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AbstractComplexKernelFilter - Class in com.xinapse.filter
This class provides a skeletal implementation of the SpatialFilter interface, to minimize the effort required to implement this interface.
AbstractDynamicContrastModel - Class in com.xinapse.apps.perfusion
A Model that can be fitted to dynamic data where contrast agent is injected, and the tissue response to an input function is measured.
AbstractDynamicContrastModel(String, String, String[], String[]) - Constructor for class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
Constructor used by sub-classes.
AbstractDynamicContrastResult - Class in com.xinapse.apps.perfusion
Superclass for the results of dynamic contrast analysis.
AbstractDynamicContrastResult(DynamicModel, float[], float, float[]) - Constructor for class com.xinapse.apps.perfusion.AbstractDynamicContrastResult
Used by sub-class constructors.
AbstractDynamicFrame - Class in com.xinapse.dynamic
AbstractDynamicFrame - a GUI for performing general image dynamic analysis.
AbstractDynamicFrame(String, List<Image>, String) - Constructor for class com.xinapse.dynamic.AbstractDynamicFrame
Creates a new DynamicFrame for a stand-alone image dynamic analysis application.
AbstractDynamicFrame(ImageDisplayer, String, List<Image>, String) - Constructor for class com.xinapse.dynamic.AbstractDynamicFrame
Creates new DynamicFrame for use with Jim.
AbstractDynamicWorker - Class in com.xinapse.apps.perfusion
MonitorWorker for running dynamic contrast analysis.
AbstractKernelFilter - Class in com.xinapse.filter
This class provides a skeletal implementation of the SpatialFilter interface, to minimize the effort required to implement this interface.
accept(File) - Method in class com.xinapse.image.ImageFileFilter
Tests whether the given file probably represents a loadable image file.
accept(File) - Method in class com.xinapse.multisliceimage.Analyze.AnalyzeFileFilter
Tests whether the given file probably represents an Analyze header file.
accept(File) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIFileFilter
Tests whether the given file probably represents a NIFTI image file.
accept(File) - Method in class com.xinapse.multisliceimage.roi.ImageJROIFileFilter
Tests whether the given file is possibly an ImageJ region of interest file.
accept(File) - Method in class com.xinapse.multisliceimage.roi.ROIFileFilter
Tests whether the given file is a region of interest file.
accept(File) - Method in class com.xinapse.multisliceimage.UNC.UNCFileFilter
Tests whether the given file probably represents a UNC image file.
add(FixedWeightsComplexKernelFilter) - Method in class com.xinapse.filter.FixedWeightsComplexKernelFilter
Adds the weights from a FixedWeightsComplexKernelFilter to the weights of this one.
add(FixedWeightsComplexKernelFilter, FixedWeightsComplexKernelFilter) - Static method in class com.xinapse.filter.FixedWeightsComplexKernelFilter
Adds the weights from two FixedWeightsComplexKernelFilters to create a new FixedWeightsComplexKernelFilter.
add(FixedWeightsKernelFilter) - Method in class com.xinapse.filter.FixedWeightsKernelFilter
Adds the weights from a FixedWeightsKernelFilter to the weights of this one.
add(FixedWeightsKernelFilter, FixedWeightsKernelFilter) - Static method in class com.xinapse.filter.FixedWeightsKernelFilter
Adds the weights from two FixedWeightsKernelFilters to create a new FixedWeightsKernelFilter.
add(Complex) - Method in class com.xinapse.image.Complex
Adds the value of this complex number to another complex number, and returns the result.
add(Complex) - Method in class com.xinapse.image.DoubleComplex
 
add(Complex) - Method in class com.xinapse.image.FloatComplex
 
add(Histogram, PixelDataType) - Method in class com.xinapse.image.Histogram
Adds the counts from a Histogram to this Histogram to produce a new Histogram that spans the data range of both.
add() - Method in class com.xinapse.image.ImageSelectionGroupPanel
Adds another ImageSelectionGroupMemberPanel to this group.
add(ROI) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
add(ROI) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
add(ROI) - Method in class com.xinapse.multisliceimage.roi.Marker
 
add(ROI) - Method in class com.xinapse.multisliceimage.roi.ROI
Morphologically adds an ROI to this ROI to create a new java.util.List<ROI> of ROIs that is the result of adding the shapes of the two ROIs.
add(List<ROI>) - Method in class com.xinapse.multisliceimage.roi.ROI
Morphologically adds a List of ROIs to this ROI to create a new java.util.List<ROI> of ROIs that is the result of adding (forming the union of) the shapes of the ROIs to this ROI.
addActionListener(ActionListener) - Method in class com.xinapse.dynamic.DynamicModel.SpecifierPanel
Adds an ActionListener that is triggered whenever the model settings are changed.
addChangeListener(ChangeListener) - Method in class com.xinapse.image.MultipleImageSelectionPanel
Add a ChangeListener to this MultipleImageSelectionPanel.
addChangeListener(ChangeListener) - Method in class com.xinapse.util.MultiContrastAnalysisFrame
 
AddChecksum - Class in com.xinapse.multisliceimage.roi
Program to add a Checksum to an ROI file.
addCol() - Method in class com.xinapse.image.ImageGrid
Adds another column of images.
addExtendedData(ExtendedData) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Adds a block of ExtendedData to this NIFTIImage.
addExtension(File, String) - Static method in class com.xinapse.multisliceimage.ImageName
Adds an extension to a File to create the name for a new file with the given extension.
addExtension(String, String) - Static method in class com.xinapse.multisliceimage.ImageName
Adds an extension to a file or URL name String to create the name for a new file or URL with the given extension.
addFileChangeCommitListener(ChangeListener) - Method in class com.xinapse.image.ImageSelectionGroupPanel
Adds a listener that listens for the file name change being committed.
addFileChangeCommitListener(ChangeListener) - Method in class com.xinapse.image.ImageSelectionPanel
Add a ChangeListener to this ImageSelectionPanel.
addFiles(List<File>) - Method in class com.xinapse.image.MultipleImageSelectionPanel
Add a List of Files to this MultipleImageSelectionPanel.
addFileTextEditListener(ChangeListener) - Method in class com.xinapse.image.ImageSelectionGroupPanel
Adds a listener that listens for the file text being edited.
addFileTextEditListener(ChangeListener) - Method in class com.xinapse.image.ImageSelectionPanel
Add a ChangeListener to this ImageSelectionPanel.
addGraph(GraphPanel, String) - Method in class com.xinapse.util.ReportGenerator
Adds a graph to the report.
addGraph(GraphPanel, String, String, String) - Method in class com.xinapse.util.ReportGenerator
Adds a graph to the report.
addImage(ReadableImage, ColourMapping, double, double, ComplexMode, String) - Method in class com.xinapse.util.ReportGenerator
Adds an image to the report.
addImage(ReadableImage, String) - Method in class com.xinapse.util.ReportGenerator
Adds a colour image to the report.
addImageInfo(ReadableImage) - Method in class com.xinapse.util.ReportGenerator
Adds basic image information to a report.
addImageInfo(ReadableImage, String) - Method in class com.xinapse.util.ReportGenerator
Adds basic image information to a report.
addInfo(List<String>) - Method in class com.xinapse.apps.cardiac.SelectableSegmentalAnalysis
Add common information for inclusion in a Report.
addMorphological(List<ROI>) - Static method in class com.xinapse.multisliceimage.roi.ROI
Morphologically adds a List of ROIs to create a new java.util.List<ROI> of ROIs that is the result of morphologically adding (forming the union of) the shapes of the ROIs.
addNColumnsChangeActionListener(ActionListener) - Method in class com.xinapse.image.ImageGrid
Add an ActionListener that is to be notified when the number of columns in the ImageGrid changes.
addNRowsChangeActionListener(ActionListener) - Method in class com.xinapse.image.ImageGrid
Add an ActionListener that is to be notified when the number of rows in the ImageGrid changes.
addParagraph(String) - Method in class com.xinapse.util.ReportGenerator
Adds a paragraph to the report.
addParagraph(Chunk) - Method in class com.xinapse.util.ReportGenerator
Adds a paragraph to the report.
addPrefix(File, String) - Static method in class com.xinapse.multisliceimage.ImageName
Adds a prefix to a File name to create the name for a new File with the given prefix.
addPrefix(String, String) - Static method in class com.xinapse.multisliceimage.ImageName
Adds a prefix to a file or URL name to create the name for a new file or URL with the given prefix.
addROI(ROI) - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Add an ROI to the frame.
addROI() - Method in class com.xinapse.multisliceimage.roi.EllipticalROICreateDialog
 
addROI() - Method in class com.xinapse.multisliceimage.roi.LineROICreateDialog
 
addROI() - Method in class com.xinapse.multisliceimage.roi.MarkerCreateDialog
 
addROI() - Method in class com.xinapse.multisliceimage.roi.RectangularROICreateDialog
 
addROI() - Method in class com.xinapse.multisliceimage.roi.ROICreateDialog
Method to cause the ROICreateDialog to read its setting and add the appropriate ROI.
addROI() - Method in class com.xinapse.multisliceimage.roi.TextCreateDialog
 
addROIs(List<ROI>) - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Add a java.util.List of ROIs to the Frame.
addRow() - Method in class com.xinapse.image.ImageGrid
Adds another row of images.
addSuffix(File, String) - Static method in class com.xinapse.multisliceimage.ImageName
Adds a suffix to a File name to create the name for a new File with the given suffix.
addSuffix(String, String) - Static method in class com.xinapse.multisliceimage.ImageName
Adds a suffix to a file or URL name to create the name for a new file or URL with the given suffix.
addTable(String, String[], double[][], DecimalFormat) - Method in class com.xinapse.util.ReportGenerator
Adds a table to the report.
addTable(TableDataSet) - Method in class com.xinapse.util.ReportGenerator
Adds a table to the report.
addTable(String, String[], String[], String[][]) - Method in class com.xinapse.util.ReportGenerator
Adds a table to the report.
addUserColourMapping(Component) - Static method in class com.xinapse.image.ColourMapping
Prompts the user to add a new user-defined ColourMapping.
addValues(Object, int, int, PixelDataType, ComplexMode) - Method in class com.xinapse.image.Histogram
Adds some pixel values to this Histogram.
AffineTransform3D - Class in com.xinapse.geom3d
The AffineTransform3D class represents a 3D affine transform that performs a linear mapping from 3D coordinates to other 3D coordinates that preserves the "straightness" and "parallelness" of lines.
AffineTransform3D() - Constructor for class com.xinapse.geom3d.AffineTransform3D
Constructs and initializes a transform to the identity transform.
AffineTransform3D(float[]) - Constructor for class com.xinapse.geom3d.AffineTransform3D
Constructs and initializes a transform from the float array of length 12; the top row of the matrix is initialized to the first four elements of the array, and so on.
AffineTransform3D(Transform3D) - Constructor for class com.xinapse.geom3d.AffineTransform3D
Constructs and initializes a transform from the Transform3D object.
AFNIExtendedData - Class in com.xinapse.multisliceimage.Analyze
This abstract class handles the NIFTI 1.1 extended data.
aif - Variable in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
The blood plasma concentration in the feeding artery, Cpa(t).
alignKnots(List<SplineROI>) - Static method in class com.xinapse.multisliceimage.roi.SplineROI
Aligns the knot points in a set of SplineROIs, so that there is spatial correspondence as far as possible across the knots.
alignKnots(SplineROI, SplineROI, int) - Static method in class com.xinapse.multisliceimage.roi.SplineROI
Aligns the knot points in a pair of SplineROIs, so that there is spatial correspondence as far as possible across the knots.
Analyze75Header - Class in com.xinapse.multisliceimage.Analyze
This class represents a multi-dimensional Analyze 7.5 image header file.
Analyze75Image - Class in com.xinapse.multisliceimage.Analyze
This class is a representation of a multi-dimensional image in the Analyze 7.5 format.
Analyze75Image() - Constructor for class com.xinapse.multisliceimage.Analyze.Analyze75Image
Creates an uninitialised instance of an Analyze75Image.
Analyze75Image(short, short, short, short, ANZPixFormat) - Constructor for class com.xinapse.multisliceimage.Analyze.Analyze75Image
Creates a new in-memory Analyze75Image.
Analyze75Image(ANZPixFormat, Short...) - Constructor for class com.xinapse.multisliceimage.Analyze.Analyze75Image
Creates a new in-memory Analyze75Image.
Analyze75Image(String, ANZPixFormat, Short...) - Constructor for class com.xinapse.multisliceimage.Analyze.Analyze75Image
Creates a new disk-based Analyze75Image.
Analyze75Image(Analyze75Header) - Constructor for class com.xinapse.multisliceimage.Analyze.Analyze75Image
Creates a new in-memory Analyze75Image, using information from an existing Analyze75header.
Analyze75Image(String, short, short, short, short, ANZPixFormat) - Constructor for class com.xinapse.multisliceimage.Analyze.Analyze75Image
Creates a new disk-based Analyze75Image.
Analyze75Image(File, Analyze75Header) - Constructor for class com.xinapse.multisliceimage.Analyze.Analyze75Image
Creates a new disk-based Analyze75Image, using an existing header as a template for the new image.
Analyze75Image(String, Analyze75Header) - Constructor for class com.xinapse.multisliceimage.Analyze.Analyze75Image
Creates a new disk-based Analyze75Image, using an existing header as a template for the new image.
Analyze75Image(String, String) - Constructor for class com.xinapse.multisliceimage.Analyze.Analyze75Image
Opens an existing Analyze75Image, with pixel data remaining on disk until requested.
AnalyzeFileFilter - Class in com.xinapse.multisliceimage.Analyze
A file filter for Analyze header files.
and(BitSet) - Method in class com.xinapse.util.BitSet
Performs the logical AND operation on this bit set and the given BitSet.
andNot(BitSet) - Method in class com.xinapse.util.BitSet
Performs the logical AND operation on this bit set and the complement of the given BitSet.
ANegativeHandle - Class in com.xinapse.multisliceimage.roi
A Class representing a Handle at the negative end of axis A on an EllipticalROI.
ANegativeHandle(int, int, int) - Constructor for class com.xinapse.multisliceimage.roi.ANegativeHandle
Creates a new ANegativeHandle at the location (x,y) with the given size in screen pixels.
ANNOTATIONTOKEN - Static variable in class com.xinapse.multisliceimage.roi.ROIStreamTokenizer
 
anonymise(String, String, Date, boolean, String, String, String, boolean, String, String, String, String, String, String, String, boolean) - Method in interface com.xinapse.image.WritableImage
 
anonymise(String, String, Date, boolean, String, String, String, boolean, String, String, String, String, String, String, String, boolean) - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
anonymise(String, String, Date, boolean, String, String, String, boolean, String, String, String, String, String, String, String, boolean) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
anonymise(String, String, Date, boolean, String, String, String, boolean, String, String, String, String, String, String, String, boolean) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
anonymise(String, String, Date, boolean, String, String, String, boolean, String, String, String, String, String, String, String, boolean) - Method in class com.xinapse.util.InfoList
 
ANZColourMapping - Class in com.xinapse.multisliceimage.Analyze
Class to handle Analyze lookup files (colour mapping files).
ANZColourMapping() - Constructor for class com.xinapse.multisliceimage.Analyze.ANZColourMapping
 
ANZDebug - Class in com.xinapse.multisliceimage.Analyze
Enables and disables debugging messages for the Analyze package.
ANZException - Exception in com.xinapse.multisliceimage.Analyze
Signals that an error in the Analyze package has occurred.
ANZException() - Constructor for exception com.xinapse.multisliceimage.Analyze.ANZException
Constructs an ANZException without a detail message.
ANZException(String) - Constructor for exception com.xinapse.multisliceimage.Analyze.ANZException
Constructs an ANZException with the specified detail message.
ANZException(String, Throwable) - Constructor for exception com.xinapse.multisliceimage.Analyze.ANZException
Constructs an ANZException with the specified cause.
ANZHeader - Class in com.xinapse.multisliceimage.Analyze
An abstract Analyze header representation.
ANZImage - Class in com.xinapse.multisliceimage.Analyze
This is an abstract class that is the superclass of a multi-dimensional image in the Analyze 7.5 format or the new NIFTI-1 format.
ANZPixFormat - Enum in com.xinapse.multisliceimage.Analyze
This class represents the pixel formats (data types) that can be used in Analyze, and NIFTI (extended Analyze) images.
APositiveHandle - Class in com.xinapse.multisliceimage.roi
A Class representing a Handle at the positive end of axis A on an EllipticalROI.
APositiveHandle(int, int, int) - Constructor for class com.xinapse.multisliceimage.roi.APositiveHandle
Creates a new APositiveHandle at the location (x,y) with the given size in screen pixels.
append(InfoList) - Method in class com.xinapse.util.InfoList
Appends an InfoList onto the end of an existing one.
appendAuditInfo(String, String) - Method in interface com.xinapse.image.WritableImage
Appends audit trail information to this image.
appendAuditInfo(String, String) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by Analyze 7.5 format, so this method does nothing.
appendAuditInfo(String, String) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Appends audit trail information to this image.
appendAuditInfo(String, String) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
appendInfoList(InfoList) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
appendInfoList(InfoList, int, int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Appends an InfoList to that for a particular dimension of this image.
appendInfoList(InfoList) - Method in interface com.xinapse.multisliceimage.InfoStorer
Appends an InfoList to the existing general file info of this image.
appendInfoList(InfoList, int, int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Appends an InfoList to that existing for a specific dimension of this image.
appendInfoList(InfoList) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
appendInfoList(InfoList, int, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
appendVertex(Point2D) - Method in class com.xinapse.multisliceimage.roi.IrregularROIInProgress
Appends a vertex to the end of this IrregularROIInProgress.
appendVertex(double, double) - Method in class com.xinapse.multisliceimage.roi.IrregularROIInProgress
Appends a vertex to the end of this IrregularROIInProgress.
APPLY_SPATIAL_FILTER_PREFERENCE_NAME - Static variable in class com.xinapse.dynamic.AbstractDynamicFrame
The Preference name for whether to apply a spatial smoothing filter.
approximate(int) - Method in class com.xinapse.multisliceimage.roi.SplineROI
Creates a new SplineROI which approximates this SplineROI, but which has the specified number of knot points and where the knot points are evenly distributed in the s-parameter.
area - Variable in class com.xinapse.multisliceimage.roi.ROIStats
The area of this ROI in square mm.
AREATOKEN - Static variable in class com.xinapse.multisliceimage.roi.ROIStreamTokenizer
 
ATOKEN - Static variable in class com.xinapse.multisliceimage.roi.EllipticalROI
The token written to ROI output files to represent the first semi-major axis length.
AUDIT_TRAIL_ACTION_TEXT - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
A String used when composing audit trail information.
AutoCorrelationEstimate - Class in com.xinapse.dynamic
Class to estimate the auto-correlation of a time-series by examining the residuals of a GLM fit.
AutoCorrelationEstimate(float[][], int, int, int, float, float, float, MonitorWorker, boolean) - Constructor for class com.xinapse.dynamic.AutoCorrelationEstimate
Estimate the auto-correlation for the supplied residuals.
autoCrop(ReadableImage) - Static method in class com.xinapse.image.ImageUtils
Automatically crop an image to remove regions of background.
autoCrop(ReadableImage, Double) - Static method in class com.xinapse.image.ImageUtils
Automatically crop an image to remove regions of background.
autoCrop(ReadableImage, MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Automatically crop an image to remove regions of background.
autoCrop(ReadableImage, Double, MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Automatically crop an image to remove regions of background.
autoCropSlices(ReadableImage) - Static method in class com.xinapse.image.ImageUtils
Automatically crop an image to remove slices that only contain background.
autoCropSlices(ReadableImage, Double) - Static method in class com.xinapse.image.ImageUtils
Automatically crop an image to remove slices that only contain background.
autoCropSlices(ReadableImage, MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Automatically crop an image to remove slices that only contain background.
autoCropSlices(ReadableImage, Double, MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Automatically crop an image to remove slices that only contain background.
autoResample(ReadableImage, int, SubSampleType, boolean, boolean) - Static method in class com.xinapse.image.ImageUtils
Automatically resamples a ReadableImage so that the resulting resampled image has no more than the given maximum number of voxels.
average(List<AffineTransform3D>) - Static method in class com.xinapse.geom3d.AffineTransform3D
Returns the AffineTransform3D that is the average of several AffineTransform3Ds.
AxisHandle - Class in com.xinapse.multisliceimage.roi
A Class representing a Handle at the end of an axis on an EllipticalROI.
AxisHandle(int, int, int) - Constructor for class com.xinapse.multisliceimage.roi.AxisHandle
Creates a new AxisHandle at the location (x,y) with the given size in screen pixels.

B

bc - Variable in class com.xinapse.filter.AbstractKernelFilter
The boundary condition for the filter.
binWidth - Variable in class com.xinapse.image.Histogram.BinSpec
The bin width.
BIRTH_DATE_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the patient's birth date.
BitSet(InputStream, BitSet) - Static method in class com.xinapse.io.Input
Reads a com.xinapse.util.BitSet from a java.io.InputStream strm ensuring that blocking occurs until all values have been read.
BitSet(DataInputStream, BitSet) - Static method in class com.xinapse.io.Input
Reads a com.xinapse.util.BitSet from a DataInputStream strm, ensuring that blocking occurs until all values have been read.
BitSet(RandomAccessFile, BitSet, int) - Static method in class com.xinapse.io.Input
Reads a com.xinapse.util.BitSet from a java.io.RandomAccessFile f, ensuring that blocking occurs until all values have been read.
BitSet(BitSet, OutputStream) - Static method in class com.xinapse.io.Output
Writes a com.xinapse.util.BitSet as individual bits to a java.io.OutputStream strm.
BitSet(BitSet, RandomAccessFile, int) - Static method in class com.xinapse.io.Output
Writes a com.xinapse.util.BitSet as individual bits to a java.io.RandomAccessFile f.
BitSet - Class in com.xinapse.util
A class representing an array of binary (1-bit) values in a more compact way than does a boolean[].
BitSet(int) - Constructor for class com.xinapse.util.BitSet
Create a new empty bit set, with a given size.
BLUE - Static variable in class com.xinapse.image.ColourMapping
The ColourMapping representing a blue intensity scale.
BLUE_FORMULA_OPTION - Static variable in class com.xinapse.filter.ColourImageFilter
A public Option to specify the formula used to calculate the new blue component values in the output image.
BLUR_FWHM - Static variable in class com.xinapse.filter.GaussianBlurFilter
A public Option to specify that the FWHM of an isotropic Gaussian blur filter.
BLUR_THREE_D - Static variable in class com.xinapse.filter.GaussianBlurFilter
A public Option to specify that a Gaussian blur filter should work in 3-D, not 2-D.
BNegativeHandle - Class in com.xinapse.multisliceimage.roi
A Class representing a Handle at the negative end of axis B on an EllipticalROI.
BNegativeHandle(int, int, int) - Constructor for class com.xinapse.multisliceimage.roi.BNegativeHandle
Creates a new BNegativeHandle at the location (x,y) with the given size in screen pixels.
BODY_PART_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the imaged body part.
BoundaryCondition - Enum in com.xinapse.image
An enumeration of possible boundary conditions when applying, for example, spatial filters and interpolators.
BPositiveHandle - Class in com.xinapse.multisliceimage.roi
A Class representing a Handle at the positive end of axis B on an EllipticalROI.
BPositiveHandle(int, int, int) - Constructor for class com.xinapse.multisliceimage.roi.BPositiveHandle
Creates a new BPositiveHandle at the location (x,y) with the given size in screen pixels.
BTOKEN - Static variable in class com.xinapse.multisliceimage.roi.EllipticalROI
The token written to ROI output files to represent the second semi-major axis length.
busyCursors() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
 
busyCursors() - Method in class com.xinapse.image.ImageSelectionPanel
 
busyCursors() - Method in class com.xinapse.image.MultipleImageSelectionPanel
 
busyCursors() - Method in interface com.xinapse.util.MessageShower
Sets the cursor for this MessageShower to indicate that an operation is in progress.
busyCursors() - Method in class com.xinapse.util.MultiContrastAnalysisFrame
 
Byte(byte, OutputStream) - Static method in class com.xinapse.io.Output
Write a single byte value to an java.io.OutputStream strm.
Byte(byte, RandomAccessFile) - Static method in class com.xinapse.io.Output
Write a single byte value to a java.io.RandomAccessFile f.
ByteArray(InputStream, int) - Static method in class com.xinapse.io.Input
Reads an array of bytes from a java.io.InputStream strm ensuring that blocking occurs until all values have been read.
ByteArray(RandomAccessFile, int) - Static method in class com.xinapse.io.Input
Reads an array of bytes from a java.io.RandomAccessFile f, ensuring that blocking occurs until all values have been read.
ByteArray(byte[], OutputStream) - Static method in class com.xinapse.io.Output
Write an array of byte values to a java.io.OutputStream strm.
ByteSwap - Class in com.xinapse.io
Abstract class to provide byte swapping facilities, allowing correct interpretation of multi-byte numbers on machines of different byte orders.

C

calcBins(double, double, PixelDataType, ComplexMode) - Static method in class com.xinapse.image.Histogram
Calculates a suitable bin width, number of bins, and minimum bin value for a histogram, for the given type of pixels over the given intensity range.
calcBins(double, double, int, PixelDataType, ComplexMode) - Static method in class com.xinapse.image.Histogram
Calculates a suitable bin width, and minimum bin value for a histogram, for the given type of pixels over the given intensity range.
CanAddROIToFrame - Interface in com.xinapse.multisliceimage.roi
An interface to indicate that a javax.swing.JFrame can receive ROIs.
cancel() - Method in class com.xinapse.image.ColourVolumeInterpolator
Signal to this ColourVolumeInterpolator to stop the current interpolation (if an interpolation is in progress) as soon as possible.
cancel() - Method in class com.xinapse.image.VolumeInterpolator
Signal to this VolumeInterpolator to stop the current interpolation (if an interpolation is in progress) as soon as possible, and throw a java.util.concurrent.CancellationException.
cancel() - Method in class com.xinapse.util.CancellableThread
Signal the CancellableThread to stop any processing and return.
CancellableThread - Class in com.xinapse.util
A class to implement a cancellable Thread.
CancellableThread() - Constructor for class com.xinapse.util.CancellableThread
 
CancellableThread.Flag - Class in com.xinapse.util
A flag that can be set to indicate that a cancellation has taken place.
CancelledException - Exception in com.xinapse.util
Thrown when an action is cancelled by the user.
CancelledException() - Constructor for exception com.xinapse.util.CancelledException
Constructs a CancelledException without a detail message, and without a user object.
CancelledException(String) - Constructor for exception com.xinapse.util.CancelledException
Constructs a CancelledException with the specified detail message.
CancelledException(String, List<ROI>) - Constructor for exception com.xinapse.util.CancelledException
Constructs a CancelledException with the specified detail message, and an associated User Object.
cardinality() - Method in class com.xinapse.util.BitSet
Returns the number of bits set to true.
CentreHandle - Class in com.xinapse.multisliceimage.roi
A Class representing a Handle at the centre of an ROI.
CentreHandle(int, int, int) - Constructor for class com.xinapse.multisliceimage.roi.CentreHandle
Creates a new CentreHandle at the location (x,y) with the given size in screen pixels.
checkCancelled() - Method in class com.xinapse.util.MonitorWorker
Tests whether this CancellableWorker has been cancelled.
checkCancelled(String) - Method in class com.xinapse.util.MonitorWorker
Tests whether this CancellableWorker has been cancelled.
checkCancelled(Integer) - Method in class com.xinapse.util.MonitorWorker
Tests whether this CancellableWorker has been cancelled, and sets the progress through this operation.
checkCancelled(String, Integer) - Method in class com.xinapse.util.MonitorWorker
Tests whether this CancellableWorker has been cancelled, and sets the progress through this operation.
checkIndices(ReadableImage, int[]) - Static method in class com.xinapse.image.ImageUtils
Checks compatibility of the pixel indices that reference a particular pixel of an image.
checkMinMax(int, int, PixelDataType) - Static method in class com.xinapse.image.ImageUtils
Checks the integrity of the minimum and maximum pixel values taking into account the data type of the image.
clear() - Method in class com.xinapse.util.BitSet
Sets all bits in the set to false.
clear(int) - Method in class com.xinapse.util.BitSet
Removes the integer bitIndex from this set.
clear(int, int) - Method in class com.xinapse.util.BitSet
Sets the bits between from (inclusive) and to (exclusive) to false.
clearAllImages() - Method in class com.xinapse.image.ImageGrid
Clear all images from this ImageGrid.
clearAllImages() - Method in class com.xinapse.image.ImageSelectionGroupPanel
Clear all images from this ImageSelectionGroupPanel.
clearDeletionHistory() - Method in class com.xinapse.multisliceimage.roi.ROI
Removed the deletion HistoryItem for this ROI.
clearFiles() - Method in class com.xinapse.image.MultipleImageSelectionPanel
Removes all files from the list.
clearFiles() - Method in class com.xinapse.image.SingleOrMultipleInputImageSelectionPanel
 
clearHisto() - Method in class com.xinapse.multisliceimage.roi.ROIStats
Clears (sets to null) the histogram for these ROIStats.
clone() - Method in class com.xinapse.geom3d.AffineTransform3D
Creates and returns a copy of this AffineTransform3D.
clone() - Method in class com.xinapse.image.ColourMapping
Returns an exact copy of this ColourMapping.
clone() - Method in class com.xinapse.image.PixArray
Returns a new PixArray object that contains pixel values and properties that are the same as the original.
clone() - Method in class com.xinapse.multisliceimage.Analyze.AFNIExtendedData
 
clone() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Header
Returns an exact copy of this Analyze header.
clone() - Method in class com.xinapse.multisliceimage.Analyze.ANZHeader
Creates a deep copy of this Analyze header.
clone() - Method in class com.xinapse.multisliceimage.Analyze.CommentExtendedData
 
clone() - Method in class com.xinapse.multisliceimage.Analyze.DICOMExtendedData
 
clone() - Method in class com.xinapse.multisliceimage.Analyze.InfoExtendedData
 
clone() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
Returns an exact copy of this NIFTI header.
clone() - Method in class com.xinapse.multisliceimage.Analyze.UnknownExtendedData
 
clone() - Method in class com.xinapse.multisliceimage.Analyze.XCEDEExtendedData
 
clone() - Method in class com.xinapse.multisliceimage.Analyze.XMLExtendedData
 
clone() - Method in class com.xinapse.multisliceimage.MultiSliceImage
Returns a copy of this MultiSliceImage.
clone() - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
clone() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
clone() - Method in class com.xinapse.multisliceimage.roi.Handle
 
clone() - Method in class com.xinapse.multisliceimage.roi.HistoryItem
 
clone() - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
clone() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
clone() - Method in class com.xinapse.multisliceimage.roi.IrregularROIInProgress
 
clone() - Method in class com.xinapse.multisliceimage.roi.LineROI
 
clone() - Method in class com.xinapse.multisliceimage.roi.Marker
 
clone() - Method in class com.xinapse.multisliceimage.roi.OpenSplineROI
 
clone() - Method in class com.xinapse.multisliceimage.roi.RadialDivider
 
clone() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
clone() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns a clone of this ROI.
clone() - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
clone() - Method in class com.xinapse.multisliceimage.roi.Text
 
clone() - Method in class com.xinapse.util.BitSet
Create a clone of this bit set, that is an instance of the same class and contains the same elements.
clone() - Method in class com.xinapse.util.InfoItem
Returns a copy of this InfoItem.
clone() - Method in class com.xinapse.util.InfoList
Makes a copy of this InfoList.
close() - Method in interface com.xinapse.image.ReadableImage
Closes an image and frees up resources.
close() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
Closes an ANZImage and frees up resources.
close() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Closes a NIFTIImage and frees up resources.
close() - Method in class com.xinapse.multisliceimage.roi.SplineROI
Closes this SplineROI so that the outline is a closed path.
close() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
Closes a UNCImage and frees up resources.
close() - Method in class com.xinapse.util.IndeterminateProgressMonitor
Indicate that the operation is complete.
closed - Variable in class com.xinapse.multisliceimage.roi.SplineROI
Whether the SplineROI is closed.
closestPoints(IrregularROI) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Returns the line that represents the line that joins the two points that are closest together (in space) between this IrregularROI and another IrregularROI.
cm - Variable in class com.xinapse.image.ColourMapping
The IndexColorModel used to contain the mapping.
CODE - Static variable in class com.xinapse.multisliceimage.Analyze.AFNIExtendedData
The ecode for an AFNI header attributes extension.
CODE - Static variable in class com.xinapse.multisliceimage.Analyze.CommentExtendedData
The ecode for an arbitrary non-NUL ASCII text extension.
CODE - Static variable in class com.xinapse.multisliceimage.Analyze.DICOMExtendedData
The ecode for a DICOM format extension.
CODE - Static variable in class com.xinapse.multisliceimage.Analyze.InfoExtendedData
The ecode for an InfoExtendedData extension.
CODE - Static variable in class com.xinapse.multisliceimage.Analyze.XCEDEExtendedData
The ecode for an XCEDE metadata extension.
CODE - Static variable in class com.xinapse.multisliceimage.Analyze.XMLExtendedData
The ecode for an arbitrary non-NULL ASCII text extension.
coerce(Object, PixelDataType, boolean) - Method in enum com.xinapse.image.PixelDataType
Coerce pixels of this PixelDataType to a new PixelDataType.
coerce(Object, PixelDataType, ComplexMode, boolean) - Method in enum com.xinapse.image.PixelDataType
Coerce pixels of this PixelDataType to a new PixelDataType.
coerce(Object, PixelDataType, int, int, ComplexMode, boolean) - Method in enum com.xinapse.image.PixelDataType
Coerce pixels of this PixelDataType to a new PixelDataType.
COLOUR_MAPPING_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the colour mapping.
ColourImageFilter - Class in com.xinapse.filter
A SpatialFilter for altering the colour components of a colour image.
ColourImageFilter(String, String, String) - Constructor for class com.xinapse.filter.ColourImageFilter
Creates a new ColourImageFilter based on three formulae used to compute the red, green and blue colour components.
ColourImageFilter.ColourImageFilterSpecifierPanel - Class in com.xinapse.filter
A FilterSpecifierPanel for a colour image filter.
colourLookup(int, int, Object, int, PixelDataType, byte[], double, double, boolean, BitSet, boolean, ComplexMode) - Method in class com.xinapse.image.ColourMapping
Converts an array of pixel intensity values into the byte values that can then be used as an argument in the getRaster().setDataElements() method of BufferedImage to put pixel colours to a BufferedImage Object.
colourLookupColourPacked(int, int, byte[], int, int[], short, short, boolean, BitSet, boolean, byte, boolean) - Static method in class com.xinapse.image.ColourMapping
Converts an array of pixel intensity values into the int values that can then be used as an argument in the getRaster().setDataElements() method of BufferedImage to put pixel colours to a BufferedImage Object.
colourLookupRGBByPlane(int, int, byte[], int, int[], short, short, boolean, BitSet, boolean, byte, boolean) - Static method in class com.xinapse.image.ColourMapping
Converts an array of pixel intensity values into the int values that can then be used as an argument in the getRaster().setDataElements() method of BufferedImage to put pixel colours to a BufferedImage Object.
colourLookupRGBInterlaced(int, int, byte[], int, int[], short, short, boolean, BitSet, boolean, byte, boolean) - Static method in class com.xinapse.image.ColourMapping
Converts an array of pixel intensity values into the int values that can then be used as an argument in the getRaster().setDataElements() method of BufferedImage to put pixel colours to a BufferedImage Object.
ColourMapping - Class in com.xinapse.image
The ColourMapping class represents a mapping from pixel presentation values (PPVs) to colours that are shown on a display device, such as a computer monitor.
COLOURTOKEN - Static variable in class com.xinapse.multisliceimage.roi.ROIStreamTokenizer
 
