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All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

AbstractComplexKernelFilter - Class in com.xinapse.filter
This class provides a skeletal implementation of the SpatialFilter interface, for complex data to minimize the effort required to implement this interface.
AbstractDynamicContrastModel - Class in com.xinapse.apps.perfusion
A Model that can be fitted to dynamic data where contrast agent is injected, and the tissue response to an input function is measured.
AbstractDynamicContrastModel(String, String, String[], String[]) - Constructor for class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
Constructor used by sub-classes.
AbstractDynamicContrastResult - Class in com.xinapse.apps.perfusion
Superclass for the results of dynamic contrast analysis.
AbstractDynamicContrastResult(DynamicModel, float[], float, float[]) - Constructor for class com.xinapse.apps.perfusion.AbstractDynamicContrastResult
Used by sub-class constructors.
AbstractDynamicFrame - Class in com.xinapse.dynamic
AbstractDynamicFrame - a GUI for performing general image dynamic analysis.
AbstractDynamicFrame(ImageDisplayer, String, List<Image>, String) - Constructor for class com.xinapse.dynamic.AbstractDynamicFrame
Creates new DynamicFrame for use with Jim.
AbstractDynamicFrame(String, List<Image>, String) - Constructor for class com.xinapse.dynamic.AbstractDynamicFrame
Creates a new DynamicFrame for a stand-alone image dynamic analysis application.
AbstractDynamicWorker - Class in com.xinapse.apps.perfusion
MonitorWorker for running dynamic contrast analysis.
AbstractKernelFilter - Class in com.xinapse.filter
This class provides a skeletal implementation of the SpatialFilter interface, to minimize the effort required to implement this interface.
accept(File) - Method in class com.xinapse.image.ImageFileFilter
Tests whether the given file probably represents a loadable image file.
accept(File) - Method in class com.xinapse.multisliceimage.Analyze.AnalyzeFileFilter
Tests whether the given file probably represents an Analyze header file.
accept(File) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIFileFilter
Tests whether the given file probably represents a NIFTI image file.
accept(File) - Method in class com.xinapse.multisliceimage.roi.ImageJROIFileFilter
Tests whether the given file is possibly an ImageJ region of interest file.
accept(File) - Method in class com.xinapse.multisliceimage.roi.ROIFileFilter
Tests whether the given file is a region of interest file.
accept(File) - Method in class com.xinapse.multisliceimage.UNC.UNCFileFilter
Tests whether the given file probably represents a UNC image file.
add() - Method in class com.xinapse.image.ImageSelectionGroupPanel
Adds another ImageSelectionGroupMemberPanel to this group.
add(FixedWeightsComplexKernelFilter) - Method in class com.xinapse.filter.FixedWeightsComplexKernelFilter
Adds the weights from a FixedWeightsComplexKernelFilter to the weights of this one.
add(FixedWeightsComplexKernelFilter, FixedWeightsComplexKernelFilter) - Static method in class com.xinapse.filter.FixedWeightsComplexKernelFilter
Adds the weights from two FixedWeightsComplexKernelFilters to create a new FixedWeightsComplexKernelFilter.
add(FixedWeightsKernelFilter) - Method in class com.xinapse.filter.FixedWeightsKernelFilter
Adds the weights from a FixedWeightsKernelFilter to the weights of this one.
add(FixedWeightsKernelFilter, FixedWeightsKernelFilter) - Static method in class com.xinapse.filter.FixedWeightsKernelFilter
Adds the weights from two FixedWeightsKernelFilters to create a new FixedWeightsKernelFilter.
add(Complex) - Method in class com.xinapse.image.Complex
Adds the value of this complex number to another complex number, and returns the result.
add(Complex) - Method in class com.xinapse.image.DoubleComplex
 
add(Complex) - Method in class com.xinapse.image.FloatComplex
 
add(Histogram, PixelDataType) - Method in class com.xinapse.image.Histogram
Adds the counts from a Histogram to this Histogram to produce a new Histogram that spans the data range of both.
ADD - Enum constant in enum class com.xinapse.multisliceimage.roi.ROIEditAction
Add an ROI.
addActionListener(ActionListener) - Method in class com.xinapse.dynamic.DynamicModel.SpecifierPanel
Adds an ActionListener that is triggered whenever the model settings are changed.
addChangeListener(ChangeListener) - Method in class com.xinapse.image.MultipleImageSelectionPanel
addChangeListener(ChangeListener) - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Adds a ChangeListener to the MultiContrastAnalysisFrame.
AddChecksum - Class in com.xinapse.multisliceimage.roi
Program to add a Checksum to an ROI file.
addCol() - Method in class com.xinapse.image.ImageGrid
Adds another column of images.
addExtendedData(ExtendedData) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Adds a block of ExtendedData to this NIFTIImage.
addExtension(File, String) - Static method in class com.xinapse.multisliceimage.ImageName
Adds an extension to a File to create the name for a new file with the given extension.
addExtension(String, String) - Static method in class com.xinapse.multisliceimage.ImageName
Adds an extension to a file or URL name String to create the name for a new file or URL with the given extension.
addFileChangeCommitListener(ChangeListener) - Method in class com.xinapse.image.ImageSelectionGroupPanel
Adds a listener that listens for the file name change being committed.
addFileChangeCommitListener(ChangeListener) - Method in class com.xinapse.image.ImageSelectionPanel
addFiles(List<File>) - Method in class com.xinapse.image.MultipleImageSelectionPanel
addFileTextEditListener(ChangeListener) - Method in class com.xinapse.image.ImageSelectionGroupPanel
Adds a listener that listens for the file text being edited.
addFileTextEditListener(ChangeListener) - Method in class com.xinapse.image.ImageSelectionPanel
addGraph(GraphPanel, String) - Method in class com.xinapse.util.ReportGenerator
Adds a graph to the report.
addGraph(GraphPanel, String, String, String) - Method in class com.xinapse.util.ReportGenerator
Adds a graph to the report.
addImage(ReadableImage, ColourMapping, double, double, ComplexMode, String) - Method in class com.xinapse.util.ReportGenerator
Adds an image to the report.
addImage(ReadableImage, String) - Method in class com.xinapse.util.ReportGenerator
Adds a colour image to the report.
addImageInfo(ReadableImage) - Method in class com.xinapse.util.ReportGenerator
Adds basic image information to a report.
addImageInfo(ReadableImage, String) - Method in class com.xinapse.util.ReportGenerator
Adds basic image information to a report.
addInfo(List<String>) - Method in class com.xinapse.apps.cardiac.SelectableCardiacAnalysis
Add common information for inclusion in a Report.
addNColumnsChangeActionListener(ActionListener) - Method in class com.xinapse.image.ImageGrid
Add an ActionListener that is to be notified when the number of columns in the ImageGrid changes.
addNRowsChangeActionListener(ActionListener) - Method in class com.xinapse.image.ImageGrid
Add an ActionListener that is to be notified when the number of rows in the ImageGrid changes.
addParagraph(Chunk) - Method in class com.xinapse.util.ReportGenerator
Adds a paragraph to the report.
addParagraph(String) - Method in class com.xinapse.util.ReportGenerator
Adds a paragraph to the report.
addPicture(BufferedImage, String, float) - Method in class com.xinapse.util.ReportGenerator
Adds a picture image 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() - 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
 
addROI(ROI) - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Add an ROI to the frame.
addROI(ROI) - Method in class com.xinapse.multisliceimage.roi.VOI
Add an ROI to this VOI.
addROIs(List<ROI>) - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Add a List of ROIs to the Frame.
addRow() - Method in class com.xinapse.image.ImageGrid
Adds another row of images.
addSuffix(File, String) - Static method in class com.xinapse.multisliceimage.ImageName
Adds a suffix to a File name to create the name for a new File with the given suffix.
addSuffix(String, String) - Static method in class com.xinapse.multisliceimage.ImageName
Adds a suffix to a file or URL name to create the name for a new file or URL with the given suffix.
addTable(TableDataSet) - Method in class com.xinapse.util.ReportGenerator
Adds a table to the report.
addTable(String, String[], double[][], DecimalFormat) - Method in class com.xinapse.util.ReportGenerator
Adds a table to the report.
addTable(String, String[], double[][], DecimalFormat[]) - Method in class com.xinapse.util.ReportGenerator
Adds a table to the report.
addTable(String, String[], String[], String[][]) - Method in class com.xinapse.util.ReportGenerator
Adds a table to the report.
addUserColourMapping(Component) - Static method in class com.xinapse.image.ColourMapping
Prompts the user to add a new user-defined ColourMapping.
addValues(Object, int, int, PixelDataType, ComplexMode) - Method in class com.xinapse.image.Histogram
Adds some pixel values to this Histogram.
AffineTransform3D - Class in com.xinapse.geom3d
The AffineTransform3D class represents a 3D affine transform that performs a linear mapping from 3D coordinates to other 3D coordinates that preserves the "straightness" and "parallelness" of lines.
AffineTransform3D() - Constructor for class com.xinapse.geom3d.AffineTransform3D
Constructs and initializes a transform to the identity transform.
AffineTransform3D(float[]) - Constructor for class com.xinapse.geom3d.AffineTransform3D
Constructs and initializes a transform from the float array of length 12; the top row of the matrix is initialized to the first four elements of the array, and so on.
AffineTransform3D(Transform3D) - Constructor for class com.xinapse.geom3d.AffineTransform3D
Constructs and initializes a transform from the Transform3D object.
AFNIExtendedData - Class in com.xinapse.multisliceimage.Analyze
This abstract class handles the NIFTI 1.1 extended data.
aif - Variable in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
The blood plasma concentration in the feeding artery, Cpa(t).
AIF - Class in com.xinapse.apps.perfusion
Class for writing and reading arterial input function data (graphs).
AIF(double[], double[]) - Constructor for class com.xinapse.apps.perfusion.AIF
Creates a new AIF from tabulated concentration values.
AIF(double[], double[], Double, boolean, String, boolean) - Constructor for class com.xinapse.apps.perfusion.AIF
Creates a new AIF from tabulated concentration values.
ALIGNED_ANAT - Enum constant in enum class com.xinapse.multisliceimage.Analyze.NIFTIXForm
Coordinates aligned to another file's, or to anatomical "truth".
alignKnots(OpenSplineROI, OpenSplineROI, int) - Static method in class com.xinapse.multisliceimage.roi.OpenSplineROI
Aligns the knot points in a pair of OpenSplineROIs, so that there is spatial correspondence as far as possible across the knots.
alignKnots(SplineROI, SplineROI, int) - Static method in class com.xinapse.multisliceimage.roi.SplineROI
Aligns the knot points in a pair of SplineROIs, so that there is spatial correspondence as far as possible across the knots.
alignKnots(List<SplineROI>, int) - Static method in class com.xinapse.multisliceimage.roi.SplineROI
Aligns the knot points in a set of SplineROIs, so that there is spatial correspondence as far as possible across the knots.
ALL - Enum constant in enum class com.xinapse.multisliceimage.roi.MaskMode
MaskMode such that all of a pixel must be inside an ROI for that pixel to be part of the mask.
ALT_DEC - Enum constant in enum class com.xinapse.multisliceimage.Analyze.SliceOrder
Interleaved slice aquisition, decreasing time with slice number.
ALT_DEC2 - Enum constant in enum class com.xinapse.multisliceimage.Analyze.SliceOrder
Interleaved slice aquisition, decreasing time with slice number.
ALT_INC - Enum constant in enum class com.xinapse.multisliceimage.Analyze.SliceOrder
Interleaved slice aquisition, increasing time with slice number.
ALT_INC2 - Enum constant in enum class com.xinapse.multisliceimage.Analyze.SliceOrder
Interleaved slice aquisition, increasing time with slice number.
Analyze75Header - Class in com.xinapse.multisliceimage.Analyze
This class represents a multi-dimensional Analyze 7.5 image header file.
Analyze75Image - Class in com.xinapse.multisliceimage.Analyze
This class is a representation of a multi-dimensional image in the Analyze 7.5 format.
Analyze75Image() - Constructor for class com.xinapse.multisliceimage.Analyze.Analyze75Image
Creates an uninitialised instance of an Analyze75Image.
Analyze75Image(short, short, short, short, ANZPixFormat) - Constructor for class com.xinapse.multisliceimage.Analyze.Analyze75Image
Creates a new in-memory Analyze75Image.
Analyze75Image(Analyze75Header) - Constructor for class com.xinapse.multisliceimage.Analyze.Analyze75Image
Creates a new in-memory Analyze75Image, using information from an existing Analyze75header.
Analyze75Image(ANZPixFormat, Short...) - Constructor for class com.xinapse.multisliceimage.Analyze.Analyze75Image
Creates a new in-memory 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, short, short, short, short, ANZPixFormat) - Constructor for class com.xinapse.multisliceimage.Analyze.Analyze75Image
Creates a new disk-based Analyze75Image.
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, ANZPixFormat, Short...) - Constructor for class com.xinapse.multisliceimage.Analyze.Analyze75Image
Creates a new disk-based Analyze75Image.
Analyze75Image(String, String) - Constructor for class com.xinapse.multisliceimage.Analyze.Analyze75Image
Opens an existing Analyze75Image, with pixel data remaining on disk until requested.
AnalyzeFileFilter - Class in com.xinapse.multisliceimage.Analyze
A file filter for Analyze header files.
and(BitSet) - Method in class com.xinapse.util.BitSet
Performs the logical AND operation on this bit set and the given BitSet.
andNot(ROI) - Method in class com.xinapse.multisliceimage.roi.ROI
Logically AND NOTs (subtracts) an ROI from this ROI to create a new java.util.List<ROI> of ROIs that is the result of subtracting the shape of the supplied ROI from this ROI.
andNot(ROI, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
andNot(ROI, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
andNot(ROI, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.Marker
 
andNot(ROI, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.ROI
Logically AND NOTs (subtracts) an ROI from this ROI to create a new java.util.List<ROI> of ROIs that is the result of subtracting the shape of the supplied ROI from this ROI.
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.
andNot(List<ROI>, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.ROI
Logically AND NOTs (subtracts) a List of ROIs from this ROI to create a new java.util.List<ROI> of ROIs that is the result of subtracting the shapes of the ROIs.
ANDNOT_ASCENDING - Enum constant in enum class com.xinapse.multisliceimage.roi.LogicalOperator
AND NOT operation, applied to ROIs in ascending size order.
ANDNOT_DESCENDING - Enum constant in enum class com.xinapse.multisliceimage.roi.LogicalOperator
AND NOT operation, applied to ROIs in descending size order.
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.
ANGIOSCOPY_RET - Enum constant in enum class com.xinapse.dicom.Modality
Angioscopy Modality (RETIRED).
ANNOTATION - Enum constant in enum class com.xinapse.multisliceimage.roi.StatsType
StatsType for ROI annotation.
ANNOTATIONTOKEN - Static variable in class com.xinapse.multisliceimage.roi.ROIStreamTokenizer
The token written to show the ROI annotation.
anonymise(String, String, Date, boolean, String, String, String, boolean, String, String, String, String, String, String, String, boolean) - Method in interface com.xinapse.image.WritableImage
Anonymise this WritableImage.
anonymise(String, String, Date, boolean, String, String, String, boolean, String, String, String, String, String, String, String, boolean) - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
anonymise(String, String, Date, boolean, String, String, String, boolean, String, String, String, String, String, String, String, boolean) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
anonymise(String, String, Date, boolean, String, String, String, boolean, String, String, String, String, String, String, String, boolean) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
anonymise(String, String, Date, boolean, String, String, String, boolean, String, String, String, String, String, String, String, boolean) - Method in class com.xinapse.util.InfoList
Anonymise the items in this InfoList.
ANY - Enum constant in enum class com.xinapse.multisliceimage.roi.MaskMode
MaskMode such that if any part of a pixel is inside an ROI, that pixel is part of the mask.
ANZColourMapping - Class in com.xinapse.multisliceimage.Analyze
Class to handle Analyze lookup files (colour mapping files).
ANZColourMapping() - Constructor for class com.xinapse.multisliceimage.Analyze.ANZColourMapping
 
ANZDebug - Class in com.xinapse.multisliceimage.Analyze
Enables and disables debugging messages for the Analyze package.
ANZException - Exception in com.xinapse.multisliceimage.Analyze
Signals that an error in the Analyze package has occurred.
ANZException() - Constructor for exception com.xinapse.multisliceimage.Analyze.ANZException
Constructs an ANZException without a detail message.
ANZException(String) - Constructor for exception com.xinapse.multisliceimage.Analyze.ANZException
Constructs an ANZException with the specified detail message.
ANZException(String, Throwable) - Constructor for exception com.xinapse.multisliceimage.Analyze.ANZException
Constructs an ANZException with the specified cause.
ANZHeader - Class in com.xinapse.multisliceimage.Analyze
An abstract Analyze header representation.
ANZHeader(boolean) - Constructor for class com.xinapse.multisliceimage.Analyze.ANZHeader
Creates an uninitialised ANZHeader.
ANZHeader(ANZPixFormat, boolean, Long...) - Constructor for class com.xinapse.multisliceimage.Analyze.ANZHeader
Constructor for a generic Analyze image header.
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 NIFTI format.
ANZPixFormat - Enum Class in com.xinapse.multisliceimage.Analyze
This class represents the pixel formats (data types) that can be used in Analyze, and NIFTI (extended Analyze) images.
APositiveHandle - Class in com.xinapse.multisliceimage.roi
A Class representing a Handle at the positive end of axis A on an EllipticalROI.
APositiveHandle(int, int, int) - Constructor for class com.xinapse.multisliceimage.roi.APositiveHandle
Creates a new APositiveHandle at the location (x,y) with the given size in screen pixels.
append(InfoList) - Method in class com.xinapse.util.InfoList
Appends an InfoList onto the end of an existing one.
appendAuditInfo(String, String) - Method in interface com.xinapse.image.WritableImage
Appends audit trail information to this image.
appendAuditInfo(String, String) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by Analyze 7.5 format, so this method does nothing.
appendAuditInfo(String, String) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Appends audit trail information to this image.
appendAuditInfo(String, String) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
appendInfoList(InfoList) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
appendInfoList(InfoList) - Method in interface com.xinapse.multisliceimage.InfoStorer
Appends an InfoList to the existing general file info of this image.
appendInfoList(InfoList) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
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, int, int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Appends an InfoList to that existing for a specific dimension of this image.
appendInfoList(InfoList, int, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
appendToTitle(String) - Method in interface com.xinapse.image.WritableImage
Append some text to the title of this WritableImage, if the image format can handle titles.
appendVertex(double, double) - Method in class com.xinapse.multisliceimage.roi.IrregularROIInProgress
Appends a vertex to the end of this IrregularROIInProgress.
appendVertex(Point2D) - Method in class com.xinapse.multisliceimage.roi.IrregularROIInProgress
Appends a vertex to the end of this IrregularROIInProgress.
APPLY_SPATIAL_FILTER_PREFERENCE_NAME - Static variable in class com.xinapse.dynamic.AbstractDynamicFrame
The Preference name for whether to apply a spatial smoothing filter.
approximate(int) - Method in class com.xinapse.multisliceimage.roi.SplineROI
Creates a new SplineROI which approximates this SplineROI, but which has the specified number of knot points and where the knot points are evenly distributed in the s-parameter.
area - Variable in class com.xinapse.multisliceimage.roi.ROIStats
The area of this ROI in square mm.
AREA - Enum constant in enum class com.xinapse.multisliceimage.roi.StatsType
StatsType for ROI area.
AREATOKEN - Static variable in class com.xinapse.multisliceimage.roi.ROIStreamTokenizer
The token written to show the ROI area.
ASMT - Enum constant in enum class com.xinapse.dicom.Modality
Content assessment results Modality.
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.
AUDIO - Enum constant in enum class com.xinapse.dicom.Modality
Audio Modality.
AUDIT_TRAIL_ACTION_TEXT - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
A String used when composing audit trail information.
AutoCorrelationEstimate - Class in com.xinapse.dynamic
Class to estimate the auto-correlation of a time-series by examining the residuals of a GLM fit.
AutoCorrelationEstimate(float[][], int, int, int, float, float, float, MonitorWorker, boolean) - Constructor for class com.xinapse.dynamic.AutoCorrelationEstimate
Estimate the auto-correlation for the supplied residuals.
autoCrop(ReadableImage) - Static method in class com.xinapse.image.ImageUtils
Automatically crop an image to remove regions of background.
autoCrop(ReadableImage[]) - Static method in class com.xinapse.image.ImageUtils
Automatically crops an array of images to remove regions which are background in any of the images.
autoCrop(ReadableImage[], MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Automatically crops an array of images to remove regions which are background in any of the images.
autoCrop(ReadableImage[], Double) - Static method in class com.xinapse.image.ImageUtils
Automatically crops an array of images to remove regions which are background in any of the images.
autoCrop(ReadableImage[], Double, MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Automatically crops an array of images to remove regions which are background in any of the images.
autoCrop(ReadableImage, MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Automatically crop an image to remove regions of background.
autoCrop(ReadableImage, Double) - Static method in class com.xinapse.image.ImageUtils
Automatically crop an image to remove regions of background.
autoCrop(ReadableImage, Double, MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Automatically crop an image to remove regions of background.
autoCropSlices(ReadableImage) - Static method in class com.xinapse.image.ImageUtils
Automatically crop an image to remove slices that only contain background.
autoCropSlices(ReadableImage, MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Automatically crop an image to remove slices that only contain background.
autoCropSlices(ReadableImage, Double) - Static method in class com.xinapse.image.ImageUtils
Automatically crop an image to remove slices that only contain background.
autoCropSlices(ReadableImage, Double, MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Automatically crop an image to remove slices that only contain background.
AUTOREFRACTION - Enum constant in enum class com.xinapse.dicom.Modality
Autorefraction Modality.
autoResample(ReadableImage, int, SubSampleType, boolean, boolean) - Static method in class com.xinapse.image.ImageUtils
Automatically resamples a ReadableImage so that the resulting resampled image has no more than the given maximum number of voxels.
AUXFILE_LEN - Static variable in class com.xinapse.multisliceimage.Analyze.ANZHeader
The length in bytes of the auxiliary file field.
average(List<AffineTransform3D>) - Static method in class com.xinapse.geom3d.AffineTransform3D
Returns the AffineTransform3D that is the average of several AffineTransform3Ds.
AXIAL - Enum constant in enum class com.xinapse.image.MostLikePlane
The MostLikePlane corresponding to an axial orientation.
AxisHandle - Class in com.xinapse.multisliceimage.roi
A Class representing a Handle at the end of an axis on an EllipticalROI.
AxisHandle(int, int, int) - Constructor for class com.xinapse.multisliceimage.roi.AxisHandle
Creates a new AxisHandle at the location (x,y) with the given size in screen pixels.

B

bc - Variable in class com.xinapse.filter.AbstractKernelFilter
The boundary condition for the filter.
BDUS - Enum constant in enum class com.xinapse.dicom.Modality
Bone densitometry (ultrasound) Modality.
BETA - Enum constant in enum class com.xinapse.multisliceimage.Analyze.NIFTIIntent
[C2, chap 25] Beta distribution (2 params): p1=a, p2=b.
BI - Enum constant in enum class com.xinapse.dicom.Modality
Biomagnetic imaging Modality; store as secondary capture.
BICUBIC - Enum constant in enum class com.xinapse.image.RenderingInterpolationType
The RenderingInterpolationType for bi-cubic interpolation.
BILINEAR - Enum constant in enum class com.xinapse.image.RenderingInterpolationType
The RenderingInterpolationType for bi-linear interpolation.
BINARY - Enum constant in enum class com.xinapse.image.PixelDataType
PixelDataType for 1-bit per pixel.
BINARY - Enum constant in enum class com.xinapse.multisliceimage.Analyze.ANZPixFormat
ANZPixFormat for binary (1-bit) pixel values.
BINOM - Enum constant in enum class com.xinapse.multisliceimage.Analyze.NIFTIIntent
[U, chap 3] Binomial distribution (2 params):
p1 = number of trials, p2 = probability per trial.
Prob(x) = (p1 choose x) * p2^x * (1-p2)^(p1-x), for x=0,1,...,p1.
binWidth - Variable in class com.xinapse.image.Histogram.BinSpec
The bin width.
BIRTH_DATE_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the patient's birth date.
BitSet - 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.
BitSet(BitSet, OutputStream) - Static method in class com.xinapse.io.Output
Writes a BitSet as individual bits to a OutputStream strm.
BitSet(BitSet, RandomAccessFile, int) - Static method in class com.xinapse.io.Output
Writes a BitSet as individual bits to a RandomAccessFile f.
BitSet(DataInputStream, BitSet) - Static method in class com.xinapse.io.Input
Reads a BitSet from a DataInputStream strm, ensuring that blocking occurs until all values have been read.
BitSet(InputStream, BitSet) - Static method in class com.xinapse.io.Input
Reads a BitSet from a InputStream 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 BitSet from a RandomAccessFile f, ensuring that blocking occurs until all values have been read.
BLUE - Static variable in class com.xinapse.image.ColourMapping
The ColourMapping representing a blue intensity scale.
BLUE_FORMULA_OPTION - Static variable in class com.xinapse.filter.ColourImageFilter
A public Option to specify the formula used to calculate the new blue component values in the output image.
BLUR_FWHM - Static variable in class com.xinapse.filter.GaussianBlurFilter
A public Option to specify that the FWHM of an isotropic Gaussian blur filter.
BMD - Enum constant in enum class com.xinapse.dicom.Modality
Bone Mineral Densitometry (X-Ray) Modality.
BNegativeHandle - Class in com.xinapse.multisliceimage.roi
A Class representing a Handle at the negative end of axis B on an EllipticalROI.
BNegativeHandle(int, int, int) - Constructor for class com.xinapse.multisliceimage.roi.BNegativeHandle
Creates a new BNegativeHandle at the location (x,y) with the given size in screen pixels.
BODY_PART_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the imaged body part.
BoundaryCondition - Enum Class in com.xinapse.image
An enumeration of possible boundary conditions when applying, for example, spatial filters and interpolators.
BPositiveHandle - Class in com.xinapse.multisliceimage.roi
A Class representing a Handle at the positive end of axis B on an EllipticalROI.
BPositiveHandle(int, int, int) - Constructor for class com.xinapse.multisliceimage.roi.BPositiveHandle
Creates a new BPositiveHandle at the location (x,y) with the given size in screen pixels.
BTOKEN - Static variable in class com.xinapse.multisliceimage.roi.EllipticalROI
The token written to ROI output files to represent the second semi-major axis length.
busyCursors() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
 
busyCursors() - Method in class com.xinapse.image.ImageSelectionPanel
 
busyCursors() - Method in class com.xinapse.image.MultipleImageSelectionPanel
 
busyCursors() - Method in interface com.xinapse.util.MessageShower
Sets the cursor for this MessageShower to indicate that an operation is in progress.
busyCursors() - Method in class com.xinapse.util.MultiContrastAnalysisFrame
 
BUTTON_ICON_SIZE - Static variable in class com.xinapse.multisliceimage.roi.ROI
The standard (square) size for icons on ROI creation buttons.
BY_AVERAGING - Enum constant in enum class com.xinapse.image.SubSampleType
Sub-sampling by averaging across nearest pixels.
Byte(byte, OutputStream) - Static method in class com.xinapse.io.Output
Write a single byte value to an OutputStream strm.
Byte(byte, RandomAccessFile) - Static method in class com.xinapse.io.Output
Write a single byte value to a RandomAccessFile f.
BYTE - Enum constant in enum class com.xinapse.image.PixelDataType
PixelDataType for signed byte.
BYTE - Enum constant in enum class com.xinapse.multisliceimage.UNC.UNCPixFormat
UNCPixFormat for unsigned byte (8-bit) pixel values.
ByteArray(byte[], OutputStream) - Static method in class com.xinapse.io.Output
Write an array of byte values to a OutputStream strm.
ByteArray(InputStream, int) - Static method in class com.xinapse.io.Input
Reads an array of bytes from a 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 RandomAccessFile f, ensuring that blocking occurs until all values have been read.
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, int, PixelDataType, ComplexMode) - Static method in class com.xinapse.image.Histogram
Calculates a suitable bin width, and minimum bin value for a histogram, for the given type of pixels over the given intensity range.
calcBins(double, double, PixelDataType, ComplexMode) - Static method in class com.xinapse.image.Histogram
Calculates a suitable bin width, number of bins, and minimum bin value for a histogram, for the given type of pixels over the given intensity range.
CanAddROIToFrame - Interface in com.xinapse.multisliceimage.roi
An interface to indicate that a JFrame can receive ROIs.
cancel() - Method in class com.xinapse.image.ColourVolumeInterpolator
Signal to this ColourVolumeInterpolator to stop the current interpolation (if an interpolation is in progress) as soon as possible.
cancel() - Method in class com.xinapse.image.VolumeInterpolator
Signal to this VolumeInterpolator to stop the current interpolation (if an interpolation is in progress) as soon as possible, and throw a CancellationException.
cancel() - Method in class com.xinapse.util.CancellableThread
Signal the CancellableThread to stop any processing and return.
CancellableThread - Class in com.xinapse.util
A class to implement a cancellable Thread.
CancellableThread() - Constructor for class com.xinapse.util.CancellableThread
 
