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

A

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, Image, String) - Constructor for class com.xinapse.dynamic.AbstractDynamicFrame

Creates new DynamicFrame for a stand-alone image dynamic analysis application.

AbstractDynamicFrame(ImageDisplayer, String, 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.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.ImageFileFilter

Tests whether the given file probably represents a MultiSliceImage file.

accept(File) - Method in class com.xinapse.multisliceimage.LogFileChooser.LogFileFilter

Whether the given file is accepted by this filter.

accept(File) - Method in class com.xinapse.multisliceimage.roi.ImageJROIFileFilter

Tests whether the given file is a 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(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(Histogram, PixelDataType) - Method in class com.xinapse.multisliceimage.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.multisliceimage.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.multisliceimage.MultipleImageSelectionPanel

Add a ChangeListener to this MultipleImageSelectionPanel.

AddChecksum - Class in com.xinapse.multisliceimage.roi

Program to add a Checksum to an ROI file.

AddChecksum() - Constructor for class com.xinapse.multisliceimage.roi.AddChecksum

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.multisliceimage.ImageSelectionGroupPanel

addFileChangeCommitListener(ChangeListener) - Method in class com.xinapse.multisliceimage.ImageSelectionPanel

Add a ChangeListener to this ImageSelectionPanel.

addFiles(List<File>) - Method in class com.xinapse.multisliceimage.MultipleImageSelectionPanel

Add a List of Files to this MultipleImageSelectionPanel.

addFileTextEditListener(ChangeListener) - Method in class com.xinapse.multisliceimage.ImageSelectionGroupPanel

addFileTextEditListener(ChangeListener) - Method in class com.xinapse.multisliceimage.ImageSelectionPanel

Add a ChangeListener to this ImageSelectionPanel.

addGraph(GraphPanel, String, String, String) - Method in class com.xinapse.util.ReportGenerator

Adds a graph to the report.

addImage(MultiSliceImage, ColourMapping, double, double, ComplexMode, String) - Method in class com.xinapse.util.ReportGenerator

Adds an image to the 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.

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.

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[][], NumberFormat) - Method in class com.xinapse.util.ReportGenerator

Adds a table to the report.

addUserColourMapping(Component) - Static method in class com.xinapse.multisliceimage.ColourMapping

Prompts the user to add a new user-defined ColourMapping.

addValues(Object, int, int, PixelDataType, ComplexMode) - Method in class com.xinapse.multisliceimage.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 matrix.

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.

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(short, short, short, short, ANZPixFormat) - Constructor for class com.xinapse.multisliceimage.Analyze.Analyze75Image

Creates a new in-memory 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.

AnalyzeFileFilter() - Constructor for class com.xinapse.multisliceimage.Analyze.AnalyzeFileFilter

The constructor for an Analyze image header file filter.

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.

ANZColourMapping - Class in com.xinapse.multisliceimage.Analyze

Class to handle Analyze lookup files (colour mapping files).

ANZColourMapping(String) - Constructor for class com.xinapse.multisliceimage.Analyze.ANZColourMapping

Constructs an ANZColourMapping Object by reading the values from the given file.

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 with null as its error 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

Sticks an InfoList onto the end of an existing one.

appendAuditInfo(String, String) - Method in interface com.xinapse.loadableimage.LoadableImage

Appends audit trail information to this image.

appendAuditInfo(String, String) - Method in class com.xinapse.loadableimage.LoadedImage

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

appendVertex(double, double) - Method in class com.xinapse.multisliceimage.roi.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.

area - Variable in class com.xinapse.multisliceimage.roi.ROIStats

The area of this ROI in square mm.

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.

autoResample(int, SubSampleType, boolean, boolean) - Method in class com.xinapse.multisliceimage.MultiSliceImage

Automatically resamples this image 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

binWidth - Variable in class com.xinapse.multisliceimage.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.multisliceimage.ColourMapping

The ColourMapping representing a blue intensity scale.

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.

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 interface com.xinapse.util.MessageShower

Sets the cursor for this MessageShower to indicate that an operation is in progress.

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.multisliceimage.Histogram

Calculates a suitable bin width, number of bins, and minimum bin value for a histogram, given the for given type of pixels over the given intensity range.

calcBins(double, double, int, PixelDataType, ComplexMode) - Static method in class com.xinapse.multisliceimage.Histogram

Calculates a suitable bin width, and minimum bin value for a histogram, given the for 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.multisliceimage.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.multisliceimage.VolumeInterpolator

Signal to this VolumeInterpolator to stop the current interpolation (if an interpolation is in progress) as soon as possible, and throw a CancelledException.

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.

CancellableThread.Flag() - Constructor for class com.xinapse.util.CancellableThread.Flag

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 with "cancelled" as its error detail message.

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.

checkMinMax(int, int, PixelDataType) - Static method in class com.xinapse.multisliceimage.MultiSliceImage

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.multisliceimage.ImageSelectionGroupPanel

Clear all files 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.multisliceimage.MultipleImageSelectionPanel

clearStats() - Method in class com.xinapse.multisliceimage.roi.ROI

Clears the cached statistics for this ROI, forcing them to be re-computed next time they are required.

clone() - Method in class com.xinapse.geom3d.AffineTransform3D

Creates and returns a copy of this AffineTransform3D.

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.ANZImage

Creates an in-memory clone of an Analyze image.

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.ColourMapping

Returns an exact copy of this ColourMapping.

clone() - Method in class com.xinapse.multisliceimage.MultiSliceImage

Returns a copy of this MultiSliceImage.

clone() - Method in class com.xinapse.multisliceimage.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.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.RectangularROI

clone() - Method in class com.xinapse.multisliceimage.roi.ROI

Returns a clone of this ROI.

clone() - Method in class com.xinapse.multisliceimage.roi.Text

clone() - Method in class com.xinapse.multisliceimage.UNC.UNCImage

Creates an in-memory copy of a UNCImage.

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.loadableimage.LoadableImage

Closes an image and frees up resources.

close() - Method in class com.xinapse.loadableimage.LoadedImage

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.UNC.UNCImage

Closes a UNCImage and frees up resources.

close() - Method in class com.xinapse.util.IndeterminateProgressMonitor

Indicate that the operation is complete.

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.multisliceimage.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.multisliceimage.PixelDataType

Coerce pixels of this PixelDataType to a new PixelDataType.

coerce(Object, PixelDataType, ComplexMode, boolean) - Method in enum com.xinapse.multisliceimage.PixelDataType

Coerce pixels of this PixelDataType to a new PixelDataType.

coerce(Object, PixelDataType, int, int, ComplexMode, boolean) - Method in enum com.xinapse.multisliceimage.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.

colourLookup(int, int, Object, int, PixelDataType, byte[], double, double, boolean, BitSet, boolean, ComplexMode) - Method in class com.xinapse.multisliceimage.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.multisliceimage.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.multisliceimage.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.multisliceimage.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.multisliceimage

The ColourMapping class represents a mapping from pixel presentation values (PPVs) to colours that are displayed on the image.

ColourMapping(short) - Constructor for class com.xinapse.multisliceimage.ColourMapping

Creates an empty ColourMapping with the specified number of slots in the map.

ColourMapping(byte[], byte[], byte[]) - Constructor for class com.xinapse.multisliceimage.ColourMapping

Creates a new ColourMapping object from a set of red, green and blue gun values.

ColourVolumeInterpolator - Class in com.xinapse.multisliceimage

An interpolator for a 3- (or fewer) dimensional array of pixels in a Colour image.

ColourVolumeInterpolator(byte[], PixelDataType, int, int, int, float, float, float, Color, InterpolationType) - Constructor for class com.xinapse.multisliceimage.ColourVolumeInterpolator

Creates a new ColourVolumeInterpolator for a block of colour (R,G,B) pixel samples.

