Serialized Form

  • Package com.xinapse.apps.active

    • Class com.xinapse.apps.active.ROICalculation.SpecifierPanel

      class SpecifierPanel extends JPanel implements Serializable

      • Serialized Fields

        • parentFrame
          com.xinapse.apps.active.ROIPropagateFrame parentFrame
          The ROIPropagateFrame that is the parent of this SpecifierPanel.

    • Class com.xinapse.apps.active.ROICalculationSelection.Panel

      class Panel extends JPanel implements Serializable

      • Serialized Fields

        • parentFrame
          com.xinapse.apps.active.ROIPropagateFrame parentFrame
          The parent frame that contains this Panel.
        • preferencesNodeName
          String preferencesNodeName
          The Preferences node name for ROICalculationSelection.Panel.
        • tabbedPane
          JTabbedPane tabbedPane
          The JTabbedPane that contains the different selections.

    • Class com.xinapse.apps.active.ROIPropagateFrame

      class ROIPropagateFrame extends com.xinapse.util.ImageOrganiserFrame implements Serializable

      • Serialized Fields

        • calcButton
          JButton calcButton
          A button to perform the selected calculation on the propagated ROIs.
        • calcSelectionPanel
          com.xinapse.apps.active.ROICalculationSelection.Panel calcSelectionPanel
          A ROICalculationSelection.Panel to select the type of calculation to be performed on the propagated ROIs.
        • contiguousPanel
          com.xinapse.util.ContiguousPanel contiguousPanel
          A JPanel to set whether slice locations or time points are contiguous in the image. Only needed if this ROIPropagateFrame is launched from within Jim.
        • inputImagesPanel
          com.xinapse.util.MultiContrastSelectionPanel inputImagesPanel
          The JPanel that contains the input configuration widgets. Only needed for a stand-alone ROIPropagateFrame.
        • lastOutputROIFileName
          String lastOutputROIFileName
          In stand-alone application, the last output ROI file name that was selected by the user. Used to set the default fine name next time ROIs are output.
        • nShapeCoeffsLabel
          JLabel nShapeCoeffsLabel
          A JLabel to go with the number of shape coefficients spinner.
        • nShapeCoeffsSpinner
          JSpinner nShapeCoeffsSpinner
          A JSpinner to manually set the number of shape coefficients.
        • nTimeCoeffsLabel
          JLabel nTimeCoeffsLabel
          A JLabel to go with the number of time coefficients spinner.
        • nTimeCoeffsSpinner
          JSpinner nTimeCoeffsSpinner
          A JSpinner to manually set the number of time coefficients.
        • periodicCheckBox
          JCheckBox periodicCheckBox
          A JCheckBox to specify that the time-series is perioic.
        • propagateButton
          JButton propagateButton
          A JButton to find the propagate the ROIs.
        • propagatedROIs
          SplineROI[][][] propagatedROIs
          The last set of ROIs that resulted from a propagation, for stand-alone GUI application.
        • roiSelectionPanel
          ROIFileSelectionPanel roiSelectionPanel
          The JPanel used to select the ROI file with the ROIs to propagate.
        • setShapeCoeffsCheckBox
          JCheckBox setShapeCoeffsCheckBox
          A JCheckBox to set the number of shape coefficients manually.
        • setTimeCoeffsCheckBox
          JCheckBox setTimeCoeffsCheckBox
          A JCheckBox to set the number of time coefficients manually.

  • Package com.xinapse.apps.cardiac

    • Class com.xinapse.apps.cardiac.CardiacAnalysis.SpecifierPanel

      class SpecifierPanel extends JPanel implements Serializable

      • Serialized Fields

        • parentFrame
          com.xinapse.apps.cardiac.CardiacFrame parentFrame
          The CardiacFrame that is the parent of this SpecifierPanel.

    • Class com.xinapse.apps.cardiac.CardiacAnalysisSelection.Panel

      class Panel extends JPanel implements Serializable

      • Serialized Fields

        • parentFrame
          com.xinapse.apps.cardiac.CardiacFrame parentFrame
          The parent frame that contains this Panel.
        • preferencesNodeName
          String preferencesNodeName
          The Preferences node name for CardiacAnalysisSelection.Panel.
        • tabbedPane
          JTabbedPane tabbedPane
          The JTabbedPane that contains the different selections.

    • Class com.xinapse.apps.cardiac.CardiacFrame

      class CardiacFrame extends MultiContrastAnalysisFrame implements Serializable

      • Serialized Fields

        • analyseButton
          JButton analyseButton
          A button to perform the selected cardiac analysis.
        • analysisSelectionPanel
          com.xinapse.apps.cardiac.CardiacAnalysisSelection.Panel analysisSelectionPanel
          A CardiacAnalysisSelection.Panel to select the type of cardiac analysis to be performed.
        • autoPropagateButton
          JButton autoPropagateButton
          A JButton to automatically propagate ROIs defined in one slice to all time points.
        • contiguousPanel
          com.xinapse.util.ContiguousPanel contiguousPanel
          A JPanel to set whether slice locations or time points are contiguous in the image.
        • copyAllButton
          JButton copyAllButton
          A JButton to copy ROIs defined at one time-point to all time-points.
        • copyBackwardsButton
          JButton copyBackwardsButton
          A JButton to copy ROIs defined at one time-point to all earlier time-points.
        • copyForwardsButton
          JButton copyForwardsButton
          A JButton to copy ROIs defined at one time-point to all later time-points.
        • divideMyocardiumCheckBox
          JCheckBox divideMyocardiumCheckBox
          A JCheckBox to set whether to split into endocardium/eipcardium.
        • endoEpiSplitSlider
          JSlider endoEpiSplitSlider
          A JSlider to set the endo/epicardial split in increments of 5%, from 5% to 95%
        • nSegmentsPanel
          com.xinapse.apps.cardiac.CardiacFrame.NSegmentsPanel nSegmentsPanel
          A JPanel to set the number of cardiac segments in each physical slice.
        • revertButton
          JButton revertButton
          A JButton to undo the propagation of ROIs and revert to the pre-propagated ROIs.
        • roisBeforePropagation
          List<ROI> roisBeforePropagation
          A record of the ROIs before they are propagated.
        • roiSelectionPanel
          ROIFileSelectionPanel roiSelectionPanel
          For selecting the input ROIs. Only needed in the stand-alone application.
        • splitLabel
          JLabel splitLabel
          The JLabel showing the current endo/epi cardial split.

