Serialized Form

Package edu.stanford.rsl.apps
- Class edu.stanford.rsl.apps.TestJang extends VOIBasedReconstructionFilter implements Serializable

Package edu.stanford.rsl.apps.gui

Class edu.stanford.rsl.apps.gui.ConfigurationFrame extends javax.swing.JFrame implements Serializable

serialVersionUID:: 979874928758716096L

Serialized Fields

jTabbedPane
```
javax.swing.JTabbedPane jTabbedPane
```
jSaveButton
```
javax.swing.JButton jSaveButton
```
exited
```
boolean exited
```
config
```
Configuration config
```
parentFrame
```
UpdateableGUI parentFrame
```
regEditor
```
RegistryEditor regEditor
```
trajEdit
```
TrajectoryEditor trajEdit
```
camAxes
```
java.lang.String[] camAxes
```
xDimensionField
```
javax.swing.JTextField xDimensionField
```
yDimensionField
```
javax.swing.JTextField yDimensionField
```
zDimensionField
```
javax.swing.JTextField zDimensionField
```
xOriginVoxel
```
javax.swing.JTextField xOriginVoxel
```
yOriginVoxel
```
javax.swing.JTextField yOriginVoxel
```
zOriginVoxel
```
javax.swing.JTextField zOriginVoxel
```
xOriginWorld
```
javax.swing.JTextField xOriginWorld
```
yOriginWorld
```
javax.swing.JTextField yOriginWorld
```
zOriginWorld
```
javax.swing.JTextField zOriginWorld
```
xSpacingField
```
javax.swing.JTextField xSpacingField
```
ySpacingField
```
javax.swing.JTextField ySpacingField
```
zSpacingField
```
javax.swing.JTextField zSpacingField
```
maxVOIPathField
```
javax.swing.JTextField maxVOIPathField
```
jCenterVolume
```
javax.swing.JButton jCenterVolume
```

detectorWidthField

javax.swing.JTextField detectorWidthField

detectorHeightField

javax.swing.JTextField detectorHeightField

pixelDimensionXField

javax.swing.JTextField pixelDimensionXField

pixelDimensionYField

javax.swing.JTextField pixelDimensionYField

projectionStackSizeField

javax.swing.JTextField projectionStackSizeField

numSweepsField
```
javax.swing.JTextField numSweepsField
```

sourceToDetectorField

javax.swing.JTextField sourceToDetectorField

sourceToPatientField

javax.swing.JTextField sourceToPatientField

projectionTableFileField

javax.swing.JTextField projectionTableFileField

jParseGeometry
```
javax.swing.JButton jParseGeometry
```
jGenerateGeometry
```
javax.swing.JButton jGenerateGeometry
```

averageAngularIncrement

javax.swing.JTextField averageAngularIncrement

detectorOffsetU
```
javax.swing.JTextField detectorOffsetU
```
detectorOffsetV
```
javax.swing.JTextField detectorOffsetV
```
rotationAxis
```
javax.swing.JTextField rotationAxis
```

DetectorUDirection

javax.swing.JComboBox<E> DetectorUDirection

DetectorVDirection

javax.swing.JComboBox<E> DetectorVDirection

optionList
```
javax.swing.JComboBox<E> optionList
```
trajectoryFromFile
```
javax.swing.JPanel trajectoryFromFile
```

trajectoryFromParameters

javax.swing.JPanel trajectoryFromParameters

trajectoryPanel
```
javax.swing.JPanel trajectoryPanel
```

trajectoryEditorButton

javax.swing.JButton trajectoryEditorButton

recentFileOneField

javax.swing.JTextField recentFileOneField

recentFileTwoField

javax.swing.JTextField recentFileTwoField

citationFormatGroup

javax.swing.ButtonGroup citationFormatGroup

bibButton
```
javax.swing.JRadioButton bibButton
```
medlineButton
```
javax.swing.JRadioButton medlineButton
```
importFromDicom
```
javax.swing.JCheckBox importFromDicom
```

extrapolateGeometry

javax.swing.JCheckBox extrapolateGeometry

houns
```
javax.swing.JCheckBox houns
```

Class edu.stanford.rsl.apps.gui.ConfigurePipelineFrame extends javax.swing.JFrame implements Serializable

serialVersionUID:: -6842659152489589850L

Serialized Fields

jScrollPane1
```
javax.swing.JScrollPane jScrollPane1
```
jMoveDownButton
```
javax.swing.JButton jMoveDownButton
```
jPipelinePanel
```
javax.swing.JPanel jPipelinePanel
```
jSaveButton
```
javax.swing.JButton jSaveButton
```
jMoveUpButton
```
javax.swing.JButton jMoveUpButton
```
jRemoveButton
```
javax.swing.JButton jRemoveButton
```
jAddButton
```
javax.swing.JButton jAddButton
```
pipeline
```
ImageFilteringTool[] pipeline
```
exited
```
boolean exited
```
parentFrame
```
UpdateableGUI parentFrame
```
saveToDisk
```
boolean saveToDisk
```

panels

GUICompatibleObjectVisualizationPanel[] panels

selectedIndex
```
int selectedIndex
```

Class edu.stanford.rsl.apps.gui.Experimenter extends javax.swing.JFrame implements Serializable

serialVersionUID:: 4087722049818451579L

Serialized Fields

jLabel1
```
javax.swing.JLabel jLabel1
```
jAddExperiment
```
javax.swing.JButton jAddExperiment
```
jScrollPane1
```
javax.swing.JScrollPane jScrollPane1
```
jRun
```
javax.swing.JButton jRun
```
jRemoveExperiment
```
javax.swing.JButton jRemoveExperiment
```
jExperimentPanel
```
javax.swing.JPanel jExperimentPanel
```
panels
```
ExperimentPanel[] panels
```
selectedIndex
```
int selectedIndex
```

experiments

edu.stanford.rsl.science.experiments.Experiment[] experiments

Class edu.stanford.rsl.apps.gui.ExperimentPanel extends javax.swing.JPanel implements Serializable

serialVersionUID:: -1533939136906031192L

Serialized Fields

jConfigurationFile

javax.swing.JTextField jConfigurationFile

jConfigurationLabel
```
javax.swing.JLabel jConfigurationLabel
```
jProjectionFile
```
javax.swing.JTextField jProjectionFile
```
jLabel2
```
javax.swing.JLabel jLabel2
```

jNoCorrectionRecon

javax.swing.JTextField jNoCorrectionRecon

jLabel1
```
javax.swing.JLabel jLabel1
```
jIdealRecon
```
javax.swing.JTextField jIdealRecon
```
jScrollPane1
```
javax.swing.JScrollPane jScrollPane1
```
jMetricLabel
```
javax.swing.JLabel jMetricLabel
```
jMetricList
```
javax.swing.JList<E> jMetricList
```
jRemoveMetric
```
javax.swing.JButton jRemoveMetric
```
jAddMetric
```
javax.swing.JButton jAddMetric
```
jProjectionsLabel
```
javax.swing.JLabel jProjectionsLabel
```

experiment

edu.stanford.rsl.science.experiments.Experiment experiment

Class edu.stanford.rsl.apps.gui.FileTextFieldTransferHandler extends javax.swing.TransferHandler implements Serializable

serialVersionUID:

-7758055750140825222L
- Serialized Fields
  - field
```
javax.swing.JTextField field
```
  - p1
```
javax.swing.text.Position p1
```
  - p0
```
javax.swing.text.Position p0
```
Class edu.stanford.rsl.apps.gui.GUICompatibleObjectVisualizationPanel extends javax.swing.JPanel implements Serializable

serialVersionUID:

126994236281825512L
- Serialized Fields
  - jConfigureButton
```
javax.swing.JButton jConfigureButton
```
  - jIsConfiguredCheckBox
```
javax.swing.JCheckBox jIsConfiguredCheckBox
```
  - jScrollPane1
```
javax.swing.JScrollPane jScrollPane1
```
  - jCitationTextField
```
javax.swing.JTextPane jCitationTextField
```
  - citation
```
Citeable citation
```
  - config
```
GUIConfigurable config
```
  - border
```
javax.swing.border.TitledBorder border
```
  - parentFrame
```
UpdateableGUI parentFrame
```
Class edu.stanford.rsl.apps.gui.PhantomMaker extends javax.swing.JFrame implements Serializable

serialVersionUID:

4782596036459267832L

Class edu.stanford.rsl.apps.gui.RawDataOpener extends javax.swing.JFrame implements Serializable

serialVersionUID:: -1952776160986620856L

Serialized Fields

jButtonLittle
```
javax.swing.JButton jButtonLittle
```
jButtonBig
```
javax.swing.JButton jButtonBig
```
jLabel2
```
javax.swing.JLabel jLabel2
```
jLabel3
```
javax.swing.JLabel jLabel3
```
jLabel4
```
javax.swing.JLabel jLabel4
```
jOffset
```
javax.swing.JTextField jOffset
```
jTextFieldStack
```
javax.swing.JTextField jTextFieldStack
```
jButtonDouble
```
javax.swing.JButton jButtonDouble
```
jTextFieldHeight
```
javax.swing.JTextField jTextFieldHeight
```
jTextFieldWidth
```
javax.swing.JTextField jTextFieldWidth
```
jLabel1
```
javax.swing.JLabel jLabel1
```
jButtonSShort
```
javax.swing.JButton jButtonSShort
```
jButtonShort
```
javax.swing.JButton jButtonShort
```
jButtonFloat
```
javax.swing.JButton jButtonFloat
```

Class edu.stanford.rsl.apps.gui.ReconstructionPipelineFrame extends javax.swing.JFrame implements Serializable

serialVersionUID:: -2788658929679662808L

Serialized Fields

jLabel1
```
javax.swing.JLabel jLabel1
```

jProjectionsTextField

javax.swing.JTextField jProjectionsTextField

jPanel1
```
javax.swing.JPanel jPanel1
```
jLoadDataButton
```
javax.swing.JButton jLoadDataButton
```

jEditConfigurationButton

javax.swing.JButton jEditConfigurationButton

jEditPipelineButton
```
javax.swing.JButton jEditPipelineButton
```

jChooseBackprojector

javax.swing.JButton jChooseBackprojector

jPipelineLabel
```
javax.swing.JLabel jPipelineLabel
```
jReconstructButton
```
javax.swing.JButton jReconstructButton
```

jProjectionDataChooseButton

javax.swing.JButton jProjectionDataChooseButton

jProjectionsLabel
```
javax.swing.JLabel jProjectionsLabel
```

sinkPanel

GUICompatibleObjectVisualizationPanel sinkPanel

sink
```
BufferedProjectionSink sink
```
debug
```
boolean debug
```
pipelineFrame
```
ConfigurePipelineFrame pipelineFrame
```
configFrame
```
ConfigurationFrame configFrame
```

filteringPipeline

ParallelImageFilterPipeliner filteringPipeline

soundClip
```
javax.sound.sampled.Clip soundClip
```
volumePreview
```
ij.ImagePlus volumePreview
```
pSource
```
ProjectionSource pSource
```

Class edu.stanford.rsl.apps.gui.RegistryEditor extends javax.swing.JPanel implements Serializable

serialVersionUID:

-8853718009928894577L
- Serialized Fields
  - config
```
Configuration config
```
  - add
```
javax.swing.JButton add
```
  - delete
```
javax.swing.JButton delete
```
  - showKeys
```
javax.swing.JButton showKeys
```
  - table
```
javax.swing.JTable table
```
  - keysDescription
```
javax.swing.JFrame keysDescription
```
  - descTable
```
javax.swing.JTable descTable
```

Class edu.stanford.rsl.apps.gui.TrajectoryEditor extends javax.swing.JFrame implements Serializable

Serialized Fields

jLabelLeft
```
javax.swing.JLabel jLabelLeft
```
jLabelMatrixRight
```
javax.swing.JLabel jLabelMatrixRight
```
JLabelPMatrix
```
javax.swing.JLabel JLabelPMatrix
```
jA11
```
javax.swing.JTextField jA11
```
jApplyToPMatrices
```
javax.swing.JButton jApplyToPMatrices
```
jB33
```
javax.swing.JTextField jB33
```
jB32
```
javax.swing.JTextField jB32
```
jB31
```
javax.swing.JTextField jB31
```
jB23
```
javax.swing.JTextField jB23
```
jB22
```
javax.swing.JTextField jB22
```
jB21
```
javax.swing.JTextField jB21
```
jB13
```
javax.swing.JTextField jB13
```
jB12
```
javax.swing.JTextField jB12
```
jB11
```
javax.swing.JTextField jB11
```
jA31
```
javax.swing.JTextField jA31
```
jA32
```
javax.swing.JTextField jA32
```
jA33
```
javax.swing.JTextField jA33
```
jA34
```
javax.swing.JTextField jA34
```
jA41
```
javax.swing.JTextField jA41
```
jA42
```
javax.swing.JTextField jA42
```
jA43
```
javax.swing.JTextField jA43
```
jA44
```
javax.swing.JTextField jA44
```
jA21
```
javax.swing.JTextField jA21
```
jA22
```
javax.swing.JTextField jA22
```
jA23
```
javax.swing.JTextField jA23
```
jA24
```
javax.swing.JTextField jA24
```
jA14
```
javax.swing.JTextField jA14
```
jA13
```
javax.swing.JTextField jA13
```
jA12
```
javax.swing.JTextField jA12
```
jLabelP
```
javax.swing.JLabel jLabelP
```

Package edu.stanford.rsl.apps.gui.blobdetection

Class edu.stanford.rsl.apps.gui.blobdetection.MarkerDetection extends javax.swing.JFrame implements Serializable

serialVersionUID:: -5274899502815414214L

Serialized Fields

jButtonRun
```
javax.swing.JButton jButtonRun
```
pWorker
```
MarkerDetectionWorker pWorker
```

jSpinnerGradientThreshold

javax.swing.JSpinner jSpinnerGradientThreshold

jTextPane4
```
javax.swing.JTextPane jTextPane4
```
jTextPane3
```
javax.swing.JTextPane jTextPane3
```
jTextPane2
```
javax.swing.JTextPane jTextPane2
```
jTextPane1
```
javax.swing.JTextPane jTextPane1
```

jTextPaneBlobRadii

javax.swing.JTextPane jTextPaneBlobRadii

jSpinnerDistance
```
javax.swing.JSpinner jSpinnerDistance
```

jCheckBoxRefineAutoDetection

javax.swing.JCheckBox jCheckBoxRefineAutoDetection

jSpinnerNumberOfBeadsToDetect

javax.swing.JSpinner jSpinnerNumberOfBeadsToDetect

jButtonSaveResults
```
javax.swing.JButton jButtonSaveResults
```
jTextPane6
```
javax.swing.JTextPane jTextPane6
```

jSpinnerNrOfIterations

javax.swing.JSpinner jSpinnerNrOfIterations

jCheckBoxAutomaticDetection

javax.swing.JCheckBox jCheckBoxAutomaticDetection

jTextPane5
```
javax.swing.JTextPane jTextPane5
```

jSpinnerCircularity

javax.swing.JSpinner jSpinnerCircularity

jSpinnerBinarizationThreshold

javax.swing.JSpinner jSpinnerBinarizationThreshold

AutoDetectioncheckBoxChecked
```
boolean AutoDetectioncheckBoxChecked
```
RefinementcheckBoxChecked
```
boolean RefinementcheckBoxChecked
```

Package edu.stanford.rsl.apps.gui.pointselector
- Class edu.stanford.rsl.apps.gui.pointselector.PointSelector extends javax.swing.JFrame implements Serializable
 
 serialVersionUID:
 
 -5274899502815414214L
 - Serialized Fields
 - jButtonAdd
```
javax.swing.JButton jButtonAdd
```
 - jButtonDelete
```
javax.swing.JButton jButtonDelete
```
 - jList
```
javax.swing.JList<E> jList
```
 - jInfoTable
```
javax.swing.JTable jInfoTable
```
 - jButtonImport
```
javax.swing.JButton jButtonImport
```
 - jButtonExport
```
javax.swing.JButton jButtonExport
```
 - jScrollPane
```
javax.swing.JScrollPane jScrollPane
```
 - jButtonOpenInROImanager
```
javax.swing.JButton jButtonOpenInROImanager
```
 - psWorker
```
PointSelectorWorker psWorker
```
Package edu.stanford.rsl.conrad.cuda
- Class edu.stanford.rsl.conrad.cuda.CUDABackProjector extends VOIBasedReconstructionFilter implements Serializable
 
 serialVersionUID:
 