CancellableThread.Flag - Class in com.xinapse.util
A flag that can be set to indicate that a cancellation has taken place.
CANCELLED_BY_USER - Enum constant in enum class com.xinapse.platform.ExitStatus
Exit status when the program has been cancelled by the user (2).
CancelledException - Exception in com.xinapse.util
Thrown when an action is cancelled by the user.
CancelledException() - Constructor for exception com.xinapse.util.CancelledException
Constructs a CancelledException without a detail message, and without a user object.
CancelledException(String) - Constructor for exception com.xinapse.util.CancelledException
Constructs a CancelledException with the specified detail message.
CancelledException(String, List<ROI>) - Constructor for exception com.xinapse.util.CancelledException
Constructs a CancelledException with the specified detail message, and an associated User Object.
CARDIAC_ELECTROPHYSIOLOGY - Enum constant in enum class com.xinapse.dicom.Modality
Cardiac electrophysiology Modality.
CardiacAnalysis - Interface in com.xinapse.apps.cardiac
An interface implemented by classes that can perform cardiac analysis.
CardiacAnalysis.SpecifierPanel - Class in com.xinapse.apps.cardiac
A JPanel that can be used to specify cardiac analysis parameters.
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 MonitorWorker has been cancelled.
checkCancelled(Integer) - Method in class com.xinapse.util.MonitorWorker
Tests whether this MonitorWorker has been cancelled, and sets the progress through this operation.
checkCancelled(String) - Method in class com.xinapse.util.MonitorWorker
Tests whether this MonitorWorker has been cancelled.
checkCancelled(String, Integer) - Method in class com.xinapse.util.MonitorWorker
Tests whether this MonitorWorker has been cancelled, and sets the progress through this operation.
checkIndices(ReadableImage, int[]) - Static method in class com.xinapse.image.ImageUtils
Checks compatibility of the pixel indices that reference a particular pixel of an image.
checkMinMax(int, int, PixelDataType) - Static method in class com.xinapse.image.ImageUtils
Checks the integrity of the minimum and maximum pixel values taking into account the data type of the image.
CHI - Enum constant in enum class com.xinapse.multisliceimage.Analyze.NIFTIIntent
[C1, chap 18] Chi distribution (1 param): p1 = DOF.
CHISQ - Enum constant in enum class com.xinapse.multisliceimage.Analyze.NIFTIIntent
[C1, chap 18] Chi-squared (1 param): p1 = DOF.
CHISQ_NONC - Enum constant in enum class com.xinapse.multisliceimage.Analyze.NIFTIIntent
[C2, chap 29] Noncentral chi-squared statistic (2 params):
p1 = DOF, p2 = noncentrality parameter.
CINE_FLUOROGRAPHY_RET - Enum constant in enum class com.xinapse.dicom.Modality
Cine fluorography Modality (RETIRED).
clear() - Method in class com.xinapse.util.BitSet
Sets all bits in the set to false.
clear(int) - Method in class com.xinapse.util.BitSet
Removes the integer bitIndex from this set.
clear(int, int) - Method in class com.xinapse.util.BitSet
Sets the bits between from (inclusive) and to (exclusive) to false.
clearAllImages() - Method in class com.xinapse.image.ImageGrid
Clear all images from this ImageGrid.
clearAllImages() - Method in class com.xinapse.image.ImageSelectionGroupPanel
Clear all images from this ImageSelectionGroupPanel.
clearDeletionHistory() - Method in class com.xinapse.multisliceimage.roi.ROI
Removed the deletion HistoryItem for this ROI.
clearFiles() - Method in class com.xinapse.image.MultipleImageSelectionPanel
Removes all files from the list.
clearFiles() - Method in class com.xinapse.image.SingleOrMultipleInputImageSelectionPanel
Clears the currently-set files names, so that the file names are un-initialised.
clearHisto() - Method in class com.xinapse.multisliceimage.roi.ROIStats
Clears (sets to null) the histogram for these ROIStats.
CLICK - Enum constant in enum class com.xinapse.multisliceimage.roi.InteractionType
InteractionType for a single click interaction.
CLICK_DRAG - Enum constant in enum class com.xinapse.multisliceimage.roi.InteractionType
InteractionType for a click, hold and drag interaction.
CLICK_OUTLINE - Enum constant in enum class com.xinapse.multisliceimage.roi.InteractionType
InteractionType for a click points/draw interaction.
CLICK_POINTS - Enum constant in enum class com.xinapse.multisliceimage.roi.InteractionType
InteractionType for a click points interaction.
CLICK_TYPE - Enum constant in enum class com.xinapse.multisliceimage.roi.InteractionType
InteractionType for a click, type, press return interaction.
clone() - Method in class com.xinapse.geom3d.AffineTransform3D
Creates and returns a copy of this AffineTransform3D.
clone() - Method in class com.xinapse.image.ColourMapping
Returns an exact copy of this ColourMapping.
clone() - Method in class com.xinapse.image.PixArray
Returns a new PixArray object that contains pixel values and properties that are the same as the original.
clone() - Method in class com.xinapse.multisliceimage.Analyze.AFNIExtendedData
 
clone() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Header
Returns an exact copy of this Analyze header.
clone() - Method in class com.xinapse.multisliceimage.Analyze.ANZHeader
Creates a deep copy of this Analyze header.
clone() - Method in class com.xinapse.multisliceimage.Analyze.CommentExtendedData
 
clone() - Method in class com.xinapse.multisliceimage.Analyze.DICOMExtendedData
 
clone() - Method in class com.xinapse.multisliceimage.Analyze.InfoExtendedData
 
clone() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
Returns an exact copy of this NIFTI-1 header.
clone() - Method in class com.xinapse.multisliceimage.Analyze.UnknownExtendedData
 
clone() - Method in class com.xinapse.multisliceimage.Analyze.XCEDEExtendedData
 
clone() - Method in class com.xinapse.multisliceimage.Analyze.XMLExtendedData
 
clone() - Method in class com.xinapse.multisliceimage.MultiSliceImage
Returns a copy of this MultiSliceImage.
clone() - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
clone() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
clone() - Method in class com.xinapse.multisliceimage.roi.Handle
 
clone() - Method in class com.xinapse.multisliceimage.roi.HistoryItem
 
clone() - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
clone() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
clone() - Method in class com.xinapse.multisliceimage.roi.IrregularROIInProgress
 
clone() - Method in class com.xinapse.multisliceimage.roi.LineROI
 
clone() - Method in class com.xinapse.multisliceimage.roi.Marker
 
clone() - Method in class com.xinapse.multisliceimage.roi.OpenSplineROI
 
clone() - Method in class com.xinapse.multisliceimage.roi.RadialDivider
 
clone() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
clone() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns a clone of this ROI.
clone() - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
clone() - Method in class com.xinapse.multisliceimage.roi.Text
 
clone() - Method in class com.xinapse.util.BitSet
Create a clone of this bit set, that is an instance of the same class and contains the same elements.
clone() - Method in class com.xinapse.util.InfoItem
Returns a copy of this InfoItem.
clone() - Method in class com.xinapse.util.InfoList
Makes a copy of this InfoList.
close() - Method in interface com.xinapse.image.ReadableImage
Closes an image and frees up resources.
close() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
Closes an ANZImage and frees up resources.
close() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Closes a NIFTIImage and frees up resources.
close() - Method in class com.xinapse.multisliceimage.roi.SplineROI
Closes this SplineROI so that the outline is a closed path.
close() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
Closes a UNCImage and frees up resources.
close() - Method in class com.xinapse.util.IndeterminateProgressMonitor
Indicate that the operation is complete.
CLOSE - Enum constant in enum class com.xinapse.filter.MorphologicalOperator.Op
Closing operation.
closed - Variable in class com.xinapse.multisliceimage.roi.SplineROI
Whether the SplineROI is closed.
closestPoints(IrregularROI) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Returns the line that represents the line that joins the two points that are closest together (in space) between this IrregularROI and another IrregularROI.
cm - Variable in class com.xinapse.image.ColourMapping
The IndexColorModel used to contain the mapping.
CODE - Static variable in class com.xinapse.multisliceimage.Analyze.AFNIExtendedData
The ecode for an AFNI header attributes extension.
CODE - Static variable in class com.xinapse.multisliceimage.Analyze.CommentExtendedData
The ecode for an arbitrary non-NUL ASCII text extension.
CODE - Static variable in class com.xinapse.multisliceimage.Analyze.DICOMExtendedData
The ecode for a DICOM format extension.
CODE - Static variable in class com.xinapse.multisliceimage.Analyze.InfoExtendedData
The ecode for an InfoExtendedData extension.
CODE - Static variable in class com.xinapse.multisliceimage.Analyze.XCEDEExtendedData
The ecode for an XCEDE metadata extension.
CODE - Static variable in class com.xinapse.multisliceimage.Analyze.XMLExtendedData
The ecode for an arbitrary non-NULL ASCII text extension.
coerce(Object, PixelDataType, boolean) - Method in enum class com.xinapse.image.PixelDataType
Coerce pixels of this PixelDataType to a new PixelDataType.
coerce(Object, PixelDataType, int, int, ComplexMode, boolean) - Method in enum class com.xinapse.image.PixelDataType
Coerce pixels of this PixelDataType to a new PixelDataType.
coerce(Object, PixelDataType, ComplexMode, boolean) - Method in enum class com.xinapse.image.PixelDataType
Coerce pixels of this PixelDataType to a new PixelDataType.
coerceOneValue(Object, PixelDataType) - Method in enum class com.xinapse.image.PixelDataType
Coerces a single pixel value to the given PixelDataType.
coerceOneValue(Object, PixelDataType, ComplexMode) - Method in enum class com.xinapse.image.PixelDataType
Coerce a single pixel of this PixelDataType to a new PixelDataType.
COLOR - Enum constant in enum class com.xinapse.multisliceimage.UNC.UNCPixFormat
UNCPixFormat for colour pixel (16-bit) values.
COLOR_FLOW_DOPPLER_RET - Enum constant in enum class com.xinapse.dicom.Modality
Color Doppler imaging Modality (RETIRED).
COLORPACKED - Enum constant in enum class com.xinapse.multisliceimage.UNC.UNCPixFormat
UNCPixFormat for packed colour (r,g,b,n) (4x8-bit) pixel values.
COLOUR_MAPPING_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the colour mapping.
ColourImageFilter - Class in com.xinapse.filter
A SpatialFilter for altering the colour components of a colour image.
ColourImageFilter(String, String, String) - Constructor for class com.xinapse.filter.ColourImageFilter
Creates a new ColourImageFilter based on three formulae used to compute the red, green and blue colour components.
ColourImageFilter.ColourImageFilterSpecifierPanel - Class in com.xinapse.filter
A FilterSpecifierPanel for a colour image filter.
colourLookup(int, int, Object, int, PixelDataType, byte[], double, double, boolean, BitSet, boolean, ComplexMode) - Method in class com.xinapse.image.ColourMapping
Converts an array of pixel intensity values into the byte values that can then be used as an argument in the BufferedImage.getRaster().setDataElements() method of BufferedImage to put pixel colours to a BufferedImage Object.
colourLookupColourPacked(int, int, byte[], int, int[], short, short, boolean, BitSet, boolean, byte, boolean) - Static method in class com.xinapse.image.ColourMapping
Converts an array of pixel intensity values into the int values that can then be used as an argument in the BufferedImage.getRaster().setDataElements() method of BufferedImage to put pixel colours to a BufferedImage Object.
colourLookupRGBByPlane(int, int, byte[], int, int[], short, short, boolean, BitSet, boolean, byte, boolean) - Static method in class com.xinapse.image.ColourMapping
Converts an array of pixel intensity values into the int values that can then be used as an argument in the BufferedImage.getRaster().setDataElements() method of BufferedImage to put pixel colours to a BufferedImage Object.
colourLookupRGBInterlaced(int, int, byte[], int, int[], short, short, boolean, BitSet, boolean, byte, boolean) - Static method in class com.xinapse.image.ColourMapping
Converts an array of pixel intensity values into the int values that can then be used as an argument in the BufferedImage.getRaster().setDataElements() method of BufferedImage to put pixel colours to a BufferedImage Object.
ColourMapping - Class in com.xinapse.image
The ColourMapping class represents a mapping from pixel presentation values (PPVs) to colours that are shown on a display device, such as a computer monitor.
COLOURPACKED - Enum constant in enum class com.xinapse.image.PixelDataType
PixelDataType for colour packed (UNC).
COLOURTOKEN - Static variable in class com.xinapse.multisliceimage.roi.ROIStreamTokenizer
The token written to show the ROI colour.
ColourVolumeInterpolator - Class in com.xinapse.image
An interpolator for a 3- (or fewer) dimensional array of pixels in a Colour image.
ColourVolumeInterpolator(byte[], PixelDataType, int, int, int, float, float, float, BoundaryCondition, Color, InterpolationType) - Constructor for class com.xinapse.image.ColourVolumeInterpolator
Creates a new ColourVolumeInterpolator for a block of colour (R,G,B) pixel samples.
ColourVolumeInterpolator(ColourVolumeInterpolator, InterpolationType) - Constructor for class com.xinapse.image.ColourVolumeInterpolator
Returns a new ColourVolumeInterpolator, constructed from an existing one.
com.xinapse.filter - package com.xinapse.filter
The package com.xinapse.filter is used to filter images.
com.xinapse.image - package com.xinapse.image
The package com.xinapse.image contains utilities for handling different types of image that can be handled by Jim.
com.xinapse.image.template - package com.xinapse.image.template
Provides access to built-in and user-selected template images, and utilities related to them.
com.xinapse.io - package com.xinapse.io
Provides basic input/output of primitive data types, with provision to read and write values to machines with different byte orders.
com.xinapse.multisliceimage - package com.xinapse.multisliceimage
The package com.xinapse.multisliceimage is used to represent and handle multi-dimensional Medical Images in different file formats.
com.xinapse.multisliceimage.Analyze - package com.xinapse.multisliceimage.Analyze
The package com.xinapse.multisliceimage.Analyze is used to represent and handle the Analyze Medical Image file format, and the NIFTI-1 and NIFTI-2 extensions 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 Class in com.xinapse.multisliceimage.roi
An enumeration of possible ROI combination operations that can be be applied to a set of ROIs to create a single resulting ROI.
CombineMode.Panel - Class in com.xinapse.multisliceimage.roi
A JPanel for selecting a CombineMode.
ComboBox() - Constructor for class com.xinapse.dicom.PatientPosition.ComboBox
ComboBox() - Constructor for class com.xinapse.dicom.PulseSequenceType.ComboBox
ComboBox() - Constructor for class com.xinapse.image.RenderingInterpolationType.ComboBox
ComboBox() - Constructor for class com.xinapse.multisliceimage.roi.ContourMode.ComboBox
Create a new ContourMode.ComboBox for selecting a ContourMode.
ComboBox(boolean) - Constructor for class com.xinapse.dicom.Modality.ComboBox
Creates a new Modality.ComboBox.
CommentExtendedData - Class in com.xinapse.multisliceimage.Analyze
This class handles the NIFTI 1.1 non-NUL ASCII text extended data.
compare(ROI, ROI) - Method in class com.xinapse.multisliceimage.roi.StatsComparator
Compares the statistics for two ROIs for order.
compareTo(ReadableImage.Position) - Method in class com.xinapse.image.ReadableImage.Position
 
compareTo(ICBMLabel) - Method in class com.xinapse.image.template.ICBMLabel
 
Complex - Class in com.xinapse.image
A complex (real, imaginary) number.
Complex() - Constructor for class com.xinapse.image.Complex
 
COMPLEX - Enum constant in enum class com.xinapse.image.PixelDataType
PixelDataType for complex (2x32-bit float in real/imaginary interlaced pairs).
COMPLEX - Enum constant in enum class com.xinapse.multisliceimage.Analyze.ANZPixFormat
ANZPixFormat for complex (2 x 32-bit float) pixel values.
COMPLEX - Enum constant in enum class com.xinapse.multisliceimage.UNC.UNCPixFormat
UNCPixFormat for complex float pixel values.
ComplexMode - Enum Class in com.xinapse.image
An enumeration of the possible display/calculation modes for complex numbers.
complexWeights - Variable in class com.xinapse.filter.FixedWeightsComplexKernelFilter
The 3-D array of weights in the kernel.
COMPRESSED_EXTENSION - Static variable in class com.xinapse.multisliceimage.Analyze.ANZHeader
The file extension for Analyze header files in lower case form.
COMPRESSED_EXTENSION - Static variable in class com.xinapse.multisliceimage.Analyze.ANZImage
The file extension for Analyze image files in lower case form.
COMPRESSED_EXTENSION - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIImage
The file extension for compressed NIFTI image files.
COMPRESSED_PROPERTY_KEY - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Image
The property value key for setting whether Analyze 7.5 images should be stored compressed, or uncompressed.
COMPRESSED_PROPERTY_KEY - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIImage
The property value key for setting whether NIFTI images should be stored compressed, or uncompressed.
COMPRESSED_UPPERCASE_EXTENSION - Static variable in class com.xinapse.multisliceimage.Analyze.ANZHeader
The file extension for Analyze header files in upper case form.
COMPRESSED_UPPERCASE_EXTENSION - Static variable in class com.xinapse.multisliceimage.Analyze.ANZImage
The file extension for Analyze image files in upper case form.
COMPUTED_RADIOGRAPHY - Enum constant in enum class com.xinapse.dicom.Modality
Computed radigraphy imaging Modality.
COMPUTED_TOMOGRAPHY - Enum constant in enum class com.xinapse.dicom.Modality
X-ray computerised tomography imaging Modality.
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.
CONFLICTING_ARGUMENTS - Enum constant in enum class com.xinapse.platform.ExitStatus
Exit status when program arguments conflict with each other (15).
conj() - Method in class com.xinapse.image.Complex
Returns the complex conjugate of this complex number.
conj() - Method in class com.xinapse.image.DoubleComplex
 
conj() - Method in class com.xinapse.image.FloatComplex
 
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
Indicates whether this CurvedLineROI contains another ROI entirely within its borders.
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
Indicates whether this EllipticalROI contains another ROI entirely within its borders.
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Indicates whether this IrregularROI contains another ROI entirely within its borders.
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.LineROI
Indicates whether this LineROI contains another ROI entirely within its borders.
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.Marker
Indicates whether this Marker ROI contains another ROI entirely within its borders.
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Indicates whether this RadialDivider ROI contains another ROI entirely within its borders.
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.RectangularROI
Indicates whether this RectangularROI contains another ROI entirely within its borders.
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.ROI
Indicates whether this ROI entirely contains another ROI entirely within its borders.
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.SplineROI
Indicates whether this SplineROI contains another ROI entirely within its borders.
contains(ROI) - Method in class com.xinapse.multisliceimage.roi.VOI
Tests whether this volume of interest (VOI) contains an ROI.
containsVertex(Point2D) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Tests whether the supplied vertex location is one of the vertex locations for this ROI.
contiguousTimes - Variable in class com.xinapse.apps.cardiac.SelectableCardiacAnalysis
True if time points are contiguous in the input image(s).
ContourMode - Enum Class in com.xinapse.multisliceimage.roi
An enumeration of the modes of operation of intensity level contour generation.
ContourMode.ComboBox - Class in com.xinapse.multisliceimage.roi
A JComboBox for selecting a ContourMode.
ContourROI - Class in com.xinapse.multisliceimage.roi
A class for edge detection and contour following.
ContourWorker - Class in com.xinapse.multisliceimage.roi
A MonitorWorker for performing edge detection and contouring from a seed point.
ContourWorker(Point3i, ReadableImage, ComplexMode, ContourMode, double, IntensityRelation, boolean, short, byte, boolean, boolean, CanAddROIToFrame, boolean) - Constructor for class com.xinapse.multisliceimage.roi.ContourWorker
Instantiates a new ContourWorker that will perform contouring from the supplied seed pixel.
ConvergenceException - Exception in com.xinapse.numerical
Signals that an iterative procedure has failed to converge.
ConvergenceException() - Constructor for exception com.xinapse.numerical.ConvergenceException
Constructs a ConvergenceException with "failed to converge" as its detail message.
ConvergenceException(int) - Constructor for exception com.xinapse.numerical.ConvergenceException
Constructs a ConvergenceException with a detail message that indicates the number of iterations tried.
ConvergenceException(String) - Constructor for exception com.xinapse.numerical.ConvergenceException
Constructs a ConvergenceException with the specified detail message.
convolve(FixedWeightsComplexKernelFilter) - Method in class com.xinapse.filter.FixedWeightsComplexKernelFilter
Convolves this FixedWeightsComplexKernelFilter with another FixedWeightsComplexKernelFilter to create a new FixedWeightsComplexKernelFilter.
convolve(FixedWeightsKernelFilter) - Method in class com.xinapse.filter.FixedWeightsKernelFilter
Convolves this FixedWeightsKernelFilter with another FixedWeightsKernelFilter to create a new FixedWeightsKernelFilter.
copyInfo(UNCImage) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
Copies all the info fields to another image.
copyPixels(Object) - Method in enum class com.xinapse.image.PixelDataType
Copies the pixel samples to a new array of the correct type for this type of pixel.
copyPixels(Object, int, Object) - Method in enum class com.xinapse.image.PixelDataType
Copies the pixel samples to an array of the correct type for this type of pixel.
copyPixels(Object, Object) - Method in enum class com.xinapse.image.PixelDataType
Copies the pixel samples to an array of the correct type for this type of pixel.
copyPixels(Object, Object, int) - Method in enum class com.xinapse.image.PixelDataType
Copies the pixel samples to an array of the correct type for this type of pixel.
copyResize(int[], boolean) - Method in class com.xinapse.filter.FixedWeightsComplexKernelFilter
Copies a FixedWeightsComplexKernelFilter, possibly resizing it, creating a new FixedWeightsComplexKernelFilter.
copyResize(int[], boolean) - Method in class com.xinapse.filter.FixedWeightsKernelFilter
Copies a FixedWeightsKernelFilter, possibly resizing it, creating a new FixedWeightsKernelFilter.
CornerHandle - Class in com.xinapse.multisliceimage.roi
An abstract Class representing a Handle at one of the four corners of an ROI.
CornerHandle(int, int, int) - Constructor for class com.xinapse.multisliceimage.roi.CornerHandle
Creates a new CornerHandle at the location (x,y) with the given size in screen pixels.
CORONAL - Enum constant in enum class com.xinapse.image.MostLikePlane
The MostLikePlane corresponding to a coronal orientation.
CORREL - Enum constant in enum class com.xinapse.multisliceimage.Analyze.NIFTIIntent
[C2, chap 32] Correlation coefficient R (1 param):
p1 = degrees of freedom;
R/sqrt(1-R*R) is t-distributed with p1 DOF.
CREATE - Enum constant in enum class com.xinapse.multisliceimage.roi.HistoryType
HistoryType for ROI creation.
CREATE_NON_FLIPPED_PROPERTY_KEY - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Header
The property value key for setting whether newly-created Analyze 7.5 images should have a non-flipped orientation.
crop(ReadableImage, int[][], MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Crops a WritableImage to produce a new image.
CT_PROTOCOL - Enum constant in enum class com.xinapse.dicom.Modality
X-ray computerised tomography protocol Modality.
CubicSplineInterpolator - Class in com.xinapse.numerical
A cubic spline interpolator for tabulated values of (x,y).
CubicSplineInterpolator(double[], double[]) - Constructor for class com.xinapse.numerical.CubicSplineInterpolator
Create a new CubicSplineInterpolator interpolator, from arrays of tabulated x and y values.
CULPOSCOPY_RET - Enum constant in enum class com.xinapse.dicom.Modality
Culcoscopy Modality (RETIRED).
currentWorkingDirectory - Variable in class com.xinapse.image.ImageSelectionPanel
The current working directory.
CurvedLineROI - Class in com.xinapse.multisliceimage.roi
A represention of a planar curved line on an image.
CurvedLineROI(double[], double[], int, ROIState) - Constructor for class com.xinapse.multisliceimage.roi.CurvedLineROI
Creates a new CurvedLineROI with the coordinates of the points forming the line given by the x and y arrays in mm coordinates.
CurvedLineROI(List<Point2D.Double>, 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.
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.
CUT - Enum constant in enum class com.xinapse.multisliceimage.roi.ROIEditAction
Cut an ROI to the clipboard.
CYAN - Static variable in class com.xinapse.image.ColourMapping
The ColourMapping representing a cyan intensity scale.
CYSTOSCOPY_RET - Enum constant in enum class com.xinapse.dicom.Modality
Cytoscopy Modality (RETIRED).

D

DATA_FORMAT_ERROR - Enum constant in enum class com.xinapse.platform.ExitStatus
Exit status when data is in the wrong format (31).
DATABASE_ERROR - Enum constant in enum class com.xinapse.platform.ExitStatus
Exit status when there is an error accessing a database (120).
dataType - Variable in class com.xinapse.image.PixArray
The type of pixel that this PixArray stores.
dataType - Variable in class com.xinapse.image.VolumeInterpolator
The PixelDataType of the pixel values to be interpolated.
DCEMRIModel - Class in com.xinapse.apps.perfusion
The superclass of models that can be fitted to DCE-MRI data.
DCEMRIModel(String, String, String[], String[]) - Constructor for class com.xinapse.apps.perfusion.DCEMRIModel
Constructor used by sub-classes.
deallocate() - Static method in class com.xinapse.io.DirectBufferDeallocator
Deallocate memory associated with all ByteBuffers.
DEFAULT - Static variable in enum class com.xinapse.image.InputConfigurationType
The default InputConfigurationType.
DEFAULT - Static variable in enum class com.xinapse.image.RenderingInterpolationType
The default RenderingInterpolationType.
DEFAULT - Static variable in enum class com.xinapse.image.template.WeightingType
The default WeightingType for applications.
DEFAULT_COMPLEX_MODE - Static variable in enum class com.xinapse.image.ComplexMode
The default ComplexMode for applications.
DEFAULT_COMPRESSED - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Whether to store Analyze 7.5 images compressed by default.
DEFAULT_COMPRESSED - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Whether to store NIFTI images compressed by default.
DEFAULT_CREATE_NON_FLIPPED - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Header
The default setting of whether newly-created Analyze 7.5 images should have a non-flipped orientation.
DEFAULT_DO_NOT_FLIP_FLIPPED - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Header
The default setting of whether not to flip vertically an image with a flipped Analyze orientation.
DEFAULT_FLIP_NON_FLIPPED - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Header
The default setting of whether to flip vertically an image with a non-flipped Analyze orientation.
DEFAULT_FSL_COMPATIBLE_NIFTI - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
The default setting of whether NIFTI-1 images that have qform and sform orientation both unset should be read as having an increasing a patient left coordinate value with stored pixel data column number, and whether NIFTI-1 images should be prevented from being written without orientation information.
DEFAULT_GAMMA - Static variable in class com.xinapse.image.ColourMapping
The default gamma value of the computer display.
DEFAULT_IMAGE_CLASS - Static variable in class com.xinapse.image.ImageUtils
The default image class to work with, if the user has no Preference.
DEFAULT_IMAGE_PREVIEW - Static variable in class com.xinapse.image.ImagePreview
The default setting for whether to generate an image preview thumbnail.
DEFAULT_INTENSITY_RELATION - Static variable in enum class com.xinapse.util.IntensityRelation
The default IntensityRelation.
DEFAULT_INTENSITY_RELATION - Static variable in class com.xinapse.util.IntensityRelation.IntensityRelationButton
The default IntensityRelation for applications.
DEFAULT_MAX_LUMINANCE - Static variable in class com.xinapse.image.ColourMapping
The default luminance of the computer display for a digital driver level (DDL) of 255, including the effects of ambient light.
DEFAULT_MIN_LUMINANCE - Static variable in class com.xinapse.image.ColourMapping
The default luminance of the computer display for a digital driver level (DDL) of zero, including the effects of ambient light.
DEFAULT_MIN_RADIUS - Static variable in class com.xinapse.multisliceimage.roi.SmootherWorker
The default minimum radius of curvature for sections.
DEFAULT_N_STEADY_STATES - Static variable in class com.xinapse.dynamic.AbstractDynamicFrame
The default number of steady state images, if not set in user preferences.
DEFAULT_NIFTI_ONE_FILE - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Whether to store NIFTI images in one file (.nii) by default.
DEFAULT_OVERWRITE - Static variable in class com.xinapse.multisliceimage.UNC.UNCImage
The default setting for the whether UNC images can be overwritten.
DEFAULT_SAVE_FSL_ORIENT - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
The default setting of whether NIFTI-1 images should be saved with an orientation that is compatible with FSL, where possible.
DEFAULT_SAVE_SPM_ORIENT - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
The default setting of whether NIFTI-1 images should be saved with an orientation that is compatible with SPM, where possible.
DEFAULT_THREE_D - Static variable in class com.xinapse.filter.GaussianBlurFilter.GaussianBlurSpecifierPanel
The default setting for whether a GaussianBlurFilter should be in 3-D.
DEFAULT_THREE_D - Static variable in class com.xinapse.filter.PatchSimilarityFilter.PatchSimilaritySpecifierPanel
The default setting for whether a PatchSimilarityFilter 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.
DELETE - Enum constant in enum class com.xinapse.multisliceimage.roi.HistoryType
HistoryType for ROI deletion.
DELETE - Enum constant in enum class com.xinapse.multisliceimage.roi.ROIEditAction
Delete an ROI.
DELETED - Enum constant in enum class com.xinapse.multisliceimage.roi.ROIState
ROIState for a deleted ROI.
DELETED_SELECTED - Enum constant in enum class com.xinapse.multisliceimage.roi.ROIState
ROIState for a deleted ROI that is selected by the user.
deleteImage(String, Class<? extends ReadableImage>) - Static method in class com.xinapse.image.ImageUtils
Attempts to delete an image of the given Class<? extends WritableImage> with the given name.
deleteUserColourMapping(ColourMapping) - Static method in class com.xinapse.image.ColourMapping
Deletes one of the user-defined ColourMappings and removes it from the list maintained in the user preferences.
deleteVertex(Handle) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
deleteVertex(Handle) - Method in interface com.xinapse.multisliceimage.roi.EditableOutlineROI
Delete a point on the outline of this EditableOutlineROI that is under a handle.
deleteVertex(Handle) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
deleteVertex(Handle) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
deleteVertex(Handle) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
deregister() - Method in class com.xinapse.image.IntensityPresetsMenu
Deregister this IntensityPresetsMenu so that it will no longer be updated when the list of user-defined presets changes.
DESCRIPTION_LEN - Static variable in class com.xinapse.multisliceimage.Analyze.ANZHeader
The length in bytes of the description field.
DESIGN_SIZE_LARGE - Static variable in class com.xinapse.multisliceimage.roi.Handle
The design size of Handles (in screen pixels) when they are drawn large, with no HiDPI scaling.
DESIGN_SIZE_SMALL - Static variable in class com.xinapse.multisliceimage.roi.Handle
The design size of Handles (in screen pixels) when they are drawn small, with no HiDPI scaling.
DEVTOKEN - Static variable in class com.xinapse.multisliceimage.roi.ROIStreamTokenizer
The token written to show the ROI intensity "deviation" in "standard deviation".
DIAPHANOGRAPHY - Enum constant in enum class com.xinapse.dicom.Modality
Diaphonography imaging Modality.
Dice - Class in com.xinapse.multisliceimage.roi
A class for calculating Dice similarity scores between two sets of ROIs.
Dice(List<ROI>, List<ROI>, float) - Constructor for class com.xinapse.multisliceimage.roi.Dice
Calculate the Dice similarity scores between two sets of ROIs.
diceKappa - Variable in class com.xinapse.image.template.ICBMLabel
The Dice Kappa score for the brain region.
DICOM_FORMAT_ERROR - Enum constant in enum class com.xinapse.platform.ExitStatus
Exit status when a badly-formatted DICOM object is encountered (50).
DICOMExtendedData - Class in com.xinapse.multisliceimage.Analyze
This class handles NIFTI 1.1 DICOM extended data.
DIGITAL_FLUOROSCOPY_RET - Enum constant in enum class com.xinapse.dicom.Modality
Digital fluoroscopy Modality (RETIRED).
DIGITAL_MICROSCOPY_RET - Enum constant in enum class com.xinapse.dicom.Modality
Digital microscopy Modality (RETIRED).
DIGITAL_RADIOGRAPHY - Enum constant in enum class com.xinapse.dicom.Modality
Digital radiography image Modality.
DIGITAL_SUBTRACTION_ANGIOGRAPHY_RET - Enum constant in enum class com.xinapse.dicom.Modality
Digital subtraction angiography Modality..
dilate(double) - Method in class com.xinapse.multisliceimage.roi.ROI
Dilates this ROI by the specified distance.
dilate(double, AtomicInteger, CancellableThread.Flag) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Dilation of a RadialDivider has no effect.
dilate(double, AtomicInteger, CancellableThread.Flag) - Method in class com.xinapse.multisliceimage.roi.Text
Dilation of a Text ROI has no effect.
DILATE - Enum constant in enum class com.xinapse.filter.MorphologicalOperator.Op
Dilate operation.
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.
DIR - Enum constant in enum class com.xinapse.dicom.PulseSequenceType
Double inversion-recovery pulse sequence type.
DirectBufferDeallocator - Class in com.xinapse.io
Class for deallocating memory associated with DirectByteBuffer.
DISCLAIMER_NOT_ACKNOWLEDGED - Enum constant in enum class com.xinapse.platform.ExitStatus
Exit status when the clinical use disclaimer has not been acknowledged by the user (101).
disposeImageData() - Method in interface com.xinapse.image.ReadableImage
Gives this image the option to free up resources by removing access to image data.
disposeImageData() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
disposeImageData() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
DISPVECT - Enum constant in enum class com.xinapse.multisliceimage.Analyze.NIFTIIntent
To signify that the vector value at each voxel is to be taken as a displacement field or vector:
- dataset must have a 5th dimension
- intent must be DISPVECT
- dim[5] must be the dimensionality of the displacment vector (e.g., 3 for spatial displacement, 2 for in-plane).
This intent is specifically for displacements.
divide(Complex) - Method in class com.xinapse.image.Complex
Divides this complex by another complex number, and returns the result.
divide(Complex) - Method in class com.xinapse.image.DoubleComplex
 
divide(Complex) - Method in class com.xinapse.image.FloatComplex
 
DO_NOT_FLIP_FLIPPED_PROPERTY_KEY - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Header
The property value key for setting whether not to flip flipped Analyze 7.5 images.
doAnalysis(CardiacFrame, RadialDivider[], Integer, ROI[][][], ReadableImage[], boolean, int, int, int, float, float, float, MonitorWorker) - Method in interface com.xinapse.apps.cardiac.CardiacAnalysis
Do the cardiac analysis.
doCalc(ROIPropagateFrame, ROI[][][], ReadableImage[], int, int, float, float) - Method in interface com.xinapse.apps.active.ROICalculation
Perform the calculation on the image/ROIs.
DOCUMENT - Enum constant in enum class com.xinapse.dicom.Modality
Document Modality.
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.LogicalOperationWorker
Perform the logical operation.
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.LogicalOperationWorker
 
done() - Method in class com.xinapse.multisliceimage.roi.MorphologicalOperationWorker
 
done() - Method in class com.xinapse.multisliceimage.roi.SmootherWorker
 
done() - Method in class com.xinapse.util.MonitorWorker
Overrides the done() method.
done() - Method in class com.xinapse.util.Twiddler
Indicates that the operation for which this twiddler was created is finished.
done(String) - Method in class com.xinapse.util.Twiddler
Indicates that the operation for which this twiddler was created is finished.
doPostLoad() - Method in class com.xinapse.image.InputImageSelectionPanel
Does nothing.
doPostLoad() - Method in class com.xinapse.image.MultipleImageSelectionPanel
 