    • Class com.xinapse.apps.cardiac.SegmentalAnalysis.SpecifierPanel

      class SpecifierPanel extends JPanel implements Serializable

      • Serialized Fields

        • parentFrame
          com.xinapse.apps.cardiac.CardiacFrame parentFrame
          The CardiacFrame that is the parent of this SpecifierPanel.

  • Package com.xinapse.apps.perfusion

    • Class com.xinapse.apps.perfusion.DCEMRIFrame

      class DCEMRIFrame extends com.xinapse.apps.perfusion.PerfusionFrame implements Serializable

      • Serialized Fields

        • analysisTypePanel
          com.xinapse.apps.perfusion.AnalysisType.Panel analysisTypePanel
          The AnalysisType.Panel that is used to select the type of analysis (pixel-by-pixel, or ROI).
        • modelPanel
          com.xinapse.apps.perfusion.DCEMRIModel.Panel modelPanel
          The DCEMRIModel.Panel that is used to select the model to fit.

    • Class com.xinapse.apps.perfusion.PerfusionFrame

      class PerfusionFrame extends AbstractDynamicFrame implements Serializable

      • Serialized Fields

        • aifSelectionModePanel
          com.xinapse.apps.perfusion.AIFSelectionMode.Panel aifSelectionModePanel
        • analysisEndTimeField
          JTextField analysisEndTimeField
          The JTextField for setting the analysis end time-point, or leave blank for the full time-course.
        • analysisEndTimeNumberLabel
          JLabel analysisEndTimeNumberLabel
          The JLabel that labels the analysis end time or frame number.
        • analysisEndTimeNumberUnitsLabel
          JLabel analysisEndTimeNumberUnitsLabel
          The JLabel that shows the analysis end time or frame number units.
        • arrivalTimeUnitsPanel
          com.xinapse.apps.perfusion.ContrastArrivalTimeUnits.Panel arrivalTimeUnitsPanel
        • arterialHaematocritField
          JTextField arterialHaematocritField
        • arterialHaematocritLabel
          JLabel arterialHaematocritLabel
        • arterialHaematocritPanel
          JPanel arterialHaematocritPanel
        • arterialRelaxivityField
          JTextField arterialRelaxivityField
        • arterialRelaxivityLabel
          JLabel arterialRelaxivityLabel
        • contrastArrivalTimeField
          JTextField contrastArrivalTimeField
        • ctButton
          JRadioButton ctButton
        • imageTypePanel
          com.xinapse.apps.perfusion.ImageType.T1WeightedPanel imageTypePanel
        • mriButton
          JRadioButton mriButton
        • presetsMenu
          com.xinapse.preset.PresetsMenu<com.xinapse.apps.perfusion.DynamicPreset> presetsMenu
          The Presets menu.
        • relaxivityPanel
          JPanel relaxivityPanel
        • scanTimeNumberLabel
          JLabel scanTimeNumberLabel
        • scanTimeNumberUnitsLabel
          JLabel scanTimeNumberUnitsLabel
        • svdPanel
          JPanel svdPanel
        • svdThresholdSpinner
          JSpinner svdThresholdSpinner
        • teField
          JTextField teField
        • tePanel
          JPanel tePanel
        • tissueHaematocritField
          JTextField tissueHaematocritField
        • tissueHaematocritPanel
          JPanel tissueHaematocritPanel
        • tissueLagPanel
          com.xinapse.apps.perfusion.TissueLagPanel tissueLagPanel
        • tissueRelaxivityField
          JTextField tissueRelaxivityField
        • tissueRelaxivityLabel
          JLabel tissueRelaxivityLabel

    • Class com.xinapse.apps.perfusion.TissueLagPanel

      class TissueLagPanel extends JPanel implements Serializable

      • Serialized Fields

        • lagInfoLabel
          JLabel lagInfoLabel
          The JLabel that tells the user what the current lag is.
        • lagLabel
          JLabel lagLabel
          The JLabel that precedes the Spinner.
        • lagSpinnerModel
          SpinnerNumberModel lagSpinnerModel
          The SpinnerNumberModel for setting the lag.
        • spinner
          JSpinner spinner
          The JSpinner used to set the lag.

  • Package com.xinapse.dicom

    • Exception com.xinapse.dicom.BadVMException

      class BadVMException extends com.xinapse.dicom.DCMException implements Serializable

    • Exception com.xinapse.dicom.BadVRException

      class BadVRException extends com.xinapse.dicom.DCMException implements Serializable

    • Class com.xinapse.dicom.BodyPart.ComboBox

      class ComboBox extends JComboBox<String> implements Serializable

    • Class com.xinapse.dicom.DatePanel

      class DatePanel extends JPanel implements Serializable

      • Serialized Fields

        • dayField
          JTextField dayField
          The JTextField to set the day.
        • monthField
          JTextField monthField
          The JTextField to set the month.
        • yearField
          JTextField yearField
          The JTextField to set the year.

