A

addBookmark(Coordinate, String) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Adds a bookmark.

addMaskValue(int, int, int, int, long) - Method in interface edu.uthscsa.ric.roi.ROIData

Adds an ROI value at a specified location.

addMaskValue(int, int, int, long) - Method in interface edu.uthscsa.ric.roi.ROIData

Adds an ROI value at a specified location.

addMoreROIColors() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Adds more ROI colors (color count starts at 8, then 16, 32, 64).

addOverlay(String, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Adds an overlay.

addOverlayOnto(VolumeManager, String) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Overlays the base volume onto another VolumeManager.

addOverlayURL(String) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Adds an overlay from a URL.

addPoint(Coordinate, int) - Method in interface edu.uthscsa.ric.roi.ROIData

Adds a point.

addROIMaskValue(int, int, int, byte) - Method in interface edu.uthscsa.ric.roi.ROIData

Deprecated. 

addROIMaskValue(int, int, int, int, byte) - Method in interface edu.uthscsa.ric.roi.ROIData

Deprecated. 

addShape(int, int, int, Shape) - Method in interface edu.uthscsa.ric.roi.ROIData

Add a shape of a specified color within a slice.

addShapeFromLogical(List<ImageVolume>, String, int, double, boolean, boolean, boolean, double, int, double, double, double, boolean, double, double, int) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Adds a surface shape from a logical.

addShapeFromOverlay(ImageVolume, String, int, double, boolean, boolean, boolean, double, int, double, double, double, boolean, double, double, int) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Adds a surface shape from an overlay.

addShapeFromROI(int, String, int, double, boolean, boolean, boolean, double, int, double, double, double, boolean, double, double, int) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Adds a surface shape from a ROI.

addShapesFromFile(String) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Adds a surface shape from file.

addSliceListener(SliceListener, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Adds a slice listener, which will be notified anytime a slice's position has changed.

addSpecialPoint(Coordinate, Color, boolean) - Method in interface edu.uthscsa.ric.roi.ROIData

Adds a point with special properties that can only be removed programmatically.

addSpecialShape(int, int, Color, Shape, Stroke, boolean, boolean) - Method in interface edu.uthscsa.ric.roi.ROIData

Add a shape with special properties that can only be remove programmatically.

Analysis - Interface in edu.uthscsa.ric.volume

A result of a statistical operation.

AnalysisPoint - Interface in edu.uthscsa.ric.volume

A point of interest.

anonymize() - Method in interface edu.uthscsa.ric.volume.EditableHeader

Perform anonymization.

anonymize() - Method in class edu.uthscsa.ric.volume.ImageDescription

Clears this data.

AppLogger - Class in edu.uthscsa.ric.utilities

A class to manage logging in the application and plugins.

associatePluginWindow(String, JFrame) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Associates a plugin window with this VolumeManager.

Atlas - Interface in edu.uthscsa.ric.mango

A class that implements Atlas can be used to provide labels for coordinate positions within an image.

B

BLUE_INDEX - Static variable in interface edu.uthscsa.ric.roi.ROIData

Deprecated.

BLUE_MASK - Static variable in interface edu.uthscsa.ric.roi.ROIData

Deprecated.

buildProjection(int, int, double, double, double, int, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Creates a ProjectionManager.

buildSurface(double, boolean, boolean, boolean, boolean, double, int, double, double, double, boolean, double, double, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Creates a SurfaceManager.

BYTE_TYPE_BINARY - Static variable in class edu.uthscsa.ric.volume.ImageType

 

BYTE_TYPE_COMPLEX - Static variable in class edu.uthscsa.ric.volume.ImageType

 

BYTE_TYPE_FLOAT - Static variable in class edu.uthscsa.ric.volume.ImageType

 

BYTE_TYPE_INTEGER - Static variable in class edu.uthscsa.ric.volume.ImageType

 

BYTE_TYPE_INTEGER_UNSIGNED - Static variable in class edu.uthscsa.ric.volume.ImageType

 

BYTE_TYPE_RGB - Static variable in class edu.uthscsa.ric.volume.ImageType

 

BYTE_TYPE_UNKNOWN - Static variable in class edu.uthscsa.ric.volume.ImageType

 

C

canCompress() - Method in interface edu.uthscsa.ric.volume.WritableHeader

Returns true if the format supports compressed data.

capture() - Method in interface edu.uthscsa.ric.mango.MangoContext

Programmatically clicks the Toolbox camera button.

captureLayout(String, int, int, int, int, boolean, boolean, boolean, boolean, String, String) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Captures a multi-slice layout.

captureSnapshot(String) - Method in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

Save a snapshot of the projection viewer to the specified location.

captureSnapshot(String) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Captures a single-slice.

captureSnapshot(String) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Save a snapshot of the surface viewer to the specified location.

captureVideoStart(String, int, int, int, boolean) - Method in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

Starts saving a captured video to the specified file location.

captureVideoStart(String, int, int, int, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Starts video capture.

captureVideoStart(String, int, int, int, boolean) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Starts saving a captured video to the specified file location.

captureVideoStop() - Method in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

Stops the video capture.

captureVideoStop() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Stops the video capture.

captureVideoStop() - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Stops the video capture.

clear() - Method in interface edu.uthscsa.ric.mango.Atlas

Call to clear atlas of resources.

clearNegativeVoxelSizes() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Replaces any stored negative voxel sizes with their absolute value.

clone() - Method in class edu.uthscsa.ric.volume.Coordinate

Returns a copy of this object.

clone() - Method in class edu.uthscsa.ric.volume.ImageDescription

Returns a copy of this object.

clone() - Method in class edu.uthscsa.ric.volume.ImageDimensions

Returns a copy of this object.

clone() - Method in class edu.uthscsa.ric.volume.ImageRange

Returns a copy of this object.

clone() - Method in class edu.uthscsa.ric.volume.ImageType

Returns a copy of this object.

clone() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Returns a copy of this object.

Cluster - Interface in edu.uthscsa.ric.volume

The result of a cluster operation.

ColorManager - Interface in edu.uthscsa.ric.roi

Manages ROI color data.

colorSelected(int) - Method in interface edu.uthscsa.ric.mango.components.MangoColorSelectedListener

Called when a new ROI color has been selected.

compareTo(EditableHeader.CodeOption) - Method in class edu.uthscsa.ric.volume.EditableHeader.CodeOption

Compare two CodeOptions.

COMPRESSION_TYPE_DICOM - Static variable in class edu.uthscsa.ric.volume.ImageType

 

COMPRESSION_TYPE_DICOM_JPEG2000 - Static variable in class edu.uthscsa.ric.volume.ImageType

 

COMPRESSION_TYPE_DICOM_JPEG_BASELINE - Static variable in class edu.uthscsa.ric.volume.ImageType

 

COMPRESSION_TYPE_DICOM_JPEG_LOSSLESS - Static variable in class edu.uthscsa.ric.volume.ImageType

 

COMPRESSION_TYPE_DICOM_RLE - Static variable in class edu.uthscsa.ric.volume.ImageType

 

COMPRESSION_TYPE_GZIP - Static variable in class edu.uthscsa.ric.volume.ImageType

 

COMPRESSION_TYPE_NONE - Static variable in class edu.uthscsa.ric.volume.ImageType

 

ConsoleLogger - Interface in edu.uthscsa.ric.utilities

A console logging interface.

ConsolePlugin - Interface in edu.uthscsa.ric.cli

A plugin that can be run at the command-line.

continueScript() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Continue a paused script.

convertIndexToOffset(int, int, int) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Converts an XYZ index into an array offset based on image orientation.

convertIndexToWorldCoordinate(Coordinate) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Converts index coordinate to world coordinate.

convertToSigned(ImageType) - Static method in class edu.uthscsa.ric.volume.ImageType

Converts datatype from unsigned integer to signed integer.

convertWorldToIndexCoordinate(Coordinate) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Converts world coordinate to index coordinate.

Coordinate - Class in edu.uthscsa.ric.volume

Coordinate stores information about a point in space.

Coordinate() - Constructor for class edu.uthscsa.ric.volume.Coordinate

Default constructor.

Coordinate(Coordinate) - Constructor for class edu.uthscsa.ric.volume.Coordinate

Copy constructor.

Coordinate(double, double, double) - Constructor for class edu.uthscsa.ric.volume.Coordinate

Constructor.

Coordinate4D - Class in edu.uthscsa.ric.volume

Coordinate4D extends Coordinate and includes a series dimension.

Coordinate4D(Coordinate, int) - Constructor for class edu.uthscsa.ric.volume.Coordinate4D

Constructor.

Coordinate4D(double, double, double, int) - Constructor for class edu.uthscsa.ric.volume.Coordinate4D

Constructor.

COORDINATE_TYPE_ATLAS - Static variable in class edu.uthscsa.ric.volume.Coordinate

 

COORDINATE_TYPE_INDEX - Static variable in class edu.uthscsa.ric.volume.Coordinate

 

COORDINATE_TYPE_MM - Static variable in class edu.uthscsa.ric.volume.Coordinate

 

COORDINATE_TYPE_WORLD - Static variable in class edu.uthscsa.ric.volume.Coordinate

 

createBitMask() - Method in class edu.uthscsa.ric.volume.ImageType

Returns a bit mask based on the number of bytes and bits stored per voxel.

createColorPickerButton(VolumeManager, MangoColorSelectedListener, boolean) - Method in interface edu.uthscsa.ric.mango.MangoContext

Creates a ROI color picker widget.

createFileLogger(File) - Static method in class edu.uthscsa.ric.utilities.AppLogger

Creates the file logger.

createMask(int) - Method in interface edu.uthscsa.ric.roi.ROIData

Creates a bit mask for a ROI color.

createWebpage(String, String, boolean, boolean, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Deprecated. 

createWebpage(String, String, boolean, boolean, boolean, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Creates a webpage.

CYAN_INDEX - Static variable in interface edu.uthscsa.ric.roi.ROIData

Deprecated.

CYAN_MASK - Static variable in interface edu.uthscsa.ric.roi.ROIData

Deprecated.

D

DATE_FORMAT - Variable in class edu.uthscsa.ric.volume.ImageDescription

 

DATETIME_FORMAT - Variable in class edu.uthscsa.ric.volume.ImageDescription

 

debug(String) - Static method in class edu.uthscsa.ric.utilities.AppLogger

Log debug.

decrement(int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Decrements the slice in the specified direction.