ColourVolumeInterpolator(ColourVolumeInterpolator, InterpolationType) - Constructor for class com.xinapse.multisliceimage.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.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.loadableimage - package com.xinapse.loadableimage

The package com.xinapse.loadableimage contains the specification for images that can be loaded into an image displayer (such as Jim).

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.

CombineMode.Panel(Preferences, CombineMode) - Constructor for class com.xinapse.multisliceimage.roi.CombineMode.Panel

Constructs a CombineMode.Panel for selecting a CombineMode.

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.

Complex - Class in com.xinapse.multisliceimage

A complex (real, imaginary) number.

Complex() - Constructor for class com.xinapse.multisliceimage.Complex

Creates a new Complex number, with zero real and imaginary parts.

Complex(float, float) - Constructor for class com.xinapse.multisliceimage.Complex

Creates a new Complex number, with the real and imaginary part specified by the arguments.

ComplexMode - Enum in com.xinapse.multisliceimage

An enumeration of the possible display/calculation modes for complex numbers.

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.

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.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.

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

ContourMode.ComboBox() - Constructor for class com.xinapse.multisliceimage.roi.ContourMode.ComboBox

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, LoadableImage, 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.

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.multisliceimage.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.multisliceimage.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.multisliceimage.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.multisliceimage.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.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.

Cpa - Variable in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel

The blood plasma concentration in the feeding artery, Cpa(t).

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(int[][], MonitorWorker, boolean) - Method in class com.xinapse.multisliceimage.MultiSliceImage

Crops an existing MultiSliceImage.

CurvedLineROI - Class in com.xinapse.multisliceimage.roi

A Class representing a 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.multisliceimage.ColourMapping

The ColourMapping representing a cyan intensity scale.

D

dataType - Variable in class com.xinapse.multisliceimage.PixArray

The type of pixel that this PixArray stores.

dataType - Variable in class com.xinapse.multisliceimage.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_COMPLEX_MODE - Static variable in enum com.xinapse.multisliceimage.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.multisliceimage.ColourMapping

The default gamma value of the computer display.

DEFAULT_IMAGE_CLASS - Static variable in class com.xinapse.multisliceimage.MultiSliceImage

The default image class to work with, if the user has no Preference.

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.multisliceimage.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.multisliceimage.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) - Static method in class com.xinapse.multisliceimage.MultiSliceImage

Attempts to delete an image of the given Class with the given name.

deleteUserColourMapping(ColourMapping) - Static method in class com.xinapse.multisliceimage.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

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.EllipticalROI

dilate(double, AtomicInteger, CancellableThread.Flag) - Method in class com.xinapse.multisliceimage.roi.HollowROI

dilate(double, AtomicInteger, CancellableThread.Flag) - Method in class com.xinapse.multisliceimage.roi.IrregularROI

dilate(double, AtomicInteger, CancellableThread.Flag) - Method in class com.xinapse.multisliceimage.roi.LineROI

dilate(double, AtomicInteger, CancellableThread.Flag) - Method in class com.xinapse.multisliceimage.roi.Marker

dilate(double, AtomicInteger, CancellableThread.Flag) - Method in class com.xinapse.multisliceimage.roi.RectangularROI

dilate(double) - Method in class com.xinapse.multisliceimage.roi.ROI

Dilates this ROI by the specified distance.

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.

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.

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.

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.multisliceimage

A complex (real, imaginary) number, with double precision.

DoubleComplex() - Constructor for class com.xinapse.multisliceimage.DoubleComplex

Creates a new DoubleComplex number, with zero real and imaginary parts.

DoubleComplex(double, double) - Constructor for class com.xinapse.multisliceimage.DoubleComplex

Creates a new DoubleComplex number, with the real and imaginary parts specified by the arguments.

DoubleComplex(DoubleComplex) - Constructor for class com.xinapse.multisliceimage.DoubleComplex

Creates a new DoubleComplex number, with the real and imaginary parts copied from an existing DoubleComplex.

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, 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, 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.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.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.Text

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 with null as its error 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.

DynamicModel.SpecifierPanel(AbstractDynamicFrame) - Constructor for class com.xinapse.dynamic.DynamicModel.SpecifierPanel

Default constructor for use by sub-classes.

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 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.multisliceimage.Complex

Determines whether another object is equal to this Complex number.

equals(Object) - Method in class com.xinapse.multisliceimage.DoubleComplex

Determines whether another object is equal to this DoubleComplex 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.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.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

erasePoints(List<Point2D>, float, int, int, float, float) - Method in interface com.xinapse.multisliceimage.roi.EditableOutlineROI

Erase points from this ROI.

erasePoints(List<Point2D>, float, int, int, float, float) - Method in class com.xinapse.multisliceimage.roi.HollowROI

erasePoints(List<Point2D>, float, int, int, float, float) - Method in class com.xinapse.multisliceimage.roi.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.

exists(String) - Static method in class com.xinapse.multisliceimage.MultiSliceImage

Tests whether a MultiSliceImage with the given name already exists on disk.

ExitStatus - Enum in com.xinapse.platform

Exit status codes on program termination.

export(String, String, ColourMapping, double, double, ComplexMode, int) - Method in class com.xinapse.multisliceimage.MultiSliceImage

Writes an image to a disk file in an external format (such as JPEG, GIF etc.), creating the disk image from this MultiSliceImage, by drawing all of the slices in a raster of slices.

export(String, ColourMapping, double, double, ComplexMode, int) - Method in class com.xinapse.multisliceimage.MultiSliceImage

Returns an InputStream from which a external format image (such as JPEG, GIF etc.) can be read, producing the external format image from this MultiSliceImage, by drawing all of the slices in a raster of slices.

export(String, ImageOutputStream, ColourMapping, double, double, ComplexMode, int) - Method in class com.xinapse.multisliceimage.MultiSliceImage

Writes an image to an ImageOutputStream in an external format (such as JPEG, GIF etc.), creating the disk image from this MultiSliceImage, 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.LogFileChooser

The extension used for log files (".log").

FILE_EXTENSION - Static variable in class com.xinapse.multisliceimage.roi.ROIFileFilter

The extension for ROI files (".roi").

filter(MultiSliceImage) - Method in class com.xinapse.filter.AbstractKernelFilter

filter(MultiSliceImage, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractKernelFilter

filter(SpatialFilter, MultiSliceImage, MonitorWorker, boolean) - Static method in class com.xinapse.filter.AbstractKernelFilter

Filter a MultiSliceImage using the supplied filter, returning a new image which is a filtered version of the supplied image.

filter(MultiSliceImage) - Method in interface com.xinapse.filter.SpatialFilter

Filter a MultiSliceImage, returning a new image which is a filtered version of the supplied image.

filter(MultiSliceImage, MonitorWorker, boolean) - Method in interface com.xinapse.filter.SpatialFilter

Filter a MultiSliceImage, 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.

FilterBoundaryCondition - Enum in com.xinapse.filter

An enumeration of possible boundary conditions when applying a SpatialFilter.

filterInPlace(MultiSliceImage) - Method in class com.xinapse.filter.AbstractKernelFilter

filterInPlace(MultiSliceImage, 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, MultiSliceImage) - Static method in class com.xinapse.filter.AbstractKernelFilter

Filter a MultiSliceImage "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, MultiSliceImage, MonitorWorker, boolean) - Static method in class com.xinapse.filter.AbstractKernelFilter

Filter an array of pixel values "in place".

filterInPlace(Object, PixelDataType, int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.MorphologicalOperator

filterInPlace(MultiSliceImage) - Method in interface com.xinapse.filter.SpatialFilter

Filter a MultiSliceImage "in place".

filterInPlace(MultiSliceImage, MonitorWorker, boolean) - Method in interface com.xinapse.filter.SpatialFilter

Filter a MultiSliceImage "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

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.