    • Exception com.xinapse.dicom.DCMAbortException

      class DCMAbortException extends com.xinapse.dicom.DCMException implements Serializable

    • Exception com.xinapse.dicom.DCMErrorException

      class DCMErrorException extends com.xinapse.dicom.DCMException implements Serializable

    • Exception com.xinapse.dicom.DCMException

      class DCMException extends Exception implements Serializable

    • Exception com.xinapse.dicom.DCMFatalException

      class DCMFatalException extends com.xinapse.dicom.DCMException implements Serializable

    • Exception com.xinapse.dicom.DCMWarningException

      class DCMWarningException extends com.xinapse.dicom.DCMException implements Serializable

    • Class com.xinapse.dicom.DebuggingOptionsDialog

      class DebuggingOptionsDialog extends JDialog implements Serializable

      • Serialized Fields

        • DULCheckBox
          JCheckBox DULCheckBox
          The JCheckBox to enable debugging of DICOM upper layer.
        • SRVCheckBox
          JCheckBox SRVCheckBox
          The JCheckBox to enable debugging of DICOM services.

    • Class com.xinapse.dicom.DicomdirFileChooser

      class DicomdirFileChooser extends JFileChooser implements Serializable

    • Class com.xinapse.dicom.DicomPreferencesPanel

      class DicomPreferencesPanel extends JPanel implements Serializable

      • Serialized Fields

        • prefsSettable
          PreferencesSettable prefsSettable
          The PreferencesSettable whose Preferences will be set.
        • queryRetrievePreferencesPanel
          com.xinapse.dicom.DicomPreferencesPanel.QueryRetrievePreferencesPanel queryRetrievePreferencesPanel
        • savePreferencesPanel
          com.xinapse.dicom.DicomPreferencesPanel.SavePreferencesPanel savePreferencesPanel

    • Exception com.xinapse.dicom.InvalidDateException

      class InvalidDateException extends Exception implements Serializable

    • Exception com.xinapse.dicom.InvalidInputException

      class InvalidInputException extends Exception implements Serializable

    • Exception com.xinapse.dicom.InvalidTagException

      class InvalidTagException extends com.xinapse.dicom.DCMException implements Serializable

    • Class com.xinapse.dicom.Laterality.Panel

      class Panel extends JPanel implements Serializable

    • Class com.xinapse.dicom.Modality.ComboBox

      class ComboBox extends JComboBox<String> implements Serializable

    • Class com.xinapse.dicom.PatientPosition.ComboBox

      class ComboBox extends JComboBox<String> implements Serializable

    • Class com.xinapse.dicom.PulseSequenceType.ComboBox

      class ComboBox extends JComboBox<PulseSequenceType> implements Serializable

    • Class com.xinapse.dicom.Sex.Panel

      class Panel extends JPanel implements Serializable

  • Package com.xinapse.dynamic

    • Class com.xinapse.dynamic.AbstractDynamicFrame

      class AbstractDynamicFrame extends MultiContrastAnalysisFrame implements Serializable

      • Serialized Fields

        • dynamicModelPanel
          JPanel dynamicModelPanel
          The JPanel that contains the analysis setup. Components for the analysis model should be added to this JPanel.
        • fwhmLabel
          JLabel fwhmLabel
          A label before the FWHMTextField.
        • fwhmMmLabel
          JLabel fwhmMmLabel
          A label after the fwhmTextField.
        • fwhmTextField
          com.xinapse.util.XinapseFormattedTextField fwhmTextField
          A JFormattedTextField to set the FWHM of the smoothing filter.
        • maskSelectorPanel
          com.xinapse.dynamic.DynamicMaskSelectorWorker.Panel maskSelectorPanel
          A JPanel for selecting an image mask.
        • nSteadyStatesSpinner
          JSpinner nSteadyStatesSpinner
        • outputImageSelectionPanel
          OutputImageSelectionPanel outputImageSelectionPanel
          ImageSelectionPanel used to select the output images basename.
        • registerCheckBox
          JCheckBox registerCheckBox
          A check box to turn on registration.
        • smoothingFilterCheckBox
          JCheckBox smoothingFilterCheckBox
          A check box to turn on spatial filtering.
        • thresholdField
          JTextField thresholdField
          The JTextField to set the intensity threshold.
        • timeBetweenImagesField
          JTextField timeBetweenImagesField
          The JTextField to set the time between images in seconds.

    • Class com.xinapse.dynamic.DynamicMaskSelectorWorker.Panel

      class Panel extends JPanel implements Serializable

      • Serialized Fields

        • allowBrainFinder
          boolean allowBrainFinder
          Whether BrainFinder use is allowed.
        • bTPanel
          com.xinapse.apps.brain.BTPanel bTPanel
          A JPanel to set the threshold fraction for brain finding.
        • maskImageCheckBox
          JCheckBox maskImageCheckBox
          A JCheckBox to turn on masking with an image.
        • maskImageSelectionPanel
          InputImageSelectionPanel maskImageSelectionPanel
          A JPanel for setting the mask image.
        • maskLabel
          JLabel maskLabel
          A JLabel for the mask.
        • maskROIsCheckBox
          JCheckBox maskROIsCheckBox
          A JCheckBox to turn on masking with ROIs.
        • maskTypeSelectionActionListeners
          List<ActionListener> maskTypeSelectionActionListeners
        • messageShower
          MessageShower messageShower
        • roiMaskSelectionPanel
          ROIFileSelectionPanel roiMaskSelectionPanel
          A JPanel for setting the ROI mask.
        • useBrainFinderCheckBox
          JCheckBox useBrainFinderCheckBox
          A JCheckBox to turn on brain finding.