 -8615490043940236889L
 - Serialized Fields
 - module
```
jcuda.driver.CUmodule module
```
 The CUDA module containing the kernel
 - function
```
jcuda.driver.CUfunction function
```
 The handle for the CUDA function of the kernel that is to be called
 - h_volume
```
float[] h_volume
```
 The volume data that is to be reconstructed
 - projectionTex
```
jcuda.driver.CUtexref projectionTex
```
 The 2D projection texture reference
 - gridSize
```
jcuda.runtime.dim3 gridSize
```
 The grid size of the kernel execution
 - cuCtx
```
jcuda.driver.CUcontext cuCtx
```
 the context
 - projectionMatrix
```
jcuda.driver.CUdeviceptr projectionMatrix
```
 The global variable of the module which stores the view matrix.
 - volStride
```
jcuda.driver.CUdeviceptr volStride
```
 - volumePointer
```
jcuda.driver.CUdeviceptr volumePointer
```
 - projectionArray
```
jcuda.driver.CUarray projectionArray
```
 - projections
```
ImageProcessorBuffer projections
```
 - projectionsAvailable
```
java.util.ArrayList<E> projectionsAvailable
```
 - projectionsDone
```
java.util.ArrayList<E> projectionsDone
```
 - largeVolumeMode
```
boolean largeVolumeMode
```
 - nSteps
```
int nSteps
```
 - subVolumeZ
```
int subVolumeZ
```
 - initialized
```
boolean initialized
```
- Class edu.stanford.rsl.conrad.cuda.CUDACompensatedBackProjector extends VOIBasedReconstructionFilter implements Serializable
 
 serialVersionUID:
 
 7732291211252379464L
 - Serialized Fields
 - mot
```
double[] mot
```
 - module
```
jcuda.driver.CUmodule module
```
 The CUDA module containing the kernel
 - function
```
jcuda.driver.CUfunction function
```
 The handle for the CUDA function of the kernel that is to be called
 - h_volume
```
float[] h_volume
```
 The volume data that is to be reconstructed
 - projectionTex
```
jcuda.driver.CUtexref projectionTex
```
 The 2D projection texture reference
 - gridSize
```
jcuda.runtime.dim3 gridSize
```
 The grid size of the kernel execution
 - cuCtx
```
jcuda.driver.CUcontext cuCtx
```
 the context
 - projectionMatrix
```
jcuda.driver.CUdeviceptr projectionMatrix
```
 The global variable of the module which stores the view matrix.
 - volStride
```
jcuda.driver.CUdeviceptr volStride
```
 - volumePointer
```
jcuda.driver.CUdeviceptr volumePointer
```
 - projectionArray
```
jcuda.driver.CUarray projectionArray
```
 - projections
```
ImageProcessorBuffer projections
```
 - projectionsAvailable
```
java.util.ArrayList<E> projectionsAvailable
```
 - projectionsDone
```
java.util.ArrayList<E> projectionsDone
```
 - largeVolumeMode
```
boolean largeVolumeMode
```
 - nSteps
```
int nSteps
```
 - subVolumeZ
```
int subVolumeZ
```
 - initialized
```
boolean initialized
```
- Class edu.stanford.rsl.conrad.cuda.ImagePlusVolumeRenderer extends JCudaDriverTextureSample implements Serializable
 
 serialVersionUID:
 
 -2120647421143268776L
 - Serialized Fields
 - multiFrameMode
```
boolean multiFrameMode
```
 - textures
```
jcuda.driver.CUtexref[] textures
```
 - volumes
```
byte[][] volumes
```
 - nFrames
```
int nFrames
```
 - time
```
int time
```
 - minmax
```
double[] minmax
```
 - playTimer
```
java.util.Timer playTimer
```
 - frameDuration
```
long frameDuration
```
- Class edu.stanford.rsl.conrad.cuda.JCudaDriverTextureSample extends javax.swing.JFrame implements Serializable
 
 serialVersionUID:
 
 3072546722050331601L
 - Serialized Fields
 - transferFunc
```
float[] transferFunc
```
 - initialized
```
boolean initialized
```
 Whether the initialization method of this GLEventListener has already been called
 - stereoMode
```
boolean stereoMode
```
 Whether the stereo mode is enabled
 - glComponentL
```
javax.media.opengl.awt.GLJPanel glComponentL
```
 The GL component which is used for rendering
 - glComponentR
```
javax.media.opengl.awt.GLJPanel glComponentR
```
 The GL component which is used for the other eye
 - renderer
```
com.jogamp.opengl.util.awt.TextRenderer renderer
```
 Text renderer for status messages
 - animatorL
```
com.jogamp.opengl.util.Animator animatorL
```
 The animator used for rendering
 - animatorR
```
com.jogamp.opengl.util.Animator animatorR
```
 The animator for the other eye
 - module
```
jcuda.driver.CUmodule module
```
 The CUDA module containing the kernel
 - function
```
jcuda.driver.CUfunction function
```
 The handle for the CUDA function of the kernel that is to be called
 - width
```
int width
```
 The width of the rendered area and the PBO
 - height
```
int height
```
 The height of the rendered area and the PBO
 - volumeSize
```
jcuda.runtime.dim3 volumeSize
```
 The size of the volume data that is to be rendered
 - h_volume
```
byte[] h_volume
```
 The volume data that is to be rendered
 - blockSize
```
jcuda.runtime.dim3 blockSize
```
 The block size for the kernel execution
 - gridSize
```
jcuda.runtime.dim3 gridSize
```
 The grid size of the kernel execution
 - c_invViewMatrix
```
jcuda.driver.CUdeviceptr c_invViewMatrix
```
 The global variable of the module which stores the inverted view matrix.
 - invViewMatrix
```
float[] invViewMatrix
```
 The inverted view matrix, which will be copied to the global variable of the kernel.
 - density
```
float density
```
 The density of the rendered volume data
 - brightness
```
float brightness
```
 The brightness of the rendered volume data
 - transferOffset
```
float transferOffset
```
 The transferOffset of the rendered volume data
 - transferScale
```
float transferScale
```
 The transferScale of the rendered volume data
 - pbo
```
int pbo
```
 The OpenGL pixel buffer object
 - tex
```
jcuda.driver.CUtexref tex
```
 The 3D texture reference
 - transferTex
```
jcuda.driver.CUtexref transferTex
```
 The 1D transfer texture reference
 - translationX
```
float translationX
```
 The translation in X-direction
 - translationY
```
float translationY
```
 The translation in Y-direction
 - translationZ
```
float translationZ
```
 The translation in Z-direction
 - rotationX
```
float rotationX
```
 The rotation about the X-axis, in degrees
 - frame
```
javax.swing.JFrame frame
```
 - rotationY
```
float rotationY
```
 The rotation about the Y-axis, in degrees
 - prevFrameNanoTime
```
long prevFrameNanoTime
```
 The System.nanoTime() of the previous rendered frame.
 - glCtx
```
jcuda.driver.CUcontext glCtx
```
Package edu.stanford.rsl.conrad.cuda.splines
- Class edu.stanford.rsl.conrad.cuda.splines.CUDABSpline extends BSpline implements Serializable
  
  serialVersionUID:
  
  -4887896401270761029L
  - Serialized Fields
    - deviceX
```
jcuda.driver.CUdeviceptr deviceX
```
Package edu.stanford.rsl.conrad.filtering
- Class edu.stanford.rsl.conrad.filtering.AbsoluteValueTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 260472749566522423L
- Class edu.stanford.rsl.conrad.filtering.ApplyHounsfieldScaling extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 6671943273538431531L
- Class edu.stanford.rsl.conrad.filtering.ApplyLambdaWeightingTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 -8909824388187619416L
 - Serialized Fields
 - measureHard
```
double measureHard
```
 - measureSoft
```
double measureSoft
```
 - lambda0
```
double lambda0
```
 - lut
```
BilinearInterpolatingDoubleArray lut
```
 - offset
```
double offset
```
 - projectionXShift
```
double projectionXShift
```
 - projectionYShift
```
double projectionYShift
```
 - slope
```
double slope
```
 - hardMaterial
```
Grid3D hardMaterial
```
- Class edu.stanford.rsl.conrad.filtering.AtractResidual2D extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 5015484026254715749L
 - Serialized Fields
 - zeroValue
```
double zeroValue
```
 - kernel
```
AtractKernel2D kernel
```
- Class edu.stanford.rsl.conrad.filtering.BilateralFilteringTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 8308762121723928775L
 - Serialized Fields
 - sigma_d
```
double sigma_d
```
 - sigma_r
```
double sigma_r
```
 - width
```
int width
```
- Class edu.stanford.rsl.conrad.filtering.CosineWeightingTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 -4985677804638655239L
 - Serialized Fields
 - cosineWeights
```
double[][] cosineWeights
```
 - detectorWidth
```
int detectorWidth
```
 - detectorHeight
```
int detectorHeight
```
 - pixelDimensionX
```
double pixelDimensionX
```
 - pixelDimensionY
```
double pixelDimensionY
```
 - sourceToDetectorDistance
```
double sourceToDetectorDistance
```
 - sourceToAxisDistance
```
double sourceToAxisDistance
```
 - weightsAvailable
```
boolean weightsAvailable
```
- Class edu.stanford.rsl.conrad.filtering.DynamicDensityOptimizationScatterCorrectionTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 -8866437142171005094L
 - Serialized Fields
 - sigma
```
double sigma
```
 - weight
```
double weight
```
- Class edu.stanford.rsl.conrad.filtering.ExtremeValueTruncationFilter extends IndividualImagePipelineFilteringTool implements Serializable
 
 serialVersionUID:
 
 -2948507386005078704L
 - Serialized Fields
 - operation
```
java.lang.String operation
```
 - deviceDependent
```
boolean deviceDependent
```
 - threshold
```
double threshold
```
- Class edu.stanford.rsl.conrad.filtering.FastRadialSymmetryTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 8801374879563931231L
 - Serialized Fields
 - radii
```
double[] radii
```
 - alpha
```
double alpha
```
 - smallGradientThreshold
```
double smallGradientThreshold
```
 - useOrientationOnly
```
boolean useOrientationOnly
```
 - usePositiveNegativeOnly
```
int usePositiveNegativeOnly
```
- Class edu.stanford.rsl.conrad.filtering.FiducialMarkerDetectionTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 -6110577475173113158L
 - Serialized Fields
 - radiusOfBeads
```
int radiusOfBeads
```
 - offset
```
double offset
```
 - start
```
double start
```
 - stop
```
double stop
```
 - distance
```
double distance
```
 - config
```
Configuration config
```
- Class edu.stanford.rsl.conrad.filtering.Filtering2DTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 6298941333447055742L
 - Serialized Fields
 - filter2D
```
Grid2D filter2D
```
 - deviceDependent
```
boolean deviceDependent
```
- Class edu.stanford.rsl.conrad.filtering.HilbertFilteringTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 -8601705506734490146L
 - Serialized Fields
 - nTimes
```
int nTimes
```
- Class edu.stanford.rsl.conrad.filtering.HorizontalFlippingTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 -727180365181022869L
- Class edu.stanford.rsl.conrad.filtering.HoughFilteringTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - radiusOfCircles
```
int radiusOfCircles
```
 - start
```
double start
```
 - stop
```
double stop
```
- Class edu.stanford.rsl.conrad.filtering.ImageConstantMathFilter extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 1576269350353505544L
 - Serialized Fields
 - operand
```
double operand
```
 - operation
```
java.lang.String operation
```
 - deviceDependent
```
boolean deviceDependent
```
- Class edu.stanford.rsl.conrad.filtering.ImageFilteringTool extends java.lang.Object implements Serializable
 
 serialVersionUID:
 
 2772279250470371073L
 - Serialized Fields
 - configured
```
boolean configured
```
- Class edu.stanford.rsl.conrad.filtering.ImageJParallelTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 -4269226968123355343L
 - Serialized Fields
 - operation
```
java.lang.String operation
```
 - parameters
```
java.lang.String parameters
```
- Class edu.stanford.rsl.conrad.filtering.ImageMathFilter extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 -1161045076404535185L
 - Serialized Fields
 - operandFileName
```
java.lang.String operandFileName
```
 - operand
```
ij.ImagePlus operand
```
 - operation
```
java.lang.String operation
```
 - deviceDependent
```
boolean deviceDependent
```
- Class edu.stanford.rsl.conrad.filtering.IndividualImageFilteringTool extends ImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 -2504582813925296457L
 - Serialized Fields
 - imageProcessor
```
Grid2D imageProcessor
```
 - latch
```
java.util.concurrent.CountDownLatch latch
```
 - imageIndex
```
int imageIndex
```
 - theFiltered
```
Grid2D theFiltered
```
- Class edu.stanford.rsl.conrad.filtering.KinectBasedDetectorSaturationCorrectionTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 450437133500604807L
 - Serialized Fields
 - config
```
Configuration config
```
 - isDisplay
```
boolean isDisplay
```
- Class edu.stanford.rsl.conrad.filtering.LaplaceFilteringTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 -741259606020972883L
 - Serialized Fields
 - twoD
```
boolean twoD
```
- Class edu.stanford.rsl.conrad.filtering.LogPoissonNoiseFilteringTool extends PoissonNoiseFilteringTool implements Serializable
 
 serialVersionUID:
 
 -6025566244585199099L
 - Serialized Fields
 - photonCountMax
```
double photonCountMax
```
- Class edu.stanford.rsl.conrad.filtering.MeanFilteringTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 5822100894598421376L
 - Serialized Fields
 - kernel
```
float[] kernel
```
 - kernelWidth
```
int kernelWidth
```
 - kernelHeight
```
int kernelHeight
```
- Class edu.stanford.rsl.conrad.filtering.MeanMarkerBasedProjectionShiftingTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 1449423447534168982L
 - Serialized Fields
 - beadBuilder
```
WeightBearingBeadPositionBuilder beadBuilder
```
 - config
```
Configuration config
```
 - initBead
```
boolean initBead
```
 - isDisplay
```
boolean isDisplay
```
- Class edu.stanford.rsl.conrad.filtering.MeanMarkerBasedProjectionShiftingToolForXCAT extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 -4287558757650497769L
 - Serialized Fields
 - config
```
Configuration config
```
 - motionField
```
MotionField motionField
```
 - variants
```
java.util.ArrayList<E> variants
```
 - markers
```
int[][] markers
```
 - fAddMarkerErr
```
boolean fAddMarkerErr
```
 - initMotionField
```
boolean initMotionField
```
 - isDisplay
```
boolean isDisplay
```
- Class edu.stanford.rsl.conrad.filtering.MedianFilteringTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 -2206224407501839982L
 - Serialized Fields
 - kernelWidth
```
int kernelWidth
```
 - kernelHeight
```
int kernelHeight
```
- Class edu.stanford.rsl.conrad.filtering.NonLinearGainCorrectionTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 -5757798244081582971L
 - Serialized Fields
 - lookUpTable
```
java.util.ArrayList<E> lookUpTable
```
 - start
```
int start
```
 - end
```
int end
```
- Class edu.stanford.rsl.conrad.filtering.NumericalDerivativeComputationTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 1549628690729735281L
 - Serialized Fields
 - nTimes
```
int nTimes
```
 - twoD
```
boolean twoD
```
 - horizontal
```
boolean horizontal
```
- Class edu.stanford.rsl.conrad.filtering.NumericalLinewiseAntiderivativeFilteringTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 7305539337599312505L
 - Serialized Fields
 - horizontal
```
boolean horizontal
```
- Class edu.stanford.rsl.conrad.filtering.PoissonNoiseFilteringTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 647343713286585178L
- Class edu.stanford.rsl.conrad.filtering.PrimaryModulationScatterCorrectionTool extends MultiProjectionFilter implements Serializable
 
 serialVersionUID:
 