FilterSelection.Panel(String) - Constructor for class com.xinapse.filter.FilterSelection.Panel

Create a new FilterSelectionPanel.

fit(float[], int, int, int, AutoCorrelationEstimate) - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel

Calculate the model parameters that best fit the data.

fit(float[], int, int, int, AutoCorrelationEstimate) - Method in interface com.xinapse.dynamic.DynamicModel

Calculate the model parameters that best fit the data.

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, FilterBoundaryCondition) - Constructor for class com.xinapse.filter.FixedWeightsKernelFilter

Constructs a 2-dimensional kernel-based filter with the given filter weights.

FixedWeightsKernelFilter(float[][][], boolean, FilterBoundaryCondition) - 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

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.RectangularROI

flipHorizontal(Point2D) - Method in class com.xinapse.multisliceimage.roi.ROI

Flip this ROI horizontally about a given location.

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.RectangularROI

flipVertical(Point2D) - Method in class com.xinapse.multisliceimage.roi.ROI

Flip this ROI vertically about a given location.

flipX(Object, int, int) - Method in enum com.xinapse.multisliceimage.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.multisliceimage.PixelDataType

Flips an array of pixels in-place about the y-axis (ie flips left-right).

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.

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 ReoprtGenerator 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.

getAllColourMappings() - Static method in class com.xinapse.multisliceimage.ColourMapping

Returns a java.util.List of all ColorMappings, both built-in and imported by the user.

getAnnotation() - Method in class com.xinapse.multisliceimage.roi.ROI

Gets the anotation string for this ROI.

getAreaUnder() - Method in class com.xinapse.multisliceimage.Histogram

Returns the total area under this histogram.

getAreaUnder(boolean) - Method in class com.xinapse.multisliceimage.Histogram

Returns the area under this histogram, optionally excluding any zero-intensity pixels.

getArg() - Method in class com.xinapse.multisliceimage.Complex

Returns the polar angle of this Complex number.

getArg() - Method in class com.xinapse.multisliceimage.DoubleComplex

Returns the polar angle of this DoubleComplex number.

getArrayElementsPerPixel() - Method in enum com.xinapse.multisliceimage.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.multisliceimage.Histogram

Returns the bin width for this Histogram.

getBitsPerPixel() - Method in enum com.xinapse.multisliceimage.PixelDataType

Returns the number of bits used to store one pixel for this data type.

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.

getBuiltInMappings() - Static method in class com.xinapse.multisliceimage.ColourMapping

Returns a java.util.List of the built-in ColorMappings.

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.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.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.

getCachedStatistics() - Method in class com.xinapse.multisliceimage.roi.ROI

Returns the cached ROI statistics, or null if there are none.

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.

getCentrePix(int, int, float, float) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI

Gets the centre of this ROI in pixel coordinates.

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.MultiSliceImage

Returns an array of classes that are known to be sub-classes of MultiSliceImage.

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.

getColour(short) - Method in class com.xinapse.multisliceimage.ColourMapping

Returns the colour in a particular slot of the colour mapping.

getCombineMode() - Method in class com.xinapse.multisliceimage.roi.CombineMode.Panel

Returns the CombineMode set in this panel.

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.multisliceimage.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.

getContourMode() - Method in class com.xinapse.multisliceimage.roi.ContourMode.ComboBox

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.RectangularROI

getCopy() - Method in class com.xinapse.multisliceimage.roi.ROI

Returns a copy of this ROI.

getCopy() - Method in class com.xinapse.multisliceimage.roi.Text

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.multisliceimage.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.RectangularROI

Returns the type of interaction needed to create a RectangularROI.

getCreateInteractionType() - Static method in class com.xinapse.multisliceimage.roi.Text

Returns the type of interaction needed to create a Text ROI.

getCumulativeHistogram() - Method in class com.xinapse.multisliceimage.Histogram

Return a new Histogram that is the cumulative histogram of this one.

getCumulativeIntensity(float, boolean) - Method in class com.xinapse.multisliceimage.Histogram

Returns an intensity value such that the specified fraction of pixels is below the returned intensity; zero-valued pixels 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.

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

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.

getDescription() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns a String description of this image.

getDescription(int) - Method in interface com.xinapse.loadableimage.LoadableImage

Returns a description of a slice of this image.

getDescription() - Method in class com.xinapse.loadableimage.LoadedImage

getDescription(int) - Method in class com.xinapse.loadableimage.LoadedImage

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.ImageFileFilter

Returns "All Images".

getDescription() - Method in class com.xinapse.multisliceimage.LogFileChooser.LogFileFilter

Returns the String "Log Files".

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.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.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 class com.xinapse.multisliceimage.Analyze.ANZImage

getDims() - Method in class com.xinapse.multisliceimage.MultiSliceImage

Returns the dimensions of this image.

getDims() - Method in class com.xinapse.multisliceimage.UNC.UNCImage

Returns the MultiSliceImage dimensions of this image.

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.

getDoBonferroni() - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel

Returns false, since Bonferroni correction is not performed because significance value 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.

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.

getDWBMatrix(int) - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the diffusion-weighting b-matrix for one slice of this image.

getDWBMatrix(int) - Method in class com.xinapse.loadableimage.LoadedImage

getDWBMatrix(int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image

This action is not supported by the Analyze file format, so this method always throws a ParameterNotSetException always.

getDWBMatrix(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage

getDWBMatrix(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage

getDWbValue(int) - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the diffusion-weighting b-value for one slice of this image.

getDWbValue(int) - Method in class com.xinapse.loadableimage.LoadedImage

getDWbValue(int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image

This action is not supported by the Analyze file format, so this method always throws a ParameterNotSetException always.

getDWbValue(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage

getDWbValue(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage

getDWGradientVector(int) - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the diffusion-weighting gradient-vector for one slice of this image.

getDWGradientVector(int) - Method in class com.xinapse.loadableimage.LoadedImage

getDWGradientVector(int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image

This action is not supported by the Analyze file format, so this method always throws a ParameterNotSetException always.

getDWGradientVector(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage

getDWGradientVector(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage

getEntriesString() - Method in class com.xinapse.multisliceimage.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.multisliceimage.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.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 this List of ROI, in mm.

getFile(int) - Method in class com.xinapse.multisliceimage.ImageSelectionGroupPanel

Returns the java.io.File for the ImageSelectionGroupMemberPanel at particular location in the group.

getFile() - Method in class com.xinapse.multisliceimage.ImageSelectionPanel

Returns the java.io.File that has been set in this ImageSelectionPanel.

getFile(int) - Method in class com.xinapse.multisliceimage.MultipleImageSelectionPanel

Returns the java.io.File for the MultipleImageSelectionMemberPanel at particular location in the list of images.

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.

getFiles() - Method in class com.xinapse.multisliceimage.MultipleImageSelectionPanel

Returns an array of java.io.File with each array member being a file currently set in the MultipleImageSelectionMemberPanel.

getFilter(LoadableImage) - Method in class com.xinapse.filter.FilterSelection.Panel

Returns the SpatialFilter currently set in this FilterSelectionPanel.

getFilter(LoadableImage) - Method in class com.xinapse.filter.GaussianBlurFilter.GaussianBlurSpecifierPanel

getFilter(LoadableImage) - Method in class com.xinapse.filter.LaplacianFilter.LaplacianSpecifierPanel

getFilter(LoadableImage) - Method in class com.xinapse.filter.MedianFilter.MedianSpecifierPanel

getFilter(LoadableImage) - Method in class com.xinapse.filter.MorphologicalOperator.MorphologicalSpecifierPanel

getFilter(LoadableImage) - Method in class com.xinapse.filter.SharpenFilter.SharpenSpecifierPanel

getFilter(LoadableImage) - Method in class com.xinapse.filter.SobelFilter.SobelSpecifierPanel

getFilter(LoadableImage) - Method in class com.xinapse.filter.SpatialFilter.SpecifierPanel

Returns the SpatialFilter that has been specified by this SpatialFilter.SpecifierPanel.

