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

com.xinapse.util.SmallButton 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

com.xinapse.util.ScaledJCheckBox periodicCheckBox

A ScaledJCheckBox to specify that the time-series is perioic.

propagateButton

com.xinapse.util.SmallButton propagateButton

A button 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

com.xinapse.util.ScaledJCheckBox setShapeCoeffsCheckBox

A ScaledJCheckBox to set the number of shape coefficients manually.

setTimeCoeffsCheckBox

com.xinapse.util.ScaledJCheckBox setTimeCoeffsCheckBox

A ScaledJCheckBox to set the number of time coefficients manually.

Package com.xinapse.apps.cardiac

Class com.xinapse.apps.cardiac.CardiacAnalysis.SpecifierPane

class SpecifierPane extends JScrollPane implements Serializable

Serialized Fields

analysisPanel

JPanel analysisPanel

The JPanel that contains the Components needed for the analysis.

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

com.xinapse.util.SmallButton 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

com.xinapse.util.SmallButton 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

com.xinapse.util.SmallButton copyAllButton

A JButton to copy ROIs defined at one time-point to all time-points.

copyBackwardsButton

com.xinapse.util.SmallButton copyBackwardsButton

A JButton to copy ROIs defined at one time-point to all earlier time-points.

copyForwardsButton

com.xinapse.util.SmallButton copyForwardsButton

A JButton to copy ROIs defined at one time-point to all later time-points.

divideMyocardiumCheckBox

com.xinapse.util.ScaledJCheckBox divideMyocardiumCheckBox

A ScaledJCheckBox 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

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

A AIFSelectionMode.Panel for setting AIF selection mode.

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

A ContrastArrivalTimeUnits.Panel for setting the contrast agent arrival time units.

arterialHaematocritField

JTextField arterialHaematocritField

A JTextField to set the arterial haematocrit.

arterialHaematocritLabel

JLabel arterialHaematocritLabel

A JLabel for the arterial haematocrit.

arterialHaematocritPanel

JPanel arterialHaematocritPanel

A JPanel to which arterial haematocrit stuff is added.

arterialRelaxivityField

JTextField arterialRelaxivityField

A JTextField to set the arterial haematocrit.

arterialRelaxivityLabel

JLabel arterialRelaxivityLabel

A JLabel for the arterial relaxivity.

contrastArrivalTimeField

JTextField contrastArrivalTimeField

A JTextField to set the contrast agent arrival time.

ctButton

com.xinapse.util.ScaledJRadioButton ctButton

A ScaledJRadioButton to select the modality CT.

imageTypePanel

com.xinapse.apps.perfusion.ImageType.T1WeightedPanel imageTypePanel

A ImageType.T1WeightedPanel to set the exact type of T1-weighted image.

mriButton

com.xinapse.util.ScaledJRadioButton mriButton

A ScaledJRadioButton to select the modality MRI.

presetsMenu

com.xinapse.preset.PresetsMenu<com.xinapse.apps.perfusion.DynamicPreset> presetsMenu

The Presets menu.

relaxivityPanel

JPanel relaxivityPanel

A JPanel to set relaxivities.

scanTimeNumberLabel

JLabel scanTimeNumberLabel

A JLabel for the scan time/number.

scanTimeNumberUnitsLabel

JLabel scanTimeNumberUnitsLabel

A JLabel for the scan time/number units.

svdPanel

JPanel svdPanel

A JPanel to which SVD stuff is added.

svdThresholdSpinner

JSpinner svdThresholdSpinner

A JSpinner for setting the singular value decomposition threshold.

teField

JTextField teField

A JTextField to set the echo time.

tePanel

JPanel tePanel

A JPanel to which echo-time stuff is added.

tissueHaematocritField

JTextField tissueHaematocritField

A JTextField to set the tissue haematocrit.

tissueHaematocritPanel

JPanel tissueHaematocritPanel

A JPanel to which tissue haematocrit stuff is added.

tissueLagPanel

com.xinapse.apps.perfusion.TissueLagPanel tissueLagPanel

A TissueLagPanel for setting the tissue lag.

tissueRelaxivityField

JTextField tissueRelaxivityField

A JTextField to set the tissue relaxivity.

tissueRelaxivityLabel

JLabel tissueRelaxivityLabel

A JLabel for the tissue relaxivity.

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 Class com.xinapse.dicom.BadVMException

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

Exception Class 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 Class com.xinapse.dicom.DCMAbortException

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

Exception Class com.xinapse.dicom.DCMErrorException

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

Exception Class com.xinapse.dicom.DCMException

class DCMException extends Exception implements Serializable

Exception Class com.xinapse.dicom.DCMFatalException

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

Exception Class 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

com.xinapse.util.ScaledJCheckBox DULCheckBox

The ScaledJCheckBox to enable debugging of DICOM upper layer.

SRVCheckBox

com.xinapse.util.ScaledJCheckBox SRVCheckBox

The ScaledJCheckBox 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

A panel for setting Preferences related to Q/R.

saveFloatPreferencesPanel

com.xinapse.dicom.DicomPreferencesPanel.SaveFloatPreferencesPanel saveFloatPreferencesPanel

A panel for setting Preferences related to saving floating-point DICOM images.

savePreferencesPanel

com.xinapse.dicom.DicomPreferencesPanel.SavePreferencesPanel savePreferencesPanel

A panel for setting Preferences related to saving DICOM images.

Exception Class com.xinapse.dicom.InvalidDateException

class InvalidDateException extends Exception implements Serializable

Exception Class com.xinapse.dicom.InvalidInputException

class InvalidInputException extends Exception implements Serializable

Exception Class 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

Serialized Fields

bothButton

com.xinapse.util.ScaledJRadioButton bothButton

A ScaledJRadioButton for selecting the Both laterality.

leftButton

com.xinapse.util.ScaledJRadioButton leftButton

A ScaledJRadioButton for selecting the Left laterality.

rightButton

com.xinapse.util.ScaledJRadioButton rightButton

A ScaledJRadioButton for selecting the Right laterality.

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

Serialized Fields

femaleButton

com.xinapse.util.ScaledJRadioButton femaleButton

A ScaledJRadioButton for selecting the Female sex.

maleButton

com.xinapse.util.ScaledJRadioButton maleButton

A ScaledJRadioButton for selecting the Male sex.

otherButton

com.xinapse.util.ScaledJRadioButton otherButton

A ScaledJRadioButton for selecting the Other sex.