    • Class com.xinapse.dynamic.DynamicModel.SpecifierPanel

      class SpecifierPanel extends JPanel implements Serializable

      • Serialized Fields

        • actionListeners
          List<ActionListener> actionListeners
          A List of ActionListeners that is maintained by this SpecifierPanel.
        • modelChangedListener
          com.xinapse.dynamic.DynamicModel.SpecifierPanel.ModelChangedListener modelChangedListener
          The ActionListener that should be notified when the DynamicModel specified in this SpecifierPanel is changed. This ActionListener should be added to all UI items that specify the DynamicModel.
        • parentFrame
          AbstractDynamicFrame parentFrame
          The AbstractDynamicFrame that is the parent of this SpecifierPanel.

    • Class com.xinapse.dynamic.DynamicModelSelection.Panel

      class Panel extends JPanel implements Serializable

    • Class com.xinapse.dynamic.SliceOrderPanel

      class SliceOrderPanel extends JPanel implements Serializable

  • Package com.xinapse.filter

  • Package com.xinapse.geom3d

    • Class com.xinapse.geom3d.CancellableParallelSorter

      class CancellableParallelSorter extends CountedCompleter<Void> implements Serializable

      • Serialized Fields

        • a
          T extends Comparable<T>[] a
        • base
          int base
        • gran
          int gran
        • size
          int size
        • w
          T extends Comparable<T>[] w
        • wbase
          int wbase

    • Class com.xinapse.geom3d.ImageDisplayCanvas3D

      class ImageDisplayCanvas3D extends com.jogamp.opengl.awt.GLCanvas implements Serializable

      • Serialized Fields

        • ambientLight
          float[] ambientLight
          The ambient light source.
        • boundingBox
          com.xinapse.geom3d.Cuboid boundingBox
          The bounding box of all elements in the display.
        • boundingBoxLock
          Object boundingBoxLock
          The synchronization lock on the bounding box.
        • cameraDistance
          double cameraDistance
          The current distance from the camera to the Model origin.
        • constrainedRotationAxis
          org.jogamp.vecmath.Vector3d constrainedRotationAxis
          If non-null, the constrained axis of rotation.
        • cutOutUpdaterThread
          com.xinapse.geom3d.ImageDisplayCanvas3D.CutOutUpdaterThread cutOutUpdaterThread
          The Thread that updates the cutout. Only one Thread is allowed to do this at a time.
        • diffuseLightBrightness
          float[] diffuseLightBrightness
          The diffuse light source.
        • diffuseLightDirection
          float[] diffuseLightDirection
          The directional light direction.
        • doNotWarnAboutHandedness
          boolean doNotWarnAboutHandedness
          If set, the user has indicated that they don't want to see a warning again.
        • geometryGenerators
          List<com.xinapse.geom3d.GeometryGenerator> geometryGenerators
          The current List of GeometryGenerator that will be displayed.
        • glu
          com.jogamp.opengl.glu.GLU glu
          GL Utilities.
        • lastMousePosition
          org.jogamp.vecmath.Point2i lastMousePosition
          The last mouse position.
        • modelViewportTransform
          double[][] modelViewportTransform
          The transform from model to viewport coordinates.
        • mouseRotationTransform
          double[][] mouseRotationTransform
          The transform created by changing the rotation by dragging the mouse.
        • mouseTranslation
          org.jogamp.vecmath.Vector2d mouseTranslation
          The translation created by changing the pan by dragging the mouse (right mouse button).
        • parentFrame
          com.xinapse.geom3d.ImageDisplayFrame3D parentFrame
          The parent to which this Canvas3D has been added.
        • phi
          double phi
          The latitude angle. Range: -PI/2..+PI/2.
        • psi
          double psi
          The rotation angle of the camera about the axis from the camera to the centre of the scene. Range: -PI..+PI.
        • showAxes
          boolean showAxes
          Whether the axes are visible.
        • showBoundingBox
          boolean showBoundingBox
          Whether the bounding box is visible.
        • theta
          double theta
          The longitude angle. Range: -PI..+PI.
        • validModelViewTransform
          AtomicBoolean validModelViewTransform
          A flag indicating whether the Model-View Transform is valid.
        • viewportModelTransform
          double[][] viewportModelTransform
          The transform from viewport to model coordinates.
        • xAxisCone
          com.xinapse.geom3d.Cone xAxisCone
        • xAxisLabel
          com.xinapse.geom3d.LetterX xAxisLabel
        • yAxisCone
          com.xinapse.geom3d.Cone yAxisCone
        • yAxisLabel
          com.xinapse.geom3d.LetterY yAxisLabel
        • zAxisCone
          com.xinapse.geom3d.Cone zAxisCone
        • zAxisLabel
          com.xinapse.geom3d.LetterZ zAxisLabel