 7870494646455524074L
 - Serialized Fields
 - meanfilterLen
```
int meanfilterLen
```
 - lowPassFilterWidth
```
double lowPassFilterWidth
```
 - lowPassFilterHeight
```
double lowPassFilterHeight
```
 - gaincutfactor
```
double gaincutfactor
```
 - scatterEstScale
```
double scatterEstScale
```
 - bUniformAlpha
```
boolean bUniformAlpha
```
 - softcutfactor
```
double softcutfactor
```
 - modulationFunctionFilename
```
java.lang.String modulationFunctionFilename
```
 - scatterEstimatesBuffer
```
ImageProcessorBuffer scatterEstimatesBuffer
```
 - blkIdxX
```
ij.process.FloatProcessor blkIdxX
```
 - blkIdxY
```
ij.process.FloatProcessor blkIdxY
```
 - blkIdxVal
```
ij.process.FloatProcessor blkIdxVal
```
 - dsModFun
```
ij.process.FloatProcessor dsModFun
```
 - dsModFunMean
```
double dsModFunMean
```
 - upsampIdxX
```
ij.process.FloatProcessor upsampIdxX
```
 - upsampIdxY
```
ij.process.FloatProcessor upsampIdxY
```
 - alphaDist
```
ij.process.FloatProcessor alphaDist
```
 - initModulation
```
boolean initModulation
```
- Class edu.stanford.rsl.conrad.filtering.RampFilteringTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 2575773201054615567L
 - Serialized Fields
 - ramp
```
RampFilter ramp
```
- Class edu.stanford.rsl.conrad.filtering.Rotate90DegreeLeftTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 865405590293794136L
- Class edu.stanford.rsl.conrad.filtering.ThinPlateSplinesBasedProjectionWarpingTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 -3377571138470875648L
 - Serialized Fields
 - beadBuilder
```
WeightBearingBeadPositionBuilder beadBuilder
```
 - config
```
Configuration config
```
 - initBead
```
boolean initBead
```
 - isDisplay
```
boolean isDisplay
```
 - isCornerIncluded
```
boolean isCornerIncluded
```
- Class edu.stanford.rsl.conrad.filtering.ThinPlateSplinesBasedProjectionWarpingToolForXCAT extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 -3377571138470875648L
 - Serialized Fields
 - config
```
Configuration config
```
 - isCornerIncluded
```
boolean isCornerIncluded
```
 - motionField
```
MotionField motionField
```
 - variants
```
java.util.ArrayList<E> variants
```
 - markers
```
int[][] markers
```
 - fAddMarkerErr
```
boolean fAddMarkerErr
```
 - initMotionField
```
boolean initMotionField
```
 - isDisplay
```
boolean isDisplay
```
 - fScaling
```
boolean fScaling
```
- Class edu.stanford.rsl.conrad.filtering.TruncationCorrectionTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 7424197576259159222L
 - Serialized Fields
 - n_ext
```
int n_ext
```
 - n_S
```
int n_S
```
 - k_SA
```
int k_SA
```
 - k_SE
```
int k_SE
```
 - tau_cos
```
double tau_cos
```
- Class edu.stanford.rsl.conrad.filtering.VolumeAttenuationFactorCorrectionTool extends IndividualImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 -4178589044274723460L
 - Serialized Fields
 - minimum
```
double minimum
```
 - measureHard
```
double measureHard
```
 - measureSoft
```
double measureSoft
```
 - debug
```
boolean debug
```
Package edu.stanford.rsl.conrad.filtering.multiprojection
- Class edu.stanford.rsl.conrad.filtering.multiprojection.BilateralFilter3D extends BlockWiseMultiProjectionFilter implements Serializable
 
 serialVersionUID:
 
 2430924392909104202L
- Class edu.stanford.rsl.conrad.filtering.multiprojection.BlockWiseMultiProjectionFilter extends MultiProjectionFilter implements Serializable
 
 serialVersionUID:
 
 -8702779450295098767L
 - Serialized Fields
 - modelBlock
```
ImageProcessingBlock modelBlock
```
 - blocks
```
ImageProcessingBlock[][][] blocks
```
 - numBlocks
```
int numBlocks
```
 - blocksX
```
int blocksX
```
 - blocksY
```
int blocksY
```
 - blocksZ
```
int blocksZ
```
 - blockSizeX
```
int blockSizeX
```
 - blockSizeY
```
int blockSizeY
```
 - blockSizeZ
```
int blockSizeZ
```
 - width
```
int width
```
 - height
```
int height
```
 - blockOverlap
```
double blockOverlap
```
 - initBlocks
```
boolean initBlocks
```
 - nInputImages
```
int nInputImages
```
 - latch
```
java.util.concurrent.CountDownLatch latch
```
- Class edu.stanford.rsl.conrad.filtering.multiprojection.BlockWiseStructureTensor extends BlockWiseMultiProjectionFilter implements Serializable
 
 serialVersionUID:
 
 -5932376637078023191L
- Class edu.stanford.rsl.conrad.filtering.multiprojection.DiaphragmTrackingTool extends MultiProjectionFilter implements Serializable
 
 serialVersionUID:
 
 334423738188161138L
 - Serialized Fields
 - a
```
java.util.ArrayList<E> a
```
 - ip
```
ij.process.ImageProcessor ip
```
 - imp
```
ij.process.ImageProcessor imp
```
 - impSeg
```
ij.process.ImageProcessor impSeg
```
- Class edu.stanford.rsl.conrad.filtering.multiprojection.IdentityTransformFilter extends BlockWiseMultiProjectionFilter implements Serializable
 
 serialVersionUID:
 
 6288980025231747250L
- Class edu.stanford.rsl.conrad.filtering.multiprojection.IterativeReconstructionFilter extends BlockWiseMultiProjectionFilter implements Serializable
 
 serialVersionUID:
 
 2430924392909104202L
- Class edu.stanford.rsl.conrad.filtering.multiprojection.Lambda3DDerivativeFilter extends MultiProjectionFilter implements Serializable
 
 serialVersionUID:
 
 -4713499234279226464L
 - Serialized Fields
 - uWeights
```
double[] uWeights
```
 - vWeights
```
double[][] vWeights
```
 - pWeights
```
double[] pWeights
```
 - detectorElementSizeX
```
double detectorElementSizeX
```
 - detectorElementSizeY
```
double detectorElementSizeY
```
 - averageAngularIncrement
```
double averageAngularIncrement
```
 - factor
```
double factor
```
 - factor2
```
double factor2
```
 - SID
```
double SID
```
- Class edu.stanford.rsl.conrad.filtering.multiprojection.MultiProjectionFilter extends ImageFilteringTool implements Serializable
 
 serialVersionUID:
 
 -2775871921675277534L
 - Serialized Fields
 - inputQueue
```
ImageProcessorBuffer inputQueue
```
 - processed
```
java.util.ArrayList<E> processed
```
 - outputQueue
```
ImageProcessorBuffer outputQueue
```
 - sink
```
ProjectionSink sink
```
 - context
```
int context
```
 - showStatus
```
boolean showStatus
```
 - closed
```
boolean closed
```
 - finalIndex
```
int finalIndex
```
 - init
```
boolean init
```
 - debug
```
int debug
```
- Class edu.stanford.rsl.conrad.filtering.multiprojection.ProjectionSortingFilter extends MultiProjectionFilter implements Serializable
 
 serialVersionUID:
 
 1767982087589043403L
- Class edu.stanford.rsl.conrad.filtering.multiprojection.Triangulation extends MultiProjectionFilter implements Serializable
 
 serialVersionUID:
 
 -8039698341980560155L
 - Serialized Fields
 - correction
```
double correction
```
Package edu.stanford.rsl.conrad.filtering.multiprojection.anisotropic
- Class edu.stanford.rsl.conrad.filtering.multiprojection.anisotropic.AnisotropicStructureTensorNoiseFilter extends MultiProjectionFilter implements Serializable
  
  serialVersionUID:
  
  -7877365673267053836L
  - Serialized Fields
    - smoothness
```
float smoothness
```
    - lowerTensorLevel
```
float lowerTensorLevel
```
    - upperTensorLevel
```
float upperTensorLevel
```
    - highPassLowerLevel
```
float highPassLowerLevel
```
    - highPassUpperLevel
```
float highPassUpperLevel
```
    - lpUpper
```
float lpUpper
```
    - showAbsoluteTensor
```
boolean showAbsoluteTensor
```
    - dimx
```
double dimx
```
    - dimy
```
double dimy
```
    - tensorBuffer
```
ImageProcessorBuffer tensorBuffer
```
    - overlap
```
boolean overlap
```
- Class edu.stanford.rsl.conrad.filtering.multiprojection.anisotropic.CUDAAnisotropicStructureTensorNoiseFilter extends AnisotropicStructureTensorNoiseFilter implements Serializable
  
  serialVersionUID:
  
  5714621818252161125L
  - Serialized Fields
    - cuop
```
CUDAVolumeOperator cuop
```
- Class edu.stanford.rsl.conrad.filtering.multiprojection.anisotropic.CUDAFFTAnisotropicStructureTensorNoiseFilter extends AnisotropicStructureTensorNoiseFilter implements Serializable
  
  serialVersionUID:
  
  5714621818252161125L
Package edu.stanford.rsl.conrad.filtering.multiprojection.blocks
- Class edu.stanford.rsl.conrad.filtering.multiprojection.blocks.AnisotropicStructureTensorBlock extends ImageProcessingBlock implements Serializable
  
  serialVersionUID:
  
  1265388205607681586L
  - Serialized Fields
    - smoothness
```
float smoothness
```
    - lowerTensorLevel
```
float lowerTensorLevel
```
    - upperTensorLevel
```
float upperTensorLevel
```
    - highPassLowerLevel
```
float highPassLowerLevel
```
    - highPassUpperLevel
```
float highPassUpperLevel
```
    - lpUpper
```
float lpUpper
```
    - showAbsoluteTensor
```
boolean showAbsoluteTensor
```
    - dimx
```
double dimx
```
    - dimy
```
double dimy
```
- Class edu.stanford.rsl.conrad.filtering.multiprojection.blocks.BilateralFilter3DBlock extends ImageProcessingBlock implements Serializable
  
  serialVersionUID:
  
  -7875829253535505054L
  - Serialized Fields
    - sigma_d
```
double sigma_d
```
    - sigma_r
```
double sigma_r
```
    - width
```
int width
```
- Class edu.stanford.rsl.conrad.filtering.multiprojection.blocks.IdentityTransformBlock extends ImageProcessingBlock implements Serializable
  
  serialVersionUID:
  
  6502352732903411093L
- Class edu.stanford.rsl.conrad.filtering.multiprojection.blocks.ImageProcessingBlock extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -5847536522784571557L
  - Serialized Fields
    - latch
```
java.util.concurrent.CountDownLatch latch
```
    - inputBlock
```
ij.ImagePlus inputBlock
```
    - outputBlock
```
ij.ImagePlus outputBlock
```
    - configured
```
boolean configured
```
- Class edu.stanford.rsl.conrad.filtering.multiprojection.blocks.IterativeReconstructionBlock extends ImageProcessingBlock implements Serializable
  
  serialVersionUID:
  
  -7875829253535505054L
  - Serialized Fields
    - sigma_d
```
double sigma_d
```
    - sigma_r
```
double sigma_r
```
    - width
```
int width
```
Package edu.stanford.rsl.conrad.filtering.rampfilters
- Class edu.stanford.rsl.conrad.filtering.rampfilters.ArbitraryRampFilter extends RampFilter implements Serializable
  
  serialVersionUID:
  
  -7312562756045270927L
  - Serialized Fields
    - filter
```
double[] filter
```
    - file
```
java.lang.String file
```
- Class edu.stanford.rsl.conrad.filtering.rampfilters.CosineRampFilter extends RampFilter implements Serializable
  
  serialVersionUID:
  
  8510178767243770599L
- Class edu.stanford.rsl.conrad.filtering.rampfilters.HammingRampFilter extends RampFilter implements Serializable
  
  serialVersionUID:
  
  8909229941245077452L
- Class edu.stanford.rsl.conrad.filtering.rampfilters.HanningRampFilter extends RampFilter implements Serializable
  
  serialVersionUID:
  
  -4538976511084471631L
- Class edu.stanford.rsl.conrad.filtering.rampfilters.RamLakRampFilter extends RampFilter implements Serializable
  
  serialVersionUID:
  
  -372550797243795367L
- Class edu.stanford.rsl.conrad.filtering.rampfilters.RampFilter extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -6709816992630498882L
  - Serialized Fields
    - debug
```
boolean debug
```
    - configured
```
boolean configured
```
    - physicalPixelWidthInMilimeters
```
double physicalPixelWidthInMilimeters
```
    - cutOffFrequency
```
double cutOffFrequency
```
    - sourceToDetectorDistance
```
double sourceToDetectorDistance
```
    - filter
```
double[] filter
```
    - currentWidth
```
int currentWidth
```
    - currentProcessor
```
ij.process.FloatProcessor currentProcessor
```
    - sourceToAxisDistance
```
double sourceToAxisDistance
```
- Class edu.stanford.rsl.conrad.filtering.rampfilters.SheppLoganRampFilter extends RampFilter implements Serializable
  
  serialVersionUID:
  
  8055940389460979441L
- Class edu.stanford.rsl.conrad.filtering.rampfilters.SheppLoganRampFilterWithRollOff extends SheppLoganRampFilter implements Serializable
  
  serialVersionUID:
  
  -4506146824678039341L
  - Serialized Fields
    - start
```
double start
```
    - scale
```
double scale
```
    - slope
```
double slope
```
Package edu.stanford.rsl.conrad.filtering.redundancy
- Class edu.stanford.rsl.conrad.filtering.redundancy.NooWeightingTool extends ParkerWeightingTool implements Serializable
  
  serialVersionUID:
  
  -9073647229814074372L
  - Serialized Fields
    - numerical
```
double numerical
```
    - deltaX
```
double deltaX
```
- Class edu.stanford.rsl.conrad.filtering.redundancy.OSCARWeightingTool extends ParkerWeightingTool implements Serializable
  
  serialVersionUID:
  
  2453380390532119284L
  - Serialized Fields
    - deltaX
```
double deltaX
```
    - numerical
```
double numerical
```
- Class edu.stanford.rsl.conrad.filtering.redundancy.ParkerWeightingTool extends IndividualImageFilteringTool implements Serializable
  
  serialVersionUID:
  
  -1342759492107420854L
  - Serialized Fields
    - detectorWidth
```
int detectorWidth
```
    - pixelDimensionX
```
double pixelDimensionX
```
    - sourceToDetectorDistance
```
double sourceToDetectorDistance
```
    - sourceToAxisDistance
```
double sourceToAxisDistance
```
    - numberOfProjections
```
int numberOfProjections
```
    - primaryAngles
```
double[] primaryAngles
```
    - delta
```
double delta
```
    - offset
```
double offset
```
- Class edu.stanford.rsl.conrad.filtering.redundancy.SilverWeightingTool extends ParkerWeightingTool implements Serializable
  
  serialVersionUID:
  
  2453380390532119284L
  - Serialized Fields
    - deltaX
```
double deltaX
```
    - numerical
```
double numerical
```
- Class edu.stanford.rsl.conrad.filtering.redundancy.TrajectoryParkerWeightingTool extends ParkerWeightingTool implements Serializable
  
  serialVersionUID:
  
  -7809768945811552837L
- Class edu.stanford.rsl.conrad.filtering.redundancy.WesargWeightingTool extends ParkerWeightingTool implements Serializable
  
  serialVersionUID:
  
  2453380390532119284L
  - Serialized Fields
    - deltaX
```
double deltaX
```
    - filter
```
boolean filter
```
    - percent
```
double percent
```
Package edu.stanford.rsl.conrad.fitting
- Class edu.stanford.rsl.conrad.fitting.ConstrainedRANSACFittedFunction extends RANSACFittedFunction implements Serializable
  
  serialVersionUID:
  
  -4078810270398436119L
  - Serialized Fields
    - upperbound
```
double[] upperbound
```
    - lowerbound
```
double[] lowerbound
```
- Class edu.stanford.rsl.conrad.fitting.Function extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  5067981485975476424L
  - Serialized Fields
    - fittingDone
```
boolean fittingDone
```
    - numberOfParameters
```
int numberOfParameters
```
- Class edu.stanford.rsl.conrad.fitting.GaussianFunction extends Function implements Serializable
  
  serialVersionUID:
  
  8345414466275108572L
  - Serialized Fields
    - mu
```
double mu
```
    - sigma
```
double sigma
```
- Class edu.stanford.rsl.conrad.fitting.IdentityFunction extends Function implements Serializable
  
  serialVersionUID:
  
  4775769211165404450L
- Class edu.stanford.rsl.conrad.fitting.LinearFunction extends Function implements Serializable
  
  serialVersionUID:
  
  7484751042707779396L
  - Serialized Fields
    - m
```
double m
```
    - t
```
double t
```
- Class edu.stanford.rsl.conrad.fitting.LogarithmicFunction extends Function implements Serializable
  
  serialVersionUID:
  
  3584939480038216387L
  - Serialized Fields
    - a
```
double a
```
    - b
```
double b
```
    - c
```
double c
```
    - d
```
double d
```
- Class edu.stanford.rsl.conrad.fitting.PolynomialFunction extends Function implements Serializable
  
  serialVersionUID:
  
  -1557807323919814217L
  - Serialized Fields
    - degree
```
int degree
```
    - params
```
double[] params
```
- Class edu.stanford.rsl.conrad.fitting.Quadric extends Surface implements Serializable
  
  serialVersionUID:
  