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

A JSpinner for setting the number of pre-steady-state images.

outputImageSelectionPanel

OutputImageSelectionPanel outputImageSelectionPanel

ImageSelectionPanel used to select the output images basename.

registerCheckBox

com.xinapse.util.ScaledJCheckBox registerCheckBox

A check box to turn on registration.

smoothingFilterCheckBox

com.xinapse.util.ScaledJCheckBox 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

allowAutoThreshold

boolean allowAutoThreshold

Whether automatic Otsu thresholding is allowed.

allowBrainFinder

boolean allowBrainFinder

Whether BrainFinder use is allowed.

autoThresholdCheckBox

com.xinapse.util.ScaledJCheckBox autoThresholdCheckBox

A ScaledJCheckBox to select using an Otsu threshold to mask the background.

bTPanel

com.xinapse.apps.brain.BTPanel bTPanel

A JPanel to set the threshold fraction for brain finding.

maskImageCheckBox

com.xinapse.util.ScaledJCheckBox maskImageCheckBox

A ScaledJCheckBox 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

com.xinapse.util.ScaledJCheckBox maskROIsCheckBox

A ScaledJCheckBox to turn on masking with ROIs.

maskTypeSelectionActionListeners

List<ActionListener> maskTypeSelectionActionListeners

A List of ActionListeners to be triggered when the mask type selection changes.

messageShower

MessageShower messageShower

The MessageShower for showing messages.

roiMaskSelectionPanel

ROIFileSelectionPanel roiMaskSelectionPanel

A JPanel for setting the ROI mask.

useBrainFinderCheckBox

com.xinapse.util.ScaledJCheckBox useBrainFinderCheckBox

A ScaledJCheckBox 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

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

Serialized Fields

parentFrame

AbstractDynamicFrame parentFrame

The AbstractDynamicFrame that is the parent of this.

preferencesNodeName

String preferencesNodeName

The Preferences node name.

tabbedPane

JTabbedPane tabbedPane

A JTabbedPane for selecting the model.

Class com.xinapse.dynamic.SliceOrderPanel

class SliceOrderPanel extends JPanel implements Serializable

Serialized Fields

actionListeners

List<ActionListener> actionListeners

A List of ActionListeners, triggered when the order is changed.

ascendingButton

com.xinapse.util.ScaledJRadioButton ascendingButton

A ScaledJRadioButton for selecting Ascending order.

descendingButton

com.xinapse.util.ScaledJRadioButton descendingButton

A ScaledJRadioButton for selecting Descending order.

doCorrectionCheckBox

com.xinapse.util.ScaledJCheckBox doCorrectionCheckBox

ScaledJCheckBox for selecting to do correction.

interleavedCheckBox

com.xinapse.util.ScaledJCheckBox interleavedCheckBox

A ScaledJRadioButton for selecting Interleaved order.

preferencesNodeName

String preferencesNodeName

The Preferences node name.

Package com.xinapse.filter

Class com.xinapse.filter.BoxBlurFilter.BoxBlurSpecifierPanel

class BoxBlurSpecifierPanel extends TwoDOrThreeDFilterSpecifierPanel implements Serializable

Serialized Fields

sizeXTextField

com.xinapse.util.XinapseFormattedTextField sizeXTextField

A XinapseFormattedTextField for setting the x-size.

sizeYTextField

com.xinapse.util.XinapseFormattedTextField sizeYTextField

A XinapseFormattedTextField for setting the y-size.

sizeZTextField

com.xinapse.util.XinapseFormattedTextField sizeZTextField

A XinapseFormattedTextField for setting the z-size.

throughSliceLabel

JLabel throughSliceLabel

A JLabel for the through-slice size.

zPixLabel

JLabel zPixLabel

A JLabel showing pixel units.

Class com.xinapse.filter.ColourImageFilter.ColourImageFilterSpecifierPanel

class ColourImageFilterSpecifierPanel extends SpatialFilter.SpecifierPanel implements Serializable

Serialized Fields

blueFormulaTextField

JTextField blueFormulaTextField

A JTextField for setting the Blue formula.

greenFormulaTextField

JTextField greenFormulaTextField

A JTextField for setting the Green formula.

preferencesNodeName

String preferencesNodeName

The Preferences node name.

redFormulaTextField

JTextField redFormulaTextField

A JTextField for setting the Red formula.

Class com.xinapse.filter.FilterSelection.Panel

class Panel extends JPanel implements Serializable

Serialized Fields

preferencesNodeName

String preferencesNodeName

The Preferences node name.

tabbedPane

JTabbedPane tabbedPane

The JTabbedPane for different filters.

Class com.xinapse.filter.GaussianBlurFilter.GaussianBlurSpecifierPanel

class GaussianBlurSpecifierPanel extends TwoDOrThreeDFilterSpecifierPanel implements Serializable

Serialized Fields

fwhmXTextField

com.xinapse.util.XinapseFormattedTextField fwhmXTextField

A XinapseFormattedTextField for setting the FWHM in the x-direction.

fwhmYTextField

com.xinapse.util.XinapseFormattedTextField fwhmYTextField

A XinapseFormattedTextField for setting the FWHM in the y-direction.

fwhmZTextField

com.xinapse.util.XinapseFormattedTextField fwhmZTextField

A XinapseFormattedTextField for setting the FWHM in the z-direction.

throughSliceLabel

JLabel throughSliceLabel

A JLabel for the through-slice FWHM.

zMMLabel

JLabel zMMLabel

A JLabel showing distance units.

Class com.xinapse.filter.KernelFilterSpecifierPanel

class KernelFilterSpecifierPanel extends TwoDOrThreeDFilterSpecifierPanel implements Serializable

Serialized Fields

kernelSizeComboBox

JComboBox<Integer> kernelSizeComboBox

The JComboBox for setting the filter kernel size.

kernelSizePanel

JPanel kernelSizePanel

A JPanel for setting the filterkernel size.

Class com.xinapse.filter.LaplacianFilter.LaplacianSpecifierPanel

class LaplacianSpecifierPanel extends KernelFilterSpecifierPanel implements Serializable

Class com.xinapse.filter.MedianFilter.MedianSpecifierPanel

class MedianSpecifierPanel extends KernelFilterSpecifierPanel implements Serializable

Class com.xinapse.filter.MorphologicalOperator.MorphologicalSpecifierPanel

class MorphologicalSpecifierPanel extends KernelFilterSpecifierPanel implements Serializable

Serialized Fields

opPanel

MorphologicalOperator.Op.Panel opPanel

The MorphologicalOperator.Op.Panel for selecting the morphological operator.

Class com.xinapse.filter.PatchSimilarityFilter.PatchSimilaritySpecifierPanel

class PatchSimilaritySpecifierPanel extends TwoDOrThreeDFilterSpecifierPanel implements Serializable

Serialized Fields

noisePercentCheckBox

com.xinapse.util.ScaledJCheckBox noisePercentCheckBox

A ScaledJCheckBox for selecting to specify a percentage noise level.

noisePercentLabel

com.xinapse.util.FixedSizeLabel noisePercentLabel

A FixedSizeLabel for showing the %age noise.

noisePercentSlider

JSlider noisePercentSlider

A JSlider for setting percentage noise level.

noiseSDTextField

com.xinapse.util.XinapseFormattedTextField noiseSDTextField

The XinapseFormattedTextField for specifying the noise standard deviation.

Class com.xinapse.filter.SharpenFilter.SharpenSpecifierPanel

class SharpenSpecifierPanel extends KernelFilterSpecifierPanel implements Serializable

Class com.xinapse.filter.SobelFilter.SobelSpecifierPanel

class SobelSpecifierPanel extends TwoDOrThreeDFilterSpecifierPanel implements Serializable

Serialized Fields

typePanel

com.xinapse.filter.SobelFilter.SobelType.Panel typePanel

A SobelFilter.SobelType.Panel for setting the Sobel filter type.

