S-Index

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

S

SafeSerializable - Interface in edu.stanford.rsl.conrad.io
save(ImagePlus, String, String) - Method in class edu.stanford.rsl.conrad.io.Nrrd_Writer
saveConfiguration() - Static method in class edu.stanford.rsl.conrad.utils.Configuration
saveConfiguration(Configuration, String) - Static method in class edu.stanford.rsl.conrad.utils.Configuration
saveForVisualization(int, double[]) - Static method in class edu.stanford.rsl.conrad.utils.DoubleArrayUtil: Stores an array for later visualization at index imageNumber
saveForVisualization(int, float[]) - Static method in class edu.stanford.rsl.conrad.utils.FloatArrayUtil: Stores an array for later visualization at index imageNumber
saveViva(ImagePlus, String) - Method in class edu.stanford.rsl.conrad.io.SEQProjectionSource
scale(double, double) - Method in class edu.stanford.rsl.conrad.io.SerializableFloatProcessor: Scales the image or selection using the specified scale factors.
ScaleRotate - Class in edu.stanford.rsl.conrad.geometry.transforms: This is a decorator class for a scale-rotation matrix.
ScaleRotate(SimpleMatrix) - Constructor for class edu.stanford.rsl.conrad.geometry.transforms.ScaleRotate: Initialize a scale-rotation transform using a rotation matrix
SceneFileParser - Interface in edu.stanford.rsl.conrad.utils.parsers: Interface for parsers that convert configuration files to a scene
SeparableFootprints - Class in edu.stanford.rsl.conrad.geometry
SeparableFootprints() - Constructor for class edu.stanford.rsl.conrad.geometry.SeparableFootprints
SeparableFootprints - Class in edu.stanford.rsl.conrad.reconstruction.iterative
SeparableFootprints() - Constructor for class edu.stanford.rsl.conrad.reconstruction.iterative.SeparableFootprints
SeparableFootprintsBasedReconstruction - Class in edu.stanford.rsl.conrad.reconstruction.iterative
SeparableFootprintsBasedReconstruction(Trajectory) - Constructor for class edu.stanford.rsl.conrad.reconstruction.iterative.SeparableFootprintsBasedReconstruction
SeparableFootprintsBasedReconstruction - Class in edu.stanford.rsl.conrad.reconstruction
SeparableFootprintsBasedReconstruction(Trajectory) - Constructor for class edu.stanford.rsl.conrad.reconstruction.SeparableFootprintsBasedReconstruction
SeparableFootprintsBasedReconstruction.FootprintsType - Enum in edu.stanford.rsl.conrad.reconstruction.iterative
SeparableFootprintsBasedReconstruction.FootprintsType - Enum in edu.stanford.rsl.conrad.reconstruction
SEQProjectionSource - Class in edu.stanford.rsl.conrad.io: Class to stream Varian's SEQ Format.
SEQProjectionSource() - Constructor for class edu.stanford.rsl.conrad.io.SEQProjectionSource
SerializableFloatProcessor - Class in edu.stanford.rsl.conrad.io
SerializableFloatProcessor(int, int, float[], ColorModel) - Constructor for class edu.stanford.rsl.conrad.io.SerializableFloatProcessor: Creates a new FloatProcessor using the specified pixel array and ColorModel.
SerializableFloatProcessor(FloatProcessor) - Constructor for class edu.stanford.rsl.conrad.io.SerializableFloatProcessor: Creates a new FloatProcessor using the specified FloatProcessor.
SerializableFloatProcessor(ImageProcessor) - Constructor for class edu.stanford.rsl.conrad.io.SerializableFloatProcessor: Creates a new FloatProcessor using the specified ImageProcessor.
SerializableFloatProcessor(int, int) - Constructor for class edu.stanford.rsl.conrad.io.SerializableFloatProcessor: Creates a blank FloatProcessor using the default grayscale LUT that displays zero as black.
SerializableFloatProcessor(int, int, int[]) - Constructor for class edu.stanford.rsl.conrad.io.SerializableFloatProcessor: Creates a FloatProcessor from an int array using the default grayscale LUT.
SerializableFloatProcessor(int, int, double[]) - Constructor for class edu.stanford.rsl.conrad.io.SerializableFloatProcessor: Creates a FloatProcessor from a double array using the default grayscale LUT.
SerializableFloatProcessor(float[][]) - Constructor for class edu.stanford.rsl.conrad.io.SerializableFloatProcessor: Creates a FloatProcessor from a 2D float array using the default LUT.
SerializableFloatProcessor(int[][]) - Constructor for class edu.stanford.rsl.conrad.io.SerializableFloatProcessor: Creates a FloatProcessor from an int[][] array.
serializeObject(File, Object) - Static method in class edu.stanford.rsl.conrad.utils.XmlUtils
serialVersionUID - Static variable in class edu.stanford.rsl.conrad.geometry.bounds.QuadricBoundingCondition
serialVersionUID - Static variable in class edu.stanford.rsl.conrad.geometry.shapes.simple.Box
serialVersionUID - Static variable in class edu.stanford.rsl.conrad.geometry.shapes.simple.Ellipsoid
serialVersionUID - Static variable in class edu.stanford.rsl.conrad.phantom.electrondensity.QuadricDisk
serialVersionUID - Static variable in class edu.stanford.rsl.conrad.phantom.forbild.shapes.ForbildCylinder
serialVersionUID - Static variable in class edu.stanford.rsl.conrad.phantom.forbild.shapes.ForbildEllipsoid
set(float) - Method in class edu.stanford.rsl.conrad.data.iterators.PointwiseIterator
set(float) - Method in class edu.stanford.rsl.conrad.data.iterators.PointwiseIterator1D
set(float) - Method in class edu.stanford.rsl.conrad.data.iterators.PointwiseIterator2D
set(float) - Method in class edu.stanford.rsl.conrad.data.iterators.PointwiseIterator3D
set(int, double) - Method in class edu.stanford.rsl.conrad.geometry.shapes.simple.PointND: Methods to set individual entries of the coordinates
set(int, int, int) - Method in class edu.stanford.rsl.conrad.io.SerializableFloatProcessor
set(int, int) - Method in class edu.stanford.rsl.conrad.io.SerializableFloatProcessor
setA(double) - Method in class edu.stanford.rsl.conrad.fitting.LogarithmicFunction
setA(float[][]) - Method in class edu.stanford.rsl.tutorial.motionEstimation.OpenCLCompensatedBackProjectorTPS
setAcc(double) - Method in class edu.stanford.rsl.conrad.geometry.motion.timewarp.SigmoidTimeWarper
setAllPointSets(Object) - Method in class edu.stanford.rsl.apps.gui.pointselector.PointSelectorWorker
setAlpha(double) - Method in class edu.stanford.rsl.conrad.filtering.FastRadialSymmetryTool
setAtIndex(int, float) - Method in class edu.stanford.rsl.conrad.data.Grid1D
setAtIndex(int, float) - Method in class edu.stanford.rsl.conrad.data.Grid1DComplex
setAtIndex(int, int, float) - Method in class edu.stanford.rsl.conrad.data.Grid2D
setAtIndex(int, int, float) - Method in class edu.stanford.rsl.conrad.data.Grid2DComplex
setAtIndex(int, int, int, float) - Method in class edu.stanford.rsl.conrad.data.Grid3D
setAtomicNumber(double) - Method in class edu.stanford.rsl.conrad.physics.materials.Element: Set the atomic number of the element
setAtomicWeight(double) - Method in class edu.stanford.rsl.conrad.physics.materials.Element: Set the atomic weight of the element
setAutomaticExposureControlConfigFile(String) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setAverageAngularIncrement(double) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setAxis(SimpleVector) - Method in class edu.stanford.rsl.conrad.geometry.Axis
setB(double) - Method in class edu.stanford.rsl.conrad.fitting.LogarithmicFunction
setB(float) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeSquaredCosineR
setB(float[][]) - Method in class edu.stanford.rsl.tutorial.motionEstimation.OpenCLCompensatedBackProjectorTPS
setBackground(Color) - Method in class edu.stanford.rsl.apps.gui.GUICompatibleObjectVisualizationPanel
setBackground(Material) - Method in class edu.stanford.rsl.conrad.rendering.AbstractScene
setBackgroundValue(double) - Method in class edu.stanford.rsl.conrad.io.SerializableFloatProcessor: Does nothing.
setBase(double) - Method in class edu.stanford.rsl.conrad.utils.interpolation.LogLinearInterpolator
setBase(double) - Method in class edu.stanford.rsl.conrad.utils.interpolation.LogLogInterpolator
setBaseFunction(Function) - Method in class edu.stanford.rsl.conrad.fitting.RANSACFittedFunction
setBeadMeanPosition3D(double[][]) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setBeadPosition2D(double[][][]) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setBeadPosition2D(int, int, int, double) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setBeamHardeningLookupTable(BilinearInterpolatingDoubleArray) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setBeginIndexX(int) - Method in class edu.stanford.rsl.conrad.volume3d.operations.ParallelVolumeOperation
setBoundsFromGeometry() - Method in class edu.stanford.rsl.conrad.geometry.splines.SurfaceBSplineVolumePhantom
setBreathing(BreathingScene) - Method in class edu.stanford.rsl.conrad.phantom.xcat.CombinedBreathingHeartScene
setBreathingHeartScene(CombinedBreathingHeartScene) - Method in class edu.stanford.rsl.conrad.geometry.motion.CombinedBreathingHeartMotionField
setBufferMaterial(Material) - Method in class edu.stanford.rsl.conrad.phantom.electrondensity.Insert
setbUniformAlpha(boolean) - Method in class edu.stanford.rsl.conrad.filtering.PrimaryModulationScatterCorrectionTool
setC(double) - Method in class edu.stanford.rsl.conrad.fitting.LogarithmicFunction
setCitationFormat(int) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setClockwise(boolean) - Method in class edu.stanford.rsl.conrad.geometry.splines.SurfaceBSpline
setCoeff(float[][]) - Method in class edu.stanford.rsl.tutorial.motionEstimation.OpenCLCompensatedBackProjectorTPS
setColor(Color) - Method in class edu.stanford.rsl.conrad.io.SerializableFloatProcessor: Sets the foreground fill/draw color.
setColValue(int, SimpleVector) - Method in class edu.stanford.rsl.conrad.numerics.SimpleMatrix: Replace col with newCol
setCompositionTable(TreeMap<String, Double>) - Method in class edu.stanford.rsl.conrad.physics.materials.utils.WeightedAtomicComposition: Set a pre-initialized composition table
setCompositionTable(TreeMap<String, Double>) - Method in class edu.stanford.rsl.conrad.physics.materials.WeightedAtomicComposition
setConfig(Configuration) - Method in class edu.stanford.rsl.conrad.utils.DicomConfigurationUpdater
setConfiguration(Configuration) - Method in class edu.stanford.rsl.conrad.filtering.CosineWeightingTool
setConfiguration(Configuration) - Method in class edu.stanford.rsl.conrad.filtering.rampfilters.RampFilter
setConfiguration(Configuration) - Method in class edu.stanford.rsl.conrad.filtering.redundancy.ParkerWeightingTool
setConfiguration(Configuration) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.SystemGeometryConfigFileTrajectory
setConfiguration(Configuration) - Method in class edu.stanford.rsl.conrad.io.ImagePlusDataSink
setConfiguration(Configuration) - Method in class edu.stanford.rsl.conrad.io.IndividualFilesProjectionDataSink
setConfiguration(Configuration) - Method in class edu.stanford.rsl.conrad.pipeline.BufferedProjectionSink
setConfiguration(Configuration) - Method in class edu.stanford.rsl.conrad.pipeline.DevNullSink
setConfiguration(Configuration) - Method in class edu.stanford.rsl.conrad.reconstruction.VOIBasedReconstructionFilter: Deprecated.