DEFAULT_COLOR - Static variable in interface edu.uthscsa.ric.visualization.surface.primitives.Surface

 

DEFAULT_DATA_SCALE_INTERCEPT - Static variable in class edu.uthscsa.ric.volume.ImageRange

 

DEFAULT_DATA_SCALE_SLOPE - Static variable in class edu.uthscsa.ric.volume.ImageRange

 

deleteROI(ROI) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Deletes the specified ROI.

DESCRIPTION_CLUSTER - Static variable in interface edu.uthscsa.ric.volume.Analysis

 

DESCRIPTION_LINE - Static variable in interface edu.uthscsa.ric.volume.Analysis

 

DESCRIPTION_LOGICAL - Static variable in interface edu.uthscsa.ric.volume.Analysis

 

DESCRIPTION_POINT - Static variable in interface edu.uthscsa.ric.volume.Analysis

 

DESCRIPTION_SLICE - Static variable in interface edu.uthscsa.ric.volume.Analysis

 

DESCRIPTION_TIMESERIES - Static variable in interface edu.uthscsa.ric.volume.Analysis

 

DESCRIPTION_VOLUME - Static variable in interface edu.uthscsa.ric.volume.Analysis

 

display(GLAutoDrawable) - Method in interface edu.uthscsa.ric.visualization.surface.SurfacePlugin

After calling addToDisplay() from a SurfaceController, this method will be called at the end of each drawing loop.

disposeVolumeManager() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Call to remove this VolumeManager from the application.

distance(Coordinate) - Method in class edu.uthscsa.ric.volume.Coordinate

Returns the distance between this Coordinate and another.

doOperation(MangoContext, String...) - Method in interface edu.uthscsa.ric.cli.ConsolePlugin

The method that is executed when the plugin is run from the command-line.

doOperation(MangoContext, VolumeManager, boolean, String...) - Method in interface edu.uthscsa.ric.cli.ScriptablePlugin

The method that is called by the script.

doOperation(MangoContext, VolumeManager) - Method in interface edu.uthscsa.ric.mango.MangoPlugin

This is the method which Mango executes when a plugin is selected.

doOperation(MangoData, ViewerController) - Method in interface edu.uthscsa.ric.mango.MangoPlugin

Deprecated. 

doOperation(SurfaceController) - Method in interface edu.uthscsa.ric.visualization.surface.SurfacePlugin

This is the method which Mango executes when a plugin is chosen.

E

EditableHeader - Interface in edu.uthscsa.ric.volume

An EditableHeader is a header with editable fields.

EditableHeader.CodeOption - Class in edu.uthscsa.ric.volume

A CodeOption consists of a code string and human-readable name.

EditableHeader.CodeOption(String, String) - Constructor for class edu.uthscsa.ric.volume.EditableHeader.CodeOption

Constructor.

edu.uthscsa.ric.cli - package edu.uthscsa.ric.cli

 

edu.uthscsa.ric.mango - package edu.uthscsa.ric.mango

 

edu.uthscsa.ric.mango.components - package edu.uthscsa.ric.mango.components

 

edu.uthscsa.ric.mango.viewerprojection - package edu.uthscsa.ric.mango.viewerprojection

 

edu.uthscsa.ric.mango.viewerslice - package edu.uthscsa.ric.mango.viewerslice

 

edu.uthscsa.ric.mango.viewersurface - package edu.uthscsa.ric.mango.viewersurface

 

edu.uthscsa.ric.roi - package edu.uthscsa.ric.roi

 

edu.uthscsa.ric.roi.mask - package edu.uthscsa.ric.roi.mask

 

edu.uthscsa.ric.utilities - package edu.uthscsa.ric.utilities

 

edu.uthscsa.ric.visualization.surface - package edu.uthscsa.ric.visualization.surface

 

edu.uthscsa.ric.visualization.surface.io - package edu.uthscsa.ric.visualization.surface.io

 

edu.uthscsa.ric.visualization.surface.primitives - package edu.uthscsa.ric.visualization.surface.primitives

 

edu.uthscsa.ric.volume - package edu.uthscsa.ric.volume

 

equals(Object) - Method in class edu.uthscsa.ric.volume.Coordinate

Tests equality.

equals(Object) - Method in class edu.uthscsa.ric.volume.Coordinate4D

Tests equality.

equals(ImageDimensions) - Method in class edu.uthscsa.ric.volume.ImageDimensions

Deprecated. 

equals(Object) - Method in class edu.uthscsa.ric.volume.ImageDimensions

Tests equality.

equals(Object) - Method in class edu.uthscsa.ric.volume.ImageRange

 

equals(Object) - Method in class edu.uthscsa.ric.volume.ImageType

Tests equality.

equals(VoxelDimensions) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Deprecated. 

equals(Object) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Tests equality.

error(String) - Static method in class edu.uthscsa.ric.utilities.AppLogger

Log error.

error(Throwable) - Static method in class edu.uthscsa.ric.utilities.AppLogger

Log error.

errorMinimal(Throwable) - Static method in class edu.uthscsa.ric.utilities.AppLogger

Log error (without stacktrace).

exit() - Method in interface edu.uthscsa.ric.mango.MangoContext

Exit the application and clear all resources.

exportTo(String, String, Surface, String) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Exports the surface data to the specified file location.

F

FILTER_TYPE_SLICE - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

FILTER_TYPE_TIME - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

FILTER_TYPE_VOLUME - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

findGoodPluginWindowLocation(Dimension) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns a point to display a plugin window next to, but not in front of, the viewer window.

flipOrientation(ImageVolume, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Flips the orientation of the data in the specified dimension.

FloatIterator - Class in edu.uthscsa.ric.visualization.surface.io

 

FloatIterator(FloatBuffer[]) - Constructor for class edu.uthscsa.ric.visualization.surface.io.FloatIterator

Constructor.

formatImageFile(File) - Method in interface edu.uthscsa.ric.volume.WritableHeader

Returns a formatted image file (string) based on a header file (i.e., a header type might have a convention for naming the image file relative to header file name).

G

get(int, int) - Method in interface edu.uthscsa.ric.roi.mask.ROIMaskBuffer

Returns the ROI mask value at the specified offset and series index.

getAddedShapes() - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Returns a list of surfaces added to the base surface.

getAllAnalyses() - Method in interface edu.uthscsa.ric.mango.MangoContext

Returns a list of all analyses.

getAllAnalysisPoints() - Method in interface edu.uthscsa.ric.mango.MangoContext

Returns a list of all analysis points.

getAllID() - Method in class edu.uthscsa.ric.volume.ImageDescription

Returns both ID and name.

getAllPointsAndLines() - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Returns a list of all points and lines.

getAllROIs() - Method in interface edu.uthscsa.ric.roi.ROIData

Returns a list of all ROIs.

getAllTime() - Method in class edu.uthscsa.ric.volume.ImageDescription

Deprecated. 

getAllVolumeManagers() - Method in interface edu.uthscsa.ric.mango.MangoContext

Returns a list of all the currently loaded VolumeManagers.

getAllVolumeManagersFrom(VolumeManager) - Method in interface edu.uthscsa.ric.mango.MangoContext

Returns a list of all currently loaded VolumeManagers, starting with the specified manager.

getAnalysis() - Method in interface edu.uthscsa.ric.volume.Cluster

Returns an analysis of this cluster region.

getAnonymizableFields() - Method in interface edu.uthscsa.ric.volume.EditableHeader

Returns a list of anonymizable fields or null if anonymization is not supported.

getAssociatedFiles() - Method in class edu.uthscsa.ric.volume.ImageDescription

Returns an array of files associated with this image (e.g., a multifile image format).

getAvailableMask() - Method in interface edu.uthscsa.ric.roi.ROIData

If there exists selected mask, it returns getSelectedMask(), otherwise it returns getUsedMaks().

getAxialArea() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Returns the area of a voxel in the axial plane.

getBaseSurface() - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Returns the base surface

getBaseVolume() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns the base volume.

getBinCounts() - Method in interface edu.uthscsa.ric.volume.Histogram

Returns an array of histogram bin counts.

getBinRangeMaximums() - Method in interface edu.uthscsa.ric.volume.Histogram

Returns an array of histogram bin range maxs.

getBinRangeMinimums() - Method in interface edu.uthscsa.ric.volume.Histogram

Returns an array of histogram bin range mins.

getBitsStored() - Method in class edu.uthscsa.ric.volume.ImageType

Returns the number of bits stored.

getBuildNumber() - Method in interface edu.uthscsa.ric.mango.MangoContext

Returns the Mango build number.

getByteType() - Method in class edu.uthscsa.ric.volume.ImageType

Returns the byte type code.

getByteTypeString(int) - Static method in class edu.uthscsa.ric.volume.ImageType

Returns the byte type name associated with a byte type code.

getByteTypeString() - Method in class edu.uthscsa.ric.volume.ImageType

Returns the byte type name.

getCenter() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the center coordinate.

getCentroidCoordinate() - Method in interface edu.uthscsa.ric.volume.Analysis

Returns the coordinate of the centroid value.

getCentroidValue() - Method in interface edu.uthscsa.ric.volume.Analysis

Returns the value at the centroid coordinate.

getCode() - Method in class edu.uthscsa.ric.volume.EditableHeader.CodeOption

Returns the code string.

getColor() - Method in interface edu.uthscsa.ric.roi.ROI

Returns the color representation of this ROI as an index in the list of specified Mango ROI colors.

getColor() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Shape

Returns a three float array of RGB values representing the surface color.

getColor() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Surface

Returns the color components (one solid color) of this Surface.

getColorsIterator() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Surface

Returns a colors iterator.

getColorTableName() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Overlay

Returns the LUT name associated with this Overlay.

getCols() - Method in class edu.uthscsa.ric.volume.ImageDimensions

Gets the number of columns in a volume of this image.

getColSize(boolean) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Returns the size of a voxel's column dimension.

getCommandLineName() - Method in interface edu.uthscsa.ric.cli.ConsolePlugin

The name of the command-line program.

getCompressionType() - Method in class edu.uthscsa.ric.volume.ImageType

Returns the compression type.

getCompressionTypeString() - Method in class edu.uthscsa.ric.volume.ImageType

 

getConsoleLogger() - Static method in class edu.uthscsa.ric.utilities.AppLogger

Returns the current ConsoleLogger.

getCoordinate() - Method in interface edu.uthscsa.ric.volume.AnalysisPoint

The coordinate.