Double(byte[], ByteOrder) - Static method in class com.xinapse.io.ByteSwap
Swap the byte order (if necessary) in a eight-byte array and return the value represented by the bit pattern as a double.
Double(double) - Static method in class com.xinapse.io.ByteSwap
Swap the byte order in a double and return the value represented by the bit pattern of the reversed bytes as a double.
Double(double, OutputStream, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single double to a OutputStream strm.
Double(double, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single double to a RandomAccessFile f.
Double(InputStream, ByteOrder) - Static method in class com.xinapse.io.Input
Reads a double value from a 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 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 OutputStream strm as a double primitive.
Double(Double, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single Double to a RandomAccessFile f as a double primitive.
DOUBLE - Enum constant in enum class com.xinapse.image.PixelDataType
PixelDataType for double (64-bit).
DOUBLE - Enum constant in enum class com.xinapse.multisliceimage.Analyze.ANZPixFormat
ANZPixFormat for double (64-bit) pixel values.
DOUBLE - Enum constant in enum class com.xinapse.multisliceimage.UNC.UNCPixFormat
UNCPixFormat for double-precision (64-bit) pixel values.
DoubleArray(double[], int, int, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of double values to a RandomAccessFile f.
DoubleArray(double[], OutputStream, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of double values to a OutputStream strm.
DoubleArray(double[], RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of double values to a RandomAccessFile f.
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(InputStream, ByteOrder, int) - Static method in class com.xinapse.io.Input
Reads an array of double values from a InputStream 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 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 RandomAccessFile f ensuring that blocking occurs until all values have been read.
DoubleComplex - Class in com.xinapse.image
A complex (real, imaginary) number, with double precision.
DoubleComplex() - Constructor for class com.xinapse.image.DoubleComplex
Creates a new DoubleComplex number, with zero real and imaginary parts.
DoubleComplex(double, double) - Constructor for class com.xinapse.image.DoubleComplex
Creates a new DoubleComplex number, with the real and imaginary parts specified by the arguments.
DoubleComplex(Complex) - Constructor for class com.xinapse.image.DoubleComplex
Creates a new DoubleComplex number, with the real and imaginary parts copied from an existing Complex number.
DOUBLECOMPLEX - Enum constant in enum class com.xinapse.image.PixelDataType
PixelDataType for double complex (2x64-bit double in real/imaginary interlaced pairs).
DOUBLEDOUBLE - Enum constant in enum class com.xinapse.image.PixelDataType
PixelDataType for double double (128-bit) - not implemented.
DOUBLEDOUBLECOMPLEX - Enum constant in enum class com.xinapse.image.PixelDataType
PixelDataType for double double complex (2x128-bit double in real/imaginary interlaced pairs) - not implemented.
DoublePixArray - Class in com.xinapse.image
A representation of an array of double-precision pixels.
DoublePixArray(int, int[], PixelDataType) - Constructor for class com.xinapse.image.DoublePixArray
Creates an empty DoublePixArray object containing the number of pixels given by nDim and dims.
DoublePixArray(DataInputStream, ByteOrder, int, int[], PixelDataType) - Constructor for class com.xinapse.image.DoublePixArray
Creates an DoublePixArray object, with the pixel intensity data coming from DataInputStream s, and containing the number of pixels specified in nDim and dims.
DoublePixArray(RandomAccessFile, ByteOrder, int, int, int[], PixelDataType) - Constructor for class com.xinapse.image.DoublePixArray
Creates an DoublePixArray object, with the pixel intensity data coming from RandomAccessFile f, and containing the number of pixels specified in nDim and dims.
DoublePixArray(Object, int, int[], PixelDataType) - Constructor for class com.xinapse.image.DoublePixArray
Creates an empty DoublePixArray object with enough pixels to contain the whole of the image.
draw(Graphics) - Method in class com.xinapse.multisliceimage.roi.CentreHandle
Draws this Handle on the given Graphics context.
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) - Method in class com.xinapse.multisliceimage.roi.InsertionPointHandle
Draws this InsertionPointHandle using the given Graphics context.
draw(Graphics) - Method in class com.xinapse.multisliceimage.roi.VertexHandle
 
draw(Graphics, int, int, Rectangle, int, int, int, int, int, int, float, float, List<ROI>) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Draws this RadialDivider if it needs to be be drawn on screen.
draw(Graphics, Rectangle, int, int, int, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
draw(Graphics, Rectangle, int, int, int, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
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.SplineROI
 
draw(Graphics, Rectangle, int, int, int, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.Text
 
drawInOrthoView(Image, Point3f, Transform3D, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
drawInOrthoView(Image, Point3f, Transform3D, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
drawInOrthoView(Image, Point3f, Transform3D, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
drawInOrthoView(Image, Point3f, Transform3D, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
drawInOrthoView(Image, Point3f, Transform3D, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.Marker
 
drawInOrthoView(Image, Point3f, Transform3D, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
 
drawInOrthoView(Image, Point3f, Transform3D, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
drawInOrthoView(Image, Point3f, Transform3D, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.ROI
Draws this ROI on top of an orthogonal view of an image.
drawInOrthoView(Image, Point3f, Transform3D, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
drawInOrthoView(Image, Point3f, Transform3D, int, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.Text
 
drawRoamingResponseGraphs(List<XYDataSet>) - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Draws the graphs into the RoamingResponseDialog.
DUPLEX_DOPPLER_RET - Enum constant in enum class com.xinapse.dicom.Modality
Duplex Doppler imaging Modality (RETIRED).
DuplicateROIException - Exception in com.xinapse.multisliceimage.roi
Signals the attempted creation and addition of an identical duplicate ROI to an image.
DuplicateROIException() - Constructor for exception com.xinapse.multisliceimage.roi.DuplicateROIException
Constructs an DuplicateROIException without a detail message.
DuplicateROIException(String) - Constructor for exception com.xinapse.multisliceimage.roi.DuplicateROIException
Constructs an ROIException with the specified detail message.
DW_B_MATRIX_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the 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 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 diffusion-weighting gradient vector.
DynamicModel - Interface in com.xinapse.dynamic
An interface implemented by classes that can fit to dynamic signals that vary as a function of time.
DynamicModel.SpecifierPanel - Class in com.xinapse.dynamic
A JPanel that can be used to specify dynamic model parameters.
dynamicModelPanel - Variable in class com.xinapse.dynamic.AbstractDynamicFrame
The JPanel that contains the analysis setup.
DynamicResult - Class in com.xinapse.dynamic
An abstract result of a computation from a dynamic signal change.
DynamicResult(DynamicModel, float[], float, float[]) - Constructor for class com.xinapse.dynamic.DynamicResult
Used by sub-class constructors.

E

EastHandle - Class in com.xinapse.multisliceimage.roi
A Class representing a Handle on the East edge of an ROI.
EastHandle(int, int, int) - Constructor for class com.xinapse.multisliceimage.roi.EastHandle
Creates a new EastHandle at the location (x,y) with the given size in screen pixels.
ECHO_TIME_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the scan echo time.
ECHO_TRAIN_LENGTH_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the scan echo train length.
ECHOCARDIOGRAPHY_RET - Enum constant in enum class com.xinapse.dicom.Modality
Echocardiography Modality (RETIRED).
EDGE_SEEKING - Enum constant in enum class com.xinapse.multisliceimage.roi.ContourMode
Edge seeking to get the intensity level.
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.
EDIT_OUTLINE - Enum constant in enum class com.xinapse.multisliceimage.roi.ROIEditAction
Edit an ROI's outline.
EDIT_OUTLINE - Enum constant in enum class com.xinapse.multisliceimage.roi.ROIState
ROIState for a normal selected irregular ROI when its outline is editable.
EDITABLE - Enum constant in enum class com.xinapse.multisliceimage.roi.ROIState
ROIState for a normal, selected and editable ROI.
EditableOutlineROI - Interface in com.xinapse.multisliceimage.roi
An interface that ROIs implement if they have an editable outline shape with handles at each vertex.
ELECTROCARDIOGRAPHY - Enum constant in enum class com.xinapse.dicom.Modality
Elecrocardiography Modality.
EllipticalROI - Class in com.xinapse.multisliceimage.roi
A Class representing an elliptical region of an image.
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.
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(Point2D.Double, double, double, double) - 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.
ENDOSCOPY - Enum constant in enum class com.xinapse.dicom.Modality
Endoscopy imaging Modality.
ENHANCED_COMPUTED_TOMOGRAPHY - Enum constant in enum class com.xinapse.dicom.Modality
X-ray computerised tomography imaging Modality.
ENHANCED_MAGNETIC_RESONANCE - Enum constant in enum class com.xinapse.dicom.Modality
Enhanced magnetic resonance imaging Modality.
ENHANCED_POSITRON_EMISSION_TOMOGRAPHY - Enum constant in enum class com.xinapse.dicom.Modality
Enhanced positron emission tomography imaging Modality.
EP - Enum constant in enum class com.xinapse.dicom.PulseSequenceType
Echo-planar pulse sequence type.
equals(Object) - Method in class com.xinapse.filter.MorphologicalOperator
Tests whether the supplied argument is equal to this MorphologicalOperator.
equals(Object) - Method in class com.xinapse.image.ColourMapping
 
equals(Object) - Method in class com.xinapse.image.DoubleComplex
Determines whether another object is equal to this DoubleComplex number.
equals(Object) - Method in class com.xinapse.image.FloatComplex
Determines whether another object is equal to this FloatComplex number.
equals(Object) - Method in class com.xinapse.image.template.ICBMLabel
 
equals(Object) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
equals(Object) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
equals(Object) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
equals(Object) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
equals(Object) - Method in class com.xinapse.multisliceimage.roi.Marker
 
equals(Object) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
 
equals(Object) - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
equals(Object) - Method in class com.xinapse.multisliceimage.roi.ROI
Indicates whether some Object is equal to this ROI.
equals(Object) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
equals(Object) - Method in class com.xinapse.util.BitSet
Returns true if the obj is a bit set that contains exactly the same elements as this bit set, otherwise false.
ERASE - Enum constant in enum class com.xinapse.multisliceimage.roi.InteractionType
InteractionType for draw-to-erase interaction.
ERASE - Enum constant in enum class com.xinapse.multisliceimage.roi.ROIEditAction
Erase points from an ROI.
erasePoints(List<Point2D>, float, int, int, float, float) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
Erase points from this CurvedLineROI.
erasePoints(List<Point2D>, float, int, int, float, float) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Erase points from this IrregularROI.
ERODE - Enum constant in enum class com.xinapse.filter.MorphologicalOperator.Op
Erode operation.
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.
ESTIMATE - Enum constant in enum class com.xinapse.multisliceimage.Analyze.NIFTIIntent
To signify that the value at each voxel is an estimate of some parameter, set intent_code = NIFTI_INTENT_ESTIMATE.
exchangeROIs(List<ROI>, List<ROI>, ROIEditAction) - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Exchange one List of ROIs with another List of ROIs in this Frame.
exclusiveOr(ROI, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
exclusiveOr(ROI, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
exclusiveOr(ROI, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.Marker
 
exclusiveOr(ROI, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.ROI
Performs an exclusive OR operation on the shape of this ROI with another ROI.
exclusiveOr(List<ROI>, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.ROI
Performs an exclusive OR (XOR) operation on the shape of this ROI with another ROI.
ExitStatus - Enum Class in com.xinapse.platform
Exit status codes on program termination.
expi() - Method in class com.xinapse.image.Complex
Returns the exponential of this complex number multiplied by i.
expi() - Method in class com.xinapse.image.DoubleComplex
 
expi() - Method in class com.xinapse.image.FloatComplex
 
export(ReadableImage, String, ColourMapping, double, double, ComplexMode, int) - Method in class com.xinapse.image.ImageUtils
Returns an InputStream from which an external format image (such as JPEG, GIF etc.) can be read, producing the external format image from this WritableImage, by drawing all of the slices in a raster of slices.
export(ReadableImage, String, String, ColourMapping, double, double, ComplexMode, int) - Static method in class com.xinapse.image.ImageUtils
Writes an image to a disk file in a picture format (such as JPEG, GIF etc.), creating the disk image from this WritableImage, by drawing all of the slices in a raster of slices.
export(ReadableImage, String, ImageOutputStream, ColourMapping, double, double, ComplexMode, int) - Static method in class com.xinapse.image.ImageUtils
Writes an image to an ImageOutputStream in an external format (such as JPEG, GIF etc.), creating the disk image from this ReadableImage, by drawing all of the slices in a raster of slices.
extData - Variable in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
The extended data, if present.
extension - Variable in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
The NIFTI extension indicator, if present.
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.
EXTERNAL_CAMERA_PHOTOGRAPHY - Enum constant in enum class com.xinapse.dicom.Modality
External camera Modality.
EXTVAL - Enum constant in enum class com.xinapse.multisliceimage.Analyze.NIFTIIntent
[C2, chap 22] Extreme value type I (2 params):
p1 = location, p2 = scale
cdf(x) = exp(-exp(-(x-p1)/p2)).

F

Feret - Class in com.xinapse.multisliceimage.roi
A Class describing the minimum and maximum Feret's diameter.
FFDL - Enum constant in enum class com.xinapse.dicom.PatientPosition
PatientPosition indicating feet-first, decubitus left.
FFDR - Enum constant in enum class com.xinapse.dicom.PatientPosition
PatientPosition indicating feet-first, decubitus right.
FFP - Enum constant in enum class com.xinapse.dicom.PatientPosition
PatientPosition indicating feet-first, prone.
FFS - Enum constant in enum class com.xinapse.dicom.PatientPosition
PatientPosition indicating feet-first, supine.
FFTConvolutionFilter - Class in com.xinapse.filter
A convolution filter that uses the Fast Fourier Transform to perform the convolution in Fourier space.
FFTConvolutionFilter() - Constructor for class com.xinapse.filter.FFTConvolutionFilter
 
FIDUCIALS - Enum constant in enum class com.xinapse.dicom.Modality
Fiducials Modality.
FILE_EXTENSION - Static variable in class com.xinapse.multisliceimage.roi.ROIFileFilter
The extension for ROI files ("roi").
fileLabel - Variable in class com.xinapse.image.ImageSelectionPanel
The JLabel to display along side the image file.
fileSelectionPanel - Variable in class com.xinapse.image.ImageSelectionPanel
A JPanel displayed to allow an image file to be selected.
fileTextField - Variable in class com.xinapse.image.ImageSelectionPanel
The JTextField to set the image file.
filter(SpatialFilter, ReadableImage, MonitorWorker, boolean) - Static method in class com.xinapse.filter.AbstractComplexKernelFilter
Filter a ReadableImage using the supplied filter, returning a new image which is a filtered version of the supplied image.
filter(SpatialFilter, ReadableImage, MonitorWorker, boolean) - Static method in class com.xinapse.filter.AbstractKernelFilter
Filter a ReadableImage using the supplied filter, returning a new image which is a filtered version of the supplied image.
filter(ReadableImage) - Method in class com.xinapse.filter.AbstractComplexKernelFilter
 
filter(ReadableImage) - Method in class com.xinapse.filter.AbstractKernelFilter
 
filter(ReadableImage) - Method in class com.xinapse.filter.ColourImageFilter
 
filter(ReadableImage) - Method in class com.xinapse.filter.PatchSimilarityFilter
 
filter(ReadableImage) - Method in class com.xinapse.filter.SobelFilter.MagnitudeFilter
 
filter(ReadableImage) - Method in interface com.xinapse.filter.SpatialFilter
Filter a ReadableImage, returning a new image which is a filtered version of the supplied image.
filter(ReadableImage, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractComplexKernelFilter
 
filter(ReadableImage, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractKernelFilter
 
filter(ReadableImage, MonitorWorker, boolean) - Method in class com.xinapse.filter.ColourImageFilter
 
filter(ReadableImage, MonitorWorker, boolean) - Method in class com.xinapse.filter.PatchSimilarityFilter
 
filter(ReadableImage, MonitorWorker, boolean) - Method in class com.xinapse.filter.SobelFilter.MagnitudeFilter
 
filter(ReadableImage, MonitorWorker, boolean) - Method in interface com.xinapse.filter.SpatialFilter
Filter a ReadableImage, returning a new image which is a filtered version of the supplied image.
FILTER_SELECTION_OPTION - Static variable in class com.xinapse.filter.FilterSelection
The Option used to select a particular filter.
filterInPlace(float[], FixedWeightsKernelFilter, int, int, int) - Static method in class com.xinapse.filter.FFTConvolutionFilter
Filter an image of floating-point values "in-place".
filterInPlace(SpatialFilter, WritableImage) - Static method in class com.xinapse.filter.AbstractComplexKernelFilter
Filter a WritableImage "in place" using the supplied filter.
filterInPlace(SpatialFilter, WritableImage) - Static method in class com.xinapse.filter.AbstractKernelFilter
Filter a WritableImage "in place" using the supplied filter.
filterInPlace(SpatialFilter, WritableImage, MonitorWorker, boolean) - Static method in class com.xinapse.filter.AbstractComplexKernelFilter
Filter an image "in place".
filterInPlace(SpatialFilter, WritableImage, MonitorWorker, boolean) - Static method in class com.xinapse.filter.AbstractKernelFilter
Filter an image "in place".
filterInPlace(SpatialFilter, Object, PixelDataType, int, int, int) - Static method in class com.xinapse.filter.AbstractComplexKernelFilter
Filter an array of pixel values "in place".
filterInPlace(SpatialFilter, Object, PixelDataType, int, int, int) - Static method in class com.xinapse.filter.AbstractKernelFilter
Filter an array of pixel values "in place".
filterInPlace(WritableImage) - Method in class com.xinapse.filter.AbstractComplexKernelFilter
 
filterInPlace(WritableImage) - Method in class com.xinapse.filter.AbstractKernelFilter
 
filterInPlace(WritableImage) - Method in class com.xinapse.filter.ColourImageFilter
 
filterInPlace(WritableImage) - Method in class com.xinapse.filter.PatchSimilarityFilter
 
filterInPlace(WritableImage) - Method in class com.xinapse.filter.SobelFilter.MagnitudeFilter
 
filterInPlace(WritableImage) - Method in interface com.xinapse.filter.SpatialFilter
Filter a WritableImage "in place".
filterInPlace(WritableImage, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractComplexKernelFilter
 
filterInPlace(WritableImage, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractKernelFilter
 
filterInPlace(WritableImage, MonitorWorker, boolean) - Method in class com.xinapse.filter.ColourImageFilter
 
filterInPlace(WritableImage, MonitorWorker, boolean) - Method in class com.xinapse.filter.PatchSimilarityFilter
 
filterInPlace(WritableImage, MonitorWorker, boolean) - Method in class com.xinapse.filter.SobelFilter.MagnitudeFilter
 
filterInPlace(WritableImage, MonitorWorker, boolean) - Method in interface com.xinapse.filter.SpatialFilter
Filter a WritableImage "in place".
filterInPlace(Object, PixelDataType, int, int, int) - Method in class com.xinapse.filter.AbstractComplexKernelFilter
 
filterInPlace(Object, PixelDataType, int, int, int) - Method in class com.xinapse.filter.AbstractKernelFilter
 
filterInPlace(Object, PixelDataType, int, int, int) - Method in class com.xinapse.filter.ColourImageFilter
 
filterInPlace(Object, PixelDataType, int, int, int) - Method in class com.xinapse.filter.PatchSimilarityFilter
 
filterInPlace(Object, PixelDataType, int, int, int) - Method in class com.xinapse.filter.SobelFilter.MagnitudeFilter
 
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 class com.xinapse.filter.AbstractComplexKernelFilter
 
filterInPlace(Object, PixelDataType, int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractKernelFilter
 
filterInPlace(Object, PixelDataType, int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.ColourImageFilter
 
filterInPlace(Object, PixelDataType, int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.MorphologicalOperator
 
filterInPlace(Object, PixelDataType, int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.PatchSimilarityFilter
 
filterInPlace(Object, PixelDataType, int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.SobelFilter.MagnitudeFilter
 
filterInPlace(Object, PixelDataType, int, int, int, MonitorWorker, boolean) - Method in interface com.xinapse.filter.SpatialFilter
Filter an array of pixel values "in place".
filterInPlaceBinary(BitSet, int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractKernelFilter
Filter an array of binary pixel values "in place".
filterInPlaceBinary(BitSet, int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.FixedWeightsKernelFilter
 
filterInPlaceByte(byte[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractKernelFilter
Filter an array of signed byte pixel values "in place".
filterInPlaceByte(byte[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.FixedWeightsKernelFilter
 
filterInPlaceDouble(double[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.AbstractKernelFilter
Filter an array of double-precision pixel values "in place".
filterInPlaceDouble(double[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.FixedWeightsKernelFilter
 
filterInPlaceDouble(double[], int, int, int, MonitorWorker, boolean) - Method in class com.xinapse.filter.MorphologicalOperator
 
filterInPlaceFloat(float[], int, int, int, int, int, int, int, int, int) - Method in class com.xinapse.filter.FixedWeightsKernelFilter
Filter a cuboid portion of an array of floating-point pixel values "in place".
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.
firstSlice - Variable in class com.xinapse.multisliceimage.roi.VOIStats
The first slice number which this VOI spans (indexed from zero).
fit(float[], int, int, int, AutoCorrelationEstimate, MonitorWorker) - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
Calculate the model parameters that best fit the data.
fit(float[], int, int, int, AutoCorrelationEstimate, MonitorWorker) - Method in interface com.xinapse.dynamic.DynamicModel
Calculate the model parameters that best fit the data.
FIXED - Enum constant in enum class com.xinapse.image.BoundaryCondition
Use a fixed value, for example if zero is used: [1 2 3 4 5] → [0 0 1 2 3 4 5 0 0].
FIXED - Enum constant in enum class com.xinapse.multisliceimage.roi.ContourMode
A fixed user-set intensity level.
FixedWeightsComplexKernelFilter - Class in com.xinapse.filter
A class for performing filtering of complex images based on a moving kernel of pixels with fixed complex weights within the kernel.
FixedWeightsComplexKernelFilter() - Constructor for class com.xinapse.filter.FixedWeightsComplexKernelFilter
Default constructor produces an identity FixedWeightsComplexKernelFilter with kernel size 1x1x1 that has no effect when applied.
FixedWeightsComplexKernelFilter(FloatComplex[][][], boolean, BoundaryCondition) - Constructor for class com.xinapse.filter.FixedWeightsComplexKernelFilter
Constructs a 3-dimensional kernel-based filter with the given filter weights.
FixedWeightsComplexKernelFilter(FloatComplex[][], boolean, BoundaryCondition) - Constructor for class com.xinapse.filter.FixedWeightsComplexKernelFilter
Constructs a 2-dimensional kernel-based filter with the given filter weights.
FixedWeightsKernelFilter - Class in com.xinapse.filter
A class for performing filtering of images based on a moving kernel of pixels with fixed weights within the kernel.
FixedWeightsKernelFilter() - Constructor for class com.xinapse.filter.FixedWeightsKernelFilter
Default constructor produces an identity FixedWeightsKernelFilter with kernel size 1x1x1 that has no effect when applied.
FixedWeightsKernelFilter(float[][][], boolean, BoundaryCondition) - Constructor for class com.xinapse.filter.FixedWeightsKernelFilter
Constructs a 3-dimensional kernel-based filter with the given filter weights.
FixedWeightsKernelFilter(float[][], boolean, BoundaryCondition) - Constructor for class com.xinapse.filter.FixedWeightsKernelFilter
Constructs a 2-dimensional kernel-based filter with the given filter weights.
flag - Variable in class com.xinapse.util.CancellableThread
The flag that is set by the cencel() method in order to cancel this Thread.
Flag() - Constructor for class com.xinapse.util.CancellableThread.Flag
 
flip() - Method in class com.xinapse.util.BitSet
Sets all bits to the opposite value.
flip(int) - Method in class com.xinapse.util.BitSet
Sets the bit at the index to the opposite value.
flip(int, int) - Method in class com.xinapse.util.BitSet
Sets a range of bits to the opposite value.
flip(ReadableImage, boolean, boolean, boolean, MonitorWorker, boolean) - Static method in class com.xinapse.image.ImageUtils
Flips the image data in a ReadableImage.
FLIP - Enum constant in enum class com.xinapse.multisliceimage.roi.ROIEditAction
Flip an ROI.
FLIP_ANGLE_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the excitation pulse flip angle.
FLIP_NON_FLIPPED_PROPERTY_KEY - Static variable in class com.xinapse.multisliceimage.Analyze.Analyze75Header
The property value key for setting whether to flip non-flipped Analyze 7.5 images.
flipHorizontal(Point2D) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
flipHorizontal(Point2D) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
flipHorizontal(Point2D) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
flipHorizontal(Point2D) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
flipHorizontal(Point2D) - Method in class com.xinapse.multisliceimage.roi.Marker
 
flipHorizontal(Point2D) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
This method does nothing.
flipHorizontal(Point2D) - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
flipHorizontal(Point2D) - Method in class com.xinapse.multisliceimage.roi.ROI
Flip this ROI horizontally about a given location.
flipHorizontal(Point2D) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
flipVertical(Point2D) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
flipVertical(Point2D) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
flipVertical(Point2D) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
flipVertical(Point2D) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
flipVertical(Point2D) - Method in class com.xinapse.multisliceimage.roi.Marker
 
flipVertical(Point2D) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
This method does nothing.
flipVertical(Point2D) - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
flipVertical(Point2D) - Method in class com.xinapse.multisliceimage.roi.ROI
Flip this ROI vertically about a given location.
flipVertical(Point2D) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
flipX(Object, int, int) - Method in enum class com.xinapse.image.PixelDataType
Flips an array of pixels in-place about the x-axis (ie, flips top to bottom).
flipY(Object, int) - Method in enum class com.xinapse.image.PixelDataType
Flips an array of pixels in-place about the y-axis (ie flips left-right).
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(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(float[], ByteOrder) - Static method in class com.xinapse.io.ByteSwap
Swap the byte order (if necessary) in an array of float values "in-place".
Float(float, OutputStream, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single float to a OutputStream strm.
Float(float, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single float to a RandomAccessFile f.
Float(InputStream, ByteOrder) - Static method in class com.xinapse.io.Input
Reads a float value from a 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 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 OutputStream strm as a float primitive.
Float(Float, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single Float to a RandomAccessFile f as a float primitive.
FLOAT - Enum constant in enum class com.xinapse.image.PixelDataType
PixelDataType for float (32-bit).
FLOAT - Enum constant in enum class com.xinapse.multisliceimage.Analyze.ANZPixFormat
ANZPixFormat for float pixel values.
FloatArray(float[], int, int, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of float values to a RandomAccessFile f.
FloatArray(float[], OutputStream, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of float values to a OutputStream strm.
FloatArray(float[], RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of float values to a RandomAccessFile f.
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(InputStream, ByteOrder, int) - Static method in class com.xinapse.io.Input
Reads an array of float values from a InputStream 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 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 RandomAccessFile f ensuring that blocking occurs until all values have been read.
FloatComplex - Class in com.xinapse.image
A complex (real, imaginary) number, with single precision.
FloatComplex() - Constructor for class com.xinapse.image.FloatComplex
Creates a new FloatComplex number, with zero real and imaginary parts.
FloatComplex(float, float) - Constructor for class com.xinapse.image.FloatComplex
Creates a new FloatComplex number, with the real and imaginary parts specified by the arguments.
FloatComplex(Complex) - Constructor for class com.xinapse.image.FloatComplex
Creates a new FloatComplex number, with the real and imaginary parts copied from an existing Complex.
FLUORESCEIN_ANGIOGRAPHY_RET - Enum constant in enum class com.xinapse.dicom.Modality
Fluorescein angiography Modality (RETIRED).
folderLabel - Variable in class com.xinapse.image.ImageSelectionPanel
The JLabel to display along side the image folder, or null if the image folder isn't shown separately.
folderTextField - Variable in class com.xinapse.image.ImageSelectionPanel
The JTextField to set the image folder, or null if the image folder isn't shown separately.
FRAME_OF_REFERENCE_UID_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the frame of reference UID for the image position/orientation.
FSL_COMPATIBLE_NIFTI_PROPERTY_KEY - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
The property value key for setting whether NIFTI-1 images that have qform and sform orientation both unset should be read as having an increasing a patient left coordinate value with stored pixel data column number, and whether NIFTI-1 images should be prevented from being written without orientation information.
FTEST - Enum constant in enum class com.xinapse.multisliceimage.Analyze.NIFTIIntent
[C2, chap 27] Fisher F statistic (2 params):
p1 = numerator DOF,
p2 = denominator DOF.
FTEST_NONC - Enum constant in enum class com.xinapse.multisliceimage.Analyze.NIFTIIntent
[C2, chap 30] Noncentral F statistic (3 params):
p1 = numerator DOF, p2 = denominator DOF,
p3 = numerator noncentrality parameter.
FUNDOSCOPY_RET - Enum constant in enum class com.xinapse.dicom.Modality
Fundoscopy Modality (RETIRED).
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

GAMMA - Enum constant in enum class com.xinapse.multisliceimage.Analyze.NIFTIIntent
[C1, chap 17] Gamma distribution (2 params):
p1 = shape, p2 = scale.
Density(x) proportional to x^(p1-1) * exp(-p2*x).
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.
GENERAL_MICROSCOPY - Enum constant in enum class com.xinapse.dicom.Modality
General microscopy Modality.
generateReport() - Method in class com.xinapse.util.ReportGenerator
Cause this ReportGenerator to generate a report.
GENMATRIX - Enum constant in enum class com.xinapse.multisliceimage.Analyze.NIFTIIntent
To store an M x N matrix at each voxel:
- dataset must have a 5th dimension (dim[0]=5 and dim[5]>1)
- intent must be GENMATRIX
- dim[5] must be M*N
- intent_p1 must be M (in float format)
- intent_p2 must be N (ditto)
- the matrix values A[i][[j] are stored in row-order:
- A[0][0] A[0][1] ...
get(int) - Static method in class com.xinapse.image.template.ICBMLabel
Returns the ICBMLabel from an integer region label.
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.
get(String) - Static method in class com.xinapse.image.template.ICBMLabel
Returns the ICBMLabel from a label name.
get(Point3f) - Static method in class com.xinapse.image.template.ICBMLabel
Returns the ICBMLabel at a given image location.
GET - Enum constant in enum class com.xinapse.image.PixelOp
The pixel PixelOp for getting pixel values from an image.
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 String.
getAffineTransform() - Method in interface com.xinapse.image.ReadableImage
Returns the AffineTransform3D that will transform the pixel indices (colIdx, rowIdx, sliceIdx) to a position in space in the patient-centric coordinate system.
getAffineTransform(Integer) - Method in interface com.xinapse.image.ReadableImage
Returns the AffineTransform3D that will transform the pixel indices (colIdx, rowIdx, sliceIdx) to a position in space in the patient-centric coordinate system for one particular slice of the image.
getAllColourMapNames() - Static method in class com.xinapse.image.ColourMapping
Returns a list of all ColourMapping names, as a comma-separated list.
getAllColourMappings() - Static method in class com.xinapse.image.ColourMapping
Returns a java.util.List&lt;ColourMapping&gt; of all ColourMappings, both built-in and imported by the user.
getAllLabels() - Static method in class com.xinapse.image.template.ICBMLabel
Returns an array of all known ICBMLabels.
getAllPresets() - Static method in class com.xinapse.image.IntensityPreset
Returns a java.util.List<IntensityPreset> of all IntensityPresets, both built-in and created by the user.
getAlwaysAsk() - Static method in enum class com.xinapse.dicom.Modality
Returns whether always to ask the user what is the Modality, if not set in an image.
getAlwaysAsk() - Static method in enum class com.xinapse.dicom.PatientPosition
Returns whether the user prefers always to be asked to set the PatientPosition.
getAlwaysAsk() - Static method in enum class com.xinapse.dicom.PulseSequenceType
Returns whether the user prefers always to be asked to set the PulseSequenceType.
getAnalysis() - Method in class com.xinapse.apps.cardiac.CardiacAnalysis.SpecifierPanel
Returns the CardiacAnalysis that has been specified by this CardiacAnalysis.SpecifierPanel.
getAnalysisDescription() - Method in interface com.xinapse.apps.cardiac.CardiacAnalysis
Returns a String describing this cardiac analysis.
getAnalysisName() - Method in interface com.xinapse.apps.cardiac.CardiacAnalysis
Returns the name of the analysis.
getAnnotation() - Method in class com.xinapse.multisliceimage.roi.ROI
Gets the anotation string for this ROI.
getAnnularThickness(ROI[], int) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Returns an array of annular thicknesses - one for each segment of this RadialDivider.
getAreaUnder() - Method in class com.xinapse.image.Histogram
Returns the total area under this histogram.
getAreaUnder(boolean) - Method in class com.xinapse.image.Histogram
Returns the area under this histogram, optionally excluding any zero-valued values.
getArg() - Method in class com.xinapse.image.Complex
Returns the polar angle of this complex number.
getArg() - Method in class com.xinapse.image.DoubleComplex
 
getArg() - Method in class com.xinapse.image.FloatComplex
 
getArrayElementsPerPixel() - Method in enum class com.xinapse.image.PixelDataType
Returns the number of array elements of a primitive type needed to store a single pixel value.
getB() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
Returns the second semi-major axis length in mm.
getBinaryMask() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
Returns the mask image if masking by an image has been selected.
getBinWidth() - Method in class com.xinapse.image.Histogram
Returns the bin width for this Histogram.
getBitsPerPixel() - Method in enum class com.xinapse.image.PixelDataType
Returns the number of bits used to store one pixel for this data type.
getBodyPart() - Method in interface com.xinapse.image.ReadableImage
Returns the body part imaged.
getBodyPart() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getBodyPart() - Method in class com.xinapse.multisliceimage.MultiSliceImage
By default, body part recording is not supported, so this method always returns null.
getBodyPart() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getBorderColor() - Static method in class com.xinapse.multisliceimage.roi.Handle
Returns the Color with which ROI Handle borders are to be drawn.
getBoundingRectangle(int, int, float, float) - Method in class com.xinapse.multisliceimage.roi.LineROI
Returns a high-precision rectangle (in pixel coordinates) that just bounds this ROI.
getBoundingRectangle(int, int, float, float) - Method in class com.xinapse.multisliceimage.roi.Marker
 