setConfiguration(Configuration) - Method in interface edu.stanford.rsl.conrad.utils.ConfigurationUpdater
setConfiguration(Configuration) - Method in class edu.stanford.rsl.conrad.utils.DicomConfigurationUpdater
setConfigured(boolean) - Method in class edu.stanford.rsl.apps.gui.roi.EvaluateROI
setConfigured(boolean) - Method in class edu.stanford.rsl.conrad.filtering.ImageFilteringTool
setConfigured(boolean) - Method in class edu.stanford.rsl.conrad.phantom.AnalyticPhantom
setContext(int) - Method in class edu.stanford.rsl.conrad.filtering.multiprojection.MultiProjectionFilter
setControlPoints(ArrayList<PointND>) - Method in class edu.stanford.rsl.conrad.geometry.splines.BSpline
setCoordinates(SimpleVector) - Method in class edu.stanford.rsl.conrad.geometry.shapes.simple.PointND
setCorrectionFactor(double) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setCosineWeights(double[][]) - Method in class edu.stanford.rsl.conrad.filtering.CosineWeightingTool
setCurrent(double[]) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setCurrentPath(String) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setCurrentRowWeights(String) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setCutOffFrequency(double) - Method in class edu.stanford.rsl.conrad.filtering.rampfilters.RampFilter
setCutOffFrequency(double) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setD(double) - Method in class edu.stanford.rsl.conrad.fitting.LogarithmicFunction
setData(int, int, int, float[][][]) - Method in class edu.stanford.rsl.conrad.volume3d.MaxEigenValue
setdCU(double) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setDebug(boolean) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.ExtrapolatedTrajectory
setDebug(boolean) - Method in class edu.stanford.rsl.conrad.pipeline.ParallelImageFilterSink
setDegree(int) - Method in class edu.stanford.rsl.conrad.fitting.PolynomialFunction: Sets the degree of the polynomial function.
setDensity(double) - Method in class edu.stanford.rsl.conrad.physics.materials.Material: Update the density and CT Value of the material with given value
setDetectorHeight(int) - Method in class edu.stanford.rsl.conrad.filtering.CosineWeightingTool
setDetectorHeight(int) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setDetectorOffsetU(int) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setDetectorOffsetV(int) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setDetectorUDirection(Projection.CameraAxisDirection) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setDetectorVDirection(Projection.CameraAxisDirection) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setDetectorWidth(int) - Method in class edu.stanford.rsl.conrad.filtering.CosineWeightingTool
setDetectorWidth(int) - Method in class edu.stanford.rsl.conrad.filtering.redundancy.ParkerWeightingTool
setDetectorWidth(int) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setDeviceDependent(boolean) - Method in class edu.stanford.rsl.conrad.filtering.ImageConstantMathFilter
setDevicePointer(CUdeviceptr) - Method in class edu.stanford.rsl.conrad.cuda.CUDAVolume3D
setDeviceSerialNumber(String) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setDeviceX(CUdeviceptr) - Method in class edu.stanford.rsl.conrad.cuda.splines.CUDABSpline
setDiagValue(SimpleVector) - Method in class edu.stanford.rsl.conrad.numerics.SimpleMatrix: Replace diagonal entries of matrix with diag
setDiaphragmCoords(double[][]) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setDiaphragmCoordsEntry(int, double[]) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setDiaphragmMax(PointND) - Method in class edu.stanford.rsl.conrad.phantom.xcat.BreathingScene
setDiaphragmMin(PointND) - Method in class edu.stanford.rsl.conrad.phantom.xcat.BreathingScene
setDiaphragmModelEntry(int, double[]) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setDiaphragmModelField(double[][]) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setDiaphragmMovement(double) - Method in class edu.stanford.rsl.conrad.phantom.xcat.BreathingScene
setDiaphragmPositionField(double[]) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setDimx(double) - Method in class edu.stanford.rsl.conrad.filtering.multiprojection.anisotropic.AnisotropicStructureTensorNoiseFilter
setDimy(double) - Method in class edu.stanford.rsl.conrad.filtering.multiprojection.anisotropic.AnisotropicStructureTensorNoiseFilter
setDirection(int...) - Method in class edu.stanford.rsl.conrad.data.iterators.FloatIterator
setDirection(SimpleVector) - Method in class edu.stanford.rsl.conrad.geometry.shapes.simple.StraightLine
setDirection(float[]) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeSquaredCosine
setDirection(float[]) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeSquaredCosineR
setDirectory(String) - Method in class edu.stanford.rsl.conrad.io.IndividualFilesProjectionDataSink
setDose(double) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setElectroCardioGramm(double[]) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setElementValue(int, int, double) - Method in class edu.stanford.rsl.conrad.numerics.SimpleMatrix: Replaces matrix entry in the specified row and column with given value
setElementValue(int, double) - Method in class edu.stanford.rsl.conrad.numerics.SimpleVector: Replaces the vector element at index i
setEndIndexX(int) - Method in class edu.stanford.rsl.conrad.volume3d.operations.ParallelVolumeOperation
setEnds(PointND, PointND) - Method in class edu.stanford.rsl.conrad.geometry.shapes.simple.Edge
setEpsilon(double) - Method in class edu.stanford.rsl.conrad.fitting.RANSACFittedFunction
setExperiment(Experiment) - Method in class edu.stanford.rsl.apps.gui.ExperimentPanel
setExponent(int) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeSquaredCosine
setExponent(int) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeSquaredCosineR
setf(int, int, float) - Method in class edu.stanford.rsl.conrad.io.SerializableFloatProcessor
setf(int, float) - Method in class edu.stanford.rsl.conrad.io.SerializableFloatProcessor
setFastVOIMode(boolean) - Method in class edu.stanford.rsl.conrad.reconstruction.VOIBasedReconstructionFilter
setfDelta(float[]) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeGaussian
setfDelta(float[]) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeHighPass
setfDelta(float[]) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeLowPass
setfDelta(float[]) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeSquaredCosine
setfDelta(float[]) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeSquaredCosineR
setFilename(String) - Method in class edu.stanford.rsl.apps.gui.blobdetection.MarkerDetectionWorker
setFilename(String) - Method in class edu.stanford.rsl.conrad.utils.DicomConfigurationUpdater
setFilter(double[]) - Method in class edu.stanford.rsl.conrad.filtering.rampfilters.ArbitraryRampFilter
setFilter2D(Grid2D) - Method in class edu.stanford.rsl.conrad.filtering.Filtering2DTool
setFilterPipeline(ImageFilteringTool[]) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setFilterType(String) - Method in class edu.stanford.rsl.conrad.filtering.rampfilters.IRRFilter
setFilterType(int) - Method in class edu.stanford.rsl.conrad.filtering.rampfilters.IRRFilter
setFilterType(VolumeOperator.FILTER_TYPE) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeSquaredCosine
setFilterType(VolumeOperator.FILTER_TYPE) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeSquaredCosineR
setfMax(float[]) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeGaussian
setfMax(float[]) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeHighPass
setfMax(float[]) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeLowPass
setfMax(float[]) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeSquaredCosine
setfMax(float[]) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeSquaredCosineR
setFormat(String) - Method in class edu.stanford.rsl.conrad.io.IndividualFilesProjectionDataSink
setFormula(String) - Method in class edu.stanford.rsl.conrad.physics.materials.Compound: Set the formula of a compound
setFreq1(float) - Method in class edu.stanford.rsl.conrad.filtering.rampfilters.IRRFilter
setFreq2(float) - Method in class edu.stanford.rsl.conrad.filtering.rampfilters.IRRFilter
setFreqPoints(int) - Method in class edu.stanford.rsl.conrad.filtering.rampfilters.IRRFilter
setGaincutfactor(double) - Method in class edu.stanford.rsl.conrad.filtering.PrimaryModulationScatterCorrectionTool
setGeometry(Trajectory) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setGlobalConfiguration(Configuration) - Static method in class edu.stanford.rsl.conrad.utils.Configuration
setHeart(HeartScene) - Method in class edu.stanford.rsl.conrad.phantom.xcat.CombinedBreathingHeartScene
setHeartPhases(double[]) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setHeartTranslation(Translation) - Method in class edu.stanford.rsl.conrad.phantom.xcat.CombinedBreathingHeartScene
setHeight(int) - Method in class edu.stanford.rsl.conrad.io.IndividualFilesProjectionDataSink
setHeight(int) - Method in class edu.stanford.rsl.conrad.phantom.renderer.RampProjectionPhantomRenderer
setHighHyst(float) - Static method in class edu.stanford.rsl.conrad.filtering.multiprojection.DiaphragmTrackingTool
setHighHyst(float) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setHighPassLowerLevel(float) - Method in class edu.stanford.rsl.conrad.filtering.multiprojection.anisotropic.AnisotropicStructureTensorNoiseFilter
setHighPassUpperLevel(float) - Method in class edu.stanford.rsl.conrad.filtering.multiprojection.anisotropic.AnisotropicStructureTensorNoiseFilter
setHorizontal(boolean) - Method in class edu.stanford.rsl.conrad.filtering.NumericalDerivativeComputationTool
setHounsfieldScaling(Function) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setHpLower(float) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeHighPass
setHpUpper(float) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeHighPass
setImag(double) - Method in class edu.stanford.rsl.conrad.data.Complex
setImagAtIndex(int, float) - Method in class edu.stanford.rsl.conrad.data.Grid1DComplex
setImagAtIndex(int, int, float) - Method in class edu.stanford.rsl.conrad.data.Grid2DComplex
setImage(ImagePlus) - Method in class edu.stanford.rsl.apps.gui.blobdetection.MarkerDetectionWorker
setImage(ImagePlus) - Method in class edu.stanford.rsl.apps.gui.roi.EvaluateROI
setImage(Grid3D) - Method in class edu.stanford.rsl.conrad.io.ImagePlusProjectionDataSource
setImageIndex(int) - Method in class edu.stanford.rsl.conrad.filtering.IndividualImageFilteringTool: Sets the number of the current image in the stack.
setImageProcessor(Grid2D) - Method in class edu.stanford.rsl.conrad.filtering.IndividualImageFilteringTool: Sets the actual ImageProcessor to be filtered.
setImageProcessorBuffer(ImageProcessorBuffer) - Method in class edu.stanford.rsl.conrad.phantom.workers.SliceWorker: Sets the volume to work on.
setImportFromDicomAutomatically(boolean) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setInputBlock(ImagePlus) - Method in class edu.stanford.rsl.conrad.filtering.multiprojection.blocks.ImageProcessingBlock
setInputSpectrum(PolychromaticXRaySpectrum) - Method in class edu.stanford.rsl.conrad.physics.absorption.PolychromaticAbsorptionModel: Change the X-Ray spectrum used by the absorption model.