  6104784792939859900L
  - Serialized Fields
    - degree
```
int degree
```
    - params
```
double[] params
```
- Class edu.stanford.rsl.conrad.fitting.RANSACFittedFunction extends Function implements Serializable
  
  serialVersionUID:
  
  -8899279893077174756L
  - Serialized Fields
    - baseFunction
```
Function baseFunction
```
      This is the function that RANSAC is computed on-
    - numberOfTries
```
int numberOfTries
```
      This paremeter defines the number of tries to compute RANSAC
    - epsilon
```
double epsilon
```
      This parameter defines the fault tolerance
- Class edu.stanford.rsl.conrad.fitting.Surface extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -91840779787161332L
  - Serialized Fields
    - fittingDone
```
boolean fittingDone
```
    - numberOfParameters
```
int numberOfParameters
```
Package edu.stanford.rsl.conrad.geometry
- Class edu.stanford.rsl.conrad.geometry.AbstractCurve extends AbstractShape implements Serializable
  
  serialVersionUID:
  
  8742936166235392950L
- Class edu.stanford.rsl.conrad.geometry.AbstractShape extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  6333594201718418159L
  - Serialized Fields
    - boundingPlanes
```
Plane3D[] boundingPlanes
```
    - min
```
PointND min
```
    - max
```
PointND max
```
    - name
```
java.lang.String name
```
- Class edu.stanford.rsl.conrad.geometry.AbstractSurface extends AbstractShape implements Serializable
  
  serialVersionUID:
  
  8336440075236081077L
- Class edu.stanford.rsl.conrad.geometry.Projection extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -6890230919386599781L
  - Serialized Fields
    - s
```
double s
```
      Scaling factor for the decomposed projection.
    - K
```
SimpleMatrix K
```
      Intrinsic parameters for the decomposed projection.
    - R
```
SimpleMatrix R
```
      Rotation matrix for the decomposed projection.
    - t
```
SimpleVector t
```
      Translation vector for the decomposed projection.
    - RTKinv
```
SimpleMatrix RTKinv
```
      Store precomputed matrix $\mathbf{R}^T \cdot \mathbf{K}^{-1}$ to speed up computeRayDirection()
Package edu.stanford.rsl.conrad.geometry.bounds
- Class edu.stanford.rsl.conrad.geometry.bounds.AbstractBoundingCondition extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  8678860762808220344L
- Class edu.stanford.rsl.conrad.geometry.bounds.BoundingBox extends AbstractBoundingCondition implements Serializable
  
  serialVersionUID:
  
  -5984414347382076217L
  - Serialized Fields
    - min
```
PointND min
```
    - max
```
PointND max
```
- Class edu.stanford.rsl.conrad.geometry.bounds.HalfSpaceBoundingCondition extends AbstractBoundingCondition implements Serializable
  
  serialVersionUID:
  
  -1161793937985226484L
  - Serialized Fields
    - plane
```
Plane3D plane
```
    - isFlipped
```
boolean isFlipped
```
- Class edu.stanford.rsl.conrad.geometry.bounds.QuadricBoundingCondition extends AbstractBoundingCondition implements Serializable
  
  serialVersionUID:
  
  -3212222341769199451L
  - Serialized Fields
    - surface
```
QuadricSurface surface
```
    - isFlipped
```
boolean isFlipped
```
Package edu.stanford.rsl.conrad.geometry.motion
- Class edu.stanford.rsl.conrad.geometry.motion.AffineMotionField extends SimpleMotionField implements Serializable
 
 serialVersionUID:
 
 6748536919627679826L
 - Serialized Fields
 - toCenter
```
Translation toCenter
```
 - back
```
Translation back
```
 - axis
```
SimpleVector axis
```
 - angle
```
double angle
```
 - center
```
PointND center
```
 - translation
```
SimpleVector translation
```
 - rotationMat
```
SimpleMatrix rotationMat
```
- Class edu.stanford.rsl.conrad.geometry.motion.CombinedBreathingHeartMotionField extends ParzenWindowMotionField implements Serializable
 
 serialVersionUID:
 
 4787248458841471038L
 - Serialized Fields
 - breathingHeartScene
```
CombinedBreathingHeartScene breathingHeartScene
```
- Class edu.stanford.rsl.conrad.geometry.motion.CompressionMotionField extends SimpleMotionField implements Serializable
 
 serialVersionUID:
 
 191865158667227329L
 - Serialized Fields
 - direction
```
SimpleVector direction
```
 - min
```
PointND min
```
 - max
```
PointND max
```
 - length
```
double length
```
- Class edu.stanford.rsl.conrad.geometry.motion.ConstantMotionField extends SimpleMotionField implements Serializable
 
 serialVersionUID:
 
 -6413969556338466583L
- Class edu.stanford.rsl.conrad.geometry.motion.DualMotionField extends SimpleMotionField implements Serializable
 
 serialVersionUID:
 
 -202437787576272143L
 - Serialized Fields
 - halfSpaceOne
```
HalfSpaceBoundingCondition halfSpaceOne
```
 - one
```
MotionField one
```
 - two
```
MotionField two
```
- Class edu.stanford.rsl.conrad.geometry.motion.MixedSurfaceBSplineMotionField extends ParzenWindowMotionField implements Serializable
 
 serialVersionUID:
 
 -4288495612235276488L
 - Serialized Fields
 - variants
```
java.util.ArrayList<E> variants
```
 - invariants
```
java.util.ArrayList<E> invariants
```
- Class edu.stanford.rsl.conrad.geometry.motion.MovingCenterRotationMotionField extends RotationMotionField implements Serializable
 
 serialVersionUID:
 
 -4231093664698586329L
 - Serialized Fields
 - centerTransform
```
MotionField centerTransform
```
- Class edu.stanford.rsl.conrad.geometry.motion.OpenCLParzenWindowMotionField extends ParzenWindowMotionField implements Serializable
 
 serialVersionUID:
 
 -322305647900119904L
 - Serialized Fields
 - motionField
```
ParzenWindowMotionField motionField
```
 - context
```
com.jogamp.opencl.CLContext context
```
 - program
```
com.jogamp.opencl.CLProgram program
```
- Class edu.stanford.rsl.conrad.geometry.motion.ParzenWindowMotionField extends java.lang.Object implements Serializable
 
 serialVersionUID:
 
 -6548767514419099244L
 - Serialized Fields
 - timePointMap
```
java.util.HashMap<K,V> timePointMap
```
 - sigma
```
double sigma
```
 Standard Deviation of the Gaussian Window in world coordinate metric, i.e. [mm] for XCat.
 - warp
```
TimeWarper warp
```
- Class edu.stanford.rsl.conrad.geometry.motion.PlanarMotionField extends SimpleMotionField implements Serializable
 
 serialVersionUID:
 
 -7264620135393212142L
 - Serialized Fields
 - normal
```
SimpleVector normal
```
 - fullMotion
```
MotionField fullMotion
```
- Class edu.stanford.rsl.conrad.geometry.motion.PointBasedMotionField extends java.lang.Object implements Serializable
 
 serialVersionUID:
 
 1286210731201948669L
 - Serialized Fields
 - warp
```
TimeWarper warp
```
 - timePoints
```
java.util.ArrayList<E> timePoints
```
 - context
```
int context
```
 - timeSamplePoints
```
int timeSamplePoints
```
- Class edu.stanford.rsl.conrad.geometry.motion.RotationMotionField extends SimpleMotionField implements Serializable
 
 serialVersionUID:
 
 -5199935079209350635L
 - Serialized Fields
 - toCenter
```
Translation toCenter
```
 - back
```
Translation back
```
 - axis
```
SimpleVector axis
```
 - angle
```
double angle
```
 - center
```
PointND center
```
- Class edu.stanford.rsl.conrad.geometry.motion.SimpleMotionField extends java.lang.Object implements Serializable
 
 serialVersionUID:
 
 -352375092478769290L
 - Serialized Fields
 - warp
```
TimeWarper warp
```
- Class edu.stanford.rsl.conrad.geometry.motion.TimeVariantSurfaceBSplineListMotionField extends ParzenWindowMotionField implements Serializable
 
 serialVersionUID:
 
 7397812496219257524L
 - Serialized Fields
 - variants
```
java.util.ArrayList<E> variants
```
- Class edu.stanford.rsl.conrad.geometry.motion.TimeVariantSurfaceBSplineMotionField extends ParzenWindowMotionField implements Serializable
 
 serialVersionUID:
 
 138799495833604748L
 - Serialized Fields
 - variant
```
TimeVariantSurfaceBSpline variant
```
- Class edu.stanford.rsl.conrad.geometry.motion.VICONMarkerMotionField extends SimpleMotionField implements Serializable
 
 serialVersionUID:
 
 -719945083192209758L
 - Serialized Fields
 - markers
```
java.util.ArrayList<E> markers
```
 - fieldNo
```
int fieldNo
```
 - beforePts
```
PointND[] beforePts
```
 - afterPts
```
PointND[] afterPts
```
 - tmpTransformation1
```
ViconAffineTransform tmpTransformation1
```
 - tmpTransformation2
```
ViconAffineTransform tmpTransformation2
```
 - part
```
java.lang.String part
```
 - splineTitle
```
java.lang.String splineTitle
```
 - vBuilder
```
ViconMarkerBuilder vBuilder
```
 - weight
```
double weight
```
- Class edu.stanford.rsl.conrad.geometry.motion.WeightBearingBeadPositionBuilder extends java.lang.Object implements Serializable
 
 serialVersionUID:
 
 -4691626378724299348L
 - Serialized Fields
 - config
```
Configuration config
```
 - noProjection
```
int noProjection
```
 - beadsIn2D
```
double[][][] beadsIn2D
```
 - beadsMeanIn3D
```
double[][] beadsMeanIn3D
```
Package edu.stanford.rsl.conrad.geometry.motion.timewarp
- Class edu.stanford.rsl.conrad.geometry.motion.timewarp.ConstantTimeWarper extends TimeWarper implements Serializable
  
  serialVersionUID:
  
  -8589588541432169559L
  - Serialized Fields
    - c
```
double c
```
- Class edu.stanford.rsl.conrad.geometry.motion.timewarp.DualPhasePeriodicTimeWarper extends TimeWarper implements Serializable
  
  serialVersionUID:
  
  2589628945345492493L
  - Serialized Fields
    - phase1
```
double phase1
```
- Class edu.stanford.rsl.conrad.geometry.motion.timewarp.HarmonicTimeWarper extends TimeWarper implements Serializable
  
  serialVersionUID:
  
  7097330258596613543L
  - Serialized Fields
    - n
```
double n
```
- Class edu.stanford.rsl.conrad.geometry.motion.timewarp.IdentityTimeWarper extends TimeWarper implements Serializable
  
  serialVersionUID:
  
  6668711012221834486L
- Class edu.stanford.rsl.conrad.geometry.motion.timewarp.PeriodicTimeWarper extends TimeWarper implements Serializable
  
  serialVersionUID:
  
  7128385122818413431L
- Class edu.stanford.rsl.conrad.geometry.motion.timewarp.RestPhaseTimeWarper extends TimeWarper implements Serializable
  
  serialVersionUID:
  
  -8951035976077197467L
  - Serialized Fields
    - restPhase
```
double restPhase
```
    - scale
```
double scale
```
- Class edu.stanford.rsl.conrad.geometry.motion.timewarp.SigmoidTimeWarper extends TimeWarper implements Serializable
  
  serialVersionUID:
  
  -5822332120091846823L
  - Serialized Fields
    - acc
```
double acc
```
- Class edu.stanford.rsl.conrad.geometry.motion.timewarp.TimeWarper extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -6032593933715940914L
Package edu.stanford.rsl.conrad.geometry.shapes
- Class edu.stanford.rsl.conrad.geometry.shapes.ArbitrarySurface extends SimpleSurface implements Serializable
 
 serialVersionUID:
 
 -3286378502393392770L
 - Serialized Fields
 - boundingClips
```
java.util.ArrayList<E> boundingClips
```
 - baseSurface
```
SimpleSurface baseSurface
```
Package edu.stanford.rsl.conrad.geometry.shapes.compound
- Class edu.stanford.rsl.conrad.geometry.shapes.compound.CompoundShape extends AbstractShape implements Serializable
 
 serialVersionUID:
 
 4296470814160586436L
 - Serialized Fields
 - list
```
java.util.ArrayList<E> list
```
 - dirty
```
boolean dirty
```
- Class edu.stanford.rsl.conrad.geometry.shapes.compound.LinearOctree extends CompoundShape implements Serializable
 
 serialVersionUID:
 
 8039686125389239903L
 - Serialized Fields
 - octant1
```
CompoundShape octant1
```
 - octant2
```
CompoundShape octant2
```
 - octant3
```
CompoundShape octant3
```
 - octant4
```
CompoundShape octant4
```
 - octant5
```
CompoundShape octant5
```
 - octant6
```
CompoundShape octant6
```
 - octant7
```
CompoundShape octant7
```
 - octant8
```
CompoundShape octant8
```
 - center
```
PointND center
```
 - dimension
```
int dimension
```
- Class edu.stanford.rsl.conrad.geometry.shapes.compound.NestedOctree extends LinearOctree implements Serializable
 
 serialVersionUID:
 
 577772012630565223L
Package edu.stanford.rsl.conrad.geometry.shapes.simple
- Class edu.stanford.rsl.conrad.geometry.shapes.simple.Box extends SimpleSurface implements Serializable
 
 serialVersionUID:
 
 1760483762488429473L
 - Serialized Fields
 - principalAxis
```
Axis principalAxis
```
 - lowerCorner
```
PointND lowerCorner
```
 - upperCorner
```
PointND upperCorner
```
- Class edu.stanford.rsl.conrad.geometry.shapes.simple.Cone extends QuadricSurface implements Serializable
 
 serialVersionUID:
 
 6986546973890638795L
 - Serialized Fields
 - principalAxis
```
Axis principalAxis
```
- Class edu.stanford.rsl.conrad.geometry.shapes.simple.Cylinder extends QuadricSurface implements Serializable
 
 serialVersionUID:
 
 6986546973890638795L
 - Serialized Fields
 - principalAxis
```
Axis principalAxis
```
 - dz
```
double dz
```
 - dx
```
double dx
```
 - dy
```
double dy
```
- Class edu.stanford.rsl.conrad.geometry.shapes.simple.Edge extends StraightLine implements Serializable
 
 serialVersionUID:
 
 3399981161692525136L
 - Serialized Fields
 - end
```
double end
```
 - endPoint
```
PointND endPoint
```
 - length
```
double length
```
- Class edu.stanford.rsl.conrad.geometry.shapes.simple.Ellipsoid extends QuadricSurface implements Serializable
 
 serialVersionUID:
 
 7869742887570580304L
 - Serialized Fields
 - principalAxis
```
Axis principalAxis
```
- Class edu.stanford.rsl.conrad.geometry.shapes.simple.Plane3D extends AbstractSurface implements Serializable
 
 serialVersionUID:
 
 -6304736161052003537L
 - Serialized Fields
 - dirU
```
SimpleVector dirU
```
 - dirV
```
SimpleVector dirV
```
 - pointP
```
PointND pointP
```
 - normalN
```
SimpleVector normalN
```
 - offsetD
```
double offsetD
```
- Class edu.stanford.rsl.conrad.geometry.shapes.simple.Point2D extends PointND implements Serializable
 
 serialVersionUID:
 
 -5759702343444016617L
- Class edu.stanford.rsl.conrad.geometry.shapes.simple.Point3D extends PointND implements Serializable
 
 serialVersionUID:
 
 -3570269971680307757L
- Class edu.stanford.rsl.conrad.geometry.shapes.simple.PointND extends java.lang.Object implements Serializable
 
 serialVersionUID:
 
 -1747968959310910786L
 - Serialized Fields
 - coordinates
```
SimpleVector coordinates
```
- Class edu.stanford.rsl.conrad.geometry.shapes.simple.QuadricSurface extends SimpleSurface implements Serializable
 
 serialVersionUID:
 
 2995274520995183991L
 - Serialized Fields
 - constMatrix
```
SimpleMatrix constMatrix
```
 - constant
```
double constant
```
 - origin
```
PointND origin
```
 - dummy
```
java.util.ArrayList<E> dummy
```
- Class edu.stanford.rsl.conrad.geometry.shapes.simple.SimpleSurface extends AbstractSurface implements Serializable
 
 serialVersionUID:
 
 1165067022561672962L
 - Serialized Fields
 - transform
```
Transform transform
```
 - boundingConditions
```
java.util.ArrayList<E> boundingConditions
```
- Class edu.stanford.rsl.conrad.geometry.shapes.simple.SortablePoint extends PointND implements Serializable
 
 serialVersionUID:
 