ColourVolumeInterpolator - Class in com.xinapse.image
An interpolator for a 3- (or fewer) dimensional array of pixels in a Colour image.
ColourVolumeInterpolator(byte[], PixelDataType, int, int, int, float, float, float, BoundaryCondition, Color, InterpolationType) - Constructor for class com.xinapse.image.ColourVolumeInterpolator
Creates a new ColourVolumeInterpolator for a block of colour (R,G,B) pixel samples.
ColourVolumeInterpolator(ColourVolumeInterpolator, InterpolationType) - Constructor for class com.xinapse.image.ColourVolumeInterpolator
Returns a new ColourVolumeInterpolator, constructed from an existing one.
com.xinapse.filter - package com.xinapse.filter
The package com.xinapse.filter is used to filter images.
com.xinapse.image - package com.xinapse.image
The package com.xinapse.image contains utilities for handling different types of image that can be handled by Jim.
com.xinapse.image.template - package com.xinapse.image.template
Provides access to built-in and user-selected template images, and utilities related to them.
com.xinapse.io - package com.xinapse.io
Provides basic input/output of primitive data types, with provision to read and write values to machines with different byte orders.
com.xinapse.multisliceimage - package com.xinapse.multisliceimage
The package com.xinapse.multisliceimage is used to represent and handle multi-dimensional Medical Images in different file formats.
com.xinapse.multisliceimage.Analyze - package com.xinapse.multisliceimage.Analyze
The package com.xinapse.multisliceimage.Analyze is used to represent and handle the Analyze Medical Image file format, and the NIFTI-1 extension of this format.
com.xinapse.multisliceimage.roi - package com.xinapse.multisliceimage.roi
The package com.xinapse.multisliceimage.roi is used to create and manipulate 2-dimensional regions of interest (ROIs).
com.xinapse.multisliceimage.UNC - package com.xinapse.multisliceimage.UNC
The package com.xinapse.multisliceimage.UNC is used to represent and handle multi-dimensional medical images in the University of North Carolina (UNC) format.
CombineMode - Enum in com.xinapse.multisliceimage.roi
An enumeration of possible ROI combination operations that can be be applied to a set of ROIs to create a single resulting ROI.
CombineMode.Panel - Class in com.xinapse.multisliceimage.roi
A JPanel for selecting a CombineMode.
ComboBox(boolean) - Constructor for class com.xinapse.dicom.Modality.ComboBox
Creates a new Modality.ComboBox.
ComboBox() - Constructor for class com.xinapse.dicom.PatientPosition.ComboBox
Creates a new PatientPosition.ComboBox.
ComboBox() - Constructor for class com.xinapse.dicom.PulseSequenceType.ComboBox
Creates a new PulseSequenceType.ComboBox.
ComboBox() - Constructor for class com.xinapse.image.RenderingInterpolationType.ComboBox
Creates a new RenderingInterpolationType.ComboBox.
ComboBox() - Constructor for class com.xinapse.multisliceimage.roi.ContourMode.ComboBox
Create a new ContourMode.ComboBox for selecting a ContourMode.
CommentExtendedData - Class in com.xinapse.multisliceimage.Analyze
This class handles the NIFTI 1.1 non-NUL ASCII text extended data.
compare(ROI, ROI) - Method in class com.xinapse.multisliceimage.roi.StatsComparator
Compares the statistics for two ROIs for order.
compareTo(ReadableImage.Position) - Method in class com.xinapse.image.ReadableImage.Position
 
Complex - Class in com.xinapse.image
A complex (real, imaginary) number.
Complex() - Constructor for class com.xinapse.image.Complex
 
ComplexMode - Enum in com.xinapse.image
An enumeration of the possible display/calculation modes for complex numbers.
complexWeights - Variable in class com.xinapse.filter.FixedWeightsComplexKernelFilter
The 3-D array of weights in the kernel.
COMPRESSED_EXTENSION - Static variable in class com.xinapse.multisliceimage.Analyze.ANZHeader
The file extension for Analyze header files in lower case form.
COMPRESSED_EXTENSION - Static variable in class com.xinapse.multisliceimage.Analyze.ANZImage
The file extension for Analyze image files in lower case form.
COMPRESSED_EXTENSION - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIImage
The file extension for compressed NIFTI image files.
COMPRESSED_PROPERTY_KEY - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Image
The property value key for setting whether Analyze 7.5 images should be stored compressed, or uncompressed.
COMPRESSED_PROPERTY_KEY - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIImage
The property value key for setting whether NIFTI images should be stored compressed, or uncompressed.
COMPRESSED_UPPERCASE_EXTENSION - Static variable in class com.xinapse.multisliceimage.Analyze.ANZHeader
The file extension for Analyze header files in upper case form.
COMPRESSED_UPPERCASE_EXTENSION - Static variable in class com.xinapse.multisliceimage.Analyze.ANZImage
The file extension for Analyze image files in upper case form.
computesRMSDiff() - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
Returns whether the dynamic contrast model computed the RMS difference between the model fit and the data.
computesRMSDiff() - Method in interface com.xinapse.dynamic.DynamicModel
Signals whether the model computes the root-mean-square (RMS) difference between the model and the data.
conj() - Method in class com.xinapse.image.Complex
Returns the complex conjugate of this complex number.
conj() - Method in class com.xinapse.image.DoubleComplex
 
conj() - Method in class com.xinapse.image.FloatComplex
 
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
Indicates whether this CurvedLineROI contains another ROI entirely within its borders.
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
Indicates whether this EllipticalROI contains another ROI entirely within its borders.
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Indicates whether this IrregularROI contains another ROI entirely within its borders.
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.LineROI
Indicates whether this LineROI contains another ROI entirely within its borders.
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.Marker
Indicates whether this Marker ROI contains another ROI entirely within its borders.
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Indicates whether this RadialDivider ROI contains another ROI entirely within its borders.
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.RectangularROI
Indicates whether this RectangularROI contains another ROI entirely within its borders.
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.ROI
Indicates whether this ROI entirely contains another ROI entirely within its borders.
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.SplineROI
Indicates whether this SplineROI contains another ROI entirely within its borders.
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.VOI
Tests whether this volume of interest (VOI) contains an ROI.
containsVertex(Point2D) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Tests whether the supplied vertex location is one of the vertex locations for this ROI.
contiguousTimes - Variable in class com.xinapse.apps.cardiac.SelectableSegmentalAnalysis
True if time points are contiguous in the input image(s).
ContourMode - Enum in com.xinapse.multisliceimage.roi
An enumeration of the modes of operation of intensity level contour generation.
ContourMode.ComboBox - Class in com.xinapse.multisliceimage.roi
A JComboBox for selecting a ContourMode.
ContourROI - Class in com.xinapse.multisliceimage.roi
A class for edge detection and contour following.
ContourWorker - Class in com.xinapse.multisliceimage.roi
A MonitorWorker for performing edge detection and contouring from a seed point.
ContourWorker(Point3i, ReadableImage, ComplexMode, ContourMode, double, IntensityRelation, boolean, int, byte, boolean, boolean, CanAddROIToFrame, boolean) - Constructor for class com.xinapse.multisliceimage.roi.ContourWorker
Instantiates a new ContourWorker that will perform contouring from the supplied seed pixel.
ConvergenceException - Exception in com.xinapse.numerical
Signals that an iterative procedure has failed to converge.
ConvergenceException() - Constructor for exception com.xinapse.numerical.ConvergenceException
Constructs a ConvergenceException with "failed to converge" as its detail message.
ConvergenceException(int) - Constructor for exception com.xinapse.numerical.ConvergenceException
Constructs a ConvergenceException with a detail message that indicates the number of iterations tried.
ConvergenceException(String) - Constructor for exception com.xinapse.numerical.ConvergenceException
Constructs a ConvergenceException with the specified detail message.
convolve(FixedWeightsComplexKernelFilter) - Method in class com.xinapse.filter.FixedWeightsComplexKernelFilter
Convolves this FixedWeightsComplexKernelFilter with another FixedWeightsComplexKernelFilter to create a new FixedWeightsComplexKernelFilter.
convolve(FixedWeightsKernelFilter) - Method in class com.xinapse.filter.FixedWeightsKernelFilter
Convolves this FixedWeightsKernelFilter with another FixedWeightsKernelFilter to create a new FixedWeightsKernelFilter.
copyInfo(UNCImage) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
Copies all the info fields to another image.
copyPixels(Object) - Method in enum com.xinapse.image.PixelDataType
Copies the pixel samples to a new array of the correct type for this type of pixel.
copyPixels(Object, Object) - Method in enum com.xinapse.image.PixelDataType
Copies the pixel samples to an array of the correct type for this type of pixel.
copyPixels(Object, int, Object) - Method in enum com.xinapse.image.PixelDataType
Copies the pixel samples to an array of the correct type for this type of pixel.
copyPixels(Object, Object, int) - Method in enum com.xinapse.image.PixelDataType
Copies the pixel samples to an array of the correct type for this type of pixel.
copyResize(int[], boolean) - Method in class com.xinapse.filter.FixedWeightsComplexKernelFilter
Copies a FixedWeightsComplexKernelFilter, possibly resizing it, creating a new FixedWeightsComplexKernelFilter.
copyResize(int[], boolean) - Method in class com.xinapse.filter.FixedWeightsKernelFilter
Copies a FixedWeightsKernelFilter, possibly resizing it, creating a new FixedWeightsKernelFilter.
CornerHandle - Class in com.xinapse.multisliceimage.roi
An abstract Class representing a Handle at one of the four corners of an ROI.
CornerHandle(int, int, int) - Constructor for class com.xinapse.multisliceimage.roi.CornerHandle
Creates a new CornerHandle at the location (x,y) with the given size in screen pixels.
CREATE_NON_FLIPPED_PROPERTY_KEY - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Header
The property value key for setting whether newly-created Analyze 7.5 images should have a non-flipped orientation.
crop(ReadableImage, int[][], MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Crops a WritableImage to produce a new image.
CubicSplineInterpolator - Class in com.xinapse.numerical
A cubic spline interpolator for tabulated values of (x,y).
currentWorkingDirectory - Variable in class com.xinapse.image.ImageSelectionPanel
The current working directory.
CurvedLineROI - Class in com.xinapse.multisliceimage.roi
A represention of a planar curved line on an image.
CurvedLineROI(double[], double[], int, ROIState) - Constructor for class com.xinapse.multisliceimage.roi.CurvedLineROI
Creates a new CurvedLineROI with the coordinates of the points forming the line given by the x and y arrays in mm coordinates.
CurvedLineROI(List<Point2D.Double>, ROIState) - Constructor for class com.xinapse.multisliceimage.roi.CurvedLineROI
Creates a new CurvedLineROI with the coordinates of the points forming the line given by the List of points in mm coordinates.
CurvedLineROI(List<Point2D.Double>, int, int, float, float, byte, ROIState) - Constructor for class com.xinapse.multisliceimage.roi.CurvedLineROI
Creates a new CurvedLineROI with the coordinates of the points forming the line given by the List of points in image pixel coordinates.
CYAN - Static variable in class com.xinapse.image.ColourMapping
The ColourMapping representing a cyan intensity scale.

D

dataType - Variable in class com.xinapse.image.PixArray
The type of pixel that this PixArray stores.
dataType - Variable in class com.xinapse.image.VolumeInterpolator
The PixelDataType of the pixel values to be interpolated.
DCEMRIModel - Class in com.xinapse.apps.perfusion
The superclass of models that can be fitted to DCE-MRI data.
DCEMRIModel(String, String, String[], String[]) - Constructor for class com.xinapse.apps.perfusion.DCEMRIModel
Constructor used by sub-classes.
DEFAULT - Static variable in enum com.xinapse.image.InputConfigurationType
The default InputConfigurationType.
DEFAULT - Static variable in enum com.xinapse.image.RenderingInterpolationType
The default RenderingInterpolationType.
DEFAULT - Static variable in enum com.xinapse.image.template.WeightingType
The default WeightingType for applications.
DEFAULT_COMPLEX_MODE - Static variable in enum com.xinapse.image.ComplexMode
The default ComplexMode for applications.
DEFAULT_COMPRESSED - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Whether to store Analyze 7.5 images compressed by default.
DEFAULT_COMPRESSED - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Whether to store NIFTI images compressed by default.
DEFAULT_CREATE_NON_FLIPPED - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Header
The default setting of whether newly-created Analyze 7.5 images should have a non-flipped orientation.
DEFAULT_DO_NOT_FLIP_FLIPPED - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Header
The default setting of whether not to flip vertically an image with a flipped Analyze orientation.
DEFAULT_FLIP_NON_FLIPPED - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Header
The default setting of whether to flip vertically an image with a non-flipped Analyze orientation.
DEFAULT_FSL_COMPATIBLE_NIFTI - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
The default setting of whether NIFTI-1 images that have qform and sform orientation both unset should be read as having an increasing a patient left coordinate value with stored pixel data column number, and whether NIFTI-1 images should be prevented from being written without orientation information.
DEFAULT_GAMMA - Static variable in class com.xinapse.image.ColourMapping
The default gamma value of the computer display.
DEFAULT_IMAGE_CLASS - Static variable in class com.xinapse.image.ImageUtils
The default image class to work with, if the user has no Preference.
DEFAULT_IMAGE_PREVIEW - Static variable in class com.xinapse.image.ImagePreview
The default setting for whether to generate an image preview thumbnail.
DEFAULT_INTENSITY_RELATION - Static variable in enum com.xinapse.util.IntensityRelation
The default IntensityRelation.
DEFAULT_INTENSITY_RELATION - Static variable in class com.xinapse.util.IntensityRelation.IntensityRelationButton
The default IntensityRelation for applications.
DEFAULT_MAX_LUMINANCE - Static variable in class com.xinapse.image.ColourMapping
The default luminance of the computer display for a digital driver level (DDL) of 255, including the effects of ambient light.
DEFAULT_MIN_LUMINANCE - Static variable in class com.xinapse.image.ColourMapping
The default luminance of the computer display for a digital driver level (DDL) of zero, including the effects of ambient light.
DEFAULT_MIN_RADIUS - Static variable in class com.xinapse.multisliceimage.roi.SmootherWorker
The default minimum radius of curvature for sections.
DEFAULT_N_STEADY_STATES - Static variable in class com.xinapse.dynamic.AbstractDynamicFrame
The default number of steady state images, if not set in user preferences.
DEFAULT_NIFTI_ONE_FILE - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Whether to store NIFTI images in one file (.nii) by default.
DEFAULT_OVERWRITE - Static variable in class com.xinapse.multisliceimage.UNC.UNCImage
The default setting for the whether UNC images can be overwritten.
DEFAULT_SAVE_FSL_ORIENT - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
The default setting of whether NIFTI-1 images should be saved with an orientation that is compatible with FSL, where possible.
DEFAULT_SAVE_SPM_ORIENT - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
The default setting of whether NIFTI-1 images should be saved with an orientation that is compatible with SPM, where possible.
DEFAULT_SIZE - Static variable in class com.xinapse.multisliceimage.roi.Marker
The size (in screen pixels) of a Marker as it is drawn on-screen (the extreme width and height).
DEFAULT_THREE_D - Static variable in class com.xinapse.filter.GaussianBlurFilter.GaussianBlurSpecifierPanel
The default setting for whether a GaussianBlurFilter should be in 3-D.
DEFAULT_WARN_NEGATIVE_PIXEL_SIZE - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Header
Whether to warn the user about negative pixel sizes by default.
deleteImage(String, Class<? extends ReadableImage>) - Static method in class com.xinapse.image.ImageUtils
Attempts to delete an image of the given Class<? extends WritableImage> with the given name.
deleteUserColourMapping(ColourMapping) - Static method in class com.xinapse.image.ColourMapping
Deletes one of the user-defined ColourMappings and removes it from the list maintained in the user preferences.
deleteVertex(Handle) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
deleteVertex(Handle) - Method in interface com.xinapse.multisliceimage.roi.EditableOutlineROI
Delete a point on the outline of this EditableOutlineROI that is under a handle.
deleteVertex(Handle) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
deleteVertex(Handle) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
deleteVertex(Handle) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
deregister() - Method in class com.xinapse.image.IntensityPresetsMenu
Deregister this IntensityPresetsMenu so that it will no longer be updated when the list of user-defined presets changes.
DEVTOKEN - Static variable in class com.xinapse.multisliceimage.roi.ROIStreamTokenizer
 
DICOMExtendedData - Class in com.xinapse.multisliceimage.Analyze
This class handles NIFTI 1.1 DICOM extended data.
dilate(double, AtomicInteger, CancellableThread.Flag) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Dilation of a RadialDivider has no effect.
dilate(double) - Method in class com.xinapse.multisliceimage.roi.ROI
Dilates this ROI by the specified distance.
dilate(double, AtomicInteger, CancellableThread.Flag) - Method in class com.xinapse.multisliceimage.roi.Text
Dilation of a Text ROI has no effect.
DILATE_2D_3_X_3 - Static variable in class com.xinapse.filter.MorphologicalOperator
A 2-D dilate operator with a 3x3 kernel.
DILATE_3D_3_X_3_X_3 - Static variable in class com.xinapse.filter.MorphologicalOperator
A 3-D dilate operator with a 3x3x3 kernel.
disposeImageData() - Method in interface com.xinapse.image.ReadableImage
Gives this image the option to free up resources by removing access to image data.
disposeImageData() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
disposeImageData() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
divide(Complex) - Method in class com.xinapse.image.Complex
Divides this complex by another complex number, and returns the result.
divide(Complex) - Method in class com.xinapse.image.DoubleComplex
 
divide(Complex) - Method in class com.xinapse.image.FloatComplex
 
DO_NOT_FLIP_FLIPPED_PROPERTY_KEY - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Header
The property value key for setting whether not to flip flipped Analyze 7.5 images.
doAnalysis(CardiacSegmentFrame, RadialDivider[], Integer, ROI[][][], ReadableImage[], boolean, int, int, int, float, float, MonitorWorker) - Method in interface com.xinapse.apps.cardiac.SegmentalAnalysis
Do the segmental analysis.
doCalc(ROIPropagateFrame, ROI[][][], ReadableImage[], int, int, float, float) - Method in interface com.xinapse.apps.active.ROICalculation
Perform the calculation on the image/ROIs.
doInBackground() - Method in class com.xinapse.apps.perfusion.AbstractDynamicWorker
 
doInBackground() - Method in class com.xinapse.multisliceimage.roi.ContourWorker
Runs this ContourWorker in the background.
doInBackground() - Method in class com.xinapse.multisliceimage.roi.MorphologicalOperationWorker
Perform the morphological operation.
doInBackground() - Method in class com.xinapse.multisliceimage.roi.SmootherWorker
Run the SmootherWorker to make an IrregularROI convex, or at least less concave.
doInBackground() - Method in class com.xinapse.util.MonitorWorker
Overrides the doInBackground() method.
done() - Method in class com.xinapse.apps.perfusion.AbstractDynamicWorker
 
done() - Method in class com.xinapse.multisliceimage.roi.ContourWorker
 
done() - Method in class com.xinapse.multisliceimage.roi.MorphologicalOperationWorker
 
done() - Method in class com.xinapse.multisliceimage.roi.SmootherWorker
 
done() - Method in class com.xinapse.util.MonitorWorker
Overrides the done() method.
done() - Method in class com.xinapse.util.Twiddler
Indicates that the operation for which this twiddler was created is finished.
done(String) - Method in class com.xinapse.util.Twiddler
Indicates that the operation for which this twiddler was created is finished.
doPostLoad() - Method in class com.xinapse.image.InputImageSelectionPanel
Does nothing.
doPostLoad() - Method in class com.xinapse.image.MultipleImageSelectionPanel
 
Double(byte[], ByteOrder) - Static method in class com.xinapse.io.ByteSwap
Swap the byte order (if necessary) in a eight-byte array and return the value represented by the bit pattern as a double.
Double(double) - Static method in class com.xinapse.io.ByteSwap
Swap the byte order in a double and return the value represented by the bit pattern of the reversed bytes as a double.
Double(InputStream, ByteOrder) - Static method in class com.xinapse.io.Input
Reads a double value from a java.io.InputStream strm, ensuring that blocking occurs until the value has been read.
Double(RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Input
Reads a double value from a java.io.RandomAccessFile f, ensuring that blocking occurs until the value has been read.
Double(Double, OutputStream, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single Double to a java.io.OutputStream strm as a double primitive.
Double(double, OutputStream, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single double to a java.io.OutputStream strm.
Double(Double, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single Double to a java.io.RandomAccessFile f as a double primitive.
Double(double, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single double to a java.io.RandomAccessFile f.
DoubleArray(InputStream, ByteOrder, int) - Static method in class com.xinapse.io.Input
Reads an array of double values from a java.io.InputStream strm ensuring that blocking occurs until all values have been read.
DoubleArray(InputStream, ByteOrder, double[]) - Static method in class com.xinapse.io.Input
Reads an array of double values from a DataInputStream strm ensuring that blocking occurs until all values have been read.
DoubleArray(RandomAccessFile, ByteOrder, double[]) - Static method in class com.xinapse.io.Input
Reads an array of double values from a java.io.RandomAccessFile f ensuring that blocking occurs until all values have been read.
DoubleArray(RandomAccessFile, ByteOrder, double[], int, int) - Static method in class com.xinapse.io.Input
Reads an array of double values from a java.io.RandomAccessFile f ensuring that blocking occurs until all values have been read.
DoubleArray(double[], OutputStream, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of double values to a java.io.OutputStream strm.
DoubleArray(double[], RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of double values to a java.io.RandomAccessFile f.
DoubleArray(double[], int, int, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of double values to a java.io.RandomAccessFile f.
DoubleComplex - Class in com.xinapse.image
A complex (real, imaginary) number, with double precision.
DoubleComplex() - Constructor for class com.xinapse.image.DoubleComplex
Creates a new DoubleComplex number, with zero real and imaginary parts.
DoubleComplex(double, double) - Constructor for class com.xinapse.image.DoubleComplex
Creates a new DoubleComplex number, with the real and imaginary parts specified by the arguments.
DoubleComplex(DoubleComplex) - Constructor for class com.xinapse.image.DoubleComplex
Creates a new DoubleComplex number, with the real and imaginary parts copied from an existing DoubleComplex.
DoublePixArray - Class in com.xinapse.image
A representation of an array of double-precision pixels.
DoublePixArray(int, int[], PixelDataType) - Constructor for class com.xinapse.image.DoublePixArray
Creates an empty DoublePixArray object containing the number of pixels given by nDim and dims.
DoublePixArray(Object, int, int[], PixelDataType) - Constructor for class com.xinapse.image.DoublePixArray
Creates an empty DoublePixArray object with enough pixels to contain the whole of the image.
DoublePixArray(DataInputStream, ByteOrder, int, int[], PixelDataType) - Constructor for class com.xinapse.image.DoublePixArray
Creates an DoublePixArray object, with the pixel intensity data coming from DataInputStream s, and containing the number of pixels specified in nDim and dims.
DoublePixArray(RandomAccessFile, ByteOrder, int, int, int[], PixelDataType) - Constructor for class com.xinapse.image.DoublePixArray
Creates an DoublePixArray object, with the pixel intensity data coming from RandomAccessFile f, and containing the number of pixels specified in nDim and dims.
draw(Graphics) - Method in class com.xinapse.multisliceimage.roi.CentreHandle
Draws this Handle on the given Graphics context.
draw(Graphics, Rectangle, int, int, int, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
draw(Graphics, Rectangle, int, int, int, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
draw(Graphics) - Method in class com.xinapse.multisliceimage.roi.EndHandle
Draws this Handle on the given Graphics context.
draw(Graphics) - Method in class com.xinapse.multisliceimage.roi.Handle
Draws this Handle using the given Graphics context.
draw(Graphics, Rectangle, int, int, int, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
draw(Graphics) - Method in class com.xinapse.multisliceimage.roi.InsertionPointHandle
Draws this InsertionPointHandle using the given Graphics context.
draw(Graphics, Rectangle, int, int, int, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
draw(Graphics, Rectangle, int, int, int, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.IrregularROIInProgress
 
draw(Graphics, Rectangle, int, int, int, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.LineROI
LineROIs are a special case, since we can't use the Bounding Rectangle to decide whether a Line is on screen, since the line may be vertical or horizontal, and therefore have an empty boundng rectangle.
draw(Graphics, Rectangle, int, int, int, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.Marker
Draws this ROI if it needs to be be drawn on screen.
draw(Graphics, int, int, Rectangle, int, int, int, int, int, int, float, float, List<ROI>) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Draws this RadialDivider if it needs to be be drawn on screen.
draw(Graphics, Rectangle, int, int, int, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
draw(Graphics, Rectangle, int, int, int, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.ROI
Draws this ROI if it needs to be be drawn on screen.
draw(Graphics, Rectangle, int, int, int, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
draw(Graphics, Rectangle, int, int, int, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.Text
 
draw(Graphics) - Method in class com.xinapse.multisliceimage.roi.VertexHandle
 
drawInOrthoView(Image, Point3f, Transform3D, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
drawInOrthoView(Image, Point3f, Transform3D, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
drawInOrthoView(Image, Point3f, Transform3D, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
drawInOrthoView(Image, Point3f, Transform3D, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
drawInOrthoView(Image, Point3f, Transform3D, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.Marker
 
drawInOrthoView(Image, Point3f, Transform3D, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
 
drawInOrthoView(Image, Point3f, Transform3D, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
drawInOrthoView(Image, Point3f, Transform3D, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.ROI
Draws this ROI on top of an orthogonal view of an image.
drawInOrthoView(Image, Point3f, Transform3D, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
drawInOrthoView(Image, Point3f, Transform3D, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.Text
 
drawRoamingResponseGraphs(List<XYDataSet>) - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Draws the graphs into the RoaminResponseDialog.
DuplicateROIException - Exception in com.xinapse.multisliceimage.roi
Signals the attempted creation and addition of an identical duplicate ROI to an image.
DuplicateROIException() - Constructor for exception com.xinapse.multisliceimage.roi.DuplicateROIException
Constructs an DuplicateROIException without a detail message.
DuplicateROIException(String) - Constructor for exception com.xinapse.multisliceimage.roi.DuplicateROIException
Constructs an ROIException with the specified detail message.
DW_B_MATRIX_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the excitation diffusion-weighting B-matrix.
DW_B_VALUE_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the excitation diffusion-weighting b-value.
DW_GRADIENT_VECTOR_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the excitation diffusion-weighting gradient vector.
DynamicModel - Interface in com.xinapse.dynamic
An interface implemented by classes that can fit to dynamic signals that vary as a function of time.
DynamicModel.SpecifierPanel - Class in com.xinapse.dynamic
A JPanel that can be used to specify dynamic model parameters.
dynamicModelPanel - Variable in class com.xinapse.dynamic.AbstractDynamicFrame
The JPanel that contains the analysis setup.
DynamicResult - Class in com.xinapse.dynamic
An abstract result of a computation from a dynamic signal change.
DynamicResult(DynamicModel, float[], float, float[]) - Constructor for class com.xinapse.dynamic.DynamicResult
Used by sub-class constructors.

E

EastHandle - Class in com.xinapse.multisliceimage.roi
A Class representing a Handle on the East edge of an ROI.
EastHandle(int, int, int) - Constructor for class com.xinapse.multisliceimage.roi.EastHandle
Creates a new EastHandle at the location (x,y) with the given size in screen pixels.
ECHO_TIME_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the scan echo time.
EdgeHandle - Class in com.xinapse.multisliceimage.roi
An abstract Class representing a Handle at one of the four edges of an ROI.
EdgeHandle(int, int, int) - Constructor for class com.xinapse.multisliceimage.roi.EdgeHandle
Creates a new EdgeHandle at the location (x,y) with the given size in screen pixels.
EditableOutlineROI - Interface in com.xinapse.multisliceimage.roi
An interface that ROIs implement if they have an editable outline shape with handles at each vertex.
EllipticalROI - Class in com.xinapse.multisliceimage.roi
A Class representing an elliptical region of an image.
EllipticalROI(Point2D.Double, double, double, double) - Constructor for class com.xinapse.multisliceimage.roi.EllipticalROI
Creates a new EllipticalROI with the specified shape in mm coordinates.
EllipticalROI(double, double, double, double, double, ROIState) - Constructor for class com.xinapse.multisliceimage.roi.EllipticalROI
Creates a new EllipticalROI with the specified shape in mm coordinates.
EllipticalROI(double, double, double, double, double, byte, ROIState) - Constructor for class com.xinapse.multisliceimage.roi.EllipticalROI
Creates a new EllipticalROI with the specified shape in mm coordinates.
EllipticalROICreateDialog - Class in com.xinapse.multisliceimage.roi
A dialog used to create Elliptical ROIs.
EllipticalROICreateDialog(CanAddROIToFrame) - Constructor for class com.xinapse.multisliceimage.roi.EllipticalROICreateDialog
Creates a new EllipticalROICreateDialog, with ROIs that are created by the dialog being added to the specified frame.
EndHandle - Class in com.xinapse.multisliceimage.roi
A Class representing a Handle at one of the two ends of a LineROI.
EndHandle(int, int, int) - Constructor for class com.xinapse.multisliceimage.roi.EndHandle
Creates a new EndHandle at the location (x,y) with the given size in screen pixels.
equals(Object) - Method in class com.xinapse.filter.MorphologicalOperator
Tests whether the supplied argument is equal to this MorphologicalOperator.
equals(Object) - Method in class com.xinapse.image.ColourMapping
 
equals(Object) - Method in class com.xinapse.image.DoubleComplex
Determines whether another object is equal to this DoubleComplex number.
equals(Object) - Method in class com.xinapse.image.FloatComplex
Determines whether another object is equal to this FloatComplex number.
equals(Object) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
equals(Object) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
equals(Object) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
equals(Object) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
equals(Object) - Method in class com.xinapse.multisliceimage.roi.Marker
 
equals(Object) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
 
equals(Object) - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
equals(Object) - Method in class com.xinapse.multisliceimage.roi.ROI
Indicates whether some Object is equal to this ROI.
equals(Object) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
equals(Object) - Method in class com.xinapse.util.BitSet
Returns true if the obj is a bit set that contains exactly the same elements as this bit set, otherwise false.
erasePoints(List<Point2D>, float, int, int, float, float) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
Erase points from this CurvedLineROI.
erasePoints(List<Point2D>, float, int, int, float, float) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Erase points from this IrregularROI.
ERODE_2D_3_X_3 - Static variable in class com.xinapse.filter.MorphologicalOperator
A 2-D erode operator with a 3x3 kernel.
ERODE_3D_3_X_3_X_3 - Static variable in class com.xinapse.filter.MorphologicalOperator
A 3-D erode operator with a 3x3x3 kernel.
errorMessage - Variable in class com.xinapse.util.MonitorWorker
An error message set when an error occurs.
exchangeROIs(List<ROI>, List<ROI>, ROIEditAction) - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Exchange one java.util.List of ROIs with another java.util.List of ROIs in this Frame.
exclusiveOr(ROI) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
exclusiveOr(ROI) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
exclusiveOr(ROI) - Method in class com.xinapse.multisliceimage.roi.Marker
 
exclusiveOr(ROI) - Method in class com.xinapse.multisliceimage.roi.ROI
Performs an exclusive OR operation on the shape of this ROI with another ROI.
ExitStatus - Enum in com.xinapse.platform
Exit status codes on program termination.
expi() - Method in class com.xinapse.image.Complex
Returns the exponential of this complex number multiplied by i.
expi() - Method in class com.xinapse.image.DoubleComplex
 
expi() - Method in class com.xinapse.image.FloatComplex
 
export(ReadableImage, String, String, ColourMapping, double, double, ComplexMode, int) - Static method in class com.xinapse.image.ImageUtils
Writes an image to a disk file in a picture format (such as JPEG, GIF etc.), creating the disk image from this WritableImage, by drawing all of the slices in a raster of slices.
export(ReadableImage, String, ColourMapping, double, double, ComplexMode, int) - Method in class com.xinapse.image.ImageUtils
Returns an InputStream from which an external format image (such as JPEG, GIF etc.) can be read, producing the external format image from this WritableImage, by drawing all of the slices in a raster of slices.
export(ReadableImage, String, ImageOutputStream, ColourMapping, double, double, ComplexMode, int) - Static method in class com.xinapse.image.ImageUtils
Writes an image to an ImageOutputStream in an external format (such as JPEG, GIF etc.), creating the disk image from this ReadableImage, by drawing all of the slices in a raster of slices.
EXTENSION - Static variable in class com.xinapse.multisliceimage.Analyze.ANZHeader
The file extension for Analyze header files in lower case form.
EXTENSION - Static variable in class com.xinapse.multisliceimage.Analyze.ANZImage
The file extension for Analyze image files in lower case form.
EXTENSION - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIImage
The file extension for NIFTI image files.