setInputStream(BufferedInputStream) - Method in class edu.stanford.rsl.conrad.utils.DicomDecoder
setInsert(int, int, Insert) - Method in class edu.stanford.rsl.conrad.phantom.electrondensity.CrisEDPhantomM062
setIntensifierSize(int) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setInterpolator(Interpolator) - Method in class edu.stanford.rsl.conrad.utils.interpolation.NumberInterpolatingTreeMap: Set the interpolating scheme used by the class.
setInvariants(ArrayList<SurfaceBSpline>) - Method in class edu.stanford.rsl.conrad.geometry.motion.MixedSurfaceBSplineMotionField
setjButtonBig(JButton) - Method in class edu.stanford.rsl.apps.gui.RawDataOpener
setjButtonDouble(JButton) - Method in class edu.stanford.rsl.apps.gui.RawDataOpener
setjButtonFloat(JButton) - Method in class edu.stanford.rsl.apps.gui.RawDataOpener
setjButtonLittle(JButton) - Method in class edu.stanford.rsl.apps.gui.RawDataOpener
setjButtonShort(JButton) - Method in class edu.stanford.rsl.apps.gui.RawDataOpener
setjButtonSShort(JButton) - Method in class edu.stanford.rsl.apps.gui.RawDataOpener
setKernel(float[]) - Method in class edu.stanford.rsl.conrad.filtering.MeanFilteringTool
setKernelHeight(int) - Method in class edu.stanford.rsl.conrad.filtering.MeanFilteringTool
setKernelHeight(int) - Method in class edu.stanford.rsl.conrad.filtering.MedianFilteringTool
setKernelWidth(int) - Method in class edu.stanford.rsl.conrad.filtering.MeanFilteringTool
setKernelWidth(int) - Method in class edu.stanford.rsl.conrad.filtering.MedianFilteringTool
setKFromDistancesSpacingsSizeOffset(double, SimpleVector, SimpleVector, SimpleVector, double, double) - Method in class edu.stanford.rsl.conrad.geometry.Projection: Constructs the K matrix from distance and offset parameters.
setKnots(double[]) - Method in class edu.stanford.rsl.conrad.geometry.splines.BSpline
setKValue(SimpleMatrix) - Method in class edu.stanford.rsl.conrad.geometry.Projection: Set the intrinsic parameters K of the projection.
setLabelMethod(int) - Method in class edu.stanford.rsl.apps.gui.blobdetection.ConnectedComponent3D: Set the value of this instance's labelMethod field
setLatch(CountDownLatch) - Method in class edu.stanford.rsl.conrad.filtering.IndividualImageFilteringTool
setLatch(CountDownLatch) - Method in class edu.stanford.rsl.conrad.filtering.multiprojection.blocks.ImageProcessingBlock
setLatch(CountDownLatch) - Method in interface edu.stanford.rsl.conrad.parallel.ParallelizableRunnable
setLatch(CountDownLatch) - Method in class edu.stanford.rsl.conrad.parallel.ParallelThread
setLatch(CountDownLatch) - Method in class edu.stanford.rsl.conrad.phantom.workers.SliceWorker
setLatch(CountDownLatch) - Method in class edu.stanford.rsl.conrad.physics.LambdaFunction
setLatch(CountDownLatch) - Method in class edu.stanford.rsl.conrad.pipeline.ParallelProjectionDataSinkFeeder
setLatch(CountDownLatch) - Method in class edu.stanford.rsl.conrad.volume3d.operations.ParallelVolumeOperation
setLittleEndian(boolean) - Method in class edu.stanford.rsl.conrad.io.IndividualFilesProjectionDataSink
setLocation(int, double) - Method in class edu.stanford.rsl.conrad.phantom.electrondensity.Insert
setLowerbound(double[]) - Method in class edu.stanford.rsl.conrad.fitting.ConstrainedRANSACFittedFunction
setLowerTensorLevel(float) - Method in class edu.stanford.rsl.conrad.filtering.multiprojection.anisotropic.AnisotropicStructureTensorNoiseFilter
setLowHyst(float) - Static method in class edu.stanford.rsl.conrad.filtering.multiprojection.DiaphragmTrackingTool
setLowHyst(float) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setLowPassFilterHeight(double) - Method in class edu.stanford.rsl.conrad.filtering.PrimaryModulationScatterCorrectionTool
setLowPassFilterWidth(double) - Method in class edu.stanford.rsl.conrad.filtering.PrimaryModulationScatterCorrectionTool
setLpUpper(float) - Method in class edu.stanford.rsl.conrad.filtering.multiprojection.anisotropic.AnisotropicStructureTensorNoiseFilter
setLpUpper(float) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeHighPass
setLpUpper(float) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeLowPass
setM(double) - Method in class edu.stanford.rsl.conrad.fitting.LinearFunction
setMap(double[], double[]) - Method in class edu.stanford.rsl.conrad.utils.LinearInterpolatingDoubleArray
setMaterial(Material) - Method in class edu.stanford.rsl.conrad.phantom.electrondensity.EDInnerDisk: Set disk material.
setMaterial(Material) - Method in class edu.stanford.rsl.conrad.phantom.electrondensity.EDOuterDisk: Set disk material.
setMaterial(Material) - Method in class edu.stanford.rsl.conrad.physics.PhysicalObject
setMatrixSerialization(String) - Method in class edu.stanford.rsl.conrad.numerics.SimpleMatrix: Initialize matrix using a serialized equivalent
setMax(PointND) - Method in class edu.stanford.rsl.conrad.rendering.AbstractScene
setMaxI(int) - Method in class edu.stanford.rsl.conrad.reconstruction.VOIBasedReconstructionFilter
setMaximumVolumeOfInterest(String) - Method in class edu.stanford.rsl.conrad.reconstruction.VOIBasedReconstructionFilter
setMaximumVolumeOfInterest(VolumeOfInterest) - Method in class edu.stanford.rsl.conrad.reconstruction.VOIBasedReconstructionFilter
setMaxIter(int) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setMaxIterations(int) - Static method in class edu.stanford.rsl.conrad.filtering.multiprojection.DiaphragmTrackingTool
setMaxMotion(double) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setMeanfilterLen(int) - Method in class edu.stanford.rsl.conrad.filtering.PrimaryModulationScatterCorrectionTool
setMin(PointND) - Method in class edu.stanford.rsl.conrad.rendering.AbstractScene
setMinAndMax(double, double) - Method in class edu.stanford.rsl.conrad.io.SerializableFloatProcessor: Sets the min and max variables that control how real pixel values are mapped to 0-255 screen values.
setModelWorker(SliceWorker) - Method in class edu.stanford.rsl.conrad.phantom.renderer.SliceParallelVolumePhantomRenderer
setModulationFunctionFilename(String) - Method in class edu.stanford.rsl.conrad.filtering.PrimaryModulationScatterCorrectionTool
setMotionField(MotionField) - Method in class edu.stanford.rsl.conrad.reconstruction.MotionCompensatedVOIBasedReconstructionFilter
setMu(double) - Method in class edu.stanford.rsl.conrad.fitting.GaussianFunction
setName(String) - Method in class edu.stanford.rsl.conrad.geometry.AbstractShape
setName(String) - Method in class edu.stanford.rsl.conrad.physics.materials.Material: Update the name of the material.
setName(String) - Method in class edu.stanford.rsl.conrad.rendering.AbstractScene
setNameString(String) - Method in class edu.stanford.rsl.conrad.physics.PhysicalObject
setNewPointsAndRecalibrate(ArrayList<PointND>, ArrayList<PointND>, int) - Method in class edu.stanford.rsl.tutorial.motionEstimation.ThinPlateSplineInterpolation: This method accepts a new pointgrid for interpolation, and the corresponding values.
setNext(float) - Method in class edu.stanford.rsl.conrad.data.iterators.PointwiseIterator
setNext(float) - Method in class edu.stanford.rsl.conrad.data.iterators.PointwiseIterator1D
setNext(float) - Method in class edu.stanford.rsl.conrad.data.iterators.PointwiseIterator2D
setNext(float) - Method in class edu.stanford.rsl.conrad.data.iterators.PointwiseIterator3D
setNormalizationImage(ImagePlus) - Method in class edu.stanford.rsl.conrad.metric.NormalizedImageMetric
setNormalizeMode(boolean) - Static method in class edu.stanford.rsl.conrad.geometry.General
setNTimes(int) - Method in class edu.stanford.rsl.conrad.filtering.HilbertFilteringTool
setnTimes(int) - Method in class edu.stanford.rsl.conrad.filtering.NumericalDerivativeComputationTool
setNumberOfBSplineTimePoints(int) - Method in class edu.stanford.rsl.conrad.phantom.xcat.BreathingScene
setNumberOfProjections(int) - Method in class edu.stanford.rsl.conrad.filtering.redundancy.ParkerWeightingTool
setNumberOfTries(int) - Method in class edu.stanford.rsl.conrad.fitting.RANSACFittedFunction
setNumberOfUPoints(int) - Method in class edu.stanford.rsl.conrad.geometry.splines.SurfaceBSpline
setNumberOfVPoints(int) - Method in class edu.stanford.rsl.conrad.geometry.splines.SurfaceBSpline
setNumProjectionMatrices(int) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setNumSweeps(int) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setObject(PhysicalObject) - Method in class edu.stanford.rsl.conrad.physics.PhysicalPoint
setOperand(double) - Method in class edu.stanford.rsl.conrad.filtering.ImageConstantMathFilter
setOperation(String) - Method in class edu.stanford.rsl.conrad.filtering.ExtremeValueTruncationFilter
setOperation(String) - Method in class edu.stanford.rsl.conrad.filtering.ImageConstantMathFilter
setOperation(String) - Method in class edu.stanford.rsl.conrad.filtering.ImageJParallelTool
setOperation(String) - Method in class edu.stanford.rsl.conrad.filtering.ImageMathFilter
setOrder(int) - Method in class edu.stanford.rsl.conrad.filtering.rampfilters.IRRFilter
setOrigin(double...) - Method in class edu.stanford.rsl.conrad.data.Grid: Set the array origin's world coordinates, given in real world units (usually mm) of the first pixel's center (excluding borders), in all dimensions.