 6976938525970166621L
 - Serialized Fields
 - sortIndex
```
int sortIndex
```
- Class edu.stanford.rsl.conrad.geometry.shapes.simple.Sphere extends QuadricSurface implements Serializable
 
 serialVersionUID:
 
 7869742887570580304L
 - Serialized Fields
 - principalAxis
```
Axis principalAxis
```
- Class edu.stanford.rsl.conrad.geometry.shapes.simple.StraightLine extends AbstractCurve implements Serializable
 
 serialVersionUID:
 
 4615305861839196846L
 - Serialized Fields
 - direction
```
SimpleVector direction
```
 - point
```
PointND point
```
- Class edu.stanford.rsl.conrad.geometry.shapes.simple.Triangle extends Plane3D implements Serializable
 
 serialVersionUID:
 
 3360323076084779150L
 - Serialized Fields
 - bUcoord
```
double bUcoord
```
 - bVcoord
```
double bVcoord
```
 - cUcoord
```
double cUcoord
```
 - cVcoord
```
double cVcoord
```
- Class edu.stanford.rsl.conrad.geometry.shapes.simple.VectorPoint3D extends Point3D implements Serializable
 
 serialVersionUID:
 
 3854685720292206922L
 - Serialized Fields
 - vector
```
SimpleVector vector
```
Package edu.stanford.rsl.conrad.geometry.splines
- Class edu.stanford.rsl.conrad.geometry.splines.BSpline extends AbstractCurve implements Serializable
 
 serialVersionUID:
 
 -1510774879340694844L
 - Serialized Fields
 - degree
```
int degree
```
 - knots
```
double[] knots
```
 - controlPoints
```
java.util.ArrayList<E> controlPoints
```
 - dimension
```
int dimension
```
- Class edu.stanford.rsl.conrad.geometry.splines.MotionDefectTimeVariantSurfaceBSpline extends TimeVariantSurfaceBSpline implements Serializable
 
 serialVersionUID:
 
 -1439361309222709769L
 - Serialized Fields
 - min
```
PointND min
```
 - max
```
PointND max
```
 - samplingStep
```
double samplingStep
```
 - phaseShift
```
double phaseShift
```
 - defectPoints
```
java.util.ArrayList<E> defectPoints
```
 - interpolationPoints
```
java.util.ArrayList<E> interpolationPoints
```
- Class edu.stanford.rsl.conrad.geometry.splines.NearestNeighborTimeVariantSurfaceBSpline extends TimeVariantSurfaceBSpline implements Serializable
 
 serialVersionUID:
 
 7390783547660669266L
- Class edu.stanford.rsl.conrad.geometry.splines.SurfaceBSpline extends AbstractSurface implements Serializable
 
 serialVersionUID:
 
 4942618494585588413L
 - Serialized Fields
 - uKnots
```
SimpleVector uKnots
```
 - vKnots
```
SimpleVector vKnots
```
 - numberOfUPoints
```
int numberOfUPoints
```
 - numberOfVPoints
```
int numberOfVPoints
```
 - points
```
java.util.ArrayList<E> points
```
 - vSplines
```
BSpline[] vSplines
```
 - uSpline
```
BSpline uSpline
```
 - dimension
```
int dimension
```
 - clockwise
```
boolean clockwise
```
 - title
```
java.lang.String title
```
- Class edu.stanford.rsl.conrad.geometry.splines.SurfaceUniformCubicBSpline extends SurfaceBSpline implements Serializable
 
 serialVersionUID:
 
 -7498785267911679836L
- Class edu.stanford.rsl.conrad.geometry.splines.TimeVariantSurfaceBSpline extends AbstractSurface implements Serializable
 
 serialVersionUID:
 
 6323388850451960550L
 - Serialized Fields
 - timeVariantShapes
```
java.util.ArrayList<E> timeVariantShapes
```
 - title
```
java.lang.String title
```
 - timeSpline
```
BSpline timeSpline
```
 - tPoints
```
int tPoints
```
 - clockwise
```
boolean clockwise
```
- Class edu.stanford.rsl.conrad.geometry.splines.UniformCubicBSpline extends BSpline implements Serializable
 
 serialVersionUID:
 
 8467214013384105086L
Package edu.stanford.rsl.conrad.geometry.trajectories
- Class edu.stanford.rsl.conrad.geometry.trajectories.CircularTrajectory extends Trajectory implements Serializable
  
  serialVersionUID:
  
  -3236098993706829039L
- Class edu.stanford.rsl.conrad.geometry.trajectories.ConfigFileBasedTrajectory extends Trajectory implements Serializable
  
  serialVersionUID:
  
  -5999736125816034590L
- Class edu.stanford.rsl.conrad.geometry.trajectories.DennerleinProjectionTableFileTrajectory extends ConfigFileBasedTrajectory implements Serializable
  
  serialVersionUID:
  
  -1392472185220533956L
  - Serialized Fields
    - success
```
boolean success
```
- Class edu.stanford.rsl.conrad.geometry.trajectories.ExtrapolatedTrajectory extends Trajectory implements Serializable
  
  serialVersionUID:
  
  800597336777372574L
  - Serialized Fields
    - debug
```
boolean debug
```
- Class edu.stanford.rsl.conrad.geometry.trajectories.MultiSweepTrajectory extends Trajectory implements Serializable
  
  serialVersionUID:
  
  800597336777372574L
- Class edu.stanford.rsl.conrad.geometry.trajectories.ProjectionTableFileTrajectory extends ConfigFileBasedTrajectory implements Serializable
  
  serialVersionUID:
  
  8539564781880779305L
  - Serialized Fields
    - version
```
int version
```
    - success
```
boolean success
```
- Class edu.stanford.rsl.conrad.geometry.trajectories.SystemGeometryConfigFileTrajectory extends ConfigFileBasedTrajectory implements Serializable
  
  serialVersionUID:
  
  2773005628961913345L
  - Serialized Fields
    - volumeSize
```
double[] volumeSize
```
    - volumeResolution
```
double[] volumeResolution
```
    - detectorResolution
```
double[] detectorResolution
```
    - detectorPixels
```
double[] detectorPixels
```
    - averageAngularIncrement
```
double averageAngularIncrement
```
    - numProjections
```
int numProjections
```
    - transformToNextProjection
```
SimpleMatrix transformToNextProjection
```
    - SID
```
double SID
```
    - SAD
```
double SAD
```
    - success
```
boolean success
```
    - config
```
Configuration config
```
- Class edu.stanford.rsl.conrad.geometry.trajectories.Trajectory extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  8005225046964549262L
  - Serialized Fields
    - numProjectionMatrices
```
int numProjectionMatrices
```
    - detectorWidth
```
int detectorWidth
```
    - detectorHeight
```
int detectorHeight
```
    - pixelDimensionX
```
double pixelDimensionX
```
    - pixelDimensionY
```
double pixelDimensionY
```
    - sourceToDetectorDistance
```
double sourceToDetectorDistance
```
    - sourceToAxisDistance
```
double sourceToAxisDistance
```
    - averageAngularIncrement
```
double averageAngularIncrement
```
    - projectionStackSize
```
int projectionStackSize
```
    - reconDimensions
```
double[] reconDimensions
```
    - reconVoxelSizes
```
double[] reconVoxelSizes
```
    - projectionMatrices
```
Projection[] projectionMatrices
```
    - primaryAngles
```
double[] primaryAngles
```
    - secondaryAngles
```
double[] secondaryAngles
```
    - primaryAnglesString
```
java.lang.String primaryAnglesString
```
    - secondaryAnglesString
```
java.lang.String secondaryAnglesString
```
    - originInPixelsX
```
double originInPixelsX
```
    - originInPixelsY
```
double originInPixelsY
```
    - originInPixelsZ
```
double originInPixelsZ
```
    - detectorUDirection
```
Projection.CameraAxisDirection detectorUDirection
```
    - detectorVDirection
```
Projection.CameraAxisDirection detectorVDirection
```
    - detectorOffsetU
```
int detectorOffsetU
```
    - detectorOffsetV
```
int detectorOffsetV
```
    - rotationAxis
```
SimpleVector rotationAxis
```
Package edu.stanford.rsl.conrad.geometry.transforms
- Class edu.stanford.rsl.conrad.geometry.transforms.AffineTransform extends ComboTransform implements Serializable
 
 serialVersionUID:
 
 -6509394061746644677L
- Class edu.stanford.rsl.conrad.geometry.transforms.ComboTransform extends Transform implements Serializable
 
 serialVersionUID:
 
 -509282426585065975L
 - Serialized Fields
 - transforms
```
java.util.ArrayList<E> transforms
```
- Class edu.stanford.rsl.conrad.geometry.transforms.ScaleRotate extends Transform implements Serializable
 
 serialVersionUID:
 
 4514828466172949672L
 - Serialized Fields
 - scaleRotate
```
SimpleMatrix scaleRotate
```
- Class edu.stanford.rsl.conrad.geometry.transforms.Transform extends java.lang.Object implements Serializable
 
 serialVersionUID:
 
 -5051528144142521617L
- Class edu.stanford.rsl.conrad.geometry.transforms.Translation extends Transform implements Serializable
 
 serialVersionUID:
 
 3605382281959086496L
 - Serialized Fields
 - translator
```
SimpleVector translator
```
Package edu.stanford.rsl.conrad.io
- Class edu.stanford.rsl.conrad.io.BetaConfigFile extends ConfigFile implements Serializable
  
  serialVersionUID:
  
  -2408878271483968174L
  - Serialized Fields
    - beta
```
double beta
```
    - calVoltage
```
double calVoltage
```
    - dCalCopper
```
double dCalCopper
```
    - success
```
boolean success
```
- Class edu.stanford.rsl.conrad.io.ConfigFile extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  4609062299901243820L
- Class edu.stanford.rsl.conrad.io.ImagePlusDataSink extends BufferedProjectionSink implements Serializable
  
  serialVersionUID:
  
  -931042578800415977L
  - Serialized Fields
    - imageBuffer
```
ImageProcessorBuffer imageBuffer
```
    - stack
```
Grid3D stack
```
    - closed
```
boolean closed
```
    - init
```
boolean init
```
    - debug
```
boolean debug
```
- Class edu.stanford.rsl.conrad.io.IndividualFilesProjectionDataSink extends BufferedProjectionSink implements Serializable
  
  serialVersionUID:
  
  -2991638524617273945L
  - Serialized Fields
    - directory
```
java.lang.String directory
```
    - prefix
```
java.lang.String prefix
```
    - format
```
java.lang.String format
```
    - width
```
int width
```
    - height
```
int height
```
    - littleEndian
```
boolean littleEndian
```
    - closed
```
boolean closed
```
- Class edu.stanford.rsl.conrad.io.LUTConfigFile extends ConfigFile implements Serializable
  
  serialVersionUID:
  
  7789626780684597594L
  - Serialized Fields
    - minCalVoltage
```
double minCalVoltage
```
    - maxCalVoltage
```
double maxCalVoltage
```
    - nFilters
```
double nFilters
```
    - filterThickness
```
double[] filterThickness
```
    - minVoltage
```
double minVoltage
```
    - maxVoltage
```
double maxVoltage
```
    - lutDCu
```
double[][][] lutDCu
```
    - lutCalVoltage
```
double[][][] lutCalVoltage
```
    - lutVoltage
```
double[][][] lutVoltage
```
    - lutData
```
double[][][] lutData
```
    - success
```
boolean success
```
- Class edu.stanford.rsl.conrad.io.SerializableFloatProcessor extends ij.process.ImageProcessor implements Serializable
  
  serialVersionUID:
  
  -5805594811209369617L
  - Serialized Fields
    - width
```
int width
```
    - height
```
int height
```
    - cm
```
java.awt.image.ColorModel cm
```
    - min
```
float min
```
    - max
```
float max
```
    - snapshotMin
```
float snapshotMin
```
    - snapshotMax
```
float snapshotMax
```
    - pixels
```
float[] pixels
```
    - pixels8
```
byte[] pixels8
```
    - snapshotPixels
```
float[] snapshotPixels
```
    - fillColor
```
float fillColor
```
    - fixedScale
```
boolean fixedScale
```
    - snapshotCopyMode
```
boolean snapshotCopyMode
```
Package edu.stanford.rsl.conrad.metric
- Class edu.stanford.rsl.conrad.metric.ImageMetric extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  6626577275910593598L
  - Serialization Methods
    - readObject
```
public void readObject(java.io.ObjectInputStream oos)
```
    - writeObject
```
public void writeObject(java.io.ObjectOutputStream ois)
```
  - Serialized Fields
    - testImage
```
ij.ImagePlus testImage
```
    - referenceImage
```
ij.ImagePlus referenceImage
```
- Class edu.stanford.rsl.conrad.metric.MeanSquareErrorMetric extends ImageMetric implements Serializable
  
  serialVersionUID:
  
  668095213557188946L
- Class edu.stanford.rsl.conrad.metric.NormalizedImageMetric extends ImageMetric implements Serializable
  
  serialVersionUID:
  
  6441213178752251933L
  - Serialized Fields
    - normalizationImage
```
ij.ImagePlus normalizationImage
```
- Class edu.stanford.rsl.conrad.metric.NormalizedImprovement extends NormalizedImageMetric implements Serializable
  
  serialVersionUID:
  
  -9211171034028752308L
- Class edu.stanford.rsl.conrad.metric.RootMeanSquareErrorMetric extends MeanSquareErrorMetric implements Serializable
  
  serialVersionUID:
  
  332165924495213426L
Package edu.stanford.rsl.conrad.numerics
- Class edu.stanford.rsl.conrad.numerics.DecompositionSVD extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  201880439875521920L
  - Serialized Fields
    - U
```
double[][] U
```
      Arrays for internal storage of U and V.
      
      internal storage of U.
    - V
```
double[][] V
```
      Arrays for internal storage of U and V.
      
      internal storage of U.
    - s
```
double[] s
```
      Array for internal storage of singular values.
      
      internal storage of singular values.
    - m
```
int m
```
      Row and column dimensions.
      
      row dimension.
    - n
```
int n
```
      Row and column dimensions.
      
      row dimension.
    - ncu
```
int ncu
```
      Row and column dimensions.
      
      row dimension.
    - thin
```
boolean thin
```
      Column specification of matrix U
      
      U column dimension toggle
- Class edu.stanford.rsl.conrad.numerics.SimpleMatrix extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -8285872089886352233L
  - Serialized Fields
    - rows
```
int rows
```
    - cols
```
int cols
```
    - buf
```
double[][] buf
```
- Class edu.stanford.rsl.conrad.numerics.SimpleVector extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -8563837337889104489L
  - Serialized Fields
    - len
```
int len
```
    - buf
```
double[] buf
```
Package edu.stanford.rsl.conrad.opencl
- Class edu.stanford.rsl.conrad.opencl.OpenCLBackProjector extends VOIBasedReconstructionFilter implements Serializable
 
 serialVersionUID:
 
 -8615490043940236889L
 - Serialized Fields
 - context
```
com.jogamp.opencl.CLContext context
```
 The OpenCL context
 - program
```
com.jogamp.opencl.CLProgram program
```
 The OpenCL program
 - device
```
com.jogamp.opencl.CLDevice device
```
 The OpenCL device
 - kernelFunction
```
com.jogamp.opencl.CLKernel kernelFunction
```
 The OpenCL kernel function binding
 - commandQueue
```
com.jogamp.opencl.CLCommandQueue commandQueue
```
 The OpenCL command queue
 - projectionTex
```
com.jogamp.opencl.CLImage2d projectionTex
```
 The 2D projection texture reference
 - h_volume
```
float[] h_volume
```
 The volume data that is to be reconstructed
 - projectionMatrix
```
com.jogamp.opencl.CLBuffer projectionMatrix
```
 The global variable of the module which stores the view matrix.
 - volStride
```
com.jogamp.opencl.CLBuffer volStride
```
 - volumePointer
```
com.jogamp.opencl.CLBuffer volumePointer
```
 - projectionArray
```
com.jogamp.opencl.CLBuffer projectionArray
```
 - projections
```
ImageProcessorBuffer projections
```
 - projectionsAvailable
```
java.util.ArrayList<E> projectionsAvailable
```
 - projectionsDone
```
java.util.ArrayList<E> projectionsDone
```
 - largeVolumeMode
```
boolean largeVolumeMode
```
 - nSteps
```
int nSteps
```
 - subVolumeZ
```
int subVolumeZ
```
 - initialized
```
boolean initialized
```
- Class edu.stanford.rsl.conrad.opencl.OpenCLCylinder extends Cylinder implements Serializable
 
 serialVersionUID:
 