F

Feret - Class in com.xinapse.multisliceimage.roi
A Class describing the minimum and maximum Feret's diameter.
FILE_EXTENSION - Static variable in class com.xinapse.multisliceimage.roi.ROIFileFilter
The extension for ROI files (".roi").
fileLabel - Variable in class com.xinapse.image.ImageSelectionPanel
The JLabel to display along side the image file.
fileSelectionPanel - Variable in class com.xinapse.image.ImageSelectionPanel
A JPanel displayed to allow an image file to be selected.
fileTextField - Variable in class com.xinapse.image.ImageSelectionPanel
The JTextField to set the image file.
filter(ReadableImage) - Method in class com.xinapse.filter.AbstractComplexKernelFilter
 
filter(ReadableImage, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractComplexKernelFilter
 
filter(SpatialFilter, ReadableImage, MonitorWorker, boolean) - Static method in class com.xinapse.filter.AbstractComplexKernelFilter
Filter a ReadableImage using the supplied filter, returning a new image which is a filtered version of the supplied image.
filter(ReadableImage) - Method in class com.xinapse.filter.AbstractKernelFilter
 
filter(ReadableImage, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractKernelFilter
 
filter(SpatialFilter, ReadableImage, MonitorWorker, boolean) - Static method in class com.xinapse.filter.AbstractKernelFilter
Filter a ReadableImage using the supplied filter, returning a new image which is a filtered version of the supplied image.
filter(ReadableImage) - Method in class com.xinapse.filter.ColourImageFilter
 
filter(ReadableImage, MonitorWorker, boolean) - Method in class com.xinapse.filter.ColourImageFilter
 
filter(ReadableImage) - Method in class com.xinapse.filter.SobelFilter.MagnitudeFilter
 
filter(ReadableImage, MonitorWorker, boolean) - Method in class com.xinapse.filter.SobelFilter.MagnitudeFilter
 
filter(ReadableImage) - Method in interface com.xinapse.filter.SpatialFilter
Filter a ReadableImage, returning a new image which is a filtered version of the supplied image.
filter(ReadableImage, MonitorWorker, boolean) - Method in interface com.xinapse.filter.SpatialFilter
Filter a ReadableImage, returning a new image which is a filtered version of the supplied image.
FILTER_SELECTION_OPTION - Static variable in class com.xinapse.filter.FilterSelection
The Option used to select a particular filter.
filterInPlace(WritableImage) - Method in class com.xinapse.filter.AbstractComplexKernelFilter
 
filterInPlace(WritableImage, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractComplexKernelFilter
 
filterInPlace(Object, PixelDataType, int, int, int) - Method in class com.xinapse.filter.AbstractComplexKernelFilter
 
filterInPlace(Object, PixelDataType, int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractComplexKernelFilter
 
filterInPlace(SpatialFilter, WritableImage) - Static method in class com.xinapse.filter.AbstractComplexKernelFilter
Filter a WritableImage "in place" using the supplied filter.
filterInPlace(SpatialFilter, Object, PixelDataType, int, int, int) - Static method in class com.xinapse.filter.AbstractComplexKernelFilter
Filter an array of pixel values "in place".
filterInPlace(SpatialFilter, WritableImage, MonitorWorker, boolean) - Static method in class com.xinapse.filter.AbstractComplexKernelFilter
Filter an image "in place".
filterInPlace(WritableImage) - Method in class com.xinapse.filter.AbstractKernelFilter
 
filterInPlace(WritableImage, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractKernelFilter
 
filterInPlace(Object, PixelDataType, int, int, int) - Method in class com.xinapse.filter.AbstractKernelFilter
 
filterInPlace(Object, PixelDataType, int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractKernelFilter
 
filterInPlace(SpatialFilter, WritableImage) - Static method in class com.xinapse.filter.AbstractKernelFilter
Filter a WritableImage "in place" using the supplied filter.
filterInPlace(SpatialFilter, Object, PixelDataType, int, int, int) - Static method in class com.xinapse.filter.AbstractKernelFilter
Filter an array of pixel values "in place".
filterInPlace(SpatialFilter, WritableImage, MonitorWorker, boolean) - Static method in class com.xinapse.filter.AbstractKernelFilter
Filter an image "in place".
filterInPlace(WritableImage) - Method in class com.xinapse.filter.ColourImageFilter
 
filterInPlace(WritableImage, MonitorWorker, boolean) - Method in class com.xinapse.filter.ColourImageFilter
 
filterInPlace(Object, PixelDataType, int, int, int) - Method in class com.xinapse.filter.ColourImageFilter
 
filterInPlace(Object, PixelDataType, int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.ColourImageFilter
 
filterInPlace(Object, PixelDataType, int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.MorphologicalOperator
 
filterInPlace(WritableImage) - Method in class com.xinapse.filter.SobelFilter.MagnitudeFilter
 
filterInPlace(WritableImage, MonitorWorker, boolean) - Method in class com.xinapse.filter.SobelFilter.MagnitudeFilter
 
filterInPlace(Object, PixelDataType, int, int, int) - Method in class com.xinapse.filter.SobelFilter.MagnitudeFilter
 
filterInPlace(Object, PixelDataType, int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.SobelFilter.MagnitudeFilter
 
filterInPlace(WritableImage) - Method in interface com.xinapse.filter.SpatialFilter
Filter a WritableImage "in place".
filterInPlace(WritableImage, MonitorWorker, boolean) - Method in interface com.xinapse.filter.SpatialFilter
Filter a WritableImage "in place".
filterInPlace(Object, PixelDataType, int, int, int) - Method in interface com.xinapse.filter.SpatialFilter
Filter an array of pixel values "in place".
filterInPlace(Object, PixelDataType, int, int, int, MonitorWorker, boolean) - Method in interface com.xinapse.filter.SpatialFilter
Filter an array of pixel values "in place".
filterInPlaceBinary(BitSet, int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractKernelFilter
Filter an array of binary pixel values "in place".
filterInPlaceBinary(BitSet, int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.FixedWeightsKernelFilter
 
filterInPlaceByte(byte[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractKernelFilter
Filter an array of signed byte pixel values "in place".
filterInPlaceByte(byte[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.FixedWeightsKernelFilter
 
filterInPlaceDouble(double[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractKernelFilter
Filter an array of double-precision pixel values "in place".
filterInPlaceDouble(double[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.FixedWeightsKernelFilter
 
filterInPlaceDouble(double[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.MorphologicalOperator
 
filterInPlaceFloat(float[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractKernelFilter
Filter an array of floating-point pixel values "in place".
filterInPlaceFloat(float[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.FixedWeightsKernelFilter
 
filterInPlaceFloat(float[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.MedianFilter
 
filterInPlaceFloat(float[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.MorphologicalOperator
 
filterInPlaceInt(int[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractKernelFilter
Filter an array of signed int pixel values "in place".
filterInPlaceInt(int[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.FixedWeightsKernelFilter
 
filterInPlaceLong(long[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractKernelFilter
Filter an array of long pixel values "in place".
filterInPlaceLong(long[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.FixedWeightsKernelFilter
 
filterInPlaceShort(short[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractKernelFilter
Filter an array of signed short pixel values "in place".
filterInPlaceShort(short[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.FixedWeightsKernelFilter
 
filterInPlaceUByte(byte[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractKernelFilter
Filter an array of unsigned byte pixel values "in place".
filterInPlaceUByte(byte[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.FixedWeightsKernelFilter
 
filterInPlaceUInt(int[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractKernelFilter
Filter an array of unsigned int pixel values "in place".
filterInPlaceUInt(int[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.FixedWeightsKernelFilter
 
filterInPlaceUShort(short[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractKernelFilter
Filter an array of unsigned short pixel values "in place".
filterInPlaceUShort(short[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.FixedWeightsKernelFilter
 
FilterSelection - Class in com.xinapse.filter
A class for selecting a SpatialFilter.
FilterSelection.Panel - Class in com.xinapse.filter
A JPanel that contains a JTabbedPane that can be used to select one of the known SpatialFilters.
fit(float[], int, int, int, AutoCorrelationEstimate, MonitorWorker) - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
Calculate the model parameters that best fit the data.
fit(float[], int, int, int, AutoCorrelationEstimate, MonitorWorker) - Method in interface com.xinapse.dynamic.DynamicModel
Calculate the model parameters that best fit the data.
FixedWeightsComplexKernelFilter - Class in com.xinapse.filter
A class for performing filtering of complex images based on a moving kernel of pixels with fixed complex weights within the kernel.
FixedWeightsComplexKernelFilter() - Constructor for class com.xinapse.filter.FixedWeightsComplexKernelFilter
Default constructor produces an identity FixedWeightsComplexKernelFilter with kernel size 1x1x1 that has no effect when applied.
FixedWeightsComplexKernelFilter(FloatComplex[][], boolean, BoundaryCondition) - Constructor for class com.xinapse.filter.FixedWeightsComplexKernelFilter
Constructs a 2-dimensional kernel-based filter with the given filter weights.
FixedWeightsComplexKernelFilter(FloatComplex[][][], boolean, BoundaryCondition) - Constructor for class com.xinapse.filter.FixedWeightsComplexKernelFilter
Constructs a 3-dimensional kernel-based filter with the given filter weights.
FixedWeightsKernelFilter - Class in com.xinapse.filter
A class for performing filtering of images based on a moving kernel of pixels with fixed weights within the kernel.
FixedWeightsKernelFilter() - Constructor for class com.xinapse.filter.FixedWeightsKernelFilter
Default constructor produces an identity FixedWeightsKernelFilter with kernel size 1x1x1 that has no effect when applied.
FixedWeightsKernelFilter(float[][], boolean, BoundaryCondition) - Constructor for class com.xinapse.filter.FixedWeightsKernelFilter
Constructs a 2-dimensional kernel-based filter with the given filter weights.
FixedWeightsKernelFilter(float[][][], boolean, BoundaryCondition) - Constructor for class com.xinapse.filter.FixedWeightsKernelFilter
Constructs a 3-dimensional kernel-based filter with the given filter weights.
flag - Variable in class com.xinapse.util.CancellableThread
 
Flag() - Constructor for class com.xinapse.util.CancellableThread.Flag
 
flip(ReadableImage, boolean, boolean, boolean, MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Flips the image data in a ReadableImage.
flip(int) - Method in class com.xinapse.util.BitSet
Sets the bit at the index to the opposite value.
flip() - Method in class com.xinapse.util.BitSet
Sets all bits to the opposite value.
flip(int, int) - Method in class com.xinapse.util.BitSet
Sets a range of bits to the opposite value.
FLIP_ANGLE_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the excitation pulse flip angle.
FLIP_NON_FLIPPED_PROPERTY_KEY - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Header
The property value key for setting whether to flip non-flipped Analyze 7.5 images.
flipHorizontal(Point2D) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
flipHorizontal(Point2D) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
flipHorizontal(Point2D) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
flipHorizontal(Point2D) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
flipHorizontal(Point2D) - Method in class com.xinapse.multisliceimage.roi.Marker
 
flipHorizontal(Point2D) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
This method does nothing.
flipHorizontal(Point2D) - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
flipHorizontal(Point2D) - Method in class com.xinapse.multisliceimage.roi.ROI
Flip this ROI horizontally about a given location.
flipHorizontal(Point2D) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
flipVertical(Point2D) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
flipVertical(Point2D) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
flipVertical(Point2D) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
flipVertical(Point2D) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
flipVertical(Point2D) - Method in class com.xinapse.multisliceimage.roi.Marker
 
flipVertical(Point2D) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
This method does nothing.
flipVertical(Point2D) - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
flipVertical(Point2D) - Method in class com.xinapse.multisliceimage.roi.ROI
Flip this ROI vertically about a given location.
flipVertical(Point2D) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
flipX(Object, int, int) - Method in enum com.xinapse.image.PixelDataType
Flips an array of pixels in-place about the x-axis (ie, flips top to bottom).
flipY(Object, int) - Method in enum com.xinapse.image.PixelDataType
Flips an array of pixels in-place about the y-axis (ie flips left-right).
Float(float[], ByteOrder) - Static method in class com.xinapse.io.ByteSwap
Swap the byte order (if necessary) in an array of float values "in-place".
Float(float) - Static method in class com.xinapse.io.ByteSwap
Swap the byte order in a float and return the value represented by the bit pattern of the reversed bytes as a float.
Float(byte[], ByteOrder) - Static method in class com.xinapse.io.ByteSwap
Swap the byte order (if necessary) in a four-byte array and return the value represented by the bit pattern as a float.
Float(InputStream, ByteOrder) - Static method in class com.xinapse.io.Input
Reads a float value from a java.io.InputStream strm, ensuring that blocking occurs until the value has been read.
Float(RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Input
Reads a float value from a java.io.RandomAccessFile f, ensuring that blocking occurs until the value has been read.
Float(Float, OutputStream, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single Float to a java.io.OutputStream strm as a float primitive.
Float(float, OutputStream, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single float to a java.io.OutputStream strm.
Float(Float, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single Float to a java.io.RandomAccessFile f as a float primitive.
Float(float, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single float to a java.io.RandomAccessFile f.
FloatArray(InputStream, ByteOrder, int) - Static method in class com.xinapse.io.Input
Reads an array of float values from a java.io.InputStream strm ensuring that blocking occurs until all values have been read.
FloatArray(DataInputStream, ByteOrder, float[]) - Static method in class com.xinapse.io.Input
Reads an array of float values from a DataInputStream strm ensuring that blocking occurs until all values have been read.
FloatArray(RandomAccessFile, ByteOrder, float[]) - Static method in class com.xinapse.io.Input
Reads an array of float values from a java.io.RandomAccessFile f ensuring that blocking occurs until all values have been read.
FloatArray(RandomAccessFile, ByteOrder, float[], int, int) - Static method in class com.xinapse.io.Input
Reads an array of float values from a java.io.RandomAccessFile f ensuring that blocking occurs until all values have been read.
FloatArray(float[], OutputStream, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of float values to a java.io.OutputStream strm.
FloatArray(float[], RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of float values to a java.io.RandomAccessFile f.
FloatArray(float[], int, int, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of float values to a java.io.RandomAccessFile f.
FloatComplex - Class in com.xinapse.image
A complex (real, imaginary) number, with single precision.
FloatComplex() - Constructor for class com.xinapse.image.FloatComplex
Creates a new FloatComplex number, with zero real and imaginary parts.
FloatComplex(float, float) - Constructor for class com.xinapse.image.FloatComplex
Creates a new FloatComplex number, with the real and imaginary parts specified by the arguments.
FloatComplex(Complex) - Constructor for class com.xinapse.image.FloatComplex
Creates a new FloatComplex number, with the real and imaginary parts copied from an existing Complex.
folderLabel - Variable in class com.xinapse.image.ImageSelectionPanel
The JLabel to display along side the image folder, or null if the image folder isn't shown separately.
folderTextField - Variable in class com.xinapse.image.ImageSelectionPanel
The JTextField to set the image folder, or null if the image folder isn't shown separately.
FRAME_OF_REFERENCE_UID_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the frame of reference UID for the image position/orientation.
FSL_COMPATIBLE_NIFTI_PROPERTY_KEY - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
The property value key for setting whether NIFTI-1 images that have qform and sform orientation both unset should be read as having an increasing a patient left coordinate value with stored pixel data column number, and whether NIFTI-1 images should be prevented from being written without orientation information.
FWHM_OPTION - Static variable in class com.xinapse.filter.GaussianBlurFilter
Command line option for setting the full-width-half-maximum values for a GaussianBlurFilter.
fwhmTextField - Variable in class com.xinapse.dynamic.AbstractDynamicFrame
A JFormattedTextField to set the FWHM of the smoothing filter.

G

GaussianBlurFilter - Class in com.xinapse.filter
A FixedWeightsKernelFilter for performing a Gaussian blurring of an image.
GaussianBlurFilter.GaussianBlurSpecifierPanel - Class in com.xinapse.filter
A FilterSpecifierPanel for a Gaussian blur filter.
generateReport() - Method in class com.xinapse.util.ReportGenerator
Cause this ReportGenerator to generate a report.
get(int) - Method in class com.xinapse.util.BitSet
Returns true if the integer bitIndex is in this bit set, otherwise false.
get(int, int) - Method in class com.xinapse.util.BitSet
Returns a new BitSet composed of a range of bits from this one.
get12(float[]) - Method in class com.xinapse.geom3d.AffineTransform3D
Sets the matrix values of this transform to the matrix values in the single precision array parameter.
getA() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
Returns the first semi-major axis length in mm.
getAction() - Method in class com.xinapse.multisliceimage.roi.HistoryItem
Return the action performed in this HistoryItem.
getActionString() - Method in class com.xinapse.multisliceimage.roi.HistoryItem
Return the action performed in this HistoryItem as a java.lang.String.
getAffineTransform() - Method in interface com.xinapse.image.ReadableImage
Returns the AffineTransform3D that will transform the pixel indices (colIdx, rowIdx, sliceIdx) to a position in space in the patient-centric coordinate system.
getAffineTransform(Integer) - Method in interface com.xinapse.image.ReadableImage
Returns the AffineTransform3D that will transform the pixel indices (colIdx, rowIdx, sliceIdx) to a position in space in the patient-centric coordinate system for one particular slice of the image.
getAllColourMappings() - Static method in class com.xinapse.image.ColourMapping
Returns a java.util.List<ColourMapping> of all ColourMappings, both built-in and imported by the user.
getAllPresets() - Static method in class com.xinapse.image.IntensityPreset
Returns a java.util.List<IntensityPreset> of all IntensityPresets, both built-in and created by the user.
getAlwaysAsk() - Static method in enum com.xinapse.dicom.Modality
Returns whether always to ask the user what is the Modality, if not set in an image.
getAlwaysAsk() - Static method in enum com.xinapse.dicom.PatientPosition
Returns whether the user prefers always to be asked to set the PatientPosition.
getAlwaysAsk() - Static method in enum com.xinapse.dicom.PulseSequenceType
Returns whether the user prefers always to be asked to set the PulseSequenceType.
getAnalysis() - Method in class com.xinapse.apps.cardiac.SegmentalAnalysis.SpecifierPanel
Returns the SegmentalAnalysis that has been specified by this SegmentalAnalysis.SpecifierPanel.
getAnalysisDescription() - Method in interface com.xinapse.apps.cardiac.SegmentalAnalysis
Returns a String describing this segmental analysis.
getAnalysisName() - Method in interface com.xinapse.apps.cardiac.SegmentalAnalysis
Returns the name of the analysis.
getAnnotation() - Method in class com.xinapse.multisliceimage.roi.ROI
Gets the anotation string for this ROI.
getAreaUnder() - Method in class com.xinapse.image.Histogram
Returns the total area under this histogram.
getAreaUnder(boolean) - Method in class com.xinapse.image.Histogram
Returns the area under this histogram, optionally excluding any zero-valued values.
getArg() - Method in class com.xinapse.image.Complex
Returns the polar angle of this complex number.
getArg() - Method in class com.xinapse.image.DoubleComplex
 
getArg() - Method in class com.xinapse.image.FloatComplex
 
getArrayElementsPerPixel() - Method in enum com.xinapse.image.PixelDataType
Returns the number of array elements of a primitive type needed to store a single pixel value.
getB() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
Returns the second semi-major axis length in mm.
getBinWidth() - Method in class com.xinapse.image.Histogram
Returns the bin width for this Histogram.
getBitsPerPixel() - Method in enum com.xinapse.image.PixelDataType
Returns the number of bits used to store one pixel for this data type.
getBodyPart() - Method in interface com.xinapse.image.ReadableImage
Returns the body part imaged.
getBodyPart() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getBodyPart() - Method in class com.xinapse.multisliceimage.MultiSliceImage
By default, body part recording is not supported, so this method always returns null.
getBodyPart() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getBorderColor() - Static method in class com.xinapse.multisliceimage.roi.Handle
Returns the Color with which ROI Handle borders are to be drawn.
getBoundingRectangle(int, int, float, float) - Method in class com.xinapse.multisliceimage.roi.LineROI
Returns a high-precision rectangle (in pixel coordinates) that just bounds this ROI.
getBoundingRectangle(int, int, float, float) - Method in class com.xinapse.multisliceimage.roi.Marker
 
getBoundingRectangle(List<ROI>, int, int, float, float) - Static method in class com.xinapse.multisliceimage.roi.ROI
Returns a high-precision rectangle (in image pixel coordinates) that bounds all the ROIs in the ROIlist.
getBoundingRectangle(int, int, float, float) - Method in class com.xinapse.multisliceimage.roi.ROI
Returns a high-precision rectangle (in image pixel coordinates) that just bounds this ROI.
getBT() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
Returns the threshold fraction to use with the Brain Finder, if this option has been set in the GUI.
getBuiltInMappings() - Static method in class com.xinapse.image.ColourMapping
Returns a java.util.List<ColourMapping> of the built-in ColourMappings.
getBuiltInPresets() - Static method in class com.xinapse.image.IntensityPreset
Returns a java.util.List<IntensityPreset> of the built-in IntensityPresets.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.ContourROI
Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.CurvedLineROI
Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.EllipticalROI
Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.IrregularROI
Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.LineROI
Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.Marker
Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.OpenSplineROI
Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.RectangularROI
Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.SplineROI
Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.Text
Returns an Icon that can be used for a button to create this type of ROI.
getByteOrder() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getByteOrder() - Method in class com.xinapse.multisliceimage.MultiSliceImage
Returns the byte order for this image.
getByteOrder() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getBytesPerPixel() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns the number of bytes per pixel for this image.
getBytesPerPixel() - Method in enum com.xinapse.multisliceimage.UNC.UNCPixFormat
Returns the number of bytes per pixel for this UNCPixFormat.
getCalc() - Method in class com.xinapse.apps.active.ROICalculation.SpecifierPanel
Returns the ROICalculation that has been specified by this ROICalculation.SpecifierPanel.
getCalcOptions() - Static method in class com.xinapse.apps.active.SelectableROICalculation
Returns an array of Options that are used with the ROICalculation.
getCalculationDescription() - Method in interface com.xinapse.apps.active.ROICalculation
Returns a String describing this ROI calculation.
getCalculationName() - Method in interface com.xinapse.apps.active.ROICalculation
Returns the name of the calculation.
getCentre() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
getCentre() - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
getCentre() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
getCentre() - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getCentre() - Method in interface com.xinapse.multisliceimage.roi.RotatableROI
Gets the centre (about which rotation will occur) of this RotatableROI in mm.
getCentre() - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
getCentreOfMass(ReadableImage, Double, boolean) - Static method in class com.xinapse.image.ImageMoments
Calculates the centre of mass of an image.
getCentreOfMass(ReadableImage, Object, PixelDataType) - Static method in class com.xinapse.image.ImageMoments
Calculates the centre of mass of an image.
getCentrePix(int, int, float, float) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
Gets the centre of this ROI in pixel coordinates.
getCentroid() - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
getCentroid() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
getCentroid() - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
getCentroid() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
getCentroid() - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getCentroid() - Method in class com.xinapse.multisliceimage.roi.Marker
 
getCentroid() - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Returns null.
getCentroid() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
getCentroid() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the centroid (centre of area) of this ROI.
getCentroid(ROI[]) - Static method in class com.xinapse.multisliceimage.roi.ROI
Returns the centroid (centre of area) of an array of ROIs.
getCentroid() - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
getChoosableColor(int) - Static method in enum com.xinapse.multisliceimage.roi.ROIState
Returns one of the user-choosable ROI colours.
getClasses() - Static method in class com.xinapse.multisliceimage.roi.ROI
Returns an array of all known sub-classes of ROI.
getColor() - Static method in class com.xinapse.multisliceimage.roi.Handle
Returns the Color with which ROI Handles are to be drawn.
getColor() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the java.awt.Color in which this ROI should be drawn.
getColor() - Method in class com.xinapse.multisliceimage.roi.Text
Returns the java.awt.Color in which this Text ROI should be drawn.
getColorValue(Object, int) - Method in enum com.xinapse.image.PixelDataType
Gets a single colour pixel value from an array of pixels.
getColour(short) - Method in class com.xinapse.image.ColourMapping
Returns the colour in a particular slot of the colour mapping.
getColourMapping(String) - Static method in class com.xinapse.multisliceimage.Analyze.ANZColourMapping
Returns a ColourMapping by reading the values from the given file which has the contain a colour lookup table in Analyze format.
getColourPixelDataType(Class<? extends ReadableImage>) - Static method in class com.xinapse.image.Image
Returns the colour PixelDataType that is supported by a particular class of ReadableImage, or null if the class does not support a colour PixelDataType.
getCombineMode() - Method in class com.xinapse.multisliceimage.roi.CombineMode.Panel
Returns the CombineMode set in this panel.
getCommonInfo(InfoList[]) - Static method in class com.xinapse.util.InfoList
Returns an InfoList which contains only those InfoItems that are found in every element of the supplied InfoList[].
getCommonName() - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Returns the common name for this type of image.
getCommonName() - Static method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the common name for this type of image.
getCommonName() - Static method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns the common name for this type of image.
getComponent(int) - Method in interface com.xinapse.image.ImageSelectionGroupPanel.ComponentGenerator
Causes this ComponentGenerator to generate a new user component.
getComponent(int) - Method in class com.xinapse.util.IntensityRelation.PanelGenerator
 
getComponent() - Method in class com.xinapse.util.MonitorWorker
Returns the component from which this MonitorWorker was launched.
getContiguousContrasts() - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Note: getContiguousContrasts has a different meaning, depending on whether a single input image is used, or whether multiple input images are used: For a single input image, getContiguousContrasts() == true indicates that all contrasts for one slice are adjacent, before moving on to the next slice.
getContourMode() - Method in class com.xinapse.multisliceimage.roi.ContourMode.ComboBox
Returns the ContourMode currently set in this ContourMode.ComboBox.
getCopy() - Method in interface com.xinapse.image.ReadableImage
Returns a copy of this ReadableImage.
getCopy() - Method in interface com.xinapse.image.WritableImage
Returns a copy of this WritableImage.
getCopy() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
Creates an in-memory copy of an Analyze image.
getCopy() - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
getCopy() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
getCopy() - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
getCopy() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
getCopy() - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getCopy() - Method in class com.xinapse.multisliceimage.roi.Marker
 
getCopy() - Method in class com.xinapse.multisliceimage.roi.OpenSplineROI
 
getCopy() - Method in class com.xinapse.multisliceimage.roi.RadialDivider
 
getCopy() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
getCopy() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns a copy of this ROI.
getCopy() - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
getCopy() - Method in class com.xinapse.multisliceimage.roi.Text
 
getCopy() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getCorrectAutoCorrelation() - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
Returns false, since the DynamicContrastModels do not do a correction for temporal autocorrelation.
getCorrectAutoCorrelation() - Method in interface com.xinapse.dynamic.DynamicModel
Signals whether the model requires the autocorrelation in the time-series to be estimated when computing significance levels.
getCount(int) - Method in class com.xinapse.image.Histogram
Returns the count in one bin of this Histogram.
getCreateDialog(CanAddROIToFrame) - Static method in class com.xinapse.multisliceimage.roi.EllipticalROI
Returns a JDialog that can be used to create Elliptical ROIs.
getCreateDialog(CanAddROIToFrame) - Static method in class com.xinapse.multisliceimage.roi.LineROI
Returns a JDialog that can be used to create Line ROIs.
getCreateDialog(CanAddROIToFrame) - Static method in class com.xinapse.multisliceimage.roi.Marker
Returns a JDialog that can be used to create Marker ROIs.
getCreateDialog(CanAddROIToFrame) - Static method in class com.xinapse.multisliceimage.roi.RectangularROI
Returns a JDialog that can be used to create Rectangular ROIs.
getCreateDialog(CanAddROIToFrame) - Static method in class com.xinapse.multisliceimage.roi.Text
Returns a JDialog that can be used to create Text ROIs.
getCreateInteractionType() - Static method in class com.xinapse.multisliceimage.roi.ContourROI
Returns the type of interaction needed to create a ContouredROI.
getCreateInteractionType() - Static method in class com.xinapse.multisliceimage.roi.CurvedLineROI
Returns the type of interaction needed to create a CurvedLineROI.
getCreateInteractionType() - Static method in class com.xinapse.multisliceimage.roi.EllipticalROI
Returns the type of interaction needed to create an EllipticalROI.
getCreateInteractionType() - Static method in class com.xinapse.multisliceimage.roi.IrregularROI
Returns the type of interaction needed to create an IrregularROI.
getCreateInteractionType() - Static method in class com.xinapse.multisliceimage.roi.LineROI
Returns the type of interaction needed to create a LineROI.
getCreateInteractionType() - Static method in class com.xinapse.multisliceimage.roi.Marker
Returns the type of interaction needed to create a Marker.
getCreateInteractionType() - Static method in class com.xinapse.multisliceimage.roi.OpenSplineROI
Returns the type of interaction needed to create an OpenSplineROI.
getCreateInteractionType() - Static method in class com.xinapse.multisliceimage.roi.RectangularROI
Returns the type of interaction needed to create a RectangularROI.
getCreateInteractionType() - Static method in class com.xinapse.multisliceimage.roi.SplineROI
Returns the type of interaction needed to create a SplineROI.
getCreateInteractionType() - Static method in class com.xinapse.multisliceimage.roi.Text
Returns the type of interaction needed to create a Text ROI.
getCSFProbTemplate() - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in csf probability template image.
getCumulativeHistogram() - Method in class com.xinapse.image.Histogram
Return a new Histogram that is the cumulative histogram of this one.
getCumulativeIntensity(float, boolean) - Method in class com.xinapse.image.Histogram
Returns a value such that the specified fraction of values is below the returned intensity; zero-valued values are optionally excluded from the calculation.
getCumulativeStats(List<ROIStats>, PixelDataType) - Static method in class com.xinapse.multisliceimage.roi.ROIStats
Returns the cumulative stats for a List of ROIStats.
getCurvature(int) - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns the signed curvature of the outline shape at a knot point.
getCurvature(double) - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns the signed curvature of the outline shape at particular value of the s-parameter.
getDataType() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
Returns the data type (ANZPixFormat) of this image.
getDateFormat() - Static method in class com.xinapse.multisliceimage.MultiSliceImage
Returns the DateFormat used when this class writes dates.
getDBName() - Method in class com.xinapse.multisliceimage.Analyze.ANZHeader
Returns the data base name for this Analyze image header.
getDeletedROIs() - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Returns a java.util.List of deleted (not current) ROIs for the image displayed.
getDeletedROIs(int) - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Returns a java.util.List of deleted (not current) ROIs for one slice of the image displayed.
getDeltaX() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
For the purposes of plotting data, returns the step between values of the independent variable.
getDeltaX() - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the δ x-value between adjacent points on a pop-up plot.
getDescription() - Method in enum com.xinapse.dicom.Modality
Returns a string describing this imaging modality.
getDescription() - Method in class com.xinapse.image.ImageFileFilter
Returns "All Images".
getDescription() - Method in interface com.xinapse.image.ReadableImage
Returns a String description of this image.
getDescription(int) - Method in interface com.xinapse.image.ReadableImage
Returns a String description of this one particular slice of this image.
getDescription() - Method in enum com.xinapse.image.template.WeightingType
Returns a string describing this image weighting type.
getDescription() - Method in class com.xinapse.multisliceimage.Analyze.AnalyzeFileFilter
Returns "Analyze Images".
getDescription() - Method in class com.xinapse.multisliceimage.Analyze.ANZHeader
Returns the description for this Analyze image header.
getDescription() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getDescription(int) - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getDescription() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIFileFilter
Returns "NIFTI Images".
getDescription() - Method in class com.xinapse.multisliceimage.roi.ContourROI
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.ImageJROIFileFilter
Returns "ImageJ Region of Interest Files".
getDescription() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.Marker
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.OpenSplineROI
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.RadialDivider
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.ROI
Return a description of this type of ROI.
getDescription() - Method in class com.xinapse.multisliceimage.roi.ROIFileFilter
Returns "Region of Interest Files".
getDescription() - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.Text
 
getDescription() - Method in class com.xinapse.multisliceimage.UNC.UNCFileFilter
Returns "UNC Images".
getDescription() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getDescription(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getDescription() - Method in enum com.xinapse.util.IntensityRelation
Returns a String describing this IntensityRelation in detail.
getDimc() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns the dimensionality of this image.
getDims() - Method in interface com.xinapse.image.ReadableImage
Returns the dimensions (numbers of samples in each image dimension) of this image.
getDims() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getDims() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getDimv() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns the dimensions of this image.
getDisplayedBounds2D(List<ROI>) - Static method in class com.xinapse.multisliceimage.roi.ROI
Returns a high-precision rectangle (in screen coordinates) that bounds all the ROIs in the ROIlist.
getDisplayedBounds2D() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns a high-precision rectangle (in screen coordinates) that just bounds this ROI.
getDisplayedBounds2D() - Method in interface com.xinapse.multisliceimage.roi.StretchableROI
Returns a high-precision rectangle (in screen coordinates) that just bounds this ROI.
getDisplayedRoiArea() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the java.awt.geom.Area of this ROI as it is displayed on-screen.
getDividerColor() - Static method in class com.xinapse.multisliceimage.roi.RadialDivider
Returns the Color to be used for drawing the end/epicardium divider.
getDoBonferroni() - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
Returns false, since Bonferroni correction is not performed because significance values for the fitted parameters are not computed.
getDoBonferroni() - Method in interface com.xinapse.dynamic.DynamicModel
Returns true if this DynmicModel does Bonferroni correction; false otherwise.
getDoubleValue(Object, int) - Method in enum com.xinapse.image.PixelDataType
Gets a single pixel value from an array of pixels.
getDoubleValue(Object, ComplexMode) - Method in enum com.xinapse.image.PixelDataType
Converts a single pixel value to a double value.
getDrawColor(byte) - Method in enum com.xinapse.multisliceimage.roi.ROIState
Returns the colour with which an ROI in this state should be drawn.
getDt() - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
Returns the time between data samples.
getDt() - Method in interface com.xinapse.dynamic.DynamicModel
Returns the time between data samples.
getDynamicModel() - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the DynamicModel set in this MultiContrastAnalysisFrame.
getEntriesString() - Method in class com.xinapse.image.ColourMapping
Returns a String showing either: The [R,G,B] entries for this ColourMapping, or If the ColourMapping is MONOCHROME1 or MONOCHROME2, the String "MONOCHROME1" or "MONOCHROME2".
getEntropy() - Method in class com.xinapse.image.Histogram
Returns the entropy of this Histogram.
getExtendedData() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns a java.util.List of ExtendedData for this NIFTIImage.
getFeret() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
getFeret() - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
getFeret() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
getFeret() - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getFeret() - Method in class com.xinapse.multisliceimage.roi.Marker
 
getFeret() - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Returns zero.
getFeret() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
getFeret() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the minimum and maximum Feret's diameter for this ROI, in mm.
getFeret(List<ROI>) - Static method in class com.xinapse.multisliceimage.roi.ROI
Returns the minimum and maximum Feret's diameter for a List of ROI, in mm.
getFeret() - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
getFile() - Method in class com.xinapse.image.ImageSelectionPanel
Returns the image File set in this ImageSelectionPanel.
getFile() - Method in class com.xinapse.image.OutputImageSelectionPanel
Returns the image File set in this OutputImageSelectionPanel.
getFileDataOffset() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getFileDataOffset() - Method in class com.xinapse.multisliceimage.MultiSliceImage
Returns the byte offset into the disk-based file format where pixel data begins.
getFileDataOffset() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns the byte offset into the disk-based file format where pixel data begins.
getFilter(ReadableImage) - Method in class com.xinapse.filter.ColourImageFilter.ColourImageFilterSpecifierPanel
 
getFilter(ReadableImage) - Method in class com.xinapse.filter.FilterSelection.Panel
Returns the SpatialFilter currently set in this FilterSelectionPanel.
getFilter(ReadableImage) - Method in class com.xinapse.filter.GaussianBlurFilter.GaussianBlurSpecifierPanel
 
getFilter(ReadableImage) - Method in class com.xinapse.filter.LaplacianFilter.LaplacianSpecifierPanel
 
getFilter(ReadableImage) - Method in class com.xinapse.filter.MedianFilter.MedianSpecifierPanel
 
getFilter(ReadableImage) - Method in class com.xinapse.filter.MorphologicalOperator.MorphologicalSpecifierPanel
 
getFilter(ReadableImage) - Method in class com.xinapse.filter.SharpenFilter.SharpenSpecifierPanel
 
getFilter(ReadableImage) - Method in class com.xinapse.filter.SobelFilter.SobelSpecifierPanel
 
getFilter(ReadableImage) - Method in class com.xinapse.filter.SpatialFilter.SpecifierPanel
Returns the SpatialFilter that has been specified by this SpatialFilter.SpecifierPanel.
getFirstDeriv(double) - Method in class com.xinapse.numerical.CubicSplineInterpolator
Returns the first derivative of the function value at a given value of x.
getFittedCurve() - Method in class com.xinapse.dynamic.DynamicResult
Returns the values of the fitted model at the same points as the data.
getFittedVarValues() - Method in class com.xinapse.dynamic.DynamicResult
Returns the values of the fit variables after they have been optimised in the model.
getFlatKernelWeights() - Method in class com.xinapse.filter.FixedWeightsKernelFilter
Returns the kernel weights as a flat array.
getFlipAngle() - Method in interface com.xinapse.image.ReadableImage
Returns the excitation pulse flip angle for this image.
getFlipAngle() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getFlipAngle() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the excitation pulse flip angle for this image.
getFlipAngle() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getFollowingVisibleHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
getFollowingVisibleHandle(Handle) - Method in interface com.xinapse.multisliceimage.roi.EditableOutlineROI
Returns the visible Handle that is immediately after the specified handle, in the order in which they were placed around the ROI.
getFollowingVisibleHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
getFollowingVisibleHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
getFollowingVisibleHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
getFrame() - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Returns the javax.swing.JFrame to which the ROI(s) will be added.
getFrameDim() - Method in class com.xinapse.multisliceimage.MultiSliceImage
Returns the index number to the "frame" dimension of the image.
getFrameDWBMatrix(int) - Method in interface com.xinapse.image.ReadableImage
Returns the diffusion-weighting b-matrix for one frame of this image.
getFrameDWBMatrix(int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getFrameDWBMatrix(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getFrameDWBMatrix(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getFrameDWbValue(int) - Method in interface com.xinapse.image.ReadableImage
Returns the diffusion-weighting b-value for one frame of this 4-D image.
getFrameDWbValue(int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getFrameDWbValue(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getFrameDWbValue(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getFrameDWGradientVector(int) - Method in interface com.xinapse.image.ReadableImage
Returns the diffusion-weighting gradient-vector for one frame of this image 4-D image.
getFrameDWGradientVector(int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getFrameDWGradientVector(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getFrameDWGradientVector(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getFrameInfo(String, int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getFrameInfo(String, int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Returns a java.lang.String representing the value of this information item in a particular frame of this image.
getFrameInfo(String, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getFrameInfoList(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getFrameInfoList(int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Returns an InfoList object applying to a particular frame of this image.
getFrameInfoList(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getFrameOfReferenceUID() - Method in interface com.xinapse.image.ReadableImage
Returns the frame of reference UID that uniquely identifies the frame of reference for an image.
getFrameOfReferenceUID() - Method in class com.xinapse.multisliceimage.MultiSliceImage
 
getGamma() - Static method in class com.xinapse.image.ColourMapping
Returns the current gamma value setting for the display.
getGMProbTemplate() - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in grey-matter probability template image.
getGroupUid() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the group UID for this ROI.
getGroupUid(List<ROI>) - Static method in class com.xinapse.multisliceimage.roi.ROI
Returns the Group UID of the ROIs supplied if they are all members of the same group (i.e., they all have the same Group UID).
getHandles() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns an array of Handles that this ROI has.
getHandleUnder(Point, int) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
If the mouse is over the InsertionPointHandle, returns the InsertionPointHandle.
getHandleUnderPoint(Point) - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the Handle of this ROI that is under the point supplied (in screen coordinates).
getHeader() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
Returns the ANZHeader image header for this image.
getHeight() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
Returns the height of this RectangularROI in mm.
getHisto(int) - Method in class com.xinapse.image.DoublePixArray
Computes a histogram of a DoublePixArray.
getHisto(int) - Method in class com.xinapse.image.PixArray
Computes a histogram of this PixArray.
getHistoMax(PixelDataType) - Method in class com.xinapse.image.Histogram
Returns the maximum value that can be added to this Histogram's bins.
getHistoMin() - Method in class com.xinapse.image.Histogram
Returns the minimum bin value of this Histogram.
getHTMLDescription() - Method in interface com.xinapse.image.ReadableImage
Returns a String description of this image in HTML format.
getHTMLDescription(int) - Method in interface com.xinapse.image.ReadableImage
Returns a String description of a slice of this image in HTML format.
getHTMLDescription() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getHTMLDescription(int) - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getHTMLDescription(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getHTMLDescription() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getHTMLDescription(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getIccMesh() - Static method in class com.xinapse.image.template.HeadTemplate
Returns a pre-calculated surface mesh of the intra-cranial cavity for any of the template images (the T1, T2 or PD templates).
getIconHeight() - Method in class com.xinapse.image.ColourMapping
Get the height of the Icon used to represent this ColourMapping.
getIconHeight() - Method in class com.xinapse.image.PreviewIcon
Returns the icon's width.
getIconHeight() - Method in enum com.xinapse.image.RenderingInterpolationType
 
getIconHeight() - Method in enum com.xinapse.util.IntensityRelation
 
getIconWidth() - Method in class com.xinapse.image.ColourMapping
Get the width of the Icon used to represent this ColourMapping.
getIconWidth() - Method in class com.xinapse.image.PreviewIcon
Returns the icon's height.
getIconWidth() - Method in enum com.xinapse.image.RenderingInterpolationType
 
getIconWidth() - Method in enum com.xinapse.util.IntensityRelation
 
getID() - Method in class com.xinapse.multisliceimage.roi.HistoryItem
Return the ID of the operator who performed the action in this HistoryItem.
getImag() - Method in class com.xinapse.image.Complex
Returns the imaginary part of this complex number.
getImag() - Method in class com.xinapse.image.DoubleComplex
 