setOrigin(double...) - Method in class edu.stanford.rsl.conrad.data.Grid2D
setOrigin(double...) - Method in class edu.stanford.rsl.conrad.data.Grid3D
setOriginInPixelsX(double) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setOriginInPixelsY(double) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setOriginInPixelsZ(double) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setOriginInWorld(PointND) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setOutputBlock(ImagePlus) - Method in class edu.stanford.rsl.conrad.filtering.multiprojection.blocks.ImageProcessingBlock
setOverlap(boolean) - Method in class edu.stanford.rsl.conrad.filtering.multiprojection.anisotropic.AnisotropicStructureTensorNoiseFilter
setParameters(double, double, double, double, String, boolean, int) - Method in class edu.stanford.rsl.apps.gui.blobdetection.AutomaticMarkerDetectionWorker
setParameters(double, double, double, double, String) - Method in class edu.stanford.rsl.apps.gui.blobdetection.MarkerDetectionWorker
setParameters(String) - Method in class edu.stanford.rsl.conrad.filtering.ImageJParallelTool
setParentFrame(UpdateableGUI) - Method in class edu.stanford.rsl.apps.gui.ConfigurationFrame
setParentFrame(UpdateableGUI) - Method in class edu.stanford.rsl.apps.gui.ConfigurePipelineFrame
setParentFrame(UpdateableGUI) - Method in class edu.stanford.rsl.apps.gui.GUICompatibleObjectVisualizationPanel
setPatellaRotationMatrix(PointND, PointND, double) - Method in class edu.stanford.rsl.conrad.phantom.xcat.ViconAffineTransform
setPhase1(double) - Method in class edu.stanford.rsl.conrad.geometry.motion.timewarp.DualPhasePeriodicTimeWarper
setPhotonCountMax(double) - Method in class edu.stanford.rsl.conrad.filtering.LogPoissonNoiseFilteringTool
setPhysicalPixelWidthInMilimeters(double) - Method in class edu.stanford.rsl.conrad.filtering.rampfilters.RampFilter
setPipeline(IndividualImageFilteringTool[]) - Method in class edu.stanford.rsl.conrad.pipeline.IndividualImagePipelineFilteringTool
setPipeline(IndividualImageFilteringTool[]) - Method in class edu.stanford.rsl.conrad.pipeline.ParallelImageFilterSink
setPixelDimensionX(double) - Method in class edu.stanford.rsl.conrad.filtering.CosineWeightingTool
setPixelDimensionX(double) - Method in class edu.stanford.rsl.conrad.filtering.redundancy.ParkerWeightingTool
setPixelDimensionX(double) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setPixelDimensionY(double) - Method in class edu.stanford.rsl.conrad.filtering.CosineWeightingTool
setPixelDimensionY(double) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setPixels(Object) - Method in class edu.stanford.rsl.conrad.io.SerializableFloatProcessor
setPixels(int, FloatProcessor) - Method in class edu.stanford.rsl.conrad.io.SerializableFloatProcessor: Sets the pixels, and min&max values from a FloatProcessor.
setPMatrixSerialization(String) - Method in class edu.stanford.rsl.conrad.geometry.Projection: This method is only used for XML serialization.
setPoint(PointND) - Method in class edu.stanford.rsl.conrad.geometry.shapes.simple.StraightLine
setPointCorrespondences(PointND[][][][]) - Method in class edu.stanford.rsl.conrad.reconstruction.MotionCompensatedVOIBasedReconstructionFilter
setPosition(int...) - Method in class edu.stanford.rsl.conrad.data.iterators.FloatIterator
setPrefix(String) - Method in class edu.stanford.rsl.conrad.io.IndividualFilesProjectionDataSink
setPrimaryAngleArray(double[]) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setPrimaryAngles(double[]) - Method in class edu.stanford.rsl.conrad.filtering.redundancy.ParkerWeightingTool
setPrimaryAnglesString(String) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setPrincipalPointValue(SimpleVector) - Method in class edu.stanford.rsl.conrad.geometry.Projection: Sets the principal point in pixels.
setProjection(Grid2D) - Method in class edu.stanford.rsl.conrad.pipeline.ParallelProjectionDataSinkFeeder
setProjectionMatrices(Projection[]) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setProjectionMatrix(SimpleMatrix) - Method in class edu.stanford.rsl.conrad.opencl.OpenCLRenderer
setProjectionNumber(int) - Method in class edu.stanford.rsl.conrad.pipeline.ParallelProjectionDataSinkFeeder
setProjectionSource(ProjectionSource) - Method in class edu.stanford.rsl.conrad.pipeline.IndividualImagePipelineFilteringTool
setProjectionStackSize(int) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setProjectionTableFileName(String) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setProjectionVolume(Grid3D) - Method in class edu.stanford.rsl.conrad.reconstruction.ReconstructionFilter: Used to set the projection volume.
setProjTurningAngle(double) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setPrototype(String) - Method in class edu.stanford.rsl.conrad.filtering.rampfilters.IRRFilter
setPrototype(int) - Method in class edu.stanford.rsl.conrad.filtering.rampfilters.IRRFilter
setPts(ArrayList<PointND>) - Method in class edu.stanford.rsl.conrad.io.VTKMeshReader: Sets a list of points
setPts(float[][]) - Method in class edu.stanford.rsl.tutorial.motionEstimation.OpenCLCompensatedBackProjectorTPS
setPtX(int) - Static method in class edu.stanford.rsl.conrad.filtering.multiprojection.DiaphragmTrackingTool
setPtY(int) - Static method in class edu.stanford.rsl.conrad.filtering.multiprojection.DiaphragmTrackingTool
setRadii(double[]) - Method in class edu.stanford.rsl.conrad.filtering.FastRadialSymmetryTool
setRamp(RampFilter) - Method in class edu.stanford.rsl.conrad.filtering.RampFilteringTool: Method to set the desired ramp for filtering.
setRate(float) - Method in class edu.stanford.rsl.conrad.filtering.rampfilters.IRRFilter
setReal(double) - Method in class edu.stanford.rsl.conrad.data.Complex
setRealAtIndex(int, float) - Method in class edu.stanford.rsl.conrad.data.Grid1DComplex
setRealAtIndex(int, int, float) - Method in class edu.stanford.rsl.conrad.data.Grid2DComplex
setRealtime(double[]) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setRecentFileOne(String) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setRecentFileTwo(String) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setReconDimensions(double...) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setReconDimensionX(int) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setReconDimensionY(int) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setReconDimensionZ(int) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setReconVoxelSizes(double[]) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setReferenceImage(ImagePlus) - Method in class edu.stanford.rsl.conrad.metric.ImageMetric
setRegistry(HashMap<String, String>) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setRegistryEntry(String, String) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setRespiratoryMotionField(double[]) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setRespiratoryMotionFieldEntry(int, double) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setRestPhase(double) - Method in class edu.stanford.rsl.conrad.geometry.motion.timewarp.RestPhaseTimeWarper
setRi(float) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeSquaredCosineR
setRingState(int, boolean) - Method in class edu.stanford.rsl.conrad.phantom.electrondensity.CrisEDPhantomM062
setRipple(float) - Method in class edu.stanford.rsl.conrad.filtering.rampfilters.IRRFilter
setRoi(Roi) - Method in class edu.stanford.rsl.apps.gui.roi.EvaluateROI
setRoiHeightBottom(int) - Static method in class edu.stanford.rsl.conrad.filtering.multiprojection.DiaphragmTrackingTool
setRoiHeightBottom(int) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setRoiHeightBottomMax(int) - Static method in class edu.stanford.rsl.conrad.filtering.multiprojection.DiaphragmTrackingTool
setRoiHeightTop(int) - Static method in class edu.stanford.rsl.conrad.filtering.multiprojection.DiaphragmTrackingTool
setRoiHeightTop(int) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setRoiHeightTopMax(int) - Static method in class edu.stanford.rsl.conrad.filtering.multiprojection.DiaphragmTrackingTool
setRoiManagerPointSet(int) - Method in class edu.stanford.rsl.apps.gui.pointselector.PointSelectorWorker
setRoiWidthHalf(int) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setRoiWidthHalfMax(int) - Static method in class edu.stanford.rsl.conrad.filtering.multiprojection.DiaphragmTrackingTool
setRoiWidthLeft(int) - Static method in class edu.stanford.rsl.conrad.filtering.multiprojection.DiaphragmTrackingTool
setRoiWidthRight(int) - Static method in class edu.stanford.rsl.conrad.filtering.multiprojection.DiaphragmTrackingTool
setRotationAxis(SimpleVector) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setRowValue(int, SimpleVector) - Method in class edu.stanford.rsl.conrad.numerics.SimpleMatrix: Replace row with newRow
setRtFromCircularTrajectory(SimpleVector, SimpleVector, double, SimpleVector, Projection.CameraAxisDirection, Projection.CameraAxisDirection, double) - Method in class edu.stanford.rsl.conrad.geometry.Projection: Constructs the extrinsic parameters (R and t) of this projection from the extrensic parameters source-to-isocenter distance, rotation axis, rotation angle, and viewing axis.
setRtValue(SimpleMatrix) - Method in class edu.stanford.rsl.conrad.geometry.Projection: Set the extrinsic parameters of the projection.
setRValue(SimpleMatrix) - Method in class edu.stanford.rsl.conrad.geometry.Projection: Set the rotation part of the extrinsic parameters of the projection.
setSamplingStep(double) - Method in class edu.stanford.rsl.conrad.geometry.splines.MotionDefectTimeVariantSurfaceBSpline
setSaveToDisk(boolean) - Method in class edu.stanford.rsl.apps.gui.ConfigurePipelineFrame
setScalar1(float) - Method in class edu.stanford.rsl.conrad.volume3d.operations.ParallelVolumeOperation
setScalar2(float) - Method in class edu.stanford.rsl.conrad.volume3d.operations.ParallelVolumeOperation
setScale(double) - Method in class edu.stanford.rsl.conrad.filtering.rampfilters.SheppLoganRampFilterWithRollOff
setScatterEstScale(double) - Method in class edu.stanford.rsl.conrad.filtering.PrimaryModulationScatterCorrectionTool
setScene(AbstractScene) - Method in class edu.stanford.rsl.conrad.geometry.splines.SurfaceBSplineVolumePhantom
setScene(AbstractScene) - Method in class edu.stanford.rsl.conrad.rendering.AbstractRayTracer
setSecondaryAngleArray(double[]) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setSecondaryAnglesString(String) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setSeedX(int) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setSeedY(int) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setShape(AbstractShape) - Method in class edu.stanford.rsl.conrad.physics.PhysicalObject
setShowAbsoluteTensor(boolean) - Method in class edu.stanford.rsl.conrad.filtering.multiprojection.anisotropic.AnisotropicStructureTensorNoiseFilter
setShowProgress(boolean) - Method in class edu.stanford.rsl.conrad.io.FileProjectionSource
setShowStatus(boolean) - Method in class edu.stanford.rsl.conrad.filtering.multiprojection.anisotropic.AnisotropicFilterFunction
setShowStatus(boolean) - Method in class edu.stanford.rsl.conrad.filtering.multiprojection.MultiProjectionFilter
setShowStatus(boolean) - Method in class edu.stanford.rsl.conrad.parallel.ParallelThreadExecutor
setShowStatus(boolean) - Method in class edu.stanford.rsl.conrad.phantom.workers.SliceWorker
setShowStatus(boolean) - Method in class edu.stanford.rsl.conrad.pipeline.BufferedProjectionSink
setShowStatus(boolean) - Method in class edu.stanford.rsl.conrad.pipeline.ParallelImageFilterSink
setShowStatus(boolean) - Method in interface edu.stanford.rsl.conrad.pipeline.ProjectionSink
setSigma(double) - Method in class edu.stanford.rsl.conrad.filtering.DynamicDensityOptimizationScatterCorrectionTool
setSigma(double) - Method in class edu.stanford.rsl.conrad.fitting.GaussianFunction
setSigma(float) - Method in class edu.stanford.rsl.conrad.volume3d.operations.InitializeGaussian
setSink(ProjectionSink) - Method in class edu.stanford.rsl.conrad.filtering.multiprojection.MultiProjectionFilter: Used to connect the filter with the rest of the pipeline.