getBoundingRectangle(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.
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.
getBT() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
Returns the threshold fraction to use with the Brain Finder, if this option has been set in the GUI.
getBuiltInMappings() - Static method in class com.xinapse.image.ColourMapping
Returns a java.util.List&lt;ColourMapping&gt; of the built-in ColourMappings.
getBuiltInPresets() - Static method in class com.xinapse.image.IntensityPreset
Returns a java.util.List<IntensityPreset> of the built-in IntensityPresets.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.ContourROI
Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.CurvedLineROI
Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.EllipticalROI
Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.IrregularROI
Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.LineROI
Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.Marker
Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.OpenSplineROI
Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.RectangularROI
Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.SplineROI
Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.Text
Returns an Icon that can be used for a button to create this type of ROI.
getByteOrder() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getByteOrder() - Method in class com.xinapse.multisliceimage.MultiSliceImage
Returns the byte order for this image.
getByteOrder() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getBytesPerPixel() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns the number of bytes per pixel for this image.
getBytesPerPixel() - Method in enum class com.xinapse.multisliceimage.UNC.UNCPixFormat
Returns the number of bytes per pixel for this UNCPixFormat.
getCalc() - Method in class com.xinapse.apps.active.ROICalculation.SpecifierPanel
Returns the ROICalculation that has been specified by this ROICalculation.SpecifierPanel.
getCalcOptions() - Static method in class com.xinapse.apps.active.SelectableROICalculation
Returns an array of Options that are used with the ROICalculation.
getCalculationDescription() - Method in interface com.xinapse.apps.active.ROICalculation
Returns a String describing this ROI calculation.
getCalculationName() - Method in interface com.xinapse.apps.active.ROICalculation
Returns the name of the calculation.
getCentre() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
getCentre() - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
getCentre() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
getCentre() - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getCentre() - Method in interface com.xinapse.multisliceimage.roi.RotatableROI
Gets the centre (about which rotation will occur) of this RotatableROI in mm.
getCentre() - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
getCentre(int) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Returns the centre position for this RadialDivider for the given movie frame number.
getCentreOfMass(ReadableImage, Double, boolean) - Static method in class com.xinapse.image.ImageMoments
Calculates the centre of mass of an image.
getCentreOfMass(ReadableImage, Object, PixelDataType) - Static method in class com.xinapse.image.ImageMoments
Calculates the centre of mass of an image.
getCentrePix(int, int, float, float) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
Gets the centre of this ROI in pixel coordinates.
getCentroid() - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
getCentroid() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
getCentroid() - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
getCentroid() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
getCentroid() - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getCentroid() - Method in class com.xinapse.multisliceimage.roi.Marker
 
getCentroid() - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Returns null.
getCentroid() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
getCentroid() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the centroid (centre of area) of this ROI.
getCentroid() - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
getCentroid(ROI[]) - Static method in class com.xinapse.multisliceimage.roi.ROI
Returns the centroid (centre of area) of an array of ROIs.
getChoosableColor(int) - Static method in enum class com.xinapse.multisliceimage.roi.ROIState
Returns one of the user-choosable ROI colours.
getClasses() - Static method in class com.xinapse.multisliceimage.roi.ROI
Returns an array of all known sub-classes of ROI.
getColor() - Static method in class com.xinapse.multisliceimage.roi.Handle
Returns the Color with which ROI Handles are to be drawn.
getColor() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the Color in which this ROI should be drawn.
getColor() - Method in class com.xinapse.multisliceimage.roi.Text
Returns the Color in which this Text ROI should be drawn.
getColorValue(Object, int) - Method in enum class com.xinapse.image.PixelDataType
Gets a single colour pixel value from an array of pixels.
getColour(short) - Method in class com.xinapse.image.ColourMapping
Returns the colour in a particular slot of the colour mapping.
getColourMapping(String) - Static method in class com.xinapse.multisliceimage.Analyze.ANZColourMapping
Returns a ColourMapping by reading the values from the given file which has the contain a colour lookup table in Analyze format.
getColourPixelDataType(Class<? extends ReadableImage>) - Static method in class com.xinapse.image.Image
Returns the colour PixelDataType that is supported by a particular class of ReadableImage, or null if the class does not support a colour PixelDataType.
getColumnFormats() - Method in class com.xinapse.multisliceimage.roi.VOIStats
Returns the column formats when writing VOIStats in columns.
getColumnHeaders() - Method in class com.xinapse.multisliceimage.roi.VOIStats
Returns the column headers when writing VOIStats in columns.
getCombineMode() - Method in class com.xinapse.multisliceimage.roi.CombineMode.Panel
Returns the CombineMode set in this panel.
getCommonInfo(InfoList[]) - Static method in class com.xinapse.util.InfoList
Returns an InfoList which contains only those InfoItems that are found in every element of the supplied InfoList[].
getCommonName() - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Returns the common name for this type of image.
getCommonName() - Static method in class com.xinapse.multisliceimage.Analyze.NIFTI2Image
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.
getComplexValue(Object, int) - Method in enum class com.xinapse.image.PixelDataType
Gets a single Complex pixel value from an array of pixels.
getComponent() - Method in class com.xinapse.util.MonitorWorker
Returns the component from which this MonitorWorker was launched.
getComponent(int) - Method in interface com.xinapse.image.ImageSelectionGroupPanel.ComponentGenerator
Causes this ImageSelectionGroupPanel.ComponentGenerator to generate a new user component.
getComponent(int) - Method in class com.xinapse.util.IntensityRelation.PanelGenerator
 
getConc(double[]) - Method in class com.xinapse.apps.perfusion.AIF
Returns the concentration values at a set of time-points.
getContiguousContrasts() - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Note: getContiguousContrasts has a different meaning, depending on whether a single input image is used, or whether multiple input images are used: For a single input image, getContiguousContrasts() == true indicates that all contrasts for one slice are adjacent, before moving on to the next slice.
getContourMode() - Method in class com.xinapse.multisliceimage.roi.ContourMode.ComboBox
Returns the ContourMode currently set in this ContourMode.ComboBox.
getCopy() - Method in interface com.xinapse.image.ReadableImage
Returns a copy of this ReadableImage.
getCopy() - Method in interface com.xinapse.image.WritableImage
Returns a copy of this WritableImage.
getCopy() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
Creates an in-memory copy of an Analyze image.
getCopy() - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
getCopy() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
getCopy() - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
getCopy() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
getCopy() - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getCopy() - Method in class com.xinapse.multisliceimage.roi.Marker
 
getCopy() - Method in class com.xinapse.multisliceimage.roi.OpenSplineROI
 
getCopy() - Method in class com.xinapse.multisliceimage.roi.RadialDivider
 
getCopy() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
getCopy() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns a copy of this ROI.
getCopy() - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
getCopy() - Method in class com.xinapse.multisliceimage.roi.Text
 
getCopy() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getCorrectAutoCorrelation() - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
Returns false, since the DynamicContrastModels do not do a correction for temporal autocorrelation.
getCorrectAutoCorrelation() - Method in interface com.xinapse.dynamic.DynamicModel
Signals whether the model requires the autocorrelation in the time-series to be estimated when computing significance levels.
getCount(int) - Method in class com.xinapse.image.Histogram
Returns the count in one bin of this Histogram.
getCreateDialog(CanAddROIToFrame) - Static method in class com.xinapse.multisliceimage.roi.EllipticalROI
Returns a JDialog that can be used to create Elliptical ROIs.
getCreateDialog(CanAddROIToFrame) - Static method in class com.xinapse.multisliceimage.roi.LineROI
Returns a JDialog that can be used to create Line ROIs.
getCreateDialog(CanAddROIToFrame) - Static method in class com.xinapse.multisliceimage.roi.Marker
Returns a JDialog that can be used to create Marker ROIs.
getCreateDialog(CanAddROIToFrame) - Static method in class com.xinapse.multisliceimage.roi.RectangularROI
Returns a JDialog that can be used to create Rectangular ROIs.
getCreateDialog(CanAddROIToFrame) - Static method in class com.xinapse.multisliceimage.roi.Text
Returns a JDialog that can be used to create Text ROIs.
getCreateInteractionType() - Static method in class com.xinapse.multisliceimage.roi.ContourROI
Returns the type of interaction needed to create a ContourROI.
getCreateInteractionType() - Static method in class com.xinapse.multisliceimage.roi.CurvedLineROI
Returns the type of interaction needed to create a CurvedLineROI.
getCreateInteractionType() - Static method in class com.xinapse.multisliceimage.roi.EllipticalROI
Returns the type of interaction needed to create an EllipticalROI.
getCreateInteractionType() - Static method in class com.xinapse.multisliceimage.roi.IrregularROI
Returns the type of interaction needed to create an IrregularROI.
getCreateInteractionType() - Static method in class com.xinapse.multisliceimage.roi.LineROI
Returns the type of interaction needed to create a LineROI.
getCreateInteractionType() - Static method in class com.xinapse.multisliceimage.roi.Marker
Returns the type of interaction needed to create a Marker.
getCreateInteractionType() - Static method in class com.xinapse.multisliceimage.roi.OpenSplineROI
Returns the type of interaction needed to create an OpenSplineROI.
getCreateInteractionType() - Static method in class com.xinapse.multisliceimage.roi.RectangularROI
Returns the type of interaction needed to create a RectangularROI.
getCreateInteractionType() - Static method in class com.xinapse.multisliceimage.roi.SplineROI
Returns the type of interaction needed to create a SplineROI.
getCreateInteractionType() - Static method in class com.xinapse.multisliceimage.roi.Text
Returns the type of interaction needed to create a Text ROI.
getCSFProbTemplate() - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in csf probability template image.
getCumulativeHistogram() - Method in class com.xinapse.image.Histogram
Return a new Histogram that is the cumulative histogram of this one.
getCumulativeIntensity(float, boolean) - Method in class com.xinapse.image.Histogram
Returns a value such that the specified fraction of values is below the returned intensity; zero-valued values are optionally excluded from the calculation.
getCumulativeStats(List<ROIStats>, PixelDataType) - Static method in class com.xinapse.multisliceimage.roi.ROIStats
Returns the cumulative stats for a List of ROIStats.
getCurvature(double) - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns the signed curvature of the outline shape at a particular value of the s-parameter.
getCurvature(int) - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns the signed curvature of the outline shape at a knot point.
getData() - Method in class com.xinapse.multisliceimage.roi.VOIStats
Returns the VOIStats statistics.
getDataType() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
Returns the data type (ANZPixFormat) of this image.
getDateFormat() - Static method in class com.xinapse.multisliceimage.MultiSliceImage
Returns the DateFormat used when this class writes dates.
getDBName() - Method in class com.xinapse.multisliceimage.Analyze.ANZHeader
Returns the data base name for this Analyze image header.
getDeletedROIs() - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Returns a List of deleted (not current) ROIs for the image displayed.
getDeletedROIs(int) - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Returns a List of deleted (not current) ROIs for one slice of the image displayed.
getDeltaX() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
For the purposes of plotting data, returns the step between values of the independent variable.
getDeltaX() - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the δ x-value between adjacent points on a pop-up plot.
getDescription() - Method in enum class com.xinapse.dicom.Modality
Returns a string describing this imaging modality.
getDescription() - Method in enum class com.xinapse.dicom.PulseSequenceType
Returns a description of the pulse-sequence type.
getDescription() - Method in class com.xinapse.image.ImageFileFilter
Returns "All Images".
getDescription() - Method in interface com.xinapse.image.ReadableImage
Returns a String description of this image.
getDescription() - Method in enum class com.xinapse.image.template.WeightingType
Returns a string describing this image weighting type.
getDescription() - Method in class com.xinapse.multisliceimage.Analyze.AnalyzeFileFilter
Returns "Analyze Images".
getDescription() - Method in class com.xinapse.multisliceimage.Analyze.ANZHeader
Returns the description for this Analyze image header.
getDescription() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getDescription() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIFileFilter
Returns "NIFTI Images".
getDescription() - Method in class com.xinapse.multisliceimage.roi.ContourROI
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.ImageJROIFileFilter
Returns "ImageJ Region of Interest Files".
getDescription() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.Marker
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.OpenSplineROI
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.RadialDivider
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.ROI
Return a description of this type of ROI.
getDescription() - Method in class com.xinapse.multisliceimage.roi.ROIFileFilter
Returns "Region of Interest Files".
getDescription() - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
getDescription() - Method in class com.xinapse.multisliceimage.roi.Text
 
getDescription() - Method in class com.xinapse.multisliceimage.UNC.UNCFileFilter
Returns "UNC Images".
getDescription() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getDescription() - Method in enum class com.xinapse.util.IntensityRelation
Returns a String describing this IntensityRelation in detail.
getDescription(int) - Method in interface com.xinapse.image.ReadableImage
Returns a String description of this one particular slice of this image.
getDescription(int) - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getDescription(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getDesignTextFontSize() - Static method in class com.xinapse.multisliceimage.roi.ROI
Returns the font size at which ROI annotation text should be rendered.
getDimc() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns the dimensionality of this image.
getDims() - Method in interface com.xinapse.image.ReadableImage
Returns the dimensions (numbers of samples in each image dimension) of this image.
getDims() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getDims() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getDimv() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns the dimensions of this image.
getDisplayedBounds2D() - 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.
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.
getDisplayedRoiArea() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the Area of this ROI as it is displayed on-screen.
getDividerColor() - Static method in class com.xinapse.multisliceimage.roi.RadialDivider
Returns the Color to be used for drawing the end/epicardium divider.
getDoBonferroni() - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
Returns false, since Bonferroni correction is not performed because significance values for the fitted parameters are not computed.
getDoBonferroni() - Method in interface com.xinapse.dynamic.DynamicModel
Returns true if this DynmicModel does Bonferroni correction; false otherwise.
getDoubleValue(Object, int) - Method in enum class com.xinapse.image.PixelDataType
Gets a single pixel value from an array of pixels.
getDoubleValue(Object, ComplexMode) - Method in enum class com.xinapse.image.PixelDataType
Converts a single pixel value to a double value.
getDrawColor(byte) - Method in enum class com.xinapse.multisliceimage.roi.ROIState
Returns the colour with which an ROI in this state should be drawn.
getDt() - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
Returns the time between data samples.
getDt() - Method in interface com.xinapse.dynamic.DynamicModel
Returns the time between data samples.
getDynamicModel() - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the DynamicModel set in this MultiContrastAnalysisFrame.
getEchoTrainLength() - Method in interface com.xinapse.image.ReadableImage
Returns the scan echo train length for this image.
getEchoTrainLength() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getEchoTrainLength() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the echo train length for this image.
getEchoTrainLength() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getEntriesString() - Method in class com.xinapse.image.ColourMapping
Returns a String showing either: The [R,G,B] entries for this ColourMapping, or If the ColourMapping is MONOCHROME1 or MONOCHROME2, the String "MONOCHROME1" or "MONOCHROME2".
getEntropy() - Method in class com.xinapse.image.Histogram
Returns the entropy of this Histogram.
getEulerAngles() - Method in class com.xinapse.geom3d.AffineTransform3D
Returns a three rotation angles (the Euler angles) about the x, y and z axes from this AffineTransform3D.
getExtendedData() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns a List of ExtendedData for this NIFTIImage.
getFeret() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
getFeret() - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
getFeret() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
getFeret() - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getFeret() - Method in class com.xinapse.multisliceimage.roi.Marker
 
getFeret() - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Returns zero.
getFeret() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
getFeret() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the minimum and maximum Feret's diameter for this ROI, in mm.
getFeret() - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
getFeret(List<ROI>) - Static method in class com.xinapse.multisliceimage.roi.ROI
Returns the minimum and maximum Feret's diameter for a List of ROI, in mm.
getFile() - Method in class com.xinapse.image.ImageSelectionPanel
Returns the image File set in this ImageSelectionPanel.
getFile() - Method in class com.xinapse.image.OutputImageSelectionPanel
Returns the image File set in this OutputImageSelectionPanel.
getFileDataOffset() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getFileDataOffset() - Method in class com.xinapse.multisliceimage.MultiSliceImage
Returns the byte offset into the disk-based file format where pixel data begins.
getFileDataOffset() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns the byte offset into the disk-based file format where pixel data begins.
getFilter(ReadableImage) - Method in class com.xinapse.filter.ColourImageFilter.ColourImageFilterSpecifierPanel
 
getFilter(ReadableImage) - Method in class com.xinapse.filter.FilterSelection.Panel
Returns the SpatialFilter currently set in this FilterSelectionPanel.
getFilter(ReadableImage) - Method in class com.xinapse.filter.GaussianBlurFilter.GaussianBlurSpecifierPanel
 
getFilter(ReadableImage) - Method in class com.xinapse.filter.LaplacianFilter.LaplacianSpecifierPanel
 
getFilter(ReadableImage) - Method in class com.xinapse.filter.MedianFilter.MedianSpecifierPanel
 
getFilter(ReadableImage) - Method in class com.xinapse.filter.MorphologicalOperator.MorphologicalSpecifierPanel
 
getFilter(ReadableImage) - Method in class com.xinapse.filter.PatchSimilarityFilter.PatchSimilaritySpecifierPanel
 
getFilter(ReadableImage) - Method in class com.xinapse.filter.SharpenFilter.SharpenSpecifierPanel
 
getFilter(ReadableImage) - Method in class com.xinapse.filter.SobelFilter.SobelSpecifierPanel
 
getFilter(ReadableImage) - Method in class com.xinapse.filter.SpatialFilter.SpecifierPanel
Returns the SpatialFilter that has been specified by this SpatialFilter.SpecifierPanel.
getFirstDeriv(double) - Method in class com.xinapse.numerical.CubicSplineInterpolator
Returns the first derivative of the function value at a given value of x.
getFittedCurve() - Method in class com.xinapse.dynamic.DynamicResult
Returns the values of the fitted model at the same points as the data.
getFittedVarValues() - Method in class com.xinapse.dynamic.DynamicResult
Returns the values of the fit variables after they have been optimised in the model.
getFlatKernelWeights() - Method in class com.xinapse.filter.FixedWeightsKernelFilter
Returns the kernel weights as a flat array.
getFlipAngle() - Method in interface com.xinapse.image.ReadableImage
Returns the excitation pulse flip angle for this image.
getFlipAngle() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getFlipAngle() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the excitation pulse flip angle for this image.
getFlipAngle() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getFollowingVisibleHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
getFollowingVisibleHandle(Handle) - Method in interface com.xinapse.multisliceimage.roi.EditableOutlineROI
Returns the visible Handle that is immediately after the specified handle, in the order in which they were placed around the ROI.
getFollowingVisibleHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
getFollowingVisibleHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
getFollowingVisibleHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
getFrame() - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Returns the JFrame to which the ROI(s) will be added.
getFrameDim() - Method in class com.xinapse.multisliceimage.MultiSliceImage
Returns the index number to the "frame" dimension of the image.
getFrameDWBMatrix(int) - Method in interface com.xinapse.image.ReadableImage
Returns the diffusion-weighting b-matrix for one frame of this image.
getFrameDWBMatrix(int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getFrameDWBMatrix(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getFrameDWBMatrix(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getFrameDWbValue(int) - Method in interface com.xinapse.image.ReadableImage
Returns the diffusion-weighting b-value for one frame of this 4-D image.
getFrameDWbValue(int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getFrameDWbValue(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getFrameDWbValue(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getFrameDWGradientVector(int) - Method in interface com.xinapse.image.ReadableImage
Returns the diffusion-weighting gradient-vector for one frame of this image 4-D image.
getFrameDWGradientVector(int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getFrameDWGradientVector(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getFrameDWGradientVector(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getFrameInfo(String, int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getFrameInfo(String, int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Returns a String representing the value of this information item in a particular frame of this image.
getFrameInfo(String, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getFrameInfoList(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getFrameInfoList(int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Returns an InfoList object applying to a particular frame of this image.
getFrameInfoList(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getFrameOfReferenceUID() - Method in interface com.xinapse.image.ReadableImage
Returns the frame of reference UID that uniquely identifies the frame of reference for an image.
getFrameOfReferenceUID() - Method in class com.xinapse.multisliceimage.MultiSliceImage
 
getFrameTriggerDelayMS(int) - Method in interface com.xinapse.image.ReadableImage
Returns the trigger delay, in milliseconds, for one frame of this image.
getFrameTriggerDelayMS(int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getFrameTriggerDelayMS(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getFrameTriggerDelayMS(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getFullDescription() - Method in enum class com.xinapse.image.template.WeightingType
Returns a "full" description of this WeightingType.
getGamma() - Static method in class com.xinapse.image.ColourMapping
Returns the current gamma value setting for the display.
getGMProbTemplate() - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in grey-matter probability template image.
getGroupUid() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the group UID for this ROI.
getGroupUid(List<ROI>) - Static method in class com.xinapse.multisliceimage.roi.ROI
Returns the Group UID of the ROIs supplied if they are all members of the same group (i.e., they all have the same Group UID).
getHandles() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns an array of Handles that this ROI has.
getHandleUnder(Point, int) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
If the mouse is over the InsertionPointHandle, returns the InsertionPointHandle.
getHandleUnderPoint(Point) - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the Handle of this ROI that is under the point supplied (in screen coordinates).
getHeader() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
Returns the ANZHeader image header for this image.
getHeaderSize() - Method in class com.xinapse.multisliceimage.Analyze.NIFTI2Header
 
getHeaderSize() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
Returns the size of this NIFTI (NIFTI-1 or NIFTI-2) header.
getHeight() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
Returns the height of this RectangularROI in mm.
getHisto(int) - Method in class com.xinapse.image.DoublePixArray
Computes a histogram of a DoublePixArray.
getHisto(int) - Method in class com.xinapse.image.PixArray
Computes a histogram of this PixArray.
getHistoMax() - Method in class com.xinapse.image.Histogram
Returns the maximum bin value of this Histogram.
getHistoMin() - Method in class com.xinapse.image.Histogram
Returns the minimum bin value of this Histogram.
getHollowROI(ROI[], int) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Returns the HollowROI that is formed from a pair of ROIs.
getHTMLDescription() - Method in interface com.xinapse.image.ReadableImage
Returns a String description of this image in HTML format.
getHTMLDescription() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getHTMLDescription() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getHTMLDescription(int) - Method in interface com.xinapse.image.ReadableImage
Returns a String description of a slice of this image in HTML format.
getHTMLDescription(int) - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getHTMLDescription(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getHTMLDescription(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getICBMCSFProbTemplate() - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in ICBM csf probability template image.
getICBMGMProbTemplate() - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in ICBM grey-matter probability template image.
getICBMICCMask() - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in ICBM intra-cranial cavity mask.
getICBMLabels() - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in ICBM labels.
getICBMLabelsImage() - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in ICBM labels image.
getICBMLesionProbTemplate() - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in lesion probability template image (which has been warped to the same space as the T1-weighted ICBM template image).
getICBMLVProbTemplate() - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in lateral ICBM ventricle probability template image.
getICBMMSLesionProbTemplate(boolean) - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in MS lesion probability image matched to the ICBM template.
getICBMMSPDHeadTemplate(boolean) - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in ICBM proton density weighted head template image.
getICBMTemplateImage(WeightingType) - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in ICBM template image of the specified weighting type.
getICBMWMProbTemplate() - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in ICBM white-matter probability template image.
getIccMesh() - Static method in class com.xinapse.image.template.HeadTemplate
Returns a pre-calculated surface mesh of the intra-cranial cavity for any of the template images (the T1, T2 or PD templates).
getIconHeight() - Method in class com.xinapse.image.ColourMapping
Get the height of the Icon used to represent this ColourMapping.
getIconHeight() - Method in class com.xinapse.image.PreviewIcon
Returns the icon's width.
getIconHeight() - Method in enum class com.xinapse.image.RenderingInterpolationType
 
getIconHeight() - Method in enum class com.xinapse.util.IntensityRelation
 
getIconWidth() - Method in class com.xinapse.image.ColourMapping
Get the width of the Icon used to represent this ColourMapping.
getIconWidth() - Method in class com.xinapse.image.PreviewIcon
Returns the icon's height.
getIconWidth() - Method in enum class com.xinapse.image.RenderingInterpolationType
 
getIconWidth() - Method in enum class com.xinapse.util.IntensityRelation
 
getID() - Method in class com.xinapse.multisliceimage.roi.HistoryItem
Return the ID of the operator who performed the action in this HistoryItem.
getImag() - Method in class com.xinapse.image.Complex
Returns the imaginary part of this complex number.
getImag() - Method in class com.xinapse.image.DoubleComplex
 
getImag() - Method in class com.xinapse.image.FloatComplex
 
getImage(Double) - Method in class com.xinapse.numerical.PolyCoeffs3D
Get an image representing the fitted polynomial surface.
getImageCentrePatient(ReadableImage) - Static method in class com.xinapse.image.ImageUtils
Returns the coordinates of the center of the block of slices of an image, in mm, in patient coordinates.
getImageFilterClass() - Method in class com.xinapse.image.ImageGrid
Returns the class of image that will be filtered when the user first chooses a new image to set in the panel.
getImageFilterClass() - Method in class com.xinapse.image.ImageSelectionGroupPanel
Returns the class of image that will be filtered when the user first chooses a new image to set in the panel.
getImageFilterClass() - Method in class com.xinapse.image.MultipleImageSelectionPanel
Returns the class of image that will be filtered when the user chooses a new image to set in the panel.
getImageName() - Method in class com.xinapse.image.ImageSelectionPanel
Returns the name of the image set in this ImageSelectionPanel.
getImageName() - Method in class com.xinapse.image.InputImageSelectionPanel
 
getImageName() - Method in class com.xinapse.image.SelectedImagePanel
Returns name of the ReadableImage set in this SelectedImagePanel.
getImageOrientationPatient() - Method in enum class com.xinapse.image.MostLikePlane
Returns the image orientation in patient coordinates for an image plane which is exactly in this MostLikePlane.
getImageOrientationPatient() - Method in interface com.xinapse.image.ReadableImage
Returns the direction cosines of the row, column and slice directions (for increasing row, column and slice) of the image, in patient (L,P,S) coordinates.
getImageOrientationPatient() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getImageOrientationPatient() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getImageOrientationPatient(int) - Method in interface com.xinapse.image.ReadableImage
Returns the direction cosines of the row, column and slice directions (for increasing row, column and slice) of the image, in patient coordinates.
getImageOrientationPatient(int) - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getImageOrientationPatient(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getImageOrientationPatient(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getImagePositionPatient() - Method in interface com.xinapse.image.ReadableImage
Returns the coordinates of the center of the first pixel of the image, in mm, in patient coordinates.
getImagePositionPatient() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getImagePositionPatient() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getImagePositionPatient(int) - Method in interface com.xinapse.image.ReadableImage
Returns the coordinates of the center of the first pixel of the specified slice of this image, in mm, in patient coordinates.
getImagePositionPatient(int) - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getImagePositionPatient(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getImagePositionPatient(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getImageSource() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the image source of this ROI.
getImageTypeName() - Method in interface com.xinapse.image.WritableImage
Returns the normal human readable name for this type of image.
getImageTypeName() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Returns the human readable name for this type of image.
getImageTypeName() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the human readable name for this type of image.
getImageTypeName() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getImplementedInterpolationTypes() - Static method in class com.xinapse.image.VolumeInterpolator
Returns the types of interpolation that are implemented by the VolumeInterpolator class.
getIndex(int, int) - Method in enum class com.xinapse.image.BoundaryCondition
For this BoundaryCondition, returns the index into an array of values for an index that is possibly outside the array of values.
getInfo(String) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getInfo(String) - Method in interface com.xinapse.multisliceimage.InfoStorer
Returns a string representing the value of this information item in the general image information.
getInfo(String) - 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".
getInfo(String, int, int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getInfo(String, int, int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Returns a String representing the value of this information item in a particular dimension of this image.
getInfo(String, int, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getInfoList() - 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() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getInfoList(int, int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getInfoList(int, int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Returns an InfoList object applying to a particular dimension/element for this image.
getInfoList(int, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getInnerROIs() - Method in class com.xinapse.multisliceimage.roi.HollowROI
Returns a list of ROIs that form the holes in this HollowROI.
getInputImages() - Method in class com.xinapse.image.SingleOrMultipleInputImageSelectionPanel
Returns the input images set in this SingleOrMultipleInputImageSelectionPanel.
getInputImages(boolean) - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the set of input images set in this MultiContrastAnalysisFrame.
getInstance() - Static method in class com.xinapse.apps.active.SelectableROICalculation
Returns an instance of this ROICalculation.
getInstance() - Static method in class com.xinapse.apps.cardiac.SelectableCardiacAnalysis
Returns an instance of this CardiacAnalysis.
getInstance(byte[], byte[], byte[]) - Static method in class com.xinapse.image.ColourMapping
Returns a ColourMapping object according to a set of red, green and blue gun values.
getInstance(byte[], int) - Static method in class com.xinapse.multisliceimage.Analyze.DICOMExtendedData
Creates a new block of NIFTI extended data.
getInstance(float[][]) - Static method in enum class com.xinapse.image.MostLikePlane
Returns the MostLikePlane corresponding to the image orientation in patient coordinates.
getInstance(DCMObject) - Static method in enum class com.xinapse.dicom.Modality
Finds the Modality in a DCMObject.
getInstance(Uid) - Static method in enum class com.xinapse.dicom.Modality
Returns a Modality corresponding to the supplied storage class SOP Uid.
getInstance(Uid, String) - Static method in enum class com.xinapse.dicom.Modality
Returns a Modality corresponding to the supplied Storage Class SOP UID and name.
getInstance(PixelDataType) - Static method in enum class com.xinapse.multisliceimage.Analyze.ANZPixFormat
Returns the ANZPixFormat corresponding to a PixelDataType.
getInstance(PixelDataType) - Static method in enum class com.xinapse.multisliceimage.UNC.UNCPixFormat
Returns the UNCPixFormat corresponding to a PixelDataType.
getInstance(PixelDataType, int, int[]) - Static method in class com.xinapse.image.PixArray
Creates one of the sub-classes of PixArray Object of the type specified by the pixel data type.
getInstance(PixelDataType, DataInputStream, ByteOrder, int, int[]) - Static method in class com.xinapse.image.PixArray
Creates one of the sub-classes of PixArray Object of the type specified by the dataType with pixel data coming from a DataInputStream.
getInstance(PixelDataType, RandomAccessFile, ByteOrder, int, int, int[]) - Static method in class com.xinapse.image.PixArray
Creates one of the sub-classes of PixArray Object of the type specified by the dataType with pixel data coming from a RandomAccessFile.
getInstance(VolumeInterpolator, InterpolationType) - Static method in class com.xinapse.image.VolumeInterpolator
Returns a new VolumeInterpolator, constructed from an existing one.
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(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(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(Point2D, Point2D, int, int, float, float, byte, ROIState) - Static method in class com.xinapse.multisliceimage.roi.LineROI
Creates a new LineROI.
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(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(Object, PixelDataType, int, int, int, float, float, float, BoundaryCondition, Float, InterpolationType) - Static method in class com.xinapse.image.VolumeInterpolator
Returns a new VolumeInterpolator for a block of pixel samples.
getInstance(String) - Static method in enum class com.xinapse.dicom.Modality
Returns a Modality corresponding to the supplied modality name.
getInstance(String) - Static method in enum class com.xinapse.dicom.PatientPosition
Returns a PatientPosition corresponding to the supplied string.
getInstance(String) - Static method in enum class com.xinapse.dicom.PulseSequenceType
Returns the PulseSequenceType corresponding to the supplied String.
getInstance(String) - Static method in enum class com.xinapse.filter.SobelFilter.SobelType
Returns a SolbelType corresponding to the given name.
getInstance(String) - Static method in enum class com.xinapse.image.BoundaryCondition
Returns the BoundaryCondition corresponding to the supplied string.
getInstance(String) - Static method in class com.xinapse.image.ColourMapping
Returns one of the "built-in" ColourMappings, selected according to its name.
getInstance(String) - Static method in enum class com.xinapse.image.ComplexMode
Returns the ComplexMode corresponding to the supplied String argument.
getInstance(String) - Static method in enum class com.xinapse.image.InputConfigurationType
Returns an InputConfigurationType Object corresponding to a string.
getInstance(String) - Static method in enum class com.xinapse.image.InterpolationType
Returns the InterpolationType corresponding to the description supplied in the argument.
getInstance(String) - Static method in enum class com.xinapse.image.MostLikePlane
Returns a MostLikePlane corresponding to a string.
getInstance(String) - Static method in enum class com.xinapse.image.RotationAngle
Returns a RotationAngle corresponding to a string.
getInstance(String) - Static method in enum class com.xinapse.image.SubSampleType
Returns the SubSampleType corresponding to a String representation.
getInstance(String) - Static method in enum class com.xinapse.image.template.WeightingType
Returns a WeightingType Object corresponding to the supplied String.
getInstance(String) - Static method in enum class com.xinapse.multisliceimage.Analyze.SliceOrder
Returns an SliceOrder corresponding to String value.
getInstance(String) - Static method in enum class com.xinapse.multisliceimage.roi.MaskMode
Returns a MaskMode corresponding to the supplied String.
getInstance(String) - Static method in enum class com.xinapse.multisliceimage.roi.StatsType
Returns the StatsType corresponding to the supplied String.
getInstance(String) - Static method in enum class com.xinapse.multisliceimage.roi.VertexHandle.Spacing
Returns a vertex handle spacing according to the supplied String.
getInstance(String) - Static method in enum class com.xinapse.util.IntensityRelation
Returns the IntensityRelation specified by the argument.
getInstance(String) - Static method in enum class com.xinapse.util.ReportGenerator.ReportType
Creates ReportType from a String.
getInstance(Vector3f[]) - Static method in enum class com.xinapse.image.MostLikePlane
Returns the MostLikePlane corresponding to the image orientation in patient coordinates.
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.
getInstances(Point3i, ContourMode, double, IntensityRelation, boolean, boolean, short, 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.
getIntensityProfile(Object, PixelDataType, int, int, int, float, float, ComplexMode) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
getIntensityProfile(Object, PixelDataType, int, int, int, float, float, ComplexMode) - Method in interface com.xinapse.multisliceimage.roi.LinearROI
Returns an array of Point2D representing the pixel intensities along this LinearROI.
getIntensityProfile(Object, PixelDataType, int, int, int, float, float, ComplexMode) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getIntensityProfile(Object, PixelDataType, int, int, int, float, float, ComplexMode) - Method in class com.xinapse.multisliceimage.roi.OpenSplineROI
 