getImag() - Method in class com.xinapse.image.FloatComplex
 
getImageCentrePatient(ReadableImage) - Static method in class com.xinapse.image.ImageUtils
Returns the coordinates of the center of the block of slices of an image, in mm, in patient coordinates.
getImageFilterClass() - Method in class com.xinapse.image.ImageGrid
Returns the class of image that will be filtered when the user first chooses a new image to set in the panel.
getImageFilterClass() - Method in class com.xinapse.image.ImageSelectionGroupPanel
Returns the class of image that will be filtered when the user first chooses a new image to set in the panel.
getImageFilterClass() - Method in class com.xinapse.image.MultipleImageSelectionPanel
Returns the class of image that will be filtered when the user chooses a new image to set in the panel.
getImageName() - Method in class com.xinapse.image.ImageSelectionPanel
Returns the name of the image set in this ImageSelectionPanel.
getImageName() - Method in class com.xinapse.image.InputImageSelectionPanel
 
getImageName() - Method in class com.xinapse.image.SelectedImagePanel
Returns name of the ReadableImage set in this SelectedImagePanel.
getImageOrientationPatient() - Method in enum com.xinapse.image.MostLikePlane
Returns the image orientation in patient coordinates for an image plane which is exactly in this MostLikePlane.
getImageOrientationPatient() - Method in interface com.xinapse.image.ReadableImage
Returns the direction cosines of the row, column and slice directions (for increasing row, column and slice) of the image, in patient (L,P,S) coordinates.
getImageOrientationPatient(int) - Method in interface com.xinapse.image.ReadableImage
Returns the direction cosines of the row, column and slice directions (for increasing row, column and slice) of the image, in patient coordinates.
getImageOrientationPatient() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getImageOrientationPatient(int) - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getImageOrientationPatient(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getImageOrientationPatient() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getImageOrientationPatient(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getImagePositionPatient() - Method in interface com.xinapse.image.ReadableImage
Returns the coordinates of the center of the first pixel of the image, in mm, in patient coordinates.
getImagePositionPatient(int) - Method in interface com.xinapse.image.ReadableImage
Returns the coordinates of the center of the first pixel of the specified slice of this image, in mm, in patient coordinates.
getImagePositionPatient() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getImagePositionPatient(int) - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getImagePositionPatient(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getImagePositionPatient() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getImagePositionPatient(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getImageSource() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the image source of this ROI.
getImageTypeName() - Method in interface com.xinapse.image.WritableImage
Returns the normal human readable name for this type of image.
getImageTypeName() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Returns the human readable name for this type of image.
getImageTypeName() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the human readable name for this type of image.
getImageTypeName() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getImplementedInterpolationTypes() - Static method in class com.xinapse.image.VolumeInterpolator
Returns the types of interpolation that are implemented by the VolumeInterpolator class.
getIndex(int, int) - Method in enum com.xinapse.image.BoundaryCondition
For this BoundaryCondition, returns the index into an array of values for an index that is possibly outside the array of values.
getInfo(String) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getInfo(String, int, int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getInfo(String) - Method in interface com.xinapse.multisliceimage.InfoStorer
Returns a string representing the value of this information item in the general image information.
getInfo(String, int, int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Returns a java.lang.String representing the value of this information item in a particular dimension of this image.
getInfo(String) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getInfo(String, int, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getInfo(String) - Method in class com.xinapse.util.InfoList
An InfoList is a list of Strings of the form "name=value".
getInfoList() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getInfoList(int, int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getInfoList() - Method in interface com.xinapse.multisliceimage.InfoStorer
Returns an InfoList object which is the general info for this image.
getInfoList(int, int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Returns an InfoList object applying to a particular dimension/element for this image.
getInfoList() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getInfoList(int, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getInnerROIs() - Method in class com.xinapse.multisliceimage.roi.HollowROI
Returns a list of ROIs that form the holes in this HollowROI.
getInputImages() - Method in class com.xinapse.image.SingleOrMultipleInputImageSelectionPanel
Returns the input images set in this SingleOrMultipleInputImageSelectionPanel.
getInputImages(boolean) - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the set of input images set in this MultiContrastAnalysisFrame.
getInstance() - Static method in class com.xinapse.apps.active.SelectableROICalculation
Returns an instance of this ROICalculation.
getInstance() - Static method in class com.xinapse.apps.cardiac.SelectableSegmentalAnalysis
Returns an instance of this SegmentalAnalysis.
getInstance(Uid, String) - Static method in enum com.xinapse.dicom.Modality
Returns a Modality corresponding to the supplied Storage Class SOP UID and name.
getInstance(Uid) - Static method in enum com.xinapse.dicom.Modality
Returns a Modality corresponding to the supplied storage class SOP Uid.
getInstance(String) - Static method in enum com.xinapse.dicom.Modality
Returns a Modality corresponding to the supplied modality name.
getInstance(DCMObject) - Static method in enum com.xinapse.dicom.Modality
Finds the Modality in a DCMObject.
getInstance(String) - Static method in enum com.xinapse.dicom.PatientPosition
Returns a PatientPosition corresponding to the supplied string.
getInstance(String) - Static method in enum com.xinapse.filter.SobelFilter.SobelType
Returns a SolbelType corresponding to the given name.
getInstance(String) - Static method in enum com.xinapse.image.BoundaryCondition
Returns the BoundaryCondition corresponding to the supplied string.
getInstance(byte[], byte[], byte[]) - Static method in class com.xinapse.image.ColourMapping
Returns a ColourMapping object according to a set of red, green and blue gun values.
getInstance(String) - Static method in class com.xinapse.image.ColourMapping
Returns one of the "built-in" ColourMappings, selected according to its name.
getInstance(String) - Static method in enum com.xinapse.image.ComplexMode
Returns the ComplexMode corresponding to the supplied String argument.
getInstance(String) - Static method in enum com.xinapse.image.InputConfigurationType
Returns an InputConfigurationType Object corresponding to a string.
getInstance(String) - Static method in enum com.xinapse.image.InterpolationType
Returns the InterpolationType corresponding to the description supplied in the argument.
getInstance(String) - Static method in enum com.xinapse.image.MostLikePlane
Returns a MostLikePlane corresponding to a string.
getInstance(float[][]) - Static method in enum com.xinapse.image.MostLikePlane
Returns the MostLikePlane corresponding to the image orientation in patient coordinates.
getInstance(Vector3f[]) - Static method in enum com.xinapse.image.MostLikePlane
Returns the MostLikePlane corresponding to the image orientation in patient coordinates.
getInstance(PixelDataType, int, int[]) - Static method in class com.xinapse.image.PixArray
Creates one of the sub-classes of PixArray Object of the type specified by the pixel data type.
getInstance(PixelDataType, RandomAccessFile, ByteOrder, int, int, int[]) - Static method in class com.xinapse.image.PixArray
Creates one of the sub-classes of PixArray Object of the type specified by the dataType with pixel data coming from a RandomAccessFile.
getInstance(PixelDataType, DataInputStream, ByteOrder, int, int[]) - Static method in class com.xinapse.image.PixArray
Creates one of the sub-classes of PixArray Object of the type specified by the dataType with pixel data coming from a DataInputStream.
getInstance(String) - Static method in enum com.xinapse.image.RotationAngle
Returns a RotationAngle corresponding to a string.
getInstance(String) - Static method in enum com.xinapse.image.SubSampleType
Returns the SubSampleType corresponding to a String representation.
getInstance(String) - Static method in enum com.xinapse.image.template.WeightingType
Returns a WeightingType Object corresponding to the supplied String.
getInstance(Object, PixelDataType, int, int, int, float, float, float, BoundaryCondition, Float, InterpolationType) - Static method in class com.xinapse.image.VolumeInterpolator
Returns a new VolumeInterpolator for a block of pixel samples.
getInstance(VolumeInterpolator, InterpolationType) - Static method in class com.xinapse.image.VolumeInterpolator
Returns a new VolumeInterpolator, constructed from an existing one.
getInstance(PixelDataType) - Static method in enum com.xinapse.multisliceimage.Analyze.ANZPixFormat
Returns the ANZPixFormat corresponding to a PixelDataType.
getInstance(String) - Static method in enum com.xinapse.multisliceimage.Analyze.SliceOrder
Returns an SliceOrder corresponding to String value.
getInstance(Rectangle, int, int, float, float, byte, ROIState) - Static method in class com.xinapse.multisliceimage.roi.EllipticalROI
Creates an instance of a EllipticalROI suitable for drawing on a window.
getInstance(Point2D, Point2D, int, int, float, float, byte, ROIState) - Static method in class com.xinapse.multisliceimage.roi.LineROI
Creates a new LineROI.
getInstance(Point2D, boolean, int, int, float, float, byte, ROIState) - Static method in class com.xinapse.multisliceimage.roi.Marker
Create a Marker at a point on an image.
getInstance(String) - Static method in enum com.xinapse.multisliceimage.roi.MaskMode
Returns a MaskMode corresponding to the supplied String.
getInstance(Rectangle, int, int, float, float, byte, ROIState) - Static method in class com.xinapse.multisliceimage.roi.RectangularROI
Creates an instance of a RectangularROI suitable for drawing on a window.
getInstance(String) - Static method in enum com.xinapse.multisliceimage.roi.StatsType
Returns the StatsType corresponding to the supplied String.
getInstance(Point2D, boolean, int, int, float, float, byte, ROIState) - Static method in class com.xinapse.multisliceimage.roi.Text
Create a Text ROI at a point on an image.
getInstance(String) - Static method in enum com.xinapse.multisliceimage.roi.VertexHandle.Spacing
Returns a vertex handle spacing according to the supplied String.
getInstance(PixelDataType) - Static method in enum com.xinapse.multisliceimage.UNC.UNCPixFormat
Returns the UNCPixFormat corresponding to a PixelDataType.
getInstance(String) - Static method in enum com.xinapse.util.IntensityRelation
Returns the IntensityRelation specified by the argument.
getInstance(ReportGenerator.ReportType, String, File) - Static method in class com.xinapse.util.ReportGenerator
Creates a new ReportGenerator.
getInstance(Component, List<String>, String, String) - Static method in class com.xinapse.util.ReportGenerator
Creates a new ReportGenerator after prompting the user to ask if she wants a report to be created.
getInstance(String) - Static method in enum com.xinapse.util.ReportGenerator.ReportType
Creates ReportType from a String.
getInstances(Point3i, ContourMode, double, IntensityRelation, boolean, boolean, int, Object, PixelDataType, ComplexMode, int, int, int, float, float, float, byte, boolean, boolean, ContourWorker) - Static method in class com.xinapse.multisliceimage.roi.ContourROI
Create a ContourROI by contouring from a start point on the image.
getInstances(Object, PixelDataType, ComplexMode, BitSet, int, int, int, float, float, byte, double, IntensityRelation, boolean, boolean) - Static method in class com.xinapse.multisliceimage.roi.ContourROI
Returns a java.util.List of ContourROIs that form all the contours at a certain intensity level on a slice of pixels.
getIntensityProfile(Object, PixelDataType, int, int, int, float, float, ComplexMode) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
getIntensityProfile(Object, PixelDataType, int, int, int, float, float, ComplexMode) - Method in interface com.xinapse.multisliceimage.roi.LinearROI
Returns an array of Point2D representing the pixel intensities along this LinearROI.
getIntensityProfile(Object, PixelDataType, int, int, int, float, float, ComplexMode) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getIntensityProfile(Object, PixelDataType, int, int, int, float, float, ComplexMode) - Method in class com.xinapse.multisliceimage.roi.OpenSplineROI
 
getIntensityRelation() - Method in class com.xinapse.util.IntensityRelation.IntensityRelationButton
Returns the intensity relation set.
getIntensityRelation() - Method in class com.xinapse.util.IntensityRelation.PanelGenerator.Panel
Returns the IntensityRelation currently set.
getIntensityRescale() - Method in interface com.xinapse.image.ReadableImage
Returns the values m and b in the relationship between pixel intensity (I) values and the output units specified in getRescaleUnits() in the expression:
Output units = m*I + b.
getIntensityRescale() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Intensity rescaling is not supported by Analyze 7.5 format, so this method always returns float[] [1.0f, 0.0f].
getIntensityRescale() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getIntensityRescale() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getIntent() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the NIFTIIntent in this NIFTIImage.
getIntersectionLength(Rectangle2D, int, int, float, float) - Method in class com.xinapse.multisliceimage.roi.LineROI
Calculates the length of the line segment where this LineROI intersects the given Rectangle argument.
getKnotPoint(int) - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns a knot point location for this SplineROI.
getKnotPoints() - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns the knot point locations for this SplineROI.
getKnownClasses() - Static method in class com.xinapse.filter.FilterSelection
Returns a List of known classes of SpatialFilter.
getLastPathComponent(String) - Static method in class com.xinapse.multisliceimage.ImageName
Returns the last path component of a file or URL name.
getLaterality() - Method in interface com.xinapse.image.ReadableImage
Returns the image laterality.
getLaterality() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getLaterality() - Method in class com.xinapse.multisliceimage.MultiSliceImage
By default, laterality recording is not supported, so this method returns Laterality.BOTH.
getLaterality() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getLength() - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
getLength() - Method in interface com.xinapse.multisliceimage.roi.LinearROI
Returns the length of this ROI in mm.
getLength() - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getLength() - Method in class com.xinapse.multisliceimage.roi.OpenSplineROI
 
getLengthPix(float, float) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
getLengthPix(float, float) - Method in interface com.xinapse.multisliceimage.roi.LinearROI
Returns the length of this ROI in image pixels.
getLengthPix(float, float) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getLengthPix(float, float) - Method in class com.xinapse.multisliceimage.roi.OpenSplineROI
 
getLesionProbTemplate() - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in lesion probability template image (which has been warped to the same space as the T1-weighted template image).
getLevel() - Method in class com.xinapse.multisliceimage.roi.ContourROI
Returns the intensity level that this ContourROI followed.
getLine() - Method in class com.xinapse.multisliceimage.roi.LineROI
Returns the line forming this LineROI in mm coordinates.
getLuminance(Color) - Static method in enum com.xinapse.image.PixelDataType
Returns the luminance value of a Color.
getLVProbTemplate() - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in lateral ventricle probability template image.
getMaskImage() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
Returns the mask image if masking by an image has been selected.
getMaskMode() - Method in class com.xinapse.multisliceimage.roi.MaskMode.Panel
Returns the MaskMode set in this panel.
getMax() - Method in class com.xinapse.image.IntensityPreset
Returns the maximum intensity value in the preset.
getMax() - Method in interface com.xinapse.image.ReadableImage
Returns the maximum pixel intensity in the image.
getMax() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
 
getMax() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getMax() - Method in class com.xinapse.multisliceimage.roi.Feret
Returns the maximum Feret's diameter.
getMax() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getMaxLuminance() - Static method in class com.xinapse.image.ColourMapping
Returns the current maximmum display luminance setting for a digital driver level (DDL) of 255.
getMean() - Method in class com.xinapse.image.Histogram
Returns the mean intensity value of this Histogram.
getMean(boolean) - Method in class com.xinapse.image.Histogram
Returns the mean intensity value of this Histogram, optionally excluding all values that are zero.
getMedian() - Method in class com.xinapse.image.Histogram
Returns the median value of this Histogram.
getMedian(boolean) - Method in class com.xinapse.image.Histogram
Returns the median value of this Histogram, optionally excluding all values that are zero.
getMedian() - Method in class com.xinapse.multisliceimage.roi.ROIStats
Returns the median pixel intensity.
getMin() - Method in class com.xinapse.image.IntensityPreset
Returns the minimum intensity value in the preset.
getMin() - Method in interface com.xinapse.image.ReadableImage
Returns the minimum pixel intensity in the image.
getMin() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
 
getMin() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getMin() - Method in class com.xinapse.multisliceimage.roi.Feret
Returns the minimum Feret's diameter.
getMin() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getMinLuminance() - Static method in class com.xinapse.image.ColourMapping
Returns the current minimum display luminance setting for a digital driver level (DDL) of zero.
getMinMax(Object, PixelDataType, ComplexMode) - Static method in class com.xinapse.image.Histogram
Returns the minimum and maximum intensity values present in an array of pixel values.
getMinMax(Object, int, int, PixelDataType, ComplexMode) - Static method in class com.xinapse.image.Histogram
Returns the minimum and maximum intensity values present in a part of an array of pixel values.
getMinMax() - Method in class com.xinapse.image.PixArray
Finds the minimum and maximum values in this PixArray.
getMinMax() - Method in class com.xinapse.multisliceimage.Analyze.ANZHeader
Gets the glMin and glMax fields for this Analyze image header.
getMod() - Method in class com.xinapse.image.Complex
Returns the modulus of this complex number.
getMod() - Method in class com.xinapse.image.DoubleComplex
 
getMod() - Method in class com.xinapse.image.FloatComplex
 
getModality() - Method in interface com.xinapse.image.ReadableImage
Returns the imaging modality with which this image was collected.
getModality() - Method in class com.xinapse.multisliceimage.MultiSliceImage
 
getModel(int, int, float, ReadableImage) - Method in class com.xinapse.dynamic.DynamicModel.SpecifierPanel
Returns the DynamicModel that has been specified by this DynamicModel.SpecifierPanel.
getModelDescription() - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
Returns a String describing this dynamic contrast model.
getModelDescription() - Method in interface com.xinapse.dynamic.DynamicModel
Returns a String describing this dynamic model.
getModelName() - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
Returns the model name.
getModelName() - Method in interface com.xinapse.dynamic.DynamicModel
Returns the model name.
getMostLikePlane() - Method in interface com.xinapse.image.ReadableImage
Returns the imaging plane that this image is "most like".
getMostLikePlane() - Method in class com.xinapse.multisliceimage.MultiSliceImage
 
getMSLesionCorrelTemplate(boolean) - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in MS lesion correlation template image.
getMSLesionProbTemplate(boolean) - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in MS lesion probability template image.
getMSPDHeadTemplate(boolean) - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in proton density weighted head template image.
getName() - Static method in class com.xinapse.filter.ColourImageFilter
Returns the human-readable name of this filter.
getName() - Static method in class com.xinapse.filter.GaussianBlurFilter
Returns the human-readable name of this filter.
getName() - Static method in class com.xinapse.filter.LaplacianFilter
Returns the human-readable name of this filter.
getName() - Static method in class com.xinapse.filter.MedianFilter
Returns the human-readable name of this filter.
getName() - Static method in class com.xinapse.filter.MorphologicalOperator
Returns the human-readable name of this filter.
getName() - Static method in class com.xinapse.filter.SharpenFilter
Returns the human-readable name of this filter.
getName() - Static method in class com.xinapse.filter.SobelFilter
Returns the human-readable name of this filter.
getName() - Static method in class com.xinapse.multisliceimage.roi.ContourROI
Returns the name of the type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.CurvedLineROI
Returns a descriptive name for this type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.EllipticalROI
Returns a descriptive name for this type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.HollowROI
Returns a descriptive name for this type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.IrregularROI
Returns a descriptive name for this type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.LineROI
Returns a descriptive name for this type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.Marker
Returns a descriptive name for this type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.OpenSplineROI
Returns a descriptive name for this type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.RadialDivider
Returns a descriptive name for this type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.RectangularROI
Returns a descriptive name for this type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.SplineROI
Returns a descriptive name for this type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.Text
Returns a descriptive name for this type of ROI.
getName() - Method in class com.xinapse.util.InfoItem
Return the keyword for this InfoItem.
getNativeColourMapping() - Method in interface com.xinapse.image.ReadableImage
Returns a ColourMapping if this image has an associated colour mapping.
getNativeColourMapping() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
Returns a ColourMapping if this Analyze image has an associated colour mapping.
getNativeColourMapping() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getNativeHeader() - Method in interface com.xinapse.image.ReadableImage
Returns a String showing the 'native' header for this image.
getNativeHeader() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getNativeHeader() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getNBins() - Method in class com.xinapse.image.Histogram
Returns the number of bins in this Histogram.
getNChoosableColors() - Static method in enum com.xinapse.multisliceimage.roi.ROIState
Returns the number of user-choosable ROI colours that may be set.
getNCols() - Method in class com.xinapse.image.ImageGrid
Returns the number of columns in the ImageGrid.
getNCols() - Method in interface com.xinapse.image.ReadableImage
Returns the number of image columns in this image.
getNCols() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getNCols() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getNContrasts() - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the number of image contrasts set in this MultiContrastAnalysisFrame.
getNContrasts(ReadableImage[], Integer, boolean, String) - Static method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the number of image contrasts in a set of input images.
getNDim() - Method in interface com.xinapse.image.ReadableImage
Returns the dimensionality of this image.
getNDim() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getNDim() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns the MultiSliceImage dimensionality of this image.
getNFrames() - Method in interface com.xinapse.image.ReadableImage
Returns the number of frames in a multi-frame image.
getNFrames() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getNFrames() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getNImages() - Method in class com.xinapse.image.ImageSelectionGroupPanel
Returns the number of ImageSelectionGroupMemberPanels in this group.
getNImages() - Method in class com.xinapse.image.MultipleImageSelectionPanel
Returns the number of images currently set in this MultipleImageSelectionPanel.
getNKernelCols() - Method in class com.xinapse.filter.AbstractComplexKernelFilter
Returns the number of columns in the filter kernel.
getNKernelCols() - Method in class com.xinapse.filter.AbstractKernelFilter
Returns the number of columns in the filter kernel.
getNKernelCols() - Method in class com.xinapse.filter.FixedWeightsComplexKernelFilter
 
getNKernelCols() - Method in class com.xinapse.filter.FixedWeightsKernelFilter
 
getNKernelCols() - Method in class com.xinapse.filter.MedianFilter
 
getNKernelCols() - Method in class com.xinapse.filter.MorphologicalOperator
 
getNKernelRows() - Method in class com.xinapse.filter.AbstractComplexKernelFilter
Returns the number of rows in the filter kernel.
getNKernelRows() - Method in class com.xinapse.filter.AbstractKernelFilter
Returns the number of rows in the filter kernel.
getNKernelRows() - Method in class com.xinapse.filter.FixedWeightsComplexKernelFilter
 
getNKernelRows() - Method in class com.xinapse.filter.FixedWeightsKernelFilter
 
getNKernelRows() - Method in class com.xinapse.filter.MedianFilter
 
getNKernelRows() - Method in class com.xinapse.filter.MorphologicalOperator
 
getNKernelSlices() - Method in class com.xinapse.filter.AbstractComplexKernelFilter
Returns the number of slices in the filter kernel.
getNKernelSlices() - Method in class com.xinapse.filter.AbstractKernelFilter
Returns the number of slices in the filter kernel.
getNKernelSlices() - Method in class com.xinapse.filter.FixedWeightsComplexKernelFilter
 
getNKernelSlices() - Method in class com.xinapse.filter.FixedWeightsKernelFilter
 
getNKernelSlices() - Method in class com.xinapse.filter.MedianFilter
 
getNKernelSlices() - Method in class com.xinapse.filter.MorphologicalOperator
 
getNormal(int) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Returns the outward normal vector at a vertex.
getNormal(int) - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns the outward normal vector at a knot point.
getNormal(double) - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns the outward normal vector at particular value of the s-parameter.
getNPixels(int, int[]) - Static method in class com.xinapse.image.ImageUtils
Returns the total number of picture elements for an image with the given dimensions.
getNPixels(Object) - Method in enum com.xinapse.image.PixelDataType
Returns the number of pixels in the supplied array of pixel samples.
getNPoints() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Returns the number of vertices that define the outline.
getNPoints() - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns the number of knot points that define the shape.
getNRows() - Method in class com.xinapse.image.ImageGrid
Returns the number of rows in the ImageGrid.
getNRows() - Method in interface com.xinapse.image.ReadableImage
Returns the number of image rows in this image.
getNRows() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getNRows() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getNSegments() - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Returns the number of segments.
getNSliceLocations() - Method in interface com.xinapse.image.ReadableImage
Returns the number of unique slice locations present in the image.
getNSliceLocations() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
For Analyze 7.5 images, all slices in a block are parallel and evenly-spaced.
getNSliceLocations() - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the number of image slice locations for the images set in this MultiContrastAnalysisFrame.
getNSliceLocations(ReadableImage[], Integer, boolean, String) - Static method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the number of physical image slice locations for a set of images.
getNSlices() - Method in interface com.xinapse.image.ReadableImage
Returns the number of physical slice locations in this image.
getNSlices() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getNSlices() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getNSlots() - Method in class com.xinapse.image.ColourMapping
Returns the number of slots in this ColourMapping.
getNSteadyStates() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
Returns the number of pre-steady-state images set in the GUI.
getOppositeEnd(EndHandle) - Method in class com.xinapse.multisliceimage.roi.LineROI
Returns the location of the end that is at the other end to the specified handle.
getOptionName() - Static method in class com.xinapse.apps.active.SelectableROICalculation
Returns the option name for selecting this ROI calculation method.
getOptionName() - Static method in class com.xinapse.filter.ColourImageFilter
Returns the name of this type of filter when specifying it in program optional arguments.
getOptionName() - Static method in class com.xinapse.filter.GaussianBlurFilter
Returns the name of this type of filter when specifying it in program optional arguments.
getOptionName() - Static method in class com.xinapse.filter.LaplacianFilter
Returns the name of this type of filter when specifying it in program optional arguments.
getOptionName() - Static method in class com.xinapse.filter.MedianFilter
Returns the name of this type of filter when specifying it in program optional arguments.
getOptionName() - Static method in class com.xinapse.filter.MorphologicalOperator
Returns the name of this type of filter when specifying it in program optional arguments.
getOptionName() - Static method in class com.xinapse.filter.SharpenFilter
Returns the name of this type of filter when specifying it in program optional arguments.
getOptionName() - Static method in class com.xinapse.filter.SobelFilter
Returns the name of this type of filter when specifying it in program optional arguments.
getOptions() - Static method in class com.xinapse.filter.ColourImageFilter
Returns the options for this type of filter.
getOptions() - Static method in class com.xinapse.filter.GaussianBlurFilter
Returns the options for this type of filter.
getOptions() - Static method in class com.xinapse.filter.LaplacianFilter
Returns the options for this type of filter.
getOptions() - Static method in class com.xinapse.filter.MedianFilter
Returns the options for this type of filter.
getOptions() - Static method in class com.xinapse.filter.MorphologicalOperator
Returns the options for this type of filter.
getOptions() - Static method in class com.xinapse.filter.SobelFilter
Returns the options for this type of filter.
getOptionSpecifier() - Method in class com.xinapse.apps.perfusion.DCEMRIModel
Returns the specifier used to select the this model.
getOrient() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Gets the orientation of this Analyze75Image.
getOuterROI() - Method in class com.xinapse.multisliceimage.roi.HollowROI
Returns the ROI that encloses all the inner ROIs.
getOutputImagesBaseName() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
Returns the basename for the output images.
getParentComponent() - Method in class com.xinapse.image.ImageSelectionPanel
 
getParentComponent() - Method in class com.xinapse.image.MultipleImageSelectionPanel
 
getParentComponent() - Method in interface com.xinapse.util.MessageShower
Returns the parent of this MessageShower.
getPatientDoB() - Method in interface com.xinapse.image.ReadableImage
Returns the patient date of birth for this image.
getPatientDoB() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Patient's Birth Date is not supported by Analyze 7.5 format.
getPatientDoB() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getPatientDoB() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getPatientID() - Method in interface com.xinapse.image.ReadableImage
Returns the patient ID for this image.
getPatientID() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Header
Returns the patient ID for this Analyze image header.
getPatientID() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Returns the Patient ID set in the image header.
getPatientID() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the patient ID for this image.
getPatientID() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getPatientName() - Method in interface com.xinapse.image.ReadableImage
Returns the patient name for this image.
getPatientName() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Patient names are not supported by Analyze 7.5 format.
getPatientName() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the patient name for this image.
getPatientName() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getPatientPosition() - Method in interface com.xinapse.image.ReadableImage
Returns the position in which the patient is lying in the scanning equipment.
getPatientPosition() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getPatientPosition() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getPatientPosition() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getPatientSex() - Method in interface com.xinapse.image.ReadableImage
Returns the patient sex for this image.
getPatientSex() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
 
getPatientSex() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getPatientSex() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getPeakHeight(boolean) - Method in class com.xinapse.image.Histogram
Returns the number of values with the most common value in this Histogram, optionally excluding the values that are zero-valued.
getPeakPosition(boolean) - Method in class com.xinapse.image.Histogram
Returns the most common value in this Histogram, optionally excluding the values that are zero-valued.
getPenSize() - Method in class com.xinapse.multisliceimage.roi.PenSizePanel
Returns the pen size set.
getPerimeter() - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
Returns the perimeter length of this ROI.
getPerimeter() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
Returns the perimeter length of this EllipticalROI.
getPerimeter() - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
getPerimeter() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
getPerimeter() - Method in class com.xinapse.multisliceimage.roi.LineROI
Returns the perimeter length of this ROI.
getPerimeter() - Method in class com.xinapse.multisliceimage.roi.Marker
 
getPerimeter() - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Returns zero.
getPerimeter() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
getPerimeter() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the perimeter length of this ROI.
getPerimeter() - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
getPhase(Object, PixelDataType) - Static method in class com.xinapse.image.PhaseImage
Return the phase values from pixel values that represent phase.
getPhase(ReadableImage, ReadableImage, List<ROI>) - Static method in class com.xinapse.image.PhaseImage
Return the phase values from an image where pixel values represent phase.
getPix() - Method in class com.xinapse.image.PixArray
Returns a copy of the array of pixel values encapulated by this PixArray.
getPix() - Method in interface com.xinapse.image.ReadableImage
Returns all the pixel values for this image in the order in which they are stored internally.
getPix(boolean) - Method in interface com.xinapse.image.ReadableImage
Returns all the pixel values for this image, optionally returning them in the correct order in which they will be presented, where the first pixel should be presented at the top left corner of the display device.
getPix(int[]) - Method in interface com.xinapse.image.ReadableImage
Returns a single pixel value from this image.
getPix(int[], int[]) - Method in interface com.xinapse.image.ReadableImage
Returns pixel values from this image.
getPix(Object, int[], int[]) - Method in interface com.xinapse.image.ReadableImage
Get pixel values from this image into a specified array.
getPix() - Method in class com.xinapse.multisliceimage.MultiSliceImage
Returns all pixel values from this image.
getPix(boolean) - Method in class com.xinapse.multisliceimage.MultiSliceImage
Returns all pixel values from this image.
getPix(int[], int[]) - Method in class com.xinapse.multisliceimage.MultiSliceImage
 
getPix(Object, int[], int[]) - Method in class com.xinapse.multisliceimage.MultiSliceImage
 
getPix(int[]) - Method in class com.xinapse.multisliceimage.MultiSliceImage
Returns a single pixel value from the image.
getPixelDataType() - Method in interface com.xinapse.image.ReadableImage
Returns a PixelDataType representing the data type of this image.
getPixelDataType() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getPixelDataType() - Method in enum com.xinapse.multisliceimage.Analyze.ANZPixFormat
Returns the PixelDataType corresponding to this ANZPixFormat.
getPixelDataType() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getPixelDataType() - Method in enum com.xinapse.multisliceimage.UNC.UNCPixFormat
Returns the PixelDataType corresponding to this UNCPixFormat.
getPixels(Object, int) - Method in enum com.xinapse.image.PixelDataType
Gets an array of pixel samples, large enough to hold a specified number of pixels.
getPixelsAsFloat(Object) - Method in enum com.xinapse.image.PixelDataType
Returns a set of pixel samples as an array of float values.
getPixelsAsFloat(Object, int, int) - Method in enum com.xinapse.image.PixelDataType
Returns a set of pixel samples as an array of float values.
getPixelValue(Object, int, int, int, int, int) - Method in enum com.xinapse.image.PixelDataType
Gets the pixel value at a particular (column, row) of an array of pixels of this PixelDataType.
getPixelValue(Object, PixelDataType, ComplexMode, int, int, int, int, int) - Static method in class com.xinapse.multisliceimage.roi.ROI
Returns the pixel value at a particular (column,row) of an array of pixels.
getPixelXSize() - Method in interface com.xinapse.image.ReadableImage
Returns the pixel size in the x (horizontal) direction for this image.
getPixelXSize() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getPixelXSize() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getPixelYSize() - Method in interface com.xinapse.image.ReadableImage
Returns the pixel size in the y (vertical) direction for this image.
getPixelYSize() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getPixelYSize() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getPixelZSize() - Method in interface com.xinapse.image.ReadableImage
Returns the separation between the centres of image planes for this image.
getPixelZSize() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getPixelZSize() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getPixformat() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns the pixel format (pixformat) of this image.
getPrecedingVisibleHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
getPrecedingVisibleHandle(Handle) - Method in interface com.xinapse.multisliceimage.roi.EditableOutlineROI
Returns the visible Handle that is immediately before the specified handle, in the order in which they were placed around the ROI.
getPrecedingVisibleHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
getPrecedingVisibleHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
getPrecedingVisibleHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
getPreferredAlwaysOnTop() - Static method in class com.xinapse.multisliceimage.roi.ROIPreferencesDialog
Returns the setting of whether to the ROI toolkit should always be on top of other windows, as set in the user preferences.
getPreferredCombineMode(Preferences, CombineMode) - Static method in enum com.xinapse.multisliceimage.roi.CombineMode
Returns the CombineMode set in the UserPreferences, or the default CombineMode, if none is set in the Preferences.
getPreferredCompressed() - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Returns the user's preference about whether Analyze 7.5 images should be stored compressed.
getPreferredCompressed() - Static method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the user's preference about whether NIFTI images should be stored compressed.
getPreferredContourMode() - Static method in enum com.xinapse.multisliceimage.roi.ContourMode
Returns the user's preferred ContourMode.
getPreferredCreateNonFlipped() - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Header
Returns the user's preference about whether newly-created Analyze 7.5 images should have a non-flipped orientation.
getPreferredDoNotFlipFlipped() - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Header
Returns the user's preference about whether an Analyze 7.5 image with a flipped orientation should be treated as if it has a non-flipped orientation.
getPreferredErodeDilateFraction() - Static method in class com.xinapse.multisliceimage.roi.ROIPreferencesDialog
Returns the erode/dilate distance as a fraction of the image pixel size as set in the user preferences.
getPreferredFlipNonFlipped() - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Header
Returns the user's preference about whether an Analyze 7.5 image with a non-flipped orientation should be treated as if it has a flipped orientation.
getPreferredFSLCompatibleNIFTI() - Static method in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
Returns the user's preference about whether NIFTI-1 images with both qform and sform orientations unset should be read as having the patient left coordinate increasing with stored pixel data column number, and whether NIFTI-1 images should be prevented from being written without orientation information.
getPreferredImageClass() - Static method in class com.xinapse.image.ImageUtils
Returns the WritableImage class set in the user's Preferences.
getPreferredImagePreview() - Static method in class com.xinapse.image.ImagePreview
Returns the user's preference for whether to generate an image preview thumbnail.
getPreferredInputConfigurationType(Preferences) - Static method in enum com.xinapse.image.InputConfigurationType
Returns the user's preferred InputConfigurationType.
getPreferredInterpolationType(Preferences, InterpolationType) - Static method in enum com.xinapse.image.InterpolationType
Returns the InterpolationType set in the preferences.
getPreferredMaskAction() - Static method in enum com.xinapse.multisliceimage.roi.MaskAction
Returns the user's preferred mask action.
getPreferredMaskMode(Preferences, MaskMode) - Static method in enum com.xinapse.multisliceimage.roi.MaskMode
Returns the MaskMode set in the UserPreferences, or the default MaskMode, if none is set in the Preferences.
getPreferredMaxUndos() - Static method in class com.xinapse.multisliceimage.roi.ROIPreferencesDialog
Returns the maximum number of undo operations set in the user preferences.
getPreferredMergeContours() - Static method in class com.xinapse.multisliceimage.roi.ROIPreferencesDialog
Returns the setting of whether contours should be merged after 3-D propagagtion as set in the user preferences.
getPreferredMinimise() - Static method in class com.xinapse.multisliceimage.roi.ROIPreferencesDialog
Returns the setting of whether to the ROI toolkit should be minimised on startup, in the user preferences.
getPreferredModality() - Static method in enum com.xinapse.dicom.Modality
Returns the user's most common-used Modality as set in the user Preferences.
getPreferredMode(Preferences) - Static method in enum com.xinapse.image.ComplexMode
Returns the ComplexMode set in the supplied Preferences, or the default ComplexMode.
getPreferredNIFTIOneFile() - Static method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the user's preference about whether NIFTI images should be stored in two separate files (.hdr and .hdr) or one (.nii).
getPreferredOp(Preferences) - Static method in enum com.xinapse.filter.MorphologicalOperator.Op
Returns the MorphologicalOperator.Op set in the given preferences.
getPreferredOverwrite() - Static method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns whether the user prefers to overwrite UNC images.
getPreferredPatientPosition() - Static method in enum com.xinapse.dicom.PatientPosition
Returns the user's preferred PatientPosition set in the user Preferences.
getPreferredRenderingInterpolationType() - Static method in enum com.xinapse.image.RenderingInterpolationType
Returns the user's preferred RenderingInterpolationType as set in the user preferences.
getPreferredRotationAngle(Preferences) - Static method in enum com.xinapse.image.RotationAngle
Gets the preferred rotation angle from the Preferences.
getPreferredSaveFolderFollowsImage() - Static method in class com.xinapse.multisliceimage.roi.ROIPreferencesDialog
Returns the setting of whether to the folder for saving ROIs follows the image as set in the user preferences.
getPreferredSaveFSLOrient() - Static method in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
Returns the user's preference about whether NIFTI-1 images should be saved with an orientation that is compatible with FSL, where possible.
getPreferredSaveSPMOrient() - Static method in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
Returns the user's preference about whether NIFTI-1 images should be saved with an orientation that is compatible with SPM, where possible.
getPreferredShowExtendedStats() - Static method in class com.xinapse.multisliceimage.roi.ROIPreferencesDialog
Returns the setting of show extended statistics set in the user preferences.
getPreferredShowStatistics() - Static method in class com.xinapse.multisliceimage.roi.ROIPreferencesDialog
Returns the setting of whether to show ROI statistics on startup, in the user preferences.
getPreferredSize() - Method in class com.xinapse.image.ImageFileChooser
Returns the preferred size of the image file chooser.
getPreferredSize() - Method in class com.xinapse.image.ImagePreview
Returns the preferred size of this component.
getPreferredSize() - Method in class com.xinapse.image.ImageSelectionPanel
Overrides the default getPreferredSize() method.
getPreferredSize() - Method in class com.xinapse.image.InputImageSelectionPanel
Override the default getPreferredSize() method.
getPreferredSize() - Method in class com.xinapse.image.MultipleImageSelectionPanel
Override the default getPreferredSize() method.
getPreferredSize() - Method in class com.xinapse.image.ScanDetailsPanel
Overrides the default getPreferredSize() method.
getPreferredSize() - Method in class com.xinapse.image.SelectedImagePanel
Overrides the default getPreferredSize() method.
getPreferredSnapCentre() - Static method in class com.xinapse.multisliceimage.roi.ROIPreferencesDialog
Returns the setting of snap to the centre of pixels set in the user preferences.
getPreferredSpacing() - Static method in enum com.xinapse.multisliceimage.roi.VertexHandle.Spacing
Returns the Spacing set in the user Preferences, or the default if not in the preferences.
getPreferredSubSampleType(Preferences, SubSampleType) - Static method in enum com.xinapse.image.SubSampleType
Returns the SubSampleType set in the preferences.
getPreferredType() - Static method in enum com.xinapse.dicom.PulseSequenceType
Returns the user's preferred PulseSequenceType set in the user Preferences.
getPreferredWarnNegativePixelHeight() - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Header
Returns the user's preference about whether the user should be warned about negative pixel height in Analyze 7.5 images.
getPreferredWarnNegativePixelWidth() - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Header
Returns the user's preference about whether the user should be warned about negative pixel width in Analyze 7.5 images.
getPreviewIcon(File, boolean) - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Returns the PreviewIcon for an Analyze75Image header, or null if the supplied File does not represent an Analyze 7.5 image header.
getPreviewIcon(File, boolean) - Static method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the PreviewIcon for an NIFTIImage, or null if the supplied File does not represent a NIFTI image.
getPreviewIcon(File, boolean) - Static method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns the PreviewIcon for a UNC image, or null if the supplied File does not represent a UNC image.
getPrincipalAxes(ReadableImage, Point3f, Double, boolean, boolean) - Static method in class com.xinapse.image.ImageMoments
Calculates the principal axes of an image.
getPrincipalAxes(ReadableImage, Object, PixelDataType, Point3f, boolean) - Static method in class com.xinapse.image.ImageMoments
Calculates the principal axes of an image.
getPrincipalAxisAngle() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
Returns the angle between the major principal axis of this ROI and the x-axis.
getPrincipalAxisAngle() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Returns the angle between the major principal axis of this ROI and the x-axis.
getPrincipalAxisAngle() - Method in class com.xinapse.multisliceimage.roi.LineROI
Returns the angle between the major principal axis of this ROI and the x-axis.
getPrincipalAxisAngle() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
Returns the angle between the major principal axis of this ROI and the x-axis.
getPrincipalAxisAngle() - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
getProgName() - Method in class com.xinapse.util.MonitorWorker
Returns the program name for this MonitorWorker.
getPulseSequence() - Method in interface com.xinapse.image.ReadableImage
Returns the name of the pulse sequence with which this image was collected.
getPulseSequence() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Pulse sequence names are not supported by Analyze 7.5 for,at.
getPulseSequence() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getPulseSequence() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getPutPix(Object, int[], int[], PixelOp) - Method in class com.xinapse.image.DoublePixArray
 