Class com.xinapse.filter.SpatialFilter.SpecifierPanel

class SpecifierPanel extends JPanel implements Serializable

Class com.xinapse.filter.TwoDOrThreeDFilterSpecifierPanel

class TwoDOrThreeDFilterSpecifierPanel extends SpatialFilter.SpecifierPanel implements Serializable

Serialized Fields

filterName

String filterName

The filter name.

filterSpecifierPanel

JPanel filterSpecifierPanel

A JPanel for the filter specifications.

preferencesNodeName

String preferencesNodeName

The Preferences node name.

threeDButton

com.xinapse.util.ScaledJRadioButton threeDButton

A ScaledJRadioButton for selecting a 3-D filter.

twoDButton

com.xinapse.util.ScaledJRadioButton twoDButton

A ScaledJRadioButton for selecting a 2-D filter.

Package com.xinapse.geom3d

Class com.xinapse.geom3d.CoordinateSystem.Panel

class Panel extends JPanel implements Serializable

Serialized Fields

buttons

com.xinapse.util.ScaledJRadioButton[] buttons

The ScaledJRadioButtons for selecting a CoordinateSystem.

Class com.xinapse.geom3d.ImageDisplayCanvas3D

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

Serialized Fields

ambientLight

float[] ambientLight

The ambient light source.

animator

com.jogamp.opengl.util.FPSAnimator animator

The FPSAnimator to run the animation loop.

backgroundColor

Color backgroundColor

The current background Color.

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 GeometryGenerators that will be displayed.

glu

com.jogamp.opengl.glu.GLU glu

GL Utilities.

isRecording

boolean isRecording

A flag set when a rotation movie recording is in progress.

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

The Cone on the x-axis.

xAxisLabel

com.xinapse.geom3d.LetterX xAxisLabel

The LetterX on the x-axis.

yAxisCone

com.xinapse.geom3d.Cone yAxisCone

The Cone on the y-axis.

yAxisLabel

com.xinapse.geom3d.LetterY yAxisLabel

The LetterY on the y-axis.

zAxisCone

com.xinapse.geom3d.Cone zAxisCone

The Cone on the z-axis.

zAxisLabel

com.xinapse.geom3d.LetterZ zAxisLabel

The LetterZ on the z-axis.

Class com.xinapse.geom3d.ImageDisplayFrame3D

class ImageDisplayFrame3D extends JFrame implements Serializable

Serialized Fields

animateDialog

com.xinapse.geom3d.AnimateDialog animateDialog

The dialog to animate rotation.

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.

exportRotationMovieDialog

com.xinapse.movie.ExportRotationMovieDialog exportRotationMovieDialog

The Dialog to make 360 degree rotation movies.

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.

logger

Logger logger

The Logger for error messages.

resetViewButton

com.xinapse.util.SmallButton resetViewButton

Button to reset to a standard view.

setViewDialog

com.xinapse.geom3d.SetViewDialog setViewDialog

The dialog to set a particular view on the scene.

statusBar

com.xinapse.util.StatusBar statusBar

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.

colorLabel

JLabel colorLabel

A JLabel for the colorButton.

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

The name of the currently loaded image.

cutOutCheckBox

com.xinapse.util.ScaledJCheckBox cutOutCheckBox

A ScaledJCheckBox 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

The name of the last loaded image.

opacitySetterThread

com.xinapse.geom3d.IsoSurfaceSelectionDialog.OpacitySetterThread opacitySetterThread

The one and only OpacitySetterThread that can be alive for this Dialog.

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.

perVertexColoursCheckBox

com.xinapse.util.ScaledJCheckBox perVertexColoursCheckBox

A ScaledJCheckBox to enable per-vertex colours for R,G,B images.

renderModePanel

com.xinapse.geom3d.RenderMode.Panel renderModePanel

For setting the rendering mode.

saveOBJMenuItem

JMenuItem saveOBJMenuItem

The JMenuItem for saving an iso-surface in OBJ format.

saveSTLMenuItem

JMenuItem saveSTLMenuItem

The JMenuItem for saving an iso-surface in STL format.

saveVRMLMenuItem

JMenuItem saveVRMLMenuItem

The JMenuItem for saving an iso-surface in VRML format.

shininessSpinner

JSpinner shininessSpinner

A JSpinner to set the surface shininess.

statusBar

com.xinapse.util.StatusBar statusBar

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

The ThreeDGeometrySelectionDialog that may pop up to select some 3-D geomertry.

Package com.xinapse.image

Class com.xinapse.image.ImageFileChooser

class ImageFileChooser extends JFileChooser implements Serializable

Class com.xinapse.image.ImageFileChooser.LoadChooser

class LoadChooser extends ImageFileChooser implements Serializable

Class com.xinapse.image.ImageFileChooser.SaveChooser

class SaveChooser extends ImageFileChooser implements Serializable

Class com.xinapse.image.ImageGrid

class ImageGrid extends JPanel implements Serializable

Serialized Fields

columnHeaders

JLabel[] columnHeaders

The Array of headers for the columns in the grid.

columnName

String columnName

The name given to a column.

columnSelectedList

List<Integer> columnSelectedList

A List of column numbers selected.

columnSelectors

com.xinapse.util.ScaledJCheckBox[] columnSelectors

The array of ScaledJCheckBoxes for the selection of columns in the grid.

columnsSelectable

boolean columnsSelectable

Whether columns can be selected using ScaledJCheckBoxes.

currentWorkingDirectory

File currentWorkingDirectory

The current working directory.

defaultNCols

int defaultNCols

The default number of columns.

defaultNRows

int defaultNRows

The default number of rows.

gridPanel

JPanel gridPanel

The JPanel that contains the grid.

imageClassToFilter

Class<? extends ReadableImage> imageClassToFilter

The image class to filter.

maximumColumnsSelectable

int maximumColumnsSelectable

The maximum number of columns selectable. A negative value indicates that all columns can be selected.

nColsLabel

JLabel nColsLabel

The label for the spinner that is used to set the number of columns.

nColsSpinner

JSpinner nColsSpinner

The JSpinner used to set the number of columns.

nColumnsChangeActionListeners

List<ActionListener> nColumnsChangeActionListeners

The List of ActionListeners that is notified when the number of columns in the ImageGrid changes.

nRowsChangeActionListeners

List<ActionListener> nRowsChangeActionListeners

The List of ActionListeners that is notified when the number of rows in the ImageGrid changes.

nRowsLabel

JLabel nRowsLabel

The label for the spinner that is used to set the number of rows.

nRowsSpinner

JSpinner nRowsSpinner

The JSpinner used to set the number of rows.

panelArray

InputImageSelectionPanel[][] panelArray

The array of InputImageSelectionPanels that form the matrix.

parentFrame

com.xinapse.util.ImageOrganiserFrame parentFrame

The parent ImageOrganiserFrame in which this ImageGrid is embedded.

rowHeaders

JLabel[] rowHeaders

The array of headers for the rows in the grid.

rowName

String rowName

If non-null, the name given to all rows.

rowSelectors

com.xinapse.util.ScaledJRadioButton[] rowSelectors

The array of ScaledJRadioButtons for the selection of rows in the grid.

rowsSelectable

boolean rowsSelectable

Whether rows can be selected using ScaledJRadioButtons.