 -578366497108607027L
 - Serialized Fields
 - context
```
com.jogamp.opencl.CLContext context
```
 - device
```
com.jogamp.opencl.CLDevice device
```
 - parameter
```
com.jogamp.opencl.CLBuffer parameter
```
- Class edu.stanford.rsl.conrad.opencl.OpenCLSphere extends Sphere implements Serializable
 
 serialVersionUID:
 
 2607437298428367616L
 - Serialized Fields
 - context
```
com.jogamp.opencl.CLContext context
```
 - device
```
com.jogamp.opencl.CLDevice device
```
 - parameter
```
com.jogamp.opencl.CLBuffer parameter
```
- Class edu.stanford.rsl.conrad.opencl.OpenCLTextureTimeVariantSurfaceBSpline extends OpenCLTimeVariantSurfaceBSpline implements Serializable
 
 serialVersionUID:
 
 -1682699329382911891L
 - Serialized Fields
 - texture
```
com.jogamp.opencl.CLImage3d texture
```
- Class edu.stanford.rsl.conrad.opencl.OpenCLTimeVariantSurfaceBSpline extends TimeVariantSurfaceBSpline implements Serializable
 
 serialVersionUID:
 
 -2373375608698854130L
 - Serialized Fields
 - context
```
com.jogamp.opencl.CLContext context
```
 - device
```
com.jogamp.opencl.CLDevice device
```
 - controlPoints
```
com.jogamp.opencl.CLBuffer controlPoints
```
- Class edu.stanford.rsl.conrad.opencl.OpenCLUniformBSpline extends BSpline implements Serializable
 
 serialVersionUID:
 
 5895570242152310515L
 - Serialized Fields
 - context
```
com.jogamp.opencl.CLContext context
```
 - device
```
com.jogamp.opencl.CLDevice device
```
 - controlPoints
```
com.jogamp.opencl.CLBuffer controlPoints
```
- Class edu.stanford.rsl.conrad.opencl.OpenCLUniformSurfaceBSpline extends SurfaceBSpline implements Serializable
 
 serialVersionUID:
 
 -7502977258317985586L
 - Serialized Fields
 - context
```
com.jogamp.opencl.CLContext context
```
 - device
```
com.jogamp.opencl.CLDevice device
```
 - controlPoints
```
com.jogamp.opencl.CLBuffer controlPoints
```
- Class edu.stanford.rsl.conrad.opencl.OpenCLUniformTextureBSpline extends OpenCLUniformBSpline implements Serializable
 
 serialVersionUID:
 
 -3769875288043610795L
 - Serialized Fields
 - texture
```
com.jogamp.opencl.CLImage2d texture
```
- Class edu.stanford.rsl.conrad.opencl.OpenCLUniformTextureSurfaceBSpline extends OpenCLUniformSurfaceBSpline implements Serializable
 
 serialVersionUID:
 
 -578366497108607026L
 - Serialized Fields
 - texture
```
com.jogamp.opencl.CLImage2d texture
```
Package edu.stanford.rsl.conrad.opencl.rendering
- Class edu.stanford.rsl.conrad.opencl.rendering.OpenCLTextureRendering extends javax.swing.JFrame implements Serializable
 
 serialVersionUID:
 
 -6181935230597653012L
 - Serialized Fields
 - transferFunc
```
float[] transferFunc
```
 - initialized
```
boolean initialized
```
 Whether the initialization method of this GLEventListener has already been called
 - stereoMode
```
boolean stereoMode
```
 Whether the stereo mode is enabled
 - glComponentL
```
javax.media.opengl.awt.GLJPanel glComponentL
```
 The GL component which is used for rendering
 - glComponentR
```
javax.media.opengl.awt.GLJPanel glComponentR
```
 The GL component which is used for the other eye
 - renderer
```
com.jogamp.opengl.util.awt.TextRenderer renderer
```
 Text renderer for status messages
 - animatorL
```
com.jogamp.opengl.util.Animator animatorL
```
 The animator used for rendering
 - animatorR
```
com.jogamp.opengl.util.Animator animatorR
```
 The animator for the other eye
 - glCtx
```
com.jogamp.opencl.gl.CLGLContext glCtx
```
 The OpenCL context
 - program
```
com.jogamp.opencl.CLProgram program
```
 The OpenCL program
 - device
```
com.jogamp.opencl.CLDevice device
```
 The OpenCL device
 - kernelFunction
```
com.jogamp.opencl.CLKernel kernelFunction
```
 The OpenCL kernel function binding
 - commandQueue
```
com.jogamp.opencl.CLCommandQueue commandQueue
```
 The OpenCL command queue
 - tex
```
com.jogamp.opencl.CLImage3d tex
```
 The 3D volume texture reference
 - transferTex
```
com.jogamp.opencl.CLImage2d transferTex
```
 The 1D transfer texture reference
 - hvolumeBuffer
```
com.jogamp.opencl.CLBuffer hvolumeBuffer
```
 - transferFctBuffer
```
com.jogamp.opencl.CLBuffer transferFctBuffer
```
 - h_volume
```
byte[] h_volume
```
 The volume data that is to be rendered
 - invViewMatrix
```
com.jogamp.opencl.CLBuffer invViewMatrix
```
 The inverted view matrix, which will be copied to the global variable of the kernel.
 - d_output
```
com.jogamp.opencl.gl.CLGLBuffer d_output
```
 The output of CL
 - width
```
int width
```
 The width of the rendered area and the PBO
 - height
```
int height
```
 The height of the rendered area and the PBO
 - volumeSize
```
int[] volumeSize
```
 The size of the volume data that is to be rendered
 - gridSize
```
float[] gridSize
```
 The block size for the kernel execution
 - density
```
float density
```
 The density of the rendered volume data
 - brightness
```
float brightness
```
 The brightness of the rendered volume data
 - transferOffset
```
float transferOffset
```
 The transferOffset of the rendered volume data
 - transferScale
```
float transferScale
```
 The transferScale of the rendered volume data
 - pbo
```
int pbo
```
 The OpenGL pixel buffer object
 - translationX
```
float translationX
```
 The translation in X-direction
 - translationY
```
float translationY
```
 The translation in Y-direction
 - translationZ
```
float translationZ
```
 The translation in Z-direction
 - rotationX
```
float rotationX
```
 The rotation about the X-axis, in degrees
 - frame
```
javax.swing.JFrame frame
```
 - rotationY
```
float rotationY
```
 The rotation about the Y-axis, in degrees
 - prevFrameNanoTime
```
long prevFrameNanoTime
```
 The System.nanoTime() of the previous rendered frame.
- Class edu.stanford.rsl.conrad.opencl.rendering.OpenCLVolumeRenderer extends OpenCLTextureRendering implements Serializable
 
 serialVersionUID:
 
 369749150640130620L
 - Serialized Fields
 - multiFrameMode
```
boolean multiFrameMode
```
 - clImages
```
java.util.ArrayList<E> clImages
```
 - volumes
```
byte[][] volumes
```
 - nFrames
```
int nFrames
```
 - time
```
int time
```
 - minmax
```
double[] minmax
```
 - playTimer
```
java.util.Timer playTimer
```
 - frameDuration
```
long frameDuration
```
Package edu.stanford.rsl.conrad.phantom
- Class edu.stanford.rsl.conrad.phantom.AnalyticPhantom extends PrioritizableScene implements Serializable
  
  serialVersionUID:
  
  9211271452251474622L
  - Serialized Fields
    - configured
```
boolean configured
```
- Class edu.stanford.rsl.conrad.phantom.AnalyticPhantom4D extends AnalyticPhantom implements Serializable
  
  serialVersionUID:
  
  -5680252649645704710L
  - Serialized Fields
    - warper
```
TimeWarper warper
```
- Class edu.stanford.rsl.conrad.phantom.BeadRemovalPhantom extends AnalyticPhantom implements Serializable
  
  serialVersionUID:
  
  572931430014588123L
  - Serialized Fields
    - noOfBeads
```
int noOfBeads
```
    - beadRadius
```
double beadRadius
```
    - beadZRangebegin
```
double beadZRangebegin
```
    - beadZRangeend
```
double beadZRangeend
```
    - outerCylRadius
```
double outerCylRadius
```
    - innerCylRadius
```
double innerCylRadius
```
    - cylHeight
```
double cylHeight
```
- Class edu.stanford.rsl.conrad.phantom.BoxPhantom extends AnalyticPhantom implements Serializable
  
  serialVersionUID:
  
  5781085850910993618L
- Class edu.stanford.rsl.conrad.phantom.CatheterPhantom extends AnalyticPhantom implements Serializable
  
  serialVersionUID:
  
  -144401635934271936L
- Class edu.stanford.rsl.conrad.phantom.CatphanCTP528 extends AnalyticPhantom implements Serializable
  
  serialVersionUID:
  
  -3843719205362984060L
- Class edu.stanford.rsl.conrad.phantom.DefrisePhantom extends AnalyticPhantom implements Serializable
  
  serialVersionUID:
  
  6331427750379955185L
- Class edu.stanford.rsl.conrad.phantom.MovingBallPhantom extends AnalyticPhantom4D implements Serializable
  
  serialVersionUID:
  
  8308889276453752657L
  - Serialized Fields
    - mf
```
RotationMotionField mf
```
    - dynamic
```
boolean dynamic
```
    - refPosition
```
PointND refPosition
```
    - periWarper
```
PeriodicTimeWarper periWarper
```
    - harmoWarper
```
HarmonicTimeWarper harmoWarper
```
    - sigWarper
```
SigmoidTimeWarper sigWarper
```
    - restWarper
```
RestPhaseTimeWarper restWarper
```
    - radius
```
double radius
```
    - angle
```
double angle
```
    - initialCentre
```
PointND initialCentre
```
- Class edu.stanford.rsl.conrad.phantom.MTFBeadPhantom extends AnalyticPhantom implements Serializable
  
  serialVersionUID:
  
  -3843719205362984060L
- Class edu.stanford.rsl.conrad.phantom.SevenBeadPhantom extends AnalyticPhantom implements Serializable
  
  serialVersionUID:
  
  6633919775510507739L
  - Serialized Fields
    - beadRadius
```
double beadRadius
```
    - beadXYdist
```
double beadXYdist
```
    - beadZdist
```
double beadZdist
```
    - cylRadius
```
double cylRadius
```
    - cylHeight
```
double cylHeight
```
- Class edu.stanford.rsl.conrad.phantom.SheppLoganPhantom extends AnalyticPhantom implements Serializable
  
  serialVersionUID:
  
  5781085850910993618L
- Class edu.stanford.rsl.conrad.phantom.SpherePhantom extends AnalyticPhantom implements Serializable
  
  serialVersionUID:
  
  5781085850910993618L
- Class edu.stanford.rsl.conrad.phantom.WaterCylinderPhantom extends AnalyticPhantom implements Serializable
  
  serialVersionUID:
  
  -2123220619757423791L
  - Serialized Fields
    - cylRadius
```
double cylRadius
```
    - cylHeight
```
double cylHeight
```
Package edu.stanford.rsl.conrad.phantom.electrondensity
- Class edu.stanford.rsl.conrad.phantom.electrondensity.CrisEDPhantomGUI extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  8752339017895320468L
  - Serialized Fields
    - gd
```
ij.gui.GenericDialog gd
```
    - innerRing
```
javax.swing.JPanel innerRing
```
    - innerRingHolder
```
javax.swing.JPanel innerRingHolder
```
    - outerRing
```
javax.swing.JPanel outerRing
```
    - innerBut
```
javax.swing.JRadioButton[] innerBut
```
    - outterBut
```
javax.swing.JRadioButton[] outterBut
```
    - insertNameField
```
javax.swing.text.JTextComponent insertNameField
```
    - materialField
```
javax.swing.JTextField materialField
```
    - innerDiskActivator
```
javax.swing.AbstractButton innerDiskActivator
```
    - insertNameLabel
```
javax.swing.JLabel insertNameLabel
```
    - materialLabel
```
javax.swing.JLabel materialLabel
```
    - instructionLabel
```
javax.swing.JLabel instructionLabel
```
    - bufferedMaterial
```
javax.swing.JCheckBox bufferedMaterial
```
    - bufferedMaterialLabel
```
javax.swing.JLabel bufferedMaterialLabel
```
    - okButton
```
javax.swing.JButton okButton
```
    - currButton
```
javax.swing.JRadioButton currButton
```
    - data
```
CrisEDPhantomM062 data
```
- Class edu.stanford.rsl.conrad.phantom.electrondensity.CrisEDPhantomM062 extends AnalyticPhantom implements Serializable
  
  serialVersionUID:
  
  -7299055837928247210L
  - Serialized Fields
    - innerDiskIns
```
Insert[] innerDiskIns
```
    - outerDiskIns
```
Insert[] outerDiskIns
```
    - useInnerDisk
```
boolean useInnerDisk
```
    - useOuterDisk
```
boolean useOuterDisk
```
    - inner
```
EDInnerDisk inner
```
    - outer
```
EDOuterDisk outer
```
- Class edu.stanford.rsl.conrad.phantom.electrondensity.EDInnerDisk extends PrioritizableScene implements Serializable
  
  serialVersionUID:
  
  -4179587831440511881L
  - Serialized Fields
    - disk
```
QuadricDisk disk
```
    - dx
```
double dx
```
    - dy
```
double dy
```
    - dz
```
double dz
```
    - insertsDistanceFromOrigin
```
double insertsDistanceFromOrigin
```
- Class edu.stanford.rsl.conrad.phantom.electrondensity.EDOuterDisk extends PrioritizableScene implements Serializable
  
  serialVersionUID:
  
  -6136623274828882139L
  - Serialized Fields
    - disk
```
QuadricDisk disk
```
    - ext_dx
```
double ext_dx
```
    - ext_dy
```
double ext_dy
```
    - int_dx
```
double int_dx
```
    - int_dy
```
double int_dy
```
    - dz
```
double dz
```
    - insertsDistanceFromOrigin
```
double insertsDistanceFromOrigin
```
    - insert6DistanceFromOrigin
```
double insert6DistanceFromOrigin
```
- Class edu.stanford.rsl.conrad.phantom.electrondensity.Insert extends PrioritizableScene implements Serializable
  
  serialVersionUID:
  
  -6549158504106309805L
  - Serialized Fields
    - dx
```
double dx
```
    - dy
```
double dy
```
    - dz
```
double dz
```
    - buffer
```
QuadricDisk buffer
```
    - disk
```
QuadricDisk disk
```
    - bufferMaterial
```
Material bufferMaterial
```
    - mat
```
SimpleMatrix mat
```
    - bufferState
```
int bufferState
```
- Class edu.stanford.rsl.conrad.phantom.electrondensity.QuadricDisk extends PhysicalObject implements Serializable
  
  serialVersionUID:
  
  1655681292265501419L
  - Serialized Fields
    - ellipt_cyl
```
Cylinder ellipt_cyl
```
Package edu.stanford.rsl.conrad.phantom.forbild
- Class edu.stanford.rsl.conrad.phantom.forbild.ForbildPhantom extends AnalyticPhantom implements Serializable
  
  serialVersionUID:
  
  -2384108143541335664L
  - Serialized Fields
    - isConfigured
```
boolean isConfigured
```
Package edu.stanford.rsl.conrad.phantom.forbild.shapes
- Class edu.stanford.rsl.conrad.phantom.forbild.shapes.ForbildBox extends Box implements Serializable
 
 serialVersionUID:
 
 4063615482635066034L
 - Serialized Fields
 - surfaceOrigin
```
PointND surfaceOrigin
```
 - boundingPlanes
```
java.util.ArrayList<E> boundingPlanes
```
 - dx
```
double dx
```
 - dy
```
double dy
```
 - dz
```
double dz
```
- Class edu.stanford.rsl.conrad.phantom.forbild.shapes.ForbildCone extends Cone implements Serializable
 
 serialVersionUID:
 
 7863208071648369579L
 - Serialized Fields
 - dx
```
double dx
```
 - dy
```
double dy
```
 - dz
```
double dz
```
 - surfaceOrigin
```
PointND surfaceOrigin
```
 - axis
```
SimpleVector axis
```
 - boundingPlanes
```
java.util.ArrayList<E> boundingPlanes
```
- Class edu.stanford.rsl.conrad.phantom.forbild.shapes.ForbildCylinder extends Cylinder implements Serializable
 
 serialVersionUID:
 
 7086658338878039459L
 - Serialized Fields
 - dx
```
double dx
```
 - dy
```
double dy
```
 - dz
```
double dz
```
 - surfaceOrigin
```
PointND surfaceOrigin
```
 - axis
```
SimpleVector axis
```
 - boundingPlanes
```
java.util.ArrayList<E> boundingPlanes
```
- Class edu.stanford.rsl.conrad.phantom.forbild.shapes.ForbildEllipsoid extends Ellipsoid implements Serializable
 
 serialVersionUID:
 