getPutPix(Object, int[], PixelOp) - Method in class com.xinapse.image.DoublePixArray
Gets/puts a single pixel value from/to an an image.
getPutPix(Object, int[], int[], PixelOp) - Method in class com.xinapse.image.PixArray
Basic pixel accessor method for images of any dimensionality.
getPutPix(Object, int[], PixelOp) - Method in class com.xinapse.image.PixArray
Gets/puts a single pixel value from/to this PixArray.
getPutPix(Object, RandomAccessFile, ByteOrder, int, PixelDataType, int, int[], int[], int[], PixelOp) - Static method in class com.xinapse.image.PixArray
Basic pixel accessor method for images of any dimensionality where pixel data is held in a RandomAccessFile.
getPutPix(Object, int[], RandomAccessFile, ByteOrder, int, PixelDataType, int, int[], PixelOp) - Static method in class com.xinapse.image.PixArray
Gets/puts a pixel value from/to an array of pixels.
getPutSlice(Object, int, PixelOp) - Method in class com.xinapse.image.DoublePixArray
Returns a 1-Dimensional array of type int, cast as an Object, with array indices [0 to (nRows * nCols)-1], representing the pixel intensity values for one slice of this image.
getPutSlice(Object, int, PixelOp) - Method in class com.xinapse.image.PixArray
Returns a 1-Dimensional array of type appropriate of the image pixel type, cast as an Object, with array indices [0 to (nRows * nCols)-1], representing the pixel intensity values for one slice of this image.
getPutSlice(Object, int, RandomAccessFile, ByteOrder, int, PixelDataType, int, int[], PixelOp) - Static method in class com.xinapse.image.PixArray
Returns a 2-Dimensional array type appropriate to the primitive type for the image, cast as an Object, with array indices [0 to (nRows * nCols) - 1], representing the pixel intensity values for one slice of this image.
getQForm() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the qForm in this NIFTIImage.
getRangeMax() - Method in enum com.xinapse.image.PixelDataType
Returns the maximum value that a pixel of this PixelDataType can take.
getRangeMin() - Method in enum com.xinapse.image.PixelDataType
Returns the minimum value that a pixel of this PixelDataType can take.
getReadableImage(int, int) - Method in class com.xinapse.image.ImageGrid
Returns the ReadableImage for the InputImageSelectionPanel at particular location in the ImageGrid.
getReadableImage(int) - Method in class com.xinapse.image.ImageSelectionGroupPanel
Returns the ReadableImage for the ImageSelectionGroupMemberPanel at particular location in the group.
getReadableImage(String) - Static method in class com.xinapse.image.ImageUtils
Returns a ReadableImage, reading the image data from a file.
getReadableImage(File) - Static method in class com.xinapse.image.ImageUtils
Returns a ReadableImage, reading the image data from a file.
getReadableImage() - Method in class com.xinapse.image.InputImageSelectionPanel
Returns the ReadableImage that has been set in this InputImageSelectionPanel.
getReadableImage(int) - Method in class com.xinapse.image.MultipleImageSelectionPanel
Returns the ReadableImage for the MultipleImageSelectionPanel at particular location in the list of images.
getReadableImage() - Method in class com.xinapse.image.SelectedImagePanel
Returns the ReadableImage set in this SelectedImagePanel.
getReadableImages() - Method in class com.xinapse.image.ImageGrid
Returns a 2-D array of images that is set in the grid.
getReadableImages() - Method in class com.xinapse.image.MultipleImageSelectionPanel
Returns an array of ReadableImages with each array member being an image currently set in the MultipleImageSelectionPanel.
getReal() - Method in class com.xinapse.image.Complex
Returns the real part of this complex number.
getReal() - Method in class com.xinapse.image.DoubleComplex
 
getReal() - Method in class com.xinapse.image.FloatComplex
 
getRenderingHint() - Method in enum com.xinapse.image.RenderingInterpolationType
Returns the rendering hint for this RenderingInterpolationType.
getRenderingInterpolationType() - Method in class com.xinapse.image.RenderingInterpolationType.RenderingInterpolationTypeButton
Returns the current RenderingInterpolationType that this button's current state represents.
getReportType() - Method in class com.xinapse.util.ReportGenerator
Returns the ReportType generated.
getRescaleUnits() - Method in interface com.xinapse.image.ReadableImage
Returns the output units of Intensity Rescale Slope and Intensity Rescale Intercept, retrieved by getIntensityRescale().
getRescaleUnits() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
 
getRescaleUnits() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getRescaleUnits() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns RescaleUnits.US.
getRescaleUnits() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getResultTitle() - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastResult
Returns a title for the type of report.
getResultTitle() - Method in class com.xinapse.dynamic.DynamicResult
Returns a title suitable for heading up this DynamicResult.
getRMSError() - Method in class com.xinapse.dynamic.DynamicResult
Returns the RMS difference between the fit and the data.
getROIMaskFile() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
Returns the mask ROI file if masking by a ROIs has been selected.
getROIOutput() - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Returns the current set of both current and deleted ROIs, outputted as text to a byte[].
getROIs() - Method in interface com.xinapse.image.ReadableImage
Returns a List of ROIs that are stored with the image.
getROIs() - Method in class com.xinapse.multisliceimage.MultiSliceImage
 
getROIs() - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Returns a java.util.List of current (not deleted) ROIs for the image displayed.
getROIs(int) - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Returns a java.util.List of current (not deleted) ROIs for one slice of the image displayed.
getROIs(File, Float, Float, Integer, Integer) - Static method in class com.xinapse.multisliceimage.roi.ROI
Returns a List of ROIs read from an input File.
getROIs(InputStream) - Static method in class com.xinapse.multisliceimage.roi.ROI
Returns a List of ROIs read from an InputStream.
getROIs(InputStream, Float, Float, Integer, Integer) - Static method in class com.xinapse.multisliceimage.roi.ROI
Returns a List of ROIs read from an InputStream.
getROIs() - Method in class com.xinapse.multisliceimage.roi.ROIFileSelectionPanel
Returns a java.util.List of ROIs from the ROI file set in this ROIFileSelectionPanel.
getRotation() - Method in class com.xinapse.image.RotationAngle.RotationPanel
Returns the current selected rotation.
getScanDate() - Method in interface com.xinapse.image.ReadableImage
Returns the scan Date for this image.
getScanDate() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Scan dates are not supported by Analyze 7.5 format.
getScanDate() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the scan date for this image.
getScanDate() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getScanDateFormat() - Static method in class com.xinapse.multisliceimage.MultiSliceImage
Returns the java.text.DateFormat with which a scan date should be formatted.
getScanDateFormat() - Static method in class com.xinapse.util.ReportGenerator
Returns a DateFormat suitable for formatting scan dates.
getScanningSequence() - Method in interface com.xinapse.image.ReadableImage
Returns the DICOM Scanning Sequence with which this image was collected.
getScanningSequence() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Scan sequences are not supported by Analyze 7.5 format.
getScanningSequence() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getScanningSequence() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getScanTE() - Method in interface com.xinapse.image.ReadableImage
Returns the scan echo time for this image if it has a single echo-time.
getScanTE(int) - Method in interface com.xinapse.image.ReadableImage
Returns the scan echo time for one dimension index of this image.
getScanTE() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getScanTE(int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getScanTE() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the scan echo time for this image if it has a single echo-time.
getScanTE(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getScanTE() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getScanTE(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getScanTI() - Method in interface com.xinapse.image.ReadableImage
Returns the scan inversion time for this image.
getScanTI() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze 7.5 format, so this method always returns null.
getScanTI() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the scan inversion time for this image.
getScanTI() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getScanTR() - Method in interface com.xinapse.image.ReadableImage
Returns the scan repetition time for this image.
getScanTR() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze 7.5 format, so this method always returns null.
getScanTR() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the scan repetition time for this image.
getScanTR() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSD() - Method in class com.xinapse.image.Histogram
Returns the standard deviation of intensity values of this Histogram.
getSD(boolean) - Method in class com.xinapse.image.Histogram
Returns the standard deviation of intensity values of this Histogram, optionally excluding all values that are zero from the calculation.
getSecondDeriv(double) - Method in class com.xinapse.numerical.CubicSplineInterpolator
Returns the second derivative of the function value at a given value of x.
getSecondDerivs() - Method in class com.xinapse.numerical.CubicSplineInterpolator
Returns the internal array of second derivatives values at the knots.
getSeedPoint() - Method in class com.xinapse.multisliceimage.roi.ContourWorker
Returns the seed point from which contouring was initiated.
getSelectedColumns() - Method in class com.xinapse.image.ImageGrid
Returns the indices of the grid columns that have been selected by the user.
getSelectedIntensityPreset() - Method in class com.xinapse.image.IntensityPresetsMenu
Return the current selected IntensityPreset in the menu.
getSelectedItem() - Method in class com.xinapse.multisliceimage.roi.VertexHandle.SpacingPanel
Returns the current spacing set in this panel.
getSelectedModality() - Method in class com.xinapse.dicom.Modality.ComboBox
Returns the Modality selected.
getSelectedPatientPosition() - Method in class com.xinapse.dicom.PatientPosition.ComboBox
Returns the PatientPosition selected.
getSelectedRenderingInterpolationType() - Method in class com.xinapse.image.RenderingInterpolationType.ComboBox
Returns the RenderingInterpolationType selected.
getSelectedROIs() - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Returns a java.util.List of selected ROIs for the image displayed.
getSelectedRow() - Method in class com.xinapse.image.ImageGrid
Returns the index of the grid row that has been selected by the user.
getSelectedSlice() - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Returns the number of the selected image slice in this CanAddROIToFrame.
getSelectedType() - Method in class com.xinapse.dicom.PulseSequenceType.ComboBox
Returns the PulseSequenceType selected.
getSequenceVariant() - Method in interface com.xinapse.image.ReadableImage
Returns the DICOM Scanning Sequence Variant with which this image was collected.
getSequenceVariant() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Scanning sequence variants are not supported by Analyze 7.5 format.
getSequenceVariant() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getSequenceVariant() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSeriesDescription() - Method in interface com.xinapse.image.ReadableImage
Returns a short description of the series (scan), such as is provided by the DICOM series description.
getSeriesDescription() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Series descriptions are not supported by Analyze 7.5 format.
getSeriesDescription() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getSeriesDescription() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSeriesNumber() - Method in interface com.xinapse.image.ReadableImage
Returns the series number for this ReadableImage.
getSeriesNumber() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Series numbers are not supported by Analyze 7.5 format.
getSeriesNumber() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getSeriesNumber() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSForm() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the sForm in this NIFTIImage.
getSFormAffineTransform() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the general (sForm) AffineTransform3D that will transform the pixel indices (colIdx, rowIdx, sliceIdx) to a position in space in a patient-centric coordinate system.
getSize() - Method in class com.xinapse.multisliceimage.roi.Handle
Returns the size of this ROI in screen pixels.
getSize(int, int) - Static method in class com.xinapse.multisliceimage.roi.Handle
Returns a suitable size of Handle for drawing an ROI of the given width and height.
getSize(int) - Static method in class com.xinapse.multisliceimage.roi.Handle
Returns a suitable size of Handle for drawing an ROI of the given size.
getSlice(Object, int) - Method in interface com.xinapse.image.ReadableImage
Returns all the pixels for a two-dimensional slice of this image, as a 1-dimensional array of primitive values.
getSlice(int) - Method in interface com.xinapse.image.ReadableImage
Returns the pixel values for one slice of an n-dimensional image, where n > 1.
getSlice(int) - Method in class com.xinapse.multisliceimage.MultiSliceImage
 
getSlice(Object, int) - Method in class com.xinapse.multisliceimage.MultiSliceImage
 
getSlice() - Method in class com.xinapse.multisliceimage.roi.InsertionPointHandle
Returns the physical slice number to which this InsertionPointHandle applies.
getSlice() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the slice number for this ROI.
getSliceDataType(int, int, ReadableImage[], boolean, int, boolean) - Static method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the PixelDataTypefor one physical slice location and one image contrast.
getSliceDim() - Method in class com.xinapse.multisliceimage.MultiSliceImage
Returns the index number to the "slice" dimension of the image.
getSliceDWBMatrix(int) - Method in interface com.xinapse.image.ReadableImage
Returns the diffusion-weighting b-matrix for one slice of this image.
getSliceDWBMatrix(int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getSliceDWBMatrix(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getSliceDWBMatrix(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSliceDWbValue(int) - Method in interface com.xinapse.image.ReadableImage
Returns the diffusion-weighting b-value for one slice of this image.
getSliceDWbValue(int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getSliceDWbValue(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getSliceDWbValue(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSliceDWGradientVector(int) - Method in interface com.xinapse.image.ReadableImage
Returns the diffusion-weighting gradient-vector for one slice of this image.
getSliceDWGradientVector(int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getSliceDWGradientVector(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getSliceDWGradientVector(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSliceInfo(String, int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getSliceInfo(String, int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Returns a java.lang.String representing the value of this information item in a particular slice of this image.
getSliceInfo(String, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSliceInfoList(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getSliceInfoList(int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Returns an InfoList object applying to a particular slice of this image.
getSliceInfoList(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSlicePix(int, int, ReadableImage[], boolean, int, ReadableImage, String, boolean) - Static method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the pixel values for one physical slice location and one image contrast.
getSlicesAreReversed(ReadableImage) - Static method in class com.xinapse.image.ImageUtils
Tests whether the supplied image has slices which are in reverse order compared to standard radiological presentation order.
getSliceThickness() - Method in interface com.xinapse.image.ReadableImage
Returns the slice thickness (in mm).
getSliceThickness() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getSliceThickness() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getSliceThickness() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSmoothedROI() - Method in class com.xinapse.multisliceimage.roi.SmootherWorker
After the SmootherWorker has run to completion, returns the smoothed ROI.
getSmoothingFWHMmm() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
Returns the full-width-at-half-maximum for the smoothing filter.
getSpacingFactor() - Method in enum com.xinapse.multisliceimage.roi.VertexHandle.Spacing
Returns the spacing factor between handles.
getSpecifierPanel(ROIPropagateFrame, String) - Method in class com.xinapse.apps.active.SelectableROICalculation
Returns a ROICalculation.SpecifierPanel that can be used to select and specify a SelectableROICalculation.
getSpecifierPanel(CardiacSegmentFrame, String) - Method in class com.xinapse.apps.cardiac.SelectableSegmentalAnalysis
Returns a SegmentalAnalysis.SpecifierPanel that can be used to select and specify a SelectableSegmentalAnalysis.
getSpecifierPanel(String) - Static method in class com.xinapse.filter.ColourImageFilter
Returns a SpatialFilter.SpecifierPanel that can be used to set the parameters for a ColourImageFilter.
getSpecifierPanel(String) - Static method in class com.xinapse.filter.GaussianBlurFilter
Returns a SpatialFilter.SpecifierPanel that can be used to set the parameters for a GaussianBlurFilter.
getSpecifierPanel(String) - Static method in class com.xinapse.filter.LaplacianFilter
Returns a SpatialFilter.SpecifierPanel that can be used to set the parameters for a LaplacianFilter.
getSpecifierPanel(String) - Static method in class com.xinapse.filter.MedianFilter
Returns a SpatialFilter.SpecifierPanel that can be used to set the parameters for a MedianFilter.
getSpecifierPanel(String) - Static method in class com.xinapse.filter.MorphologicalOperator
Returns a SpatialFilter.SpecifierPanel that can be used to set the parameters for a MorphologicalOperator.
getSpecifierPanel(String) - Static method in class com.xinapse.filter.SharpenFilter
Returns a SpatialFilter.SpecifierPanel that can be used to set the parameters for a SharpenFilter.
getSpecifierPanel(String) - Static method in class com.xinapse.filter.SobelFilter
Returns a SpatialFilter.SpecifierPanel that can be used to set the parameters for a SobelFilter.
getSquareArea() - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
Returns zero - a curved line has no area.
getSquareArea() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
getSquareArea() - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getSquareArea() - Method in class com.xinapse.multisliceimage.roi.Marker
 
getSquareArea() - Method in class com.xinapse.multisliceimage.roi.OpenSplineROI
Returns zero - an Open Spline has no area.
getSquareArea() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
getSquareArea() - Method in interface com.xinapse.multisliceimage.roi.RegularROI
Returns the area of this regular ROI in square mm.
getState() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the state of this ROI.
getStats(Object, PixelDataType, int, int, int, float, float, MaskAction, MaskMode, double, PrintStream, boolean, ComplexMode) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
getStats(Object, PixelDataType, int, int, int, float, float, MaskAction, MaskMode, double, PrintStream, boolean, ComplexMode) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getStats(Object, PixelDataType, int, int, int, float, float, MaskAction, MaskMode, double, PrintStream, boolean, ComplexMode) - Method in class com.xinapse.multisliceimage.roi.Marker
 
getStats(Object, PixelDataType, int, int, int, float, float, MaskAction, MaskMode, double, PrintStream, boolean, ComplexMode) - Method in class com.xinapse.multisliceimage.roi.OpenSplineROI
 
getStats(ROI[], int, Object, PixelDataType, int, int, int, float, float, ComplexMode) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Returns an array of ROIStats - one for each segment, and possibly two for each segment if there is an endo- epi-cardial split.
getStats(List<? extends ROI>, Object, PixelDataType, int, int, int, float, float, CombineMode, MaskAction, MaskMode, double, ComplexMode) - Static method in class com.xinapse.multisliceimage.roi.ROI
Find combined statistics about a list of ROIs.
getStats(Object, PixelDataType, int, int, int, float, float, ComplexMode) - Method in class com.xinapse.multisliceimage.roi.ROI
Returns statistics about this ROI.
getStats(Object, PixelDataType, int, int, int, float, float, MaskAction, MaskMode, double, PrintStream, boolean, ComplexMode) - Method in class com.xinapse.multisliceimage.roi.ROI
Returns statistics about this ROI, and (optionally) performs a masking operation.
getStatus() - Method in enum com.xinapse.platform.ExitStatus
Returns the integer exit status code for this ExitStatus.
getStorageClassUID() - Method in enum com.xinapse.dicom.Modality
Returns a UID of the Storage Class with which Objects of this Modality can be stored.
getStudyID() - Method in interface com.xinapse.image.ReadableImage
Returns the study ID for this ReadableImage.
getStudyID() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Study ID is not supported by Analyze 7.5 format.
getStudyID() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getStudyID() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSuggestedFileName() - Method in interface com.xinapse.image.ReadableImage
Returns the suggested file name for in-memory images that are to be saved to disk.
getSuggestedFileName() - Method in class com.xinapse.multisliceimage.MultiSliceImage
 
getTemplateImage(WeightingType) - Static method in class com.xinapse.image.template.HeadTemplate
Returns the a built-in template image of the specified weighting type.
getTextColor() - Static method in class com.xinapse.multisliceimage.roi.ROI
Returns the java.awt.Color with which ROI annotation text should be rendered.
getTextFontSize() - Static method in class com.xinapse.multisliceimage.roi.ROI
Returns the font size at which ROI annotation text should be rendered.
getTheta() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
getTheta() - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
getTheta() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
getTheta() - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getTheta() - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Returns the insertion point angle.
getTheta() - Method in interface com.xinapse.multisliceimage.roi.RotatableROI
Returns the current rotation angle for this RotatableROI.
getTheta() - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
getThreshold() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
Returns the intensity threshold for pixel processing.
getTimeBetweenFrames() - Method in interface com.xinapse.image.ReadableImage
Returns the time between frames in a 4- or higher dimensional image.
getTimeBetweenFrames() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getTimeBetweenFrames() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getTimeBetweenImages() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
Returns the time between images set in the GUI.
getTimeShift(float, int, int) - Method in enum com.xinapse.multisliceimage.Analyze.SliceOrder
Calculates the time difference (in seconds) between the acquisition of the first slice and the given slice, for this SliceOrder.
getTimeStamp() - Method in class com.xinapse.multisliceimage.roi.HistoryItem
Return the time at which the action was performed in this HistoryItem.
getTimeStampString() - Method in class com.xinapse.multisliceimage.roi.HistoryItem
Return the time at which the action was performed in this HistoryItem as a java.lang.String.
getTitle() - Method in class com.xinapse.image.MultipleImageSelectionPanel
Returns the title for the list of images.
getTitle() - Method in interface com.xinapse.image.ReadableImage
Returns the title of this image.
getTitle() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getTitle() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns the title of this image.
getToolTipString() - Method in enum com.xinapse.multisliceimage.roi.MaskMode
Returns a String that is useful for building a ToolTip or description of this MaskMode.
getTotalCount() - Method in class com.xinapse.image.Histogram
Returns the total number of values that contributed to this histogram.
getTotalCount(boolean) - Method in class com.xinapse.image.Histogram
Returns the total number of values that contributed to this histogram, optionally excluding any zero-valued values.
getTotalCount(double) - Method in class com.xinapse.image.Histogram
Returns the number of values in this histogram that are above the supplied threshold.
getTotalNSlices() - Method in interface com.xinapse.image.ReadableImage
Returns the total number of slices in this image.
getTotalNSlices() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getTotalNSlices() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getType() - Method in class com.xinapse.image.template.WeightingType.Panel
Returns the WeightingType set in this Panel.
getUseBrainFinder() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
Returns whether the Brain Finder option has been set in the GUI.
getUserColour() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the user-defined colour for this ROI.
getUserComponent(int) - Method in class com.xinapse.image.ImageSelectionGroupPanel
Returns the user component associated with the image selection panel at the given index.
getUserComponents() - Method in class com.xinapse.image.ImageSelectionGroupPanel
Returns all user components.
getUserMappings() - Static method in class com.xinapse.image.ColourMapping
Returns a java.util.List<ColourMapping> of the ColourMappings imported by the user and stored in the user preferences.
getUserObject() - Method in exception com.xinapse.util.CancelledException
Retrieves the User Object associated with this CancelledException.
getUserPresets() - Static method in class com.xinapse.image.IntensityPreset
Returns a java.util.List<IntensityPreset> of the IntensityPresets created by the user and stored in the user preferences.
getValidIntensityStats() - Method in class com.xinapse.multisliceimage.roi.ROIStats
Returns whether this ROIStats has valid intensity-related statistics.
getValue() - Method in class com.xinapse.util.InfoItem
Return the value for this InfoItem.
getVarColourMappings() - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
Returns an array of ColourMappings, applicable for each of the output images.
getVarColourMappings() - Method in interface com.xinapse.dynamic.DynamicModel
Returns an array of the ColourMappings, in an order that matches the order of the variable names returned by getVarNames().
getVarContrasts(List<GLMContrastVector>, int, int, int, float[][], float[][], float[][], double) - Method in class com.xinapse.dynamic.AutoCorrelationEstimate
Get the estimated variances of a set of contrast of Beta (fitted parameter) estimates for a single pixel using this auto-correlation estimate.
getVarNames() - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
Returns an array of the names of the fitted variables, in an order that matches the order of the variable units returned by getVarUnits().
getVarNames() - Method in interface com.xinapse.dynamic.DynamicModel
Returns an array of the names of the fitted variables, in an order that matches the order of the variable units returned by getVarUnits().
getVarNames() - Method in class com.xinapse.dynamic.DynamicResult
Returns the fitted variable names.
getVarUnits() - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
Returns an array of the fitted variable units, in an order that matches the order of the variable names returned by getVarNames().
getVarUnits() - Method in interface com.xinapse.dynamic.DynamicModel
Returns an array of the fitted variable units, in an order that matches the order of the variable names returned by getVarNames().
getVarUnits() - Method in class com.xinapse.dynamic.DynamicResult
Returns the fitted variable units.
getVertex(int) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Returns a vertex location for this IrregularROI.
getVertexHandles() - Method in interface com.xinapse.multisliceimage.roi.EditableOutlineROI
Returns an array of VertexHandles.
getVertexHandles() - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
getVertexHandles() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
getVertexHandles() - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
getVertices() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Returns the vertex locations for this IrregularROI.
getVOIs(List<ROI>) - Static method in class com.xinapse.multisliceimage.roi.VOI
Returns a List of VOIs (3-D volumes of interest) created from a List of ROIs.
getVolume(float) - Method in class com.xinapse.multisliceimage.roi.VOI
Returns the volume of a VOI.
getWidth() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
Returns the width of this RectangularROI in mm.
getWMProbTemplate() - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in white-matter probability template image.
getWorkingDirectory() - Method in class com.xinapse.image.ImageGrid
Returns the "current working directory" for this ImageGrid.
getWorkingDirectory() - Method in class com.xinapse.image.ImageSelectionGroupPanel
Returns the "current working directory" for this ImageSelectionGroupPanel.
getWorkingDirectory() - Method in class com.xinapse.image.ImageSelectionPanel
Returns the "current working directory" for this ImageSelectionPanel.
getWorkingDirectory() - Method in class com.xinapse.image.MultipleImageSelectionPanel
Returns the "current working directory" for this MultipleImageSelectionPanel.
getWritableImage(String) - Static method in class com.xinapse.image.ImageUtils
Returns a WritableImage (opened read-write), reading the image data from a file.
getWritableImage(File) - Static method in class com.xinapse.image.ImageUtils
Returns a WritableImage (opened read-write), reading the image data from a file.
getWritableImage(ReadableImage) - Static method in class com.xinapse.image.ImageUtils
Returns an in-memory WritableImage that is a copy of the image supplied.
getWritableImage(ReadableImage, int) - Static method in class com.xinapse.image.ImageUtils
Returns an in-memory WritableImage that is a copy of the image supplied except that the number of image slices may be changed.
getWritableImage(ReadableImage, int, int[]) - Static method in class com.xinapse.image.ImageUtils
Returns an in-memory WritableImage that is a copy of the image supplied except that the image dimensionality and dimensions may be changed.
getWritableImage(ReadableImage, Class<? extends WritableImage>) - Static method in class com.xinapse.image.ImageUtils
Returns an in-memory WritableImage that is a copy of the image supplied except that the class of the image may be changed.
getWritableImage(ReadableImage, Class<? extends WritableImage>, int, PixelDataType) - Static method in class com.xinapse.image.ImageUtils
Creates a new in-memory WritableImage with the class of WritableImage class given by the argument, possibly changing the number of slices in the image and the PixelDataType.
getWritableImage(ReadableImage, Class<? extends WritableImage>, int, int[], PixelDataType) - Static method in class com.xinapse.image.ImageUtils
Creates a new in-memory WritableImage with the class of WritableImage class given by the argument, possibly changing the number of slices in the image and the PixelDataType.
getWritableImage() - Method in class com.xinapse.image.OutputImageSelectionPanel
Returns the WritableImage that has been set in this OutputImageSelectionPanel.
getWritableImageClass(String) - Static method in class com.xinapse.image.ImageUtils
Returns the WritableImage Class that is assignable from the supplied class name.
getWritableImageClass(Class) - Static method in class com.xinapse.image.ImageUtils
Returns the WritableImage Class that is assignable from the supplied class.
getWritableImageClasses() - Static method in class com.xinapse.image.ImageUtils
Returns a List of classes that are known to implement WritableImage.
getWritableImageCommonName(Class<? extends WritableImage>) - Static method in class com.xinapse.image.ImageUtils
Returns the "common name" (e.g.
getWriteDescription(boolean, boolean, boolean, boolean, boolean, boolean, PixelDataType, ComplexMode) - Method in class com.xinapse.multisliceimage.roi.ROIStats
Returns a java.util.List<String> of each of the requested statistics, correctly formatted for writing.
getX() - Method in class com.xinapse.multisliceimage.roi.Marker
Returns the x-coordinate of this Marker.
getX() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
Returns the x-coordinate of the top left corner of this RectangularROI in mm.
getX1() - Method in class com.xinapse.multisliceimage.roi.LineROI
Returns the x-coordinate of the first end of the line.
getX2() - Method in class com.xinapse.multisliceimage.roi.LineROI
Returns the x-coordinate of the second end of the line.
getXAxisLabel() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
For the purposes of plotting data, returns the x-axis label.
getXAxisLabel() - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the x-axis label for a pop-up plot.
getXStart() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
For the purposes of plotting data, returns the starting value of the independent variable.
getXStart() - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the minimum x-value for a pop-up plot.
getY() - Method in class com.xinapse.multisliceimage.roi.Marker
Returns the y-coordinate of this Marker.
getY() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
Returns the y-coordinate of the top left corner of this RectangularROI in mm.
getY1() - Method in class com.xinapse.multisliceimage.roi.LineROI
Returns the y-coordinate of the first end of the line.
getY2() - Method in class com.xinapse.multisliceimage.roi.LineROI
Returns the y-coordinate of the second end of the line.
GREEN - Static variable in class com.xinapse.image.ColourMapping
The ColourMapping representing a green intensity scale.
GREEN_FORMULA_OPTION - Static variable in class com.xinapse.filter.ColourImageFilter
A public Option to specify the formula used to calculate the new green component values in the output image.
group(List<ROI>) - Static method in class com.xinapse.multisliceimage.roi.ROI
Form an ROI group from a List of ROIs.

H

Handle - Class in com.xinapse.multisliceimage.roi
A Class representing an ROI Handle, used for changing the shape of an ROI.
Handle(int, int, int) - Constructor for class com.xinapse.multisliceimage.roi.Handle
Creates a new Handle at the location (x,y) with the given size in screen pixels.
handles - Variable in class com.xinapse.multisliceimage.roi.ROI
If an ROI is editable, it will be drawn with handles.
hasCurrentROIs() - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Tests whether a CanAddROIToFrame has current (not deleted) ROIs.
hashCode() - Method in class com.xinapse.image.DoubleComplex
Returns a hash code value for this DoubleComplex number.
hashCode() - Method in class com.xinapse.image.FloatComplex
Returns a hash code value for this FloatComplex number.
hashCode() - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
Returns a hash code value for this CurvedLine ROI.
hashCode() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
Returns a hash code value for this EllipticalROI.
hashCode() - Method in class com.xinapse.multisliceimage.roi.HollowROI
Returns a hash code value for this IrregularROI.
hashCode() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Returns a hash code value for this IrregularROI.
hashCode() - Method in class com.xinapse.multisliceimage.roi.LineROI
Returns a hash code value for this LineROI.
hashCode() - Method in class com.xinapse.multisliceimage.roi.Marker
Returns a hash code value for this Marker ROI.
hashCode() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
Returns a hash code value for this RectangularROI.
hashCode() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns a hash code value for the ROI.
hashCode() - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns a hash code value for this SplineROI.
hashCode() - Method in class com.xinapse.multisliceimage.roi.Text
Returns a hash code value for this Marker ROI.
hashCode() - Method in class com.xinapse.util.BitSet
Returns a hash code value for this bit set.
HeadTemplate - Class in com.xinapse.image.template
Access to the built-in and head template images.
HEIGHTTOKEN - Static variable in class com.xinapse.multisliceimage.roi.RectangularROI
The token written to ROI output files to represent the height of a rectangular ROI.
histo - Variable in class com.xinapse.multisliceimage.roi.ROIStats
The histogram of pixel intensities inside an ROI in intensity units.
Histogram - Class in com.xinapse.image
A class for creating histograms and finding statistics about arrays of values (normally pixel intensities).
Histogram(double[], double, double) - Constructor for class com.xinapse.image.Histogram
Creates a Histogram of intensities from pre-computed values.
Histogram(Object, PixelDataType) - Constructor for class com.xinapse.image.Histogram
Creates a Histogram of intensities from an array of values of a given PixelDataType.
Histogram(Object, PixelDataType, ComplexMode) - Constructor for class com.xinapse.image.Histogram
Creates a Histogram of intensities from an array of values of a given PixelDataType.
Histogram(Object, int, int, PixelDataType) - Constructor for class com.xinapse.image.Histogram
Creates a Histogram of intensities from an array of values of a given PixelDataType.
Histogram(Object, int, int, PixelDataType, ComplexMode) - Constructor for class com.xinapse.image.Histogram
Creates a Histogram of intensities from an array of values, with an option to specifiy the mode of calculation for PixelDataType.COMPLEX, or PixelDataType.DOUBLECOMPLEX images.
Histogram(Object, int, int, PixelDataType, double, double, double, ComplexMode) - Constructor for class com.xinapse.image.Histogram
Creates a Histogram of intensities from an array of values over a specified intensity range, and width a specified bin width.
Histogram(Object, int, int, PixelDataType, double, double, ComplexMode) - Constructor for class com.xinapse.image.Histogram
Creates a Histogram of intensities from an array of values over a specified intensity range.
Histogram(Object, int, int, PixelDataType, double, double, int, ComplexMode) - Constructor for class com.xinapse.image.Histogram
Creates a Histogram of intensities from an array of values over a specified intensity range, and with the specified number of bins.
Histogram(Histogram) - Constructor for class com.xinapse.image.Histogram
Creates a new Histogram, copying all values from an existing Histogram.
Histogram.BinSpec - Class in com.xinapse.image
A specification for Histogram bins.
HistoryDialog - Class in com.xinapse.multisliceimage.roi
A JDialog that is used to display ROI audit-trail information.
HistoryDialog(JFrame) - Constructor for class com.xinapse.multisliceimage.roi.HistoryDialog
Creates a HistoryDialog with a JFrame as its parent.
HistoryDialog(JDialog) - Constructor for class com.xinapse.multisliceimage.roi.HistoryDialog
Creates a HistoryDialog with a JDialog as its parent.
HistoryItem - Class in com.xinapse.multisliceimage.roi
A Class representing an item in the life and history of an ROI.
HistoryItem(HistoryType) - Constructor for class com.xinapse.multisliceimage.roi.HistoryItem
Create a new HistoryItem with the specfied action,.
HistoryType - Enum in com.xinapse.multisliceimage.roi
An enumeration of the types of HistoryItem that are associated with ROIs.
HOBS - Static variable in class com.xinapse.image.ColourMapping
The ColourMapping representing a hot body (black to white via red) intensity scale.
HollowROI - Class in com.xinapse.multisliceimage.roi
A Class representing an irregularly-shaped region but with one or more holes.
HollowROI(List<ROI>, ROIState) - Constructor for class com.xinapse.multisliceimage.roi.HollowROI
Creates a new HollowROI, created from a List of ROIs, where one ROI completely contains all the others.