getCoronalArea() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Returns the area of a voxel in the coronal plane.

getCount() - Method in interface edu.uthscsa.ric.volume.Analysis

Returns the voxel count.

getCurrent() - Method in interface edu.uthscsa.ric.mango.ProgressMeter

Returns the current value.

getCurrent(int) - Method in interface edu.uthscsa.ric.roi.mask.ROIMaskBuffer

Returns the ROI mask value at the specified offset for the current series index.

getCurrentAtlas() - Method in interface edu.uthscsa.ric.mango.MangoContext

Returns the current Atlas.

getCurrentPosition() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns the currently selected position.

getCurrentSeriesPoint() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the current series point.

getCurrentVolume() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns the currently selected volume.

getCurrentVolumeManager() - Method in interface edu.uthscsa.ric.mango.MangoContext

Returns the currently selected VolumeManager.

getCurrentVolumeManagerIndex() - Method in interface edu.uthscsa.ric.mango.MangoContext

Returns the index of the currently selected VolumeManager.

getCurrentWorldPosition() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns the currently selected position in world space.

getData() - Method in interface edu.uthscsa.ric.mango.ImageLoader

(Not yet implemented.)

getDataScaleIntercepts() - Method in class edu.uthscsa.ric.volume.ImageRange

Returns the data scale intercepts.

getDataScaleSlopes() - Method in class edu.uthscsa.ric.volume.ImageRange

Returns the data scale slopes.

getDate() - Method in class edu.uthscsa.ric.volume.ImageDescription

Deprecated. 

getDescription() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Surface

Returns a description of this Surface.

getDescription() - Method in interface edu.uthscsa.ric.volume.Analysis

Returns a string description of this analysis.

getDescription() - Method in interface edu.uthscsa.ric.volume.AnalysisPoint

Returns a string description of this analysis.

getDescription() - Method in class edu.uthscsa.ric.volume.ImageDescription

Returns the description.

getDicomItems() - Method in class edu.uthscsa.ric.volume.ImageDescription

Returns a map of DICOM tag id to string value (see setDicomItems() for more explanation).

getDisplayMax() - Method in class edu.uthscsa.ric.volume.ImageRange

Returns the display max.

getDisplayMin() - Method in class edu.uthscsa.ric.volume.ImageRange

Returns the display min.

getDistance() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Shape

Returns the length of the shape.

getEditableFieldValues() - Method in interface edu.uthscsa.ric.volume.EditableHeader

Returns a map of field names to field values.

getFile() - Method in class edu.uthscsa.ric.volume.ImageDescription

Returns the URI of this image.

getFrame() - Method in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

Returns the parent window of the projection.

getFrame() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns the parent window of this viewer.

getFrame() - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Returns the parent window of the surface view.

getHistogramAnalysis() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns the result of the last Histogram analysis.

getHumanReadableFieldOptions() - Method in interface edu.uthscsa.ric.volume.EditableHeader

Returns a map of field names to lists of human readable code names.

getID() - Method in class edu.uthscsa.ric.volume.ImageDescription

Returns the scan ID.

getImage() - Method in interface edu.uthscsa.ric.volume.ReadableHeader

Deprecated. 

getImageBuffers() - Method in interface edu.uthscsa.ric.volume.ReadableHeader

Return null to have the application handle reading the image data or return an array of ByteBuffers.

getImageDescription() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the ImageDescription.

getImageDescription() - Method in interface edu.uthscsa.ric.volume.ReadableHeader

Returns the image description.

getImageDimensions() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the ImageDimensions.

getImageDimensions() - Method in interface edu.uthscsa.ric.volume.ReadableHeader

Returns the image dimensions.

getImageFile() - Method in interface edu.uthscsa.ric.volume.ReadableHeader

Returns the image file (could be the same as the header file).

getImageMax() - Method in class edu.uthscsa.ric.volume.ImageRange

Returns the image max.

getImageMaxOffset() - Method in class edu.uthscsa.ric.volume.ImageRange

Returns the offset of the maximum voxel.

getImageMin() - Method in class edu.uthscsa.ric.volume.ImageRange

Returns the image min.

getImageMinOffset() - Method in class edu.uthscsa.ric.volume.ImageRange

Returns the offset of the minimum voxel.

getImageOffset() - Method in class edu.uthscsa.ric.volume.ImageDimensions

Gets the image offset.

getImageOffsets() - Method in class edu.uthscsa.ric.volume.ImageDimensions

Returns an array of image offsets for multi-file images.

getImageRange() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the ImageRange.

getImageRange() - Method in interface edu.uthscsa.ric.volume.ReadableHeader

Returns the image range.

getImageSelectionPanel(JButton) - Method in interface edu.uthscsa.ric.mango.ImageLoader

This method should return a GUI allowing the user to select a base image.

getImageTrailer() - Method in class edu.uthscsa.ric.volume.ImageDimensions

Returns the number of bytes in the image trailer.

getImageTransform() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the ImageTransform.

getImageType() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the ImageType.

getImageType() - Method in interface edu.uthscsa.ric.volume.ReadableHeader

Returns the image type.

getImageTypeDescription() - Method in class edu.uthscsa.ric.volume.ImageDescription

Returns a description of the image type.

getIndiciesIterator() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Surface

Returns a triangles iterator.

getInputStream() - Method in interface edu.uthscsa.ric.mango.ImageLoader

(Not yet implemented.)

getLabel(double, double, double) - Method in interface edu.uthscsa.ric.mango.Atlas

Returns labels based on a coordinate position.

getLabel(boolean) - Method in interface edu.uthscsa.ric.roi.ROI

Returns the label of this ROI.

getLabel(int) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the series label for the specified index.

getLabel(int, String) - Method in interface edu.uthscsa.ric.volume.LabelManager

Returns a label for the specified index.

getLabelData() - Method in interface edu.uthscsa.ric.volume.LabelManager

Returns a serialized byte array of label data.

getLabelManager() - Method in interface edu.uthscsa.ric.roi.ROIData

Returns the ROI mask LabelManager.

getLabelModel() - Method in interface edu.uthscsa.ric.volume.LabelManager

Returns the label model.

getLabels() - Method in interface edu.uthscsa.ric.volume.AnalysisPoint

Returns the atlas labels at this point.

getLibDir() - Method in interface edu.uthscsa.ric.mango.MangoContext

Returns the lib directory.

getLines() - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Returns a list of lines.

getLoadedURI() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns the URI of the file used to load the base volume of this viewer.

getLoadedURI(ImageVolume) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns the URI of the file used to load the specified volume.

getLogFile() - Static method in class edu.uthscsa.ric.utilities.AppLogger

Returns the log file.

getMainImage() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns a rendering of the main slice view.

getMainImage(boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns a rendering of the main slice view.

getMainImage(BufferedImage, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns a rendering of the main slice view.

getMainImage(BufferedImage, int, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns a rendering of the main slice view.

getMainImage(BufferedImage, int, int, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns a rendering of the main slice view.

getManagerTitle() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns a nicely formatted title for this VolumeManager

getMangoData() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Deprecated. 

getMaskValue(int, int, int) - Method in interface edu.uthscsa.ric.roi.ROIData

Gets the ROI value at a specified location.

getMaskValue(int, int, int, int) - Method in interface edu.uthscsa.ric.roi.ROIData

Gets the ROI value at a specified location.

getMatrixCopy() - Method in interface edu.uthscsa.ric.volume.ImageTransform

Returns a copy of the 4x4 image transformation matrix.

getMax() - Method in interface edu.uthscsa.ric.mango.ProgressMeter

Returns the maximum value.

getMax() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Overlay

Returns the LUT maximum.

getMax() - Method in interface edu.uthscsa.ric.volume.Histogram

Returns the histogram range max.

getMaxCoordinate() - Method in interface edu.uthscsa.ric.volume.Analysis

Returns the coordinate of the max value.

getMaximumColors() - Method in interface edu.uthscsa.ric.roi.ColorManager

Returns the current maximum number of colors.

getMaximumColors() - Method in interface edu.uthscsa.ric.roi.mask.ROIMaskBuffer

Returns the maximum number of ROI colors that this buffer supports.

getMaxReturnedLabels() - Method in interface edu.uthscsa.ric.mango.Atlas

This is the maximum number of labels that will be displayed using this atlas, not to exceed MAX_RETURN_LABELS_LENGTH;

getMaxT() - Method in class edu.uthscsa.ric.volume.ImageBounds

Returns T upper bound.

getMaxValue() - Method in interface edu.uthscsa.ric.volume.Analysis

Returns the value at the max coordinate.

getMaxX() - Method in class edu.uthscsa.ric.volume.ImageBounds

Returns X upper bound.

getMaxY() - Method in class edu.uthscsa.ric.volume.ImageBounds

Returns Y upper bound.

getMaxZ() - Method in class edu.uthscsa.ric.volume.ImageBounds

Returns Z upper bound.

getMean() - Method in interface edu.uthscsa.ric.volume.Analysis

Returns the mean.

getMin() - Method in interface edu.uthscsa.ric.mango.ProgressMeter

Returns the minimum value.

getMin() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Overlay

Returns the LUT minimum.

getMin() - Method in interface edu.uthscsa.ric.volume.Histogram

Returns the histogram range min.

getMinCoordinate() - Method in interface edu.uthscsa.ric.volume.Analysis

Returns the coordinate of the min value.

getMinimumVersionSupported() - Method in interface edu.uthscsa.ric.mango.MangoPluginType

Returns the minimum version of Mango that will support this plugin (e.g., "2.5").

getMinT() - Method in class edu.uthscsa.ric.volume.ImageBounds

Returns T lower bound.

getMinValue() - Method in interface edu.uthscsa.ric.volume.Analysis

Returns the value at the min coordinate.

getMinX() - Method in class edu.uthscsa.ric.volume.ImageBounds

Returns X lower bound.

getMinY() - Method in class edu.uthscsa.ric.volume.ImageBounds

Returns Y lower bound.

getMinZ() - Method in class edu.uthscsa.ric.volume.ImageBounds

Returns Z lower bound.

getName(ImageVolume) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns a nice name for this volume;

getName() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Surface

Returns the name of this Surface.

getName() - Method in interface edu.uthscsa.ric.volume.Analysis

Returns the name of this analysis.

getName() - Method in interface edu.uthscsa.ric.volume.AnalysisPoint

Returns the name of this analysis.