setSink(ProjectionSink) - Method in class edu.stanford.rsl.conrad.pipeline.IndividualImagePipelineFilteringTool
setSink(ProjectionSink) - Method in class edu.stanford.rsl.conrad.pipeline.ParallelImageFilterSink
setSink(ProjectionSink) - Method in class edu.stanford.rsl.conrad.pipeline.ParallelProjectionDataSinkFeeder
setSink(BufferedProjectionSink) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setSize(CalibrationBead.Property) - Method in class edu.stanford.rsl.conrad.calibration.CalibrationBead
setSliceList(Iterator<Integer>) - Method in class edu.stanford.rsl.conrad.phantom.workers.SliceWorker: Sets the sliceList which is being processed
setSlope(double) - Method in class edu.stanford.rsl.conrad.phantom.renderer.RampProjectionPhantomRenderer
setSmallGradientThreshold(double) - Method in class edu.stanford.rsl.conrad.filtering.FastRadialSymmetryTool
setSmoothness(float) - Method in class edu.stanford.rsl.conrad.filtering.multiprojection.anisotropic.AnisotropicStructureTensorNoiseFilter
setSnapshotPixels(Object) - Method in class edu.stanford.rsl.conrad.io.SerializableFloatProcessor
setSoftcutfactor(double) - Method in class edu.stanford.rsl.conrad.filtering.PrimaryModulationScatterCorrectionTool
setSortIndex(int) - Method in class edu.stanford.rsl.conrad.geometry.shapes.simple.SortablePoint
setSourceToAxisDistance(double) - Method in class edu.stanford.rsl.conrad.filtering.CosineWeightingTool
setSourceToAxisDistance(double) - Method in class edu.stanford.rsl.conrad.filtering.rampfilters.RampFilter
setSourceToAxisDistance(double) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setSourceToDetectorDistance(double) - Method in class edu.stanford.rsl.conrad.filtering.CosineWeightingTool
setSourceToDetectorDistance(double) - Method in class edu.stanford.rsl.conrad.filtering.rampfilters.RampFilter
setSourceToDetectorDistance(double) - Method in class edu.stanford.rsl.conrad.filtering.redundancy.ParkerWeightingTool
setSourceToDetectorDistance(double) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setSpacing(double...) - Method in class edu.stanford.rsl.conrad.data.Grid: Set the array's spacings.
setSpacing(double...) - Method in class edu.stanford.rsl.conrad.data.Grid2D
setSpacing(double...) - Method in class edu.stanford.rsl.conrad.data.Grid3D
setSplineList(ArrayList<SurfaceBSpline>) - Method in class edu.stanford.rsl.conrad.geometry.splines.SurfaceBSplineVolumePhantom
setStack(int) - Method in class edu.stanford.rsl.conrad.phantom.renderer.RampProjectionPhantomRenderer
setStart(double) - Method in class edu.stanford.rsl.conrad.filtering.rampfilters.SheppLoganRampFilterWithRollOff
setSubColValue(int, int, SimpleVector) - Method in class edu.stanford.rsl.conrad.numerics.SimpleMatrix: Replace the entries of sub column starting at [col,firstRow] with subCol
setSubGrid(int, Grid2D) - Method in class edu.stanford.rsl.conrad.data.Grid3D
setSubMatrixValue(int, int, SimpleMatrix) - Method in class edu.stanford.rsl.conrad.numerics.SimpleMatrix: Replaces matrix entries starting at firsRow and firstCol with entries from subMatrix
setSubRowValue(int, int, SimpleVector) - Method in class edu.stanford.rsl.conrad.numerics.SimpleMatrix: Replace the entries of sub row starting at [row,firstCol] with subRow
setSubVecValue(int, SimpleVector) - Method in class edu.stanford.rsl.conrad.numerics.SimpleVector
setSValue(double) - Method in class edu.stanford.rsl.conrad.geometry.Projection: Set the (positive) scaling of the projection.
setSymbol(String) - Method in class edu.stanford.rsl.conrad.physics.materials.Element: Set the atomic symbol of the element.
setT(double) - Method in class edu.stanford.rsl.conrad.fitting.LinearFunction
setTestImage(ImagePlus) - Method in class edu.stanford.rsl.conrad.metric.ImageMetric
setTex3D(ImagePlus) - Method in class edu.stanford.rsl.conrad.cuda.CUDAForwardProjector: Sets the volume to project
setTex3D(ImagePlus) - Method in class edu.stanford.rsl.conrad.cuda.CUDAForwardProjectorWithMotion: Sets the volume to project
setTex3D(ImagePlus) - Method in class edu.stanford.rsl.conrad.opencl.OpenCLForwardProjector: Sets the volume to project
setTex3D(ImagePlus) - Method in class edu.stanford.rsl.conrad.opencl.OpenCLForwardProjectorWithMotion: Sets the volume to project
setThreadNumber(int) - Method in class edu.stanford.rsl.conrad.cuda.CUDAFFTVolumeHandle
setThreadNumber(int) - Method in class edu.stanford.rsl.conrad.filtering.multiprojection.anisotropic.AnisotropicFilterFunction: Method to limit the number of threads used by the FFT of the filter.
setThreadNumber(int) - Method in class edu.stanford.rsl.conrad.volume3d.FFTVolumeHandle: Sets the maximal number of threads used for the FFT.
setThreadNumber(int) - Method in class edu.stanford.rsl.conrad.volume3d.JTransformsFFTVolumeHandle
setThreshold(double) - Method in class edu.stanford.rsl.conrad.filtering.ExtremeValueTruncationFilter
setThreshold(double, double, int) - Method in class edu.stanford.rsl.conrad.io.SerializableFloatProcessor
setTime(double[]) - Method in class edu.stanford.rsl.conrad.utils.Configuration: Sets the exposure time in [s]
setTimeWarper(TimeWarper) - Method in interface edu.stanford.rsl.conrad.geometry.motion.MotionField
setTimeWarper(TimeWarper) - Method in class edu.stanford.rsl.conrad.geometry.motion.ParzenWindowMotionField
setTimeWarper(TimeWarper) - Method in class edu.stanford.rsl.conrad.geometry.motion.PlanarMotionField
setTimeWarper(TimeWarper) - Method in class edu.stanford.rsl.conrad.geometry.motion.PointBasedMotionField
setTimeWarper(TimeWarper) - Method in class edu.stanford.rsl.conrad.geometry.motion.SimpleMotionField
setTimeWarper(TimeWarper) - Method in class edu.stanford.rsl.conrad.phantom.AnalyticPhantom4D
setTimeWarper(TimeWarper) - Method in class edu.stanford.rsl.conrad.phantom.xcat.BreathingScene
setTimeWarper(TimeWarper) - Method in class edu.stanford.rsl.conrad.phantom.xcat.CoronaryScene
setTimeWarper(TimeWarper) - Method in class edu.stanford.rsl.conrad.phantom.xcat.HeartScene
setTimeWarper(TimeWarper) - Method in class edu.stanford.rsl.conrad.phantom.xcat.SquatScene
setTimeWarper(TimeWarper) - Method in class edu.stanford.rsl.conrad.phantom.xcat.XCatScene
setTitle(String) - Method in class edu.stanford.rsl.conrad.geometry.splines.SurfaceBSpline
setTitle(String) - Method in class edu.stanford.rsl.conrad.geometry.splines.TimeVariantSurfaceBSpline
setTitle(String) - Method in class edu.stanford.rsl.tutorial.phantoms.Phantom
setTitle(String) - Method in class edu.stanford.rsl.tutorial.phantoms.Phantom3D
setTrajectory(int, double, double, double, double, Projection.CameraAxisDirection, Projection.CameraAxisDirection, SimpleVector) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.CircularTrajectory
setTVector(SimpleVector) - Method in class edu.stanford.rsl.conrad.geometry.Projection: Set the translation part of the extrinsic parameters of the projection.
setTwoD(boolean) - Method in class edu.stanford.rsl.conrad.filtering.NumericalDerivativeComputationTool
setU(double) - Method in class edu.stanford.rsl.conrad.calibration.CalibrationBead
setuCtrl(int) - Method in class edu.stanford.rsl.tutorial.motionEstimation.EstimateBSplineSurface: Setter for number of u-controlpoints
setup() - Static method in class edu.stanford.rsl.conrad.utils.CONRAD
setUpperbound(double[]) - Method in class edu.stanford.rsl.conrad.fitting.ConstrainedRANSACFittedFunction
setUpperTensorLevel(float) - Method in class edu.stanford.rsl.conrad.filtering.multiprojection.anisotropic.AnisotropicStructureTensorNoiseFilter
setUseExtrapolatedGeometry(boolean) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setUseGarbageCollection(boolean) - Static method in class edu.stanford.rsl.conrad.utils.CONRAD
setUseHounsfieldScaling(boolean) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setUseOrientationOnly(boolean) - Method in class edu.stanford.rsl.conrad.filtering.FastRadialSymmetryTool
setUsePositiveNegativeOnly(int) - Method in class edu.stanford.rsl.conrad.filtering.FastRadialSymmetryTool
setV(double) - Method in class edu.stanford.rsl.conrad.calibration.CalibrationBead
setValue(double) - Method in class edu.stanford.rsl.conrad.io.SerializableFloatProcessor: Sets the default fill/draw value.
setVariant(TimeVariantSurfaceBSpline) - Method in class edu.stanford.rsl.conrad.geometry.motion.TimeVariantSurfaceBSplineMotionField
setVariants(ArrayList<TimeVariantSurfaceBSpline>) - Method in class edu.stanford.rsl.conrad.geometry.motion.MixedSurfaceBSplineMotionField
setVariants(ArrayList<TimeVariantSurfaceBSpline>) - Method in class edu.stanford.rsl.conrad.geometry.motion.TimeVariantSurfaceBSplineListMotionField
setvCtrl(int) - Method in class edu.stanford.rsl.tutorial.motionEstimation.EstimateBSplineSurface: Setter for number of v-controlpoints
setVector(SimpleVector) - Method in class edu.stanford.rsl.conrad.geometry.shapes.simple.VectorPoint3D
setVectorSerialization(String) - Method in class edu.stanford.rsl.conrad.numerics.SimpleVector
setViewingDirectionValue(double) - Method in class edu.stanford.rsl.conrad.geometry.Projection: Set the viewing direction of the camera with respect to the z axis of the camera coordinate system.