    • Class com.xinapse.geom3d.ImageDisplayFrame3D

      class ImageDisplayFrame3D extends JFrame implements Serializable

      • Serialized Fields

        • cineDialog
          com.xinapse.cinerecorder.CineDialog cineDialog
          The Dialog to capture movies.
        • controlPanel3D
          com.xinapse.geom3d.ControlPanel3D controlPanel3D
          The ControlPanel3D that controls the common features of the scene.
        • displayer
          com.xinapse.displayer.ImageDisplayer displayer
          The display from which this ImageDisplayCanvas3D was launched, or null.
        • displayPanel
          JPanel displayPanel
          The JPanel into which the imageDisplayCanvas3D will be added.
        • doneButton
          com.xinapse.util.DoneButton doneButton
          Button to close this Frame.
        • imageDisplayCanvas3D
          com.xinapse.geom3d.ImageDisplayCanvas3D imageDisplayCanvas3D
          The ImageDisplayCanvas3D in which the scene will be drawn.
        • imageSelectionDialogs
          List<com.xinapse.geom3d.ThreeDObjectDialog> imageSelectionDialogs
          A List of dialogs for adding 3-D objects to the scene.
        • quitMe
          boolean quitMe
          A flag which when set to true when this ImageDisplayFrame3D's setVisible(false) method is called. Can be used by an application to identify when to quit.
        • resetViewButton
          JButton resetViewButton
          Button to reset to a standard view.
        • setViewDialog
          com.xinapse.geom3d.SetViewDialog setViewDialog
          The dialog to set a particular view on the scene.
        • statusText
          JTextField statusText
          Status text area.
        • userPanel
          JPanel userPanel
          The JPanel into which specific applications can add GUI components.

    • Class com.xinapse.geom3d.IsoSurfaceSelectionDialog

      class IsoSurfaceSelectionDialog extends com.xinapse.geom3d.ThreeDObjectDialog implements Serializable

      • Serialized Fields

        • alphaPanel
          com.xinapse.util.AlphaPanel alphaPanel
          A panel to set the surface opacity.
        • colorButton
          com.xinapse.util.ColorSelectionButton colorButton
          A button to set the uniform surface color.
        • computedThreshold
          Float computedThreshold
          The threshold value that has already been computed or set for this image, and which will be reused when the only Fidelity setting is changed. Changing the Fidelity causes the image to be reloaded so that it can be downsampled to give the right Fidelity.
        • currentImageName
          String currentImageName
        • cutOutCheckBox
          JCheckBox cutOutCheckBox
          A JCheckBox for setting whether the iso-surface is to be cut away.
        • doneButton
          com.xinapse.util.DoneButton doneButton
          The button to close the dialog.
        • fidelityPanel
          com.xinapse.geom3d.Fidelity.Panel fidelityPanel
          A panel for setting the surface fidelity (number of triangular faces) of the iso-surface.
        • imageLoaderWorker
          com.xinapse.util.ImageLoaderWorker imageLoaderWorker
          The one and only ImageLoaderWorker that can be alive for this Dialog.
        • inputImageSelectionPanel
          InputImageSelectionPanel inputImageSelectionPanel
          The JPanel for selecting the input image.
        • isoSurfaceGenerator
          com.xinapse.geom3d.IsoSurfaceGenerator isoSurfaceGenerator
          The GeometryGenerator to generate the iso-surface.
        • isoSurfaceLoaderThread
          com.xinapse.geom3d.IsoSurfaceSelectionDialog.IsoSurfaceLoaderThread isoSurfaceLoaderThread
          The one IsoSurfaceLoaderThread that is allowed to run at a time.
        • lastImageName
          String lastImageName
        • optionalItemsPanel
          JPanel optionalItemsPanel
          A Panel for optional items that are not used by sub-classes.
        • parentFrame
          com.xinapse.geom3d.ImageDisplayFrame3D parentFrame
          The parent ImageDisplayFrame3D where the iso-surface will be displayed.
        • renderModePanel
          com.xinapse.geom3d.RenderMode.Panel renderModePanel
          For setting the rendering mode.
        • saveOBJMenuItem
          JMenuItem saveOBJMenuItem
        • saveSTLMenuItem
          JMenuItem saveSTLMenuItem
        • saveVRMLMenuItem
          JMenuItem saveVRMLMenuItem
        • shininessSpinner
          JSpinner shininessSpinner
          A JSpinner to set the surface shininess.
        • statusText
          JTextField statusText
          A status text line.
        • thresholdSliderPanel
          com.xinapse.util.IntensitySliderPanel thresholdSliderPanel
          A sliders to set the background separation threshold.

    • Class com.xinapse.geom3d.ThreeDGeometryFileSelectionPanel

      class ThreeDGeometryFileSelectionPanel extends com.xinapse.util.FileSelectionPanel implements Serializable

      • Serialized Fields

        • dialog
          com.xinapse.geom3d.ThreeDGeometrySelectionDialog dialog

  • Package com.xinapse.image

  • Package com.xinapse.image.template

  • Package com.xinapse.io

  • Package com.xinapse.multisliceimage

  • Package com.xinapse.multisliceimage.Analyze

  • Package com.xinapse.multisliceimage.roi

  • Package com.xinapse.multisliceimage.UNC

  • Package com.xinapse.numerical

  • Package com.xinapse.platform

    • Class com.xinapse.platform.LookAndFeelPanel

      class LookAndFeelPanel extends JPanel implements Serializable

    • Exception com.xinapse.platform.PlatformException

      class PlatformException extends Exception implements Serializable

  • Package com.xinapse.util

    • Class com.xinapse.util.AlphaPanel

      class AlphaPanel extends JPanel implements Serializable

      • Serialized Fields

        • alphaChangeListeners
          List<com.xinapse.util.AlphaPanel.AlphaChangeListener> alphaChangeListeners
        • currentText
          JTextField currentText
          The JTextField showing the current setting of the slider.
        • slider
          JSlider slider
          The slider.