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.

getFlipAngle() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the excitation pulse flip angle for this image.

getFlipAngle() - Method in class com.xinapse.loadableimage.LoadedImage

getFlipAngle() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image

This action is not supported by the Analyze file format, so this method always throws a ParameterNotSetException always.

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

getFollowingHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI

getFollowingHandle(Handle) - Method in interface com.xinapse.multisliceimage.roi.EditableOutlineROI

Returns the Handle that is immediately after the specified handle, in the order in which they were placed around the ROI.

getFollowingHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.HollowROI

getFollowingHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.IrregularROI

getFrame() - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame

Returns the javax.swing.JFrame to which the ROI(s) will be added.

getFrameOfReferenceUID() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the frame of reference UID that uniquely identifies the frame of reference for an image.

getFrameOfReferenceUID() - Method in class com.xinapse.loadableimage.LoadedImage

getFrameOfReferenceUID() - Method in class com.xinapse.multisliceimage.MultiSliceImage

getGamma() - Static method in class com.xinapse.multisliceimage.ColourMapping

Returns the current gamma value setting for the display.

getHandles() - Method in class com.xinapse.multisliceimage.roi.ROI

Returns an array of Handles that this ROI has.

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.multisliceimage.PixArray

Computes a histogram of this PixArray.

getHistoMax(PixelDataType) - Method in class com.xinapse.multisliceimage.Histogram

Returns the maximum value that can be added to this Histogram's bins.

getHistoMin() - Method in class com.xinapse.multisliceimage.Histogram

Returns the minimum bin value of this Histogram.

getHTMLDescription() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns a String description of this image in HTML format.

getHTMLDescription(int) - Method in interface com.xinapse.loadableimage.LoadableImage

Returns a String description of a slice of this image in HTML format.

getHTMLDescription() - Method in class com.xinapse.loadableimage.LoadedImage

getHTMLDescription(int) - Method in class com.xinapse.loadableimage.LoadedImage

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

getIconHeight() - Method in class com.xinapse.multisliceimage.ColourMapping

Get the height of the Icon used to represent this ColourMapping.

getIconHeight() - Method in class com.xinapse.multisliceimage.PreviewIcon

Returns the icon's width.

getIconHeight() - Method in enum com.xinapse.util.IntensityRelation

getIconWidth() - Method in class com.xinapse.multisliceimage.ColourMapping

Get the width of the Icon used to represent this ColourMapping.

getIconWidth() - Method in class com.xinapse.multisliceimage.PreviewIcon

Returns the icon's height.

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.multisliceimage.Complex

Returns the imaginary part of this Complex number.

getImag() - Method in class com.xinapse.multisliceimage.DoubleComplex

Returns the imaginary part of this DoubleComplex number.

getImageCentrePatient(LoadableImage) - Static method in class com.xinapse.loadableimage.LoadedImage

Returns the coordinates of the center of the block of slices of an image, in mm, in patient coordinates.

getImageClass() - Method in class com.xinapse.loadableimage.LoadedImage

Returns the class of image that this LoadedImage was loaded from, e.g.

getImageFilterClass() - Method in class com.xinapse.multisliceimage.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.multisliceimage.ImageSelectionPanel

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.multisliceimage.MultipleImageSelectionPanel

Returns the class of image that will be filtered when the user chooses a new image to set in the panel.

getImageOrientationPatient() - Method in interface com.xinapse.loadableimage.LoadableImage

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.loadableimage.LoadableImage

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.loadableimage.LoadedImage

getImageOrientationPatient(int) - Method in class com.xinapse.loadableimage.LoadedImage

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 enum com.xinapse.multisliceimage.MostLikePlane

Returns the image orientation in patient coordinates for an image plane which is exactly in this MostLikePlane.

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.loadableimage.LoadableImage

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.loadableimage.LoadableImage

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.loadableimage.LoadedImage

getImagePositionPatient(int) - Method in class com.xinapse.loadableimage.LoadedImage

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.

getImplementedTypes() - Static method in class com.xinapse.multisliceimage.VolumeInterpolator

Returns the types of interpolation that are implemented by the VolumeInterpolator class.

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

getInstance(String) - Static method in enum com.xinapse.dicom.Modality

Returns a Modality Object corresponding to the supplied string.

getInstance(String) - Static method in enum com.xinapse.dicom.PatientPosition

Returns a PatientPosition Object corresponding to the supplied string.

getInstance(String) - Static method in enum com.xinapse.filter.FilterBoundaryCondition

Returns the FilterBoundaryCondition 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(Class, int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image

getInstance(Class, int) - Method in class com.xinapse.multisliceimage.Analyze.ANZImage

getInstance(PixelDataType) - Static method in enum com.xinapse.multisliceimage.Analyze.ANZPixFormat

Returns the ANZPixFormat corresponding to a PixelDataType.

getInstance(Class, int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage

getInstance(String) - Static method in enum com.xinapse.multisliceimage.Analyze.SliceOrder

Returns an SliceOrder corresponding to String value.

getInstance(String) - Static method in class com.xinapse.multisliceimage.ColourMapping

Returns one of the "built-in" ColourMappings, selected according to its name.

getInstance(String) - Static method in enum com.xinapse.multisliceimage.ComplexMode

Returns the ComplexMode corresponding to the supplied String argument.

getInstance(LoadableImage) - Static method in class com.xinapse.multisliceimage.Histogram

Creates a Histogram of intensities from a com.xinapse.loadableimage.LoadableImage.

getInstance(String) - Static method in enum com.xinapse.multisliceimage.InterpolationType

Returns the InterpolationType corresponding to the description supplied in the argument.

getInstance(String) - Static method in enum com.xinapse.multisliceimage.MostLikePlane

Returns a MostLikePlane corresponding to a string.

getInstance(float[][]) - Static method in enum com.xinapse.multisliceimage.MostLikePlane

Returns the MostLikePlane corresponding to the image orientation in patient coordinates.

getInstance(Vector3f[]) - Static method in enum com.xinapse.multisliceimage.MostLikePlane

Returns the MostLikePlane corresponding to the image orientation in patient coordinates.

getInstance(Class, int) - Method in class com.xinapse.multisliceimage.MultiSliceImage

Creates a new in-memory MultiSliceImage with the MultiSliceImage class given by the argument, possibly changing the number of slices in the image.

getInstance(int) - Method in class com.xinapse.multisliceimage.MultiSliceImage

Creates a new in-memory MultiSliceImage, based on this MultiSliceImage, but possibly changing the number of slices in the image.

getInstance(String) - Static method in class com.xinapse.multisliceimage.MultiSliceImage

Returns an instance of an image class gotten from a file.

getInstance(String, String) - Static method in class com.xinapse.multisliceimage.MultiSliceImage

Returns an instance of an image class gotten from a file, opened according to the mode.

getInstance(Component, MultiSliceImage) - Static method in class com.xinapse.multisliceimage.MultiSliceImage

Returns an instance of an image class using the supplied MultiSliceImage as a template for the image to be created.

getInstance(Component, MultiSliceImage, int) - Static method in class com.xinapse.multisliceimage.MultiSliceImage

Returns an instance of an image class using the supplied MultiSliceImage as a template for the image to be created.

getInstance(Component, MultiSliceImage, Class) - Static method in class com.xinapse.multisliceimage.MultiSliceImage

Returns an instance of an image class using the supplied MultiSliceImage as a template for the image to be created.

getInstance(MultiSliceImage, Class, int) - Static method in class com.xinapse.multisliceimage.MultiSliceImage