I

Image - Class in com.xinapse.image
Contains settings that are common across all images, together with some utilities for images.
IMAGE_ORIENTATION_PATIENT_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the orientation (direction cosines) of the matrix of image pixels, in patient coordinates.
IMAGE_POSITION_PATIENT_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the location of the first pixel of the image, in patient coordinates.
imageChooser - Variable in class com.xinapse.image.ImageSelectionPanel
The ImageFileChooser that can be popped up to select a new image.
imageClassToFilter - Variable in class com.xinapse.image.ImageSelectionPanel
The class of image that will intially be filtered when the user first selects the image.
ImageDebug - Class in com.xinapse.image
Enables and disables debugging messages for the image package.
imageExists(String, Class<? extends WritableImage>) - Static method in class com.xinapse.image.ImageUtils
Tests whether a WritableImage with the given name already exists on disk.
imageExists(String) - Static method in class com.xinapse.multisliceimage.Analyze.ANZImage
Tests whether an ANZImage with the given name already exists on disk.
imageExists(String) - Static method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Tests whether a NIFTIImage with the given name already exists on disk.
ImageFileChooser - Class in com.xinapse.image
Abstract Class for File Choosers for opening ReadableImages, and saving WritableImages, Includes appropriate file filters, titles and button labels.
ImageFileChooser.LoadChooser - Class in com.xinapse.image
ImageFileChooser suitable for selecting a ReadableImage file for loading.
ImageFileChooser.SaveChooser - Class in com.xinapse.image
ImageFileChooser suitable for selecting a WritableImage file for saving.
ImageFileFilter - Class in com.xinapse.image
A file filter for all images that can be loaded directly into Jim.
ImageGrid - Class in com.xinapse.image
An ImageGrid allows the selection of a 2-D 'matrix' of ReadableImages and contains the mechanism for adding images to the matrix, removing images from the matrix, etc.
ImageGrid(MessageShower, Preferences) - Constructor for class com.xinapse.image.ImageGrid
Creates a new ImageGrid, that is contained within a parent MessageShower, and with initially one image in the set of images, and a minimum of one image in the set.
ImageGrid(MessageShower, Preferences, int, int, int, int, int, int, int, int, boolean, boolean) - Constructor for class com.xinapse.image.ImageGrid
Creates a new ImageGrid, that is contained within a parent JFrame, and with minimum number and initial number of images in the set given by the argument.
imageInputPanel - Variable in class com.xinapse.util.MultiContrastAnalysisFrame
The JPanel that contains the input configuration widgets.
ImageJROIFileFilter - Class in com.xinapse.multisliceimage.roi
A FileFilter for ImageJ region of interest files.
ImageJROIFileFilter() - Constructor for class com.xinapse.multisliceimage.roi.ImageJROIFileFilter
Constructor for ImageJROIFileFilter.
ImageMoments - Class in com.xinapse.image
Calculation of factors derived from the moments of an image.
ImageName - Class in com.xinapse.multisliceimage
Class to add extensions, prefixes and suffices to image file and URL names.
ImagePreview - Class in com.xinapse.image
JComponent that is used to preview an image file.
ImagePreview(JFileChooser) - Constructor for class com.xinapse.image.ImagePreview
Creates a new ImagePreview.
ImageSaveException - Exception in com.xinapse.image
Signals that an error has occurred when trying to save an image.
ImageSaveException() - Constructor for exception com.xinapse.image.ImageSaveException
Constructs an ImageSaveException with "image couldn't be saved" as its detail message.
ImageSaveException(String) - Constructor for exception com.xinapse.image.ImageSaveException
Constructs an ImageSaveException with the specified detail message.
ImageSelectionGroupPanel - Class in com.xinapse.image
An ImageSelectionGroupPanel allows the selection of a group of ReadableImages and contains the mechanism for adding images to the group, removing images from the group, etc.
ImageSelectionGroupPanel(MessageShower) - Constructor for class com.xinapse.image.ImageSelectionGroupPanel
Creates a new ImageSelectionGroupPanel, that is contained within a parent JFrame, and with initially one image in the set of images, and a minimum of one image in the set.
ImageSelectionGroupPanel(MessageShower, int, ImageSelectionGroupPanel.ComponentGenerator, double) - Constructor for class com.xinapse.image.ImageSelectionGroupPanel
Creates a new ImageSelectionGroupPanel, that is contained within a parent JFrame, and with minimum number and initial number of images in the set given by the argument.
ImageSelectionGroupPanel.ComponentGenerator - Interface in com.xinapse.image
An interface implemented by classes that want to be able to generate user components to put into an ImageSelectionGroupPanel.
ImageSelectionPanel - Class in com.xinapse.image
An ImageSelectionPanel is a javax.swing.JPanel that can be used to select an image, either for reading or for writing.
ImageSelectionPanel(MessageShower, File, Class<? extends ReadableImage>, boolean) - Constructor for class com.xinapse.image.ImageSelectionPanel
Creates new ImageSelectionPanel, with the default Folder given by argument, and with the image file selection field optionally on only one line.
ImageUtils - Class in com.xinapse.image
Contains various image utility static methods.
ImageWriter - Class in com.xinapse.image
Contains static methods for writing images.
incState() - Method in class com.xinapse.image.RenderingInterpolationType.RenderingInterpolationTypeButton
Increment to the next RenderingInterpolationType.
indeterminateMonitor - Variable in class com.xinapse.util.MonitorWorker
An IndeterminateProgressMonitor which may pop up.
IndeterminateProgressMonitor - Class in com.xinapse.util
A JDialog for showing progress through an operation that will take an indeterminate number of steps, or an unknown time to complete.
IndeterminateProgressMonitor(Component, Object, String) - Constructor for class com.xinapse.util.IndeterminateProgressMonitor
Constructs a JDialog that shows progress that will take place over an indeterminate time, typically by making a rectangular bar oscillate from side to side.
InfoExtendedData - Class in com.xinapse.multisliceimage.Analyze
NIFTI 1.1 extended data that allows artibrary text to be associated with an image.
InfoItem - Class in com.xinapse.util
An image information item key-value pair.
InfoList - Class in com.xinapse.util
Representation of a list of information to be associated either with an image as a whole, or with a particular element of a particular dimension of an image.
InfoList() - Constructor for class com.xinapse.util.InfoList
Construct an empty InfoList.
InfoList(DataInputStream) - Constructor for class com.xinapse.util.InfoList
Creates a InfoList Object by reading it from a DataInputStream.
InfoList(String) - Constructor for class com.xinapse.util.InfoList
Creates an InfoList from an HTML description of that list.
InfoListException - Exception in com.xinapse.util
Signals that an error has occurred while creating or handling an InfoList.
InfoListException() - Constructor for exception com.xinapse.util.InfoListException
Constructs an InfoListException with null as its detail message.
InfoListException(String) - Constructor for exception com.xinapse.util.InfoListException
Constructs an InfoListException with the specified detail message.
InfoNotFoundException - Exception in com.xinapse.multisliceimage
Signals that information about an InfoStorer has not been found.
InfoNotFoundException() - Constructor for exception com.xinapse.multisliceimage.InfoNotFoundException
Constructs an InfoNotFoundException with null as its detail message.
InfoNotFoundException(String) - Constructor for exception com.xinapse.multisliceimage.InfoNotFoundException
Constructs an InfoNotFoundException with the specified detail message.
InfoNotFoundException(String, Throwable) - Constructor for exception com.xinapse.multisliceimage.InfoNotFoundException
Constructs an InfoNotFoundException with the specified cause.
InfoStorer - Interface in com.xinapse.multisliceimage
An interface that classes implement to indicate that they can store arbitrary textual information.
INNERPOINTSTOKEN - Static variable in class com.xinapse.multisliceimage.roi.HollowROI
The token written to ROI output files to indicate that a list of inner points is to follow.
Input - Class in com.xinapse.io
Abstract class providing methods to read primitve data values from input sources.
InputConfigurationType - Enum in com.xinapse.image
The types of input image configuration: either a single input image, or multiple input images.
InputImageSelectionPanel - Class in com.xinapse.image
A component that can be used to select a ReadableImage for input.
InputImageSelectionPanel(MessageShower) - Constructor for class com.xinapse.image.InputImageSelectionPanel
Creates new InputImageSelectionPanel, with the default Folder set to the System Property user.dir.
InputImageSelectionPanel(MessageShower, boolean) - Constructor for class com.xinapse.image.InputImageSelectionPanel
Creates new InputImageSelectionPanel, with the default Folder set to the System Property user.dir, and with the image file selection field on only one line.
InputImageSelectionPanel(MessageShower, File, Class<? extends ReadableImage>, boolean) - Constructor for class com.xinapse.image.InputImageSelectionPanel
Creates new InputImageSelectionPanel, with the default Folder given by argument, and with the image file selection field optionally on only one line.
InsertionPointHandle - Class in com.xinapse.multisliceimage.roi
A Handle to indicate and move the insertion point for a RadialDivider.
InsertionPointHandle(int, int, int, Point2D, boolean) - Constructor for class com.xinapse.multisliceimage.roi.InsertionPointHandle
Creates a new InsertionPointHandle at the location (x,y), in screen pixels.
insertTwoVertices(Handle) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
insertTwoVertices(Handle) - Method in interface com.xinapse.multisliceimage.roi.EditableOutlineROI
Insert two points into the outline of this EditableOutlineROI: one just before the one that is under a handle, and one just after.
insertTwoVertices(Handle) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
insertTwoVertices(Handle) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
insertTwoVertices(Handle) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
insertVertex(Point2D) - Method in class com.xinapse.multisliceimage.roi.IrregularROIInProgress
Inserts a vertex at the beginning of this IrregularROIInProgress.
insertVertex(double, double) - Method in class com.xinapse.multisliceimage.roi.IrregularROIInProgress
Inserts a vertex at the beginning of this IrregularROIInProgress.
INSTANCE - Static variable in class com.xinapse.image.ImageFileFilter
An ImageFileFilter used for testing whether a File refers to a WritableImage.
INSTANCE - Static variable in class com.xinapse.multisliceimage.Analyze.AnalyzeFileFilter
The only instance of a NIFTIFileFilter.
INSTANCE - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIFileFilter
The only instance of a NIFTIFileFilter.
INSTANCE - Static variable in class com.xinapse.multisliceimage.UNC.UNCFileFilter
The only instance of a UNCFileFilter.
IntArray(InputStream, ByteOrder, int) - Static method in class com.xinapse.io.Input
Reads an array of int values from a java.io.InputStream strm ensuring that blocking occurs until all values have been read.
IntArray(DataInputStream, ByteOrder, int[]) - Static method in class com.xinapse.io.Input
Reads an array of int values from a DataInputStream strm ensuring that blocking occurs until all values have been read.
IntArray(RandomAccessFile, ByteOrder, int[]) - Static method in class com.xinapse.io.Input
Reads an array of int values from a java.io.RandomAccessFile f ensuring that blocking occurs until all values have been read.
IntArray(RandomAccessFile, ByteOrder, int[], int, int) - Static method in class com.xinapse.io.Input
Reads an array of int values from a java.io.RandomAccessFile f ensuring that blocking occurs until all values have been read.
IntArray(int[], OutputStream, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of int values to a java.io.OutputStream strm.
IntArray(int[], RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of int values to a java.io.RandomAccessFile f.
IntArray(int[], int, int, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of int values to a java.io.RandomAccessFile f.
Integer(int) - Static method in class com.xinapse.io.ByteSwap
Swap the byte order in an an int and return the value represented by the bit pattern of the reversed bytes as an int.
Integer(int[], ByteOrder) - Static method in class com.xinapse.io.ByteSwap
Swap the byte order (if necessary) in an array of int values "in-place".
Integer(byte[], ByteOrder) - Static method in class com.xinapse.io.ByteSwap
Swap the byte order (if necessary) in a four-byte array and return the value represented by the bit pattern as an int.
Integer(byte[], int, ByteOrder) - Static method in class com.xinapse.io.ByteSwap
Swap the byte order (if necessary) in quartets of bytes in an array of bytes and return the values represented by the bit patterns as an array of ints.
Integer(InputStream, ByteOrder) - Static method in class com.xinapse.io.Input
Reads an integer value from a java.io.InputStream strm, ensuring that blocking occurs until the value has been read.
Integer(RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Input
Reads an integer value from a java.io.RandomAccessFile f, ensuring that blocking occurs until the value has been read.
Integer(byte[], int) - Static method in class com.xinapse.io.Input
Gets an int value from an array of 4 bytes.
Integer(Integer, OutputStream, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single Integer to a java.io.OutputStream strm as a primitive int value.
Integer(int, OutputStream, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single int to a java.io.OutputStream strm.
Integer(Integer, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single Integer to a java.io.RandomAccessFile f as a primitive int value.
Integer(int, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single int to a java.io.RandomAccessFile f.
INTENSITY_RESCALE_INTERCEPT_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the intensity rescale intercept.
INTENSITY_RESCALE_SLOPE_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the intensity rescale slope.
INTENSITY_RESCALE_UNITS_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the intensity rescale units.
intensityMatch(ReadableImage, WritableImage[], int, double, Double, boolean, MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Broadly match the intensities of a set of input images to an intensity standard image.
intensityMatch(float[], float[], int, int, int, int, double, Double, boolean, MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Broadly match a set of pixel intensities images to an standard set of pixel intensities.
IntensityPreset - Class in com.xinapse.image
An intensity preset, particularly for CT images.
IntensityPresetsMenu - Class in com.xinapse.image
A JMenu containing a list of IntensityPresets and allied operations.
IntensityPresetsMenu(ChangeableContrast) - Constructor for class com.xinapse.image.IntensityPresetsMenu
Creates a new IntensityPresetsMenu.
IntensityRelation - Enum in com.xinapse.util
An enumeration of possible intensity relationships.
IntensityRelation.IntensityRelationButton - Class in com.xinapse.util
A Button for setting an intensity relation.
IntensityRelation.PanelGenerator - Class in com.xinapse.util
Class for generating JPanels for selecting an IntensityRelation.
IntensityRelation.PanelGenerator.Panel - Class in com.xinapse.util
 
IntensityRelationButton(Preferences) - Constructor for class com.xinapse.util.IntensityRelation.IntensityRelationButton
Create a new IntensityRelationButton.
InteractionType - Enum in com.xinapse.multisliceimage.roi
An enumeration of the different ways in which a user can interact with an ROI.
interpolate(float[], byte[]) - Method in class com.xinapse.image.ColourVolumeInterpolator
Interpolate the intensity samples at a set of supplied coordinates.
interpolate(Object, double, double) - Method in enum com.xinapse.image.PixelDataType
Interpolates between two pixel intensity values.
interpolate(float[], float[]) - Method in class com.xinapse.image.VolumeInterpolator
Interpolate the intensity samples at a set of supplied coordinates.
interpolate(SplineROI, SplineROI, double) - Static method in class com.xinapse.multisliceimage.roi.SplineROI
Creates a new SplineROI by interpolating between two SplineROIs.
interpolate(double) - Method in class com.xinapse.numerical.CubicSplineInterpolator
Returns an interpolated value of y for a value of x.
InterpolationType - Enum in com.xinapse.image
An enumeration of the types of interpolation that can be used for resampling images.
intersect(ROI) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
intersect(ROI) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
intersect(ROI) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
intersect(ROI) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
intersect(ROI) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
intersect(ROI) - Method in class com.xinapse.multisliceimage.roi.Marker
 
intersect(ROI) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
 
intersect(ROI) - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
intersect(ROI) - Method in class com.xinapse.multisliceimage.roi.ROI
Performs an intersection operation on the shape of this ROI with another ROI.
intersect(ROI) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
intersect(ROI) - Method in class com.xinapse.multisliceimage.roi.Text
 
intersects(ROI) - Method in class com.xinapse.multisliceimage.roi.ROI
Tests whether this ROI intersects another ROI.
intersects(ROI) - Method in class com.xinapse.multisliceimage.roi.VOI
Tests whether this volume of interest (VOI) intersects an ROI.
intersects(BitSet) - Method in class com.xinapse.util.BitSet
Returns true if the specified BitSet and this one share at least one common true bit.
InvalidArgumentException - Exception in com.xinapse.util
Signals that an invalid parameter has been passed to a constructor or method, and that error must be handled by the caller.
InvalidArgumentException() - Constructor for exception com.xinapse.util.InvalidArgumentException
Constructs an InvalidArgumentException without a detail message.
InvalidArgumentException(String) - Constructor for exception com.xinapse.util.InvalidArgumentException
Constructs an InvalidArgumentException with the specified detail message.
InvalidArgumentException(String, Throwable) - Constructor for exception com.xinapse.util.InvalidArgumentException
Constructs an InvalidArgumentException with the specified cause.
InvalidColourMappingException - Exception in com.xinapse.image
Signals that an error has occurred while trying to read or generate a colour mapping.
InvalidColourMappingException(String) - Constructor for exception com.xinapse.image.InvalidColourMappingException
Constructs an InvalidColourMappingException with the specified detail message.
InvalidImageException - Exception in com.xinapse.image
Signals that an error has occurred when performing an operation on an image.
InvalidImageException() - Constructor for exception com.xinapse.image.InvalidImageException
Constructs an InvalidImageException with "invalid image" as its detail message.
InvalidImageException(String) - Constructor for exception com.xinapse.image.InvalidImageException
Constructs an InvalidImageException with the specified detail message.
InvalidImageException(String, Throwable) - Constructor for exception com.xinapse.image.InvalidImageException
Constructs an InvalidImageException with the specified cause.
INVERSION_TIME_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the scan inversion time.
invert() - Method in class com.xinapse.image.ColourMapping
Creates a new ColourMapping by inverting this ColourMapping.
IrregularROI - Class in com.xinapse.multisliceimage.roi
A Class representing an irregularly-shaped closed region on an image.
IrregularROI(double[], double[], int, ROIState) - Constructor for class com.xinapse.multisliceimage.roi.IrregularROI
Creates a new IrregularROI with the specified shape in mm coordinates.
IrregularROI(List<? extends Point2D>, ROIState) - Constructor for class com.xinapse.multisliceimage.roi.IrregularROI
Creates a new IrregularROI with the specified shape in mm coordinates.
IrregularROIInProgress - Class in com.xinapse.multisliceimage.roi
A Class representing an IrregularROI being drawn on an image.
IrregularROIInProgress(double[], double[], byte) - Constructor for class com.xinapse.multisliceimage.roi.IrregularROIInProgress
Creates a new IrregularROIInProgress with the specified shape in mm coordinates.
isAnalyze() - Method in enum com.xinapse.multisliceimage.Analyze.ANZPixFormat
Indicates whether this is an original Analyze (not NIFTI) ANZPixFormat.
isCanceled() - Method in class com.xinapse.util.IndeterminateProgressMonitor
Returns true if the user has hit the Cancel button in the progress dialog.
isCancelled() - Method in class com.xinapse.util.CancellableThread
Tests whether this CancellableThread has been cancelled.
isClosed() - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns whether this SplineROI forms a closed path.
isColourType() - Method in enum com.xinapse.image.PixelDataType
Tests whether this PixelDataType specifies explicitly the red,green,blue colour components to display, rather than needing a ColourMapping to display.
isComplex() - Method in enum com.xinapse.image.PixelDataType
Returns true if this PixelDataType is a complex (real/imaginary) data type.
isCompressed() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
Tests whether this ANZImage is compressed when on disk.
isDeleted() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns true if this ROI has been deleted.
isEditable() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns true if this ROI is currently editable.
isEmpty() - Method in class com.xinapse.util.BitSet
Returns true if this set contains no true bits.
isEnhanced() - Method in enum com.xinapse.dicom.Modality
Returns true if this is an enhanced Modality.
isFlipped() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Returns true if this Analyze75Image is flipped.
isFloatingPointType() - Method in enum com.xinapse.image.PixelDataType
Tests whether this PixelDataType is a floating-point (single or double precision) data type.
isGreyScale() - Method in class com.xinapse.image.ColourMapping
Returns true if this is a grey scale ColourMapping.
isGroup(List<ROI>) - Static method in class com.xinapse.multisliceimage.roi.ROI
Tests whether all the ROIs supplied are members of the same group (i.e., they all have the same Group UID).
isImage(File) - Static method in class com.xinapse.image.ImageUtils
Tests whether the supplied File refers to a WritableImage file.
isImagingModality() - Method in enum com.xinapse.dicom.Modality
Returns true if this is an imaging Modality.
isIntegerType() - Method in enum com.xinapse.image.PixelDataType
Tests whether a sample of this PixelDataType can be represented by a single int value (Note: not integer).
isLoadInProgress() - Method in class com.xinapse.image.InputImageSelectionPanel
 
isLoadInProgress() - Method in class com.xinapse.image.MultipleImageSelectionPanel
 
isMagneticResonance() - Method in enum com.xinapse.dicom.Modality
Returns true if this is a magnetic resonance Modality.
isModified() - Method in class com.xinapse.multisliceimage.MultiSliceImage
Tests whether this MultiSliceImage has been modified since instantiation.
isOn() - Static method in class com.xinapse.image.ImageDebug
Tests whether debugging of the image package is on.
isOn() - Static method in class com.xinapse.multisliceimage.Analyze.ANZDebug
Tests whether debugging of the Analyze package is on.
isOn() - Static method in class com.xinapse.multisliceimage.MultiSliceImageDebug
Tests whether debugging of the MultiSliceImage package is on.
isOn() - Static method in class com.xinapse.multisliceimage.UNC.UNCDebug
Tests whether debugging of the UNC package is on.
isOpen() - Method in interface com.xinapse.image.ReadableImage
Tests whether this image is still open.
isOpen() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
isOpen() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
isReloaded() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns true if this ROI has been reloaded from disk.
isSameAnnotation(List<ROI>) - Static method in class com.xinapse.multisliceimage.roi.ROI
Tests whether all the ROIs supplied have the same annotation.
isSameColour(List<ROI>) - Static method in class com.xinapse.multisliceimage.roi.ROI
Tests whether all the ROIs supplied have the same colour.
isSelected() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns true if this ROI is currently selected.
isSet() - Method in class com.xinapse.util.CancellableThread.Flag
Test whether the flag has been set.
isSingleInputImage() - Method in class com.xinapse.image.SingleOrMultipleInputImageSelectionPanel
Returns whether configured with a single input image.
isSingleInputImage() - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Tests whether there is a single or multiple input images.
isStatistic() - Method in enum com.xinapse.multisliceimage.Analyze.NIFTIIntent
Indicates whether this NIFTIIntent is a statistic intent.
isUNCImage(URL) - Static method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns true if the URL produces a UNCImage input stream.
isUNCImage(String) - Static method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns true if the fileName is the name of a UNC Image file.
isUNCImage(File) - Static method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns true if the File is a UNC Image File.
isZero() - Method in class com.xinapse.image.Complex
Tests whether this complex number is zero.
isZero() - Method in class com.xinapse.image.DoubleComplex
 
isZero() - Method in class com.xinapse.image.FloatComplex
 

J

join(IrregularROI) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Joins this ROI to another IrregularROI with a waisted join - a join at the nearest point.
join(List<ROI>) - Static method in class com.xinapse.multisliceimage.roi.ROI
Joins a List of ROIs with a waisted join at the nearest point.

L

LaplacianFilter - Class in com.xinapse.filter
A FixedWeightsKernelFilter for performing a Laplacian filtering of an image.
LaplacianFilter(float[][][]) - Constructor for class com.xinapse.filter.LaplacianFilter
 
LaplacianFilter.LaplacianSpecifierPanel - Class in com.xinapse.filter
A FilterSpecifierPanel for a Laplacian edge-detection filter.
LATERALITY_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the image laterality.
LENGTHTOKEN - Static variable in class com.xinapse.multisliceimage.roi.ROIStreamTokenizer
 
LinearROI - Interface in com.xinapse.multisliceimage.roi
Interface that ROIs having the property of linearity implement.
LineROI - Class in com.xinapse.multisliceimage.roi
A Class representing a straight line on an image.
LineROI(double, double, double, double) - Constructor for class com.xinapse.multisliceimage.roi.LineROI
Creates a new LineROI with the coordinates of the points forming the line in mm coordinates.
LineROI(double, double, double, double, ROIState) - Constructor for class com.xinapse.multisliceimage.roi.LineROI
Creates a new LineROI with the coordinates of the points forming the line in mm coordinates.
LineROI(double, double, double, double, byte, ROIState) - Constructor for class com.xinapse.multisliceimage.roi.LineROI
Creates a new LineROI with the coordinates of the points forming the line in mm coordinates.
LineROICreateDialog - Class in com.xinapse.multisliceimage.roi
A dialog used to create Line ROIs.
LineROICreateDialog(CanAddROIToFrame) - Constructor for class com.xinapse.multisliceimage.roi.LineROICreateDialog
Creates a new LineROICreateDialog, with ROIs that are created by the dialog being added to the specified frame.
LoadChooser() - Constructor for class com.xinapse.image.ImageFileChooser.LoadChooser
Creates an ImageFileChooser.LoadChooser suitable for selecting a ReadableImage file for loading, with the directory set to the current working directory.
LoadChooser(File) - Constructor for class com.xinapse.image.ImageFileChooser.LoadChooser
Creates an ImageFileChooser.LoadChooser suitable for selecting a ReadableImage file for loading, with the directory set to the supplied directory (if a directory) or the parent directory containing the file (if a regular file).
LoadChooser(File, Class<? extends ReadableImage>) - Constructor for class com.xinapse.image.ImageFileChooser.LoadChooser
Creates an ImageFileChooser.LoadChooser suitable for selecting a ReadableImage file for loading, with the directory set to the supplied directory (if a directory) or the parent directory containing the file (if a regular file).
loadImage(ReadableImage, ImageLoaderWorker) - Method in class com.xinapse.image.InputImageSelectionPanel
 
loadImage(ReadableImage, ImageLoaderWorker) - Method in class com.xinapse.image.MultipleImageSelectionPanel
 
Long(long) - Static method in class com.xinapse.io.ByteSwap
Swap the byte order in a long and return the value represented by the bit pattern of the reversed bytes as a long.
Long(byte[], ByteOrder) - Static method in class com.xinapse.io.ByteSwap
Swap the byte order (if necessary) in a eight-byte array and return the value represented by the bit pattern as a long.
Long(InputStream, ByteOrder) - Static method in class com.xinapse.io.Input
Reads a long value from a java.io.InputStream strm, ensuring that blocking occurs until the value has been read.
Long(RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Input
Reads a long value from a java.io.RandomAccessFile f, ensuring that blocking occurs until the value has been read.
Long(long, OutputStream, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single long to a java.io.OutputStream strm.
Long(long, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single long to a java.io.RandomAccessFile f.
LongArray(InputStream, ByteOrder, int) - Static method in class com.xinapse.io.Input
Reads an array of long values from a java.io.InputStream strm ensuring that blocking occurs until all values have been read.
LongArray(DataInputStream, ByteOrder, long[]) - Static method in class com.xinapse.io.Input
Reads an array of long values from a DataInputStream strm ensuring that blocking occurs until all values have been read.
LongArray(RandomAccessFile, ByteOrder, long[]) - Static method in class com.xinapse.io.Input
Reads an array of long values from a java.io.RandomAccessFile f ensuring that blocking occurs until all values have been read.
LongArray(RandomAccessFile, ByteOrder, long[], int, int) - Static method in class com.xinapse.io.Input
Reads an array of long values from a java.io.RandomAccessFile f, ensuring that blocking occurs until all values have been read.
LongArray(long[], OutputStream, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of long values to a java.io.OutputStream strm.
LongArray(long[], RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of long values to a java.io.RandomAccessFile f.
LongArray(long[], int, int, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of long values to a java.io.RandomAccessFile f.
LOWERCASEEXTENSION - Static variable in class com.xinapse.multisliceimage.Analyze.ANZColourMapping
The file extension for Analyze lookup files in lower case form.

M

MAGENTA - Static variable in class com.xinapse.image.ColourMapping
The ColourMapping representing a magenta intensity scale.
main(String[]) - Static method in enum com.xinapse.dicom.Modality
Run the unit test on the Modality class.
main(String[]) - Static method in enum com.xinapse.dicom.PulseSequenceType
Run the unit test on the PulseSequenceType class.
main(String[]) - Static method in class com.xinapse.filter.ColourImageFilter
Runs a self-test of this class.
main(String[]) - Static method in class com.xinapse.filter.FilterSelection
Runs the unit test of this class.
main(String[]) - Static method in class com.xinapse.filter.GaussianBlurFilter
Runs a self-test of this class.
main(String[]) - Static method in class com.xinapse.filter.LaplacianFilter
Runs a self-test of this class.
main(String[]) - Static method in class com.xinapse.filter.MedianFilter
Runs a self-test of this class.
main(String[]) - Static method in class com.xinapse.filter.MorphologicalOperator
Runs a self-test of this class.
main(String[]) - Static method in class com.xinapse.filter.SharpenFilter
Runs a self-test of this class.
main(String[]) - Static method in class com.xinapse.geom3d.AffineTransform3D
Runs the self-test for AffineTransform3D.
main(String[]) - Static method in enum com.xinapse.image.BoundaryCondition
Runs the self-test for this class.
main(String[]) - Static method in class com.xinapse.image.ColourMapping
Runs the self-test on this class.
main(String[]) - Static method in class com.xinapse.image.ColourVolumeInterpolator
Run the self-test for ColourVolumeInterpolator.
main(String[]) - Static method in class com.xinapse.image.Histogram
Run the self-test of the Histogram class.
main(String[]) - Static method in class com.xinapse.image.ImageGrid
Runs the self-test on this Class.
main(String[]) - Static method in class com.xinapse.image.ImageMoments
Runs the self-test on this Class.
main(String[]) - Static method in class com.xinapse.image.ImageUtils
Run the self-test of this class.
main(String[]) - Static method in class com.xinapse.image.IntensityPreset
Runs the self-test on this class.
main(String[]) - Static method in class com.xinapse.image.template.WeightingType.Panel
Runs the self-test for WeightingType.
main(String[]) - Static method in class com.xinapse.image.VolumeInterpolator
Run the self-test for VolumeInterpolator.
main(String[]) - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Run the self-test for the Analyze75Image class.
main(String[]) - Static method in enum com.xinapse.multisliceimage.Analyze.ANZPixFormat
Run a self-test on the ANZPixFormat class.
main(String[]) - Static method in class com.xinapse.multisliceimage.Analyze.InfoExtendedData
Runs the self-test of the InfoExtendedData class.
main(String[]) - Static method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Run the self-test for the NIFTIImage class.
main(String[]) - Static method in enum com.xinapse.multisliceimage.Analyze.NIFTIIntent
Run a self-test on the NIFTIIntent class.
main(String[]) - Static method in enum com.xinapse.multisliceimage.Analyze.NIFTIXForm
Run a self-test on the NIFTIXForm class.
main(String[]) - Static method in enum com.xinapse.multisliceimage.Analyze.SliceOrder
Run a self-test on the SliceOrder class.
main(String[]) - Static method in enum com.xinapse.multisliceimage.Analyze.TUnits
Run a self-test on the TUnits class.
main(String[]) - Static method in enum com.xinapse.multisliceimage.Analyze.XYZUnits
Run a self-test on the XYZUnits class.
main(String[]) - Static method in class com.xinapse.multisliceimage.MultiSliceImage
Run the self-test on the MultiSliceImage class.
main(String[]) - Static method in class com.xinapse.multisliceimage.roi.AddChecksum
Run the program to add a checksum to existing ROI files.
main(String[]) - Static method in class com.xinapse.multisliceimage.roi.ContourROI
Run the self-test on this class.
main(String[]) - Static method in class com.xinapse.multisliceimage.roi.IrregularROI
 
main(String[]) - Static method in class com.xinapse.multisliceimage.roi.ROI
Run the self-test for the ROI class.
main(String[]) - Static method in class com.xinapse.multisliceimage.roi.ROIStreamTokenizer
Runs the self-test for the ROIStreamTokenizer class.
main(String[]) - Static method in enum com.xinapse.util.IntensityRelation
Run the self-test of the IntensityRelation class.
makeConvex(CanAddROIToFrame, float, float, float) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
makeConvex(float, float, float) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Make this IrregularROI convex, or at least less concave.
makeConvex(CanAddROIToFrame, float, float, float) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Make this IrregularROI convex, or at least less concave.
makeTransparent(byte, boolean) - Method in class com.xinapse.image.ColourMapping
Add transparency (an alpha channel) to an existing ColourMapping.
markDeleted() - Method in class com.xinapse.multisliceimage.roi.ROI
Mark this ROI as deleted.
Marker - Class in com.xinapse.multisliceimage.roi
A Class representing a point on an image.
Marker(Point2D.Double) - Constructor for class com.xinapse.multisliceimage.roi.Marker
Creates a new Marker at the given point.
Marker(double, double) - Constructor for class com.xinapse.multisliceimage.roi.Marker
Creates a new Marker at the given (x, y) coordinate.
Marker(double, double, ROIState) - Constructor for class com.xinapse.multisliceimage.roi.Marker
Creates a new Marker at the given (x, y) coordinate, and sets the state of the ROI.
MarkerCreateDialog - Class in com.xinapse.multisliceimage.roi
A dialog used to create Marker ROIs.
MarkerCreateDialog(CanAddROIToFrame) - Constructor for class com.xinapse.multisliceimage.roi.MarkerCreateDialog
Creates a new MarkerCreateDialog, with ROIs that are created by the dialog being added to the specified frame.
MaskAction - Enum in com.xinapse.multisliceimage.roi
An enumeration of possible masking operation actions that can be applied to an ROI to mask out some of an image's pixels.
maskImage(int, List<ROI>, MaskAction, double, CombineMode) - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Use the supplied ROIs in the slice to mask the image.
MaskMode - Enum in com.xinapse.multisliceimage.roi
An enumeration of possible masking mode.
MaskMode.Panel - Class in com.xinapse.multisliceimage.roi
A JPanel for selecting a MaskMode.
maskSelectorPanel - Variable in class com.xinapse.dynamic.AbstractDynamicFrame
A JPanel for selecting an image mask.
match(Histogram, double) - Method in class com.xinapse.image.Histogram
Returns the intensity scaling factor that will best match this Histogram to another Histogram.
max - Variable in class com.xinapse.image.Histogram.BinSpec
The maximum histogram value for the last bin.
max - Variable in class com.xinapse.multisliceimage.roi.ROIStats
The maximum pixel intensity inside an ROI in intensity units.
MAX_GAMMA - Static variable in class com.xinapse.image.ColourMapping
The maximum display gamma value that is allowed.
MAX_LUMINANCE - Static variable in class com.xinapse.image.ColourMapping
The maximum value of display luminance (for a DDL of 255) that is allowed (including ambient light).
MAX_N_TIMES - Static variable in class com.xinapse.dynamic.AbstractDynamicFrame
The maximum number of time points that can be selected in various spinners.
MAX_PEN_SIZE - Static variable in class com.xinapse.multisliceimage.roi.PenSizePanel
The maximum size (in pixels) for the ROI eraser/paint pen.
MAXDIM - Static variable in class com.xinapse.image.Image
The maximum dimensionality of an image.
MAXDIM - Static variable in class com.xinapse.multisliceimage.Analyze.ANZHeader
The maximum dimensionality of an Analyze image.
MAXTOKEN - Static variable in class com.xinapse.multisliceimage.roi.ROIStreamTokenizer
 
mean - Variable in class com.xinapse.multisliceimage.roi.ROIStats
The mean pixel intensity inside an ROI in intensity units.
MEANTOKEN - Static variable in class com.xinapse.multisliceimage.roi.ROIStreamTokenizer
 
