Index (Xinapse Systems Medical Image A.P.I.)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _
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: Add a ChangeListener to this 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: Add a ChangeListener to this ImageSelectionPanel.
addFiles(List<File>) - Method in class com.xinapse.image.MultipleImageSelectionPanel: Add a List of Files to this MultipleImageSelectionPanel.
addFileTextEditListener(ChangeListener) - Method in class com.xinapse.image.ImageSelectionGroupPanel: Adds a listener that listens for the file text being edited.
addFileTextEditListener(ChangeListener) - Method in class com.xinapse.image.ImageSelectionPanel: Add a ChangeListener to this ImageSelectionPanel.
addGraph(GraphPanel, String) - Method in class com.xinapse.util.ReportGenerator: Adds a graph to the report.
addGraph(GraphPanel, String, String, String) - Method in class com.xinapse.util.ReportGenerator: Adds a graph to the report.
addImage(ReadableImage, ColourMapping, double, double, ComplexMode, String) - Method in class com.xinapse.util.ReportGenerator: Adds an image to the report.
addImage(ReadableImage, String) - Method in class com.xinapse.util.ReportGenerator: Adds a colour image to the report.
addImageInfo(ReadableImage) - Method in class com.xinapse.util.ReportGenerator: Adds basic image information to a report.
addImageInfo(ReadableImage, String) - Method in class com.xinapse.util.ReportGenerator: Adds basic image information to a report.
addInfo(List<String>) - Method in class com.xinapse.apps.cardiac.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: Creates a new PatientPosition.ComboBox.
ComboBox() - Constructor for class com.xinapse.dicom.PulseSequenceType.ComboBox: Creates a new PulseSequenceType.ComboBox.
ComboBox() - Constructor for class com.xinapse.image.RenderingInterpolationType.ComboBox: Creates a new RenderingInterpolationType.ComboBox.
ComboBox() - Constructor for class com.xinapse.multisliceimage.roi.ContourMode.ComboBox: Create a new ContourMode.ComboBox for selecting a ContourMode.
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<ColourMapping> 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<ColourMapping> of the built-in ColourMappings.
getBuiltInPresets() - Static method in class com.xinapse.image.IntensityPreset: Returns a java.util.List<IntensityPreset> of the built-in IntensityPresets.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.ContourROI: Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.CurvedLineROI: Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.EllipticalROI: Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.IrregularROI: Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.LineROI: Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.Marker: Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.OpenSplineROI: Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.RectangularROI: Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.SplineROI: Returns an Icon that can be used for a button to create this type of ROI.
getButtonIcon() - Static method in class com.xinapse.multisliceimage.roi.Text: Returns an Icon that can be used for a button to create this type of ROI.
getByteOrder() - Method in class com.xinapse.multisliceimage.Analyze.ANZImage
getByteOrder() - Method in class com.xinapse.multisliceimage.MultiSliceImage: Returns the byte order for this image.
getByteOrder() - Method in class com.xinapse.multisliceimage.UNC.UNCImage
getBytesPerPixel() - Method in class com.xinapse.multisliceimage.UNC.UNCImage: Returns the number of bytes per pixel for this image.
getBytesPerPixel() - Method in enum 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<ColourMapping> of the ColourMappings imported by the user and stored in the user preferences.
getUserObject() - Method in exception com.xinapse.util.CancelledException: Retrieves the User Object associated with this CancelledException.
getUserPresets() - Static method in class com.xinapse.image.IntensityPreset: Returns a java.util.List<IntensityPreset> of the IntensityPresets created by the user and stored in the user preferences.
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.