 -5672890761680090611L
 - Serialized Fields
 - surfaceOrigin
```
PointND surfaceOrigin
```
 - axis
```
SimpleVector axis
```
 - dx
```
double dx
```
 - dy
```
double dy
```
 - dz
```
double dz
```
 - a_x
```
SimpleVector a_x
```
 - a_y
```
SimpleVector a_y
```
 - a_z
```
SimpleVector a_z
```
 - boundingPlanes
```
java.util.ArrayList<E> boundingPlanes
```
- Class edu.stanford.rsl.conrad.phantom.forbild.shapes.ForbildSphere extends Sphere implements Serializable
 
 serialVersionUID:
 
 4059584393163102548L
 - Serialized Fields
 - radius
```
double radius
```
 - surfaceOrigin
```
PointND surfaceOrigin
```
 - boundingPlanes
```
java.util.ArrayList<E> boundingPlanes
```
Package edu.stanford.rsl.conrad.phantom.xcat
- Class edu.stanford.rsl.conrad.phantom.xcat.BreathingScene extends WholeBodyScene implements Serializable
 
 serialVersionUID:
 
 -4935602839572704230L
 - Serialized Fields
 - chestExpansion
```
double chestExpansion
```
 - rotationsMap
```
java.util.HashMap<K,V> rotationsMap
```
 - diaphragmMovement
```
double diaphragmMovement
```
 - numberOfBSplineTimePoints
```
int numberOfBSplineTimePoints
```
 - chestMotion
```
MotionField chestMotion
```
 - diaphragmMin
```
PointND diaphragmMin
```
 - diaphragmMax
```
PointND diaphragmMax
```
 - diaphragmTop
```
PointND diaphragmTop
```
 - dualPhaseWarper
```
DualPhasePeriodicTimeWarper dualPhaseWarper
```
 - ignoreArms
```
boolean ignoreArms
```
- Class edu.stanford.rsl.conrad.phantom.xcat.CombinedBreathingHeartScene extends WholeBodyScene implements Serializable
 
 serialVersionUID:
 
 -4691335601630948952L
 - Serialized Fields
 - breathing
```
BreathingScene breathing
```
 - heart
```
HeartScene heart
```
 - heartTranslation
```
Translation heartTranslation
```
 - motionField
```
MotionField motionField
```
- Class edu.stanford.rsl.conrad.phantom.xcat.CoronaryScene extends XCatScene implements Serializable
 
 serialVersionUID:
 
 -8901686267381868405L
 - Serialized Fields
 - arteries
```
java.util.ArrayList<E> arteries
```
 - renderHeartBody
```
boolean renderHeartBody
```
 - heartMotionField
```
MotionField heartMotionField
```
 - heartRotation
```
ScaleRotate heartRotation
```
- Class edu.stanford.rsl.conrad.phantom.xcat.DynamicSquatScene extends WholeBodyScene implements Serializable
 
 serialVersionUID:
 
 -5961188801136828415L
 - Serialized Fields
 - viconBuilder
```
ViconMarkerBuilder viconBuilder
```
- Class edu.stanford.rsl.conrad.phantom.xcat.HeartScene extends XCatScene implements Serializable
 
 serialVersionUID:
 
 -8901686267381865405L
 - Serialized Fields
 - arteries
```
java.util.ArrayList<E> arteries
```
 - renderHeartBody
```
boolean renderHeartBody
```
 - heartMotionField
```
MotionField heartMotionField
```
 - heartRotation
```
ScaleRotate heartRotation
```
 - heartCycles
```
double heartCycles
```
 - motionFieldSigma
```
double motionFieldSigma
```
 - ventricularLesions
```
double[][] ventricularLesions
```
 - atrialLesions
```
double[][] atrialLesions
```
- Class edu.stanford.rsl.conrad.phantom.xcat.SquatScene extends WholeBodyScene implements Serializable
 
 serialVersionUID:
 
 5833963135277640258L
 - Serialized Fields
 - lowerBodyMotionField
```
MotionField lowerBodyMotionField
```
 - rotationOnly
```
boolean rotationOnly
```
 - sigmaParzen
```
double sigmaParzen
```
 - numberOfNeighborsLinInterp
```
int numberOfNeighborsLinInterp
```
 - numberOfBSplineTimePoints
```
int numberOfBSplineTimePoints
```
 - angleInDegrees
```
double angleInDegrees
```
- Class edu.stanford.rsl.conrad.phantom.xcat.ViconMarkerBuilder extends java.lang.Object implements Serializable
 
 serialVersionUID:
 
 -2023706815633141182L
 - Serialized Fields
 - markers
```
java.util.ArrayList<E> markers
```
- Class edu.stanford.rsl.conrad.phantom.xcat.WholeBodyScene extends XCatScene implements Serializable
 
 serialVersionUID:
 
 7514545759333848517L
 - Serialized Fields
 - autoResize
```
boolean autoResize
```
- Class edu.stanford.rsl.conrad.phantom.xcat.XCatScene extends AnalyticPhantom4D implements Serializable
 
 serialVersionUID:
 
 7268743275585203174L
 - Serialized Fields
 - XCatDirectory
```
java.lang.String XCatDirectory
```
 This reads in the position of the XCat files from the registry.
 - warper
```
TimeWarper warper
```
 Time warping is used for animation. A time warper is a function that get an input time and return an output time.
 - splines
```
java.util.ArrayList<E> splines
```
 - variants
```
java.util.ArrayList<E> variants
```
Package edu.stanford.rsl.conrad.physics
- Class edu.stanford.rsl.conrad.physics.PhysicalObject extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -5731264279770114544L
  - Serialized Fields
    - nameString
```
java.lang.String nameString
```
    - material
```
Material material
```
    - shape
```
AbstractShape shape
```
- Class edu.stanford.rsl.conrad.physics.PhysicalPoint extends SortablePoint implements Serializable
  
  serialVersionUID:
  
  1259588295137355141L
  - Serialized Fields
    - object
```
PhysicalObject object
```
Package edu.stanford.rsl.conrad.physics.materials
- Class edu.stanford.rsl.conrad.physics.materials.Compound extends Material implements Serializable
  
  serialVersionUID:
  
  -5197674861970729455L
  - Serialized Fields
    - formula
```
java.lang.String formula
```
- Class edu.stanford.rsl.conrad.physics.materials.Element extends Material implements Serializable
  
  serialVersionUID:
  
  -761247784943296794L
  - Serialized Fields
    - symbol
```
java.lang.String symbol
```
    - atomicWeight
```
double atomicWeight
```
    - atomicNumber
```
double atomicNumber
```
- Class edu.stanford.rsl.conrad.physics.materials.Material extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -335499247531855579L
  - Serialized Fields
    - name
```
java.lang.String name
```
    - density
```
double density
```
    - comp
```
WeightedAtomicComposition comp
```
- Class edu.stanford.rsl.conrad.physics.materials.Mixture extends Material implements Serializable
  
  serialVersionUID:
  
  1224182801808270337L
Package edu.stanford.rsl.conrad.physics.materials.utils
- Class edu.stanford.rsl.conrad.physics.materials.utils.WeightedAtomicComposition extends java.lang.Object implements Serializable
 
 serialVersionUID:
 
 3049665041572231953L
 - Serialized Fields
 - composition
```
java.util.TreeMap<K,V> composition
```
Package edu.stanford.rsl.conrad.pipeline
- Class edu.stanford.rsl.conrad.pipeline.BufferedProjectionSink extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  8818811805620422888L
  - Serialized Fields
    - projectionVolume
```
Grid3D projectionVolume
```
    - configured
```
boolean configured
```
    - showStatus
```
boolean showStatus
```
- Class edu.stanford.rsl.conrad.pipeline.DevNullSink extends BufferedProjectionSink implements Serializable
  
  serialVersionUID:
  
  -6582927447254656308L
- Class edu.stanford.rsl.conrad.pipeline.IndividualImagePipelineFilteringTool extends IndividualImageFilteringTool implements Serializable
  
  serialVersionUID:
  
  -1573824644614146404L
  - Serialized Fields
    - debug
```
boolean debug
```
    - tools
```
IndividualImageFilteringTool[] tools
```
    - sink
```
ProjectionSink sink
```
    - projectionSource
```
ProjectionSource projectionSource
```
    - stack
```
Grid2D[] stack
```
Package edu.stanford.rsl.conrad.reconstruction
- Class edu.stanford.rsl.conrad.reconstruction.CPUSuperShortScanBackprojector extends VOIBasedReconstructionFilter implements Serializable
 
 serialVersionUID:
 
 -1248364198978750688L
 - Serialized Fields
 - mapped
```
boolean mapped
```
- Class edu.stanford.rsl.conrad.reconstruction.DistanceDrivenBasedReconstruction extends ModelBasedIterativeReconstruction implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - Debug
```
boolean Debug
```
 - Debug1
```
boolean Debug1
```
 - Debug2
```
boolean Debug2
```
- Class edu.stanford.rsl.conrad.reconstruction.FBPReconstructionFilter extends ReconstructionFilter implements Serializable
 
 serialVersionUID:
 
 4294553655322598313L
- Class edu.stanford.rsl.conrad.reconstruction.IterativeReconstruction extends ReconstructionFilter implements Serializable
 
 serialVersionUID:
 
 1L
- Class edu.stanford.rsl.conrad.reconstruction.LolaBunnyBackprojector extends VOIBasedReconstructionFilter implements Serializable
 
 serialVersionUID:
 
 4887607829631536252L
- Class edu.stanford.rsl.conrad.reconstruction.ModelBasedIterativeReconstruction extends IterativeReconstruction implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - Debug
```
boolean Debug
```
 - time
```
long time
```
 - volumeImage
```
Grid3D volumeImage
```
 - projectionViews
```
Grid3D projectionViews
```
 - lineOffset
```
double lineOffset
```
 - maxK
```
int maxK
```
 - maxI
```
int maxI
```
 - maxJ
```
int maxJ
```
 - maxU
```
int maxU
```
 - maxV
```
int maxV
```
 - dx
```
double dx
```
 - dy
```
double dy
```
 - dz
```
double dz
```
 - dataTrajectory
```
Trajectory dataTrajectory
```
- Class edu.stanford.rsl.conrad.reconstruction.MotionCompensatedSubVolumeBackprojector extends SubVolumeBackprojector implements Serializable
 
 serialVersionUID:
 
 6027629320244326462L
 - Serialized Fields
 - motionField
```
MotionField motionField
```
- Class edu.stanford.rsl.conrad.reconstruction.MotionCompensatedVOIBasedReconstructionFilter extends VOIBasedReconstructionFilter implements Serializable
 
 serialVersionUID:
 
 4449313613390154787L
 - Serialized Fields
 - motionField
```
MotionField motionField
```
 - pointCorrespondences
```
PointND[][][][] pointCorrespondences
```
- Class edu.stanford.rsl.conrad.reconstruction.RayDrivenBasedReconstruction extends IterativeReconstruction implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - projectionImage
```
Grid3D projectionImage
```
 - lineOffset
```
int lineOffset
```
 - maxU
```
int maxU
```
 - maxV
```
int maxV
```
 - maxK
```
int maxK
```
 - maxI
```
int maxI
```
 - maxJ
```
int maxJ
```
 - dx
```
double dx
```
 - dy
```
double dy
```
 - dz
```
double dz
```
 - umin
```
int umin
```
 - umax
```
int umax
```
 - vmin
```
int vmin
```
 - vmax
```
int vmax
```
 - weights
```
double[] weights
```
 - mat
```
SimpleMatrix mat
```
- Class edu.stanford.rsl.conrad.reconstruction.RayWeightCorrectingCPUSuperShortScanBackprojector extends VOIBasedReconstructionFilter implements Serializable
 
 serialVersionUID:
 
 -9058395760356947846L
 - Serialized Fields
 - rayMap1
```
ij.process.FloatProcessor rayMap1
```
 - rayMap2
```
ij.process.FloatProcessor rayMap2
```
 - mapped
```
boolean mapped
```
 - silver
```
ParkerWeightingTool silver
```
 - ramp
```
RampFilter ramp
```
- Class edu.stanford.rsl.conrad.reconstruction.ReconstructionFilter extends MultiProjectionFilter implements Serializable
 
 serialVersionUID:
 
 3325343968370683491L
 - Serialized Fields
 - offsetX
```
double offsetX
```
 - offsetY
```
double offsetY
```
 - offsetZ
```
double offsetZ
```
 - init
```
boolean init
```
 - projectionVolume
```
Grid3D projectionVolume
```
 - nImages
```
int nImages
```
- Class edu.stanford.rsl.conrad.reconstruction.RigidBody3DTransformationVOIBasedReconstructionFilter extends VOIBasedReconstructionFilter implements Serializable
 
 serialVersionUID:
 
 4449313613390154787L
 - Serialized Fields
 - TranslationTransform
```
java.util.ArrayList<E> TranslationTransform
```
 - RotationTransform
```
java.util.ArrayList<E> RotationTransform
```
 - rotationTranslationFilename
```
java.lang.String rotationTranslationFilename
```
- Class edu.stanford.rsl.conrad.reconstruction.RigidBody3DTransformationVOIBasedReconstructionFilterForXCAT extends VOIBasedReconstructionFilter implements Serializable
 
 serialVersionUID:
 
 4449313613390154787L
 - Serialized Fields
 - TranslationTransform
```
java.util.ArrayList<E> TranslationTransform
```
 - RotationTransform
```
java.util.ArrayList<E> RotationTransform
```
- Class edu.stanford.rsl.conrad.reconstruction.SeparableFootprintsBasedReconstruction extends ModelBasedIterativeReconstruction implements Serializable
 
 serialVersionUID:
 
 1L
 - Serialized Fields
 - Debug
```
boolean Debug
```
 - Debug1
```
boolean Debug1
```
 - Debug2
```
boolean Debug2
```
- Class edu.stanford.rsl.conrad.reconstruction.SimpleIterativeReconstruction extends ReconstructionFilter implements Serializable
 
 serialVersionUID:
 
 7404570438691680164L
- Class edu.stanford.rsl.conrad.reconstruction.SubVolumeBackprojector extends VOIBasedReconstructionFilter implements Serializable
 
 serialVersionUID:
 
 -3452972435131680120L
 - Serialized Fields
 - numThreads
```
int numThreads
```
 - projectors
```
VOIBasedReconstructionFilter[] projectors
```
 - subVolumes
```
Grid3D[] subVolumes
```
 - debug
```
boolean debug
```
 - volumeRewritten
```
boolean volumeRewritten
```
- Class edu.stanford.rsl.conrad.reconstruction.SuperShortScanBackprojection extends ReconstructionFilter implements Serializable
 
 serialVersionUID:
 
 8744415315605892588L
 - Serialized Fields
 - primaryAngles
```
double[] primaryAngles
```
 Deprecated.
 - SID
```
double SID
```
 Deprecated.
 - width
```
double width
```
 Deprecated.
 - height
```
double height
```
 Deprecated.
 - detectorElementSizeX
```
double detectorElementSizeX
```
 Deprecated.
 - detectorElementSizeY
```
double detectorElementSizeY
```
 Deprecated.
 - closed
```
boolean closed
```
 Deprecated.
 - projector
```
ReconstructionFilter projector
```
 Deprecated.
 - imageBuffer
```
ImageProcessorBuffer imageBuffer
```
 Deprecated.
 - projections
```
Grid2D[] projections
```
 Deprecated.
- Class edu.stanford.rsl.conrad.reconstruction.VOIBasedReconstructionFilter extends FBPReconstructionFilter implements Serializable
 
 serialVersionUID:
 
 -4469835421293447988L
 - Serialized Fields
 - time
```
long time
```
 - lineOffset
```
double lineOffset
```
 - maxK
```
int maxK
```
 - maxI
```
int maxI
```
 - maxJ
```
int maxJ
```
 - fastVOIMode
```
boolean fastVOIMode
```
 - voiMap
```
boolean[][][] voiMap
```
 - useVOImap
```
boolean useVOImap
```
 - interestedInVolume
```
VolumeOfInterest interestedInVolume
```
Package edu.stanford.rsl.conrad.reconstruction.iterative
- Class edu.stanford.rsl.conrad.reconstruction.iterative.DistanceDrivenBasedReconstruction extends ModelBasedIterativeReconstruction implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - Debug
```
boolean Debug
```
    - Debug1
```
boolean Debug1
```
    - Debug2
```
boolean Debug2
```
- Class edu.stanford.rsl.conrad.reconstruction.iterative.IterativeReconstruction extends ReconstructionFilter implements Serializable
  
  serialVersionUID:
  