getName() - Method in class edu.uthscsa.ric.volume.EditableHeader.CodeOption

Returns the human-readable name.

getName() - Method in class edu.uthscsa.ric.volume.ImageDescription

Returns the scan name.

getNativeIntegerValueAtIndex(int, int, int, int) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the native integer value at a specified image index.

getNativeType() - Method in class edu.uthscsa.ric.volume.ImageType

If image data was loaded as a different type than what is specified in the header, store the native type here.

getNormalsIterator() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Surface

Returns a normals iterator.

getNumBins() - Method in interface edu.uthscsa.ric.volume.Histogram

Returns the number of histogram bins.

getNumBytesPerVoxel() - Method in class edu.uthscsa.ric.volume.ImageType

Returns the number of bytes per voxel.

getNumPoints() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Surface

Returns the number of points in this Surface.

getNumTriangles() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Surface

Returns the number of triangles in this Surface.

getNumVoxels() - Method in class edu.uthscsa.ric.volume.ImageDimensions

Deprecated. 

getNumVoxelsSlice() - Method in class edu.uthscsa.ric.volume.ImageDimensions

Gets the number of voxels in a slice of this image.

getNumVoxelsSlice(int) - Method in class edu.uthscsa.ric.volume.ImageDimensions

Gets the number of voxels in a slice of this image.

getNumVoxelsTimeseries() - Method in class edu.uthscsa.ric.volume.ImageDimensions

Gets the number of voxels in this image.

getNumVoxelsVolume() - Method in class edu.uthscsa.ric.volume.ImageDimensions

Gets the number of voxels in a volume of this image.

getOptions() - Method in interface edu.uthscsa.ric.visualization.surface.io.SurfaceFormat

Returns options.

getOptionsPanel(Surface[], Shape[], SurfaceController) - Method in interface edu.uthscsa.ric.visualization.surface.io.SurfaceFormat

Deprecated.

getOrientation() - Method in interface edu.uthscsa.ric.volume.ReadableHeader

Returns the orientation (e.g., XYZ+--).

getOrientationCertainty() - Method in interface edu.uthscsa.ric.volume.ReadableHeader

Returns the orientation certainty (0=Unknown/Default, 1=Incomplete/Suspicious, 2=Complete/Sufficient).

getOrientationString() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns a string representation of this volume's data orientation (e.g., XYZ+--).

getOrigin() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns the origin of the base volume.

getOrigin() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the origin voxel location relative to the left-anterior-superior edge of the image.

getOrigin() - Method in interface edu.uthscsa.ric.volume.ReadableHeader

Returns the origin voxel location relative to the native orientation of the data.

getOriginNativeOffsets() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the original offsets.

getOtherVolumeManagers(VolumeManager) - Method in interface edu.uthscsa.ric.mango.MangoContext

Returns a list of all the currently loaded VolumeManagers, except the specified.

getOverlays() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns a list of overlays volumes.

getOverlays() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Surface

Returns an array of Overlay objects associated with this Surface.

getOverlaySelectionPanel(String, ImageDimensions, VoxelDimensions, JButton) - Method in interface edu.uthscsa.ric.mango.ImageLoader

This method should return a GUI allowing the user to select an overlay image.

getPluginName() - Method in interface edu.uthscsa.ric.mango.MangoPluginType

Returns the name of this plugin.

getPluginURL() - Method in interface edu.uthscsa.ric.mango.MangoPluginType

Returns a URL to download this plugin.

getPoints() - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Returns a list of points.

getPoints() - Method in interface edu.uthscsa.ric.roi.Line

Returns the points in this line.

getPoints(int) - Method in interface edu.uthscsa.ric.roi.ROIData

Gets all points of a specified color.

getPoints() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Shape

Returns point array

getPointsIterator() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Surface

Returns a points iterator.

getPreferredFileExtension() - Method in interface edu.uthscsa.ric.visualization.surface.io.SurfaceFormat

Returns the preferred file extension of this format.

getPreferredFileExtension() - Method in interface edu.uthscsa.ric.volume.ReadableHeader

Returns the preferred file extension of this format.

getPreviewImage() - Method in interface edu.uthscsa.ric.volume.ReadableHeader

Return null to have the application handle reading the image preview.

getProjectionManager() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns the ProjectionManager.

getRawVoxelValueAtIndex(int, int, int) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the raw (without data scaling) voxel value at a specified image index.

getRawVoxelValueAtIndex(int, int, int, int) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the raw (without data scaling) voxel value at a specified image index and timepoint.

getRawVoxelValueAtIndex(int, int, int, int, ImageTransform) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the raw (without data scaling) voxel value at a specified image index and timepoint in transformed volume.

getRawVoxelValueForOffset(long) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the raw (without data scaling) voxel value at a specified offset.

getReadableHeader() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the ReadableHeader of this ImageVolume.

getRegionSize() - Method in interface edu.uthscsa.ric.volume.Analysis

Returns the size of the region of this analysis.

getROI() - Method in interface edu.uthscsa.ric.volume.Analysis

Returns the ROI color index.

getROI() - Method in interface edu.uthscsa.ric.volume.AnalysisPoint

Returns the ROI color index.

getROIBounds(long, int) - Method in interface edu.uthscsa.ric.roi.mask.ROIMaskBuffer

Returns the ImageBounds of the specified mask and series index.

getROIBounds(boolean) - Method in interface edu.uthscsa.ric.roi.ROI

Returns the bounds of this ROI.

getROIBoundsCurrent(long) - Method in interface edu.uthscsa.ric.roi.mask.ROIMaskBuffer

Returns the ImageBounds of the specified mask for the current series index.

getRoiColor() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns the currently selected ROI color index.

getROIColor(int) - Method in interface edu.uthscsa.ric.roi.ROIData

Returns the color of this ROI.

getRoiData() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns a ROIData object.

getROIDataBuffer() - Method in interface edu.uthscsa.ric.roi.ROIData

Returns the ROI data buffer.

getROILabel(int) - Method in interface edu.uthscsa.ric.roi.ROIData

Returns the label of this ROI.

getROIMaskBuffer() - Method in interface edu.uthscsa.ric.roi.ROIData

Deprecated. 

getROIMaskValue(int, int, int) - Method in interface edu.uthscsa.ric.roi.ROIData

Deprecated. 

getROIMaskValue(int, int, int, int) - Method in interface edu.uthscsa.ric.roi.ROIData

Deprecated. 

getROISelectedMask() - Method in interface edu.uthscsa.ric.roi.ROIData

Deprecated. 

getROISelectionPanel(String, ImageDimensions, VoxelDimensions, JButton) - Method in interface edu.uthscsa.ric.mango.ImageLoader

This method should return a GUI allowing the user to select a ROI.

getROIUsedMask() - Method in interface edu.uthscsa.ric.roi.ROIData

Deprecated. 

getRows() - Method in class edu.uthscsa.ric.volume.ImageDimensions

Gets the number of rows in a volume of this image.

getRowSize(boolean) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Returns the size of a voxel's row dimension.

getSagittalArea() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Returns the area of a voxel in the sagittal plane.

getScalars() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Overlay

Returns an array of scalar buffers.

getScalarsIterator() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Overlay

Returns the scalars iterator.

getScalarsSize() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Overlay

Returns the number of scalar values.

getScriptObjectName() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns the name reference of this viewer during the recording of a script.

getSelectedAbsolutePath() - Method in interface edu.uthscsa.ric.mango.ImageLoader

This method is called after the dialog has been closed using the load button.

getSelectedBinEndIndex(int) - Method in interface edu.uthscsa.ric.volume.Histogram

Returns the selection end bin index for the specified ROI color.

getSelectedBinStartIndex(int) - Method in interface edu.uthscsa.ric.volume.Histogram

Returns the selection start bin index for the specified ROI color.

getSelectedColors() - Method in interface edu.uthscsa.ric.volume.Histogram

Returns a list of ROI color indices currently used in selection.

getSelectedLines() - Method in interface edu.uthscsa.ric.roi.ROIData

Returns a list of selected ROI lines.

getSelectedMask() - Method in interface edu.uthscsa.ric.roi.ROIData

Returns a bit mask of selected ROI colors.

getSelectedMasks() - Method in interface edu.uthscsa.ric.roi.ROIData

Returns a list of selected ROI masks.

getSelectedPoints() - Method in interface edu.uthscsa.ric.roi.ROIData

Returns a list of selected ROI points.

getSelectedRelativePath() - Method in interface edu.uthscsa.ric.mango.ImageLoader

This method is called after the dialog has been closed using the load button (applet use only).

getSelectedROIs() - Method in interface edu.uthscsa.ric.roi.ROIData

Returns a list of selected ROIs.

getSeriesIndex() - Method in interface edu.uthscsa.ric.roi.mask.ROIMaskBuffer

Returns the current ROI series index.

getSeriesLength() - Method in interface edu.uthscsa.ric.roi.mask.ROIMaskBuffer

Returns the length of the ROI series.

getSeriesLength() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the series length.

getSeriesPoint() - Method in class edu.uthscsa.ric.volume.Coordinate4D

Returns the series point.

getShapes(int, int, int) - Method in interface edu.uthscsa.ric.roi.ROIData

Gets all shapes of a specified color within a slice.

getSliceAnnotation(int, int) - Method in interface edu.uthscsa.ric.volume.ReadableHeader

Returns a bitmap of annotation data associated with the specified slice.

getSliceDirection() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns the currently selected slice direction.

getSliceDirection() - Method in interface edu.uthscsa.ric.roi.Line

The slice direction of this line (see VolumeManager constants).

getSliceDirection() - Method in interface edu.uthscsa.ric.volume.Analysis

Returns the slice direction.

getSliceMetadata(int, int) - Method in interface edu.uthscsa.ric.volume.ReadableHeader

Returns a formatted text representation of the image header associated with the specified slice.

getSliceNum() - Method in interface edu.uthscsa.ric.roi.Line

The slice number of this line.

getSliceNum() - Method in interface edu.uthscsa.ric.volume.Analysis

Returns the slice number.

getSliceNumber() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns the currently selected slice number.

getSlices() - Method in class edu.uthscsa.ric.volume.ImageDimensions

Gets the number of slices in a volume of this image.

getSliceThickness(boolean) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Returns the size of a voxel's slice dimension.

getSpatialUnit() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Returns the spatial unit code.