Returns an instance of an image class using the supplied MultiSliceImage as a template for the image to be created.

getInstance(MultiSliceImage, int) - Static method in class com.xinapse.multisliceimage.MultiSliceImage

Returns an in-memory instance of an image class using the supplied MultiSliceImage as a template for the image to be created.

getInstance(PixelDataType, int, int[]) - Static method in class com.xinapse.multisliceimage.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.multisliceimage.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.multisliceimage.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(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

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.SubSampleType

Returns the SubSampleType corresponding to a String representation.

getInstance(Class, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage

getInstance(PixelDataType) - Static method in enum com.xinapse.multisliceimage.UNC.UNCPixFormat

Returns the UNCPixFormat corresponding to a PixelDataType.

getInstance(Object, PixelDataType, int, int, int, float, float, float, Float, InterpolationType) - Static method in class com.xinapse.multisliceimage.VolumeInterpolator

Returns a new VolumeInterpolator for a block of pixel samples.

getInstance(Object, PixelDataType, int, int, int, float, float, float, InterpolationType, Float) - Static method in class com.xinapse.multisliceimage.VolumeInterpolator

Returns a new VolumeInterpolator for a block of pixel samples, with progress through the interpolation optionally being shown.

getInstance(VolumeInterpolator, InterpolationType) - Static method in class com.xinapse.multisliceimage.VolumeInterpolator

Returns a new VolumeInterpolator, constructed from an existing one.

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 report type from a String.

getInstances(String[], TimePointSplitType, boolean, MonitorWorker) - Static method in class com.xinapse.loadableimage.LoadedImage

Create a List of LoadedImages, from an array of individual file names, where each file will (typically) contain a single slice of header and pixel data.

getInstances(File[], TimePointSplitType, boolean, MonitorWorker) - Static method in class com.xinapse.loadableimage.LoadedImage

Create a List of LoadedImages, from an array of individual files, where each file will (typically) contain a single slice of header and pixel data.

getInstances(List<ImportableImage>, TimePointSplitType, boolean) - Static method in class com.xinapse.loadableimage.LoadedImage

Create a List of LoadedImages, from an array of ImportableImages, where each ImportableImage will (typically) contain a single slice of header and pixel data.

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

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.loadableimage.LoadableImage

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(int) - Method in interface com.xinapse.loadableimage.LoadableImage

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
for a particular slice.

getIntensityRescale() - Method in class com.xinapse.loadableimage.LoadedImage

getIntensityRescale(int) - Method in class com.xinapse.loadableimage.LoadedImage

getIntensityRescale() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image

Intensity rescaling is not supported by Analyze 7.5 format, so this method always the float[] [1.0f, 0.0f].

getIntensityRescale(int) - Method in class com.xinapse.multisliceimage.Analyze.ANZImage

getIntensityRescale() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage

getIntensityRescale() - Method in class com.xinapse.multisliceimage.UNC.UNCImage

getIntensityRescale(int) - 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.

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.

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

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

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.

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 interface com.xinapse.loadableimage.LoadableImage

Returns the maximum pixel intensity in the image.

getMax() - Method in class com.xinapse.loadableimage.LoadedImage

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.multisliceimage.ColourMapping

Returns the current maximmum display luminance setting for a digital driver level (DDL) of 255.

getMean() - Method in class com.xinapse.multisliceimage.Histogram

Returns the mean intensity value of this Histogram.

getMean(boolean) - Method in class com.xinapse.multisliceimage.Histogram

Returns the mean intensity value of this Histogram, optionally excluding all pixel intensities that are zero.

getMedian() - Method in class com.xinapse.multisliceimage.Histogram

Returns the median value of this Histogram.

getMedian(boolean) - Method in class com.xinapse.multisliceimage.Histogram

Returns the median value of this Histogram, optionally excluding all pixel intensities that are zero.

getMedian() - Method in class com.xinapse.multisliceimage.roi.ROIStats

getMin() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the minimum pixel intensity in the image.

getMin() - Method in class com.xinapse.loadableimage.LoadedImage

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.multisliceimage.ColourMapping

Returns the current minimum display luminance setting for a digital driver level (DDL) of zero.

getMinMax() - Method in class com.xinapse.multisliceimage.Analyze.ANZHeader

Gets the glMin and glMax fields for this Analyze image header.

getMinMax(Object, PixelDataType, ComplexMode) - Static method in class com.xinapse.multisliceimage.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.multisliceimage.Histogram

Returns the minimum and maximum intensity values present in a part of an array of pixel values.

getMinMax() - Method in class com.xinapse.multisliceimage.PixArray

Finds the minimum and maximum values in this PixArray.

getMod() - Method in class com.xinapse.multisliceimage.Complex

Returns the modulus of this Complex number.

getMod() - Method in class com.xinapse.multisliceimage.DoubleComplex

Returns the modulus of this DoubleComplex number.

getModality() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the imaging modality with which this image was collected.

getModality() - Method in class com.xinapse.loadableimage.LoadedImage

getModality() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image

Modality recording is not supported by the Analyze file format, so this method always returns Modality.UNKNOWN

getModality() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage

getModality() - Method in class com.xinapse.multisliceimage.MultiSliceImage

Returns the modality with which this image was acquired.

getModality() - Method in class com.xinapse.multisliceimage.UNC.UNCImage

getModel(int, int, float, LoadableImage) - 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.loadableimage.LoadableImage

Returns the imaging plane that this image is "most like".

getMostLikePlane() - Method in class com.xinapse.loadableimage.LoadedImage

getMostLikePlane() - Method in class com.xinapse.multisliceimage.MultiSliceImage

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.RectangularROI

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.loadableimage.LoadableImage

Returns a ColourMapping if this image has an associated colour mapping.

getNativeColourMapping() - Method in class com.xinapse.loadableimage.LoadedImage

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

getNBins() - Method in class com.xinapse.multisliceimage.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 interface com.xinapse.loadableimage.LoadableImage

Returns the number of image columns in this image.

getNCols() - Method in class com.xinapse.loadableimage.LoadedImage

getNCols() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage

getNCols() - Method in class com.xinapse.multisliceimage.UNC.UNCImage

getNDim() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the dimensionality of this image.

getNDim() - Method in class com.xinapse.loadableimage.LoadedImage

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.loadableimage.LoadableImage

Returns the number of frames in a multi-frame image.

getNFrames() - Method in class com.xinapse.loadableimage.LoadedImage

getNFrames() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage

getNFrames() - Method in class com.xinapse.multisliceimage.UNC.UNCImage

getNImages() - Method in class com.xinapse.multisliceimage.ImageSelectionGroupPanel

Returns the number of ImageSelectionGroupMemberPanels in this group.

getNImages() - Method in class com.xinapse.multisliceimage.MultipleImageSelectionPanel

Returns the number of images currently set in this MultipleImageSelectionMemberPanel.

getNKernelCols() - Method in class com.xinapse.filter.AbstractKernelFilter

Returns the number of columns in the filter kernel.

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.AbstractKernelFilter

Returns the number of rows in the filter kernel.