getIntensityRelation() - Method in class com.xinapse.util.IntensityRelation.IntensityRelationButton
Returns the intensity relation set.
getIntensityRelation() - Method in class com.xinapse.util.IntensityRelation.PanelGenerator.Panel
Returns the IntensityRelation currently set.
getIntensityRescale() - Method in interface com.xinapse.image.ReadableImage
Returns the values m and b in the relationship between pixel intensity (I) values and the output units specified in getRescaleUnits() in the expression:
Output units = m*I + b.
getIntensityRescale() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Intensity rescaling is not supported by Analyze 7.5 format, so this method always returns float[] [1.0f, 0.0f].
getIntensityRescale() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getIntensityRescale() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getIntent() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the NIFTIIntent in this NIFTIImage.
getIntersectionLength(Rectangle2D, int, int, float, float) - Method in class com.xinapse.multisliceimage.roi.LineROI
Calculates the length of the line segment where this LineROI intersects the given Rectangle argument.
getKnotPoint(int) - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns a knot point location for this SplineROI.
getKnotPoints() - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns the knot point locations for this SplineROI.
getKnownClasses() - Static method in class com.xinapse.filter.FilterSelection
Returns a List of known classes of SpatialFilter.
getKnownInstance(String) - Static method in class com.xinapse.image.ColourMapping
Returns one of "known" ColourMappings (either built-in or user-defined), selected according to its name.
getLastPathComponent(String) - Static method in class com.xinapse.multisliceimage.ImageName
Returns the last path component of a file or URL name.
getLaterality() - Method in interface com.xinapse.image.ReadableImage
Returns the image laterality.
getLaterality() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getLaterality() - Method in class com.xinapse.multisliceimage.MultiSliceImage
By default, laterality recording is not supported, so this method returns Laterality.BOTH.
getLaterality() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getLeftLabel(String) - Static method in class com.xinapse.image.template.ICBMLabel
Returns the integer code for the region name for the left side of the brain.
getLength() - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
getLength() - Method in interface com.xinapse.multisliceimage.roi.LinearROI
Returns the length of this ROI in mm.
getLength() - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getLength() - Method in class com.xinapse.multisliceimage.roi.OpenSplineROI
 
getLengthPix(float, float) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
getLengthPix(float, float) - Method in interface com.xinapse.multisliceimage.roi.LinearROI
Returns the length of this ROI in image pixels.
getLengthPix(float, float) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getLengthPix(float, float) - Method in class com.xinapse.multisliceimage.roi.OpenSplineROI
 
getLesionProbTemplate() - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in lesion probability template image (which has been warped to the same space as the T1-weighted template image).
getLevel() - Method in class com.xinapse.multisliceimage.roi.ContourROI
Returns the intensity level that this ContourROI followed.
getLine() - Method in class com.xinapse.multisliceimage.roi.LineROI
Returns the line forming this LineROI in mm coordinates.
getLocation(double) - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns the position of the SplineROI outline at a particular value of the s-parameter.
getLuminance(Color) - Static method in enum class com.xinapse.image.PixelDataType
Returns the luminance value of a Color.
getLVProbTemplate() - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in lateral ventricle probability template image.
getMaskMode() - Method in class com.xinapse.multisliceimage.roi.MaskMode.Panel
Returns the MaskMode set in this panel.
getMaskROIFile() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
Returns the mask ROI file if masking by a ROIs has been selected.
getMaskROIs() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
Returns the mask ROIs if masking by a ROIs has been selected.
getMax() - Method in class com.xinapse.image.IntensityPreset
Returns the maximum intensity value in the preset.
getMax() - Method in interface com.xinapse.image.ReadableImage
Returns the maximum pixel intensity in the image.
getMax() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
 
getMax() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getMax() - Method in class com.xinapse.multisliceimage.roi.Feret
Returns the maximum Feret's diameter.
getMax() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getMaxBinnableValue(PixelDataType) - Method in class com.xinapse.image.Histogram
Returns the maximum value that can be added to this Histogram's bins.
getMaxLuminance() - Static method in class com.xinapse.image.ColourMapping
Returns the current maximmum display luminance setting for a digital driver level (DDL) of 255.
getMean() - Method in class com.xinapse.image.Histogram
Returns the mean intensity value of this Histogram.
getMean(boolean) - Method in class com.xinapse.image.Histogram
Returns the mean intensity value of this Histogram, optionally excluding all values that are zero.
getMeanSD(float[], float[], float[], int, int, int) - Static method in class com.xinapse.image.template.TissueNormaliser
Returns mean and standard deviation statistics about a T1-weighted image and a FLAIR image.
getMeanSD(ReadableImage, ReadableImage, ReadableImage) - Static method in class com.xinapse.image.template.TissueNormaliser
Returns mean and standard deviation statistics about a T1-weighted image and a FLAIR image.
getMedian() - Method in class com.xinapse.image.Histogram
Returns the median value of this Histogram.
getMedian() - Method in class com.xinapse.multisliceimage.roi.ROIStats
Returns the median pixel intensity.
getMedian() - Method in class com.xinapse.multisliceimage.roi.VOIStats
Returns the median pixel intensity.
getMedian(boolean) - Method in class com.xinapse.image.Histogram
Returns the median value of this Histogram, optionally excluding all values that are zero.
getMedian(float[], float[], float[], int, int, int) - Static method in class com.xinapse.image.template.TissueNormaliser
Returns median intensities for a T1-weighted image and a FLAIR image.
getMedian(ReadableImage, ReadableImage, ReadableImage) - Static method in class com.xinapse.image.template.TissueNormaliser
Returns median intensity statistics for a T1-weighted image and a FLAIR image.
getMin() - Method in class com.xinapse.image.IntensityPreset
Returns the minimum intensity value in the preset.
getMin() - Method in interface com.xinapse.image.ReadableImage
Returns the minimum pixel intensity in the image.
getMin() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
 
getMin() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getMin() - Method in class com.xinapse.multisliceimage.roi.Feret
Returns the minimum Feret's diameter.
getMin() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getMinimumSize() - Method in class com.xinapse.image.MultipleImageSelectionPanel
 
getMinLuminance() - Static method in class com.xinapse.image.ColourMapping
Returns the current minimum display luminance setting for a digital driver level (DDL) of zero.
getMinMax() - Method in class com.xinapse.image.PixArray
Finds the minimum and maximum values in this PixArray.
getMinMax() - Method in class com.xinapse.multisliceimage.Analyze.ANZHeader
Gets the glMin and glMax fields for this Analyze image header.
getMinMax(Object) - Method in enum class com.xinapse.image.PixelDataType
Returns the minimum and maximum intensity values that are present in an array of pixel values.
getMinMax(Object, int, int, ComplexMode) - Method in enum class com.xinapse.image.PixelDataType
Returns the minimum and maximum intensity values that are present in subset of an array of pixel values.
getMinMax(Object, int, int, PixelDataType, ComplexMode) - Static method in class com.xinapse.image.Histogram
Returns the minimum and maximum intensity values present in a part of an array of pixel values.
getMinMax(Object, ComplexMode) - Method in enum class com.xinapse.image.PixelDataType
Returns the minimum and maximum intensity values that are present in an array of pixel values.
getMinMax(Object, PixelDataType, ComplexMode) - Static method in class com.xinapse.image.Histogram
Returns the minimum and maximum intensity values present in an array of pixel values.
getMod() - Method in class com.xinapse.image.Complex
Returns the modulus of this complex number.
getMod() - Method in class com.xinapse.image.DoubleComplex
 
getMod() - Method in class com.xinapse.image.FloatComplex
 
getModality() - Method in interface com.xinapse.image.ReadableImage
Returns the imaging modality with which this image was collected.
getModality() - Method in class com.xinapse.multisliceimage.MultiSliceImage
 
getModel(int, int, float, ReadableImage) - Method in class com.xinapse.dynamic.DynamicModel.SpecifierPanel
Returns the DynamicModel that has been specified by this DynamicModel.SpecifierPanel.
getModelDescription() - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
Returns a String describing this dynamic contrast model.
getModelDescription() - Method in interface com.xinapse.dynamic.DynamicModel
Returns a String describing this dynamic model.
getModelName() - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
Returns the model name.
getModelName() - Method in interface com.xinapse.dynamic.DynamicModel
Returns the model name.
getModSq() - Method in class com.xinapse.image.Complex
Returns the square of the modulus of this complex number.
getModSq() - Method in class com.xinapse.image.DoubleComplex
 
getModSq() - Method in class com.xinapse.image.FloatComplex
 
getMostLikePlane() - Method in interface com.xinapse.image.ReadableImage
Returns the imaging plane that this image is "most like".
getMostLikePlane() - Method in class com.xinapse.multisliceimage.MultiSliceImage
 
getMSLesionCorrelTemplate(boolean) - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in MS lesion correlation template image.
getMSLesionProbTemplate(boolean) - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in MS lesion probability template image.
getMSPDHeadTemplate(boolean) - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in proton density weighted head template image.
getName() - Static method in class com.xinapse.filter.ColourImageFilter
Returns the human-readable name of this filter.
getName() - Static method in class com.xinapse.filter.GaussianBlurFilter
Returns the human-readable name of this filter.
getName() - Static method in class com.xinapse.filter.LaplacianFilter
Returns the human-readable name of this filter.
getName() - Static method in class com.xinapse.filter.MedianFilter
Returns the human-readable name of this filter.
getName() - Static method in class com.xinapse.filter.MorphologicalOperator
Returns the human-readable name of this filter.
getName() - Static method in class com.xinapse.filter.PatchSimilarityFilter
Returns the human-readable name of this filter.
getName() - Static method in class com.xinapse.filter.SharpenFilter
Returns the human-readable name of this filter.
getName() - Static method in class com.xinapse.filter.SobelFilter
Returns the human-readable name of this filter.
getName() - Static method in class com.xinapse.multisliceimage.roi.ContourROI
Returns the name of the type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.CurvedLineROI
Returns a descriptive name for this type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.EllipticalROI
Returns a descriptive name for this type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.HollowROI
Returns a descriptive name for this type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.IrregularROI
Returns a descriptive name for this type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.LineROI
Returns a descriptive name for this type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.Marker
Returns a descriptive name for this type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.OpenSplineROI
Returns a descriptive name for this type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.RadialDivider
Returns a descriptive name for this type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.RectangularROI
Returns a descriptive name for this type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.SplineROI
Returns a descriptive name for this type of ROI.
getName() - Static method in class com.xinapse.multisliceimage.roi.Text
Returns a descriptive name for this type of ROI.
getName() - Method in class com.xinapse.util.InfoItem
Return the keyword for this InfoItem.
getNativeColourMapping() - Method in interface com.xinapse.image.ReadableImage
Returns a ColourMapping if this image has an associated colour mapping.
getNativeColourMapping() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
Returns a ColourMapping if this Analyze image has an associated colour mapping.
getNativeColourMapping() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getNativeHeader() - Method in interface com.xinapse.image.ReadableImage
Returns a String showing the 'native' header for this image.
getNativeHeader() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getNativeHeader() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getNBins() - Method in class com.xinapse.image.Histogram
Returns the number of bins in this Histogram.
getNChoosableColors() - Static method in enum class com.xinapse.multisliceimage.roi.ROIState
Returns the number of user-choosable ROI colours that may be set.
getNCols() - Method in class com.xinapse.image.ImageGrid
Returns the number of columns in the ImageGrid.
getNCols() - Method in interface com.xinapse.image.ReadableImage
Returns the number of image columns in this image.
getNCols() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getNCols() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getNContrasts() - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the number of image contrasts set in this MultiContrastAnalysisFrame.
getNContrasts(ReadableImage[], Integer, boolean, String) - Static method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the number of image contrasts in a set of input images.
getNDim() - Method in interface com.xinapse.image.ReadableImage
Returns the dimensionality of this image.
getNDim() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getNDim() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns the MultiSliceImage dimensionality of this image.
getNFrames() - Method in interface com.xinapse.image.ReadableImage
Returns the number of frames in a multi-frame image.
getNFrames() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getNFrames() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getNImages() - Method in class com.xinapse.image.ImageSelectionGroupPanel
Returns the number of ImageSelectionGroupMemberPanels in this group.
getNImages() - Method in class com.xinapse.image.MultipleImageSelectionPanel
Returns the number of images currently set in this MultipleImageSelectionPanel.
getNKernelCols() - Method in class com.xinapse.filter.AbstractComplexKernelFilter
Returns the number of columns in the filter kernel.
getNKernelCols() - Method in class com.xinapse.filter.AbstractKernelFilter
Returns the number of columns in the filter kernel.
getNKernelCols() - Method in class com.xinapse.filter.FixedWeightsComplexKernelFilter
 
getNKernelCols() - Method in class com.xinapse.filter.FixedWeightsKernelFilter
 
getNKernelCols() - Method in class com.xinapse.filter.MedianFilter
 
getNKernelCols() - Method in class com.xinapse.filter.MorphologicalOperator
 
getNKernelRows() - Method in class com.xinapse.filter.AbstractComplexKernelFilter
Returns the number of rows in the filter kernel.
getNKernelRows() - Method in class com.xinapse.filter.AbstractKernelFilter
Returns the number of rows in the filter kernel.
getNKernelRows() - Method in class com.xinapse.filter.FixedWeightsComplexKernelFilter
 
getNKernelRows() - Method in class com.xinapse.filter.FixedWeightsKernelFilter
 
getNKernelRows() - Method in class com.xinapse.filter.MedianFilter
 
getNKernelRows() - Method in class com.xinapse.filter.MorphologicalOperator
 
getNKernelSlices() - Method in class com.xinapse.filter.AbstractComplexKernelFilter
Returns the number of slices in the filter kernel.
getNKernelSlices() - Method in class com.xinapse.filter.AbstractKernelFilter
Returns the number of slices in the filter kernel.
getNKernelSlices() - Method in class com.xinapse.filter.FixedWeightsComplexKernelFilter
 
getNKernelSlices() - Method in class com.xinapse.filter.FixedWeightsKernelFilter
 
getNKernelSlices() - Method in class com.xinapse.filter.MedianFilter
 
getNKernelSlices() - Method in class com.xinapse.filter.MorphologicalOperator
 
getNormal(double) - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns the outward normal vector at a particular value of the s-parameter.
getNormal(int) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Returns the outward normal vector at a vertex.
getNormal(int) - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns the outward normal vector at a knot point.
getNPixels(int, int[]) - Static method in class com.xinapse.image.ImageUtils
Returns the total number of picture elements for an image with the given dimensions.
getNPixels(Object) - Method in enum class com.xinapse.image.PixelDataType
Returns the number of pixels in the supplied array of pixel samples.
getNPoints() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Returns the number of vertices that define the outline.
getNPoints() - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns the number of knot points that define the shape.
getNRows() - Method in class com.xinapse.image.ImageGrid
Returns the number of rows in the ImageGrid.
getNRows() - Method in interface com.xinapse.image.ReadableImage
Returns the number of image rows in this image.
getNRows() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getNRows() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getNSegments() - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Returns the number of segments.
getNSliceLocations() - Method in interface com.xinapse.image.ReadableImage
Returns the number of unique slice locations present in the image.
getNSliceLocations() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
For Analyze 7.5 images, all slices in a block are parallel and evenly-spaced.
getNSliceLocations() - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the number of image slice locations for the images set in this MultiContrastAnalysisFrame.
getNSliceLocations(ReadableImage[], Integer, boolean, String) - Static method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the number of physical image slice locations for a set of images.
getNSlices() - Method in interface com.xinapse.image.ReadableImage
Returns the number of physical slice locations in this image.
getNSlices() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getNSlices() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getNSlots() - Method in class com.xinapse.image.ColourMapping
Returns the number of slots in this ColourMapping.
getNSteadyStates() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
Returns the number of pre-steady-state images set in the GUI.
getOppositeEnd(EndHandle) - Method in class com.xinapse.multisliceimage.roi.LineROI
Returns the location of the end that is at the other end to the specified handle.
getOptionName() - Static method in class com.xinapse.apps.active.SelectableROICalculation
Returns the option name for selecting this ROI calculation method.
getOptionName() - Static method in class com.xinapse.filter.ColourImageFilter
Returns the name of this type of filter when specifying it in program optional arguments.
getOptionName() - Static method in class com.xinapse.filter.GaussianBlurFilter
Returns the name of this type of filter when specifying it in program optional arguments.
getOptionName() - Static method in class com.xinapse.filter.LaplacianFilter
Returns the name of this type of filter when specifying it in program optional arguments.
getOptionName() - Static method in class com.xinapse.filter.MedianFilter
Returns the name of this type of filter when specifying it in program optional arguments.
getOptionName() - Static method in class com.xinapse.filter.MorphologicalOperator
Returns the name of this type of filter when specifying it in program optional arguments.
getOptionName() - Static method in class com.xinapse.filter.PatchSimilarityFilter
Returns the name of this type of filter when specifying it in program optional arguments.
getOptionName() - Static method in class com.xinapse.filter.SharpenFilter
Returns the name of this type of filter when specifying it in program optional arguments.
getOptionName() - Static method in class com.xinapse.filter.SobelFilter
Returns the name of this type of filter when specifying it in program optional arguments.
getOptions() - Static method in class com.xinapse.filter.ColourImageFilter
Returns the options for this type of filter.
getOptions() - Static method in class com.xinapse.filter.GaussianBlurFilter
Returns the options for this type of filter.
getOptions() - Static method in class com.xinapse.filter.LaplacianFilter
Returns the options for this type of filter.
getOptions() - Static method in class com.xinapse.filter.MedianFilter
Returns the options for this type of filter.
getOptions() - Static method in class com.xinapse.filter.MorphologicalOperator
Returns the options for this type of filter.
getOptions() - Static method in class com.xinapse.filter.PatchSimilarityFilter
Returns the options for this type of filter.
getOptions() - Static method in class com.xinapse.filter.SobelFilter
Returns the options for this type of filter.
getOptionSpecifier() - Method in class com.xinapse.apps.perfusion.DCEMRIModel
Returns the specifier used to select the this model.
getOrient() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Gets the orientation of this Analyze75Image.
getOuterROI() - Method in class com.xinapse.multisliceimage.roi.HollowROI
Returns the ROI that encloses all the inner ROIs.
getOutputImagesBaseName() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
Returns the basename for the output images.
getParentWindow() - Method in class com.xinapse.image.ImageSelectionPanel
 
getParentWindow() - Method in class com.xinapse.image.MultipleImageSelectionPanel
 
getParentWindow() - Method in interface com.xinapse.util.MessageShower
Returns the parent of this MessageShower.
getPatientDoB() - Method in interface com.xinapse.image.ReadableImage
Returns the patient date of birth for this image.
getPatientDoB() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Patient's Birth Date is not supported by Analyze 7.5 format.
getPatientDoB() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getPatientDoB() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getPatientID() - Method in interface com.xinapse.image.ReadableImage
Returns the patient ID for this image.
getPatientID() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Header
Returns the patient ID for this Analyze image header.
getPatientID() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Returns the Patient ID set in the image header.
getPatientID() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the patient ID for this image.
getPatientID() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getPatientName() - Method in interface com.xinapse.image.ReadableImage
Returns the patient name for this image.
getPatientName() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Patient names are not supported by Analyze 7.5 format.
getPatientName() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the patient name for this image.
getPatientName() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getPatientPosition() - Method in interface com.xinapse.image.ReadableImage
Returns the position in which the patient is lying in the scanning equipment.
getPatientPosition() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getPatientPosition() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getPatientPosition() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getPatientSex() - Method in interface com.xinapse.image.ReadableImage
Returns the patient sex for this image.
getPatientSex() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
 
getPatientSex() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getPatientSex() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getPeakHeight(boolean) - Method in class com.xinapse.image.Histogram
Returns the number of values with the most common value in this Histogram, optionally excluding the values that are zero-valued.
getPeakPosition(boolean) - Method in class com.xinapse.image.Histogram
Returns the most common value in this Histogram, optionally excluding the values that are zero-valued.
getPenSize() - Method in class com.xinapse.multisliceimage.roi.PenSizePanel
Returns the pen size set.
getPerimeter() - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
Returns the perimeter length of this ROI.
getPerimeter() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
Returns the perimeter length of this EllipticalROI.
getPerimeter() - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
getPerimeter() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
getPerimeter() - Method in class com.xinapse.multisliceimage.roi.LineROI
Returns the perimeter length of this ROI.
getPerimeter() - Method in class com.xinapse.multisliceimage.roi.Marker
 
getPerimeter() - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Returns zero.
getPerimeter() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
getPerimeter() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the perimeter length of this ROI.
getPerimeter() - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
getPhase(ReadableImage, ReadableImage, List<ROI>) - Static method in class com.xinapse.image.PhaseImage
Return the phase values from an image where pixel values represent phase.
getPhase(ReadableImage, Object, PixelDataType, Object, PixelDataType) - Static method in class com.xinapse.image.PhaseImage
Return the phase values from pixel values that represent phase and (optionally) magnitude.
getPhase(ReadableImage, Object, PixelDataType, Object, PixelDataType, List<ROI>) - Static method in class com.xinapse.image.PhaseImage
Return the phase values from pixel values that represent phase and (optionally) magnitude.
getPhase(Object, PixelDataType) - Static method in class com.xinapse.image.PhaseImage
Return the phase values from pixel values that represent phase.
getPix() - Method in class com.xinapse.image.PixArray
Returns a copy of the array of pixel values encapulated by this PixArray.
getPix() - Method in interface com.xinapse.image.ReadableImage
Returns all the pixel values for this image in the order in which they are stored internally, and with intensity values as they are to be presented to the user (i.e., after any intensity rescaling).
getPix() - Method in class com.xinapse.multisliceimage.MultiSliceImage
Returns all pixel values from this image.
getPix(boolean) - Method in interface com.xinapse.image.ReadableImage
Returns all the pixel values for this image, optionally returning them in the correct order in which they will be presented, where the first pixel should be presented at the top left corner of the display device.
getPix(boolean) - Method in class com.xinapse.multisliceimage.MultiSliceImage
Returns all pixel values from this image.
getPix(int[]) - Method in interface com.xinapse.image.ReadableImage
Returns a single pixel value from this image.
getPix(int[]) - Method in class com.xinapse.multisliceimage.MultiSliceImage
Returns a single pixel value from the image.
getPix(int[], int[]) - Method in interface com.xinapse.image.ReadableImage
Returns pixel values from this image.
getPix(int[], int[]) - Method in class com.xinapse.multisliceimage.MultiSliceImage
 
getPix(Object, int[], int[]) - Method in interface com.xinapse.image.ReadableImage
Get pixel values from this image into a specified array.
getPix(Object, int[], int[]) - Method in class com.xinapse.multisliceimage.MultiSliceImage
 
getPixelDataType() - Method in enum class com.xinapse.multisliceimage.Analyze.ANZPixFormat
Returns the PixelDataType corresponding to this ANZPixFormat.
getPixelDataType() - Method in enum class com.xinapse.multisliceimage.UNC.UNCPixFormat
Returns the PixelDataType corresponding to this UNCPixFormat.
getPixels(Object, int) - Method in enum class com.xinapse.image.PixelDataType
Gets an array of pixel samples, large enough to hold a specified number of pixels.
getPixelsAsFloat(Object) - Method in enum class com.xinapse.image.PixelDataType
Returns a set of pixel samples as an array of float values.
getPixelsAsFloat(Object, int, int) - Method in enum class com.xinapse.image.PixelDataType
Returns a set of pixel samples as an array of float values.
getPixelValue(Object, int, int, int, int, int) - Method in enum class com.xinapse.image.PixelDataType
Gets the pixel value at a particular (column, row) of an array of pixels of this PixelDataType.
getPixelValue(Object, PixelDataType, ComplexMode, int, int, int, int, int) - Static method in class com.xinapse.multisliceimage.roi.ROI
Returns the pixel value at a particular (column,row) of an array of pixels.
getPixelXSize() - Method in interface com.xinapse.image.ReadableImage
Returns the pixel size in the x (horizontal) direction for this image.
getPixelXSize() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getPixelXSize() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getPixelYSize() - Method in interface com.xinapse.image.ReadableImage
Returns the pixel size in the y (vertical) direction for this image.
getPixelYSize() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getPixelYSize() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getPixelZSize() - Method in interface com.xinapse.image.ReadableImage
Returns the separation between the centres of image planes for this image.
getPixelZSize() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getPixelZSize() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getPixformat() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns the pixel format (pixformat) of this image.
getPrecedingVisibleHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
getPrecedingVisibleHandle(Handle) - Method in interface com.xinapse.multisliceimage.roi.EditableOutlineROI
Returns the visible Handle that is immediately before the specified handle, in the order in which they were placed around the ROI.
getPrecedingVisibleHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
getPrecedingVisibleHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
getPrecedingVisibleHandle(Handle) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
getPreferredAlwaysOnTop() - Static method in class com.xinapse.multisliceimage.roi.ROIPreferencesDialog
Returns the setting of whether to the ROI toolkit should always be on top of other windows, as set in the user preferences.
getPreferredCombineMode(Preferences, CombineMode) - Static method in enum class 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 class com.xinapse.multisliceimage.roi.ContourMode
Returns the user's preferred ContourMode.
getPreferredCreateNonFlipped() - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Header
Returns the user's preference about whether newly-created Analyze 7.5 images should have a non-flipped orientation.
getPreferredDoNotFlipFlipped() - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Header
Returns the user's preference about whether an Analyze 7.5 image with a flipped orientation should be treated as if it has a non-flipped orientation.
getPreferredErodeDilateFraction() - Static method in class com.xinapse.multisliceimage.roi.ROIPreferencesDialog
Returns the erode/dilate distance as a fraction of the image pixel size as set in the user preferences.
getPreferredFlipNonFlipped() - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Header
Returns the user's preference about whether an Analyze 7.5 image with a non-flipped orientation should be treated as if it has a flipped orientation.
getPreferredFSLCompatibleNIFTI() - Static method in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
Returns the user's preference about whether NIFTI-1 images with both qform and sform orientations unset should be read as having the patient left coordinate increasing with stored pixel data column number, and whether NIFTI-1 images should be prevented from being written without orientation information.
getPreferredImageClass() - Static method in class com.xinapse.image.ImageUtils
Returns the WritableImage class set in the user's Preferences.
getPreferredImagePreview() - Static method in class com.xinapse.image.ImagePreview
Returns the user's preference for whether to generate an image preview thumbnail.
getPreferredInputConfigurationType(Preferences) - Static method in enum class com.xinapse.image.InputConfigurationType
Returns the user's preferred InputConfigurationType.
getPreferredInterpolationType(Preferences, InterpolationType) - Static method in enum class com.xinapse.image.InterpolationType
Returns the InterpolationType set in the preferences.
getPreferredMaskAction() - Static method in enum class com.xinapse.multisliceimage.roi.MaskAction
Returns the user's preferred mask action.
getPreferredMaskMode(Preferences, MaskMode) - Static method in enum class com.xinapse.multisliceimage.roi.MaskMode
Returns the MaskMode set in the UserPreferences, or the default MaskMode, if none is set in the Preferences.
getPreferredMaxUndos() - Static method in class com.xinapse.multisliceimage.roi.ROIPreferencesDialog
Returns the maximum number of undo operations set in the user preferences.
getPreferredMergeContours() - Static method in class com.xinapse.multisliceimage.roi.ROIPreferencesDialog
Returns the setting of whether contours should be merged after 3-D propagagtion as set in the user preferences.
getPreferredMinimise() - Static method in class com.xinapse.multisliceimage.roi.ROIPreferencesDialog
Returns the setting of whether to the ROI toolkit should be minimised on startup, in the user preferences.
getPreferredModality() - Static method in enum class com.xinapse.dicom.Modality
Returns the user's most common-used Modality as set in the user Preferences.
getPreferredMode(Preferences) - Static method in enum class com.xinapse.image.ComplexMode
Returns the ComplexMode set in the supplied Preferences, or the default ComplexMode.
getPreferredNIFTIOneFile() - Static method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the user's preference about whether NIFTI images should be stored in two separate files (.hdr and .hdr) or one (.nii).
getPreferredOp(Preferences) - Static method in enum class com.xinapse.filter.MorphologicalOperator.Op
Returns the MorphologicalOperator.Op set in the given preferences.
getPreferredOp(Preferences) - Static method in enum class com.xinapse.multisliceimage.roi.LogicalOperator
Returns the LogicalOperator.Op set in the given preferences.
getPreferredOverwrite() - Static method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns whether the user prefers to overwrite UNC images.
getPreferredPatientPosition() - Static method in enum class com.xinapse.dicom.PatientPosition
Returns the user's preferred PatientPosition set in the user Preferences.
getPreferredRenderingInterpolationType() - Static method in enum class com.xinapse.image.RenderingInterpolationType
Returns the user's preferred RenderingInterpolationType as set in the user preferences.
getPreferredRotationAngle(Preferences) - Static method in enum class com.xinapse.image.RotationAngle
Gets the preferred rotation angle from the Preferences.
getPreferredSaveFolderFollowsImage() - Static method in class com.xinapse.multisliceimage.roi.ROIPreferencesDialog
Returns the setting of whether to the folder for saving ROIs follows the image as set in the user preferences.
getPreferredSaveFSLOrient() - Static method in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
Returns the user's preference about whether NIFTI-1 images should be saved with an orientation that is compatible with FSL, where possible.
getPreferredSaveSPMOrient() - Static method in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
Returns the user's preference about whether NIFTI-1 images should be saved with an orientation that is compatible with SPM, where possible.
getPreferredShowExtendedStats() - Static method in class com.xinapse.multisliceimage.roi.ROIPreferencesDialog
Returns the setting of show extended statistics set in the user preferences.
getPreferredShowStatistics() - Static method in class com.xinapse.multisliceimage.roi.ROIPreferencesDialog
Returns the setting of whether to show ROI statistics on startup, in the user preferences.
getPreferredSize() - Method in class com.xinapse.image.ImageFileChooser
Returns the preferred size of the image file chooser.
getPreferredSize() - Method in class com.xinapse.image.ImagePreview
Returns the preferred size of this component.
getPreferredSize() - Method in class com.xinapse.image.ImageSelectionPanel
Overrides the default getPreferredSize() method.
getPreferredSize() - Method in class com.xinapse.image.InputImageSelectionPanel
Override the default getPreferredSize() method.
getPreferredSize() - Method in class com.xinapse.image.MultipleImageSelectionPanel
Override the default getPreferredSize() method.
getPreferredSize() - Static method in class com.xinapse.image.PreviewIcon
Returns the icon's preferred size.
getPreferredSize() - Method in class com.xinapse.image.ScanDetailsPanel
Overrides the default getPreferredSize() method.
getPreferredSize() - Method in class com.xinapse.image.SelectedImagePanel
Overrides the default getPreferredSize() method.
getPreferredSize() - Method in class com.xinapse.multisliceimage.roi.HistoryDialog
 