setVisualizedObject(BufferedProjectionSink) - Method in class edu.stanford.rsl.apps.gui.GUICompatibleObjectVisualizationPanel
setVol(Volume3D) - Method in class edu.stanford.rsl.conrad.volume3d.operations.ParallelVolumeOperation
setVol1(Volume3D) - Method in class edu.stanford.rsl.conrad.volume3d.operations.ParallelVolumeOperation
setVol2(Volume3D) - Method in class edu.stanford.rsl.conrad.volume3d.operations.ParallelVolumeOperation
setVoltage(double[]) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setVolumeOfInterestFileName(String) - Method in class edu.stanford.rsl.conrad.utils.Configuration
setVolumeOperator(VolumeOperator) - Method in class edu.stanford.rsl.conrad.volume3d.FFTVolumeHandle
setVoxel(byte[], int, int, int, double) - Method in class edu.stanford.rsl.conrad.cuda.ImagePlusVolumeRenderer
setVoxel(byte[], int, int, int, double) - Method in class edu.stanford.rsl.conrad.opencl.rendering.OpenCLVolumeRenderer
setVoxelSpacingX(double) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setVoxelSpacingY(double) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setVoxelSpacingZ(double) - Method in class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory
setWeight(double) - Method in class edu.stanford.rsl.conrad.filtering.DynamicDensityOptimizationScatterCorrectionTool
setWeightedAtomicComposition(WeightedAtomicComposition) - Method in class edu.stanford.rsl.conrad.physics.materials.Material: Update the atomic composition of material by mass
setWidth(int) - Method in class edu.stanford.rsl.conrad.io.IndividualFilesProjectionDataSink
setWidth(int) - Method in class edu.stanford.rsl.conrad.phantom.renderer.RampProjectionPhantomRenderer: sets the width of the image to be rendered
setWorkload(int) - Static method in class edu.stanford.rsl.conrad.filtering.multiprojection.DiaphragmTrackingTool
setX(double) - Method in class edu.stanford.rsl.conrad.calibration.CalibrationBead
setX(double) - Method in class edu.stanford.rsl.conrad.geometry.shapes.simple.Point2D: sets the x coordinate
setX(double) - Method in class edu.stanford.rsl.conrad.geometry.shapes.simple.Point3D: sets the x coordinate
setXPoints(double, double) - Method in class edu.stanford.rsl.conrad.utils.interpolation.Interpolator
setY(double) - Method in class edu.stanford.rsl.conrad.calibration.CalibrationBead
setY(double) - Method in class edu.stanford.rsl.conrad.geometry.shapes.simple.Point2D: sets the y coordinate
setY(double) - Method in class edu.stanford.rsl.conrad.geometry.shapes.simple.Point3D: sets the y coordinate
setYPoints(double, double) - Method in class edu.stanford.rsl.conrad.utils.interpolation.Interpolator
setZ(double) - Method in class edu.stanford.rsl.conrad.calibration.CalibrationBead
setZ(double) - Method in class edu.stanford.rsl.conrad.geometry.shapes.simple.Point3D: sets the z coordinate
setZeroValue(double) - Method in class edu.stanford.rsl.conrad.filtering.AtractResidual2D
SevenBeadPhantom - Class in edu.stanford.rsl.conrad.phantom: Phantom to test forward and back projection resolution.
SevenBeadPhantom() - Constructor for class edu.stanford.rsl.conrad.phantom.SevenBeadPhantom
sharpenFloat(FloatProcessor, double, float) - Method in class edu.stanford.rsl.conrad.filtering.DynamicDensityOptimizationScatterCorrectionTool: Dynamic Density Optimization of a float image.
SheppLogan - Class in edu.stanford.rsl.tutorial.phantoms
SheppLogan(int, boolean) - Constructor for class edu.stanford.rsl.tutorial.phantoms.SheppLogan
SheppLogan(int) - Constructor for class edu.stanford.rsl.tutorial.phantoms.SheppLogan
SheppLogan3D - Class in edu.stanford.rsl.conrad.phantom: Three-dimensional Shepp-Logan Phantom in both the Fourier and image domains.
SheppLogan3D() - Constructor for class edu.stanford.rsl.conrad.phantom.SheppLogan3D: Creates a new instance of SheppLogan3D
SheppLogan3D(double[][]) - Constructor for class edu.stanford.rsl.conrad.phantom.SheppLogan3D: User may add new ellipsoids and change their properties with this constructor.
SheppLoganPhantom - Class in edu.stanford.rsl.conrad.phantom: 3-D definition of the Shepp-Logan Phantom.
SheppLoganPhantom() - Constructor for class edu.stanford.rsl.conrad.phantom.SheppLoganPhantom
SheppLoganPhantomWorker - Class in edu.stanford.rsl.conrad.phantom.workers: Wrapper class to create a volume phantom from the SheppLogan3D Class.
SheppLoganPhantomWorker() - Constructor for class edu.stanford.rsl.conrad.phantom.workers.SheppLoganPhantomWorker
SheppLoganRampFilter - Class in edu.stanford.rsl.conrad.filtering.rampfilters
SheppLoganRampFilter() - Constructor for class edu.stanford.rsl.conrad.filtering.rampfilters.SheppLoganRampFilter
SheppLoganRampFilterWithRollOff - Class in edu.stanford.rsl.conrad.filtering.rampfilters
SheppLoganRampFilterWithRollOff() - Constructor for class edu.stanford.rsl.conrad.filtering.rampfilters.SheppLoganRampFilterWithRollOff
show() - Method in class edu.stanford.rsl.conrad.data.Grid: Show the object in an imageJ window
show(String) - Method in class edu.stanford.rsl.conrad.data.Grid: Show the object in an imageJ window with title
show(String) - Method in class edu.stanford.rsl.conrad.data.Grid1D
show() - Method in class edu.stanford.rsl.conrad.data.Grid1D
show(String) - Method in class edu.stanford.rsl.conrad.data.Grid2D
show() - Method in class edu.stanford.rsl.conrad.data.Grid2D
show(String) - Method in class edu.stanford.rsl.conrad.data.Grid2DComplex
show() - Method in class edu.stanford.rsl.conrad.data.Grid2DComplex
show(String) - Method in class edu.stanford.rsl.conrad.data.Grid3D
show() - Method in class edu.stanford.rsl.conrad.data.Grid3D
showGrid2D(Grid2D, String) - Static method in class edu.stanford.rsl.conrad.utils.VisualizationUtil
showGrid3DX(Grid3D, String) - Static method in class edu.stanford.rsl.conrad.utils.VisualizationUtil
showGrid3DX(Grid3D) - Static method in class edu.stanford.rsl.conrad.utils.VisualizationUtil
showGrid3DZ(Grid3D, String) - Static method in class edu.stanford.rsl.conrad.utils.VisualizationUtil
showGrid3DZ(Grid3D) - Static method in class edu.stanford.rsl.conrad.utils.VisualizationUtil
showImageProcessor(ImageProcessor, String) - Static method in class edu.stanford.rsl.conrad.utils.VisualizationUtil
showImageProcessor(ImageProcessor) - Static method in class edu.stanford.rsl.conrad.utils.VisualizationUtil
sigmoid(Volume3D, float, float, float, float, float) - Method in class edu.stanford.rsl.conrad.cuda.CUDAVolumeOperator
sigmoid(Volume3D, float, float, float, float, float) - Method in class edu.stanford.rsl.conrad.volume3d.VolumeOperator: Remaps gray values using a sigmoid function.
SigmoidTimeWarper - Class in edu.stanford.rsl.conrad.geometry.motion.timewarp: Implements an accelerated/deaccelerated time warping.
SigmoidTimeWarper() - Constructor for class edu.stanford.rsl.conrad.geometry.motion.timewarp.SigmoidTimeWarper
SignedShort - Static variable in class edu.stanford.rsl.conrad.io.IndividualFilesProjectionDataSink
SilverWeightingTool - Class in edu.stanford.rsl.conrad.filtering.redundancy
SilverWeightingTool() - Constructor for class edu.stanford.rsl.conrad.filtering.redundancy.SilverWeightingTool
SilverWeights - Class in edu.stanford.rsl.tutorial.fan.redundancy
SilverWeights(double, double, double, double, double) - Constructor for class edu.stanford.rsl.tutorial.fan.redundancy.SilverWeights
Simple1DRayTracer - Class in edu.stanford.rsl.conrad.rendering
Simple1DRayTracer() - Constructor for class edu.stanford.rsl.conrad.rendering.Simple1DRayTracer
SimpleCubes3D - Class in edu.stanford.rsl.tutorial.phantoms: Simple class to show the Grid3D functionality.
SimpleCubes3D(int, int, int) - Constructor for class edu.stanford.rsl.tutorial.phantoms.SimpleCubes3D: The constructor takes three arguments to initialize the grid.
SimpleIterativeReconstruction - Class in edu.stanford.rsl.conrad.reconstruction: A simple approach for iterative reconstruction.
SimpleIterativeReconstruction() - Constructor for class edu.stanford.rsl.conrad.reconstruction.SimpleIterativeReconstruction
SimpleMatrix - Class in edu.stanford.rsl.conrad.numerics
SimpleMatrix() - Constructor for class edu.stanford.rsl.conrad.numerics.SimpleMatrix: Create an empty matrix.
SimpleMatrix(int, int) - Constructor for class edu.stanford.rsl.conrad.numerics.SimpleMatrix: Create a matrix with row rows and column cols
SimpleMatrix(SimpleMatrix) - Constructor for class edu.stanford.rsl.conrad.numerics.SimpleMatrix: Creates a new matrix from another
SimpleMatrix(double[][]) - Constructor for class edu.stanford.rsl.conrad.numerics.SimpleMatrix: Creates a new matrix from 2x2 double array
SimpleMatrix(String) - Constructor for class edu.stanford.rsl.conrad.numerics.SimpleMatrix: Creates a new matrix from string data
SimpleMatrix(Matrix) - Constructor for class edu.stanford.rsl.conrad.numerics.SimpleMatrix: Creates a new matrix from a jama matrix
SimpleMatrix.InversionType - Enum in edu.stanford.rsl.conrad.numerics: Set the algorithm to be used during inversion
SimpleMatrix.MatrixNormType - Enum in edu.stanford.rsl.conrad.numerics
SimpleMatrixTest - Class in edu.stanford.rsl.conrad.numerics.test
SimpleMatrixTest() - Constructor for class edu.stanford.rsl.conrad.numerics.test.SimpleMatrixTest
SimpleMotionField - Class in edu.stanford.rsl.conrad.geometry.motion
SimpleMotionField() - Constructor for class edu.stanford.rsl.conrad.geometry.motion.SimpleMotionField
simpleObjects - Static variable in class edu.stanford.rsl.conrad.opencl.OpenCLUtil
SimpleOperators - Class in edu.stanford.rsl.conrad.numerics
SimpleOperators() - Constructor for class edu.stanford.rsl.conrad.numerics.SimpleOperators
SimpleOperatorsTest - Class in edu.stanford.rsl.conrad.numerics.test
SimpleOperatorsTest() - Constructor for class edu.stanford.rsl.conrad.numerics.test.SimpleOperatorsTest
SimpleParallelThread - Class in edu.stanford.rsl.conrad.parallel
SimpleParallelThread(int) - Constructor for class edu.stanford.rsl.conrad.parallel.SimpleParallelThread
SimpleRayTracer - Class in edu.stanford.rsl.conrad.rendering
SimpleRayTracer() - Constructor for class edu.stanford.rsl.conrad.rendering.SimpleRayTracer
SimpleScene - Class in edu.stanford.rsl.conrad.rendering
SimpleScene() - Constructor for class edu.stanford.rsl.conrad.rendering.SimpleScene
SimpleSurface - Class in edu.stanford.rsl.conrad.geometry.shapes.simple: CONRAD Class to model surfaces that can efficiently determine the membership of an arbitrary point.
SimpleSurface() - Constructor for class edu.stanford.rsl.conrad.geometry.shapes.simple.SimpleSurface
SimpleVector - Class in edu.stanford.rsl.conrad.numerics
SimpleVector() - Constructor for class edu.stanford.rsl.conrad.numerics.SimpleVector: Creates a null vector.