Class com.xinapse.image.ImagePreview

class ImagePreview extends JComponent implements Serializable

Serialized Fields

file

File file

The file containing the image to be previewed.

previewIcon

PreviewIcon previewIcon

The PreviewIcon - null until generated.

previewIconGeneratorWorker

ImagePreview.PreviewIconGeneratorWorker previewIconGeneratorWorker

The PreviewIconGeneratorWorker that will generate the PreviewIcon.

Exception Class com.xinapse.image.ImageSaveException

class ImageSaveException extends Exception implements Serializable

Class com.xinapse.image.ImageSelectionGroupPanel

class ImageSelectionGroupPanel extends JPanel implements Serializable

Serialized Fields

addImageButton

com.xinapse.util.SmallButton addImageButton

The button to add another image to the set.

componentGenerator

ImageSelectionGroupPanel.ComponentGenerator componentGenerator

If non-null the ImageSelectionGroupPanel.ComponentGenerator for generating user components.

currentWorkingDirectory

File currentWorkingDirectory

The current working directory.

fileChangeCommitListeners

List<ChangeListener> fileChangeCommitListeners

A List of ChangeListener to be notified when a file is changed.

fileTextEditListeners

List<ChangeListener> fileTextEditListeners

A List of ChangeListener to be notified when the file name text is edited.

imageClassToFilter

Class<? extends ReadableImage> imageClassToFilter

If non-null, the ReadableImage class to filter.

maxNImages

int maxNImages

The maximum number of images in the group of images.

minNImages

int minNImages

The minimum number of images in the group of images.

panelList

List<ImageSelectionGroupMemberPanel> panelList

The List of ImageSelectionGroupMemberPanels that form the group.

parentFrame

com.xinapse.util.ImageOrganiserFrame parentFrame

The parent ImageOrganiserFrame in which this ImageSelectionGroupPanel is embedded.

weight

double weight

The weight applied to the ImageSelectionGroupMemberPanel.

Class com.xinapse.image.ImageSelectionPanel

class ImageSelectionPanel extends JPanel implements Serializable

Serialized Fields

currentWorkingDirectory

File currentWorkingDirectory

The current working directory.

enableFileTextChangeListener

boolean enableFileTextChangeListener

A flag to cause generation of events to FileTextChangeListeners. Disabled during programmatic changes to the file text.

fileChangeCommitListeners

List<ChangeListener> fileChangeCommitListeners

A List of ChangeListeners that will be notified if an image file change is committed (by the user pressing the return key).

fileLabel

JLabel fileLabel

The JLabel to display along side the image file.

fileSelectionPanel

JPanel fileSelectionPanel

A JPanel displayed to allow an image file to be selected.

fileTextEditListeners

List<ChangeListener> fileTextEditListeners

A List of ChangeListeners that will be notified if the text is edited without being committed.

fileTextField

JTextField fileTextField

The JTextField to set the image file.

folderLabel

JLabel folderLabel

The JLabel to display along side the image folder, or null if the image folder isn't shown separately.

folderTextField

JTextField folderTextField

The JTextField to set the image folder, or null if the image folder isn't shown separately.

imageChooser

ImageFileChooser imageChooser

The ImageFileChooser that can be popped up to select a new image.

imageClassToFilter

Class<? extends ReadableImage> imageClassToFilter

The class of image that will intially be filtered when the user first selects the image.

initialSize

Dimension initialSize

The size used to get the preferredSize() once the components in this ImageSelectionPanel have been added to it.

messageShower

MessageShower messageShower

The Component that can show messages generated by this ImageSelectionPanel.

setImageButton

com.xinapse.util.SVG.Button setImageButton

The SVG.Button to set the image file.

Class com.xinapse.image.InputImageSelectionPanel

class InputImageSelectionPanel extends ImageSelectionPanel implements Serializable

Serialized Fields

importedImage

ReadableImage importedImage

If non-null, the ReadableImage that has been set by a drag-and-drop action.

importedImageDetailsPanel

ScanDetailsPanel importedImageDetailsPanel

A JPanel shown when an ImportedImage has been dragged-and-dropped.

loadInProgress

AtomicBoolean loadInProgress

A flag set when an image load is in progress.

oneLine

boolean oneLine

A flag set if the file and folder text fields are to be condensed onto one line.

Class com.xinapse.image.IntensityPresetsMenu

class IntensityPresetsMenu extends JMenu implements Serializable

Serialized Fields

changeableContrast

com.xinapse.util.ChangeableContrast changeableContrast

The ChangeableContrast whose contrast is set when an IntensityPreset is selected.

noPresetMenuItem

JRadioButtonMenuItem noPresetMenuItem

The item to select no intensity preset.

presetsButtonGroup

ButtonGroup presetsButtonGroup

The ButtonGroup for all JRadioButtonMenuItem that select IntensityPresets.

separator

JSeparator separator

A JSeparator used to identify the end of the list of IntensityPresets.

Exception Class com.xinapse.image.InvalidColourMappingException

class InvalidColourMappingException extends Exception implements Serializable

Exception Class com.xinapse.image.InvalidImageException

class InvalidImageException extends Exception implements Serializable

Class com.xinapse.image.MostLikePlane.ComboBox

class ComboBox extends JComboBox<String> implements Serializable

Class com.xinapse.image.MultipleImageSelectionPanel

class MultipleImageSelectionPanel extends JPanel implements Serializable

Serialized Fields

addImagesButton

com.xinapse.util.SmallButton addImagesButton

A button to add images to the current list of images.

changeListeners

List<ChangeListener> changeListeners

A List of ChangeListeners that will be notified if the image files change in any way.

currentWorkingDirectory

File currentWorkingDirectory

The current working directory.

downButton

com.xinapse.util.SmallButton downButton

A button to move selected images down the list of images.

imageChooser

ImageFileChooser.LoadChooser imageChooser

The ImageFileChooser.LoadChooser that is used to select the image(s).

imageClassToFilter

Class<? extends WritableImage> imageClassToFilter

The current class of images that is being filtered.

imagesList

JList<SelectedImagePanel> imagesList

The JList that displays the list of images.

initialSize

Dimension initialSize

The size used to get the preferredSize() once the components in this MultipleImageSelectionPanel have been added to it.

listModel

DefaultListModel<SelectedImagePanel> listModel

The DefaultListModel that contains the current list of images.

listTitleLabel

JLabel listTitleLabel

The title that is displayed above the list of images.

loadInProgress

AtomicBoolean loadInProgress

A flag set when an image load is in progress.

parentWindow

Window parentWindow

The Window in which this MultipleImageSelectionPanel is embedded.

removeAllButton

com.xinapse.util.SmallButton removeAllButton

A button to remove all images from the list of images.

removeSelectedButton

com.xinapse.util.SmallButton removeSelectedButton

A button to remove selected images from the list of images.

selectImagesButton

com.xinapse.util.SmallButton selectImagesButton

A button to select a new list of images.

upButton

com.xinapse.util.SmallButton upButton

A button to move selected images up the list of images.