getPreferredSnapCentre() - Static method in class com.xinapse.multisliceimage.roi.ROIPreferencesDialog
Returns the setting of snap to the centre of pixels set in the user preferences.
getPreferredSpacing() - Static method in enum class com.xinapse.multisliceimage.roi.VertexHandle.Spacing
Returns the Spacing set in the user Preferences, or the default if not in the preferences.
getPreferredSubSampleType(Preferences, SubSampleType) - Static method in enum class com.xinapse.image.SubSampleType
Returns the SubSampleType set in the preferences.
getPreferredType() - Static method in enum class com.xinapse.dicom.PulseSequenceType
Returns the user's preferred PulseSequenceType set in the user Preferences.
getPreferredWarnNegativePixelHeight() - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Header
Returns the user's preference about whether the user should be warned about negative pixel height in Analyze 7.5 images.
getPreferredWarnNegativePixelWidth() - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Header
Returns the user's preference about whether the user should be warned about negative pixel width in Analyze 7.5 images.
getPreferredWeightingType(Preferences) - Static method in enum class com.xinapse.image.template.WeightingType
Gets the WeightingType set in the preferences.
getPresentationPixelDataType() - Method in interface com.xinapse.image.ReadableImage
Returns a PixelDataType representing the data type of pixel values for this image, after any intensity scaling has taken place.
getPresentationPixelDataType() - Method in class com.xinapse.multisliceimage.MultiSliceImage
 
getPreviewIcon(File, boolean) - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Returns the PreviewIcon for an Analyze75Image header, or null if the supplied File does not represent an Analyze 7.5 image header.
getPreviewIcon(File, boolean) - Static method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the PreviewIcon for an NIFTIImage, or null if the supplied File does not represent a NIFTI image.
getPreviewIcon(File, boolean) - Static method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns the PreviewIcon for a UNC image, or null if the supplied File does not represent a UNC image.
getPrimitiveClass() - Method in enum class com.xinapse.image.PixelDataType
Returns the Class of primitive used to store pixel values of this PixelDataType.
getPrincipalAxes(ReadableImage, Object, PixelDataType, Point3f, boolean) - Static method in class com.xinapse.image.ImageMoments
Calculates the principal axes of an image.
getPrincipalAxes(ReadableImage, Point3f, Double, boolean, boolean) - Static method in class com.xinapse.image.ImageMoments
Calculates the principal axes of an image.
getPrincipalAxisAngle() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
Returns the angle between the major principal axis of this ROI and the x-axis.
getPrincipalAxisAngle() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Returns the angle between the major principal axis of this ROI and the x-axis.
getPrincipalAxisAngle() - Method in class com.xinapse.multisliceimage.roi.LineROI
Returns the angle between the major principal axis of this ROI and the x-axis.
getPrincipalAxisAngle() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
Returns the angle between the major principal axis of this ROI and the x-axis.
getPrincipalAxisAngle() - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns the angle between the major principal axis of this ROI and the x-axis.
getProgName() - Method in class com.xinapse.util.MonitorWorker
Returns the program name for this MonitorWorker.
getPulseSequence() - Method in interface com.xinapse.image.ReadableImage
Returns the name of the pulse sequence with which this image was collected.
getPulseSequence() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Pulse sequence names are not supported by Analyze 7.5 for,at.
getPulseSequence() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getPulseSequence() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getPutPix(Object, int[], int[], PixelOp) - Method in class com.xinapse.image.DoublePixArray
 
getPutPix(Object, int[], int[], PixelOp) - Method in class com.xinapse.image.PixArray
Basic pixel accessor method for images of any dimensionality.
getPutPix(Object, int[], PixelOp) - Method in class com.xinapse.image.DoublePixArray
Gets/puts a single pixel value from/to an an image.
getPutPix(Object, int[], PixelOp) - Method in class com.xinapse.image.PixArray
Gets/puts a single pixel value from/to this PixArray.
getPutPix(Object, int[], RandomAccessFile, ByteOrder, int, PixelDataType, int, int[], PixelOp) - Static method in class com.xinapse.image.PixArray
Gets/puts a pixel value from/to an array of pixels.
getPutPix(Object, RandomAccessFile, ByteOrder, int, PixelDataType, int, int[], int[], int[], PixelOp) - Static method in class com.xinapse.image.PixArray
Basic pixel accessor method for images of any dimensionality where pixel data is held in a RandomAccessFile.
getPutSlice(Object, int, PixelOp) - Method in class com.xinapse.image.DoublePixArray
Returns a 1-Dimensional array of type int, cast as an Object, with array indices [0 to (nRows * nCols)-1], representing the pixel intensity values for one slice of this image.
getPutSlice(Object, int, PixelOp) - Method in class com.xinapse.image.PixArray
Returns a 1-Dimensional array of type appropriate of the image pixel type, cast as an Object, with array indices [0 to (nRows * nCols)-1], representing the pixel intensity values for one slice of this image.
getPutSlice(Object, int, RandomAccessFile, ByteOrder, int, PixelDataType, int, int[], PixelOp) - Static method in class com.xinapse.image.PixArray
Returns a 2-Dimensional array type appropriate to the primitive type for the image, cast as an Object, with array indices [0 to (nRows * nCols) - 1], representing the pixel intensity values for one slice of this image.
getQForm() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the qForm in this NIFTIImage.
getRangeMax() - Method in enum class com.xinapse.image.PixelDataType
Returns the maximum value that a pixel of this PixelDataType can take.
getRangeMin() - Method in enum class com.xinapse.image.PixelDataType
Returns the minimum value that a pixel of this PixelDataType can take.
getReadableImage() - Method in class com.xinapse.image.InputImageSelectionPanel
Returns the ReadableImage that has been set in this InputImageSelectionPanel.
getReadableImage() - Method in class com.xinapse.image.SelectedImagePanel
Returns the ReadableImage set in this SelectedImagePanel.
getReadableImage(int) - Method in class com.xinapse.image.ImageSelectionGroupPanel
Returns the ReadableImage for the ImageSelectionGroupMemberPanel at particular location in the group.
getReadableImage(int) - Method in class com.xinapse.image.MultipleImageSelectionPanel
Returns the ReadableImage for the MultipleImageSelectionPanel at particular location in the list of images.
getReadableImage(int, int) - Method in class com.xinapse.image.ImageGrid
Returns the ReadableImage for the InputImageSelectionPanel at particular location in the ImageGrid.
getReadableImage(File) - Static method in class com.xinapse.image.ImageUtils
Returns a ReadableImage, reading the image data from a file.
getReadableImage(String) - Static method in class com.xinapse.image.ImageUtils
Returns a ReadableImage, reading the image data from a file.
getReadableImages() - Method in class com.xinapse.image.ImageGrid
Returns a 2-D array of images that is set in the grid.
getReadableImages() - Method in class com.xinapse.image.MultipleImageSelectionPanel
Returns an array of ReadableImages with each array member being an image currently set in the MultipleImageSelectionPanel.
getReal() - Method in class com.xinapse.image.Complex
Returns the real part of this complex number.
getReal() - Method in class com.xinapse.image.DoubleComplex
 
getReal() - Method in class com.xinapse.image.FloatComplex
 
getRenderingHint() - Method in enum class com.xinapse.image.RenderingInterpolationType
Returns the rendering hint for this RenderingInterpolationType.
getRenderingInterpolationType() - Method in class com.xinapse.image.RenderingInterpolationType.RenderingInterpolationTypeButton
Returns the current RenderingInterpolationType that this button's current state represents.
getReportType() - Method in class com.xinapse.util.ReportGenerator
Returns the ReportType generated.
getRescaleUnits() - Method in interface com.xinapse.image.ReadableImage
Returns the output units of Intensity Rescale Slope and Intensity Rescale Intercept, retrieved by getIntensityRescale().
getRescaleUnits() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
 
getRescaleUnits() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getRescaleUnits() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns RescaleUnits.US.
getRescaleUnits() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getResultTitle() - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastResult
Returns a title for the type of report.
getResultTitle() - Method in class com.xinapse.dynamic.DynamicResult
Returns a title suitable for heading up this DynamicResult.
getRightLabel(String) - Static method in class com.xinapse.image.template.ICBMLabel
Returns the integer code for the region name for the right side of the brain.
getRMSError() - Method in class com.xinapse.dynamic.DynamicResult
Returns the RMS difference between the fit and the data.
getROIOutput() - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Returns the current set of both current and deleted ROIs, outputted as text to a byte[].
getROIs() - Method in interface com.xinapse.image.ReadableImage
Returns a List of ROIs that are stored with the image.
getROIs() - Method in class com.xinapse.multisliceimage.MultiSliceImage
 
getROIs() - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Returns a List of current (not deleted) ROIs for the image displayed.
getROIs() - Method in class com.xinapse.multisliceimage.roi.ROIFileSelectionPanel
Returns a List of ROIs from the ROI file set in this ROIFileSelectionPanel.
getROIs(int) - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Returns a 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(File, Float, Float, Integer, Integer, MonitorWorker) - 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(InputStream, Float, Float, Integer, Integer, MonitorWorker) - Static method in class com.xinapse.multisliceimage.roi.ROI
Returns a List of ROIs read from an InputStream.
getRotation() - Method in class com.xinapse.image.RotationAngle.RotationPanel
Returns the current selected rotation.
getSaturationFreqOffsetPPM() - Method in interface com.xinapse.image.ReadableImage
Returns the scan saturation frequency offset for this image if it has a single saturation frequency offset in parts-per-million.
getSaturationFreqOffsetPPM() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getSaturationFreqOffsetPPM() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the saturation pulse frequency offset for this image if it has a single saturation pulse frequency offset.
getSaturationFreqOffsetPPM() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSaturationFreqOffsetPPM(int) - Method in interface com.xinapse.image.ReadableImage
Returns the scan saturation frequency offset for one dimension index of this image in parts-per-million.
getSaturationFreqOffsetPPM(int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getSaturationFreqOffsetPPM(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getSaturationFreqOffsetPPM(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getScanDate() - Method in interface com.xinapse.image.ReadableImage
Returns the scan Date for this image.
getScanDate() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Scan dates are not supported by Analyze 7.5 format.
getScanDate() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the scan date for this image.
getScanDate() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getScanDateFormat() - Static method in class com.xinapse.multisliceimage.MultiSliceImage
Returns the DateFormat with which a scan date should be formatted.
getScanDateFormat() - Static method in class com.xinapse.util.ReportGenerator
Returns a DateFormat suitable for formatting scan dates.
getScanningSequence() - Method in interface com.xinapse.image.ReadableImage
Returns the DICOM Scanning Sequence with which this image was collected.
getScanningSequence() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Scan sequences are not supported by Analyze 7.5 format.
getScanningSequence() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getScanningSequence() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getScanTE() - Method in interface com.xinapse.image.ReadableImage
Returns the scan echo time for this image if it has a single echo-time.
getScanTE() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getScanTE() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the scan echo time for this image if it has a single echo-time.
getScanTE() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getScanTE(int) - Method in interface com.xinapse.image.ReadableImage
Returns the scan echo time for one dimension index of this image.
getScanTE(int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getScanTE(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getScanTE(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getScanTI() - Method in interface com.xinapse.image.ReadableImage
Returns the scan inversion time for this image.
getScanTI() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze 7.5 format, so this method always returns null.
getScanTI() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the scan inversion time for this image.
getScanTI() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getScanTR() - Method in interface com.xinapse.image.ReadableImage
Returns the scan repetition time for this image.
getScanTR() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze 7.5 format, so this method always returns null.
getScanTR() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the scan repetition time for this image.
getScanTR() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getScore() - Method in class com.xinapse.multisliceimage.roi.Dice
Returns the Dice similarity score.
getSD() - Method in class com.xinapse.image.Histogram
Returns the standard deviation of intensity values of this Histogram.
getSD(boolean) - Method in class com.xinapse.image.Histogram
Returns the standard deviation of intensity values of this Histogram, optionally excluding all values that are zero from the calculation.
getSecondDeriv(double) - Method in class com.xinapse.numerical.CubicSplineInterpolator
Returns the second derivative of the function value at a given value of x.
getSecondDerivs() - Method in class com.xinapse.numerical.CubicSplineInterpolator
Returns the internal array of second derivatives values at the knots.
getSeedPoint() - Method in class com.xinapse.multisliceimage.roi.ContourWorker
Returns the seed point from which contouring was initiated.
getSelectedColumns() - Method in class com.xinapse.image.ImageGrid
Returns the indices of the grid columns that have been selected by the user.
getSelectedIntensityPreset() - Method in class com.xinapse.image.IntensityPresetsMenu
Return the current selected IntensityPreset in the menu.
getSelectedItem() - Method in class com.xinapse.multisliceimage.roi.VertexHandle.SpacingPanel
Returns the current spacing set in this panel.
getSelectedModality() - Method in class com.xinapse.dicom.Modality.ComboBox
Returns the Modality selected.
getSelectedPatientPosition() - Method in class com.xinapse.dicom.PatientPosition.ComboBox
Returns the PatientPosition selected.
getSelectedRenderingInterpolationType() - Method in class com.xinapse.image.RenderingInterpolationType.ComboBox
Returns the RenderingInterpolationType selected.
getSelectedROIs() - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Returns a List of selected ROIs for the image displayed.
getSelectedRow() - Method in class com.xinapse.image.ImageGrid
Returns the index of the grid row that has been selected by the user.
getSelectedSlice() - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Returns the number of the selected image slice in this CanAddROIToFrame.
getSelectedType() - Method in class com.xinapse.dicom.PulseSequenceType.ComboBox
Returns the PulseSequenceType selected.
getSequenceVariant() - Method in interface com.xinapse.image.ReadableImage
Returns the DICOM Scanning Sequence Variant with which this image was collected.
getSequenceVariant() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Scanning sequence variants are not supported by Analyze 7.5 format.
getSequenceVariant() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getSequenceVariant() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSeriesDescription() - Method in interface com.xinapse.image.ReadableImage
Returns a short description of the series (scan), such as is provided by the DICOM series description.
getSeriesDescription() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Series descriptions are not supported by Analyze 7.5 format.
getSeriesDescription() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getSeriesDescription() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSeriesNumber() - Method in interface com.xinapse.image.ReadableImage
Returns the series number for this ReadableImage.
getSeriesNumber() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Series numbers are not supported by Analyze 7.5 format.
getSeriesNumber() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getSeriesNumber() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSForm() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the sForm in this NIFTIImage.
getSFormAffineTransform() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Returns the general (sForm) AffineTransform3D that will transform the pixel indices (colIdx, rowIdx, sliceIdx) to a position in space in a patient-centric coordinate system.
getSize() - Method in class com.xinapse.multisliceimage.roi.Handle
Returns the size of this ROI in screen pixels.
getSize(int) - Static method in class com.xinapse.multisliceimage.roi.Handle
Returns a suitable size of Handle for drawing an ROI of the given size.
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.
getSlice() - Method in class com.xinapse.multisliceimage.roi.InsertionPointHandle
Returns the physical slice number to which this InsertionPointHandle applies.
getSlice() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the slice number for this ROI.
getSlice(int) - Method in interface com.xinapse.image.ReadableImage
Returns the pixel values for one slice of an n-dimensional image, where n > 1.
getSlice(int) - Method in class com.xinapse.multisliceimage.MultiSliceImage
 
getSlice(Object, int) - Method in interface com.xinapse.image.ReadableImage
Returns all the pixels for a two-dimensional slice of this image, as a 1-dimensional array of primitive values.
getSlice(Object, int) - Method in class com.xinapse.multisliceimage.MultiSliceImage
 
getSliceDataType(int, int, ReadableImage[], boolean, int, boolean) - Static method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the PixelDataTypefor one physical slice location and one image contrast.
getSliceDim() - Method in class com.xinapse.multisliceimage.MultiSliceImage
Returns the index number to the "slice" dimension of the image.
getSliceDWBMatrix(int) - Method in interface com.xinapse.image.ReadableImage
Returns the diffusion-weighting b-matrix for one slice of this image.
getSliceDWBMatrix(int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getSliceDWBMatrix(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getSliceDWBMatrix(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSliceDWbValue(int) - Method in interface com.xinapse.image.ReadableImage
Returns the diffusion-weighting b-value for one slice of this image.
getSliceDWbValue(int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getSliceDWbValue(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getSliceDWbValue(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSliceDWGradientVector(int) - Method in interface com.xinapse.image.ReadableImage
Returns the diffusion-weighting gradient-vector for one slice of this image.
getSliceDWGradientVector(int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getSliceDWGradientVector(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getSliceDWGradientVector(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSliceInfo(String, int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getSliceInfo(String, int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Returns a String representing the value of this information item in a particular slice of this image.
getSliceInfo(String, int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSliceInfoList(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getSliceInfoList(int) - Method in interface com.xinapse.multisliceimage.InfoStorer
Returns an InfoList object applying to a particular slice of this image.
getSliceInfoList(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSlicePix(int, int, ReadableImage[], boolean, int, BinaryMask, String, boolean) - Static method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the pixel values for one physical slice location and one image contrast.
getSlicesAreReversed(ReadableImage) - Static method in class com.xinapse.image.ImageUtils
Tests whether the supplied image has slices which are in reverse order compared to standard radiological presentation order.
getSliceThickness() - Method in interface com.xinapse.image.ReadableImage
Returns the slice thickness (in mm).
getSliceThickness() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getSliceThickness() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getSliceThickness() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSliceTriggerDelayMS(int) - Method in interface com.xinapse.image.ReadableImage
Returns the trigger delay, in milliseconds, for one slice of this image.
getSliceTriggerDelayMS(int) - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
This action is not supported by the Analyze file format, so this method always returns null.
getSliceTriggerDelayMS(int) - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getSliceTriggerDelayMS(int) - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSMax() - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns that maximum s-parameter value for this SplineROI.
getSmoothedROI() - Method in class com.xinapse.multisliceimage.roi.SmootherWorker
After the SmootherWorker has run to completion, returns the smoothed ROI.
getSmoothingFWHMmm() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
Returns the full-width-at-half-maximum for the smoothing filter.
getSpacingFactor() - Method in enum class com.xinapse.multisliceimage.roi.VertexHandle.Spacing
Returns the spacing factor between handles.
getSpecifierPanel(ROIPropagateFrame, String) - Method in class com.xinapse.apps.active.SelectableROICalculation
Returns a ROICalculation.SpecifierPanel that can be used to select and specify a SelectableROICalculation.
getSpecifierPanel(CardiacFrame, String) - Method in class com.xinapse.apps.cardiac.SelectableCardiacAnalysis
Returns a CardiacAnalysis.SpecifierPanel that can be used to select and specify a SelectableCardiacAnalysis.
getSpecifierPanel(String) - Static method in class com.xinapse.filter.ColourImageFilter
Returns a SpatialFilter.SpecifierPanel that can be used to set the parameters for a ColourImageFilter.
getSpecifierPanel(String) - Static method in class com.xinapse.filter.GaussianBlurFilter
Returns a SpatialFilter.SpecifierPanel that can be used to set the parameters for a GaussianBlurFilter.
getSpecifierPanel(String) - Static method in class com.xinapse.filter.LaplacianFilter
Returns a SpatialFilter.SpecifierPanel that can be used to set the parameters for a LaplacianFilter.
getSpecifierPanel(String) - Static method in class com.xinapse.filter.MedianFilter
Returns a SpatialFilter.SpecifierPanel that can be used to set the parameters for a MedianFilter.
getSpecifierPanel(String) - Static method in class com.xinapse.filter.MorphologicalOperator
Returns a SpatialFilter.SpecifierPanel that can be used to set the parameters for a MorphologicalOperator.
getSpecifierPanel(String) - Static method in class com.xinapse.filter.PatchSimilarityFilter
Returns a SpatialFilter.SpecifierPanel that can be used to set the parameters for a PatchSimilarityFilter.
getSpecifierPanel(String) - Static method in class com.xinapse.filter.SharpenFilter
Returns a SpatialFilter.SpecifierPanel that can be used to set the parameters for a SharpenFilter.
getSpecifierPanel(String) - Static method in class com.xinapse.filter.SobelFilter
Returns a SpatialFilter.SpecifierPanel that can be used to set the parameters for a SobelFilter.
getSquareArea() - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
Returns zero - a curved line has no area.
getSquareArea() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
getSquareArea() - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getSquareArea() - Method in class com.xinapse.multisliceimage.roi.Marker
 
getSquareArea() - Method in class com.xinapse.multisliceimage.roi.OpenSplineROI
Returns zero - an Open Spline has no area.
getSquareArea() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
getSquareArea() - Method in interface com.xinapse.multisliceimage.roi.RegularROI
Returns the area of this regular ROI in square mm.
getState() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the state of this ROI.
getStats(ROI[], int, Object, PixelDataType, int, int, int, float, float, ComplexMode) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Returns an array of ROIStats - one for each segment, or two for each segment if there is an endo- epi-cardial split.
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.CurvedLineROI
 
getStats(Object, PixelDataType, int, int, int, float, float, MaskAction, MaskMode, double, PrintStream, boolean, ComplexMode) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getStats(Object, PixelDataType, int, int, int, float, float, MaskAction, MaskMode, double, PrintStream, boolean, ComplexMode) - Method in class com.xinapse.multisliceimage.roi.Marker
 
getStats(Object, PixelDataType, int, int, int, float, float, MaskAction, MaskMode, double, PrintStream, boolean, ComplexMode) - Method in class com.xinapse.multisliceimage.roi.OpenSplineROI
 
getStats(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.
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.
getStatus() - Method in enum class com.xinapse.platform.ExitStatus
Returns the integer exit status code for this ExitStatus.
getStorageClassUID() - Method in enum class com.xinapse.dicom.Modality
Returns a UID of the Storage Class with which Objects of this Modality can be stored.
getStoredPix() - Method in interface com.xinapse.image.ReadableImage
Returns all the pixel values for this image in the order in which they are stored internally, and in the format they are stored internally.
getStoredPix() - Method in class com.xinapse.multisliceimage.MultiSliceImage
 
getStoredPixelDataType() - Method in interface com.xinapse.image.ReadableImage
Returns a PixelDataType representing the data type of this image, as the pixel values are stored on disk.
getStoredPixelDataType() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getStoredPixelDataType() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getStudyID() - Method in interface com.xinapse.image.ReadableImage
Returns the study ID for this ReadableImage.
getStudyID() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Study ID is not supported by Analyze 7.5 format.
getStudyID() - Method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
 
getStudyID() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getSuggestedFileName() - Method in interface com.xinapse.image.ReadableImage
Returns the suggested file name for in-memory images that are to be saved to disk.
getSuggestedFileName() - Method in class com.xinapse.multisliceimage.MultiSliceImage
 
getTemplateImage(WeightingType) - Static method in class com.xinapse.image.template.HeadTemplate
Returns the a built-in template image of the specified weighting type.
getTextColor() - Static method in class com.xinapse.multisliceimage.roi.ROI
Returns the Color with which ROI annotation text should be rendered.
getTheta() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
getTheta() - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
getTheta() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
getTheta() - Method in class com.xinapse.multisliceimage.roi.LineROI
 
getTheta() - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Returns the insertion point angle.
getTheta() - Method in interface com.xinapse.multisliceimage.roi.RotatableROI
Returns the current rotation angle for this RotatableROI.
getTheta() - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
getThreshold() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
Returns the intensity threshold for pixel processing.
getTimeBetweenFrames() - Method in interface com.xinapse.image.ReadableImage
Returns the time between frames in a 4- or higher dimensional image.
getTimeBetweenFrames() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getTimeBetweenFrames() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getTimeBetweenImages() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
Returns the time between images set in the GUI.
getTimeShift(float, int, int) - Method in enum class 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 String.
getTitle() - Method in class com.xinapse.image.MultipleImageSelectionPanel
Returns the title for the list of images.
getTitle() - Method in interface com.xinapse.image.ReadableImage
Returns the title of this image.
getTitle() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getTitle() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns the title of this image.
getToolTipString() - Method in enum class com.xinapse.multisliceimage.roi.MaskMode
Returns a String that is useful for building a ToolTip or description of this MaskMode.
getTotalCount() - Method in class com.xinapse.image.Histogram
Returns the total number of values that contributed to this histogram.
getTotalCount(boolean) - Method in class com.xinapse.image.Histogram
Returns the total number of values that contributed to this histogram, optionally excluding any zero-valued values.
getTotalCount(double) - Method in class com.xinapse.image.Histogram
Returns the number of values in this histogram that are above the supplied threshold.
getTotalNSlices() - Method in interface com.xinapse.image.ReadableImage
Returns the total number of slices in this image.
getTotalNSlices() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
getTotalNSlices() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
getType() - Method in class com.xinapse.image.template.WeightingType.Panel
Returns the WeightingType set in this Panel.
getUseBrainFinder() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
Returns whether the Brain Finder option has been set in the GUI.
getUserColour() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns the user-defined colour for this ROI.
getUserComponent(int) - Method in class com.xinapse.image.ImageSelectionGroupPanel
Returns the user component associated with the image selection panel at the given index.
getUserComponents() - Method in class com.xinapse.image.ImageSelectionGroupPanel
Returns all user components.
getUserInstance(String) - Static method in class com.xinapse.image.ColourMapping
Returns one of the user-defined ColourMappings, selected according to its name.
getUserMappings() - Static method in class com.xinapse.image.ColourMapping
Returns a java.util.List&lt;ColourMapping&gt; of the ColourMappings imported by the user and stored in the user preferences.
getUserObject() - Method in exception com.xinapse.util.CancelledException
Retrieves the User Object associated with this CancelledException.
getUserPresets() - Static method in class com.xinapse.image.IntensityPreset
Returns a java.util.List<IntensityPreset> of the IntensityPresets created by the user and stored in the user preferences.
getV1() - Method in class com.xinapse.multisliceimage.roi.Dice
Returns the volume of the first set of ROIs.
getV2() - Method in class com.xinapse.multisliceimage.roi.Dice
Returns the volume of the second set of ROIs.
getValidIntensityStats() - Method in class com.xinapse.multisliceimage.roi.ROIStats
Returns whether this ROIStats has valid intensity-related statistics.
getValidIntensityStats() - Method in class com.xinapse.multisliceimage.roi.VOIStats
Returns whether this VOIStats has valid intensity-related statistics.
getValue() - Method in class com.xinapse.util.InfoItem
Return the value for this InfoItem.
getValue(ComplexMode) - Method in class com.xinapse.image.Complex
Returns a (real-valued) component of this Complex.
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 AbstractDynamicContrastModel.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 DynamicModel.getVarUnits().
getVarNames() - Method in class com.xinapse.dynamic.DynamicResult
Returns the fitted variable names.
getVarUnits() - Method in class com.xinapse.apps.perfusion.AbstractDynamicContrastModel
Returns an array of the fitted variable units, in an order that matches the order of the variable names returned by AbstractDynamicContrastModel.getVarNames().
getVarUnits() - Method in interface com.xinapse.dynamic.DynamicModel
Returns an array of the fitted variable units, in an order that matches the order of the variable names returned by #getVarNames().
getVarUnits() - Method in class com.xinapse.dynamic.DynamicResult
Returns the fitted variable units.
getVertex(int) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Returns a vertex location for this IrregularROI.
getVertexHandles() - Method in interface com.xinapse.multisliceimage.roi.EditableOutlineROI
Returns an array of VertexHandles.
getVertexHandles() - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
getVertexHandles() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
getVertexHandles() - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
getVertices() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Returns the vertex locations for this IrregularROI.
getVOIs(List<ROI>) - Static method in class com.xinapse.multisliceimage.roi.VOI
Returns a List of VOIs (3-D volumes of interest) created from a List of ROIs.
getVOIStats(ReadableImage, List<ROI>, boolean, ComplexMode, MonitorWorker) - Static method in class com.xinapse.multisliceimage.roi.VOIStats
Returns a List of the VOIStats for the 3-D connected VOIs formed by a set of ROIs.
getVolume(float) - Method in class com.xinapse.multisliceimage.roi.VOI
Returns the volume of a VOI.
getVolumePix(int, ReadableImage[], boolean, int, Integer, BinaryMask, String, boolean) - Static method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the pixels for one particular 3-D volume.
getWidth() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
Returns the width of this RectangularROI in mm.
getWMProbTemplate() - Static method in class com.xinapse.image.template.HeadTemplate
Returns the built-in white-matter probability template image.
getWorkingDirectory() - Method in class com.xinapse.image.ImageGrid
Returns the "current working directory" for this ImageGrid.
getWorkingDirectory() - Method in class com.xinapse.image.ImageSelectionGroupPanel
Returns the "current working directory" for this ImageSelectionGroupPanel.
getWorkingDirectory() - Method in class com.xinapse.image.ImageSelectionPanel
Returns the "current working directory" for this ImageSelectionPanel.
getWorkingDirectory() - Method in class com.xinapse.image.MultipleImageSelectionPanel
Returns the "current working directory" for this MultipleImageSelectionPanel.
getWritableImage() - Method in class com.xinapse.image.OutputImageSelectionPanel
Returns the WritableImage that has been set in this OutputImageSelectionPanel.
getWritableImage(ReadableImage) - Static method in class com.xinapse.image.ImageUtils
Returns an in-memory WritableImage that is a copy of the image supplied.
getWritableImage(ReadableImage, int) - Static method in class com.xinapse.image.ImageUtils
Returns an in-memory WritableImage that is a copy of the image supplied except that the number of image slices may be changed.
getWritableImage(ReadableImage, int, int[]) - Static method in class com.xinapse.image.ImageUtils
Returns an in-memory WritableImage that is a copy of the image supplied except that the image dimensionality and dimensions may be changed.
getWritableImage(ReadableImage, PixelDataType) - Static method in class com.xinapse.image.ImageUtils
Returns an in-memory WritableImage that is a copy of the image supplied except that the stored PixelDataType may be changed.
getWritableImage(ReadableImage, Class<? extends WritableImage>) - Static method in class com.xinapse.image.ImageUtils
Returns an in-memory WritableImage that is a copy of the image supplied except that the class of the image may be changed.
getWritableImage(ReadableImage, Class<? extends WritableImage>, int, int[], PixelDataType) - Static method in class com.xinapse.image.ImageUtils
Creates a new in-memory WritableImage with the class of WritableImage class given by the argument, possibly changing the number of slices in the image and the PixelDataType.
getWritableImage(ReadableImage, Class<? extends WritableImage>, int, PixelDataType) - Static method in class com.xinapse.image.ImageUtils
Creates a new in-memory WritableImage with the class of WritableImage class given by the argument, possibly changing the number of slices in the image and the PixelDataType.
getWritableImage(File) - Static method in class com.xinapse.image.ImageUtils
Returns a WritableImage (opened read-write), reading the image data from a file.
getWritableImage(String) - Static method in class com.xinapse.image.ImageUtils
Returns a WritableImage (opened read-write), reading the image data from a file.
getWritableImageClass(Class) - Static method in class com.xinapse.image.ImageUtils
Returns the WritableImage Class that is assignable from the supplied class, or if not assignable, the WritableImage Class set in the user's Preferences.
getWritableImageClass(Object) - Static method in class com.xinapse.image.ImageUtils
Returns the WritableImage Class that can be deduced from the supplied image, or the WritableImage Class set in the user's Preferences.
getWritableImageClass(String) - Static method in class com.xinapse.image.ImageUtils
Returns the WritableImage Class that is assignable from the supplied class name.
getWritableImageClasses() - Static method in class com.xinapse.image.ImageUtils
Returns a List of classes that are known to implement WritableImage.
getWritableImageCommonName(Class<? extends WritableImage>) - Static method in class com.xinapse.image.ImageUtils
Returns the "common name" (for example, "NIFTI-1") for a Class of WritableImage.
getWriteDescription(boolean, boolean, boolean, boolean, boolean, boolean, PixelDataType, ComplexMode) - Method in class com.xinapse.multisliceimage.roi.ROIStats
Returns a java.util.List<String> of each of the requested statistics, correctly formatted for writing.
getWriteDescription(boolean, boolean, boolean, boolean, boolean, boolean, PixelDataType, ComplexMode) - Method in class com.xinapse.multisliceimage.roi.VOIStats
Returns a java.util.List<String> of each of the requested statistics, correctly formatted for writing.
getX() - Method in class com.xinapse.multisliceimage.roi.Marker
Returns the x-coordinate of this Marker.
getX() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
Returns the x-coordinate of the top left corner of this RectangularROI in mm.
getX1() - Method in class com.xinapse.multisliceimage.roi.LineROI
Returns the x-coordinate of the first end of the line.
getX2() - Method in class com.xinapse.multisliceimage.roi.LineROI
Returns the x-coordinate of the second end of the line.
getXAxisLabel() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
For the purposes of plotting data, returns the x-axis label.
getXAxisLabel() - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the x-axis label for a pop-up plot.
getXStart() - Method in class com.xinapse.dynamic.AbstractDynamicFrame
For the purposes of plotting data, returns the starting value of the independent variable.
getXStart() - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Returns the minimum x-value for a pop-up plot.
getY() - Method in class com.xinapse.multisliceimage.roi.Marker
Returns the y-coordinate of this Marker.
getY() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
Returns the y-coordinate of the top left corner of this RectangularROI in mm.
getY1() - Method in class com.xinapse.multisliceimage.roi.LineROI
Returns the y-coordinate of the first end of the line.
getY2() - Method in class com.xinapse.multisliceimage.roi.LineROI
Returns the y-coordinate of the second end of the line.
GR - Enum constant in enum class com.xinapse.dicom.PulseSequenceType
Gradient-echo pulse sequence type.
GREEN - Static variable in class com.xinapse.image.ColourMapping
The ColourMapping representing a green intensity scale.
GREEN_FORMULA_OPTION - Static variable in class com.xinapse.filter.ColourImageFilter
A public Option to specify the formula used to calculate the new green component values in the output image.
GREY - Enum constant in enum class com.xinapse.multisliceimage.UNC.UNCPixFormat
UNCPixFormat for grey (aka short 16-bit) pixel values.
group(List<ROI>) - Static method in class com.xinapse.multisliceimage.roi.ROI
Form an ROI group from a List of ROIs.
GROUP - Enum constant in enum class com.xinapse.multisliceimage.roi.ROIEditAction
Group ROIs.