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.AbstractKernelFilter

Returns the number of slices in the filter kernel.

getNKernelSlices() - Method in class com.xinapse.filter.FixedWeightsKernelFilter

getNKernelSlices() - Method in class com.xinapse.filter.MedianFilter

getNKernelSlices() - Method in class com.xinapse.filter.MorphologicalOperator

getNPixels(int, int[]) - Static method in class com.xinapse.multisliceimage.MultiSliceImage

Returns the total number of picture elements for a MultiSliceImage with the given dimensions.

getNPixels(Object) - Method in enum com.xinapse.multisliceimage.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.

getNRows() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the number of image rows in this image.

getNRows() - Method in class com.xinapse.loadableimage.LoadedImage

getNRows() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage

getNRows() - Method in class com.xinapse.multisliceimage.UNC.UNCImage

getNSlices() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the number of physical slice locations in this image.

getNSlices() - Method in class com.xinapse.loadableimage.LoadedImage

getNSlices() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage

getNSlices() - Method in class com.xinapse.multisliceimage.UNC.UNCImage

getNSlots() - Method in class com.xinapse.multisliceimage.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.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.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.

getOutputImagesBaseName() - Method in class com.xinapse.dynamic.AbstractDynamicFrame

Returns the basename for the output images.

getParentComponent() - Method in interface com.xinapse.util.MessageShower

Returns the parent of this MessageShower.

getPatientDoB() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the patient date of birth for this image.

getPatientDoB() - Method in class com.xinapse.loadableimage.LoadedImage

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

Returns the patient's date of birth for this image.

getPatientDoB() - Method in class com.xinapse.multisliceimage.UNC.UNCImage

getPatientID() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the patient ID for this image.

getPatientID() - Method in class com.xinapse.loadableimage.LoadedImage

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.loadableimage.LoadableImage

Returns the patient name for this image.

getPatientName() - Method in class com.xinapse.loadableimage.LoadedImage

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.loadableimage.LoadableImage

Returns the position in which the patient is lying in the scanning equipment.

getPatientPosition() - Method in class com.xinapse.loadableimage.LoadedImage

getPatientPosition() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image

This action is not supported by the Analyze file format, so this method always returns PatientPosition.UNKNOWN;

getPatientPosition() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage

getPatientPosition() - Method in class com.xinapse.multisliceimage.UNC.UNCImage

getPeakHeight(boolean) - Method in class com.xinapse.multisliceimage.Histogram

Returns the number of pixels with the most common pixel intensity in this Histogram, optionally excluding the pixel intensities that are zero-valued.

getPeakPosition(boolean) - Method in class com.xinapse.multisliceimage.Histogram

Returns the most common pixel intensity in this Histogram, optionally excluding the pixel intensities that are zero-valued.

getPenSize() - Method in class com.xinapse.multisliceimage.roi.PenSizePanel

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.RectangularROI

getPerimeter() - Method in class com.xinapse.multisliceimage.roi.ROI

Returns the perimeter length of this ROI.

getPix() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns all the pixel values for this image in the order in which they are stored internally.

getPix(boolean) - Method in interface com.xinapse.loadableimage.LoadableImage

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() - Method in class com.xinapse.loadableimage.LoadedImage

getPix(boolean) - Method in class com.xinapse.loadableimage.LoadedImage

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

Returns pixel values from this image.

getPix(Object, int[], int[]) - Method in class com.xinapse.multisliceimage.MultiSliceImage

Get pixel values from this image into a specified array.

getPix(int[]) - Method in class com.xinapse.multisliceimage.MultiSliceImage

Returns a single pixel value from the image.

getPixelDataType() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns a PixelDataType representing the data type of this image.

getPixelDataType() - Method in class com.xinapse.loadableimage.LoadedImage

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.multisliceimage.PixelDataType

Gets an array of pixel samples, large enough to hold a specified number of pixels.

getPixelsAsFloat(Object) - Method in enum com.xinapse.multisliceimage.PixelDataType

Returns a set of pixel samples as an array of float values.

getPixelsAsFloat(Object, int, int) - Method in enum com.xinapse.multisliceimage.PixelDataType

Returns a set of pixel samples as an array of float values.

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.loadableimage.LoadableImage

Returns the pixel size in the x (horizontal) direction for this image.

getPixelXSize() - Method in class com.xinapse.loadableimage.LoadedImage

getPixelXSize() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage

getPixelXSize() - Method in class com.xinapse.multisliceimage.UNC.UNCImage

getPixelYSize() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the pixel size in the y (vertical) direction for this image.

getPixelYSize() - Method in class com.xinapse.loadableimage.LoadedImage

getPixelYSize() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage

getPixelYSize() - Method in class com.xinapse.multisliceimage.UNC.UNCImage

getPixelZSize() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the separation between the centres of image planes for this image.

getPixelZSize() - Method in class com.xinapse.loadableimage.LoadedImage

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.

getPrecedingHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI

getPrecedingHandle(Handle) - Method in interface com.xinapse.multisliceimage.roi.EditableOutlineROI

Returns the Handle that is immediately before the specified handle, in the order in which they were placed around the ROI.

getPrecedingHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.HollowROI

getPrecedingHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.IrregularROI

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.multisliceimage.MultiSliceImage

Returns the MultiSliceImage class set in the user's Preferences.

getPreferredInterpolationType(Preferences, InterpolationType) - Static method in enum com.xinapse.multisliceimage.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.

getPreferredMode(Preferences) - Static method in enum com.xinapse.multisliceimage.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.

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.multisliceimage.ImageFileChooser

Returns the preferred size of the image file chooser.

getPreferredSize() - Method in class com.xinapse.multisliceimage.ImagePreview

getPreferredSize() - Method in class com.xinapse.multisliceimage.ImageSelectionPanel

Override the default getPreferredSize() method.

getPreferredSize() - Method in class com.xinapse.multisliceimage.MultipleImageSelectionPanel

Override 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.

getPreferredSubSampleType(Preferences, SubSampleType) - Static method in enum com.xinapse.multisliceimage.SubSampleType

Returns the SubSampleType set in the 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.

getPreview(File) - Static method in class com.xinapse.multisliceimage.MultiSliceImage

Gets a PreviewIcon for a LoadableImage contained within the supplied File.

getPreviewIcon(File) - 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) - 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) - 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.

getProgName() - Method in class com.xinapse.util.MonitorWorker

Returns the program name for this MonitorWorker.

getPulseSequence() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the name of the pulse sequence with which this image was collected.

getPulseSequence() - Method in class com.xinapse.loadableimage.LoadedImage

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

Returns the pulse sequence name for this image.

getPulseSequence() - Method in class com.xinapse.multisliceimage.UNC.UNCImage

getPutPix(Object, int[], int[], boolean) - Method in class com.xinapse.multisliceimage.PixArray

Basic pixel accessor method for images of any dimensionality.

getPutPix(Object, int[], boolean) - Method in class com.xinapse.multisliceimage.PixArray

Gets/puts a single pixel value from/to an an image.

getPutSlice(Object, int, boolean) - Method in class com.xinapse.multisliceimage.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.

getQForm() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage

Returns the qForm in this NIFTIImage.

getRangeMax() - Method in enum com.xinapse.multisliceimage.PixelDataType

Returns the maximum value that a pixel of this PixelDataType can take.

getRangeMin() - Method in enum com.xinapse.multisliceimage.PixelDataType

Returns the minimum value that a pixel of this PixelDataType can take.

getReal() - Method in class com.xinapse.multisliceimage.Complex

Returns the real part of this Complex number.

getReal() - Method in class com.xinapse.multisliceimage.DoubleComplex

Returns the real part of this DoubleComplex number.

getReportType() - Method in class com.xinapse.util.ReportGenerator

Returns the ReportType generated.

getRescaleUnits() - Method in interface com.xinapse.loadableimage.LoadableImage

Specifies the output units of Intensity Rescale Slope and Intensity Rescale Intercept, retrieved by getIntensityRescale().

getRescaleUnits() - Method in class com.xinapse.loadableimage.LoadedImage

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 the intent name, or "arbitrary units", if the intent name is not set.