getSpatialUnitMultiplier() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Returns a multiplier to convert units to mm.

getSpecialPoints(Color) - Method in interface edu.uthscsa.ric.roi.ROIData

Gets all special points of a specified color.

getSpecialShapes(int, int, Color) - Method in interface edu.uthscsa.ric.roi.ROIData

Gets all special shapes of a specified color within a slice.

getStandardDev() - Method in interface edu.uthscsa.ric.volume.Analysis

Returns the standard deviation.

getStats() - Method in interface edu.uthscsa.ric.roi.ROI

Returns the stats of this ROI

getStats(int) - Method in interface edu.uthscsa.ric.roi.ROI

Returns the stats at a specified series point.

getStudyDate() - Method in class edu.uthscsa.ric.volume.ImageDescription

Returns the study date.

getStudyDateString() - Method in class edu.uthscsa.ric.volume.ImageDescription

 

getStudyDateTimeString() - Method in class edu.uthscsa.ric.volume.ImageDescription

 

getStudyTimeString() - Method in class edu.uthscsa.ric.volume.ImageDescription

 

getSum() - Method in interface edu.uthscsa.ric.volume.Analysis

Returns the sum.

getSupportedBytesForType(int) - Method in interface edu.uthscsa.ric.volume.WritableHeader

Returns an array of byte counts that supported for a datatype.

getSupportedOrientations() - Method in interface edu.uthscsa.ric.volume.WritableHeader

Returns an array of valid data orientations in the format "XYZ+--" where the first character represents the fastest moving dimension and that third character represents the slowest moving dimension.

getSupportedTypesForBytes(int) - Method in interface edu.uthscsa.ric.volume.WritableHeader

Returns an array of datatypes that are supported for a number of bytes.

getSurfaceManager() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns the SurfaceManager

getSurfaces() - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Returns an array of loaded surfaces.

getTE1() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Returns the TE1.

getTE2() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Returns the TE2.

getTemporalUnit() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Returns the temporal unit code.

getTemporalUnitMultiplier() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Returns a multiplier to convert units to seconds.

getThreshold() - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Returns the threshold used to build the base surface.

getThreshold() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Surface

Returns the threshold used to build this Surface.

getTime() - Method in class edu.uthscsa.ric.volume.ImageDescription

Deprecated. 

getTimepoints() - Method in class edu.uthscsa.ric.volume.ImageDimensions

Gets the number of timepoints in this image.

getTitle() - Method in class edu.uthscsa.ric.volume.ImageDescription

Returns a nice title for this image.

getTool() - Method in interface edu.uthscsa.ric.mango.MangoContext

Returns the current ROI tool (see tool code constants).

getTR() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Returns the TR.

getTransforms() - Method in interface edu.uthscsa.ric.volume.ReadableHeader

Returns an array of any transforms stored in the header.

getType() - Method in interface edu.uthscsa.ric.volume.Analysis

Returns the analysis type (see constants).

getType() - Method in interface edu.uthscsa.ric.volume.AnalysisPoint

Returns the analysis type.

getTypeMax(boolean) - Method in class edu.uthscsa.ric.volume.ImageType

Get the maximum value of this type.

getTypeMin(boolean) - Method in class edu.uthscsa.ric.volume.ImageType

Get the minimum value of this type.

getTypeMin(boolean, boolean) - Method in class edu.uthscsa.ric.volume.ImageType

Get the minimum value of this type.

getUnitSize() - Method in interface edu.uthscsa.ric.volume.Analysis

Returns the unit size.

getUsage() - Method in interface edu.uthscsa.ric.cli.ConsolePlugin

A Unix-style usage message

getUsedLines() - Method in interface edu.uthscsa.ric.roi.ROIData

Returns a list of used ROI lines.

getUsedMask() - Method in interface edu.uthscsa.ric.roi.ROIData

Returns a bit mask of used ROI colors.

getUsedMasks() - Method in interface edu.uthscsa.ric.roi.ROIData

Returns a list of used ROIs.

getUsedPoints() - Method in interface edu.uthscsa.ric.roi.ROIData

Returns a list of used ROI points.

getValue() - Method in interface edu.uthscsa.ric.volume.AnalysisPoint

Returns the value at this point.

getValues() - Method in class edu.uthscsa.ric.volume.Coordinate

Returns an array of coordinate values.

getVariableSpacing() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Returns an array of variable slice spacings.

getVariableTiming() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Returns an array of variable volume durations.

getVersion() - Method in interface edu.uthscsa.ric.mango.MangoContext

Returns the Mango version.

getVersion() - Method in interface edu.uthscsa.ric.mango.MangoPluginType

Returns the version of this plugin (e.g., "1.0").

getVersion() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns the Mango version.

getViewTransform() - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Returns the view transform (4x4).

getVolume(int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Gets the ImageVolume at the specified index.

getVolume() - Method in interface edu.uthscsa.ric.volume.Cluster

Returns the ImageVolume associated with this cluster.

getVolume() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Returns the volume of a voxel.

getVolumeDisplayAlpha(ImageVolume) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns the screen display alpha value of the specified ImageVolume.

getVolumeDisplayColorTable(ImageVolume) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns the screen display color table for the specified ImageVolume.

getVolumeDisplayRangeMax(ImageVolume) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns the screen display range maximum for the specified ImageVolume.

getVolumeDisplayRangeMin(ImageVolume) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns the screen display range minimum for the specified ImageVolume.

getVolumeIndex(ImageVolume) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns the index of the specified volume.

getVolumeIntercept() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the intercept value of the image [(0 - intercept) / scale] -- the value that should be on disk so that the screen value is 0.

getVolumeInterceptScreen() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the intercept value of the image [(intercept) / scale] -- if the value on disk is 0, this is the screen value.

getVolumes() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns a list of all loaded ImageVolumes.

getVoxelDimensions() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the VoxelDimensions.

getVoxelDimensions() - Method in interface edu.uthscsa.ric.volume.ReadableHeader

Returns the voxel dimensions.

getVoxelValueAtCoordinate(double, double, double) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the voxel value at a specified coordinate in real world space.

getVoxelValueAtCoordinate(double, double, double, int) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the voxel value at a specified coordinate and timepoint in real world space.

getVoxelValueAtCoordinate(double, double, double, int, ImageTransform) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the voxel value at a specified coordinate and timepoint in a transformed world space.

getVoxelValueAtIndex(int, int, int) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the voxel value at a specified image index.

getVoxelValueAtIndex(int, int, int, int) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the voxel value at a specified image index and timepoint.

getVoxelValueAtIndex(int, int, int, int, ImageTransform) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the voxel value at a specified image index and timepoint in transformed volume.

getVoxelValueForOffset(long) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the voxel value at a specified offset.

getWorkBuffer() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Deprecated. 

getWorkBufferImageType() - Static method in class edu.uthscsa.ric.volume.ImageType

Returns an ImageType which is a 4-byte float, 32 bits stored, and big endian.

getWorkBuffers() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns the work buffer (a float buffer), for use with advanced methods.

getX() - Method in interface edu.uthscsa.ric.roi.Point

The X location of the point.

getX() - Method in class edu.uthscsa.ric.volume.ImageDimensions

Gets the X dimension.

getXDim() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns x image dimension.

getXSize() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns x voxel size.

getXSize() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Returns the size of a voxel along the X dimension.

getY() - Method in interface edu.uthscsa.ric.roi.Point

The Y location of the point.

getY() - Method in class edu.uthscsa.ric.volume.ImageDimensions

Gets the Y dimension.

getYDim() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns y image dimension.

getYSize() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns y voxel size.

getYSize() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Returns the size of a voxel along the Y dimension.

getZ() - Method in interface edu.uthscsa.ric.roi.Point

The Z location of the point.

getZ() - Method in class edu.uthscsa.ric.volume.ImageDimensions

Gets the Z dimension.

getZDim() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns z image dimension.

getZSize() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns z voxel size.

getZSize() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Returns the size of a voxel along the Z dimension.

goToShape(Shape) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Move the current coordinate to the specified line or point shape.

GREEN_INDEX - Static variable in interface edu.uthscsa.ric.roi.ROIData

Deprecated.

GREEN_MASK - Static variable in interface edu.uthscsa.ric.roi.ROIData

Deprecated.

H

hasBeenEdited() - Method in class edu.uthscsa.ric.volume.ImageDescription

Returns true if this object has been edited since construction.

hasDefaultDataScaleIntercept(float[]) - Static method in class edu.uthscsa.ric.volume.ImageRange

Checks if all data scale intercepts are default.

hasDefaultDataScaleIntercept() - Method in class edu.uthscsa.ric.volume.ImageRange

Checks if all data scale intercepts are default.

hasDefaultDataScaleSlope(float[]) - Static method in class edu.uthscsa.ric.volume.ImageRange

Checks if all data scale slopes are default.

hasDefaultDataScaleSlope() - Method in class edu.uthscsa.ric.volume.ImageRange

Checks if all data scale slopes are default.

hasGlobalDataScaleIntercept() - Method in class edu.uthscsa.ric.volume.ImageRange

Checks if all data scale intercepts are the same.

hasGlobalDataScaleSlope() - Method in class edu.uthscsa.ric.volume.ImageRange

Checks if all data scale slopes are the same.

hashCode() - Method in class edu.uthscsa.ric.volume.Coordinate

Compute hash code.

hashCode() - Method in class edu.uthscsa.ric.volume.Coordinate4D

Compute hash code.

hashCode() - Method in class edu.uthscsa.ric.volume.ImageDimensions

Computes hash code.

hashCode() - Method in class edu.uthscsa.ric.volume.ImageRange

 

hashCode() - Method in class edu.uthscsa.ric.volume.ImageType

Computes hash code.

hashCode() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Compute hash code.

hasLabels() - Method in interface edu.uthscsa.ric.volume.LabelManager

Returns true if labels are found.

hasNewerVersion() - Method in interface edu.uthscsa.ric.mango.MangoPluginType

Returns true if a newer version of this plugin exists.

hasNext() - Method in class edu.uthscsa.ric.visualization.surface.io.FloatIterator

Returns true if there is more data.

hasNext() - Method in class edu.uthscsa.ric.visualization.surface.io.IndexIterator

Returns true if there is more data.

hasSelectedMaskInRange(int, int, int, int, int, int) - Method in interface edu.uthscsa.ric.roi.ROIData

Test if there is a selected ROI mask in the specified bounds.