H

HAEMODYNAMIC_WAVEFORM - Enum constant in enum class com.xinapse.dicom.Modality
Haemodynamic waveform Modality.
HALF - Enum constant in enum class com.xinapse.multisliceimage.roi.MaskMode
MaskMode such that if at least 50% of a pixel is inside an ROI, that pixel is part of the mask.
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.
HARD_COPY - Enum constant in enum class com.xinapse.dicom.Modality
Hard copy Modality; cannot store.
hasCurrentROIs() - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Tests whether a CanAddROIToFrame has current (not deleted) ROIs.
hashCode() - Method in class com.xinapse.filter.MorphologicalOperator
 
hashCode() - Method in class com.xinapse.image.ColourMapping
 
hashCode() - Method in class com.xinapse.image.DoubleComplex
Returns a hash code value for this DoubleComplex number.
hashCode() - Method in class com.xinapse.image.FloatComplex
Returns a hash code value for this FloatComplex number.
hashCode() - Method in class com.xinapse.image.template.ICBMLabel
 
hashCode() - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
Returns a hash code value for this CurvedLineROI.
hashCode() - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
Returns a hash code value for this EllipticalROI.
hashCode() - Method in class com.xinapse.multisliceimage.roi.HollowROI
Returns a hash code value for this IrregularROI.
hashCode() - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Returns a hash code value for this IrregularROI.
hashCode() - Method in class com.xinapse.multisliceimage.roi.LineROI
Returns a hash code value for this LineROI.
hashCode() - Method in class com.xinapse.multisliceimage.roi.Marker
Returns a hash code value for this Marker ROI.
hashCode() - Method in class com.xinapse.multisliceimage.roi.RectangularROI
Returns a hash code value for this RectangularROI.
hashCode() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns a hash code value for the ROI.
hashCode() - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns a hash code value for this SplineROI.
hashCode() - Method in class com.xinapse.multisliceimage.roi.Text
Returns a hash code value for this Marker ROI.
hashCode() - Method in class com.xinapse.util.BitSet
Returns a hash code value for this bit set.
HeadTemplate - Class in com.xinapse.image.template
Access to the built-in and head template images.
HEIGHTTOKEN - Static variable in class com.xinapse.multisliceimage.roi.RectangularROI
The token written to ROI output files to represent the height of a rectangular ROI.
HELP_REQUESTED - Enum constant in enum class com.xinapse.platform.ExitStatus
Exit status for termination when help has been requested (1).
HERTZ - Enum constant in enum class com.xinapse.multisliceimage.Analyze.TUnits
Time units of Hertz.
HFDL - Enum constant in enum class com.xinapse.dicom.PatientPosition
PatientPosition indicating head-first, decubitus left.
HFDR - Enum constant in enum class com.xinapse.dicom.PatientPosition
PatientPosition indicating head-first, decubitus right.
HFP - Enum constant in enum class com.xinapse.dicom.PatientPosition
PatientPosition indicating head-first, prone.
HFS - Enum constant in enum class com.xinapse.dicom.PatientPosition
PatientPosition indicating head-first, supine.
HIGH - Enum constant in enum class com.xinapse.multisliceimage.roi.VertexHandle.Spacing
Far apart spacing.
histo - Variable in class com.xinapse.multisliceimage.roi.ROIStats
The histogram of pixel intensities inside an ROI in intensity units.
histo - Variable in class com.xinapse.multisliceimage.roi.VOIStats
The histogram of pixel intensities inside the VOI in intensity units.
Histogram - Class in com.xinapse.image
A class for creating histograms and finding statistics about arrays of values (normally pixel intensities).
Histogram(double[], double, double) - Constructor for class com.xinapse.image.Histogram
Creates a Histogram of intensities from pre-computed values.
Histogram(float[], double, double) - Constructor for class com.xinapse.image.Histogram
Creates a Histogram of intensities from pre-computed values.
Histogram(Histogram) - Constructor for class com.xinapse.image.Histogram
Creates a new Histogram, copying all values from an existing Histogram.
Histogram(Object, int, int, PixelDataType) - Constructor for class com.xinapse.image.Histogram
Creates a Histogram of intensities from an array of values of a given PixelDataType.
Histogram(Object, int, int, PixelDataType, double, double, double, ComplexMode) - Constructor for class com.xinapse.image.Histogram
Creates a Histogram of intensities from an array of values over a specified intensity range, and width a specified bin width.
Histogram(Object, int, int, PixelDataType, double, double, int, ComplexMode) - Constructor for class com.xinapse.image.Histogram
Creates a Histogram of intensities from an array of values over a specified intensity range, and with the specified number of bins.
Histogram(Object, int, int, PixelDataType, double, double, ComplexMode) - Constructor for class com.xinapse.image.Histogram
Creates a Histogram of intensities from an array of values over a specified intensity range.
Histogram(Object, int, int, PixelDataType, ComplexMode) - Constructor for class com.xinapse.image.Histogram
Creates a Histogram of intensities from an array of values, with an option to specifiy the mode of calculation for PixelDataType.COMPLEX, or PixelDataType.DOUBLECOMPLEX images.
Histogram(Object, PixelDataType) - Constructor for class com.xinapse.image.Histogram
Creates a Histogram of intensities from an array of values of a given PixelDataType.
Histogram(Object, PixelDataType, ComplexMode) - Constructor for class com.xinapse.image.Histogram
Creates a Histogram of intensities from an array of values of a given PixelDataType.
Histogram.BinSpec - Class in com.xinapse.image
A specification for Histogram bins.
HistoryDialog - Class in com.xinapse.multisliceimage.roi
A JDialog that is used to display ROI audit-trail information as a table.
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 Class in com.xinapse.multisliceimage.roi
An enumeration of the types of HistoryItem that are associated with ROIs.
HOBS - Static variable in class com.xinapse.image.ColourMapping
The ColourMapping representing a hot body (black to white via red) intensity scale.
HollowROI - Class in com.xinapse.multisliceimage.roi
A Class representing an irregularly-shaped region but with one or more holes.
HollowROI(List<ROI>, ROIState) - Constructor for class com.xinapse.multisliceimage.roi.HollowROI
Creates a new HollowROI, created from a List of ROIs, where one ROI completely contains all the others.
HYPERINTENSE - Enum constant in enum class com.xinapse.util.IntensityRelation
A feature is hyperintense.
HYPOINTENSE - Enum constant in enum class com.xinapse.util.IntensityRelation
A feature is hypointense.

I

ICBMLabel - Class in com.xinapse.image.template
Class for handling the ICBM atlas labels.
Image - Class in com.xinapse.image
Contains settings that are common across all images, together with some utilities for images.
IMAGE_CREATE_ERROR - Enum constant in enum class com.xinapse.platform.ExitStatus
Exit status when an output image cannot be created (23).
IMAGE_OPEN_ERROR - Enum constant in enum class com.xinapse.platform.ExitStatus
Exit status when an image cannot be opened (21).
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.
IMAGE_WRITE_ERROR - Enum constant in enum class com.xinapse.platform.ExitStatus
Exit status when an output image cannot be written (24).
imageChooser - Variable in class com.xinapse.image.ImageSelectionPanel
The ImageFileChooser that can be popped up to select a new image.
imageClassToFilter - Variable in class com.xinapse.image.ImageSelectionPanel
The class of image that will intially be filtered when the user first selects the image.
ImageDebug - Class in com.xinapse.image
Enables and disables debugging messages for the image package.
imageExists(String) - 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, Class<? extends WritableImage>) - Static method in class com.xinapse.image.ImageUtils
Tests whether a WritableImage with the given name already exists on disk.
ImageFileChooser - Class in com.xinapse.image
Abstract Class for File Choosers for opening ReadableImages, and saving WritableImages, Includes appropriate file filters, titles and button labels.
ImageFileChooser.LoadChooser - Class in com.xinapse.image
ImageFileChooser suitable for selecting a ReadableImage file for loading.
ImageFileChooser.SaveChooser - Class in com.xinapse.image
ImageFileChooser suitable for selecting a WritableImage file for saving.
ImageFileFilter - Class in com.xinapse.image
A file filter for all images that can be loaded directly into Jim.
ImageGrid - Class in com.xinapse.image
An ImageGrid allows the selection of a 2-D 'matrix' of ReadableImages and contains the mechanism for adding images to the matrix, removing images from the matrix, etc.
ImageGrid(MessageShower, Preferences) - Constructor for class com.xinapse.image.ImageGrid
Creates a new ImageGrid, that is contained within a parent MessageShower, and with initially one image in the set of images, and a minimum of one image in the set.
ImageGrid(MessageShower, Preferences, int, int, int, int, int, int, int, int, boolean, boolean) - Constructor for class com.xinapse.image.ImageGrid
Creates a new ImageGrid, that is contained within a parent JFrame, and with minimum number and initial number of images in the set given by the argument.
imageInputPanel - Variable in class com.xinapse.util.MultiContrastAnalysisFrame
The JPanel that contains the input configuration widgets.
ImageJROIFileFilter - Class in com.xinapse.multisliceimage.roi
A FileFilter for ImageJ region of interest files.
ImageJROIFileFilter() - Constructor for class com.xinapse.multisliceimage.roi.ImageJROIFileFilter
Constructor for ImageJROIFileFilter.
ImageMoments - Class in com.xinapse.image
Calculation of factors derived from the moments of an image.
ImageName - Class in com.xinapse.multisliceimage
Class to add extensions, prefixes and suffices to image file and URL names.
ImagePreview - Class in com.xinapse.image
JComponent that is used to preview an image file.
ImagePreview(JFileChooser) - Constructor for class com.xinapse.image.ImagePreview
Creates a new ImagePreview.
ImageSaveException - Exception in com.xinapse.image
Signals that an error has occurred when trying to save an image.
ImageSaveException() - Constructor for exception com.xinapse.image.ImageSaveException
Constructs an ImageSaveException with "image couldn't be saved" as its detail message.
ImageSaveException(String) - Constructor for exception com.xinapse.image.ImageSaveException
Constructs an ImageSaveException with the specified detail message.
ImageSelectionGroupPanel - Class in com.xinapse.image
An ImageSelectionGroupPanel allows the selection of a group of ReadableImages and contains the mechanism for adding images to the group, removing images from the group, etc.
ImageSelectionGroupPanel(MessageShower) - Constructor for class com.xinapse.image.ImageSelectionGroupPanel
Creates a new ImageSelectionGroupPanel, that is contained within a parent JFrame, and with initially one image in the set of images, and a minimum of one image in the set.
ImageSelectionGroupPanel(MessageShower, int, ImageSelectionGroupPanel.ComponentGenerator, double) - Constructor for class com.xinapse.image.ImageSelectionGroupPanel
Creates a new ImageSelectionGroupPanel, that is contained within a parent JFrame, and with minimum number and initial number of images in the set given by the argument.
ImageSelectionGroupPanel.ComponentGenerator - Interface in com.xinapse.image
An interface implemented by classes that want to be able to generate user components to put into an ImageSelectionGroupPanel.
ImageSelectionPanel - Class in com.xinapse.image
An ImageSelectionPanel is a JPanel that can be used to select an image, either for reading or for writing.
ImageSelectionPanel(MessageShower, File, Class<? extends ReadableImage>, boolean) - Constructor for class com.xinapse.image.ImageSelectionPanel
Creates new ImageSelectionPanel, with the default Folder given by argument, and with the image file selection field optionally on only one line.
ImageUtils - Class in com.xinapse.image
Contains various image utility static methods.
ImageWriter - Class in com.xinapse.image
Contains static methods for writing images.
IMAGINARY - Enum constant in enum class com.xinapse.image.ComplexMode
Selects the imaginary part of a complex number.
incState() - Method in class com.xinapse.image.RenderingInterpolationType.RenderingInterpolationTypeButton
Increment to the next RenderingInterpolationType.
indeterminateMonitor - Variable in class com.xinapse.util.MonitorWorker
An IndeterminateProgressMonitor which may pop up.
IndeterminateProgressMonitor - Class in com.xinapse.util
A JDialog for showing progress through an operation that will take an indeterminate number of steps, or an unknown time to complete.
IndeterminateProgressMonitor(Component, Object, String) - Constructor for class com.xinapse.util.IndeterminateProgressMonitor
Constructs a JDialog that shows progress that will take place over an indeterminate time, typically by making a rectangular bar oscillate from side to side.
InfoExtendedData - Class in com.xinapse.multisliceimage.Analyze
NIFTI 1.1 extended data that allows artibrary text to be associated with an image.
InfoItem - Class in com.xinapse.util
An image information item key-value pair.
InfoList - Class in com.xinapse.util
Representation of a list of information to be associated either with an image as a whole, or with a particular element of a particular dimension of an image.
InfoList() - Constructor for class com.xinapse.util.InfoList
Construct an empty InfoList.
InfoList(DataInputStream) - Constructor for class com.xinapse.util.InfoList
Creates a InfoList Object by reading it from a DataInputStream.
InfoList(String) - Constructor for class com.xinapse.util.InfoList
Creates an InfoList from an HTML description of that list.
InfoListException - Exception in com.xinapse.util
Signals that an error has occurred while creating or handling an InfoList.
InfoListException() - Constructor for exception com.xinapse.util.InfoListException
Constructs an InfoListException with null as its detail message.
InfoListException(String) - Constructor for exception com.xinapse.util.InfoListException
Constructs an InfoListException with the specified detail message.
InfoNotFoundException - Exception in com.xinapse.multisliceimage
Signals that information about an InfoStorer has not been found.
InfoNotFoundException() - Constructor for exception com.xinapse.multisliceimage.InfoNotFoundException
Constructs an InfoNotFoundException with null as its detail message.
InfoNotFoundException(String) - Constructor for exception com.xinapse.multisliceimage.InfoNotFoundException
Constructs an InfoNotFoundException with the specified detail message.
InfoNotFoundException(String, Throwable) - Constructor for exception com.xinapse.multisliceimage.InfoNotFoundException
Constructs an InfoNotFoundException with the specified cause.
InfoStorer - Interface in com.xinapse.multisliceimage
An interface that classes implement to indicate that they can store arbitrary textual information.
INNERPOINTSTOKEN - Static variable in class com.xinapse.multisliceimage.roi.HollowROI
The token written to ROI output files to indicate that a list of inner points is to follow.
Input - Class in com.xinapse.io
Abstract class providing methods to read primitve data values from input sources.
InputConfigurationType - Enum Class in com.xinapse.image
The types of input image configuration: either a single input image, or multiple input images.
InputImageSelectionPanel - Class in com.xinapse.image
A component that can be used to select a ReadableImage for input.
InputImageSelectionPanel(MessageShower) - Constructor for class com.xinapse.image.InputImageSelectionPanel
Creates new InputImageSelectionPanel, with the default Folder set to the System Property user.dir.
InputImageSelectionPanel(MessageShower, boolean) - Constructor for class com.xinapse.image.InputImageSelectionPanel
Creates new InputImageSelectionPanel, with the default Folder set to the System Property user.dir, and with the image file selection field on only one line.
InputImageSelectionPanel(MessageShower, File, Class<? extends ReadableImage>, boolean) - Constructor for class com.xinapse.image.InputImageSelectionPanel
Creates new InputImageSelectionPanel, with the default Folder given by argument, and with the image file selection field optionally on only one line.
InsertionPointHandle - Class in com.xinapse.multisliceimage.roi
A Handle to indicate and move the insertion point for a RadialDivider.
InsertionPointHandle(int, int, int, Point2D) - Constructor for class com.xinapse.multisliceimage.roi.InsertionPointHandle
Creates a new InsertionPointHandle at the location (x,y), in screen pixels.
insertTwoVertices(Handle) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
insertTwoVertices(Handle) - Method in interface com.xinapse.multisliceimage.roi.EditableOutlineROI
Insert two points into the outline of this EditableOutlineROI: one just before the one that is under a handle, and one just after.
insertTwoVertices(Handle) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
insertTwoVertices(Handle) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
insertTwoVertices(Handle) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
insertVertex(double, double) - Method in class com.xinapse.multisliceimage.roi.IrregularROIInProgress
Inserts a vertex at the beginning of this IrregularROIInProgress.
insertVertex(Point2D) - Method in class com.xinapse.multisliceimage.roi.IrregularROIInProgress
Inserts a vertex at the beginning of this IrregularROIInProgress.
INSTANCE - Static variable in class com.xinapse.image.ImageFileFilter
An ImageFileFilter used for testing whether a File refers to a WritableImage.
INSTANCE - Static variable in class com.xinapse.multisliceimage.Analyze.AnalyzeFileFilter
The only instance of a NIFTIFileFilter.
INSTANCE - Static variable in class com.xinapse.multisliceimage.Analyze.NIFTIFileFilter
The only instance of a NIFTIFileFilter.
INSTANCE - Static variable in class com.xinapse.multisliceimage.UNC.UNCFileFilter
The only instance of a UNCFileFilter.
INSUFFICIENT_RESOURCES - Enum constant in enum class com.xinapse.platform.ExitStatus
Exit status when there are insufficient resources available to perform the operation (80).
INT - Enum constant in enum class com.xinapse.image.PixelDataType
PixelDataType for signed int (32-bit).
INT - Enum constant in enum class com.xinapse.multisliceimage.Analyze.ANZPixFormat
ANZPixFormat for signed int (32-bit) pixel values.
IntArray(int[], int, int, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of int values to a RandomAccessFile f.
IntArray(int[], OutputStream, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of int values to a OutputStream strm.
IntArray(int[], RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of int values to a RandomAccessFile f.
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(InputStream, ByteOrder, int) - Static method in class com.xinapse.io.Input
Reads an array of int values from a InputStream 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 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 RandomAccessFile f ensuring that blocking occurs until all values have been read.
Integer(byte[], int) - Static method in class com.xinapse.io.Input
Gets an int value from an array of 4 bytes.
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(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(int) - Static method in class com.xinapse.io.ByteSwap
Swap the byte order in an an int and return the value represented by the bit pattern of the reversed bytes as an int.
Integer(int[], ByteOrder) - Static method in class com.xinapse.io.ByteSwap
Swap the byte order (if necessary) in an array of int values "in-place".
Integer(int, OutputStream, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single int to a OutputStream strm.
Integer(int, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single int to a RandomAccessFile f.
Integer(InputStream, ByteOrder) - Static method in class com.xinapse.io.Input
Reads an integer value from a 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 RandomAccessFile f, ensuring that blocking occurs until the value has been read.
Integer(Integer, OutputStream, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single Integer to a OutputStream strm as a primitive int value.
Integer(Integer, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single Integer to a RandomAccessFile f as a primitive int value.
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.
IntensityPreset - Class in com.xinapse.image
An intensity preset, particularly for CT images.
IntensityPresetsMenu - Class in com.xinapse.image
A JMenu containing a list of IntensityPresets and allied operations.
IntensityPresetsMenu(ChangeableContrast) - Constructor for class com.xinapse.image.IntensityPresetsMenu
Creates a new IntensityPresetsMenu.
IntensityRelation - Enum Class in com.xinapse.util
An enumeration of possible intensity relationships.
IntensityRelation.IntensityRelationButton - Class in com.xinapse.util
A Button for setting an intensity relation.
IntensityRelation.PanelGenerator - Class in com.xinapse.util
Class for generating JPanels for selecting an IntensityRelation.
IntensityRelation.PanelGenerator.Panel - Class in com.xinapse.util
A JPanel for selecting an IntensityRelation.
IntensityRelationButton(Preferences) - Constructor for class com.xinapse.util.IntensityRelation.IntensityRelationButton
Create a new IntensityRelationButton.
InteractionType - Enum Class in com.xinapse.multisliceimage.roi
An enumeration of the different ways in which a user can interact with an ROI.
INTERNAL_ERROR - Enum constant in enum class com.xinapse.platform.ExitStatus
Exit status when an internal (programming) error has occurred (90).
interpolate(double) - Method in class com.xinapse.numerical.CubicSplineInterpolator
Returns an interpolated value of y for a value of x.
interpolate(float[], byte[]) - Method in class com.xinapse.image.ColourVolumeInterpolator
Interpolate the intensity samples at a set of supplied coordinates.
interpolate(float[], float[]) - Method in class com.xinapse.image.VolumeInterpolator
Interpolate the intensity samples at a set of supplied coordinates.
interpolate(SplineROI, SplineROI, double) - Static method in class com.xinapse.multisliceimage.roi.SplineROI
Creates a new SplineROI by interpolating between two SplineROIs.
interpolate(Object, double, double) - Method in enum class com.xinapse.image.PixelDataType
Interpolates between two pixel intensity values.
InterpolationType - Enum Class in com.xinapse.image
An enumeration of the types of interpolation that can be used for resampling images.
intersect(ROI) - Method in class com.xinapse.multisliceimage.roi.ROI
Intersects this ROI with another ROI.
intersect(ROI, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
intersect(ROI, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
intersect(ROI, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
intersect(ROI, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
intersect(ROI, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
intersect(ROI, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.Marker
 
intersect(ROI, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
 
intersect(ROI, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
intersect(ROI, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.ROI
Performs an intersection operation on the shape of this ROI with another ROI.
intersect(ROI, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
intersect(ROI, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.Text
 
intersect(List<ROI>, IndeterminateProgressMonitor) - Method in class com.xinapse.multisliceimage.roi.ROI
Performs an intersection operation on the shape of this ROI with a List of other ROIs.
INTERSECT - Enum constant in enum class com.xinapse.multisliceimage.roi.LogicalOperator
INTERSECT operation.
INTERSECTION - Enum constant in enum class com.xinapse.multisliceimage.roi.CombineMode
CombineMode for creating the intersection of all ROIs.
intersects(ROI) - Method in class com.xinapse.multisliceimage.roi.ROI
Tests whether this ROI intersects another ROI.
intersects(ROI) - Method in class com.xinapse.multisliceimage.roi.VOI
Tests whether this volume of interest (VOI) intersects an ROI.
intersects(BitSet) - Method in class com.xinapse.util.BitSet
Returns true if the specified BitSet and this one share at least one common true bit.
INTRA_OCCULAR_LENS_DATA - Enum constant in enum class com.xinapse.dicom.Modality
Intra-occular lens data Modality.
INTRA_ORAL_RADIOGRAPHY - Enum constant in enum class com.xinapse.dicom.Modality
Intra-oral radiography Modality.
INVALID_ARGUMENT - Enum constant in enum class com.xinapse.platform.ExitStatus
Exit status for when a program argument is invalid (11).
INVALID_IMAGE_ERROR - Enum constant in enum class com.xinapse.platform.ExitStatus
Exit status when an image is invalid (22).
INVALID_JVM - Enum constant in enum class com.xinapse.platform.ExitStatus
Exit status when the java virtual machine used is not suitable for running this release of the software (102).
INVALID_PROPERTY_VALUE - Enum constant in enum class com.xinapse.platform.ExitStatus
Exit status for when a system property used by the program has an invalid value (12).
InvalidArgumentException - Exception in com.xinapse.util
Signals that an invalid parameter has been passed to a constructor or method, and that error must be handled by the caller.
InvalidArgumentException() - Constructor for exception com.xinapse.util.InvalidArgumentException
Constructs an InvalidArgumentException without a detail message.
InvalidArgumentException(String) - Constructor for exception com.xinapse.util.InvalidArgumentException
Constructs an InvalidArgumentException with the specified detail message.
InvalidArgumentException(String, Throwable) - Constructor for exception com.xinapse.util.InvalidArgumentException
Constructs an InvalidArgumentException with the specified cause.
InvalidColourMappingException - Exception in com.xinapse.image
Signals that an error has occurred while trying to read or generate a colour mapping.
InvalidColourMappingException(String) - Constructor for exception com.xinapse.image.InvalidColourMappingException
Constructs an InvalidColourMappingException with the specified detail message.
InvalidImageException - Exception in com.xinapse.image
Signals that an error has occurred when performing an operation on an image.
InvalidImageException() - Constructor for exception com.xinapse.image.InvalidImageException
Constructs an InvalidImageException with "invalid image" as its detail message.
InvalidImageException(String) - Constructor for exception com.xinapse.image.InvalidImageException
Constructs an InvalidImageException with the specified detail message.
InvalidImageException(String, Throwable) - Constructor for exception com.xinapse.image.InvalidImageException
Constructs an InvalidImageException with the specified cause.
INVERSION_TIME_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the scan inversion time.
invert() - Method in class com.xinapse.image.ColourMapping
Creates a new ColourMapping by inverting this ColourMapping.
INVGAUSS - Enum constant in enum class com.xinapse.multisliceimage.Analyze.NIFTIIntent
[C1, chap 15] Inverse Gaussian (2 params):
p1 = mu, p2 = lambda
Density(x) proportional to exp(-p2*(x-p1)^2/(2*p1^2*x)) / x^3 for x > 0.
IO_ERROR - Enum constant in enum class com.xinapse.platform.ExitStatus
Exit status when a general input/output error occurs (50).
IR - Enum constant in enum class com.xinapse.dicom.PulseSequenceType
Inversion-recovery pulse sequence type.
IrregularROI - Class in com.xinapse.multisliceimage.roi
A Class representing an irregularly-shaped closed region on an image.
IrregularROI(double[], double[], int, ROIState) - Constructor for class com.xinapse.multisliceimage.roi.IrregularROI
Creates a new IrregularROI with the specified shape in mm coordinates.
IrregularROI(List<? extends Point2D>, ROIState) - Constructor for class com.xinapse.multisliceimage.roi.IrregularROI
Creates a new IrregularROI with the specified shape in mm coordinates.
IrregularROIInProgress - Class in com.xinapse.multisliceimage.roi
A Class representing an IrregularROI being drawn on an image.
IrregularROIInProgress(double[], double[], byte) - Constructor for class com.xinapse.multisliceimage.roi.IrregularROIInProgress
Creates a new IrregularROIInProgress with the specified shape in mm coordinates.
isAccumbens() - Method in class com.xinapse.image.template.ICBMLabel
Tests whether this ICBMLabel is Accumbens.
isAccumbens(Point3f) - Static method in class com.xinapse.image.template.ICBMLabel
Tests whether the brain region at the given point is Accumbens.
isAmygdala() - Method in class com.xinapse.image.template.ICBMLabel
Tests whether this ICBMLabel is amygdala.
isAmygdala(Point3f) - Static method in class com.xinapse.image.template.ICBMLabel
Tests whether the brain region at the given point is amygdala.
isAnalyze() - Method in enum class com.xinapse.multisliceimage.Analyze.ANZPixFormat
Indicates whether this is an original Analyze (not NIFTI) ANZPixFormat.
isBasalGanglia() - Method in class com.xinapse.image.template.ICBMLabel
Tests whether this ICBMLabel is part of the basal ganglia.
isBasalGanglia(Point3f) - Static method in class com.xinapse.image.template.ICBMLabel
Tests whether the brain region at the given point is part of the basal ganglia.
isCanceled() - Method in class com.xinapse.util.IndeterminateProgressMonitor
Returns true if the user has hit the Cancel button in the progress dialog.
isCancelled() - Method in class com.xinapse.util.CancellableThread
Tests whether this CancellableThread has been cancelled.
isCentral() - Method in class com.xinapse.image.template.ICBMLabel
Tests whether this ICBMLabel is part of the central.
isCentral(Point3f) - Static method in class com.xinapse.image.template.ICBMLabel
Tests whether the brain region at the given point is part of the central.
isCerebellum() - Method in class com.xinapse.image.template.ICBMLabel
Tests whether this ICBMLabel is part of the cerebellum.
isCerebellum(Point3f) - Static method in class com.xinapse.image.template.ICBMLabel
Tests whether the brain region at the given point is cerebellum.
isCingulate() - Method in class com.xinapse.image.template.ICBMLabel
Tests whether this ICBMLabel is part of the cingulate.
isCingulate(Point3f) - Static method in class com.xinapse.image.template.ICBMLabel
Tests whether the brain region at the given point is part of the cingulate.
isClosed() - Method in class com.xinapse.multisliceimage.roi.SplineROI
Returns whether this SplineROI forms a closed path.
isColourType() - Method in enum class com.xinapse.image.PixelDataType
Tests whether this PixelDataType specifies explicitly the red,green,blue colour components to display, rather than needing a ColourMapping to display.
isComplex() - Method in enum class com.xinapse.image.PixelDataType
Returns true if this PixelDataType is a complex (real/imaginary) data type.
isCompressed() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
Tests whether this ANZImage is compressed when on disk.
isComputedTomography() - Method in enum class com.xinapse.dicom.Modality
Returns true if this is a CT Modality.
isCSF() - Method in class com.xinapse.image.template.ICBMLabel
Tests whether this ICBMLabel is for a region that contains CSF.
isCSF(Point3f) - Static method in class com.xinapse.image.template.ICBMLabel
Tests whether the region at the given point contains CSF.
isCuneus() - Method in class com.xinapse.image.template.ICBMLabel
Tests whether this ICBMLabel is part of the cuneus.
isCuneus(Point3f) - Static method in class com.xinapse.image.template.ICBMLabel
Tests whether the brain region at the given point is part of the cuneus.
isDeleted() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns true if this ROI has been deleted.
isEditable() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns true if this ROI is currently editable.
isEmpty() - Method in class com.xinapse.util.BitSet
Returns true if this set contains no true bits.
isEnhanced() - Method in enum class com.xinapse.dicom.Modality
Returns true if this is an enhanced Modality.
isFlipped() - Method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Returns true if this Analyze75Image is flipped.
isFloatingPointType() - Method in enum class com.xinapse.image.PixelDataType
Tests whether this PixelDataType is a floating-point (single or double precision) data type.
isFrontal() - Method in class com.xinapse.image.template.ICBMLabel
Tests whether this ICBMLabel is part of the frontal lobe cortex.
isFrontal(Point3f) - Static method in class com.xinapse.image.template.ICBMLabel
Tests whether the brain region at the given point is part of the frontal lobe cortex.
isGreyScale() - Method in class com.xinapse.image.ColourMapping
Returns true if this is a grey scale ColourMapping.
isGroup(List<ROI>) - Static method in class com.xinapse.multisliceimage.roi.ROI
Tests whether all the ROIs supplied are members of the same group (i.e., they all have the same Group UID).
isHippocampus() - Method in class com.xinapse.image.template.ICBMLabel
Tests whether this ICBMLabel is hippocampus.
isHippocampus(Point3f) - Static method in class com.xinapse.image.template.ICBMLabel
Tests whether the brain region at the given point is hippocampus.
isImage(File) - Static method in class com.xinapse.image.ImageUtils
Tests whether the supplied File refers to a WritableImage file.
isImagingModality() - Method in enum class com.xinapse.dicom.Modality
Returns true if this is an imaging Modality.
isIntegerType() - Method in enum class com.xinapse.image.PixelDataType
Tests whether a sample of this PixelDataType can be represented by a single int value (Note: not integer).
isLoadInProgress() - Method in class com.xinapse.image.InputImageSelectionPanel
 
isLoadInProgress() - Method in class com.xinapse.image.MultipleImageSelectionPanel
 
isMagneticResonance() - Method in enum class com.xinapse.dicom.Modality
Returns true if this is a magnetic resonance Modality.
isMedioTemporal() - Method in class com.xinapse.image.template.ICBMLabel
Tests whether this ICBMLabel is part of the medio-temporal cortex.
isMedioTemporal(Point3f) - Static method in class com.xinapse.image.template.ICBMLabel
Tests whether the brain region at the given point is part of the medio-temporal cortex.
isModified() - Method in class com.xinapse.multisliceimage.MultiSliceImage
Tests whether this MultiSliceImage has been modified since instantiation.
isNarrowerThan(PixelDataType) - Method in enum class com.xinapse.image.PixelDataType
Tests whether this PixelDataType is not capable of storing all values that can be stored by the supplied type without clipping.
isOn() - Static method in class com.xinapse.image.ImageDebug
Tests whether debugging of the image package is on.
isOn() - Static method in class com.xinapse.multisliceimage.Analyze.ANZDebug
Tests whether debugging of the Analyze package is on.
isOn() - Static method in class com.xinapse.multisliceimage.MultiSliceImageDebug
Tests whether debugging of the MultiSliceImage package is on.
isOn() - Static method in class com.xinapse.multisliceimage.UNC.UNCDebug
Tests whether debugging of the UNC package is on.
isOpen() - Method in interface com.xinapse.image.ReadableImage
Tests whether this image is still open.
isOpen() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
 
isOpen() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
 
isOrbito() - Method in class com.xinapse.image.template.ICBMLabel
Tests whether this ICBMLabel is part of the orbito-frontal/lateral cortex.
isOrbito(Point3f) - Static method in class com.xinapse.image.template.ICBMLabel
Tests whether the brain region at the given point is part of the orbito-frontal/lateral cortex.
isPallidum() - Method in class com.xinapse.image.template.ICBMLabel
Tests whether this ICBMLabel is part of the pallidum.
isPallidum(Point3f) - Static method in class com.xinapse.image.template.ICBMLabel
Tests whether the brain region at the given point is part of the pallidum.
isParietal() - Method in class com.xinapse.image.template.ICBMLabel
Tests whether this ICBMLabel is part of the parietal.
isParietal(Point3f) - Static method in class com.xinapse.image.template.ICBMLabel
Tests whether the brain region at the given point is part of the parietal.
isPutamen() - Method in class com.xinapse.image.template.ICBMLabel
Tests whether this ICBMLabel is part of the putamen.
isPutamen(Point3f) - Static method in class com.xinapse.image.template.ICBMLabel
Tests whether the brain region at the given point is part of the putamen.
isReloaded() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns true if this ROI has been reloaded from disk.
isSameAnnotation(List<ROI>) - Static method in class com.xinapse.multisliceimage.roi.ROI
Tests whether all the ROIs supplied have the same annotation.
isSameColour(List<ROI>) - Static method in class com.xinapse.multisliceimage.roi.ROI
Tests whether all the ROIs supplied have the same colour.
isSelected() - Method in class com.xinapse.multisliceimage.roi.ROI
Returns true if this ROI is currently selected.
isSeptum(Point3f) - Static method in class com.xinapse.image.template.ICBMLabel
Tests whether the region at the given point is septum.
isSet() - Method in class com.xinapse.util.CancellableThread.Flag
Test whether the flag has been set.
isSingleInputImage() - Method in class com.xinapse.image.SingleOrMultipleInputImageSelectionPanel
Returns whether configured with a single input image.
isSingleInputImage() - Method in class com.xinapse.util.MultiContrastAnalysisFrame
Tests whether there is a single or multiple input images.
isStatistic() - Method in enum class com.xinapse.multisliceimage.Analyze.NIFTIIntent
Indicates whether this NIFTIIntent is a statistic intent.
isTemporal() - Method in class com.xinapse.image.template.ICBMLabel
Tests whether this ICBMLabel is part of the temporal lobe cortex.
isTemporal(Point3f) - Static method in class com.xinapse.image.template.ICBMLabel
Tests whether the brain region at the given point is part of the temporal lobe cortex.
isUNCImage(File) - Static method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns true if the File is a UNC Image File.
isUNCImage(String) - Static method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns true if the fileName is the name of a UNC Image file.
isUNCImage(URL) - Static method in class com.xinapse.multisliceimage.UNC.UNCImage
Returns true if the URL produces a UNCImage input stream.
isVermis() - Method in class com.xinapse.image.template.ICBMLabel
Tests whether this ICBMLabel is part of the vermis.
isVermis(Point3f) - Static method in class com.xinapse.image.template.ICBMLabel
Tests whether the brain region at the given point is vermis.
isVisible(int, List<ROI>) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
Returns whether this RadialDivider is visible on screen.
isZero() - Method in class com.xinapse.image.Complex
Tests whether this complex number is zero.
isZero() - Method in class com.xinapse.image.DoubleComplex
 
isZero() - Method in class com.xinapse.image.FloatComplex
 
IVOC - Enum constant in enum class com.xinapse.dicom.Modality
Intravascular optical coherence tomography Modality.
IVUS - Enum constant in enum class com.xinapse.dicom.Modality
Intravascular ultrasound Modality.