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.

getROIs() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns a List of ROIs that are stored with the image.

getROIs() - Method in class com.xinapse.loadableimage.LoadedImage

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.

getScanDate() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the scan Date for this image.

getScanDate() - Method in class com.xinapse.loadableimage.LoadedImage

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.loadableimage.LoadableImage

Returns the DICOM Scanning Sequence with which this image was collected.

getScanningSequence() - Method in class com.xinapse.loadableimage.LoadedImage

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

Returns the scanning sequence for this image.

getScanningSequence() - Method in class com.xinapse.multisliceimage.UNC.UNCImage

getScanTE() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the scan echo time for this image if it has a single echo-time.

getScanTE(int) - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the scan echo time for one slice of this image.

getScanTE() - Method in class com.xinapse.loadableimage.LoadedImage

getScanTE(int) - Method in class com.xinapse.loadableimage.LoadedImage

getScanTE() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image

This action is not supported by the Analyze file format, so this method always throws a ParameterNotSetException.

getScanTE(int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image

This action is not supported by the Analyze file format, so this method always throws a ParameterNotSetException.

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

Returns the scan echo time for one slice of this image.

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.loadableimage.LoadableImage

Returns the scan inversion time for this image.

getScanTI() - Method in class com.xinapse.loadableimage.LoadedImage

getScanTI() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image

This action is not supported by the Analyze 7.5 format, so this method always throws a ParameterNotSetException.

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.loadableimage.LoadableImage

Returns the scan repetition time for this image.

getScanTR() - Method in class com.xinapse.loadableimage.LoadedImage

getScanTR() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image

This action is not supported by the Analyze 7.5 format, so this method always throws a ParameterNotSetException.

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.multisliceimage.Histogram

Returns the standard deviation of intensity values of this Histogram.

getSD(boolean) - Method in class com.xinapse.multisliceimage.Histogram

Returns the standard deviation of intensity values of this Histogram, optionally excluding all pixel intensities that are zero from the calculation.

getSeedPoint() - Method in class com.xinapse.multisliceimage.roi.ContourWorker

Returns the seed point from which contouring was initiated.

getSelectedModality() - Method in class com.xinapse.dicom.Modality.ComboBox

Returns the Modality selected.

getSelectedROIs() - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame

Returns a java.util.List of selected ROIs for the image displayed.

getSelectedSlice() - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame

Returns the number of the selected image slice in this CanAddROIToFrame.

getSequenceVariant() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the DICOM Scanning Sequence Variant with which this image was collected.

getSequenceVariant() - Method in class com.xinapse.loadableimage.LoadedImage

getSequenceVariant() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image

Scan sequence variants are not supported by Analyze 7.5 format.

getSequenceVariant() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage

Returns the scanning sequence variant for this image.

getSequenceVariant() - 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.

getSimpleName() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image

getSimpleName() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage

getSimpleName() - Method in class com.xinapse.multisliceimage.MultiSliceImage

Returns the simple name for this type of image - the String that should be seen by the users to identify this type of image.

getSimpleName() - Method in class com.xinapse.multisliceimage.UNC.UNCImage

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(int) - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the pixel values for one slice of an n-dimensional image, where n > 1.

getSlice(int) - Method in class com.xinapse.loadableimage.LoadedImage

getSlice(int) - Method in class com.xinapse.multisliceimage.MultiSliceImage

Returns all the pixels for a two-dimensional slice of this image, as a 1-dimensional array of primitive values.

getSlice(Object, int) - Method in class com.xinapse.multisliceimage.MultiSliceImage

Returns all the pixels for a two-dimensional slice of this image, as a 1-dimensional array of primitive values.

getSlice() - Method in class com.xinapse.multisliceimage.roi.ROI

Returns the slice number for this ROI.

getSliceDim(int) - Method in class com.xinapse.multisliceimage.MultiSliceImage

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

getSlicesAreReversed(LoadableImage) - Static method in class com.xinapse.loadableimage.LoadedImage

Tests whether the supplied image has slices which are in reverse order compared to standard radiological presentation order.

getSliceThickness() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the slice thickness (in mm).

getSliceThickness() - Method in class com.xinapse.loadableimage.LoadedImage

getSliceThickness() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image

This action is not supported by the Analyze file format, so this method always throws ParameterNotSetException

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.

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.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(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 the UID of the Storage Class with which Objects of this Modality should be stored.

getSuggestedFileName() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the suggested file name for in-memory images that are to be saved to disk.

getSuggestedFileName() - Method in class com.xinapse.loadableimage.LoadedImage

getSuggestedFileName() - Method in class com.xinapse.multisliceimage.MultiSliceImage

getSupportedInterpolationTypes() - Static method in class com.xinapse.multisliceimage.VolumeInterpolator

Returns an array of interpolation types currently supported by the VolumeInterpolator class.

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 interface com.xinapse.multisliceimage.roi.RotatableROI

Returns the current rotation angle for this RotatableROI.

getThreshold() - Method in class com.xinapse.dynamic.AbstractDynamicFrame

Returns the intensity threshold for pixel processing.

getTimeBetweenFrames() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the time between frames in a 4- or higher dimensional image.

getTimeBetweenFrames() - Method in class com.xinapse.loadableimage.LoadedImage

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 interface com.xinapse.loadableimage.LoadableImage

Returns the title of this image.

getTitle() - Method in class com.xinapse.loadableimage.LoadedImage

getTitle() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage

getTitle() - Method in class com.xinapse.multisliceimage.MultipleImageSelectionPanel

Returns the title for the list of images.

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.multisliceimage.Histogram

Returns the total number of pixels that contributed to this histogram.

getTotalCount(boolean) - Method in class com.xinapse.multisliceimage.Histogram

Returns the total number of pixels that contributed to this histogram, optionally excluding any zero-intensity pixels.

getTotalCount(double) - Method in class com.xinapse.multisliceimage.Histogram

Returns the number of pixels in this histogram that are above the supplied threshold.

getTotalNSlices() - Method in interface com.xinapse.loadableimage.LoadableImage

Returns the total number of slices in this image.

getTotalNSlices() - Method in class com.xinapse.loadableimage.LoadedImage

getTotalNSlices() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage

getTotalNSlices() - Method in class com.xinapse.multisliceimage.UNC.UNCImage

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.multisliceimage.ImageSelectionGroupPanel

getUserComponents() - Method in class com.xinapse.multisliceimage.ImageSelectionGroupPanel

getUserMappings() - Static method in class com.xinapse.multisliceimage.ColourMapping

Returns a java.util.List of the ColorMappings 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.

getValidIntensityStats() - Method in class com.xinapse.multisliceimage.roi.ROIStats

Returns whether this ROIStats has valid intensity-related statistics.

getValue(Object, int) - Method in enum com.xinapse.multisliceimage.PixelDataType

Gets a single pixel value from an array of pixels.

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 variables 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 variables 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

getVertices() - Method in class com.xinapse.multisliceimage.roi.IrregularROI

Returns the vertex locations for this IrregularROI.

getWidth() - Method in class com.xinapse.multisliceimage.roi.RectangularROI

Returns the width of this RectangularROI in mm.

getWorkingDirectory() - Method in class com.xinapse.multisliceimage.ImageSelectionGroupPanel

Returns the "current working directory" for this ImageSelectionGroupPanel.

getWorkingDirectory() - Method in class com.xinapse.multisliceimage.ImageSelectionPanel

Returns the "current working directory" for this ImageSelectionPanel.

getWorkingDirectory() - Method in class com.xinapse.multisliceimage.MultipleImageSelectionPanel

Returns the "current working directory" for this MultipleImageSelectionPanel.

getWriteDescription(boolean, boolean, boolean, boolean, boolean, boolean, PixelDataType, ComplexMode) - Method in class com.xinapse.multisliceimage.roi.ROIStats

Returns a String showing the 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.

getXStart() - Method in class com.xinapse.dynamic.AbstractDynamicFrame

For the purposes of plotting data, returns the starting value of the independent variable.

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.multisliceimage.ColourMapping

The ColourMapping representing a green intensity scale.