    • Exception com.xinapse.util.AlreadyProcessedException

      class AlreadyProcessedException extends Exception implements Serializable

    • Class com.xinapse.util.BitSet

      class BitSet extends Object implements Serializable
      serialVersionUID:
      7997698588986878753L

      • Serialized Fields

        • bits
          long[] bits
          The actual bits.
          the i'th bit is in bits[i/64] at position i%64 (where position 0 is the least significant).
        • cachedCardinality
          int cachedCardinality
        • nbits
          int nbits
          The number of bits that can be stored and accessed in this BitSet.

    • Class com.xinapse.util.ButtonTabComponent

      class ButtonTabComponent extends JPanel implements Serializable

    • Exception com.xinapse.util.CancelledException

      class CancelledException extends Exception implements Serializable

      • Serialized Fields

    • Class com.xinapse.util.ColorSelectionButton

      class ColorSelectionButton extends JButton implements Serializable

      • Serialized Fields

        • colourChangeListeners
          List<com.xinapse.util.ColorSelectionButton.ColorChangeListener> colourChangeListeners
        • colourIcon
          com.xinapse.util.ColorSelectionButton.ColorIcon colourIcon

    • Class com.xinapse.util.ColourScalesMenu

      class ColourScalesMenu extends JMenu implements Serializable

      • Serialized Fields

        • colourMenuListener
          ActionListener colourMenuListener
          An action listener that is fired when a new ColourMapping is selected.
        • coloursButtonGroup
          ButtonGroup coloursButtonGroup
          The ButtonGroup for all JRadioButtonMenuItem that select ColourMappings.
        • defaultColourMappingMenuItem
          JRadioButtonMenuItem defaultColourMappingMenuItem
          The default JRadioButtonMenuItem to select.
        • invertCheckBoxMenuItem
          JCheckBoxMenuItem invertCheckBoxMenuItem
          A JCheckBox to invert the colour mapping.
        • nativeColourMapping
          ColourMapping nativeColourMapping
          The ColourMapping associated with the Native Colours menu entry, if non-null. If null, then there is no native colour mapping.
        • nativeColoursMenuItem
          JRadioButtonMenuItem nativeColoursMenuItem
          A special JRadioButtonMenuItem to select the Native Colours colour mapping.

    • Class com.xinapse.util.ContiguousPanel

      class ContiguousPanel extends JPanel implements Serializable

      • Serialized Fields

        • contiguousContrastsRadioButton
          JRadioButton contiguousContrastsRadioButton
          A JRadioButton to select contiguous contrasts.
        • contiguousSlicesRadioButton
          JRadioButton contiguousSlicesRadioButton
          A JRadioButton to select contiguous slice positions.
        • parent
          PreferencesSettable parent
          The PreferencesSettable in which this ContiguousPanel is embedded.

    • Class com.xinapse.util.ContrastAdjusterPanel

      class ContrastAdjusterPanel extends JPanel implements Serializable

      • Serialized Fields

        • autoContrastButton
          JButton autoContrastButton
          A button to automatically adjust the contrast settings in the ChangeableContrast.
        • buttonsPanel
          JPanel buttonsPanel
          A Panel that contains the buttons.
        • changeableContrast
          com.xinapse.util.ChangeableContrast changeableContrast
          A ChangeableContrast whose contrast will be affected by this ContrastAdjusterPanel.
        • contrastMaxAdj
          com.xinapse.util.IntensitySliderPanel contrastMaxAdj
          A slider to adjust the mapping from intensity to the mast entry in the colour mapping.
        • contrastMinAdj
          com.xinapse.util.IntensitySliderPanel contrastMinAdj
          A slider to adjust the mapping from intensity to the first entry in the colour mapping.
        • expandContrastRangeButton
          com.xinapse.util.SVG.Button expandContrastRangeButton
          A button to expand the contrast range.
        • resetContrastRangeButton
          com.xinapse.util.SVG.Button resetContrastRangeButton
          A button to reset the contrast range to its full range.

    • Class com.xinapse.util.DoneButton

      class DoneButton extends JButton implements Serializable

    • Class com.xinapse.util.FileChooser

      class FileChooser extends JFileChooser implements Serializable

      • Serialized Fields

        • extensions
          String[] extensions

    • Class com.xinapse.util.FileChooser.LoadChooser

      class LoadChooser extends com.xinapse.util.FileChooser implements Serializable

    • Class com.xinapse.util.FileChooser.SaveChooser

      class SaveChooser extends com.xinapse.util.FileChooser implements Serializable

    • Class com.xinapse.util.FileSelectionPanel

      class FileSelectionPanel extends JPanel implements Serializable

    • Class com.xinapse.util.FixedSizeLabel

      class FixedSizeLabel extends JLabel implements Serializable

      • Serialized Fields

        • size
          Dimension size
          After initialisation, the fixed size of the label.

    • Class com.xinapse.util.FolderSelectionPanel

      class FolderSelectionPanel extends JPanel implements Serializable

      • Serialized Fields

        • changeListeners
          List<ChangeListener> changeListeners
        • fileChooser
          com.xinapse.util.FileChooser fileChooser
        • folderSelectButton
          JButton folderSelectButton
        • folderTextField
          JTextField folderTextField
        • messageShower
          MessageShower messageShower
        • useDescription
          String useDescription