HEADER_FORMAT_ANALYZE - Static variable in interface edu.uthscsa.ric.volume.ImageVolume

 

HEADER_FORMAT_DES - Static variable in interface edu.uthscsa.ric.volume.ImageVolume

 

HEADER_FORMAT_DICOM_MR - Static variable in interface edu.uthscsa.ric.volume.ImageVolume

 

HEADER_FORMAT_DICOM_PET - Static variable in interface edu.uthscsa.ric.volume.ImageVolume

 

HEADER_FORMAT_DICOM_SC - Static variable in interface edu.uthscsa.ric.volume.ImageVolume

 

HEADER_FORMAT_NIFTI - Static variable in interface edu.uthscsa.ric.volume.ImageVolume

 

HEADER_TYPE_AVW - Static variable in interface edu.uthscsa.ric.volume.ImageVolume

Deprecated.

HEADER_TYPE_NEMA - Static variable in interface edu.uthscsa.ric.volume.ImageVolume

Deprecated.

HEADER_TYPE_NIFTI - Static variable in interface edu.uthscsa.ric.volume.ImageVolume

Deprecated.

HEADER_TYPE_WRITABLE - Static variable in interface edu.uthscsa.ric.volume.ImageVolume

Deprecated.

hideAll(boolean) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Hide/show all the added surface shapes, lines, and points.

Histogram - Interface in edu.uthscsa.ric.volume

The result of a histogram operation.

I

ImageBounds - Class in edu.uthscsa.ric.volume

Stores image bounds.

ImageBounds() - Constructor for class edu.uthscsa.ric.volume.ImageBounds

Default constructor.

ImageBounds(ImageBounds) - Constructor for class edu.uthscsa.ric.volume.ImageBounds

Copy constructor.

ImageBounds(int, int) - Constructor for class edu.uthscsa.ric.volume.ImageBounds

 

ImageBounds(int, int, int, int, int, int) - Constructor for class edu.uthscsa.ric.volume.ImageBounds

Constructor.

ImageDescription - Class in edu.uthscsa.ric.volume

ImageDescription contains textual information describing the image.

ImageDescription() - Constructor for class edu.uthscsa.ric.volume.ImageDescription

The default class constructor.

ImageDescription(String, String, String, String, String) - Constructor for class edu.uthscsa.ric.volume.ImageDescription

Deprecated. 

ImageDescription(String, String, Date, String) - Constructor for class edu.uthscsa.ric.volume.ImageDescription

Class constructor.

ImageDimensions - Class in edu.uthscsa.ric.volume

ImageDimensions contains information related to image size in columns/rows/slices and x/y/z orientations, as well as timepoints and offset.

ImageDimensions(int, int, int, int) - Constructor for class edu.uthscsa.ric.volume.ImageDimensions

The only class constructor.

ImageLoader - Interface in edu.uthscsa.ric.mango

An ImageLoader provides the application with a way to access an online library of images.

ImageRange - Class in edu.uthscsa.ric.volume

ImageRange stores information related to the value range of the image and value scaling.

ImageRange(double, double, double, double) - Constructor for class edu.uthscsa.ric.volume.ImageRange

The only class constructor.

ImageTransform - Interface in edu.uthscsa.ric.volume

ImageTransform provides access to volume transform.

ImageType - Class in edu.uthscsa.ric.volume

ImageType stores information related to data type and data mask.

ImageType(int, int, int, boolean) - Constructor for class edu.uthscsa.ric.volume.ImageType

The only class constructor.

ImageVolume - Interface in edu.uthscsa.ric.volume

ImageVolume is an interface that allows access to the image volume, with methods to get and put voxel values.

inBounds(int, int, int) - Method in class edu.uthscsa.ric.volume.ImageBounds

Returns true of the specified location is within bounds.

increment(int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Increments the slice in the specified direction.

INDEX_BLUE - Static variable in interface edu.uthscsa.ric.roi.ROIData

 

INDEX_GREEN - Static variable in interface edu.uthscsa.ric.roi.ROIData

 

INDEX_RED - Static variable in interface edu.uthscsa.ric.roi.ROIData

 

IndexIterator - Class in edu.uthscsa.ric.visualization.surface.io

An iterator of surface index data.

IndexIterator(IntBuffer[], int[]) - Constructor for class edu.uthscsa.ric.visualization.surface.io.IndexIterator

Constructor.

info(String) - Static method in class edu.uthscsa.ric.utilities.AppLogger

Log info.

info(Throwable) - Static method in class edu.uthscsa.ric.utilities.AppLogger

Log info.

initMask(long) - Method in interface edu.uthscsa.ric.roi.ROIData

Initializes one or more ROI colors.

initROIMask(byte) - Method in interface edu.uthscsa.ric.roi.ROIData

Deprecated. 

inRange(Coordinate) - Method in class edu.uthscsa.ric.volume.ImageDimensions

Returns true if the specified coordinate is within the range of these dimensions.

INTERPOLATION_TYPE_LINEAR - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

INTERPOLATION_TYPE_NN - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

INTERPOLATION_TYPE_SINC - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

InvalidHeaderException - Exception in edu.uthscsa.ric.volume

An exception class used to pass along specific error messages about why a file header cannot be read or is read successfully but found not to be valid.

InvalidHeaderException() - Constructor for exception edu.uthscsa.ric.volume.InvalidHeaderException

Default constructor.

InvalidHeaderException(String) - Constructor for exception edu.uthscsa.ric.volume.InvalidHeaderException

Constructor that takes a string.

InvalidHeaderException(String, Exception) - Constructor for exception edu.uthscsa.ric.volume.InvalidHeaderException

Constructor.

isAllZeros() - Method in class edu.uthscsa.ric.volume.Coordinate

This method can be used to check if all values are zero.

isAscii() - Method in class edu.uthscsa.ric.volume.ImageType

Returns true if ascii state flag is set.

isBaseSurface() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Surface

True if this Surface is the base surface, false otherwise.

isCompressed() - Method in class edu.uthscsa.ric.volume.ImageType

Returns true if this data was compressed.

isCurrentVolumeOverlay() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns true if the currently selected volume is an overlay.

isCurrentVolumeUsingTransform() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns true if the currently selected volume is using a transform.

isDebugEnabled() - Static method in class edu.uthscsa.ric.utilities.AppLogger

Returns true if debug is enabled.

isEmptyOf(int) - Method in interface edu.uthscsa.ric.roi.mask.ROIMaskBuffer

Returns true if the ROI color index is not found.

isFlip() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

 

isHidden() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Surface

Returns true if the surface is hidden.

isImportingInWorldSpace() - Method in interface edu.uthscsa.ric.mango.ImageLoader

In the case of ROIs, this method should return true if the ROI is to be imported in world space.

isImportingROI() - Method in interface edu.uthscsa.ric.mango.ImageLoader

In the case of ROIs, this method should return true if the ROI is to be imported as an image, rather than ROI format.

isInsideSelectedMaskAtOffset(int) - Method in interface edu.uthscsa.ric.roi.ROIData

Test if there is a selected ROI mask at the specified offset.

isInteger() - Method in class edu.uthscsa.ric.volume.ImageType

Returns true if the byte type is integer.

isLittleEndian() - Method in class edu.uthscsa.ric.volume.ImageType

Returns the byte order state.

isMultisliceMode() - Method in interface edu.uthscsa.ric.mango.MangoContext

Returns true if multislice mode is set, false otherwise

isMultiSliceMode() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns true if the application is in multi-slice ROI mode.

isOutOfRange() - Method in class edu.uthscsa.ric.volume.Coordinate

Returns true if any coordinate value is NaN.

isParametricOverlay() - Method in interface edu.uthscsa.ric.mango.ImageLoader

In the case of overlay, this method should return true if the overlay should load both in the positive and negative range.

isPublic() - Method in interface edu.uthscsa.ric.mango.ImageLoader

If an image is not public, its address will not be displayed (e.g., in the Image Info dialog) and it will not be added to the recent files list.

isRadiologicalMode() - Method in interface edu.uthscsa.ric.mango.MangoContext

Returns true for radiological display, false for neurological display

isRGB() - Method in class edu.uthscsa.ric.volume.ImageType

 

isRGBBySample() - Method in class edu.uthscsa.ric.volume.ImageType

Returns true if RGB data is stored by sample, rather than location.

isRGBMode() - Method in class edu.uthscsa.ric.volume.ImageType

Returns true if the RGB data is to interpreted as color rather than intensity.

isRGBPalette() - Method in class edu.uthscsa.ric.volume.ImageType

Returns true if this data uses a RGB palette.

isSaveable() - Method in interface edu.uthscsa.ric.mango.ImageLoader

(Not yet implemented.)

isSelected(int) - Method in interface edu.uthscsa.ric.roi.ColorManager

Returns true if the specified color is currently selected.

isSingleSlice() - Method in class edu.uthscsa.ric.volume.ImageBounds

Returns true if the upper and lower bounds of X, Y, or Z are the same.

isSupportedBigEndian() - Method in interface edu.uthscsa.ric.volume.WritableHeader

Returns true if this image format supports writing in big endian byte order.

isSupportedDataScaleIntercept() - Method in interface edu.uthscsa.ric.volume.WritableHeader

Returns true if this image format supports a data scale intercept.

isSupportedDataScaleSlope() - Method in interface edu.uthscsa.ric.volume.WritableHeader

Returns true if this image format supports a data scale slope.

isSupportedLittleEndian() - Method in interface edu.uthscsa.ric.volume.WritableHeader

Returns true if this image format supports writing in little endian byte order.

isSupportedMultipleDataScales() - Method in interface edu.uthscsa.ric.volume.WritableHeader

Returns true if this image format supports multiple data scale values, such as a data scale per slice or per volume.

isTextEditableHeader() - Method in interface edu.uthscsa.ric.volume.EditableHeader

Returns true if this header is text-editable.

isThisFormat(File) - Method in interface edu.uthscsa.ric.visualization.surface.io.SurfaceFormat

Used to determine if a file is of this format (e.g., read magic number, check file size, check file extension, etc).

isThisFormat(File) - Method in interface edu.uthscsa.ric.volume.ReadableHeader

Used to determine if a file is of this format (e.g., read magic number, check file size, check file extension, etc.).

isTiled() - Method in class edu.uthscsa.ric.volume.ImageDimensions

Returns true if the data is tiled (e.g., DICOM mosaic data).