Class com.xinapse.image.OutputImageSelectionPanel

class OutputImageSelectionPanel extends ImageSelectionPanel implements Serializable

Exception Class com.xinapse.image.ParameterNotSetException

class ParameterNotSetException extends Exception implements Serializable

Class com.xinapse.image.RenderingInterpolationType.ComboBox

class ComboBox extends JComboBox<String> implements Serializable

Class com.xinapse.image.RenderingInterpolationType.RenderingInterpolationTypeButton

class RenderingInterpolationTypeButton extends com.xinapse.util.NStateButton<RenderingInterpolationType> implements Serializable

Serialized Fields

frame

com.xinapse.apps.jim.ImageDisplayFrame frame

The ImageDisplayFrame in which this RenderingInterpolationTypeButton is embedded.

Class com.xinapse.image.RotationAngle.RotationPanel

class RotationPanel extends JPanel implements Serializable

Serialized Fields

minus90Button

com.xinapse.util.ScaledJRadioButton minus90Button

A ScaledJRadioButton for selecting a -90 rotation button.

minus90Label

JLabel minus90Label

A JLabel for the -90 rotation button.

plus180Button

com.xinapse.util.ScaledJRadioButton plus180Button

A ScaledJRadioButton for selecting a +180 rotation button.

plus180Label

JLabel plus180Label

A JLabel for the +180 rotation button.

plus90Button

com.xinapse.util.ScaledJRadioButton plus90Button

A ScaledJRadioButton for selecting a +90 rotation button.

plus90Label

JLabel plus90Label

A JLabel for the +90 rotation button.

preferencesNodeName

String preferencesNodeName

The Preferences node name.

Class com.xinapse.image.ScanDetailsPanel

class ScanDetailsPanel extends JPanel implements Serializable

Serialized Fields

descriptionLabel

JLabel descriptionLabel

The JLabel that shows the image description.

idLabel

JLabel idLabel

The JLabel that shows the patient ID.

nameLabel

JLabel nameLabel

The JLabel that shows the patient name.

nSlicesLabel

JLabel nSlicesLabel

The JLabel that shows the number of slices in the image.

preferredSize

Dimension preferredSize

The preferred size of this ScanDetailsPanel.

seriesLabel

JLabel seriesLabel

The JLabel that shows the image series.

Class com.xinapse.image.SelectedImagePanel

class SelectedImagePanel extends JPanel implements Serializable

Serialized Fields

fileLabel

JLabel fileLabel

If non-null, the JLabel showing the selected image file.

importedImage

ReadableImage importedImage

If non-null, the ReadableImage that has been set by a drag-and-drop action.

importedImageDetailsPanel

ScanDetailsPanel importedImageDetailsPanel

A JPanel shown when an ImportedImage has been dragged-and-dropped.

initialSize

Dimension initialSize

The size used to get the preferredSize() once the components in this SelectedImagePanel have been added to it.

Class com.xinapse.image.SingleOrMultipleInputImageSelectionPanel

class SingleOrMultipleInputImageSelectionPanel extends JPanel implements Serializable

Serialized Fields

messageShower

MessageShower messageShower

The MessageShower that shows messages emanating from this SingleOrMultipleInputImageSelectionPanel.

multipleInputButton

com.xinapse.util.ScaledJRadioButton multipleInputButton

A ScaledJRadioButton for selecting multiple images for input.

multipleInputImagesSelectionPanel

MultipleImageSelectionPanel multipleInputImagesSelectionPanel

MultipleImageSelectionPanel if multiple input images are used.

singleInputButton

com.xinapse.util.ScaledJRadioButton singleInputButton

A ScaledJRadioButton for selecting single image for input.

singleInputFillerPanel

JPanel singleInputFillerPanel

A filler JPanel visible when the singleInputImageSelectionPanel is visible.

singleInputImageSelectionPanel

InputImageSelectionPanel singleInputImageSelectionPanel

ImageSelectionPanel if a single input image is used.

Package com.xinapse.image.template

Class com.xinapse.image.template.WeightingType.Panel

class Panel extends JPanel implements Serializable

Serialized Fields

buttons

com.xinapse.util.ScaledJRadioButton[] buttons

A ScaledJRadioButton used to select Isotropic tensor fitting.

Package com.xinapse.io

Exception Class com.xinapse.io.UnsetFileException

class UnsetFileException extends Exception implements Serializable

Exception Class com.xinapse.io.UnsetImageException

class UnsetImageException extends Exception implements Serializable

Package com.xinapse.multisliceimage.analyze

Exception Class com.xinapse.multisliceimage.analyze.ANZException

class ANZException extends InvalidImageException implements Serializable

Package com.xinapse.multisliceimage.roi

Class com.xinapse.multisliceimage.roi.ANegativeHandle

class ANegativeHandle extends AxisHandle implements Serializable

Class com.xinapse.multisliceimage.roi.APositiveHandle

class APositiveHandle extends AxisHandle implements Serializable

Class com.xinapse.multisliceimage.roi.AxisHandle

class AxisHandle extends Handle implements Serializable

Class com.xinapse.multisliceimage.roi.BNegativeHandle

class BNegativeHandle extends AxisHandle implements Serializable

Class com.xinapse.multisliceimage.roi.BPositiveHandle

class BPositiveHandle extends AxisHandle implements Serializable

Class com.xinapse.multisliceimage.roi.CentreHandle

class CentreHandle extends Handle implements Serializable

Class com.xinapse.multisliceimage.roi.CombineMode.Panel

class Panel extends JPanel implements Serializable

Serialized Fields

defaultButton

com.xinapse.util.ScaledJRadioButton defaultButton

A ScaledJRadioButton to set the default.

modeButtons

List<com.xinapse.util.ScaledJRadioButton> modeButtons

A List of ScaledJRadioButton to select the mode.

Class com.xinapse.multisliceimage.roi.ContourMode.ComboBox

class ComboBox extends JComboBox<ContourMode> implements Serializable

Class com.xinapse.multisliceimage.roi.CornerHandle

class CornerHandle extends Handle implements Serializable

Exception Class com.xinapse.multisliceimage.roi.DuplicateROIException

class DuplicateROIException extends Exception implements Serializable

Class com.xinapse.multisliceimage.roi.EastHandle

class EastHandle extends EdgeHandle implements Serializable

Class com.xinapse.multisliceimage.roi.EdgeHandle

class EdgeHandle extends Handle implements Serializable

Class com.xinapse.multisliceimage.roi.EllipticalROICreateDialog

class EllipticalROICreateDialog extends ROICreateDialog implements Serializable

Serialized Fields

axis1Field

JTextField axis1Field

A JTextField to set the ellipse first semi-axis length.

axis2Field

JTextField axis2Field

A JTextField to set the ellipse second semi-axis length.

centreXField

JTextField centreXField

A JTextField to set the x-position of the centre of the ellipse.

centreYField

JTextField centreYField

A JTextField to set the y-position of the centre of the ellipse.

thetaField

JTextField thetaField

A JTextField to set the ellipse axis angle.