    • Class com.xinapse.util.ImageOrganiserFrame

      class ImageOrganiserFrame extends JFrame implements Serializable

      • Serialized Fields

        • actionDescription
          String actionDescription
          String describing the action that this tool will perform
        • actionWorkers
          List<SwingWorker> actionWorkers
          A List of SwingWorkers that can be started by this JFrame.
        • bottomPanel
          JPanel bottomPanel
          An optional JPanel consisting of a JPanel relating to user preferences, a status text area, a button to do the action, and a done button.
        • doItButton
          JButton doItButton
          A button to do the action required of this JFrame.
        • doneButton
          JButton doneButton
          A button to finish with this JFrame.
        • imageDisplayer
          com.xinapse.displayer.ImageDisplayer imageDisplayer
          The parent of this frame, if not a stand-alone application.
        • loadResultButton
          JRadioButton loadResultButton
          The JRadioButton for loading the result into Jim.
        • outputPanel
          JPanel outputPanel
          A JPanel containing items pertaining to image output (save-to-disk / load result).
        • preferencesPanel
          com.xinapse.util.PreferencesPanel preferencesPanel
          The panel from which defaults and user preferences can be set, if non-null.
        • quitMe
          boolean quitMe
          A flag that is set for stand-alone applications to indicate that the program should quit.
        • saveToDiskButton
          JRadioButton saveToDiskButton
          The JRadioButton for saving the result to disk.
        • scrollableContentsPane
          JScrollPane scrollableContentsPane
          The JScrollPane that wil contain the scrollable contents.
        • statusText
          JTextField statusText
          A status text area - shows messages to the user via the ImageOrganiserFrame.showStatus(String) method.

    • Class com.xinapse.util.InfoList

      class InfoList extends ArrayList<InfoItem> implements Serializable

    • Exception com.xinapse.util.InfoListException

      class InfoListException extends Exception implements Serializable

    • Class com.xinapse.util.IntensityRelation.IntensityRelationButton

      class IntensityRelationButton extends com.xinapse.util.NStateButton<IntensityRelation> implements Serializable

      • Serialized Fields

        • prefs
          Preferences prefs
          The Preferences to which any changes to this button will be saved.

    • Class com.xinapse.util.IntensityRelation.PanelGenerator.Panel

      class Panel extends JPanel implements Serializable

      • Serialized Fields

        • intensityRelationButtons
          JRadioButton[] intensityRelationButtons

    • Class com.xinapse.util.IntensitySliderPanel

      class IntensitySliderPanel extends JPanel implements Serializable

      • Serialized Fields

        • autoContrastButton
          JButton autoContrastButton
          The auto contrast button to be enabled when the contrast is changed.
        • changeListeners
          List<ChangeListener> changeListeners
        • currentDataType
          PixelDataType currentDataType
          The PixelDataType of the image currently displayed. May be null if no image is displayed.
        • currentText
          JTextField currentText
          The JTextField showing the current setting of the slider.
        • intercept
          double intercept
          The intercept in the relationship between an intensity value to its integer equivalent in the world of the slider.
        • minimised
          boolean minimised
        • slider
          JSlider slider
          The slider.
        • slope
          double slope
          The slope in the relationship between an intensity value to its integer equivalent in the world of the slider.
        • title
          String title

    • Exception com.xinapse.util.InvalidArgumentException

      class InvalidArgumentException extends Exception implements Serializable

    • Exception com.xinapse.util.InvalidComponentStateException

      class InvalidComponentStateException extends Exception implements Serializable

    • Class com.xinapse.util.LogFileChooser

      class LogFileChooser extends JFileChooser implements Serializable

    • Class com.xinapse.util.MultiContrastAnalysisFrame

      class MultiContrastAnalysisFrame extends com.xinapse.util.ImageOrganiserFrame implements Serializable

      • Serialized Fields

        • changeListeners
          List<ChangeListener> changeListeners
        • contrastDescription
          String contrastDescription
          A description of the difference betwen one image to the next. For example "time point" or "diffusion weighting".
        • imageInputPanel
          com.xinapse.util.MultiContrastSelectionPanel imageInputPanel
          The JPanel that contains the input configuration widgets.
        • roamingResponseDialog
          com.xinapse.util.RoamingResponseDialog roamingResponseDialog
          The RoamingResponseDialog used to display the roaming response, if non-null.
        • roiStatsCache
          com.xinapse.util.ROIStatsCache roiStatsCache
          An ROIStatsCache to hold cached ROI statistics for possible re-use if the ROIs used in the roaming response do not change.
        • showResponseWorker
          com.xinapse.util.MultiContrastAnalysisFrame.ShowResponseWorker showResponseWorker
          The SwingWorker that updates the roaming response.

    • Class com.xinapse.util.MultiContrastSelectionPanel

      class MultiContrastSelectionPanel extends JPanel implements Serializable

      • Serialized Fields

        • cacheLock
          Object cacheLock
          A synchronization lock on the input images cache.
        • changeListeners
          List<ChangeListener> changeListeners
        • contiguousPanel
          com.xinapse.util.ContiguousPanel contiguousPanel
          A JPanel to set whether contrasts or slice locations are contiguous in a single input image.
        • contrastDescription
          String contrastDescription
        • defaultNContrasts
          int defaultNContrasts
          The default number of contrasts for this MultiContrastSelectionPanel.
        • inputImages
          ReadableImage[] inputImages
          An cached array of input images. This array is reset to null whenever the input images are changed by the user, so that the input images must be re-instantiated.
        • inputImageSelectionPanel
          InputImageSelectionPanel inputImageSelectionPanel
          ImageSelectionPanel if a single input image is used, containing all contrasts and slices.
        • messageShower
          MessageShower messageShower
        • multipleImageSelectionPanel
          MultipleImageSelectionPanel multipleImageSelectionPanel
          MultipleImageSelectionPanel if multiple input images are used - one for each contrast or slice position.
        • multipleInputOnePerContrastButton
          JRadioButton multipleInputOnePerContrastButton
        • multipleInputOnePerSliceButton
          JRadioButton multipleInputOnePerSliceButton
        • nContrastsSpinner
          JSpinner nContrastsSpinner
          The JSpinner to set the number of image contrasts in a single input image.
        • singleInputButton
          JRadioButton singleInputButton
        • singleInputImageSetupPanel
          JPanel singleInputImageSetupPanel
          A JPanel for selecting a single input image and setting the number of contrasts.