isUsed(int) - Method in interface edu.uthscsa.ric.roi.ColorManager

Returns true if the specified color is currently used.

isUseTransform() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Surface

Returns whether the viewer transform is applied to the surface.

isValid() - Method in class edu.uthscsa.ric.volume.ImageDimensions

Use to verify that columns, rows, slices, and timepoints have valid values.

isValid(StringBuffer) - Method in class edu.uthscsa.ric.volume.ImageDimensions

Use to verify that columns, rows, slices, and timepoints have valid values.

isValid() - Method in class edu.uthscsa.ric.volume.ImageType

Use to verify that values are valid.

isValid(StringBuffer) - Method in class edu.uthscsa.ric.volume.ImageType

Returns true if this ImageType is valid, false otherwise.

isValid() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Use to verify that column, row, and slice sizes and TR have valid values.

isValid(StringBuffer) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Use to verify that column, row, and slice sizes and TR have valid values.

isVisible() - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Shape

Returns true if the shape is visible

isVolumeDisplayHidden(ImageVolume) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns true if the screen display of the specified ImageVolume is hidden

isVolumeDisplayNegative(ImageVolume) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns true if the screen display range is negative.

isVolumeOverlay(ImageVolume) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns true if the specified ImageVolume is an overlay.

isVolumeUsingTransform(ImageVolume) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns true if the specified ImageVolume is using a transform.

isWorldMode() - Method in interface edu.uthscsa.ric.mango.MangoContext

Returns true if world mode is set, false otherwise

isWorldMode() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns true if the application is using world mode.

L

labelChanged() - Method in interface edu.uthscsa.ric.volume.LabelManager

Notifies listener that labels have changed.

LabelManager - Interface in edu.uthscsa.ric.volume

A LabelManager stores a series of labels.

Line - Interface in edu.uthscsa.ric.roi

A ROI line can consist of two or more points.

lineToShape(Shape, Shape) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Adds a direct line between two shapes.

loadAtlas(File) - Method in interface edu.uthscsa.ric.mango.Atlas

Loads the atlas.

loadROI(String) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Loads an ROI.

loadROIURL(String, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Loads an ROI from a URL.

loadSurface(String) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Loads a surface.

loadTransform(double[][], int, Coordinate) - Method in interface edu.uthscsa.ric.volume.ImageTransform

Load a different transform.

LOG_FILENAME - Static variable in class edu.uthscsa.ric.utilities.AppLogger

 

logPoint(Coordinate, String) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Logs a point in the All Results table.

M

MAGENTA_INDEX - Static variable in interface edu.uthscsa.ric.roi.ROIData

Deprecated.

MAGENTA_MASK - Static variable in interface edu.uthscsa.ric.roi.ROIData

Deprecated.

makeFilename(String) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Builds a filename based on the base volume with the specified extension.

makeInterpolatedPoints() - Method in interface edu.uthscsa.ric.roi.Line

Creates a list of points of all intersected voxels.

makeInterpolatedPointsMM(double) - Method in interface edu.uthscsa.ric.roi.Line

Creates a list of points at a specified interval.

makeNewVolume() - Method in interface edu.uthscsa.ric.mango.MangoContext

Creates a new ImageVolume.

makeNewVolume() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Creates a new ImageVolume.

makeNewVolumeManager(String) - Method in interface edu.uthscsa.ric.mango.MangoContext

Creates a new VolumeManager by loading an ImageVolume from the specified location.

makeNewVolumeManager(ImageDimensions, VoxelDimensions, ImageType, ByteBuffer[], boolean, String) - Method in interface edu.uthscsa.ric.mango.MangoContext

Create a new VolumeManager with an empty image.

makeNewVolumeManagerURL(String) - Method in interface edu.uthscsa.ric.mango.MangoContext

Creates a new VolumeManager by loading an ImageVolume from the specified URL.

makePluginOverlay(int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Makes a static slice overlay for painting by a plugin.

makeProgressMeter() - Method in interface edu.uthscsa.ric.mango.MangoContext

Creates a ProgressMeter.

makeProgressMeter() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Creates a new ProgressMeter.

MangoColorSelectedListener - Interface in edu.uthscsa.ric.mango.components

A MangoColorSelectedListener listens for changes in color selection.

MangoContext - Interface in edu.uthscsa.ric.mango

An application context.

MangoPlugin - Interface in edu.uthscsa.ric.mango

A MangoPlugin can extend the functionality of Mango.

MangoPluginType - Interface in edu.uthscsa.ric.mango

 

MASK_BLUE - Static variable in interface edu.uthscsa.ric.roi.ROIData

 

MASK_GREEN - Static variable in interface edu.uthscsa.ric.roi.ROIData

 

MASK_RED - Static variable in interface edu.uthscsa.ric.roi.ROIData

 

MASL_BLUE - Static variable in interface edu.uthscsa.ric.roi.ROIData

Deprecated.

MAX_LABEL_LENGTH_ONE_COLUMN - Static variable in interface edu.uthscsa.ric.mango.Atlas

 

MAX_LABEL_LENGTH_TWO_COLUMN - Static variable in interface edu.uthscsa.ric.mango.Atlas

 

MAX_RETURN_LABELS_LENGTH - Static variable in interface edu.uthscsa.ric.mango.Atlas

 

measureAll() - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Measure all added surface shapes, lines, and points.

N

next() - Method in class edu.uthscsa.ric.visualization.surface.io.FloatIterator

Returns the next float element.

next() - Method in class edu.uthscsa.ric.visualization.surface.io.IndexIterator

Returns the next float element.

NO_DATA_MESSAGE - Static variable in interface edu.uthscsa.ric.mango.ImageLoader

 

O

ORANGE_INDEX - Static variable in interface edu.uthscsa.ric.roi.ROIData

Deprecated.

ORANGE_MASK - Static variable in interface edu.uthscsa.ric.roi.ROIData

Deprecated.

ORIENTATION_CERTAINTY_HIGH - Static variable in interface edu.uthscsa.ric.volume.ReadableHeader

 

ORIENTATION_CERTAINTY_LOW - Static variable in interface edu.uthscsa.ric.volume.ReadableHeader

 

ORIENTATION_CERTAINTY_MID - Static variable in interface edu.uthscsa.ric.volume.ReadableHeader

 

OUT_OF_RANGE - Static variable in class edu.uthscsa.ric.volume.Coordinate

 

Overlay - Interface in edu.uthscsa.ric.visualization.surface.primitives

A surface overlay.

P

ParameterNameAnnotation - Annotation Type in edu.uthscsa.ric.cli

 

pauseScriptForUserInput() - Method in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

Pauses execution of a running script.

pauseScriptForUserInput() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Pauses script execution.

pauseScriptForUserInput() - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Pauses execution of a running script.

Point - Interface in edu.uthscsa.ric.roi

A ROI point.

PREFERRED_ROTATION_CENTER - Static variable in interface edu.uthscsa.ric.volume.ImageTransform

 

PREFERRED_ROTATION_CURRENT - Static variable in interface edu.uthscsa.ric.volume.ImageTransform

 

PREFERRED_ROTATION_ORIGIN - Static variable in interface edu.uthscsa.ric.volume.ImageTransform

 

println(String) - Method in interface edu.uthscsa.ric.utilities.ConsoleLogger

Prints a line to the console.

ProgressMeter - Interface in edu.uthscsa.ric.mango

A meter that can be used to provide feedback to users about the progress of a process.

ProjectionManager - Interface in edu.uthscsa.ric.mango.viewerprojection

Manages projection data.

put(int, int, long) - Method in interface edu.uthscsa.ric.roi.mask.ROIMaskBuffer

Sets a mask value at a specified offset and series index.

putCurrent(int, long) - Method in interface edu.uthscsa.ric.roi.mask.ROIMaskBuffer

Sets a mask value at a specified offset for the current series index.

putVoxelValueAtCoordinate(double, double, double, double) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Deprecated. 

putVoxelValueAtCoordinate(double, double, double, int, double) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Deprecated. 

putVoxelValueAtCoordinate(double, double, double, int, double, ImageTransform) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Deprecated. 

putVoxelValueAtIndex(int, int, int, double) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Replaces a voxel value at a specified image index.

putVoxelValueAtIndex(int, int, int, int, double) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Replaces a voxel value at a specified image index and timepoint.

putVoxelValueAtIndex(int, int, int, int, double, ImageTransform) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Deprecated. 

putVoxelValueAtOffset(int, double) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Replaces a voxel value at a specified offset.

Q

QUALITY_BEST - Static variable in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

 

QUALITY_DEFAULT - Static variable in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

 

QUALITY_FAST - Static variable in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

 

QUALITY_FASTEST - Static variable in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

 

QUALITY_GOOD - Static variable in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

 

R

RANK_TYPE_MAX - Static variable in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

 

RANK_TYPE_MAX - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

RANK_TYPE_MEDIAN - Static variable in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

 

RANK_TYPE_MEDIAN - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

RANK_TYPE_MIN - Static variable in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

 

RANK_TYPE_MIN - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

ReadableHeader - Interface in edu.uthscsa.ric.volume

A class that implements ReadableHeader can be registered with Mango to extend the types of image header formats that can be read.

readFiles(File) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Deprecated. 

readFiles(URI) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Reads a file into an ImageVolume.

readFiles(URI, boolean) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Reads a file into an ImageVolume.

readHeader(File, File) - Method in interface edu.uthscsa.ric.volume.ReadableHeader

Reads the file.

readHeader(URI, File) - Method in interface edu.uthscsa.ric.volume.ReadableHeader

Reads the URI.

readSurfaceFile(File, ViewerController, Vector<Shape>, boolean) - Method in interface edu.uthscsa.ric.visualization.surface.io.SurfaceFormat

Deprecated. 

readSurfaceHeader(File, Vector<Shape>) - Method in interface edu.uthscsa.ric.visualization.surface.io.SurfaceFormat

Reads surface header (meta data) from file.

recordPluginAction(String, String...) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Records a scripted plugin action.

RED_INDEX - Static variable in interface edu.uthscsa.ric.roi.ROIData

Deprecated.