Class com.xinapse.multisliceimage.roi.EndHandle

class EndHandle extends Handle implements Serializable

Class com.xinapse.multisliceimage.roi.Handle

class Handle extends Point implements Serializable

Serialized Fields

size

int size

The size of the handle in screen pixels.

Class com.xinapse.multisliceimage.roi.HistoryDialog

class HistoryDialog extends JDialog implements Serializable

Serialized Fields

historyTable

JTable historyTable

The JTable of history information.

Class com.xinapse.multisliceimage.roi.InsertionPointHandle

class InsertionPointHandle extends Handle implements Serializable

Serialized Fields

centreOfRotation

Point2D centreOfRotation

The centre of rotation for this InsertionPointHandle.

slice

int slice

The slice number on which this InsertionPointHandle is placed.

Class com.xinapse.multisliceimage.roi.LineROICreateDialog

class LineROICreateDialog extends ROICreateDialog implements Serializable

Serialized Fields

x1Field

JTextField x1Field

A JTextField to set the x-position of the first end of the line.

x2Field

JTextField x2Field

A JTextField to set the x-position of the second end of the line.

y1Field

JTextField y1Field

A JTextField to set the y-position of the first end of the line.

y2Field

JTextField y2Field

A JTextField to set the y-position of the second end of the line.

Class com.xinapse.multisliceimage.roi.MarkerCreateDialog

class MarkerCreateDialog extends ROICreateDialog implements Serializable

Serialized Fields

xPositionField

JTextField xPositionField

A JTextField to set the Marker x-position.

yPositionField

JTextField yPositionField

A JTextField to set the Marker y-position.

Class com.xinapse.multisliceimage.roi.MaskMode.Panel

class Panel extends JPanel implements Serializable

Serialized Fields

defaultButton

com.xinapse.util.ScaledJRadioButton defaultButton

A ScaledJRadioButton to set the default.

modeButtons

List<com.xinapse.util.ScaledJRadioButton> modeButtons

A List of ScaledJRadioButtons to select the mode.

Class com.xinapse.multisliceimage.roi.NorthEastHandle

class NorthEastHandle extends CornerHandle implements Serializable

Class com.xinapse.multisliceimage.roi.NorthHandle

class NorthHandle extends EdgeHandle implements Serializable

Class com.xinapse.multisliceimage.roi.NorthWestHandle

class NorthWestHandle extends CornerHandle implements Serializable

Class com.xinapse.multisliceimage.roi.PenSizePanel

class PenSizePanel extends JPanel implements Serializable

Serialized Fields

penSizeSpinner

JSpinner penSizeSpinner

The JSpinner used to retain the pen size.

titleLabel

JLabel titleLabel

The label on the spinner.

Class com.xinapse.multisliceimage.roi.RectangularROICreateDialog

class RectangularROICreateDialog extends ROICreateDialog implements Serializable

Serialized Fields

heightField

JTextField heightField

A JTextField to set the height of the ROI.

widthField

JTextField widthField

A JTextField to set the width of the ROI.

xField

JTextField xField

A JTextField to set the x-position of the ROI.

yField

JTextField yField

A JTextField to set the y-position of the ROI.

Class com.xinapse.multisliceimage.roi.ROICoordinatesFileChooser

class ROICoordinatesFileChooser extends ROIStatsFileChooser implements Serializable

Class com.xinapse.multisliceimage.roi.ROICreateDialog

class ROICreateDialog extends JDialog implements Serializable

Serialized Fields

addButton

JButton addButton

A button to add the ROI to the image.

doneButton

JButton doneButton

A button to close the dialog.

listener

CanAddROIToFrame listener

The CanAddROIToFrame that listens for ROIs being added using this dialog.

specificationPanel

JPanel specificationPanel

The JPanel that is used to specify the different types of ROI.

Exception Class com.xinapse.multisliceimage.roi.ROIException

class ROIException extends Exception implements Serializable

Class com.xinapse.multisliceimage.roi.ROIFileChooser

class ROIFileChooser extends JFileChooser implements Serializable

Class com.xinapse.multisliceimage.roi.ROIFileSelectionPanel

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

Class com.xinapse.multisliceimage.roi.ROIIntensitiesFileChooser

class ROIIntensitiesFileChooser extends ROIStatsFileChooser implements Serializable

Class com.xinapse.multisliceimage.roi.ROIPreferencesDialog

class ROIPreferencesDialog extends JDialog implements Serializable

Serialized Fields

alwaysOnTopCheckBox

com.xinapse.util.ScaledJCheckBox alwaysOnTopCheckBox

A ScaledJCheckBox for selecting whether the ROI toolkit should always be on top of other windows.

deletedColorButton

com.xinapse.util.ColorSelectionButton deletedColorButton

A ColorSelectionButton for selecting the delected ROI color.

displayer

com.xinapse.displayer.ImageDisplayer displayer

The ImageDisplayer where ROIs will be redisplayed with new colours if the settings change.

erodeDilatePercentSpinner

JSpinner erodeDilatePercentSpinner

A JSpinner for the erode/dilate percentage.

handleBorderColorButton

com.xinapse.util.ColorSelectionButton handleBorderColorButton

A ColorSelectionButton for selecting the ROI handle border color.

handleColorButton

com.xinapse.util.ColorSelectionButton handleColorButton

A ColorSelectionButton for selecting the ROI handle color.

maskInsideButton

com.xinapse.util.ScaledJRadioButton maskInsideButton

A ScaledJRadioButton for setting masking inside on startup.

maskOutsideButton

com.xinapse.util.ScaledJRadioButton maskOutsideButton

A ScaledJRadioButton for setting masking outside on startup.

mergeContoursCheckBox

com.xinapse.util.ScaledJCheckBox mergeContoursCheckBox

A ScaledJCheckBox for selecting whether overlapping contours should be merged after 3-D propagationROIs.

minimiseCheckBox

com.xinapse.util.ScaledJCheckBox minimiseCheckBox

A ScaledJCheckBox for selecting whether the ROI toolkit should be minimised on startup.

nUndosSpinner

JSpinner nUndosSpinner

A JSpinner for the number of undos retained.

penSizePanel

PenSizePanel penSizePanel

The panel for setting the pen size.

saveFolderFollowsImageCheckBox

com.xinapse.util.ScaledJCheckBox saveFolderFollowsImageCheckBox

A ScaledJCheckBox for setting whether the folder for saving ROIs follows the image.

selectedColorButton

com.xinapse.util.ColorSelectionButton selectedColorButton

A ColorSelectionButton for selecting the ROI selected color.

showExtendedStatsCheckBox

com.xinapse.util.ScaledJCheckBox showExtendedStatsCheckBox

A ScaledJCheckBox for selecting whether the ROI toolkit should show extended ROI stats on startup.

showStatisticsCheckBox

com.xinapse.util.ScaledJCheckBox showStatisticsCheckBox

A ScaledJCheckBox for selecting whether the ROI toolkit should show ROI statistics on startup.

snapCentreCheckBox

com.xinapse.util.ScaledJCheckBox snapCentreCheckBox

A ScaledJCheckBox for selecting whether ROIs should snap to centre rather than corner of pixels.

spacingPanel

VertexHandle.SpacingPanel spacingPanel

The panel for setting vertex handle spacing.

textColorButton

com.xinapse.util.ColorSelectionButton textColorButton

A ColorSelectionButton for selecting the ROI text color.

textSizeSpinner

JSpinner textSizeSpinner

A JSpinner for the annotation text font size.

unselectedColorButton

com.xinapse.util.ColorSelectionButton unselectedColorButton

A ColorSelectionButton for selecting the ROI unselected color.

userColorButtons

com.xinapse.util.ColorSelectionButton[] userColorButtons

An array of ColorSelectionButtons, used for selecting the user colors.

