3D position from subsequent projections.

Uses of Citeable in edu.stanford.rsl.conrad.filtering.multiprojection.anisotropic

Classes in edu.stanford.rsl.conrad.filtering.multiprojection.anisotropic that implement Citeable

Modifier and Type	Class and Description
class	AnisotropicStructureTensorNoiseFilter MultiProjectionFilter which implements an anisotropic structure tensor noise filter.
class	CUDAAnisotropicStructureTensorNoiseFilter MultiProjectionFilter which implements an anisotropic structure tensor noise filter on CUDA.
class	CUDAFFTAnisotropicStructureTensorNoiseFilter MultiProjectionFilter which implements an anisotropic structure tensor noise filter.

Uses of Citeable in edu.stanford.rsl.conrad.filtering.redundancy

Classes in edu.stanford.rsl.conrad.filtering.redundancy that implement Citeable

Modifier and Type	Class and Description
class	NooWeightingTool
class	OSCARWeightingTool
class	ParkerWeightingTool Implementation of Parker weights.
class	SilverWeightingTool
class	TrajectoryParkerWeightingTool This version of the Parker weights computes the primary angles from the trajectory rather than from preconfigured "primaryAngles".
class	WesargWeightingTool

Uses of Citeable in edu.stanford.rsl.conrad.geometry.splines

Classes in edu.stanford.rsl.conrad.geometry.splines that implement Citeable

Modifier and Type	Class and Description
class	SurfaceBSplineVolumePhantom

Uses of Citeable in edu.stanford.rsl.conrad.io

Classes in edu.stanford.rsl.conrad.io that implement Citeable

Modifier and Type	Class and Description
class	ImagePlusDataSink Class to model an ImagePlus projection source, i.e.
class	IndividualFilesProjectionDataSink Class to model a directory as projection data sink.

Uses of Citeable in edu.stanford.rsl.conrad.metric

Classes in edu.stanford.rsl.conrad.metric that implement Citeable

Modifier and Type	Class and Description
class	ImageMetric
class	MeanSquareErrorMetric
class	NormalizedImageMetric
class	NormalizedImprovement
class	RootMeanSquareErrorMetric

Uses of Citeable in edu.stanford.rsl.conrad.opencl

Classes in edu.stanford.rsl.conrad.opencl that implement Citeable

Modifier and Type	Class and Description
class	OpenCLBackProjector
class	OpenCLForwardProjector Forward projection expects input of a volumetric phantom scaled to mass density.
class	OpenCLForwardProjectorWithMotion Forward projection expects input of a volumetric phantom scaled to mass density.
class	OpenCLProjectionPhantomRenderer Class to enable creation of projections using OpenCL.

Uses of Citeable in edu.stanford.rsl.conrad.phantom

Classes in edu.stanford.rsl.conrad.phantom that implement Citeable

Modifier and Type	Class and Description
class	AnalyticPhantom The class AnalyticPhantom defines a scene with different PhysicalObjects, i.e.
class	AnalyticPhantom4D
class	BeadRemovalPhantom Phantom to test forward and back projection resolution.
class	BoxPhantom Phantom to test forward and back projection.
class	CatheterPhantom Phantom to test Subtract-and-Shift (SaS).
class	CatphanCTP528 MTF phantom defined by Lars Wigstroem.
class	DefrisePhantom Creates a phantom that is scaled to the field of view of the trajectory with five disks in it.
class	MovingBallPhantom A simple 4D phantom similar to a swinging pendulum - spherical version.
class	MTFBeadPhantom MTF phantom defined by Lars Wigstroem.
class	SevenBeadPhantom Phantom to test forward and back projection resolution.
class	SheppLoganPhantom 3-D definition of the Shepp-Logan Phantom.
class	SpherePhantom Phantom to test forward and back projection resolution.
class	WaterCylinderPhantom Phantom to test forward and back projection.

Uses of Citeable in edu.stanford.rsl.conrad.phantom.electrondensity

Classes in edu.stanford.rsl.conrad.phantom.electrondensity that implement Citeable

Modifier and Type

Class and Description

class

CrisEDPhantomM062 This class models CRIS's Electron Density Phantom Model 062 . This phantom enables precise correlation of CT data in hounsfield units to electron density and includes eight different tissue references. Model 062 consists of a small cylindrical disk (Inner) nested within a large spherical disk (Outer). Phantom can be configured to simulate head or abdomen, by positioning tissue equivalent samples at 17 different locations within the scan field.

Uses of Citeable in edu.stanford.rsl.conrad.phantom.forbild

Classes in edu.stanford.rsl.conrad.phantom.forbild that implement Citeable

Modifier and Type	Class and Description
class	ForbildPhantom This class creates forbild phantoms from configuration files

Uses of Citeable in edu.stanford.rsl.conrad.phantom.renderer

Classes in edu.stanford.rsl.conrad.phantom.renderer that implement Citeable

Modifier and Type	Class and Description
class	AnalyticPhantomProjector will implement a version which streams projections as they are projected.
class	CylinderPhantomRenderer Phantom of a homogeneous cylinder.
class	MetricPhantomRenderer
class	ParallelProjectionPhantomRenderer Class to enable parallel processing of slices of the target volume.
class	PhantomRenderer Abstract class to describe a numerical phantom.
class	RampProjectionPhantomRenderer Class which generates an intensity ramp across the image in each image of the stack.
class	SliceParallelVolumePhantomRenderer Class to enable parallel processing of slices of the target volume.
class	StreamingPhantomRenderer