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.multisliceimage.Complex

Returns a hash code value for this Complex number.

hashCode() - Method in class com.xinapse.multisliceimage.DoubleComplex

Returns a hash code value for this Complex 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.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.

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.multisliceimage

A class for creating and finding statistics about arrays of pixel intensities, histograms of pixel intensities, and statistics about those histograms.

Histogram(double[], double, double) - Constructor for class com.xinapse.multisliceimage.Histogram

Creates a Histogram of intensities from pre-computed values.

Histogram(Object, PixelDataType) - Constructor for class com.xinapse.multisliceimage.Histogram

Creates a Histogram of intensities from an array of values.

Histogram(Object, PixelDataType, ComplexMode) - Constructor for class com.xinapse.multisliceimage.Histogram

Creates a Histogram of intensities from an array of values.

Histogram(Object, int, int, PixelDataType) - Constructor for class com.xinapse.multisliceimage.Histogram

Creates a Histogram of intensities from an array of values.

Histogram(Object, int, int, PixelDataType, ComplexMode) - Constructor for class com.xinapse.multisliceimage.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.multisliceimage.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.multisliceimage.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.multisliceimage.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.multisliceimage.Histogram

Creates a new Histogram, copying all values from an existing Histogram.

Histogram.BinSpec - Class in com.xinapse.multisliceimage

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.multisliceimage.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 hollows.

HollowROI(List<ROI>, ROIState) - Constructor for class com.xinapse.multisliceimage.roi.HollowROI

Creates a new HollowROI, created from a List of ROIs, where one completely contains all the other.

I

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.multisliceimage.ImageSelectionPanel

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

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.

imageExists(String) - Static method in class com.xinapse.multisliceimage.UNC.UNCImage

Tests whether a UNCImage with the given name already exists on disk.

ImageFileChooser - Class in com.xinapse.multisliceimage

Abstract Class for File Choosers for opening and saving MultiSliceImages, and DICOM images.

ImageFileChooser.LoadChooser - Class in com.xinapse.multisliceimage

ImageFileChooser suitable for selecting a MultiSliceImage file for loading.

ImageFileChooser.LoadChooser(boolean) - Constructor for class com.xinapse.multisliceimage.ImageFileChooser.LoadChooser

Creates an ImageFileChooser.LoadChooser suitable for selecting a MultiSliceImage file for loading, with the directory set to the current working directory.

ImageFileChooser.LoadChooser(File, boolean) - Constructor for class com.xinapse.multisliceimage.ImageFileChooser.LoadChooser

Creates an ImageFileChooser.LoadChooser suitable for selecting a MultiSliceImage 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).

ImageFileChooser.LoadChooser(File, Class, boolean) - Constructor for class com.xinapse.multisliceimage.ImageFileChooser.LoadChooser

Creates an ImageFileChooser.LoadChooser suitable for selecting a MultiSliceImage 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).

ImageFileChooser.SaveChooser - Class in com.xinapse.multisliceimage

ImageFileChooser suitable for selecting a MultiSliceImage file for saving.

ImageFileChooser.SaveChooser(Class, String) - Constructor for class com.xinapse.multisliceimage.ImageFileChooser.SaveChooser

Creates an ImageFileChooser.SaveChooser suitable for selecting a MultiSliceImage file for saving.

ImageFileChooser.SaveChooser() - Constructor for class com.xinapse.multisliceimage.ImageFileChooser.SaveChooser

Creates an ImageFileChooser.SaveChooser suitable for selecting a MultiSliceImage file for saving.

ImageFileChooser.SaveChooser(File) - Constructor for class com.xinapse.multisliceimage.ImageFileChooser.SaveChooser

Creates an ImageFileChooser.SaveChooser suitable for selecting a MultiSliceImage file for saving.

ImageFileFilter - Class in com.xinapse.multisliceimage

A file filter for all MultiSliceImages.

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.

ImageName - Class in com.xinapse.multisliceimage

Class to add extensions, prefixes and suffices to image file and URL names.

imageOrientationPatient - Variable in class com.xinapse.loadableimage.LoadedImage

The global image orientation in patient coordinates of a block of slices, or null if this image doesn't contain a block of parallel slices.

imagePositionPatient - Variable in class com.xinapse.loadableimage.LoadedImage

The global image position in patient coordinates of a block of slices, or null if this image doesn't contain a block of parallel slices.

ImagePreview - Class in com.xinapse.multisliceimage

JComponent that is used to preview an image file.

ImagePreview(JFileChooser) - Constructor for class com.xinapse.multisliceimage.ImagePreview

ImageSaveException - Exception in com.xinapse.multisliceimage

Signals that an error has occurred when trying to save an image.

ImageSaveException() - Constructor for exception com.xinapse.multisliceimage.ImageSaveException

Constructs an ImageSaveException with "image couldn't be saved" as its error detail message.

ImageSaveException(String) - Constructor for exception com.xinapse.multisliceimage.ImageSaveException

Constructs an ImageSaveException with the specified detail message.

ImageSelectionGroupPanel - Class in com.xinapse.multisliceimage

An ImageSelectionGroupPanel allows the selection of a group of MultiSliceImages and contains the mechanism for adding images to the group, removing images from the group, etc.

ImageSelectionGroupPanel() - Constructor for class com.xinapse.multisliceimage.ImageSelectionGroupPanel

Creates a new ImageSelectionGroupPanel with initially one image in the set of images, and a minimum of one image in the set.

ImageSelectionGroupPanel(JFrame) - Constructor for class com.xinapse.multisliceimage.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(JFrame, int, ImageSelectionGroupPanel.ComponentGenerator, double) - Constructor for class com.xinapse.multisliceimage.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.multisliceimage

An interface implemented by classes that want to be able to generate user components to put into an ImageSelectionGroupPanel.

ImageSelectionPanel - Class in com.xinapse.multisliceimage

An ImageSelectioPanel is a javax.swing.JPanel that can be used to select a MultiSliceImage for input.

ImageSelectionPanel() - Constructor for class com.xinapse.multisliceimage.ImageSelectionPanel

Creates new ImageSelectionPanel, with the default Folder set to the System Property user.dir.

ImageSelectionPanel(boolean) - Constructor for class com.xinapse.multisliceimage.ImageSelectionPanel

Creates new ImageSelectionPanel, with the default Folder set to the System Property user.dir.

ImageSelectionPanel(boolean, boolean) - Constructor for class com.xinapse.multisliceimage.ImageSelectionPanel

Creates new ImageSelectionPanel, with the default Folder set to the System Property user.dir, and with the image file selection field on only one line.

ImageSelectionPanel(File, Class, boolean) - Constructor for class com.xinapse.multisliceimage.ImageSelectionPanel

Creates new ImageSelectionPanel, with the default Folder given by argument.

ImageSelectionPanel(File, Class, boolean, boolean) - Constructor for class com.xinapse.multisliceimage.ImageSelectionPanel

Creates new ImageSelectionPanel, with the default Folder given by argument, and with the image file selection field on only one line.

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 error 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 error 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 the MultiSliceImage 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.

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

insertVertex(Point2D) - Method in class com.xinapse.multisliceimage.roi.IrregularROIInProgress

insertVertex(double, double) - Method in class com.xinapse.multisliceimage.roi.IrregularROIInProgress

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(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.

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.IntensityRelationButton(Preferences) - Constructor for class com.xinapse.util.IntensityRelation.IntensityRelationButton

Create a new IntensityRelationButton.

IntensityRelation.PanelGenerator - Class in com.xinapse.util

Class for generating JPanels for selecting an IntensityRelation.

IntensityRelation.PanelGenerator() - Constructor for class com.xinapse.util.IntensityRelation.PanelGenerator

IntensityRelation.PanelGenerator.Panel - Class in com.xinapse.util

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.multisliceimage.