Class com.xinapse.multisliceimage.roi.ROIStatsFileChooser

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

Class com.xinapse.multisliceimage.roi.SouthEastHandle

class SouthEastHandle extends CornerHandle implements Serializable

Class com.xinapse.multisliceimage.roi.SouthHandle

class SouthHandle extends EdgeHandle implements Serializable

Class com.xinapse.multisliceimage.roi.SouthWestHandle

class SouthWestHandle extends CornerHandle implements Serializable

Class com.xinapse.multisliceimage.roi.StatsComparator

class StatsComparator extends Object implements Serializable

Serialized Fields

complexMode

ComplexMode complexMode

The ComplexMode for Complex images.

dataType

PixelDataType dataType

The pixel data type.

nCols

int nCols

The number of image columns.

nRows

int nRows

The number of image rows.

pix

Object pix

The pixel values.

pixelXSize

float pixelXSize

The pixel width.

pixelYSize

float pixelYSize

The pixel height.

statsType

StatsType statsType

The StatsType.

Class com.xinapse.multisliceimage.roi.TextCreateDialog

class TextCreateDialog extends ROICreateDialog implements Serializable

Serialized Fields

annotationField

JTextField annotationField

A JTextField for setting the text annotation.

xPositionField

JTextField xPositionField

A JTextField for setting the x-position.

yPositionField

JTextField yPositionField

A JTextField for setting the y-position.

Class com.xinapse.multisliceimage.roi.VertexHandle

class VertexHandle extends Handle implements Serializable

Serialized Fields

visible

boolean visible

Whether this handle should be drawn on screen.

Class com.xinapse.multisliceimage.roi.VertexHandle.SpacingPanel

class SpacingPanel extends JPanel implements Serializable

Serialized Fields

comboBox

JComboBox<VertexHandle.Spacing> comboBox

The JComboBox for selecting the spacing.

Class com.xinapse.multisliceimage.roi.VOI

class VOI extends LinkedList<ROI> implements Serializable

Class com.xinapse.multisliceimage.roi.WestHandle

class WestHandle extends EdgeHandle implements Serializable

Package com.xinapse.multisliceimage.unc

Exception Class com.xinapse.multisliceimage.unc.UNCException

class UNCException extends InvalidImageException implements Serializable

Package com.xinapse.numerical

Class com.xinapse.numerical.AbstractInterpolator

class AbstractInterpolator extends Object implements Serializable

serialVersionUID:

42L

Serialized Fields

nPoints

int nPoints

Number of tabulated points.

x

double[] x

Tabulated abscissa values.

xMax

double xMax

Maximum x value.

xMin

double xMin

Minimum x value.

y

double[] y

Tabulated function values.

Exception Class com.xinapse.numerical.ConvergenceException

class ConvergenceException extends NumericalException implements Serializable

Class com.xinapse.numerical.CubicSplineInterpolator

class CubicSplineInterpolator extends com.xinapse.numerical.AbstractInterpolator implements Serializable

serialVersionUID:

42L

Serialized Fields

d2ydx2

double[] d2ydx2

Second derivatives of y at the knots. Only calculated when needed.

dydx1

Double dydx1

First derivative at point one. Leaving as null gives a natural spline.

dydxn

Double dydxn

First derivative at point n. Leaving as null gives a natural spline.

Class com.xinapse.numerical.LinearInterpolator

class LinearInterpolator extends com.xinapse.numerical.AbstractInterpolator implements Serializable

Class com.xinapse.numerical.LoessInterpolator

class LoessInterpolator extends CubicSplineInterpolator implements Serializable

Exception Class com.xinapse.numerical.NumericalError

class NumericalError extends IllegalArgumentException implements Serializable

Exception Class com.xinapse.numerical.NumericalException

class NumericalException extends Exception implements Serializable

Class com.xinapse.numerical.SavitzkyGolayInterpolator

class SavitzkyGolayInterpolator extends CubicSplineInterpolator implements Serializable

serialVersionUID:

42L

Package com.xinapse.platform

Class com.xinapse.platform.LookAndFeelPanel

class LookAndFeelPanel extends JPanel implements Serializable

Serialized Fields

buttons

com.xinapse.util.ScaledJRadioButton[] buttons

An array of ScaledJRadioButton for selecting the Look & Feel.

Package com.xinapse.util

Class com.xinapse.util.ActionButton

class ActionButton extends com.xinapse.util.SmallButton implements Serializable

Class com.xinapse.util.AlphaPanel

class AlphaPanel extends JPanel implements Serializable

Serialized Fields

alphaChangeListeners

List<com.xinapse.util.AlphaPanel.AlphaChangeListener> alphaChangeListeners

A List of AlphaChangeListeners that listen for changes in alpha.

currentText

JTextField currentText

The JTextField showing the current setting of the slider.

slider

JSlider slider

The slider.

Exception Class 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

The cached cardinality. Set to -1 if the cardinality needs to be recalculated.

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

Serialized Fields

pane

JTabbedPane pane

The JTabbedPane on which this ButtonTabComponent is displayed.

Exception Class com.xinapse.util.CancelledException

class CancelledException extends Exception implements Serializable

Serialized Fields

userObject

List<ROI> userObject

A List that may contain ROIs generated before cancellation.

Class com.xinapse.util.ColorSelectionButton

class ColorSelectionButton extends com.xinapse.util.SmallButton implements Serializable

Serialized Fields

colorChangeListeners

List<com.xinapse.util.ColorSelectionButton.ColorChangeListener> colorChangeListeners

The current registered ColorSelectionButton.ColorChangeListeners.

colorIcon

com.xinapse.util.ColorSelectionButton.ColorIcon colorIcon

The ColorSelectionButton.ColorIcon that shows the current selected Color.

Class com.xinapse.util.ColourKey

class ColourKey extends LinkedList<com.xinapse.util.ColourKey.ColourKeyItem> implements Serializable

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 JCheckBoxMenuItem 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

com.xinapse.util.ScaledJRadioButton contiguousContrastsRadioButton

A ScaledJRadioButton to select contiguous contrasts.

contiguousSlicesRadioButton

com.xinapse.util.ScaledJRadioButton contiguousSlicesRadioButton

A ScaledJRadioButton to select contiguous slice positions.

parentPrefsSettable

PreferencesSettable parentPrefsSettable

The PreferencesSettable in which this ContiguousPanel is embedded.