SimpleVector(int) - Constructor for class edu.stanford.rsl.conrad.numerics.SimpleVector: Creates a len dimensional vector
SimpleVector(SimpleVector) - Constructor for class edu.stanford.rsl.conrad.numerics.SimpleVector: Creates a new vector from otherVec.
SimpleVector(double...) - Constructor for class edu.stanford.rsl.conrad.numerics.SimpleVector: Creates a new vector initialized by an ordered list of numbers
SimpleVector(String) - Constructor for class edu.stanford.rsl.conrad.numerics.SimpleVector: Creates a new vector from a string equivalent
SimpleVector(Matrix) - Constructor for class edu.stanford.rsl.conrad.numerics.SimpleVector: Creates a new vector from a jama equivalent
SimpleVector.VectorNormType - Enum in edu.stanford.rsl.conrad.numerics
SimpleVectorTest - Class in edu.stanford.rsl.conrad.numerics.test
SimpleVectorTest() - Constructor for class edu.stanford.rsl.conrad.numerics.test.SimpleVectorTest
size() - Method in class edu.stanford.rsl.conrad.geometry.shapes.compound.CompoundShape
size() - Method in class edu.stanford.rsl.conrad.geometry.shapes.compound.LinearOctree
size() - Method in class edu.stanford.rsl.conrad.physics.materials.utils.WeightedAtomicComposition: Returns the number of elements that constitute the material of interest
size() - Method in class edu.stanford.rsl.conrad.physics.materials.WeightedAtomicComposition
size() - Method in class edu.stanford.rsl.conrad.physics.PolychromaticXRaySpectrum: Determine the number of discrete energies used to describe the spectrum
size() - Method in class edu.stanford.rsl.conrad.rendering.PrioritizableScene
size() - Method in class edu.stanford.rsl.conrad.rendering.SimpleScene
size() - Method in class edu.stanford.rsl.conrad.utils.ImageProcessorBuffer: returns the number of stored ImageProcessors
size() - Method in class edu.stanford.rsl.conrad.utils.LinearInterpolatingDoubleArray
size - Variable in class edu.stanford.rsl.conrad.volume3d.Volume3D
sizes - Variable in class edu.stanford.rsl.conrad.io.NrrdFileInfo
SliceParallelVolumePhantomRenderer - Class in edu.stanford.rsl.conrad.phantom.renderer: Class to enable parallel processing of slices of the target volume.
SliceParallelVolumePhantomRenderer() - Constructor for class edu.stanford.rsl.conrad.phantom.renderer.SliceParallelVolumePhantomRenderer
SliceWorker - Class in edu.stanford.rsl.conrad.phantom.workers: Class to model an abstract slice worker.
SliceWorker() - Constructor for class edu.stanford.rsl.conrad.phantom.workers.SliceWorker
SliceWorkerParser - Interface in edu.stanford.rsl.conrad.utils.parsers
SLOW_DOWN_MS - Static variable in class edu.stanford.rsl.conrad.utils.RegKeys: Entry to describe the slow down value, if the memory gets too full during the processing.
SMALL_VALUE - Static variable in class edu.stanford.rsl.conrad.utils.CONRAD
SmoothKernel1D - Class in edu.stanford.rsl.tutorial.motionEstimation: This class implements the 1-D version of a smoothing kernel (1 1 1)
SmoothKernel1D(int, int) - Constructor for class edu.stanford.rsl.tutorial.motionEstimation.SmoothKernel1D
snapshot() - Method in class edu.stanford.rsl.conrad.io.SerializableFloatProcessor
SobelKernel1D - Class in edu.stanford.rsl.tutorial.motionEstimation: This class implements the 1-D version of the Sobel Kernel (-2 0 2)
SobelKernel1D(int, int) - Constructor for class edu.stanford.rsl.tutorial.motionEstimation.SobelKernel1D
SoftBone_mdensity - Static variable in class edu.stanford.rsl.conrad.physics.Constants: B-100 Bone-Equivalent Plastic mass density 1.450E+00 (g/cm3)
SoftBoneCTValue - Static variable in class edu.stanford.rsl.conrad.physics.Constants
softBoneEnergies - Static variable in class edu.stanford.rsl.conrad.physics.EnergyDependentCoefficients: Deprecated.

Energies [Mev] at which the coefficients were meassured.
softBoneMuEnOverRho - Static variable in class edu.stanford.rsl.conrad.physics.EnergyDependentCoefficients: Deprecated.

mass energy-absorption coefficient (mu_\text{en}/rho) in [cm^2/g]
softBoneMuOverRho - Static variable in class edu.stanford.rsl.conrad.physics.EnergyDependentCoefficients: Deprecated.

Photon mass attenuation coefficients (mu/rho) in [cm^2/g]
SoftTissue_mdensity - Static variable in class edu.stanford.rsl.conrad.physics.Constants: soft tissue mass density 1.00 (g/cm3)
SoftTissueCTValue - Static variable in class edu.stanford.rsl.conrad.physics.Constants
softTissueEnergies - Static variable in class edu.stanford.rsl.conrad.physics.EnergyDependentCoefficients: Deprecated.

Energies [Mev] at which the coefficients were meassured.
softTissueMuEnOverRho - Static variable in class edu.stanford.rsl.conrad.physics.EnergyDependentCoefficients: Deprecated.

mass energy-absorption coefficient (mu_\text{en}/rho) in [cm^2/g]
softTissueMuOverRho - Static variable in class edu.stanford.rsl.conrad.physics.EnergyDependentCoefficients: Deprecated.

Photon mass attenuation coefficients (mu/rho) in [cm^2/g]
solve(SimpleVector) - Method in class edu.stanford.rsl.conrad.numerics.DecompositionQR: Computes solution Vector $\mathbf x$ for the right-hand-side $\mathbf b$ .
solve(SimpleMatrix) - Method in class edu.stanford.rsl.conrad.numerics.DecompositionQR: Computes solution Matrix $\mathbf X$ for the right-hand-side $\mathbf B$ .
solve(SimpleVector) - Method in class edu.stanford.rsl.conrad.numerics.DecompositionRQ: Computes solution Vector $\mathbf{x}$ for the right-hand-side $\mathbf b$ .
solve(SimpleMatrix) - Method in class edu.stanford.rsl.conrad.numerics.DecompositionRQ: Computes solution Matrix $\mathbf X$ for the right-hand-side $\mathbf B$ .
solveLinearLeastSquares(SimpleMatrix, SimpleVector) - Static method in class edu.stanford.rsl.conrad.numerics.Solvers: Solves the linear least squares problem $\min_{\mathbf{x}} \| \mathbf{A} \cdot \mathbf{x} - \mathbf{b} \|^2$ with a matrix A (with as least as much rows as columns).
solveLinearSysytemOfEquations(SimpleMatrix, SimpleVector) - Static method in class edu.stanford.rsl.conrad.numerics.Solvers: Solves the linear system of equations $\mathbf{A} \cdot \mathbf{x} = \mathbf{b}$ with a square matrix A.
solveLowerTriangular(SimpleMatrix, SimpleVector) - Static method in class edu.stanford.rsl.conrad.numerics.Solvers: Solves the linear system of equations L*x = b with a square, lower-triangular matrix L using forward substitution.
solveMaximumEigenvalue(Volume3D[][]) - Method in class edu.stanford.rsl.conrad.cuda.CUDAVolumeOperator
solveMaximumEigenvalue(Volume3D[][]) - Method in class edu.stanford.rsl.conrad.volume3d.ParallelVolumeOperator
solveMaximumEigenvalue(Volume3D[][]) - Method in class edu.stanford.rsl.conrad.volume3d.VolumeOperator: Method to compute the maximal eigenvalue $%preamble{\usepackage{amsmath}} $\lambda_1$$ per volume element for a volume structure tensor.
Solvers - Class in edu.stanford.rsl.conrad.numerics
Solvers() - Constructor for class edu.stanford.rsl.conrad.numerics.Solvers
SolversTest - Class in edu.stanford.rsl.conrad.numerics.test
SolversTest() - Constructor for class edu.stanford.rsl.conrad.numerics.test.SolversTest
solveUpperTriangular(SimpleMatrix, SimpleVector) - Static method in class edu.stanford.rsl.conrad.numerics.Solvers: Solves the linear system of equations U*x = b with a square, upper-triangular matrix U using backward substitution.
SortablePoint - Class in edu.stanford.rsl.conrad.geometry.shapes.simple
SortablePoint(double...) - Constructor for class edu.stanford.rsl.conrad.geometry.shapes.simple.SortablePoint
SortablePoint(PointND) - Constructor for class edu.stanford.rsl.conrad.geometry.shapes.simple.SortablePoint: Copy constructor for PointND
SortablePoint(SimpleVector) - Constructor for class edu.stanford.rsl.conrad.geometry.shapes.simple.SortablePoint
SOUND_FILE - Static variable in class edu.stanford.rsl.conrad.utils.RegKeys: Entry to store the path to the sound file that is played when reconstruction finishes.
The value is a String indicating the path and filename of a supported sound file (WAV, AIFF, AU).
spacing - Variable in class edu.stanford.rsl.conrad.volume3d.Volume3D
Sphere - Class in edu.stanford.rsl.conrad.geometry.shapes.simple: Creates a Sphere.
Sphere() - Constructor for class edu.stanford.rsl.conrad.geometry.shapes.simple.Sphere
Sphere(double, PointND) - Constructor for class edu.stanford.rsl.conrad.geometry.shapes.simple.Sphere
Sphere(double) - Constructor for class edu.stanford.rsl.conrad.geometry.shapes.simple.Sphere
Sphere3D - Class in edu.stanford.rsl.tutorial.phantoms: Simple class to show the Grid2D functionality.
Sphere3D(int, int, int) - Constructor for class edu.stanford.rsl.tutorial.phantoms.Sphere3D: The constructor takes two arguments to initialize the grid.
SpherePhantom - Class in edu.stanford.rsl.conrad.phantom: Phantom to test forward and back projection resolution.
SpherePhantom() - Constructor for class edu.stanford.rsl.conrad.phantom.SpherePhantom
SPLINE1DTO3D - Static variable in class edu.stanford.rsl.conrad.geometry.splines.BSpline
SPLINE2DTO3D - Static variable in class edu.stanford.rsl.conrad.geometry.splines.BSpline
SPLINE3DTO3D - Static variable in class edu.stanford.rsl.conrad.geometry.splines.BSpline
SPLINE_4D_LOCATION - Static variable in class edu.stanford.rsl.conrad.utils.RegKeys: Entry to select a preprocessed 4D time spline.
The value is a String representation of a file location.