MedianFilter - Class in com.xinapse.filter
A SpatialFilter for performing median filtering of an image.
MedianFilter(int[], BoundaryCondition) - Constructor for class com.xinapse.filter.MedianFilter
Construct a MedianFilter with a kernel size specified by the argument.
MedianFilter.MedianSpecifierPanel - Class in com.xinapse.filter
A FilterSpecifierPanel for a median filter.
MEDIANTOKEN - Static variable in class com.xinapse.multisliceimage.roi.ROIStreamTokenizer
 
MessageShower - Interface in com.xinapse.util
An interface for showing messages to the user.
min - Variable in class com.xinapse.image.Histogram.BinSpec
The minimun histogram value for the first bin.
min - Variable in class com.xinapse.multisliceimage.roi.ROIStats
The minimum pixel intensity inside an ROI in intensity units.
MIN_GAMMA - Static variable in class com.xinapse.image.ColourMapping
The minimum display gamma value that is allowed.
MIN_LUMINANCE - Static variable in class com.xinapse.image.ColourMapping
The minimum value of display luminance (for a DDL of zero) that is allowed (including ambient light).
MIN_PEN_SIZE - Static variable in class com.xinapse.multisliceimage.roi.PenSizePanel
The minimum size (in pixels) for the ROI eraser/paint pen.
MINTOKEN - Static variable in class com.xinapse.multisliceimage.roi.ROIStreamTokenizer
 
mmPosToPix(double, float, int) - Static method in class com.xinapse.multisliceimage.roi.ROI
Convert from a position in mm to a pixel number coordinate.
Modality - Enum in com.xinapse.dicom
An enumeration of the known imaging and other modalities.
Modality.ComboBox - Class in com.xinapse.dicom
A javax.swing.JComboBox that is used for selecting a Modality.
MODALITY_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the imaging modality.
MODALITY_PREFERENCE_NAME - Static variable in enum com.xinapse.dicom.Modality
The Preference name for the imaging modality.
mode - Variable in class com.xinapse.multisliceimage.MultiSliceImage
The "mode" with which the image was opened, if a disk-file: either "r" or "rw".
modelChangedListener - Variable in class com.xinapse.dynamic.DynamicModel.SpecifierPanel
The ActionListener that should be notified when the DynamicModel specified in this SpecifierPanel is changed.
monitor - Variable in class com.xinapse.util.MonitorWorker
A ProgressMonitor which may pop up.
MonitorWorker - Class in com.xinapse.util
A class to implement a SwingWorker that can pop up a ProgressMonitor to allow user cancellation.
MonitorWorker(Component, String) - Constructor for class com.xinapse.util.MonitorWorker
Creates a new MonitorWorker with a parent component and a program name.
MONOCHROME1 - Static variable in class com.xinapse.image.ColourMapping
The ColourMapping representing a grey (white to black) intensity scale.
MONOCHROME2 - Static variable in class com.xinapse.image.ColourMapping
The ColourMapping representing a grey (black to white) intensity scale.
MorphologicalOperationWorker - Class in com.xinapse.multisliceimage.roi
This SwingWorker is used to perform morphological operations (dilation and erosion) on ROIs.
MorphologicalOperationWorker(CanAddROIToFrame, List<ROI>, double) - Constructor for class com.xinapse.multisliceimage.roi.MorphologicalOperationWorker
Creates a new MorphologicalOperationWorker to operate on a set of ROIs.
MorphologicalOperator - Class in com.xinapse.filter
A SpatialFilter for performing a morphological operation on an image.
MorphologicalOperator.MorphologicalSpecifierPanel - Class in com.xinapse.filter
A FilterSpecifierPanel for a moprphological operation filter.
MorphologicalOperator.Op - Enum in com.xinapse.filter
An enumeration of the possible morphological operations on an image.
MorphologicalSpecifierPanel(String) - Constructor for class com.xinapse.filter.MorphologicalOperator.MorphologicalSpecifierPanel
Creates a new MorphologicalSpecifierPanel.
MostLikePlane - Enum in com.xinapse.image
The radiological planes that can be used to describe the approximate orientation of a scan plane.
move(double, double) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
move(double, double) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
move(EllipticalROI, boolean) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
Moves and rehapes this EllipticalROI so that the size and location are the same as the given EllipticalROI.
move(double, double) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
move(double, double, double, double) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
move(double, double) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
move(double, double, double, double) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
move(Point2D, Point2D) - Method in class com.xinapse.multisliceimage.roi.LineROI
Moves this LineROI so that the ends are at the new specified locations.
move(double, double) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
move(double, double) - Method in class com.xinapse.multisliceimage.roi.Marker
 
move(double, double) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
This method does nothing.
move(double, double) - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
move(double, double, double, double) - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
move(double, double) - Method in class com.xinapse.multisliceimage.roi.ROI
Move this ROI by specified distances (in mm) in the x and y directions.
move(double, double) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
move(double, double, double, double) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
move(double, double, double, double) - Method in interface com.xinapse.multisliceimage.roi.StretchableROI
Moves and stretches an ROI.
moveROIs(List<ROI>, double, double) - Static method in class com.xinapse.multisliceimage.roi.ROI
Move a List of ROIs by specified distances (in mm) in the x and y directions.
moveVertex(Point2D, Handle, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
moveVertex(Point2D, Handle, int, int, float, float, boolean) - Method in interface com.xinapse.multisliceimage.roi.EditableOutlineROI
Move a point on the outline of this EditableOutlineROI to a new position.
moveVertex(Point2D, Handle, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
moveVertex(Point2D, Handle, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
moveVertex(Point2D, Handle, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
MS_PD_IMAGE_NAME - Static variable in class com.xinapse.image.template.HeadTemplate
The name of the proton-density-weighted MS template image.
MultiContrastAnalysisFrame - Class in com.xinapse.util
A JFrame for performing an analysis of images where the contrast changes from one image to the next.
MultiContrastAnalysisFrame(ImageDisplayer, String, String, int, String) - Constructor for class com.xinapse.util.MultiContrastAnalysisFrame
Creates a new MultiContrastAnalysisFrame connected with a displayer, with the given title.
MultipleImageSelectionPanel - Class in com.xinapse.image
A MultipleImageSelectionPanel shows a list of images, and contains the mechanism for selecting a new list of images, adding images to the list, removing images from the list, and changing the order of images in the list.
MultipleImageSelectionPanel() - Constructor for class com.xinapse.image.MultipleImageSelectionPanel
Creates a new MultipleImageSelectionPanel with an empty list of images.
MultipleImageSelectionPanel(Component) - Constructor for class com.xinapse.image.MultipleImageSelectionPanel
Creates a new MultipleImageSelectionPanel, that is contained within a parent Component, and with an empty list of images.
multiply(Complex) - Method in class com.xinapse.image.Complex
Multiplies this complex number by another complex number, and returns the result.
multiply(Complex) - Method in class com.xinapse.image.DoubleComplex
 
multiply(Complex) - Method in class com.xinapse.image.FloatComplex
 
MultiSliceImage - Class in com.xinapse.multisliceimage
An abstract representation of a multi-dimensional image.
MultiSliceImage() - Constructor for class com.xinapse.multisliceimage.MultiSliceImage
Default constructor for MultiSliceImage for use by sub-classes.
MultiSliceImageDebug - Class in com.xinapse.multisliceimage
Enables and disables debugging messages for the MultiSliceImage package.

N

N_DIMV - Static variable in class com.xinapse.multisliceimage.UNC.UNCImage
The maximum dimensionality of an image.
N_DOTS - Static variable in interface com.xinapse.filter.SpatialFilter
The number of dots to show as the filter progresses.
N_HISTOGRAM - Static variable in class com.xinapse.multisliceimage.UNC.UNCImage
The number of entries in an image histogram
N_STEADY_STATES_PREFERENCE_NAME - Static variable in class com.xinapse.dynamic.AbstractDynamicFrame
The Preference name for the number of steady-state images.
nAIF - Variable in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
The number of points in the AIF if it is resampled with a time step of dt.
NAME - Static variable in interface com.xinapse.apps.cardiac.SegmentalAnalysis
The name of SegmentalAnalysis.
nBins - Variable in class com.xinapse.image.Histogram.BinSpec
The number of bins.
nCols - Variable in class com.xinapse.image.VolumeInterpolator
The number of columns in the block of pixels.
NENTRIES - Static variable in class com.xinapse.multisliceimage.Analyze.ANZColourMapping
The number of entries in an Analyze colour mapping lookup file.
new2DInstance(ReadableImage, int) - Static method in class com.xinapse.filter.LaplacianFilter
Creates a new 2-D LaplacianFilter suitable for filtering the supplied image.
new2DInstance(float, float, int) - Static method in class com.xinapse.filter.LaplacianFilter
Creates a new 2-D LaplacianFilter suitable for filtering an image with the given pixel sizes.
new2DInstance(ReadableImage, int) - Static method in class com.xinapse.filter.SharpenFilter
Creates a new 2-D SharpenFilter suitable for filtering the supplied image.
new2DInstance(float, float, int) - Static method in class com.xinapse.filter.SharpenFilter
Creates a new 2-D SharpenFilter suitable for filtering an image with the given pixel sizes.
new2DInstance(ReadableImage) - Static method in class com.xinapse.filter.SobelFilter.MagnitudeFilter
Creates a new 2-D SobelFilter.MagnitudeFilter suitable for filtering the supplied image to obtain the magnitude of the intensity gradient.
new2DInstance(float, float) - Static method in class com.xinapse.filter.SobelFilter.MagnitudeFilter
Creates a new 2-D SobelFilter.MagnitudeFilter suitable for filtering images with the given pixel sizes, to obtain the magnitude of the intensity gradient.
new2DXInstance(ReadableImage) - Static method in class com.xinapse.filter.SobelFilter
Creates a new 2-D SobelFilter suitable for filtering the supplied image to obtain the intensity gradient in the x-direction.
new2DXInstance(float) - Static method in class com.xinapse.filter.SobelFilter
Creates a new 2-D SobelFilter suitable for filtering an image to obtain the intensity gradient in the x-direction.
new2DYInstance(ReadableImage) - Static method in class com.xinapse.filter.SobelFilter
Creates a new 2-D SobelFilter suitable for filtering the supplied image to obtain the intensity gradient in the y-direction.
new2DYInstance(float) - Static method in class com.xinapse.filter.SobelFilter
Creates a new 2-D SobelFilter suitable for filtering an image to obtain the intensity gradient in the y-direction.
new3DInstance(ReadableImage, int) - Static method in class com.xinapse.filter.LaplacianFilter
Creates a new 3-D LaplacianFilter suitable for filtering the supplied image to obtain the intensity gradient.
new3DInstance(float, float, float, int) - Static method in class com.xinapse.filter.LaplacianFilter
Creates a new 3-D LaplacianFilter suitable for filtering an image to obtain the intensity gradient.
new3DInstance(ReadableImage, int) - Static method in class com.xinapse.filter.SharpenFilter
Creates a new 3-D SharpenFilter suitable for sharpening the supplied image.
new3DInstance(float, float, float, int) - Static method in class com.xinapse.filter.SharpenFilter
Creates a new 3-D SharpenFilter suitable for sharpening an image.
new3DInstance(ReadableImage) - Static method in class com.xinapse.filter.SobelFilter.MagnitudeFilter
Creates a new 3-D SobelFilter.MagnitudeFilter suitable for filtering the supplied image to obtain the magnitude of the intensity gradient.
new3DInstance(float, float, float) - Static method in class com.xinapse.filter.SobelFilter.MagnitudeFilter
Creates a new 3-D SobelFilter.MagnitudeFilter suitable for filtering images with the given pixel sizes, to obtain the magnitude of the intensity gradient.
new3DXInstance(ReadableImage) - Static method in class com.xinapse.filter.SobelFilter
Creates a new 3-D SobelFilter suitable for filtering the supplied image to obtain the intensity gradient in the x-direction.
new3DXInstance(float) - Static method in class com.xinapse.filter.SobelFilter
Creates a new 3-D SobelFilter suitable for filtering an image to obtain the intensity gradient in the x-direction.
new3DYInstance(ReadableImage) - Static method in class com.xinapse.filter.SobelFilter
Creates a new 3-D SobelFilter suitable for filtering the supplied image to obtain the intensity gradient in the y-direction.
new3DYInstance(float) - Static method in class com.xinapse.filter.SobelFilter
Creates a new 3-D SobelFilter suitable for filtering an image to obtain the intensity gradient in the y-direction.
new3DZInstance(ReadableImage) - Static method in class com.xinapse.filter.SobelFilter
Creates a new 3-D SobelFilter suitable for filtering the supplied image to obtain the intensity gradient in the z-direction.
new3DZInstance(float) - Static method in class com.xinapse.filter.SobelFilter
Creates a new 3-D SobelFilter suitable for filtering an image to obtain the intensity gradient in the z-direction.
newCircular2DInstance(int, MorphologicalOperator.Op, BoundaryCondition) - Static method in class com.xinapse.filter.MorphologicalOperator
Creates a new MorphologicalOperator with a 2-D circular kernel.
newCubic3DInstance(int, MorphologicalOperator.Op, BoundaryCondition) - Static method in class com.xinapse.filter.MorphologicalOperator
Creates a new MorphologicalOperator with a 3-D cubic kernel.
newInstance(String) - Static method in class com.xinapse.apps.perfusion.DCEMRIModel
Returns an DCEMRIModel Object corresponding to a string.
newInstance(CommandLine, ReadableImage) - Static method in class com.xinapse.filter.ColourImageFilter
Creates a new ColourImageFilter using the supplied command line arguments, suitable for filtering the supplied image.
newInstance(CommandLine, ReadableImage) - Static method in class com.xinapse.filter.GaussianBlurFilter
Creates a new GaussianBlurFilter using the supplied command line arguments, suitable for blurring the supplied image.
newInstance(ReadableImage, float[]) - Static method in class com.xinapse.filter.GaussianBlurFilter
Creates a new GaussianBlurFilter suitable for blurring the supplied image.
newInstance(float[], float[]) - Static method in class com.xinapse.filter.GaussianBlurFilter
Creates a new GaussianBlurFilter suitable for blurring an image with the given pixel sizes.
newInstance(CommandLine, ReadableImage) - Static method in class com.xinapse.filter.LaplacianFilter
Creates a new LaplacianFilter using the supplied command line arguments.
newInstance(CommandLine, ReadableImage) - Static method in class com.xinapse.filter.MedianFilter
Creates a new MedianFilter using the supplied command line arguments.
newInstance(CommandLine, ReadableImage) - Static method in class com.xinapse.filter.MorphologicalOperator
Creates a new MorphologicalOperator using the supplied command line arguments.
newInstance(CommandLine, ReadableImage) - Static method in class com.xinapse.filter.SharpenFilter
Creates a new SharpenFilter using the supplied command line arguments.
newInstance(CommandLine, ReadableImage) - Static method in class com.xinapse.filter.SobelFilter
Creates a new SobelFilter using the supplied command line arguments.
newInstance(String) - Static method in class com.xinapse.image.ColourMapping
Creates a new ColourMapping object from a String representation of the ColourMapping name, or the list of entries in the ColourMapping.
newInstance(ReadableImage) - Static method in class com.xinapse.image.Histogram
Creates a Histogram of intensities from a com.xinapse.image.ReadableImage.
newInstance(URL) - Static method in class com.xinapse.multisliceimage.UNC.UNCImage
Creates an in-memory UNCImage, loading all information from a URL.
newInstance(URL, boolean) - Static method in class com.xinapse.multisliceimage.UNC.UNCImage
Creates an in-memory UNCImage, loading information from a URL.
newInstance(String, String) - Static method in class com.xinapse.multisliceimage.UNC.UNCImage
Opens an existing disk-based UNC image.
newInstance(File, String) - Static method in class com.xinapse.multisliceimage.UNC.UNCImage
Opens an existing disk-based UNC image.
newInstance(InputStream) - Static method in class com.xinapse.multisliceimage.UNC.UNCImage
Creates an in-memory UNCImage, loading information from an input stream.
newInstance(InputStream, boolean) - Static method in class com.xinapse.multisliceimage.UNC.UNCImage
Creates an in-memory UNCImage, loading information from the input stream.
newInstance(double[], double[]) - Static method in class com.xinapse.numerical.CubicSplineInterpolator
Create a new CubicSplineInterpolator interpolator, from arrays of tabulated x and y values.
newRectangular2DInstance(int, MorphologicalOperator.Op, BoundaryCondition) - Static method in class com.xinapse.filter.MorphologicalOperator
Creates a new MorphologicalOperator with a 2-D rectangular kernel.
newSpherical3DInstance(int, MorphologicalOperator.Op, BoundaryCondition) - Static method in class com.xinapse.filter.MorphologicalOperator
Creates a new MorphologicalOperator with a 3-D spherical kernel.
nextClearBit(int) - Method in class com.xinapse.util.BitSet
Returns the index of the next false bit, from the specified bit (inclusive).
nextSetBit(int) - Method in class com.xinapse.util.BitSet
Returns the index of the next true bit, from the specified bit (inclusive).
NIFTIFileFilter - Class in com.xinapse.multisliceimage.Analyze
A file filter for NIFTI images.
NIFTIHeader - Class in com.xinapse.multisliceimage.Analyze
This class represents a multi-dimensional NIFTI image header file.
NIFTIImage - Class in com.xinapse.multisliceimage.Analyze
This class is a representation of a multi-dimensional image in the NIFTI-1 format (see The Neuroimaging Informatics Technology Initiative), an extension of the original Analyze 7.5 format (see The Biomedical Imaging Resource).
NIFTIImage() - Constructor for class com.xinapse.multisliceimage.Analyze.NIFTIImage
Creates an uninitialised instance of a NIFTIImage.
NIFTIImage(short, short, short, short, ANZPixFormat) - Constructor for class com.xinapse.multisliceimage.Analyze.NIFTIImage
Creates a new in-memory NINFIImage.
NIFTIImage(ANZPixFormat, Short...) - Constructor for class com.xinapse.multisliceimage.Analyze.NIFTIImage
Creates a new in-memory NIFTIImage.
NIFTIImage(NIFTIHeader) - Constructor for class com.xinapse.multisliceimage.Analyze.NIFTIImage
Creates a new in-memory NIFTIImage, using information from an existing NIFTIHeader.
NIFTIImage(String, short, short, short, short, ANZPixFormat) - Constructor for class com.xinapse.multisliceimage.Analyze.NIFTIImage
Creates a new disk-based NIFTIImage.
NIFTIImage(String, ANZPixFormat, Short...) - Constructor for class com.xinapse.multisliceimage.Analyze.NIFTIImage
Creates a new disk-based NIFTIImage.
NIFTIImage(File, NIFTIHeader) - Constructor for class com.xinapse.multisliceimage.Analyze.NIFTIImage
Creates a new disk-based NIFTIImage, using an existing header as a template for the new image.
NIFTIImage(String, NIFTIHeader) - Constructor for class com.xinapse.multisliceimage.Analyze.NIFTIImage
Creates a new disk-based NIFTIImage, using an existing header as a template for the new image.
NIFTIImage(String, String) - Constructor for class com.xinapse.multisliceimage.Analyze.NIFTIImage
Opens an existing NIFTIImage, with pixel data remaining on disk until requested.
NIFTIIntent - Enum in com.xinapse.multisliceimage.Analyze
This class represents the NIFTI intents.
NIFTIXForm - Enum in com.xinapse.multisliceimage.Analyze
This class represents the NIFTI qforms and sforms.
normalise() - Method in class com.xinapse.image.Histogram
Normalises this Histogram, so that the sum of all the counts is unity.
NorthEastHandle - Class in com.xinapse.multisliceimage.roi
A Class representing a Handle at of the North East corner of an ROI.
NorthEastHandle(int, int, int) - Constructor for class com.xinapse.multisliceimage.roi.NorthEastHandle
Creates a new NorthEastHandle at the location (x,y) with the given size in screen pixels.
NorthHandle - Class in com.xinapse.multisliceimage.roi
A Class representing a Handle on the North edge of an ROI.
NorthHandle(int, int, int) - Constructor for class com.xinapse.multisliceimage.roi.NorthHandle
Creates a new NorthHandle at the location (x,y) with the given size in screen pixels.
NorthWestHandle - Class in com.xinapse.multisliceimage.roi
A Class representing a Handle at of the North West corner of an ROI.
NorthWestHandle(int, int, int) - Constructor for class com.xinapse.multisliceimage.roi.NorthWestHandle
Creates a new NorthWestHandle at the location (x,y) with the given size in screen pixels.
nPoints - Variable in class com.xinapse.multisliceimage.roi.IrregularROI
The number of points forming the outline.
nRows - Variable in class com.xinapse.image.VolumeInterpolator
The number of rows in the block of pixels.
NSEG_TOKEN - Static variable in class com.xinapse.multisliceimage.roi.RadialDivider
The token written to ROI output files to represent the number of segments.
nSlices - Variable in class com.xinapse.image.VolumeInterpolator
The number of slices in the block of pixels.
nTimePoints - Variable in class com.xinapse.apps.cardiac.SelectableSegmentalAnalysis
The number of time points in the input image(s).
NullOutputStream - Class in com.xinapse.io
An OutputStream where anything written to the stream is discarded.
NullOutputStream() - Constructor for class com.xinapse.io.NullOutputStream
Constructor for a NullOutputStream.
NumericalException - Exception in com.xinapse.numerical
Signals that an error has occurred when performing a numerical operation.
NumericalException() - Constructor for exception com.xinapse.numerical.NumericalException
Constructs a NumericalException without a detail message.
NumericalException(String) - Constructor for exception com.xinapse.numerical.NumericalException
Constructs a NumerialException with the specified detail message.

O

ONE_FILE_PROPERTY_KEY - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIImage
The property value key for setting whether NIFTI images should be stored in one file, or two.
OpenSplineROI - Class in com.xinapse.multisliceimage.roi
A Class representing a curved line on an image, represented by a set of knots, with spline interpolators between the knots to define the shape of the curve.
OpenSplineROI(double[], double[], ROIState) - Constructor for class com.xinapse.multisliceimage.roi.OpenSplineROI
Creates a new OpenSplineROI with the specified knot points in mm coordinates.
OpenSplineROI(double[], double[], byte, ROIState, boolean) - Constructor for class com.xinapse.multisliceimage.roi.OpenSplineROI
Creates a new OpenSplineROI with the specified knot points in mm coordinates.
OpenSplineROI(SplineROI) - Constructor for class com.xinapse.multisliceimage.roi.OpenSplineROI
Creates a new OpenSplineROI with the positions of the knot points taken from the supplied SplineROI.
OPTION - Static variable in enum com.xinapse.image.template.WeightingType
 
OPTION - Static variable in enum com.xinapse.util.IntensityRelation
An Option that can be used for command-line processing of an optional list of intensity relations.
OPTIONS - Static variable in class com.xinapse.filter.MorphologicalOperator
The Options for selecting a MorphologicalOperator.
or(BitSet) - Method in class com.xinapse.util.BitSet
Performs the logical OR operation on this bit set and the given BitSet.
orderPoints(IrregularROI) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Sets the order of the outline points of this ROI so that they are in the closest possible correspondence (spatially) with the outline points of the supplied IrregularROI.
ORIENT_AXIAL - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Header
The constant used to indicate an axial orientation.
ORIENT_AXIAL_FLIPPED - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Header
The constant used to indicate a flipped axial orientation.
ORIENT_CORONAL - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Header
The constant used to indicate a coronal orientation.
ORIENT_CORONAL_FLIPPED - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Header
The constant used to indicate a flipped coronal orientation.
ORIENT_SAGITTAL - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Header
The constant used to indicate a sagittal orientation.
ORIENT_SAGITTAL_FLIPPED - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Header
The constant used to indicate a flipped sagittal orientation.
otsuThreshold() - Method in class com.xinapse.image.Histogram
Calculates a threshold to separate the foreground from the background using Ostu's method of maximsing between-class variance for two classes of pixel values, where one class is assumed to be the foreground, and the other is the background.
OUTERPOINTSTOKEN - Static variable in class com.xinapse.multisliceimage.roi.HollowROI
The token written to ROI output files to indicate that a list of outer points is to follow.
Output - Class in com.xinapse.io
Abstract class providing methods to write primitve data values to output files and streams.
outputImageSelectionPanel - Variable in class com.xinapse.dynamic.AbstractDynamicFrame
ImageSelectionPanel used to select the output images basename.
OutputImageSelectionPanel - Class in com.xinapse.image
An OutputImageSelectioPanel is a javax.swing.JPanel that can be used to select an image name for output.
OutputImageSelectionPanel(MessageShower) - Constructor for class com.xinapse.image.OutputImageSelectionPanel
Creates new OutputImageSelectionPanel, with the default Folder set from the System Property "user.dir".

P

pad(ReadableImage, int[], MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Pads a WritableImage with zero-intensity pixels around the edge of the image.
pageBreak() - Method in class com.xinapse.util.ReportGenerator
Insert an (optional) page break in the report.
paintComponent(Graphics) - Method in class com.xinapse.image.ImagePreview
 
paintIcon(Component, Graphics, int, int) - Method in class com.xinapse.image.ColourMapping
Paints the Icon used to represent this ColourMapping.
paintIcon(Component, Graphics, int, int) - Method in class com.xinapse.image.PreviewIcon
Draw the icon at the specified location.
paintIcon(Component, Graphics, int, int) - Method in enum com.xinapse.image.RenderingInterpolationType
 
paintIcon(Component, Graphics, int, int) - Method in enum com.xinapse.util.IntensityRelation
 
Panel(String) - Constructor for class com.xinapse.filter.FilterSelection.Panel
Create a new FilterSelectionPanel.
Panel(Preferences) - Constructor for class com.xinapse.image.template.WeightingType.Panel
Creates a WeightingType.Panel.
Panel(Preferences, CombineMode) - Constructor for class com.xinapse.multisliceimage.roi.CombineMode.Panel
Constructs a CombineMode.Panel for selecting a CombineMode.
Panel(Preferences, MaskMode) - Constructor for class com.xinapse.multisliceimage.roi.MaskMode.Panel
Constructs a MaskMode.Panel for selecting a MaskMode.
PanelGenerator() - Constructor for class com.xinapse.util.IntensityRelation.PanelGenerator
Create a new PanelGenerator.
ParameterNotSetException - Exception in com.xinapse.image
Indicates that a parameter is not stored in an image.
ParameterNotSetException() - Constructor for exception com.xinapse.image.ParameterNotSetException
Constructs an ParameterNotSetException with "parameter not set" as its detail message.
ParameterNotSetException(String) - Constructor for exception com.xinapse.image.ParameterNotSetException
Constructs a ParameterNotSetException with the specified detail message.
ParameterNotSetException(String, Throwable) - Constructor for exception com.xinapse.image.ParameterNotSetException
Constructs a ParameterNotSetException with the specified cause.
parent - Variable in class com.xinapse.image.ImageSelectionGroupPanel
The parent MessageShower in which this ImageSelectionGroupPanel is embedded.
parentFrame - Variable in class com.xinapse.apps.active.ROICalculation.SpecifierPanel
The ROIPropagateFrame that is the parent of this SpecifierPanel.
parentFrame - Variable in class com.xinapse.apps.cardiac.SegmentalAnalysis.SpecifierPanel
The CardiacSegmentFrame that is the parent of this SpecifierPanel.
parentFrame - Variable in class com.xinapse.dynamic.DynamicModel.SpecifierPanel
The AbstractDynamicFrame that is the parent of this SpecifierPanel.
parseMultiValuedString(String, int) - Static method in class com.xinapse.multisliceimage.MultiSliceImage
Convenience method to parse Strings of the form "value1\value2\value3\…\valueN", where value1 to valueN are numerical values.
parseRelations(String) - Static method in enum com.xinapse.util.IntensityRelation
Get an array of IntenstyRelations from a String comma-separated list of relations.
PATIENT_ID_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the patient ID.
PATIENT_NAME_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the patient name.
PATIENT_POSITION_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the way in which the patient is positioned in the scanner.
PATIENT_POSITION_PREFERENCE_NAME - Static variable in enum com.xinapse.dicom.PatientPosition
The Preference name for the imaging patient position.
PATIENT_SEX_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the patient's sex.
PatientPosition - Enum in com.xinapse.dicom
An enumeration of the possible positions in which a patient may be lying in the scanning equipment (e.g, head-first, supine).
PatientPosition.ComboBox - Class in com.xinapse.dicom
A javax.swing.JComboBox that is used for selecting a PatientPosition.
pdfReport - Variable in class com.xinapse.apps.cardiac.SelectableSegmentalAnalysis
True if a PDF report has been requested (command-line program only).
PenSizePanel - Class in com.xinapse.multisliceimage.roi
A JPanel that can be used to select the size of a "pen" used to erase parts of IrregularROIs.
PenSizePanel(String, int) - Constructor for class com.xinapse.multisliceimage.roi.PenSizePanel
Creates a new PenSizePanel with the specified title.
PhaseImage - Class in com.xinapse.image
A Class for converting an image where the intensity values represent phase, to the phase values in the range -pi ..
pix - Variable in class com.xinapse.image.VolumeInterpolator
The array of pixel values to be interpolated.
PixArray - Class in com.xinapse.image
An abstract representation of an array of pixels of varying type.
PixArray(Object, int, int[], PixelDataType) - Constructor for class com.xinapse.image.PixArray
Creates a new PixArray taking the pixel values from the supplied sourceArray.
pixArray - Variable in class com.xinapse.multisliceimage.MultiSliceImage
If non-null, pixel data held in this PixArray object.
PIXEL_SPACING_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the physical distance in the patient between the center of each pixel.
PIXEL_X_SIZE_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the width of an image pixel in mm.
PIXEL_Y_SIZE_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the height of an image pixel in mm.
PIXEL_Z_SIZE_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the thickness of an image pixel in mm.
PixelDataType - Enum in com.xinapse.image
An enumeration of the pixel formats (data types) that can be used in images.
PixelOp - Enum in com.xinapse.image
An Enumeration of the two types of operation for pixel accessor methods.
pixelXSize - Variable in class com.xinapse.image.VolumeInterpolator
Horizontal pixel size in the block of pixels to be interpolated.
pixelYSize - Variable in class com.xinapse.image.VolumeInterpolator
Vertical pixel size in the block of pixels to be interpolated.
pixelZSize - Variable in class com.xinapse.image.VolumeInterpolator
Pixel depth in the block of pixels to be interpolated.
pixPosToMm(double, int, float) - Static method in class com.xinapse.multisliceimage.roi.ROI
Convert from a pixel number to a position in mm.
pointOver(Point) - Method in class com.xinapse.multisliceimage.roi.Handle
Returns true if the specified point is over this handle; false otherwise.
pointOver(Point) - Method in class com.xinapse.multisliceimage.roi.VertexHandle
Returns true if the specified point is over this handle; false otherwise.
POINTSTOKEN - Static variable in class com.xinapse.multisliceimage.roi.IrregularROI
The token written to ROI output files to indicate that a list of points is to follow.
polar(double, double) - Static method in class com.xinapse.image.DoubleComplex
Creates a new DoubleComplex given the modulus and argument (in radians).
polar(float, float) - Static method in class com.xinapse.image.FloatComplex
Creates a new FloatComplex given the modulus and argument (in radians).
PREFERENCE_NAME - Static variable in enum com.xinapse.image.RenderingInterpolationType
The Preference name for rendering interpolation type setting.
PREFERENCES_NODE_NAME - Static variable in class com.xinapse.multisliceimage.roi.ROI
The node name for all Preferences to do with ROIs.
PREFERENCES_NODE_NAME - Static variable in class com.xinapse.util.ReportGenerator
The node name for all Preferences to do with ReportGenerator.
PreferencesSettable - Interface in com.xinapse.util
An interface that is implemented by components that can save their settings to user preferences.
PreviewIcon - Class in com.xinapse.image
An Icon that is used to preview an image (UNC, Analyze, NIFTI, DICOM).
PreviewIcon(String, int, int, int, int) - Constructor for class com.xinapse.image.PreviewIcon
Create a PreviewIcon without a preview of the image.
PreviewIcon(String, ReadableImage) - Constructor for class com.xinapse.image.PreviewIcon
Create a PreviewIcon with a preview of the image.
previewROIs(List<ROI>) - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Previews a java.util.List of ROIs in the frame.
previousSetBit(int) - Method in class com.xinapse.util.BitSet
Returns the index of the nearest bit that is set to true that occurs on or before the specified starting index.
print(String) - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastResult
Prints the results to System.out.
printStats(PrintStream, Object, int, int, float, float, PixelDataType, ComplexMode, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, String) - Method in class com.xinapse.multisliceimage.roi.ROI
Prints the statistics about this ROI in output format to a PrintStream.
process(List<Integer>) - Method in class com.xinapse.multisliceimage.roi.MorphologicalOperationWorker
 
propertyChange(PropertyChangeEvent) - Method in class com.xinapse.image.ImagePreview
Signals that a selected folder or file has changed.
PULSE_SEQUENCE_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the pulse sequence name.
PulseSequenceType - Enum in com.xinapse.dicom
An enumeration of DICOM pulse sequence types.
PulseSequenceType.ComboBox - Class in com.xinapse.dicom
A javax.swing.JComboBox that is used for selecting a PulseSequenceType.
PulseSequenceVariant - Enum in com.xinapse.dicom
An enumeration of recognised DICOM pulse sequence variants.
putFrameInfo(InfoList, int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
putFrameInfo(String, String, int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
putFrameInfo(String, String, int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Adds an item to the frame-specific information.
putFrameInfo(InfoList, int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Adds all the items in an InfoList to the frame-specific information.
putFrameInfo(InfoList, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
putFrameInfo(String, String, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
putInfo(String, int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
putInfo(String, float) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
putInfo(String, String) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
putInfo(String, int, int, int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
putInfo(String, float, int, int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
putInfo(String, String, int, int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
putInfo(String, int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Adds an item to the general file info.
putInfo(String, float) - Method in interface com.xinapse.multisliceimage.InfoStorer
Adds an item to the general file info.
putInfo(String, String) - Method in interface com.xinapse.multisliceimage.InfoStorer
Adds an item to the general file info.
putInfo(String, int, int, int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Adds an item to the dimension-specific information.
putInfo(String, float, int, int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Adds an item to the dimension-specific information.
putInfo(String, String, int, int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Adds an item to the dimension-specific information.
putInfo(String, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
putInfo(String, float) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
putInfo(String, String) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
putInfo(String, int, int, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
putInfo(String, float, int, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
putInfo(String, String, int, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
putInfo(String, String) - Method in class com.xinapse.util.InfoList
Adds "name=value" to the InfoList.
putInfo(String, int) - Method in class com.xinapse.util.InfoList
Adds "name=value" to the InfoList.
putInfo(String, long) - Method in class com.xinapse.util.InfoList
Adds "name=value" to the InfoList.
putInfo(String, float) - Method in class com.xinapse.util.InfoList
Adds "name=value" to the InfoList.
putInfo(String, double) - Method in class com.xinapse.util.InfoList
Adds "name=value" to the InfoList.
putInfo(String, Date) - Method in class com.xinapse.util.InfoList
Adds "name=value" to the InfoList.
putPix(Object, boolean) - Method in interface com.xinapse.image.WritableImage
Put pixel values from a specified array to this image.
putPix(Object, int[]) - Method in interface com.xinapse.image.WritableImage
Puts a single pixel value to the image.
putPix(Object, int[], int[]) - Method in interface com.xinapse.image.WritableImage
Put pixel values from a specified array to this image.
putPix(Object) - Method in class com.xinapse.multisliceimage.MultiSliceImage
Put pixel values from a specified array to this image.
putPix(Object, boolean) - Method in class com.xinapse.multisliceimage.MultiSliceImage
Put pixel values from a specified array to this image.
putPix(Object, int[], int[]) - Method in class com.xinapse.multisliceimage.MultiSliceImage
Put pixel values from a specified array to this image.
putPix(Object, int[]) - Method in class com.xinapse.multisliceimage.MultiSliceImage
Puts a single pixel value to the image.
putPix(Object, int[], int[]) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
putPix(Object, int[]) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
putSlice(Object, int) - Method in interface com.xinapse.image.WritableImage
Puts the pixel values to one slice of an n-dimensional image, where n > 1.
putSlice(Object, int) - Method in class com.xinapse.multisliceimage.MultiSliceImage
Puts the pixel values to one slice of an n-dimensional image, where n > 1.
putSlice(Object, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
putSliceInfo(InfoList, int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
putSliceInfo(String, String, int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
putSliceInfo(String, String, int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Adds an item to the slice-specific information.
putSliceInfo(InfoList, int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Adds all the items in an InfoList to the slice-specific information.
putSliceInfo(InfoList, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
putSliceInfo(String, String, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
putSlicePix(float[], int, int, WritableImage[], boolean, int, String) - Static method in class com.xinapse.util.MultiContrastAnalysisFrame
Puts the pixel values to one physical slice location and one image contrast.