Uses of Citeable in edu.stanford.rsl.conrad.phantom.workers

Classes in edu.stanford.rsl.conrad.phantom.workers that implement Citeable

Modifier and Type	Class and Description
class	AnalyticPhantom3DVolumeRenderer Renders arbitrarily defined phantoms Works now with the correct origin computations.
class	AnalyticPhantomProjectorWorker Projects arbitrarily defined phantoms to a detector using ray casting. The pixel value on the detector is determined by the absorption model. If you change anything in this class, notify the conrad-dev mailing list.
class	DiracProjectionPhantom Phantom to create a Dirac pulse in the center of the projection.
class	SheppLoganPhantomWorker Wrapper class to create a volume phantom from the SheppLogan3D Class.
class	SliceWorker Class to model an abstract slice worker.
class	VolumeOfInterestPhantom

Uses of Citeable in edu.stanford.rsl.conrad.phantom.xcat

Classes in edu.stanford.rsl.conrad.phantom.xcat that implement Citeable

Modifier and Type	Class and Description
class	BreathingScene
class	CombinedBreathingHeartScene
class	CoronaryScene
class	DynamicSquatScene Class to simulate very simple knee joint motion in XCat.
class	HeartScene
class	SquatScene Class to simluate very simple knee joint motion in XCat.
class	WholeBodyScene Simple scene for XCat to display the whole body.
class	XCatScene Class to model scenes involving Paul Seagar's XCAT.

Uses of Citeable in edu.stanford.rsl.conrad.pipeline

Classes in edu.stanford.rsl.conrad.pipeline that implement Citeable

Modifier and Type	Class and Description
class	BufferedProjectionSink
class	DevNullSink Class for debugging pipelines.
class	IndividualImagePipelineFilteringTool Class to describe the thread which runs in a parallel image pipeline.

Uses of Citeable in edu.stanford.rsl.conrad.reconstruction

Classes in edu.stanford.rsl.conrad.reconstruction that implement Citeable

Modifier and Type	Class and Description
class	CPUSuperShortScanBackprojector Implementation of the backprojector which is required for Noo's super-short-scan reconstruction.
class	DistanceDrivenBasedReconstruction
class	FBPReconstructionFilter The FBP reconstruction filter is the abstract class that describes a general outline for a filtered backprojection algorithm.
class	IterativeReconstruction All iterative reconstruction algorithms are based on the iterative reconstruction filter The iterative reconstruction is the abstract class that describe a general outline for a iterative reconstruction algorithm.
class	LolaBunnyBackprojector The most simple implementation of the backprojection using no speed-up methods.
class	ModelBasedIterativeReconstruction
class	MotionCompensatedSubVolumeBackprojector This FBP-based mathod splits the reconstruction volume into sub volumes which can be processed in parallel to speed up the reconstruction further.
class	MotionCompensatedVOIBasedReconstructionFilter The VOIBasedReconstructionFilter is an implementation of the backprojection which employs a volume-of-interest (VOI) to speed up reconstruction.
class	RayDrivenBasedReconstruction
class	RayWeightCorrectingCPUSuperShortScanBackprojector A FBP-based reconstruction algorithm which evaluates whether 180 degrees of angular coverage have been achieved during the reconstruction.
class	ReconstructionFilter All reconstruction algorithms are based on the reconstruction filter.
class	RigidBody3DTransformationVOIBasedReconstructionFilter The VOIBasedReconstructionFilter is an implementation of the backprojection which employs a volume-of-interest (VOI) to speed up reconstruction.
class	RigidBody3DTransformationVOIBasedReconstructionFilterForXCAT The VOIBasedReconstructionFilter is an implementation of the backprojection which employs a volume-of-interest (VOI) to speed up reconstruction.
class	SeparableFootprintsBasedReconstruction
class	SimpleIterativeReconstruction A simple approach for iterative reconstruction.
class	SubVolumeBackprojector This FBP-based mathod splits the reconstruction volume into sub volumes which can be processed in parallel to speed up the reconstruction further.
class	SuperShortScanBackprojection Deprecated.
class	VOIBasedReconstructionFilter The VOIBasedReconstructionFilter is an implementation of the backprojection which employs a volume-of-interest (VOI) to speed up reconstruction.

Uses of Citeable in edu.stanford.rsl.conrad.reconstruction.iterative

Classes in edu.stanford.rsl.conrad.reconstruction.iterative that implement Citeable

Modifier and Type	Class and Description
class	LeastSquaresCG
class	PenalizedLeastSquareART

Uses of Citeable in edu.stanford.rsl.tutorial.motionEstimation

Classes in edu.stanford.rsl.tutorial.motionEstimation that implement Citeable

Modifier and Type	Class and Description
class	OpenCLCompensatedBackProjector DO NOT USE IN LARGEVOLUMEMODE
class	OpenCLCompensatedBackProjector1DCompressionField DO NOT USE IN LARGEVOLUMEMODE
class	OpenCLCompensatedBackProjectorTPS DO NOT USE IN LARGEVOLUMEMODE

Uses of Citeable in edu.stanford.rsl.tutorial.truncation

Classes in edu.stanford.rsl.tutorial.truncation that implement Citeable

Modifier and Type	Class and Description
class	ConstantValueZeroArtifactImage In this class we investigate the paper Yu, H., Yang, J., Jiang, M., & Wang, G.
class	NonZeroArtifactImage Test implementation to show that a constant offset inside the ROI in the artifact image is not possible.