Class com.xinapse.util.ContrastAdjusterPanel

class ContrastAdjusterPanel extends JPanel implements Serializable

Serialized Fields

autoContrastButton

com.xinapse.util.SmallButton 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 com.xinapse.util.ActionButton implements Serializable

Class com.xinapse.util.FileChooser

class FileChooser extends JFileChooser implements Serializable

Serialized Fields

extensions

String[] extensions

The file name extensions that the FileChooser will accept.

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

Serialized Fields

changeListeners

List<ChangeListener> changeListeners

The current registered ChangeListeners.

extensions

String[] extensions

The file extensions that are accepted.

fileChooser

JFileChooser fileChooser

The JFileChooser that will pop up for selecting a new File.

fileFilter

FileFilter fileFilter

A FileFilter for filtering the type of file.

fileNameField

JTextField fileNameField

A JTextField showing the selected file name.

fileSelectButton

com.xinapse.util.SmallButton fileSelectButton

A SmallButton for selecting a new File.

fileTypeDescription

String fileTypeDescription

A human-friendly description of the file type.

icon

Icon icon

An Icon representing the file type.

load

boolean load

Whether the file is for loading, or saving data.

messageShower

MessageShower messageShower

The MessageShower for showing messages.

useDescription

String useDescription

A description of the use of the type of files.

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

The current registered ChangeListeners.

fileChooser

com.xinapse.util.FileChooser fileChooser

The FileChooser that will pop up for selecting a folder.

folderSelectButton

com.xinapse.util.SmallButton folderSelectButton

A SmallButton for selecting a folder.

folderTextField

JTextField folderTextField

A JTextField for showing the current selected folder.

messageShower

MessageShower messageShower

The MessageShower for showing messages.

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<ExitStatus, Integer>> 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

com.xinapse.util.SmallButton doItButton

A button to do the action required of this JFrame.

doneButton

com.xinapse.util.DoneButton 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

com.xinapse.util.ScaledJRadioButton loadResultButton

The JRadioButton for loading the result into Jim.

logger

Logger logger

The Logger for error and warning messages.

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.

saveToDiskButton

com.xinapse.util.ScaledJRadioButton saveToDiskButton

The JRadioButton for saving the result to disk.

scrollableContentsPane

JScrollPane scrollableContentsPane

The JScrollPane that wil contain the scrollable contents.

statusBar

com.xinapse.util.StatusBar statusBar

A status text area - shows messages to the user via the ImageOrganiserFrame.showStatus(String) method.

Class com.xinapse.util.InfoList

class InfoList extends LinkedHashMap<String,String> implements Serializable

Exception Class 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

com.xinapse.util.ScaledJRadioButton[] intensityRelationButtons

The buttons for selecting an IntensityRelation.

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

The current 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

Whether the slider in a minimised configuration.

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

The title for intensity slider.

Exception Class com.xinapse.util.InvalidArgumentException

class InvalidArgumentException extends Exception implements Serializable

Exception Class 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

The current List of ChangeListeners that want to hear about chnages in configuration.

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

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

The ChangeListeners looking out for changes in the configuration.

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

A description of the type of contrast in the images.

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

The MessageShower that shows messages.

multipleImageSelectionPanel

MultipleImageSelectionPanel multipleImageSelectionPanel

MultipleImageSelectionPanel if multiple input images are used - one for each contrast or slice position.

multipleInputOnePerContrastButton

com.xinapse.util.ScaledJRadioButton multipleInputOnePerContrastButton

ScaledJRadioButton for selecting multiple input image with one image per contrast configuration.

multipleInputOnePerSliceButton

com.xinapse.util.ScaledJRadioButton multipleInputOnePerSliceButton

ScaledJRadioButton for selecting multiple input image configuration.

nContrastsSpinner

JSpinner nContrastsSpinner

The JSpinner to set the number of image contrasts in a single input image.

singleInputButton

com.xinapse.util.ScaledJRadioButton singleInputButton

The ScaledJRadioButton for selecting single input image configuration.

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

com.xinapse.util.SmallButton addFilesButton

A button to add files to the current list of files.

currentWorkingDirectory

File currentWorkingDirectory

The current working directory.

downButton

com.xinapse.util.SmallButton 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

com.xinapse.util.SmallButton removeAllButton

A button to remove all files from the list of files.

removeSelectedButton

com.xinapse.util.SmallButton removeSelectedButton

A button to remove selected files from the list of files.

selectFilesButton

com.xinapse.util.SmallButton selectFilesButton

A button to select a new list of files.

upButton

com.xinapse.util.SmallButton 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

com.xinapse.util.SmallButton 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

com.xinapse.util.SmallButton removeAllButton

A button to remove all folders from the list of folders.

removeSelectedButton

com.xinapse.util.SmallButton removeSelectedButton

A button to remove selected folders from the list of folders.

selectFoldersButton

com.xinapse.util.SmallButton selectFoldersButton

A button to select a new list of folders.

Class com.xinapse.util.NStateButton

class NStateButton extends com.xinapse.util.SmallButton implements Serializable

Serialized Fields

stateIndex

int stateIndex

The index to the current state.

states

T extends Icon[] states

The 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

The number of columns in the image.

pixelsPerSlice

int pixelsPerSlice

The number of pixels in one slice of the image.

Class com.xinapse.util.PreferencesPanel

class PreferencesPanel extends JPanel implements Serializable

Serialized Fields

preferencesNodeName

String preferencesNodeName

The preferences node name.

prefsSettable

PreferencesSettable prefsSettable

The PreferencesSettable to which the preferences apply.

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

The parent of this RoamingResponseDialog.

plotModePanel

com.xinapse.util.RoamingResponseDialog.MultiROIPlotMode.Panel plotModePanel

The MultiROIPlotMode.Panel for setting the multi-roi-plot mode.

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

class Panel extends JPanel implements Serializable

Serialized Fields

buttons

com.xinapse.util.ScaledJRadioButton[] buttons

The array of ScaledJRadioButtons for setting the MultiROIPlotMode.

registeredListeners

List<ActionListener> registeredListeners

The registered listeners for changes in the MultiROIPlotMode.

Class com.xinapse.util.ScaledJCheckBox

class ScaledJCheckBox extends JCheckBox implements Serializable

Class com.xinapse.util.ScaledJRadioButton

class ScaledJRadioButton extends JRadioButton implements Serializable

Class com.xinapse.util.SmallButton

class SmallButton extends JButton implements Serializable

Class com.xinapse.util.StatusBar

class StatusBar extends JPanel implements Serializable

Serialized Fields

prefix

String prefix

If non-null, the prefix applied to any message.

textField

JTextField textField

The JTextField that shows the current message.

Class com.xinapse.util.SVG.Button

class Button extends com.xinapse.util.SmallButton 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

The preferred width of the field. -1 indicated unset.

Class com.xinapse.util.XinOptions

class XinOptions extends org.apache.commons.cli.Options implements Serializable

Class com.xinapse.util.XMLFileChooser

class XMLFileChooser extends JFileChooser implements Serializable