SplineTests - Class in edu.stanford.rsl.conrad.geometry.splines
SplineTests() - Constructor for class edu.stanford.rsl.conrad.geometry.splines.SplineTests
splitHomAffineMotionMatrix(SimpleMatrix, SimpleMatrix, SimpleVector) - Static method in class edu.stanford.rsl.conrad.geometry.General
sqr(Grid) - Static method in class edu.stanford.rsl.conrad.data.PointwiseOperators
sqr() - Method in class edu.stanford.rsl.conrad.io.SerializableFloatProcessor
sqrcopy(Grid) - Static method in class edu.stanford.rsl.conrad.data.PointwiseOperators
sqrt(Volume3D) - Method in class edu.stanford.rsl.conrad.cuda.CUDAVolumeOperator
sqrt(Grid) - Static method in class edu.stanford.rsl.conrad.data.PointwiseOperators
sqrt() - Method in class edu.stanford.rsl.conrad.io.SerializableFloatProcessor
sqrt(Volume3D) - Method in class edu.stanford.rsl.conrad.volume3d.ParallelVolumeOperator
sqrt(Volume3D) - Method in class edu.stanford.rsl.conrad.volume3d.VolumeOperator: Replaces every element in the volume with the output of Math.sqrt(), i.e.
sqrtcopy(Grid) - Static method in class edu.stanford.rsl.conrad.data.PointwiseOperators
SQUARE - Static variable in class edu.stanford.rsl.conrad.filtering.ImageConstantMathFilter
SQUAREROOT - Static variable in class edu.stanford.rsl.conrad.filtering.ImageConstantMathFilter
SquareRootSlab - Class in edu.stanford.rsl.conrad.volume3d.operations
SquareRootSlab() - Constructor for class edu.stanford.rsl.conrad.volume3d.operations.SquareRootSlab
SquatScene - Class in edu.stanford.rsl.conrad.phantom.xcat: Class to simluate very simple knee joint motion in XCat.
SquatScene() - Constructor for class edu.stanford.rsl.conrad.phantom.xcat.SquatScene
SquatScene(int, double, int, double) - Constructor for class edu.stanford.rsl.conrad.phantom.xcat.SquatScene
StandardCoordinateSystem - Class in edu.stanford.rsl.conrad.geometry.shapes
StandardCoordinateSystem(int) - Constructor for class edu.stanford.rsl.conrad.geometry.shapes.StandardCoordinateSystem
start() - Method in class edu.stanford.rsl.conrad.cuda.JCudaDriverTextureSample
start() - Method in class edu.stanford.rsl.conrad.filtering.multiprojection.MultiProjectionFilter: Packs the filter into a Thread and starts it.
start() - Method in class edu.stanford.rsl.conrad.opencl.rendering.OpenCLTextureRendering
start(int) - Method in class edu.stanford.rsl.conrad.pipeline.ParallelImageFilterSink
startMarkerDetectionTool() - Method in class edu.stanford.rsl.apps.gui.pointselector.PointSelector
stateChanged(ChangeEvent) - Method in class edu.stanford.rsl.apps.gui.blobdetection.MarkerDetection
StatisticsUtil - Class in edu.stanford.rsl.conrad.utils
StatisticsUtil() - Constructor for class edu.stanford.rsl.conrad.utils.StatisticsUtil
stddev(Grid, double) - Static method in class edu.stanford.rsl.conrad.data.PointwiseOperators
STLFileUtil - Class in edu.stanford.rsl.conrad.io
STLFileUtil() - Constructor for class edu.stanford.rsl.conrad.io.STLFileUtil
StraightLine - Class in edu.stanford.rsl.conrad.geometry.shapes.simple
StraightLine(PointND, SimpleVector) - Constructor for class edu.stanford.rsl.conrad.geometry.shapes.simple.StraightLine: Creates a StraightLine from point with direction dir
StraightLine(PointND, PointND) - Constructor for class edu.stanford.rsl.conrad.geometry.shapes.simple.StraightLine: Creates a new Straight line passing from point to point2
StreamingPhantomRenderer - Class in edu.stanford.rsl.conrad.phantom.renderer
StreamingPhantomRenderer() - Constructor for class edu.stanford.rsl.conrad.phantom.renderer.StreamingPhantomRenderer
StringFileFilter - Class in edu.stanford.rsl.conrad.utils
StringFileFilter(String) - Constructor for class edu.stanford.rsl.conrad.utils.StringFileFilter
sub(Complex) - Method in class edu.stanford.rsl.conrad.data.Complex
sub(double) - Method in class edu.stanford.rsl.conrad.data.Complex
subAtIndex(int, float) - Method in class edu.stanford.rsl.conrad.data.Grid1D
subAtIndex(int, int, float) - Method in class edu.stanford.rsl.conrad.data.Grid2D
SUBTRACT - Static variable in class edu.stanford.rsl.conrad.filtering.ImageConstantMathFilter
SUBTRACT - Static variable in class edu.stanford.rsl.conrad.filtering.ImageMathFilter
subtract(double) - Method in class edu.stanford.rsl.conrad.numerics.SimpleMatrix: Subtract subtrahend from all entries in matrix in place
subtract(SimpleMatrix...) - Method in class edu.stanford.rsl.conrad.numerics.SimpleMatrix: Method to subtract a set of matrices to this matrix in place.
subtract(SimpleVector, SimpleVector) - Static method in class edu.stanford.rsl.conrad.numerics.SimpleOperators: subtracts v2 from v1
subtract(SimpleMatrix, SimpleMatrix) - Static method in class edu.stanford.rsl.conrad.numerics.SimpleOperators: Subtracts M2 from M1
subtract(double) - Method in class edu.stanford.rsl.conrad.numerics.SimpleVector
subtract(SimpleVector...) - Method in class edu.stanford.rsl.conrad.numerics.SimpleVector
subtractBy(Grid, Grid) - Static method in class edu.stanford.rsl.conrad.data.PointwiseOperators: Compute grid1 = grid1 - grid2
subtractBy(Grid, float) - Static method in class edu.stanford.rsl.conrad.data.PointwiseOperators: Compute grid = grid - a
subtractedBy(Grid, Grid) - Static method in class edu.stanford.rsl.conrad.data.PointwiseOperators: Compute grid3 = grid1 - grid2
subtractFromElement(int, int, double) - Method in class edu.stanford.rsl.conrad.numerics.SimpleMatrix: Subtract subtrahend from entry at [row,col] in place
subtractFromElement(int, double) - Method in class edu.stanford.rsl.conrad.numerics.SimpleVector
subtractProcessors(ImageProcessor, ImageProcessor) - Static method in class edu.stanford.rsl.conrad.utils.ImageUtil: Subtracts two image processors.
subtractVolume(Volume3D, Volume3D) - Method in class edu.stanford.rsl.conrad.volume3d.VolumeOperator: Subtracts the second volume from the first volume.
SubVolumeBackprojector - Class in edu.stanford.rsl.conrad.reconstruction: This FBP-based mathod splits the reconstruction volume into sub volumes which can be processed in parallel to speed up the reconstruction further.
SubVolumeBackprojector() - Constructor for class edu.stanford.rsl.conrad.reconstruction.SubVolumeBackprojector
sum(Grid) - Static method in class edu.stanford.rsl.conrad.data.PointwiseOperators: Get sum of all grid elements
sum(Quaternion) - Method in class edu.stanford.rsl.conrad.geometry.transforms.Quaternion
SuperShortScanBackprojection - Class in edu.stanford.rsl.conrad.reconstruction: Deprecated.
SuperShortScanBackprojection() - Constructor for class edu.stanford.rsl.conrad.reconstruction.SuperShortScanBackprojection: Deprecated.
suppressCenter(double[], int) - Static method in class edu.stanford.rsl.conrad.utils.DoubleArrayUtil
suppressCenter(float[], int) - Static method in class edu.stanford.rsl.conrad.utils.FloatArrayUtil
Surface - Class in edu.stanford.rsl.conrad.fitting: Class to describe an abstract surface that can be fitted to a set of 3D Points.
Surface() - Constructor for class edu.stanford.rsl.conrad.fitting.Surface
SurfaceBSpline - Class in edu.stanford.rsl.conrad.geometry.splines: Class to model a surface made of BSplines.
SurfaceBSpline(ArrayList<PointND>, SimpleVector, SimpleVector) - Constructor for class edu.stanford.rsl.conrad.geometry.splines.SurfaceBSpline: Constructor for a surface BSpline.
SurfaceBSpline(ArrayList<PointND>, double[], double[]) - Constructor for class edu.stanford.rsl.conrad.geometry.splines.SurfaceBSpline: Constructor for a surface BSpline.
SurfaceBSpline(String, ArrayList<PointND>, double[], double[]) - Constructor for class edu.stanford.rsl.conrad.geometry.splines.SurfaceBSpline: Constructor for a surface BSpline.
SurfaceBSpline(String, ArrayList<PointND>, SimpleVector, SimpleVector) - Constructor for class edu.stanford.rsl.conrad.geometry.splines.SurfaceBSpline: Constructor for a surface BSpline.
SurfaceBSpline(SurfaceBSpline) - Constructor for class edu.stanford.rsl.conrad.geometry.splines.SurfaceBSpline
SurfaceBSplineRenderingAppendBuffer(AbstractShape) - Method in class edu.stanford.rsl.tutorial.motionEstimation.OpenCLSplineRenderer: This method renders a time variant spline and displays the projections in an imagej window
SurfaceBSplineRenderingAppendBufferToGrid(AbstractShape) - Method in class edu.stanford.rsl.tutorial.motionEstimation.OpenCLSplineRenderer: This method renders a timevariant spline, displays it in an imagej window and returns the result as a Grid3D
SurfaceBSplineVolumePhantom - Class in edu.stanford.rsl.conrad.geometry.splines
SurfaceBSplineVolumePhantom() - Constructor for class edu.stanford.rsl.conrad.geometry.splines.SurfaceBSplineVolumePhantom
SurfaceTests - Class in edu.stanford.rsl.conrad.geometry.test
SurfaceTests() - Constructor for class edu.stanford.rsl.conrad.geometry.test.SurfaceTests
SurfaceUniformCubicBSpline - Class in edu.stanford.rsl.conrad.geometry.splines
SurfaceUniformCubicBSpline(ArrayList<PointND>, double[], double[]) - Constructor for class edu.stanford.rsl.conrad.geometry.splines.SurfaceUniformCubicBSpline
SurfaceUniformCubicBSpline(String, ArrayList<PointND>, double[], double[]) - Constructor for class edu.stanford.rsl.conrad.geometry.splines.SurfaceUniformCubicBSpline
SurfaceUniformCubicBSpline(String, ArrayList<PointND>, SimpleVector, SimpleVector) - Constructor for class edu.stanford.rsl.conrad.geometry.splines.SurfaceUniformCubicBSpline
SurfaceUniformCubicBSpline(ArrayList<PointND>, SimpleVector, SimpleVector) - Constructor for class edu.stanford.rsl.conrad.geometry.splines.SurfaceUniformCubicBSpline
SurfaceUniformCubicBSpline(SurfaceBSpline) - Constructor for class edu.stanford.rsl.conrad.geometry.splines.SurfaceUniformCubicBSpline
swapPixelArrays() - Method in class edu.stanford.rsl.conrad.io.SerializableFloatProcessor: Not implemented.
SystemGeometryConfigFileTrajectory - Class in edu.stanford.rsl.conrad.geometry.trajectories
SystemGeometryConfigFileTrajectory(String, Trajectory) - Constructor for class edu.stanford.rsl.conrad.geometry.trajectories.SystemGeometryConfigFileTrajectory
SystemGeometryConfigFileTrajectory(Trajectory) - Constructor for class edu.stanford.rsl.conrad.geometry.trajectories.SystemGeometryConfigFileTrajectory

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