Q

qForm - Variable in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
The NIFTI qform parameter.
qOffsetX - Variable in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
The NIFTI qoffset_x parameter.
qOffsetY - Variable in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
The NIFTI qoffset_y parameter.
qOffsetZ - Variable in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
The NIFTI qoffset_z parameter.
quaternB - Variable in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
The NIFTI quatern_b parameter.
quaternC - Variable in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
The NIFTI quatern_c parameter.
quaternD - Variable in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
The NIFTI quatern_d parameter.

R

RadialDivider - Class in com.xinapse.multisliceimage.roi
A radial divider, for cardiac segental analysis.
RadialDivider(int, int, double, boolean, Integer) - Constructor for class com.xinapse.multisliceimage.roi.RadialDivider
Creates a RadialDivider to be applied to one physical slice of a (possibly) multi-slice, multiple time-point dataset.
randomAccessFile - Variable in class com.xinapse.multisliceimage.MultiSliceImage
If non-null, pixel data kept on disk and accessed via this RandomAccessFile.
RBOW1 - Static variable in class com.xinapse.image.ColourMapping
The ColourMapping representing a rainbow of colours intensity scale.
RBOW2 - Static variable in class com.xinapse.image.ColourMapping
The ColourMapping representing an alternative rainbow of colours intensity scale.
ReadableImage - Interface in com.xinapse.image
Interface implemented by classes that ensure an image of that class can be read.
ReadableImage.Position - Class in com.xinapse.image
 
readyCursors() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
 
readyCursors() - Method in class com.xinapse.image.ImageSelectionPanel
 
readyCursors() - Method in class com.xinapse.image.MultipleImageSelectionPanel
 
readyCursors() - Method in interface com.xinapse.util.MessageShower
Sets the cursor for this MessageShower to indicate that it is ready for user input.
readyCursors() - Method in class com.xinapse.util.MultiContrastAnalysisFrame
 
recalculateSplines() - Method in class com.xinapse.multisliceimage.roi.SplineROI
Recalculate the splines that defined the shape of this SplineROI.
RectangularROI - Class in com.xinapse.multisliceimage.roi
An Class representing a rectangular region of an image.
RectangularROI(Rectangle2D.Double, ROIState) - Constructor for class com.xinapse.multisliceimage.roi.RectangularROI
Creates a new RectangularROI with the dimension given by the supplied Rectangle2D in mm coordinates.
RectangularROI(double, double, double, double) - Constructor for class com.xinapse.multisliceimage.roi.RectangularROI
Creates a new RectangularROI with the supplied dimensions in mm coordinates.
RectangularROI(double, double, double, double, ROIState) - Constructor for class com.xinapse.multisliceimage.roi.RectangularROI
Creates a new RectangularROI with the supplied dimensions in mm.
RectangularROICreateDialog - Class in com.xinapse.multisliceimage.roi
A dialog used to create Rectangular ROIs.
RectangularROICreateDialog(CanAddROIToFrame) - Constructor for class com.xinapse.multisliceimage.roi.RectangularROICreateDialog
Creates a new RectangularROICreateDialog, with ROIs that are created by the dialog being added to the specified frame.
RED - Static variable in class com.xinapse.image.ColourMapping
The ColourMapping representing a red intensity scale.
RED_FORMULA_OPTION - Static variable in class com.xinapse.filter.ColourImageFilter
A public Option to specify the formula used to calculate the new red component values in the image.
reduce(float) - Method in class com.xinapse.multisliceimage.roi.SplineROI
Creates a new SplineROI which approximates this SplineROI, but which has the miniumum number of knot points to appoximate this SplineROI with the specified fractional error.
registerCheckBox - Variable in class com.xinapse.dynamic.AbstractDynamicFrame
A check box to turn on registration.
REGISTRATION_PREFERENCE_NAME - Static variable in class com.xinapse.dynamic.AbstractDynamicFrame
The Preference name for whether to perform registration.
RegularROI - Interface in com.xinapse.multisliceimage.roi
Interface that regularly-shaped ROIs implement.
removeActionListener(ActionListener) - Method in class com.xinapse.dynamic.DynamicModel.SpecifierPanel
Removes an ActionListener that is triggered whenever the model settings are changed.
removeChangeListener(ChangeListener) - Method in class com.xinapse.image.MultipleImageSelectionPanel
Remove a ChangeListener from this MultipleImageSelectionPanel.
removeChangeListener(ChangeListener) - Method in class com.xinapse.util.MultiContrastAnalysisFrame
 
removeCol() - Method in class com.xinapse.image.ImageGrid
Removes the last column of images.
removeExtendedData(ExtendedData) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Removes a block of ExtendedData from this NIFTIImage.
removeExtension(String) - Static method in class com.xinapse.multisliceimage.ImageName
Remove any extension ".img", ".hdr", ".img.gz", etc.
removeFileChangeCommitListener(ChangeListener) - Method in class com.xinapse.image.ImageSelectionGroupPanel
Removes a listener that listens for the file name change being committed.
removeFileChangeCommitListener(ChangeListener) - Method in class com.xinapse.image.ImageSelectionPanel
Remove a ChangeListener from this ImageSelectionPanel.
removeFileTextEditListener(ChangeListener) - Method in class com.xinapse.image.ImageSelectionGroupPanel
removed a listener that listens for the file text being edited.
removeFileTextEditListener(ChangeListener) - Method in class com.xinapse.image.ImageSelectionPanel
Remove a ChangeListener from this ImageSelectionPanel.
removeFirstKnotPoint() - Method in class com.xinapse.multisliceimage.roi.SplineROI
Removes the first knot point of this SplineROI.
removeFirstVertex() - Method in class com.xinapse.multisliceimage.roi.IrregularROIInProgress
Removes the first vertex from this IrregularROIInProgress.
removeInfo(String) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
removeInfo(String, int, int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
removeInfo(String) - Method in interface com.xinapse.multisliceimage.InfoStorer
Removes an item from the general file information.
removeInfo(String, int, int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Removes an item from the dimension-specific information.
removeInfo(String) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
removeInfo(String, int, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
removeInfo(String) - Method in class com.xinapse.util.InfoList
Removes "name=value" from the InfoList.
removeLastKnotPoint() - Method in class com.xinapse.multisliceimage.roi.SplineROI
Removes the last knot point of this SplineROI.
removeLastVertex() - Method in class com.xinapse.multisliceimage.roi.IrregularROIInProgress
Removes the last vertex from this IrregularROIInProgress.
removeNaNs(float[], int, int, int, int, BoundaryCondition, MonitorWorker, boolean) - Static method in interface com.xinapse.filter.SpatialFilter
Remove NaN (not-a-number) pixel intensity values from an array of single-precision floating-point pixel values.
removeNaNs(double[], int, int, int, int, BoundaryCondition, MonitorWorker, boolean) - Static method in interface com.xinapse.filter.SpatialFilter
Remove NaN (not-a-number) pixel intensity values from an array of double-precision floating-point pixel values.
removeNColumnsChangeActionListener(ActionListener) - Method in class com.xinapse.image.ImageGrid
Remove an ActionListener to be notified when the number of columns in the ImageGrid changes.
removeNRowsChangeActionListener(ActionListener) - Method in class com.xinapse.image.ImageGrid
Remove an ActionListener to be notified when the number of rows in the ImageGrid changes.
removeROIsUsed(List<ROI>) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
From a List of ROIs, remove those used to create a HollowROI forming an annulus, which can then be usd for segmental analysis using this RadialDivider.
removeRow() - Method in class com.xinapse.image.ImageGrid
Removes the last row of images.
removeSelfIntersections() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Modifies this IrregularROI, converting any self-intersecting segments so that after this method call, the ROI does not self-intersect.
RenderingInterpolationType - Enum in com.xinapse.image
An Enumeration of the types rendering interpolation when drawing pixel values to screen.
RenderingInterpolationType.ComboBox - Class in com.xinapse.image
A javax.swing.JComboBox that is used for selecting a RenderingInterpolationType.
RenderingInterpolationType.RenderingInterpolationTypeButton - Class in com.xinapse.image
A JButton for setting the RenderingInterpolationType.
RenderingInterpolationTypeButton(ImageDisplayFrame) - Constructor for class com.xinapse.image.RenderingInterpolationType.RenderingInterpolationTypeButton
Create a RenderingInterpolationTypeButton.
reorient(ReadableImage, MostLikePlane, MostLikePlane, Boolean, MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Reorients a ReadableImage.
reorientRadiological(ReadableImage, Object) - Static method in class com.xinapse.image.ImageUtils
Reorients a set of pixels for an image so that they will be presented in standard radiological orientation.
REPETITION_TIME_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the scan repetition time.
ReportGenerator - Class in com.xinapse.util
Abstract Class to generate reports.
ReportGenerator.ReportType - Enum in com.xinapse.util
An enumration of the types of report that can be generated.
requiresPositionalInformation() - Method in enum com.xinapse.dicom.Modality
Returns true if images of this Modality requires positional information.
reSample(ReadableImage, int[], InterpolationType, SubSampleType, MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Resamples an existing image to have different numbers of pixels.
reSample(ReadableImage, float[], InterpolationType, SubSampleType, MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Resamples an existing ReadableImage to have different pixel sizes.
reverseSlices(WritableImage, MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Reverses the slice order of a WritableImage in place.
revert() - Method in class com.xinapse.image.RenderingInterpolationType.ComboBox
Revert to the user's preferred RenderingInterpolationType.
roamingResponseDialog - Variable in class com.xinapse.util.MultiContrastAnalysisFrame
The RoamingResponseDialog used to display the roaming response, if non-null.
ROI - Class in com.xinapse.multisliceimage.roi
A Class representing a region of interest.
ROICalculation - Interface in com.xinapse.apps.active
An interface implemented by classes that can perform analysis on propagated ROIs.
ROICalculation.SpecifierPanel - Class in com.xinapse.apps.active
A JPanel that can be used to specify ROI calculation parameters.
ROICreateDialog - Class in com.xinapse.multisliceimage.roi
An abstract class of dialogs use to create ROIs.
ROIEditAction - Enum in com.xinapse.multisliceimage.roi
An enumeration of the different types of (undoable) actions that can be performed on an ROI.
ROIException - Exception in com.xinapse.multisliceimage.roi
Signals that an error has occurred while handling an ROI.
ROIException() - Constructor for exception com.xinapse.multisliceimage.roi.ROIException
Constructs an ROIException without a detail message.
ROIException(String) - Constructor for exception com.xinapse.multisliceimage.roi.ROIException
Constructs an ROIException with the specified detail message.
ROIException(String, Throwable) - Constructor for exception com.xinapse.multisliceimage.roi.ROIException
Constructs an ROIException with the specified cause.
ROIFileChooser - Class in com.xinapse.multisliceimage.roi
A JFileChooser for choosing region of interest files (files with extension ".roi", or ".zip" for ImageJ ROI files).
ROIFileChooser(boolean, String) - Constructor for class com.xinapse.multisliceimage.roi.ROIFileChooser
Creates an ROIFileChooser suitable for selecting an roi file either for saving or loading ROIs, with the directory set to the supplied directory (if a directory) or the parent directory containing the file (if a regular file).
ROIFileFilter - Class in com.xinapse.multisliceimage.roi
A FileFilter for region of interest files.
ROIFileFilter() - Constructor for class com.xinapse.multisliceimage.roi.ROIFileFilter
Constructor for ROIFileFilter.
ROIFileSelectionPanel - Class in com.xinapse.multisliceimage.roi
A FileSelectionPanel for selecting an ROI file.
ROIFileSelectionPanel(MessageShower, String) - Constructor for class com.xinapse.multisliceimage.roi.ROIFileSelectionPanel
Create a new ROIFIleSelectionPanel for selecting an ROI file for input.
ROIFileSelectionPanel(MessageShower, String, boolean) - Constructor for class com.xinapse.multisliceimage.roi.ROIFileSelectionPanel
Create a new ROIFIleSelectionPanel.
ROIIntensitiesFileChooser - Class in com.xinapse.multisliceimage.roi
A JFileChooser for choosing a file (a file with extension ".txt") into which region of interest intensities will be written.
ROIIntensitiesFileChooser(String) - Constructor for class com.xinapse.multisliceimage.roi.ROIIntensitiesFileChooser
A JFileChooser for writing ROI pixel intensities to file.
ROIPreferencesDialog - Class in com.xinapse.multisliceimage.roi
A javax.swing.JDialog used to set the user Preferences related to ROIs.
ROIPreferencesDialog(JDialog, ImageDisplayer) - Constructor for class com.xinapse.multisliceimage.roi.ROIPreferencesDialog
Created a new ROIPreferencesDialog with the specified owner.
ROIState - Enum in com.xinapse.multisliceimage.roi
An enumeration of the different states in which an ROI can be.
ROIStats - Class in com.xinapse.multisliceimage.roi
A Class containing the statistics that are computed for an ROI.
ROIStats(double) - Constructor for class com.xinapse.multisliceimage.roi.ROIStats
Creates an ROIStats object without valid intensity statistics or histogram of intensities but with a valid area statistic.
ROIStats(double, double, double, double, double) - Constructor for class com.xinapse.multisliceimage.roi.ROIStats
Creates an ROIStats object with valid intensity and area statistics, but no histogram of intensities.
ROIStats(double, double, double, double, double, Histogram) - Constructor for class com.xinapse.multisliceimage.roi.ROIStats
Creates an ROIStats object with valid intensity and area statistics, and a histogram of intensities.
ROIStats(ROIStats) - Constructor for class com.xinapse.multisliceimage.roi.ROIStats
Creates a new ROIStats object, copying all values from existing ROIStats.
ROIStats(ROIStats, double) - Constructor for class com.xinapse.multisliceimage.roi.ROIStats
Creates a new ROIStats object, copying all values except the area from existing ROIStats.
ROIStatsFileChooser - Class in com.xinapse.multisliceimage.roi
A JFileChooser for choosing region of interest statistics files (files with extension ".txt") into which ROI stats will be written.
ROIStatsFileChooser(String) - Constructor for class com.xinapse.multisliceimage.roi.ROIStatsFileChooser
Creates an ROIStatsFileChooser suitable for selecting a stats file for into which ROI stats will be written, with the directory set to the supplied directory (if a directory) or the parent directory containing the file (if a regular file).
ROIStreamTokenizer - Class in com.xinapse.multisliceimage.roi
An ROIStreamTokenizer used to parse ROIs from an input stream.
RotatableROI - Interface in com.xinapse.multisliceimage.roi
Interface that rotatable ROIs implement.
rotate(ReadableImage, RotationAngle, MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Rotates a ReadableImage in multiples of 90 degrees.
rotate(Object, RotationAngle, int, int) - Method in enum com.xinapse.image.PixelDataType
Rotates (slice-by-slice) an array of pixels in-place, by multiples of 90 degrees.
RotationAngle - Enum in com.xinapse.image
The rotation angles that can be used to rotate an image in steps of 90 degrees.
RotationAngle.RotationPanel - Class in com.xinapse.image
A JPanel for selecting an image rotation angle in steps of 90 degrees.
RotationPanel(String) - Constructor for class com.xinapse.image.RotationAngle.RotationPanel
Creates a new RotationPanel.

S

SAVE_FSL_ORIENT_PROPERTY_KEY - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
The property value key for setting whether NIFTI-1 images should be saved with an orientation that is compatible with FSL, where possible.
SAVE_SPM_ORIENT_PROPERTY_KEY - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
The property value key for setting whether NIFTI-1 images should be saved with an orientation that is compatible with SPM, where possible.
saveAlwaysAsk(boolean) - Static method in enum com.xinapse.dicom.Modality
Saves whether always to ask the user what is the Modality, if not set in an image.
saveAlwaysAsk(boolean) - Static method in enum com.xinapse.dicom.PatientPosition
Saves whether the user prefers always to be asked to set the PatientPosition.
saveAlwaysAsk(boolean) - Static method in enum com.xinapse.dicom.PulseSequenceType
Saves whether the user prefers always to be asked to set the PulseSequenceType.
SaveChooser(Class<? extends ReadableImage>, String) - Constructor for class com.xinapse.image.ImageFileChooser.SaveChooser
Creates an ImageFileChooser.SaveChooser suitable for selecting a WritableImage file for saving.
SaveChooser() - Constructor for class com.xinapse.image.ImageFileChooser.SaveChooser
Creates an ImageFileChooser.SaveChooser suitable for selecting a WritableImage file for saving.
SaveChooser(File) - Constructor for class com.xinapse.image.ImageFileChooser.SaveChooser
Creates an ImageFileChooser.SaveChooser suitable for selecting a WritableImage file for saving.
savePreferences(Preferences) - Method in class com.xinapse.dynamic.AbstractDynamicFrame
 
savePreferences(Preferences) - Method in class com.xinapse.dynamic.DynamicModel.SpecifierPanel
 
savePreferences() - Static method in class com.xinapse.image.ColourMapping
Saves the display settings for the DICOM standard display in the user's preferences.
savePreferences(ComplexMode, Preferences) - Static method in enum com.xinapse.image.ComplexMode
Saves the supplied ComplexMode to the user's Preferences as the user's preferred ComplexMode.
savePreferences(Preferences) - Method in class com.xinapse.image.ImageGrid
 
savePreferences(InputConfigurationType, Preferences) - Static method in enum com.xinapse.image.InputConfigurationType
 
savePreferences() - Method in class com.xinapse.image.RenderingInterpolationType.ComboBox
Saves the current selection to the user's preferences.
savePreferences(Preferences) - Method in class com.xinapse.image.SingleOrMultipleInputImageSelectionPanel
 
savePreferences(Preferences) - Method in class com.xinapse.image.template.WeightingType.Panel
 
savePreferences(Preferences) - Method in class com.xinapse.multisliceimage.roi.CombineMode.Panel
Saves the current CombineMode to the user Preferences.
savePreferences(CombineMode, Preferences) - Static method in enum com.xinapse.multisliceimage.roi.CombineMode
Saves the supplied CombineMode as the user's preferrred CombineMode.
savePreferences(Preferences) - Method in class com.xinapse.multisliceimage.roi.MaskMode.Panel
Saves the current MaskMode to the user Preferences.
savePreferences(MaskMode, Preferences) - Static method in enum com.xinapse.multisliceimage.roi.MaskMode
Saves the supplied MaskMode as the user's preferrred MaskMode.
savePreferences() - Method in class com.xinapse.multisliceimage.roi.PenSizePanel
Saves the current setting of the pen size in this PenSizePanel in the user Preferences.
savePreferences(Preferences) - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Save the current setting to the user preferences.
savePreferences(Preferences) - Method in interface com.xinapse.util.PreferencesSettable
Save the current settings to the user Preferences at the given node name.
savePreferredCompressed(boolean) - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Sets the user's preference about whether Analyze 7.5 images should be stored compressed.
savePreferredCompressed(boolean) - Static method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Sets the user's preference about whether NIFTI images should be stored compressed.
savePreferredContourMode(ContourMode) - Static method in enum com.xinapse.multisliceimage.roi.ContourMode
Saves the user's preferred ContourMode to the user preferences.
savePreferredCreateNonFlipped(boolean) - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Header
Saves the user's preference about whether newly-created Analyze 7.5 images should have a non-flipped orientation.
savePreferredDoNotFlipFlipped(boolean) - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Header
Saves the user's preference about whether an Analyze 7.5 image with a flipped orientation should be treated as if it has a non-flipped orientation.
savePreferredFlipNonFlipped(boolean) - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Header
Saves the user's preference about whether an Analyze 7.5 image with a non-flipped orientation should be treated as if it has a flipped orientation.
savePreferredFSLCompatibleNIFTI(boolean) - Static method in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
Saves the user's preference about whether NIFTI-1 images should be read as having the patient left coordinate increasing with stored pixel data column number.
savePreferredImageClass(Class<? extends WritableImage>) - Static method in class com.xinapse.image.ImageUtils
Saves the supplied class to the user's Preferences.
savePreferredImagePreview(boolean) - Static method in class com.xinapse.image.ImagePreview
Saves the user's preference for whether to generate an image preview thumbnail.
savePreferredInterpolationType(Preferences, InterpolationType) - Static method in enum com.xinapse.image.InterpolationType
Save an InterpolationType to the preferences.
savePreferredMaskAction(MaskAction) - Static method in enum com.xinapse.multisliceimage.roi.MaskAction
Sets the user's preferred mask action.
savePreferredModality(Modality) - Static method in enum com.xinapse.dicom.Modality
Saves the user's most common-used Modality to the user Preferences.
savePreferredNIFTIOneFile(boolean) - Static method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Sets the user's preference about whether NIFTI images should be stored in two separate files (.hdr and .hdr) or one (.nii).
savePreferredOp(MorphologicalOperator.Op, Preferences) - Static method in enum com.xinapse.filter.MorphologicalOperator.Op
Saves the MorphologicalOperator.Op set in the given preferences.
savePreferredOverwrite(boolean) - Static method in class com.xinapse.multisliceimage.UNC.UNCImage
Saves whether the user prefers to overwrite UNC images.
savePreferredPatientPosition(PatientPosition) - Static method in enum com.xinapse.dicom.PatientPosition
Saves the user's preferred PatientPosition to the user Preferences.
savePreferredRenderingInterpolationType(RenderingInterpolationType) - Static method in enum com.xinapse.image.RenderingInterpolationType
Saves the user's preferred RenderingInterpolationType to the user preferences.
savePreferredRotationAngle(Preferences, RotationAngle) - Static method in enum com.xinapse.image.RotationAngle
Saves the supplied rotation angle to the Preferences as the preferred RotationAngle.
savePreferredSaveFSLOrient(boolean) - Static method in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
Saves the user's preference about whether NIFTI-1 images should be saved with an orientation that is compatible with FSL, where possible.
savePreferredSaveSPMOrient(boolean) - Static method in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
Saves the user's preference about whether NIFTI-1 images should be saved with an orientation that is compatible with SPM, where possible.
savePreferredSpacing(VertexHandle.Spacing) - Static method in enum com.xinapse.multisliceimage.roi.VertexHandle.Spacing
Saves the supplied Spacing to the user Preferences.
savePreferredSubSampleType(Preferences, SubSampleType) - Static method in enum com.xinapse.image.SubSampleType
Save a SubSampleType to the preferences.
savePreferredType(PulseSequenceType) - Static method in enum com.xinapse.dicom.PulseSequenceType
Saves the user's preferred PulseSequenceType to the user Preferences.
savePreferredWarnNegativePixelHeight(boolean) - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Header
Saves the user's preference about whether the user should be warned about negative pixel height in Analyze 7.5 images.
savePreferredWarnNegativePixelWidth(boolean) - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Header
Saves the user's preference about whether the user should be warned about negative pixel width in Analyze 7.5 images.
scale(float) - Method in class com.xinapse.filter.FixedWeightsComplexKernelFilter
Scale all kernel weights (both real and imaginary parts) by the given scaling factor.
scale(float) - Method in class com.xinapse.filter.FixedWeightsKernelFilter
Scale all kernel weights by the given scaling factor.
scale(double) - Method in class com.xinapse.image.Complex
Scales this Complex by a real scalar value and returns the result.
scale(double) - Method in class com.xinapse.image.DoubleComplex
 
scale(double) - Method in class com.xinapse.image.FloatComplex
 
scale(double) - Method in class com.xinapse.image.Histogram
Scales the counts in this Histogram, mutiplying all the count values by the supplied scaling factor.
scale(Object, double) - Method in enum com.xinapse.image.PixelDataType
Scale pixel intensities "in-place".
scale(Object, double, int, int) - Method in enum com.xinapse.image.PixelDataType
Scale pixel intensities "in-place".
SCAN_DATE_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the scan date.
ScanDetailsPanel - Class in com.xinapse.image
A JPanel for showing the details of a ReadableImage.
ScanDetailsPanel(boolean) - Constructor for class com.xinapse.image.ScanDetailsPanel
Creates a ScanDetailsPanel, optionally showing all details on one line.
SCANNING_SEQUENCE_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the DICOM scanning sequence.
SEARCH_SIZE - Static variable in class com.xinapse.multisliceimage.roi.ContourROI
The size of the area of pixels to search for the maximum gradient.
SegmentalAnalysis - Interface in com.xinapse.apps.cardiac
An interface implemented by classes that can perform cardiac segmental analysis.
SegmentalAnalysis.SpecifierPanel - Class in com.xinapse.apps.cardiac
A JPanel that can be used to specify segmental analysis parameters.
SelectableROICalculation - Class in com.xinapse.apps.active
An interface implemented by classes that can perform calculations on propagated ROIs.
SelectableROICalculation() - Constructor for class com.xinapse.apps.active.SelectableROICalculation
Default constructor for use by sub-classes.
SelectableSegmentalAnalysis - Class in com.xinapse.apps.cardiac
An interface implemented by classes that can perform segmental analysis.
SelectableSegmentalAnalysis() - Constructor for class com.xinapse.apps.cardiac.SelectableSegmentalAnalysis
Creates a new SelectableSegmentalAnalysis.
SelectableSegmentalAnalysis(boolean, Integer, boolean, boolean) - Constructor for class com.xinapse.apps.cardiac.SelectableSegmentalAnalysis
Creates a new SelectableSegmentalAnalysis.
selectColumn(int) - Method in class com.xinapse.image.ImageGrid
Select a grid column.
selectDeselect(Point, boolean, boolean, int) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
selectDeselect(Point, boolean, boolean, int) - Method in class com.xinapse.multisliceimage.roi.Marker
 
selectDeselect(Point, boolean, boolean, int) - Method in class com.xinapse.multisliceimage.roi.ROI
Selects or deselects an ROI after a user click at the point.
selectDeselect(Point, boolean, boolean, int) - Method in class com.xinapse.multisliceimage.roi.Text
 
SelectedImagePanel - Class in com.xinapse.image
An SelectedImagePanel is a javax.swing.JPanel that shows a selected image.
SelectedImagePanel(File) - Constructor for class com.xinapse.image.SelectedImagePanel
Creates new SelectedImagePanel showing the given File name.
SelectedImagePanel(ReadableImage) - Constructor for class com.xinapse.image.SelectedImagePanel
Creates new SelectedImagePanel showing the given ReadableImage.
selectPlane(Component) - Static method in enum com.xinapse.image.MostLikePlane
Shows a dialog prompting the user to select a scan plane.
selfIntersects() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Returns true if this ROI has line segments that cross.
selfIntersects() - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns true if this ROI has outline segments that cross.
SEQUENCE_VARIANT_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the DICOM scanning sequence variant.
SERIES_DESCRIPTION_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the series (scan) description.
SERIES_NUMBER_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the series (scan) number.
set(ROI) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
set(ROI) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
set(ROI) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
set(ROI) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
set(double, double) - Method in class com.xinapse.multisliceimage.roi.Marker
Sets the location of this Marker to the given location.
set(ROI) - Method in class com.xinapse.multisliceimage.roi.Marker
 
set(ROI) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
 
set(ROI) - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
set(ROI) - Method in class com.xinapse.multisliceimage.roi.ROI
Sets the shape of this ROI to the shape of the supplied argument ROI.
set(ROI) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
set() - Method in class com.xinapse.util.BitSet
Sets all bits in the set to true.
set(int) - Method in class com.xinapse.util.BitSet
Add the integer bitIndex to this set.
set(int, boolean) - Method in class com.xinapse.util.BitSet
Sets the bit at the given index to the specified value.
set(int, int) - Method in class com.xinapse.util.BitSet
Sets the bits between from (inclusive) and to (exclusive) to true.
set(int, int, boolean) - Method in class com.xinapse.util.BitSet
Sets the bits between from (inclusive) and to (exclusive) to the specified value.
set() - Method in class com.xinapse.util.CancellableThread.Flag
Set the flag.
set12(float[]) - Method in class com.xinapse.geom3d.AffineTransform3D
Sets the matrix values of this transform to the matrix values in the single precision array parameter.
set3DBlockParameters(WritableImage) - Static method in class com.xinapse.image.ImageUtils
For an image which contains multiple slices with all slices parallel and regularly-spaced, this method will modify the image position (patient coords), image orientation (patient coords) and pixel spacing (pixel sizes) according to the block.
setAction(String, int, int) - Method in class com.xinapse.util.MonitorWorker
Set the action description for the ProgressMonitor.
setAction(String) - Method in class com.xinapse.util.MonitorWorker
Set the action description for the Progress monitor or IndeterminateProgressMonitor.
setAnnotation(String) - Method in class com.xinapse.multisliceimage.roi.ROI
Sets the anotation string for this ROI.
setBodyPart(BodyPart) - Method in interface com.xinapse.image.WritableImage
Sets the body part imaged.
setBodyPart(BodyPart) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
setBodyPart(BodyPart) - Method in class com.xinapse.multisliceimage.MultiSliceImage
By default, body part recording is not supported, so this method does nothing.
setBodyPart(BodyPart) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
setBonferroniN(float) - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
Does nothing, since Bonferroni correction is not performed because significance values for the fitted parameters are not computed.
setBonferroniN(float) - Method in interface com.xinapse.dynamic.DynamicModel
Sets the number of independent fits that will be performed by the model.
setBorderColor(Color) - Static method in class com.xinapse.multisliceimage.roi.Handle
Sets the Color with which ROI Handle borders are to be drawn.
setChoosableColor(int, Color) - Static method in enum com.xinapse.multisliceimage.roi.ROIState
Sets one of the user-choosable ROI colours.
setColor(Color) - Static method in class com.xinapse.multisliceimage.roi.Handle
Sets the Color with which ROI Handles are to be drawn.
setColor(Color) - Static method in enum com.xinapse.multisliceimage.roi.ROIState
Sets the colour with which ROIs in their normal, unselected state should be drawn.
setColorValue(Object, Color, int) - Method in enum com.xinapse.image.PixelDataType
Sets a single colour pixel value into an array of pixels.
setColumnLabel(String) - Method in class com.xinapse.image.ImageGrid
Sets the column label to "Number of labels".
setColumnSelectionLabel(String) - Method in class com.xinapse.image.ImageGrid
Sets the labels for the JCheckBoxes that are used to select the grid columns.
setColumnSelectionToolTipText(String) - Method in class com.xinapse.image.ImageGrid
Sets the tool tip text for the JCheckBoxes that are used to select the grid columns.
setComplexValue(Object, Complex, int) - Method in enum com.xinapse.image.PixelDataType
Sets a single complex pixel value into an array of pixels.
setCount(int, double) - Method in class com.xinapse.image.Histogram
Sets the count in one bin of this Histogram.
setCounterClockwiseSegments(boolean) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Sets the insertion point angle.
setCreationHistory(HistoryItem) - Method in class com.xinapse.multisliceimage.roi.ROI
Sets the creation history HistoryItem for this ROI.
setDBName(String) - Method in class com.xinapse.multisliceimage.Analyze.ANZHeader
Sets the data base name for this Analyze image header.
setDBName(String) - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
Sets the data base name for this ANZImage.
setDefaults() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
 
setDefaults() - Method in class com.xinapse.dynamic.DynamicModel.SpecifierPanel
 
setDefaults() - Method in class com.xinapse.image.ImageGrid
 
setDefaults() - Method in class com.xinapse.image.RenderingInterpolationType.ComboBox
Sets the default RenderingInterpolationType in the JComoBox.
setDefaults() - Method in class com.xinapse.image.SingleOrMultipleInputImageSelectionPanel
 
setDefaults() - Method in class com.xinapse.image.template.WeightingType.Panel
 
setDefaults() - Method in class com.xinapse.multisliceimage.roi.CombineMode.Panel
Sets the CombineMode in this panel to the default.
setDefaults() - Method in class com.xinapse.multisliceimage.roi.MaskMode.Panel
Sets the MaskMode in this panel to the default.
setDefaults() - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Put the default settings to this MultiContrastAnalysisFrame.
setDefaults() - Method in interface com.xinapse.util.PreferencesSettable
Set the default values.
setDeletedColor(Color) - Static method in enum com.xinapse.multisliceimage.roi.ROIState
Sets the colour with which deleted ROIs should be drawn.
setDescription(String) - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
Sets the description for this ANZImage.
setDims(Short...) - Method in class com.xinapse.multisliceimage.Analyze.ANZHeader
Sets the number of samples in each dimension of this Analyze image header.
setDisplaySettings(float, float, float) - Static method in class com.xinapse.image.ColourMapping
Set the display characteristics.
setEditable(boolean) - Method in class com.xinapse.image.InputImageSelectionPanel
Sets whether text for folder/file selection is editable.
setEnabled(boolean) - Method in class com.xinapse.image.ImageSelectionPanel
Enables or disables this ImageSelectionPanel, depending on the value of the parameter b.
setEnabled(boolean) - Method in class com.xinapse.image.InputImageSelectionPanel
 
setEnabled(boolean) - Method in class com.xinapse.image.RenderingInterpolationType.RenderingInterpolationTypeButton
 
setEnabled(boolean) - Method in class com.xinapse.image.RotationAngle.RotationPanel
Enables and disables this RotationPanel.
setEnabled(boolean) - Method in class com.xinapse.multisliceimage.roi.CombineMode.Panel
 
setEnabled(boolean) - Method in class com.xinapse.multisliceimage.roi.MaskMode.Panel
 
setEnabled(boolean) - Method in class com.xinapse.multisliceimage.roi.PenSizePanel
 
setEndDerivs(double, double) - Method in class com.xinapse.numerical.CubicSplineInterpolator
Set the first derivative values of the CubicSplineInterpolator at the end points of the abscissa range, overriding a natural spline.
setEndoEpicardiumSplitPercent(Integer) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Sets the endo- epi-cardium split percentage.
setFile(File) - Method in class com.xinapse.image.ImageSelectionPanel
Sets the file in this ImageSelectionPanel to the specified file.
setFile(File) - Method in class com.xinapse.image.InputImageSelectionPanel
 
setFileLabel(String) - Method in class com.xinapse.image.ImageSelectionPanel
Sets the label for the file selection text field.
setFileText(String) - Method in class com.xinapse.image.ImageSelectionPanel
Sets the text for the file selection text field.
setFileText(String) - Method in class com.xinapse.image.InputImageSelectionPanel
 
setFileToolTipText(String) - Method in class com.xinapse.image.ImageSelectionPanel
Sets the tool tip text for the file selection text field.
setFlipAngle(Float) - Method in interface com.xinapse.image.WritableImage
Sets the excitation pulse flip angle for this image.
setFlipAngle(Float) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by Analyze 7.5 format, so this method does nothing.
setFlipAngle(Float) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Sets the excitation pulse flip angle for this image.
setFlipAngle(Float) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
setFolderLabel(String) - Method in class com.xinapse.image.ImageSelectionPanel
Sets the label for the folder selection text field.
setFolderText(String) - Method in class com.xinapse.image.ImageSelectionPanel
Sets the text for the folder selection text field.
setFolderToolTipText(String) - Method in class com.xinapse.image.ImageSelectionPanel
Sets the tool tip text for the folder selection text field.
setFrameDWBMatrix(float[], int) - Method in interface com.xinapse.image.WritableImage
Sets the diffusion-weighting B-matrix for one "frame" of this 4-D image.
setFrameDWBMatrix(float[], int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by Analyze 7.5 format, so this method does nothing.
setFrameDWBMatrix(float[], int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
setFrameDWBMatrix(float[], int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
setFrameDWbValue(float, int) - Method in interface com.xinapse.image.WritableImage
Sets the diffusion-weighting b-value for one "frame" of this 4-D image.
setFrameDWbValue(float, int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by Analyze 7.5 format, so this method does nothing.
setFrameDWbValue(float, int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
setFrameDWbValue(float, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
setFrameDWGradientVector(Vector3f, int) - Method in interface com.xinapse.image.WritableImage
Sets the diffusion-weighting gradient vector for one "frame" of this 4-D image.
setFrameDWGradientVector(Vector3f, int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by Analyze 7.5 format, so this method does nothing.
setFrameDWGradientVector(Vector3f, int) - Method in class com.xinapse.multisliceimage.Analyze.