J

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

K

KERATOMETRY - Enum constant in enum class com.xinapse.dicom.Modality
Keratometry Modality.
KEY_OBJECT_SELECTION - Enum constant in enum class com.xinapse.dicom.Modality
Key object selection Modality; cannot store.

L

LABEL - Enum constant in enum class com.xinapse.multisliceimage.Analyze.NIFTIIntent
To signify that the value at each voxel is an index into some set of labels, set intent_code = NIFTI_INTENT_LABEL.
labelLeft - Variable in class com.xinapse.image.template.ICBMLabel
The integer label for the region in the left side of the brain.
labelRight - Variable in class com.xinapse.image.template.ICBMLabel
The integer label for the region in the right side of the brain.
LAPAROSCOPY_RET - Enum constant in enum class com.xinapse.dicom.Modality
Laparoscopy Modality Modality (RETIRED).
LAPLACE - Enum constant in enum class com.xinapse.multisliceimage.Analyze.NIFTIIntent
[C2, chap 24] Laplace distribution (2 params):
p1 = location, p2 = scale.
Density(x) proportional to exp(-abs(x-p1)/p2).
LaplacianFilter - Class in com.xinapse.filter
A FixedWeightsKernelFilter for performing a Laplacian filtering of an image.
LaplacianFilter(float[][][]) - Constructor for class com.xinapse.filter.LaplacianFilter
Creates 3-D a LaplacianFilter with the supplied weights.
LaplacianFilter.LaplacianSpecifierPanel - Class in com.xinapse.filter
A FilterSpecifierPanel for a Laplacian edge-detection filter.
LASER_SURFACE_SCAN - Enum constant in enum class com.xinapse.dicom.Modality
Laser surface scan imaging Modality.
lastSlice - Variable in class com.xinapse.multisliceimage.roi.VOIStats
The last slice number which this VOI spans (indexed from zero).
LATERALITY_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the image laterality.
LENGTH - Enum constant in enum class com.xinapse.multisliceimage.roi.StatsType
StatsType for length.
LENGTHTOKEN - Static variable in class com.xinapse.multisliceimage.roi.ROIStreamTokenizer
The token written to show the ROI length (for linear ROIs).
LINEAR - Enum constant in enum class com.xinapse.image.InterpolationType
Linear interpolation resampling.
LinearROI - Interface in com.xinapse.multisliceimage.roi
Interface that ROIs having the property of linearity implement.
LineROI - Class in com.xinapse.multisliceimage.roi
A Class representing a straight line on an image.
LineROI(double, double, double, double) - Constructor for class com.xinapse.multisliceimage.roi.LineROI
Creates a new LineROI with the coordinates of the points forming the line in mm coordinates.
LineROI(double, double, double, double, byte, ROIState) - Constructor for class com.xinapse.multisliceimage.roi.LineROI
Creates a new LineROI with the coordinates of the points forming the line in mm coordinates.
LineROI(double, double, double, double, ROIState) - Constructor for class com.xinapse.multisliceimage.roi.LineROI
Creates a new LineROI with the coordinates of the points forming the line in mm coordinates.
LineROICreateDialog - Class in com.xinapse.multisliceimage.roi
A dialog used to create Line ROIs.
LineROICreateDialog(CanAddROIToFrame) - Constructor for class com.xinapse.multisliceimage.roi.LineROICreateDialog
Creates a new LineROICreateDialog, with ROIs that are created by the dialog being added to the specified frame.
LoadChooser() - Constructor for class com.xinapse.image.ImageFileChooser.LoadChooser
Creates an ImageFileChooser.LoadChooser suitable for selecting a ReadableImage file for loading, with the directory set to the current working directory.
LoadChooser(File) - Constructor for class com.xinapse.image.ImageFileChooser.LoadChooser
Creates an ImageFileChooser.LoadChooser suitable for selecting a ReadableImage file for loading, with the directory set to the supplied directory (if a directory) or the parent directory containing the file (if a regular file).
LoadChooser(File, Class<? extends ReadableImage>) - Constructor for class com.xinapse.image.ImageFileChooser.LoadChooser
Creates an ImageFileChooser.LoadChooser suitable for selecting a ReadableImage file for loading, with the directory set to the supplied directory (if a directory) or the parent directory containing the file (if a regular file).
loadImage(ReadableImage, ImageLoaderWorker) - Method in class com.xinapse.image.InputImageSelectionPanel
 
loadImage(ReadableImage, ImageLoaderWorker) - Method in class com.xinapse.image.MultipleImageSelectionPanel
 
log() - Method in class com.xinapse.image.Complex
Returns the natural log of this complex number.
log() - Method in class com.xinapse.image.DoubleComplex
 
log() - Method in class com.xinapse.image.FloatComplex
 
LOGICAL_OP - Enum constant in enum class com.xinapse.multisliceimage.roi.ROIEditAction
Do a logical operation (union, andNot, union, intersect, XOR) on a set of ROIs.
LogicalOperationWorker - Class in com.xinapse.multisliceimage.roi
This SwingWorker is used to perform logical operations (AND, AND NOT, UNION, INTERSECTION, XOR) on ROIs.
LogicalOperationWorker(CanAddROIToFrame, List<ROI>, LogicalOperator) - Constructor for class com.xinapse.multisliceimage.roi.LogicalOperationWorker
Creates a new LogicalOperationWorker to operate on a set of ROIs.
LogicalOperator - Enum Class in com.xinapse.multisliceimage.roi
An enumeration of logical operation on ROIs.
logicalUnion(List<ROI>, IndeterminateProgressMonitor) - Static method in class com.xinapse.multisliceimage.roi.ROI
Logically adds a List of ROIs to create a new java.util.List<ROI> of ROIs that is the result of logically adding (forming the union of) the shapes of the ROIs.
LOGISTIC - Enum constant in enum class com.xinapse.multisliceimage.Analyze.NIFTIIntent
[C2, chap 23] Logistic distribution (2 params):
p1 = location, p2 = scale.
Density(x) proportional to sech^2((x-p1)/(2*p2)).
Long(byte[], ByteOrder) - Static method in class com.xinapse.io.ByteSwap
Swap the byte order (if necessary) in a eight-byte array and return the value represented by the bit pattern as a long.
Long(long) - Static method in class com.xinapse.io.ByteSwap
Swap the byte order in a long and return the value represented by the bit pattern of the reversed bytes as a long.
Long(long, OutputStream, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single long to a OutputStream strm.
Long(long, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write a single long to a RandomAccessFile f.
Long(InputStream, ByteOrder) - Static method in class com.xinapse.io.Input
Reads a long value from a InputStream strm, ensuring that blocking occurs until the value has been read.
Long(RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Input
Reads a long value from a RandomAccessFile f, ensuring that blocking occurs until the value has been read.
LONG - Enum constant in enum class com.xinapse.image.PixelDataType
PixelDataType for signed long (64-bit integer).
LONG - Enum constant in enum class com.xinapse.multisliceimage.UNC.UNCPixFormat
UNCPixFormat for 32-bit signed int pixel values.
LongArray(long[], int, int, RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of long values to a RandomAccessFile f.
LongArray(long[], OutputStream, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of long values to a OutputStream strm.
LongArray(long[], RandomAccessFile, ByteOrder) - Static method in class com.xinapse.io.Output
Write an array of long values to a RandomAccessFile f.
LongArray(DataInputStream, ByteOrder, long[]) - Static method in class com.xinapse.io.Input
Reads an array of long values from a DataInputStream strm ensuring that blocking occurs until all values have been read.
LongArray(InputStream, ByteOrder, int) - Static method in class com.xinapse.io.Input
Reads an array of long values from a InputStream strm ensuring that blocking occurs until all values have been read.
LongArray(RandomAccessFile, ByteOrder, long[]) - Static method in class com.xinapse.io.Input
Reads an array of long values from a RandomAccessFile f ensuring that blocking occurs until all values have been read.
LongArray(RandomAccessFile, ByteOrder, long[], int, int) - Static method in class com.xinapse.io.Input
Reads an array of long values from a RandomAccessFile f, ensuring that blocking occurs until all values have been read.
LOW - Enum constant in enum class com.xinapse.multisliceimage.roi.VertexHandle.Spacing
Close together spacing.
LOWERCASEEXTENSION - Static variable in class com.xinapse.multisliceimage.Analyze.ANZColourMapping
The file extension for Analyze lookup files in lower case form.
LPF - Enum constant in enum class com.xinapse.image.SubSampleType
Sub-sampling by low-pass filtering and sinc interpolation.

M

MAGENTA - Static variable in class com.xinapse.image.ColourMapping
The ColourMapping representing a magenta intensity scale.
magic - Variable in class com.xinapse.multisliceimage.Analyze.NIFTIHeader
The magic number that is used to differentiate NIFTI-1, NIFTI-2 and Analyze 7.5 images.
MAGNETIC_RESONANCE - Enum constant in enum class com.xinapse.dicom.Modality
Magnetic resonance imaging Modality.
MAGNETIC_RESONANCE_ANGIOGRAPHY_RET - Enum constant in enum class com.xinapse.dicom.Modality
Magnetic resonance angiography Modality (RETIRED).
MAGNETIC_RESONANCE_SPECTROSCOPY_RET - Enum constant in enum class com.xinapse.dicom.Modality
Magnetic resonance spectroscopy Modality (RETIRED).
MAGNITUDE - Enum constant in enum class com.xinapse.filter.SobelFilter.SobelType
The SobelType for a filter that computes the magnitude of the gradient.
MAGNITUDE - Enum constant in enum class com.xinapse.image.ComplexMode
Selects the magnitude of a complex number.
main(String[]) - Static method in enum class com.xinapse.dicom.Modality
Run the unit test on the Modality class.
main(String[]) - Static method in enum class com.xinapse.dicom.PulseSequenceType
Run the unit test on the PulseSequenceType class.
main(String[]) - Static method in class com.xinapse.filter.ColourImageFilter
Runs a self-test of this class.
main(String[]) - Static method in class com.xinapse.filter.FilterSelection
Runs the unit test of this class.
main(String[]) - Static method in class com.xinapse.filter.GaussianBlurFilter
Runs a self-test of this class.
main(String[]) - Static method in class com.xinapse.filter.LaplacianFilter
Runs a self-test of this class.
main(String[]) - Static method in class com.xinapse.filter.MedianFilter
Runs a self-test of this class.
main(String[]) - Static method in class com.xinapse.filter.MorphologicalOperator
Runs a self-test of this class.
main(String[]) - Static method in class com.xinapse.filter.SharpenFilter
Runs a self-test of this class.
main(String[]) - Static method in class com.xinapse.geom3d.AffineTransform3D
Runs the self-test for AffineTransform3D.
main(String[]) - Static method in enum class com.xinapse.image.BoundaryCondition
Runs the self-test for this class.
main(String[]) - Static method in class com.xinapse.image.ColourMapping
Runs the self-test on this class.
main(String[]) - Static method in class com.xinapse.image.ColourVolumeInterpolator
Run the self-test for ColourVolumeInterpolator.
main(String[]) - Static method in class com.xinapse.image.Histogram
Run the self-test of the Histogram class.
main(String[]) - Static method in class com.xinapse.image.ImageGrid
Runs the self-test on this Class.
main(String[]) - Static method in class com.xinapse.image.ImageMoments
Runs the self-test on this Class.
main(String[]) - Static method in class com.xinapse.image.ImageUtils
Run the self-test of this class.
main(String[]) - Static method in class com.xinapse.image.IntensityPreset
Runs the self-test on this class.
main(String[]) - Static method in enum class com.xinapse.image.PixelDataType
Runs the self-test of this class.
main(String[]) - Static method in class com.xinapse.image.template.ICBMLabel
Run the self-test on the ICBMLabel class.
main(String[]) - Static method in class com.xinapse.image.template.TissueNormaliser
Runs the self-test of this class.
main(String[]) - Static method in enum class com.xinapse.image.template.WeightingType
Runs the self-test for WeightingType.
main(String[]) - Static method in class com.xinapse.image.TestAutoCrop
Run the test of auto cropping on multiple input images.
main(String[]) - Static method in class com.xinapse.image.VolumeInterpolator
Run the self-test for VolumeInterpolator.
main(String[]) - Static method in class com.xinapse.multisliceimage.Analyze.Analyze75Image
Run the self-test for the Analyze75Image class.
main(String[]) - Static method in enum class com.xinapse.multisliceimage.Analyze.ANZPixFormat
Run a self-test on the ANZPixFormat class.
main(String[]) - Static method in class com.xinapse.multisliceimage.Analyze.InfoExtendedData
Runs the self-test of the InfoExtendedData class.
main(String[]) - Static method in class com.xinapse.multisliceimage.Analyze.NIFTI2Image
Run the self-test for the NIFTI2Image class.
main(String[]) - Static method in class com.xinapse.multisliceimage.Analyze.NIFTIImage
Run the self-test for the NIFTIImage class.
main(String[]) - Static method in enum class com.xinapse.multisliceimage.Analyze.NIFTIIntent
Run a self-test on the NIFTIIntent class.
main(String[]) - Static method in enum class com.xinapse.multisliceimage.Analyze.NIFTIXForm
Run a self-test on the NIFTIXForm class.
main(String[]) - Static method in enum class com.xinapse.multisliceimage.Analyze.SliceOrder
Run a self-test on the SliceOrder class.
main(String[]) - Static method in enum class com.xinapse.multisliceimage.Analyze.TUnits
Run a self-test on the TUnits class.
main(String[]) - Static method in enum class com.xinapse.multisliceimage.Analyze.XYZUnits
Run a self-test on the XYZUnits class.
main(String[]) - Static method in class com.xinapse.multisliceimage.MultiSliceImage
Run the self-test on the MultiSliceImage class.
main(String[]) - Static method in class com.xinapse.multisliceimage.roi.AddChecksum
Run the program to add a checksum to existing ROI files.
main(String[]) - Static method in class com.xinapse.multisliceimage.roi.ContourROI
Run the self-test on this class.
main(String[]) - Static method in class com.xinapse.multisliceimage.roi.Dice
Calculates and prints the Dice score and volume for two sets of ROIs read from disk files.
main(String[]) - Static method in class com.xinapse.multisliceimage.roi.IrregularROI
Run the self-test on this class.
main(String[]) - Static method in class com.xinapse.multisliceimage.roi.ROI
Run the self-test for the ROI class.
main(String[]) - Static method in class com.xinapse.multisliceimage.roi.ROIStreamTokenizer
Runs the self-test for the ROIStreamTokenizer class.
main(String[]) - Static method in class com.xinapse.numerical.PolyCoeffs3D
Run the self-test of this class.
main(String[]) - Static method in enum class com.xinapse.util.IntensityRelation
Run the self-test of the IntensityRelation class.
MAKE_HOLLOW - Enum constant in enum class com.xinapse.multisliceimage.roi.ROIEditAction
Make a hollow ROI.
makeConvex(float, float, float) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Make this IrregularROI convex, or at least less concave.
makeConvex(CanAddROIToFrame, float, float, float) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
makeConvex(CanAddROIToFrame, float, float, float) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
Make this IrregularROI convex, or at least less concave.
makeTransparent(byte, boolean) - Method in class com.xinapse.image.ColourMapping
Add transparency (an alpha channel) to an existing ColourMapping.
MAMMOGRAPHY - Enum constant in enum class com.xinapse.dicom.Modality
Mammography Modality.
markDeleted() - Method in class com.xinapse.multisliceimage.roi.ROI
Mark this ROI as deleted.
Marker - Class in com.xinapse.multisliceimage.roi
A Class representing a point on an image.
Marker(double, double) - Constructor for class com.xinapse.multisliceimage.roi.Marker
Creates a new Marker at the given (x, y) coordinate.
Marker(double, double, ROIState) - Constructor for class com.xinapse.multisliceimage.roi.Marker
Creates a new Marker at the given (x, y) coordinate, and sets the state of the ROI.
Marker(Point2D.Double) - Constructor for class com.xinapse.multisliceimage.roi.Marker
Creates a new Marker at the given point.
MarkerCreateDialog - Class in com.xinapse.multisliceimage.roi
A dialog used to create Marker ROIs.
MarkerCreateDialog(CanAddROIToFrame) - Constructor for class com.xinapse.multisliceimage.roi.MarkerCreateDialog
Creates a new MarkerCreateDialog, with ROIs that are created by the dialog being added to the specified frame.
MASK_INSIDE - Enum constant in enum class com.xinapse.multisliceimage.roi.MaskAction
MaskAction for masking pixels inside the ROI.
MASK_INSIDE_SOFT - Enum constant in enum class com.xinapse.multisliceimage.roi.MaskAction
MaskAction for soft masking pixels inside the ROI.
MASK_OUTSIDE - Enum constant in enum class com.xinapse.multisliceimage.roi.MaskAction
MaskAction for masking pixels outside the ROI.
MASK_OUTSIDE_SOFT - Enum constant in enum class com.xinapse.multisliceimage.roi.MaskAction
MaskAction for soft masking pixels outside the ROI.
MaskAction - Enum Class in com.xinapse.multisliceimage.roi
An enumeration of possible masking operation actions that can be applied to an ROI to mask out some of an image's pixels.
maskImage(int, List<ROI>, MaskAction, double, CombineMode) - Method in interface com.xinapse.multisliceimage.roi.CanAddROIToFrame
Use the supplied ROIs in the slice to mask the image.
MaskMode - Enum Class in com.xinapse.multisliceimage.roi
An enumeration of possible masking mode.
MaskMode.Panel - Class in com.xinapse.multisliceimage.roi
A JPanel for selecting a MaskMode.
maskSelectorPanel - Variable in class com.xinapse.dynamic.AbstractDynamicFrame
A JPanel for selecting an image mask.
match(Histogram, double) - Method in class com.xinapse.image.Histogram
Returns the intensity scaling factor that will best match this Histogram to another Histogram.
max - Variable in class com.xinapse.image.Histogram.BinSpec
The maximum histogram value for the last bin.
max - Variable in class com.xinapse.multisliceimage.roi.ROIStats
The maximum pixel intensity inside an ROI in intensity units.
max - Variable in class com.xinapse.multisliceimage.roi.VOIStats
The maximum pixel intensity inside the VOI in intensity units.
MAX - Enum constant in enum class com.xinapse.multisliceimage.roi.StatsType
StatsType for maximum intensity.
MAX_FERET - Enum constant in enum class com.xinapse.multisliceimage.roi.StatsType
StatsType for maximum Feret's diameter.
MAX_GAMMA - Static variable in class com.xinapse.image.ColourMapping
The maximum display gamma value that is allowed.
MAX_INTERPOLATIONS_BEFORE_MULTITHREADING - Static variable in class com.xinapse.image.VolumeInterpolator
The maximum number of interpolations that is performed in a singkle method call before the procedure is multi-threaded.
MAX_LUMINANCE - Static variable in class com.xinapse.image.ColourMapping
The maximum value of display luminance (for a DDL of 255) that is allowed (including ambient light).
MAX_N_TIMES - Static variable in class com.xinapse.dynamic.AbstractDynamicFrame
The maximum number of time points that can be selected in various spinners.
MAX_ORDER - Static variable in class com.xinapse.numerical.PolyCoeffs3D
The maximum polynomial order that can be fitted.
MAX_PEN_SIZE - Static variable in class com.xinapse.multisliceimage.roi.PenSizePanel
The maximum size (in pixels) for the ROI eraser/paint pen.
MAXDIM - Static variable in class com.xinapse.image.Image
The maximum dimensionality of an image.
MAXDIM - Static variable in class com.xinapse.multisliceimage.Analyze.ANZHeader
The maximum dimensionality of an Analyze image.
MAXTOKEN - Static variable in class com.xinapse.multisliceimage.roi.ROIStreamTokenizer
The token written to show the ROI maximum intensity.
mean - Variable in class com.xinapse.multisliceimage.roi.ROIStats
The mean pixel intensity inside an ROI in intensity units.
mean - Variable in class com.xinapse.multisliceimage.roi.VOIStats
The mean pixel intensity inside the VOI in intensity units.
MEAN - Enum constant in enum class com.xinapse.multisliceimage.roi.StatsType
StatsType for mean intensity.
MEANTOKEN - Static variable in class com.xinapse.multisliceimage.roi.ROIStreamTokenizer
The token written to show the ROI mean intensity.
MEDIAN - Enum constant in enum class com.xinapse.multisliceimage.roi.StatsType
StatsType for median intensity.
MedianFilter - Class in com.xinapse.filter
A SpatialFilter for performing median filtering of an image.
MedianFilter(int[], BoundaryCondition) - Constructor for class com.xinapse.filter.MedianFilter
Construct a MedianFilter with a kernel size specified by the argument.
MedianFilter.MedianSpecifierPanel - Class in com.xinapse.filter
A FilterSpecifierPanel for a median filter.
MEDIANTOKEN - Static variable in class com.xinapse.multisliceimage.roi.ROIStreamTokenizer
The token written to show the ROI intensity median.
MEDIUM - Enum constant in enum class com.xinapse.multisliceimage.roi.VertexHandle.Spacing
Medium-density spacing.
MessageShower - Interface in com.xinapse.util
An interface for showing messages to the user.
METRE - Enum constant in enum class com.xinapse.multisliceimage.Analyze.XYZUnits
Length units of metres.
MICRON - Enum constant in enum class com.xinapse.multisliceimage.Analyze.XYZUnits
Length units of microns.
min - Variable in class com.xinapse.image.Histogram.BinSpec
The minimun histogram value for the first bin.
min - Variable in class com.xinapse.multisliceimage.roi.ROIStats
The minimum pixel intensity inside an ROI in intensity units.
min - Variable in class com.xinapse.multisliceimage.roi.VOIStats
The minimum pixel intensity inside the VOI in intensity units.
MIN - Enum constant in enum class com.xinapse.multisliceimage.roi.StatsType
StatsType for minimum intensity.
MIN_FERET - Enum constant in enum class com.xinapse.multisliceimage.roi.StatsType
StatsType for minimum Feret's diameter.
MIN_GAMMA - Static variable in class com.xinapse.image.ColourMapping
The minimum display gamma value that is allowed.
MIN_LUMINANCE - Static variable in class com.xinapse.image.ColourMapping
The minimum value of display luminance (for a DDL of zero) that is allowed (including ambient light).
MIN_PEN_SIZE - Static variable in class com.xinapse.multisliceimage.roi.PenSizePanel
The minimum size (in pixels) for the ROI eraser/paint pen.
mindboggleID - Variable in class com.xinapse.image.template.ICBMLabel
The Mindboggle ID for the label.
MINTOKEN - Static variable in class com.xinapse.multisliceimage.roi.ROIStreamTokenizer
The token written to show the ROI minimum intensity.
MINUS_90 - Enum constant in enum class com.xinapse.image.RotationAngle
The RotationAngle corresponding to an anticlockwise rotation of 90 degrees.
MISSING_ARGUMENT - Enum constant in enum class com.xinapse.platform.ExitStatus
Exit status when a compulsory argument is missing (16).
MM - Enum constant in enum class com.xinapse.multisliceimage.Analyze.XYZUnits
Length units of mm.
mmPosToPix(double, float, int) - Static method in class com.xinapse.multisliceimage.roi.ROI
Convert from a position in mm to a pixel number coordinate.
MNI_152 - Enum constant in enum class com.xinapse.multisliceimage.Analyze.NIFTIXForm
MNI 152 normalized coordinates.
Modality - Enum Class in com.xinapse.dicom
An enumeration of the known imaging and other modalities.
MODALITY_NAME - Static variable in class com.xinapse.multisliceimage.MultiSliceImage
The information field name that is written into image headers to indicate the imaging modality.
MODALITY_PREFERENCE_NAME - Static variable in enum class com.xinapse.dicom.Modality
The Preference name for the imaging modality.
Modality.ComboBox - Class in com.xinapse.dicom
A javax.swing.JComboBox that is used for selecting a Modality.
mode - Variable in class com.xinapse.multisliceimage.MultiSliceImage
The "mode" with which the image was opened, if a disk-file: either "r" or "rw".
modelChangedListener - Variable in class com.xinapse.dynamic.DynamicModel.SpecifierPanel
The ActionListener that should be notified when the DynamicModel specified in this SpecifierPanel is changed.
MODIFY - Enum constant in enum class com.xinapse.multisliceimage.roi.HistoryType
HistoryType for ROI modification.
monitor - Variable in class com.xinapse.util.MonitorWorker
A ProgressMonitor which may pop up.
MonitorWorker - Class in com.xinapse.util
A class to implement a SwingWorker that can pop up a ProgressMonitor to allow user cancellation.
MonitorWorker(Component, String) - Constructor for class com.xinapse.util.MonitorWorker
Creates a new MonitorWorker with a parent component and a program name.
MONOCHROME1 - Static variable in class com.xinapse.image.ColourMapping
The ColourMapping representing a grey (white to black) intensity scale.
MONOCHROME2 - Static variable in class com.xinapse.image.ColourMapping
The ColourMapping representing a grey (black to white) intensity scale.
MORPHOLOGICAL_OP - Enum constant in enum class com.xinapse.multisliceimage.roi.ROIEditAction
Do a morphological operation (erode/dilate) on an ROI.
MorphologicalOperationWorker - Class in com.xinapse.multisliceimage.roi
This SwingWorker is used to perform morphological operations (dilation and erosion) on ROIs.
MorphologicalOperationWorker(CanAddROIToFrame, List<ROI>, double) - Constructor for class com.xinapse.multisliceimage.roi.MorphologicalOperationWorker
Creates a new MorphologicalOperationWorker to operate on a set of ROIs.
MorphologicalOperator - Class in com.xinapse.filter
A SpatialFilter for performing a morphological operation on an image.
MorphologicalOperator(boolean[][][], MorphologicalOperator.Op, BoundaryCondition) - Constructor for class com.xinapse.filter.MorphologicalOperator
Creates a new MorphologicalOperator with the given structuring element, operation and image boundary condition.
MorphologicalOperator.MorphologicalSpecifierPanel - Class in com.xinapse.filter
A FilterSpecifierPanel for a moprphological operation filter.
MorphologicalOperator.Op - Enum Class in com.xinapse.filter
An enumeration of the possible morphological operations on an image.
MorphologicalSpecifierPanel(String) - Constructor for class com.xinapse.filter.MorphologicalOperator.MorphologicalSpecifierPanel
Creates a new MorphologicalSpecifierPanel.
MostLikePlane - Enum Class in com.xinapse.image
The radiological planes that can be used to describe the approximate orientation of a scan plane.
MOUSE_MINUS_DELTA - Enum constant in enum class com.xinapse.multisliceimage.roi.ContourMode
The intensity level under the mouse minus delta.
MOUSE_PLUS_DELTA - Enum constant in enum class com.xinapse.multisliceimage.roi.ContourMode
The intensity level under the mouse plus delta.
move(double, double) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
move(double, double) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
 
move(double, double) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
move(double, double) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
move(double, double) - Method in class com.xinapse.multisliceimage.roi.LineROI
 
move(double, double) - Method in class com.xinapse.multisliceimage.roi.Marker
 
move(double, double) - Method in class com.xinapse.multisliceimage.roi.RadialDivider
This method does nothing.
move(double, double) - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
move(double, double) - Method in class com.xinapse.multisliceimage.roi.ROI
Move this ROI by specified distances (in mm) in the x and y directions.
move(double, double) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
move(double, double, double, double) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
move(double, double, double, double) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
move(double, double, double, double) - Method in class com.xinapse.multisliceimage.roi.RectangularROI
 
move(double, double, double, double) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
move(double, double, double, double) - Method in interface com.xinapse.multisliceimage.roi.StretchableROI
Moves and stretches an ROI.
move(EllipticalROI, boolean) - Method in class com.xinapse.multisliceimage.roi.EllipticalROI
Moves and rehapes this EllipticalROI so that the size and location are the same as the given EllipticalROI.
move(Point2D, Point2D) - Method in class com.xinapse.multisliceimage.roi.LineROI
Moves this LineROI so that the ends are at the new specified locations.
MOVE - Enum constant in enum class com.xinapse.multisliceimage.roi.ROIEditAction
Move an ROI.
moveROIs(List<ROI>, double, double) - Static method in class com.xinapse.multisliceimage.roi.ROI
Move a List of ROIs by specified distances (in mm) in the x and y directions.
moveVertex(Point2D, Handle, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.CurvedLineROI
 
moveVertex(Point2D, Handle, int, int, float, float, boolean) - Method in interface com.xinapse.multisliceimage.roi.EditableOutlineROI
Move a point on the outline of this EditableOutlineROI to a new position.
moveVertex(Point2D, Handle, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.HollowROI
 
moveVertex(Point2D, Handle, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.IrregularROI
 
moveVertex(Point2D, Handle, int, int, float, float, boolean) - Method in class com.xinapse.multisliceimage.roi.SplineROI
 
MP - Enum constant in enum class com.xinapse.dicom.PulseSequenceVariant
Magnetization prepared variant.
MS_PD_IMAGE_NAME - Static variable in class com.xinapse.image.template.