  1L
- Class edu.stanford.rsl.conrad.reconstruction.iterative.LeastSquaresCG extends DistanceDrivenBasedReconstruction implements Serializable
  
  serialVersionUID:
  
  1L
- Class edu.stanford.rsl.conrad.reconstruction.iterative.ModelBasedIterativeReconstruction extends IterativeReconstruction implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - Debug
```
boolean Debug
```
    - time
```
long time
```
    - volumeImage
```
Grid3D volumeImage
```
    - projectionViews
```
Grid3D projectionViews
```
    - lineOffset
```
double lineOffset
```
    - maxK
```
int maxK
```
    - maxI
```
int maxI
```
    - maxJ
```
int maxJ
```
    - maxU
```
int maxU
```
    - maxV
```
int maxV
```
    - dx
```
double dx
```
    - dy
```
double dy
```
    - dz
```
double dz
```
    - dataTrajectory
```
Trajectory dataTrajectory
```
- Class edu.stanford.rsl.conrad.reconstruction.iterative.PenalizedLeastSquareART extends DistanceDrivenBasedReconstruction implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - maxNumOfIterations
```
int maxNumOfIterations
```
    - beta
```
float beta
```
    - delta
```
float delta
```
    - pfun
```
huberPenalty pfun
```
- Class edu.stanford.rsl.conrad.reconstruction.iterative.RayDrivenBasedReconstruction extends IterativeReconstruction implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - projectionImage
```
Grid3D projectionImage
```
    - lineOffset
```
int lineOffset
```
    - maxU
```
int maxU
```
    - maxV
```
int maxV
```
    - maxK
```
int maxK
```
    - maxI
```
int maxI
```
    - maxJ
```
int maxJ
```
    - dx
```
double dx
```
    - dy
```
double dy
```
    - dz
```
double dz
```
    - umin
```
int umin
```
    - umax
```
int umax
```
    - vmin
```
int vmin
```
    - vmax
```
int vmax
```
    - weights
```
double[] weights
```
    - mat
```
SimpleMatrix mat
```
- Class edu.stanford.rsl.conrad.reconstruction.iterative.SeparableFootprintsBasedReconstruction extends ModelBasedIterativeReconstruction implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - Debug
```
boolean Debug
```
    - Debug1
```
boolean Debug1
```
    - Debug2
```
boolean Debug2
```
Package edu.stanford.rsl.conrad.reconstruction.voi
- Class edu.stanford.rsl.conrad.reconstruction.voi.CylinderBasedVolumeOfInterest extends VolumeOfInterest implements Serializable
 
 serialVersionUID:
 
 431870065424171642L
 - Serialized Fields
 - radius
```
double radius
```
 - minz
```
double minz
```
 - maxz
```
double maxz
```
 - cylinderminz
```
double cylinderminz
```
 - cylindermaxz
```
double cylindermaxz
```
 - success
```
boolean success
```
- Class edu.stanford.rsl.conrad.reconstruction.voi.PolygonBasedVolumeOfInterest extends VolumeOfInterest implements Serializable
 
 serialVersionUID:
 
 -8511498569857161802L
 - Serialized Fields
 - sliceRegionOfInterest
```
java.awt.Polygon sliceRegionOfInterest
```
 - maxZ
```
double maxZ
```
 - minZ
```
double minZ
```
 - numberOfPointsInPolygon
```
int numberOfPointsInPolygon
```
 - success
```
boolean success
```
 - sliceVoi
```
java.util.HashMap<K,V> sliceVoi
```
- Class edu.stanford.rsl.conrad.reconstruction.voi.VolumeOfInterest extends java.lang.Object implements Serializable
 
 serialVersionUID:
 
 -9014453765525455074L
 - Serialized Fields
 - debug
```
boolean debug
```
Package edu.stanford.rsl.conrad.rendering
- Class edu.stanford.rsl.conrad.rendering.AbstractScene extends java.lang.Object implements Serializable
 
 serialVersionUID:
 
 66628416515634675L
 - Serialized Fields
 - background
```
Material background
```
 - name
```
java.lang.String name
```
 - min
```
PointND min
```
 - max
```
PointND max
```
- Class edu.stanford.rsl.conrad.rendering.PrioritizableScene extends AbstractScene implements Serializable
 
 serialVersionUID:
 
 -8239645378207352898L
 - Serialized Fields
 - objects
```
java.util.ArrayList<E> objects
```
 - priorityMap
```
java.util.HashMap<K,V> priorityMap
```
 - dirty
```
boolean dirty
```
 - highest
```
int highest
```
 - lowest
```
int lowest
```
- Class edu.stanford.rsl.conrad.rendering.SimpleScene extends AbstractScene implements Serializable
 
 serialVersionUID:
 
 -4715971665107096973L
 - Serialized Fields
 - objects
```
java.util.ArrayList<E> objects
```

Package edu.stanford.rsl.conrad.utils

Class edu.stanford.rsl.conrad.utils.BilinearInterpolatingDoubleArray extends java.lang.Object implements Serializable

serialVersionUID:

1183806565056190746L
- Serialized Fields
  - meshx
```
double[] meshx
```
  - meshy
```
double[] meshy
```
  - values
```
double[][] values
```
  - minx
```
double minx
```
  - maxx
```
double maxx
```
  - miny
```
double miny
```
  - maxy
```
double maxy
```

Class edu.stanford.rsl.conrad.utils.Configuration extends java.lang.Object implements Serializable

serialVersionUID:: 3887275696746174804L

Serialized Fields

geometry
```
Trajectory geometry
```

volumeOfInterestFileName

java.lang.String volumeOfInterestFileName

projectionTableFileName

java.lang.String projectionTableFileName

cutOffFrequency
```
double cutOffFrequency
```

AutomaticExposureControlConfigFile

java.lang.String AutomaticExposureControlConfigFile

currentRowWeights
```
java.lang.String currentRowWeights
```
deviceSerialNumber
```
java.lang.String deviceSerialNumber
```
realtime
```
double[] realtime
```
electroCardioGramm
```
double[] electroCardioGramm
```
voltage
```
double[] voltage
```
current
```
double[] current
```
time
```
double[] time
```
dCU
```
double dCU
```
dose
```
double dose
```
intensifierSize
```
int intensifierSize
```
currentPath
```
java.lang.String currentPath
```
recentFileOne
```
java.lang.String recentFileOne
```
recentFileTwo
```
java.lang.String recentFileTwo
```
filterPipeline
```
ImageFilteringTool[] filterPipeline
```
sink
```
BufferedProjectionSink sink
```
citationFormat
```
int citationFormat
```
importFromDicomAutomatically
```
boolean importFromDicomAutomatically
```
useExtrapolatedGeometry
```
boolean useExtrapolatedGeometry
```
useHounsfieldScaling
```
boolean useHounsfieldScaling
```

beamHardeningLookupTable

BilinearInterpolatingDoubleArray beamHardeningLookupTable

hounsfieldScaling
```
Function hounsfieldScaling
```
heartPhases
```
double[] heartPhases
```
numSweeps
```
int numSweeps
```
registry
```
java.util.HashMap<K,V> registry
```
beadPosition2D
```
double[][][] beadPosition2D
```
beadMeanPosition3D
```
double[][] beadMeanPosition3D
```
fAccessed
```
boolean[] fAccessed
```
respiratoryMotionField
```
double[] respiratoryMotionField
```
diaphragmPositionField
```
double[] diaphragmPositionField
```
diaphragmModelField
```
double[][] diaphragmModelField
```
maxMotion
```
double maxMotion
```
lowHyst
```
float lowHyst
```
highHyst
```
float highHyst
```
seedX
```
int seedX
```
seedY
```
int seedY
```
roiWidthHalf
```
int roiWidthHalf
```
roiHeightTop
```
int roiHeightTop
```
roiHeightBottom
```
int roiHeightBottom
```
maxIter
```
int maxIter
```
projTurningAngle
```
double projTurningAngle
```
correctionFactor
```
double correctionFactor
```
diaphragmCoords
```
double[][] diaphragmCoords
```

Package edu.stanford.rsl.conrad.utils.interpolation
- Class edu.stanford.rsl.conrad.utils.interpolation.Interpolator extends java.lang.Object implements Serializable
 
 serialVersionUID:
 
 5165462540768302312L
 - Serialized Fields
 - xFloor
```
double xFloor
```
 - xCeiling
```
double xCeiling
```
 - yFloor
```
double yFloor
```
 - yCeiling
```
double yCeiling
```
- Class edu.stanford.rsl.conrad.utils.interpolation.LinearInterpolator extends Interpolator implements Serializable
 
 serialVersionUID:
 
 4895659448323575250L
- Class edu.stanford.rsl.conrad.utils.interpolation.LogLinearInterpolator extends Interpolator implements Serializable
 
 serialVersionUID:
 
 -7390032425709597726L
 - Serialized Fields
 - base
```
double base
```
- Class edu.stanford.rsl.conrad.utils.interpolation.LogLogInterpolator extends Interpolator implements Serializable
 
 serialVersionUID:
 
 -9085956175263105185L
 - Serialized Fields
 - base
```
double base
```
- Class edu.stanford.rsl.conrad.utils.interpolation.NumberInterpolatingTreeMap extends java.util.TreeMap<java.lang.Number,java.lang.Number> implements Serializable
 
 serialVersionUID:
 
 -5328843102124736133L
 - Serialized Fields
 - interpolator
```
Interpolator interpolator
```

Package edu.stanford.rsl.tutorial.motionEstimation

Class edu.stanford.rsl.tutorial.motionEstimation.OpenCLCompensatedBackProjector extends VOIBasedReconstructionFilter implements Serializable

serialVersionUID:: -8615490043940236889L

Serialized Fields

inputQueue
```
ImageProcessorBuffer inputQueue
```
context
```
com.jogamp.opencl.CLContext context
```
The OpenCL context
program
```
com.jogamp.opencl.CLProgram program
```
The OpenCL program
device
```
com.jogamp.opencl.CLDevice device
```
The OpenCL device
kernelFunction
```
com.jogamp.opencl.CLKernel kernelFunction
```
The OpenCL kernel function binding

commandQueue

com.jogamp.opencl.CLCommandQueue commandQueue

The OpenCL command queue

projectionTex

com.jogamp.opencl.CLImage2d<B extends java.nio.Buffer> projectionTex

The 2D projection texture reference

h_volume
```
float[] h_volume
```
The volume data that is to be reconstructed
projectionMatrix
```
com.jogamp.opencl.CLBuffer projectionMatrix
```
The global variable of the module which stores the view matrix.

volStride

com.jogamp.opencl.CLBuffer<B extends java.nio.Buffer> volStride

volumePointer

com.jogamp.opencl.CLBuffer<B extends java.nio.Buffer> volumePointer

projectionArray

com.jogamp.opencl.CLBuffer<B extends java.nio.Buffer> projectionArray

projections
```
ImageProcessorBuffer projections
```

projectionsAvailable

java.util.ArrayList<E> projectionsAvailable

projectionsDone
```
java.util.ArrayList<E> projectionsDone
```
largeVolumeMode
```
boolean largeVolumeMode
```
nSteps
```
int nSteps
```
subVolumeZ
```
int subVolumeZ
```
initialized
```
boolean initialized
```

Class edu.stanford.rsl.tutorial.motionEstimation.OpenCLCompensatedBackProjector1DCompressionField extends VOIBasedReconstructionFilter implements Serializable

serialVersionUID:: -8615490043940236889L

Serialized Fields

inputQueue
```
ImageProcessorBuffer inputQueue
```
context
```
com.jogamp.opencl.CLContext context
```
The OpenCL context
program
```
com.jogamp.opencl.CLProgram program
```
The OpenCL program
device
```
com.jogamp.opencl.CLDevice device
```
The OpenCL device
kernelFunction
```
com.jogamp.opencl.CLKernel kernelFunction
```
The OpenCL kernel function binding

commandQueue

com.jogamp.opencl.CLCommandQueue commandQueue

The OpenCL command queue

projectionTex

com.jogamp.opencl.CLImage2d<B extends java.nio.Buffer> projectionTex

The 2D projection texture reference

h_volume
```
float[] h_volume
```
The volume data that is to be reconstructed
projectionMatrix
```
com.jogamp.opencl.CLBuffer projectionMatrix
```
The global variable of the module which stores the view matrix.

volStride

com.jogamp.opencl.CLBuffer<B extends java.nio.Buffer> volStride

volumePointer

com.jogamp.opencl.CLBuffer<B extends java.nio.Buffer> volumePointer

projectionArray

com.jogamp.opencl.CLBuffer<B extends java.nio.Buffer> projectionArray

projections
```
ImageProcessorBuffer projections
```

projectionsAvailable

java.util.ArrayList<E> projectionsAvailable

projectionsDone
```
java.util.ArrayList<E> projectionsDone
```
largeVolumeMode
```
boolean largeVolumeMode
```
nSteps
```
int nSteps
```
subVolumeZ
```
int subVolumeZ
```
initialized
```
boolean initialized
```

Class edu.stanford.rsl.tutorial.motionEstimation.OpenCLCompensatedBackProjectorTPS extends VOIBasedReconstructionFilter implements Serializable

serialVersionUID:: -8615490043940236889L

Serialized Fields

inputQueue
```
ImageProcessorBuffer inputQueue
```
context
```
com.jogamp.opencl.CLContext context
```
The OpenCL context
program
```
com.jogamp.opencl.CLProgram program
```
The OpenCL program
device
```
com.jogamp.opencl.CLDevice device
```
The OpenCL device
kernelFunction
```
com.jogamp.opencl.CLKernel kernelFunction
```
The OpenCL kernel function binding

commandQueue

com.jogamp.opencl.CLCommandQueue commandQueue

The OpenCL command queue

projectionTex

com.jogamp.opencl.CLImage2d<B extends java.nio.Buffer> projectionTex

The 2D projection texture reference

h_volume
```
float[] h_volume
```
The volume data that is to be reconstructed
projectionMatrix
```
com.jogamp.opencl.CLBuffer projectionMatrix
```
The global variable of the module which stores the view matrix.

volStride

com.jogamp.opencl.CLBuffer<B extends java.nio.Buffer> volStride

volumePointer

com.jogamp.opencl.CLBuffer<B extends java.nio.Buffer> volumePointer

projectionArray

com.jogamp.opencl.CLBuffer<B extends java.nio.Buffer> projectionArray

projections
```
ImageProcessorBuffer projections
```

projectionsAvailable

java.util.ArrayList<E> projectionsAvailable

projectionsDone
```
java.util.ArrayList<E> projectionsDone
```
largeVolumeMode
```
boolean largeVolumeMode
```
nSteps
```
int nSteps
```
subVolumeZ
```
int subVolumeZ
```
initialized
```
boolean initialized
```
coeff
```
float[][] coeff
```
pts
```
float[][] pts
```
A
```
float[][] A
```
b
```
float[][] b
```

Serialized Form

Package edu.stanford.rsl.apps

Class edu.stanford.rsl.apps.TestJang extends VOIBasedReconstructionFilter implements Serializable

Package edu.stanford.rsl.apps.gui

Class edu.stanford.rsl.apps.gui.ConfigurationFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

jTabbedPane

jSaveButton

exited

config

parentFrame

regEditor

trajEdit

camAxes

xDimensionField

yDimensionField

zDimensionField

xOriginVoxel

yOriginVoxel

zOriginVoxel

xOriginWorld

yOriginWorld

zOriginWorld

xSpacingField

ySpacingField

zSpacingField

maxVOIPathField

jCenterVolume

detectorWidthField

detectorHeightField

pixelDimensionXField

pixelDimensionYField

projectionStackSizeField

numSweepsField

sourceToDetectorField

sourceToPatientField

projectionTableFileField

jParseGeometry

jGenerateGeometry

averageAngularIncrement

detectorOffsetU

detectorOffsetV

rotationAxis

DetectorUDirection

DetectorVDirection

optionList

trajectoryFromFile

trajectoryFromParameters

trajectoryPanel

trajectoryEditorButton

recentFileOneField

recentFileTwoField

citationFormatGroup

bibButton

medlineButton

importFromDicom

extrapolateGeometry

houns

Class edu.stanford.rsl.apps.gui.ConfigurePipelineFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

jScrollPane1

jMoveDownButton

jPipelinePanel

jSaveButton

jMoveUpButton

jRemoveButton

jAddButton

pipeline

exited

parentFrame

saveToDisk

panels

selectedIndex

Class edu.stanford.rsl.apps.gui.Experimenter extends javax.swing.JFrame implements Serializable

Serialized Fields

jLabel1

jAddExperiment

jScrollPane1

jRun

jRemoveExperiment