    • Class com.xinapse.util.MultipleFileSelectionPanel

      class MultipleFileSelectionPanel extends JPanel implements Serializable

      • Serialized Fields

        • addFilesButton
          JButton addFilesButton
          A button to add files to the current list of files.
        • currentWorkingDirectory
          File currentWorkingDirectory
          The current working directory.
        • downButton
          JButton downButton
          A button to move selected files down the list of files.
        • fileFilter
          FileFilter fileFilter
          If non-null, the FileFilter that will be applied to filter selectable files.
        • filesList
          JList<String> filesList
          The JList that displays the list of files.
        • initialWidth
          Integer initialWidth
          The width used to get the preferredSize() once the components in this MultipleFileSelectionPanel have been added to it.
        • listModel
          DefaultListModel<String> listModel
          The ListModel that contains the current list of files.
        • listTitleLabel
          JLabel listTitleLabel
          The title that is displayed above the list of files.
        • parentFrame
          JFrame parentFrame
          The JFrame in which this MultipleFileSelectionPanel is embedded.
        • removeAllButton
          JButton removeAllButton
          A button to remove all files from the list of files.
        • removeSelectedButton
          JButton removeSelectedButton
          A button to remove selected files from the list of files.
        • selectFilesButton
          JButton selectFilesButton
          A button to select a new list of files.
        • upButton
          JButton upButton
          A button to move selected files up the list of files.

    • Class com.xinapse.util.MultipleFolderSelectionPanel

      class MultipleFolderSelectionPanel extends JPanel implements Serializable

      • Serialized Fields

        • addFoldersButton
          JButton addFoldersButton
          A button to add folders to the current list of folders.
        • currentWorkingDirectory
          File currentWorkingDirectory
          The current working directory.
        • foldersList
          JList<String> foldersList
          The JList that displays the list of folders.
        • initialWidth
          Integer initialWidth
          The width used to get the preferredSize() once the components in this MultipleFolderSelectionPanel have been added to it.
        • listModel
          DefaultListModel<String> listModel
          The ListModel that contains the current list of files.
        • listTitleLabel
          JLabel listTitleLabel
          The title that is displayed above the list of folders.
        • parentFrame
          JFrame parentFrame
          The JFrame in which this MultipleFolderSelectionPanel is embedded.
        • removeAllButton
          JButton removeAllButton
          A button to remove all folders from the list of folders.
        • removeSelectedButton
          JButton removeSelectedButton
          A button to remove selected folders from the list of folders.
        • selectFoldersButton
          JButton selectFoldersButton
          A button to select a new list of folders.

    • Class com.xinapse.util.NStateButton

      class NStateButton extends JButton implements Serializable

      • Serialized Fields

        • stateIndex
          int stateIndex
        • states
          T extends Icon[] states

    • Class com.xinapse.util.PageOrientationComboBox

      class PageOrientationComboBox extends JComboBox<com.xinapse.util.PageOrientation> implements Serializable

    • Class com.xinapse.util.PageSizeComboBox

      class PageSizeComboBox extends JComboBox<com.xinapse.util.PageSize> implements Serializable

    • Class com.xinapse.util.PDFFileChooser

      class PDFFileChooser extends JFileChooser implements Serializable

    • Class com.xinapse.util.PixelComparator

      class PixelComparator extends Object implements Serializable

      • Serialized Fields

        • nCols
          int nCols
        • pixelsPerSlice
          int pixelsPerSlice

    • Class com.xinapse.util.PreferencesPanel

      class PreferencesPanel extends JPanel implements Serializable

    • Class com.xinapse.util.RecentImagesMenu

      class RecentImagesMenu extends JMenu implements Serializable

      • Serialized Fields

        • canLoadImage
          com.xinapse.util.CanLoadImage canLoadImage
          If non-null, the CanLoadImage where an image will be loaded if selected from the Recent Images list.

    • Class com.xinapse.util.RecentImagesMenu.RecentImagesPopupMenu

      class RecentImagesPopupMenu extends JPopupMenu implements Serializable

    • Class com.xinapse.util.RoamingResponseDialog

      class RoamingResponseDialog extends com.xinapse.graph.GraphDialog implements Serializable

      • Serialized Fields

        • parentFrame
          MultiContrastAnalysisFrame parentFrame
        • plotModePanel
          com.xinapse.util.RoamingResponseDialog.MultiROIPlotMode.Panel plotModePanel

    • Class com.xinapse.util.RoamingResponseDialog.MultiROIPlotMode.Panel

      class Panel extends JPanel implements Serializable

    • Class com.xinapse.util.SVG.Button

      class Button extends JButton implements Serializable

    • Class com.xinapse.util.UndoButton

      class UndoButton extends com.xinapse.util.SVG.Button implements Serializable

    • Class com.xinapse.util.XinapseEditorPane

      class XinapseEditorPane extends JEditorPane implements Serializable

    • Class com.xinapse.util.XinapseFormattedTextField

      class XinapseFormattedTextField extends JFormattedTextField implements Serializable

      • Serialized Fields

        • actionListeners
          List<ActionListener> actionListeners
          A list of ActionListeners to be notified when an edit is committed.
        • preferredWidth
          int preferredWidth

    • Class com.xinapse.util.XMLFileChooser

      class XMLFileChooser extends JFileChooser implements Serializable