RED_MASK - Static variable in interface edu.uthscsa.ric.roi.ROIData

Deprecated.

reload() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Reload this VolumeManager.

removeAll() - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Remove all the added surface shapes, lines, and points.

removeAllOverlays() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Remove all overlays from this VolumeManager.

removeOverlay(ImageVolume) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Remove overlay from this VolumeManager.

removePluginOverlay(BufferedImage, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Remove a plugin overlay.

removePluginOverlays() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Deprecated. 

removePoint(Coordinate, int) - Method in interface edu.uthscsa.ric.roi.ROIData

Removes a point.

removeShape(Shape) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Remove a line or point shape.

removeShape(int, Shape) - Method in interface edu.uthscsa.ric.roi.ROIData

Remove a shape.

removeSliceListener(SliceListener, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Removes a slice listener.

removeSpecialPoint(Coordinate, Color) - Method in interface edu.uthscsa.ric.roi.ROIData

Removes a special point.

removeSpecialShape(int, Shape) - Method in interface edu.uthscsa.ric.roi.ROIData

Remove a special shape.

removeSurface(Surface) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Remove an added surface shape.

RENDER_TYPE_POINTS - Static variable in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

 

RENDER_TYPE_TRIANGLES - Static variable in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

 

RENDER_TYPE_WIREFRAME - Static variable in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

 

replaceMaskValue(int, int, int, int, long) - Method in interface edu.uthscsa.ric.roi.ROIData

Replace a ROI value at a specified location.

replaceMaskValue(int, int, int, long) - Method in interface edu.uthscsa.ric.roi.ROIData

Replace a ROI value at a specified location.

replaceROIMaskValue(int, int, int, byte) - Method in interface edu.uthscsa.ric.roi.ROIData

Deprecated. 

replaceROIMaskValue(int, int, int, int, byte) - Method in interface edu.uthscsa.ric.roi.ROIData

Deprecated. 

reset() - Static method in class edu.uthscsa.ric.utilities.AppLogger

 

ROI - Interface in edu.uthscsa.ric.roi

A ROI.

ROIData - Interface in edu.uthscsa.ric.roi

ROIData can be used to access and edit ROI mask, line, and point data.

ROIMaskBuffer - Interface in edu.uthscsa.ric.roi.mask

A ROI data buffer.

roiMaskOperationCompleted() - Method in interface edu.uthscsa.ric.roi.ROIData

Call this following an ROI operation (e.g., after iterating through the entire volume making changes).

roiMaskOperationCompleted(String) - Method in interface edu.uthscsa.ric.roi.ROIData

Call this following an ROI operation (e.g., after iterating through the entire volume making changes).

ROTATION_AXIS_X - Static variable in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

 

ROTATION_AXIS_Y - Static variable in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

 

ROTATION_AXIS_Z - Static variable in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

 

runAddROI(Coordinate, double, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Adds ROI mask data in the currently selected ROI color at the specified location.

runAddROISlice(int, Coordinate, double, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Adds ROI mask data in the currently selected ROI color at the specified location.

runAllSliceStats(int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs slice statistics on all slices of the currently selected ImageVolume in the specified slice direction.

runAllSliceStatsROI(int, long, boolean, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs slice statistics on all ROI slices of the currently selected ImageVolume in the specified slice direction.

runAllVolumeStats() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs volume statistics on all volumes in a series of the currently selected ImageVolume.

runAllVolumeStatsROI(long, boolean, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs volume statistics on all ROI volumes in a series of the currently selected ImageVolume.

runCloseROI(long, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs a close ROI operation.

runCloseROISlice(int, int, long, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs a close ROI slice operation.

runClusterAnalysis(ImageVolume, double) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs a cluster analysis.

runComponentAnalysisROI(int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs a ROI component anlaysis.

runComponentSplitROI(int, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Splits ROI components into different colors [runComponentAnalysisROI() must precede this call].

runConvexHull(ROI) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs a convex hull on the specified ROI.

runConvexHullROI(long, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs convex hull on the specified ROI mask.

runConvexHullROISlice(int, int, long, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs convex hull on the specified ROI mask.

runCrosssectionMM(Line, double) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs a cross-section on the specified Line.

runCrosssectionVoxels(Line) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs a cross-section on the specified line.

runDilateROI(long, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs a dilate ROI operation.

runDilateROISlice(int, int, long, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs a dilate ROI slice operation.

runErodeROI(long, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs an erode ROI operation.

runErodeROISlice(int, int, long, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs a erode ROI slice operation.

runFilter(String) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs a filter.

runGenerateClusterROI(ImageVolume, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Generate ROIs from clusters [runClusterAnalysis() must precede this call].

runGenerateHistogramROI(Histogram) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Adds new ROI mask data for voxels included in this histogram.

runGenerateHistogramROISlice(int, int, Histogram) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Adds new ROI mask data for voxels included in this histogram.

runGenerateHistogramWithinROI(Histogram, long) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Adds new ROI mask data for voxels included in this histogram, but only within the specified ROI mask.

runGenerateHistogramWithinROISlice(int, int, Histogram, long) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Adds new ROI mask data for voxels included in this histogram, but only within the specified ROI mask.

runGenerateLogicalROI(List<ImageVolume>) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Creates a ROI based on the intersection of a list of ImageVolumes.

runHistogram(int, double, double, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs a histogram.

runHistogramROI(int, double, double, long, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs a histogram within a ROI mask.

runLogicalAnalysis(List<ImageVolume>) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs statistics on the intersection of a list of ImageVolumes.

runOpenROI(long, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs an open ROI operation.

runOpenROISlice(int, int, long, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs an open ROI slice operation.

runOperation(String, int, boolean, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs an operation.

runOperationROILogic(String, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs a ROI logic operation.

runOperationSeriesStatistic(int, int, int, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs a series operation.

runPlugin(String, String[]) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs a plugin.

runPlugin(String, String[]) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Runs a surface plugin.

runPropagateROISlice(int, int, int, int, long, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Propagates an ROI slice.

runRangeToROI(double, double, boolean, boolean, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Creates new ROI mask data based on a range.

runRangeToROISlice(double, double, int, int, boolean, boolean, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Creates new ROI mask data based on a range.

runRankFilter(int, int, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs a rank filter.

runReflectROI(int, int, boolean, boolean, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Reflects a ROI.

runReflectROISlice(int, int, int, boolean, boolean, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

runScript(String) - Method in interface edu.uthscsa.ric.mango.MangoContext

Runs the specified script.

runScript(String) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs a script.

runSeriesROI(ROI) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs statistics on a series ROI.

runSeriesStats() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs series statistics on the currently selected ImageVolume.

runSeriesStatsROI(long, boolean, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs ROI series statistics.

runShrinkWrapROI(double, long, int, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Shrink wraps (3D) a ROI mask.

runShrinkWrapROI(long, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Shrink wraps (3D) a ROI mask.

runShrinkWrapROIAllSlices(double, int, long, int, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Shrink wraps (2D) a ROI mask in a specified slice direction.

runShrinkWrapROIAllSlices(int, long, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Shrink wraps (2D) a ROI mask in a specified slice direction.

runShrinkWrapROISlice(double, int, int, long, int, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Shrink wraps (2D) a ROI mask in a specified slice direction.

runShrinkWrapROISlice(int, int, long, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Shrink wraps (2D) a ROI mask in a specified slice direction.

runSliceStats(int, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Run statistics on a slice.

runSliceStatsROI(int, int, long, boolean, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs statistics on a ROI slice.

runSmooth(ROI) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Smooths a ROI (only applies to Lines).

runStat(ROI) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs statistics on a specified ROI.

runSurfaceAreaStats(Surface) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Runs surface area stats on the specified surface.

runSurfaceVolumeStats(Surface) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Runs surface volume stats on the specified surface.

runThresholdToConvexHullROI(double, boolean, boolean, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Adds new ROI mask data based on a threshold and in a convex hull.

runThresholdToConvexHullROISlice(double, int, int, boolean, boolean, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Adds new ROI mask data based on a threshold and in a convex hull.

runThresholdToROI(double, boolean, boolean, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Adds new ROI mask data based on a threshold.

runThresholdToROISlice(double, int, int, boolean, boolean, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Adds new ROI mask data based on a threshold.

runThresholdToShrinkWrapROI(double, boolean, boolean, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Adds new ROI mask data based on a threshold and shrink wrap (3D).

runThresholdToShrinkWrapROIAllSlices(double, int, boolean, boolean, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Adds new ROI mask data based on a threshold and shrink wrap (2D).

runThresholdToShrinkWrapROISlice(double, int, int, boolean, boolean, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Adds new ROI mask data based on a threshold and shrink wrap (2D).

runVolumeStats() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs volume statistics on the currently selected series point of the currently selected ImageVolume.

runVolumeStatsROI(long, boolean, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Runs volume ROI statistics.

S

save() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Saves this VolumeManager.

saveAs(String, String, int, int, boolean, boolean, int, int, int, int, int, int, int, int, double, double, double, double, String, boolean, boolean, boolean, boolean, int, boolean, boolean, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Saves this VolumeManager.

saveAs(String, Surface, boolean) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Saves the surface data in the Mango surface format.

saveOverlays() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Saves overlays.

saveROI(String) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Saves ROI.

saveSingleROI(String, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Saves a single ROI color.

saveWithName(String) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Saves this VolumeManager

ScriptablePlugin - Interface in edu.uthscsa.ric.cli

A plugin that can be called by a script.

select(ROI, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Selects or unselects a specified ROI.

selectAll() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Selects all ROI masks, lines, and points.

SELECTION_TYPE_ROI_INSIDE - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

SELECTION_TYPE_ROI_OUTSIDE - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

SELECTION_TYPE_SLICE - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

SELECTION_TYPE_VOLUME - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

selectMenuOption(String) - Method in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

Selects menu options.

selectMenuOption(String) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Selects a menu option.

selectMenuOption(String) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Selects menu options.

SERIES_TYPE_MAX - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

SERIES_TYPE_MEAN - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

SERIES_TYPE_MIN - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

SERIES_TYPE_STDEV - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

SERIES_TYPE_SUM - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

seriesPoint - Variable in class edu.uthscsa.ric.volume.Coordinate4D

 

setAscii(boolean) - Method in class edu.uthscsa.ric.volume.ImageType

Set the ASCII state flag.

setAssociatedFiles(URI[]) - Method in class edu.uthscsa.ric.volume.ImageDescription

Sets an array of files associated with this image.

setAtlas(String) - Method in interface edu.uthscsa.ric.mango.MangoContext

Sets the current Atlas.

setBackground(int) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Sets the surface background

setColNegativeState(boolean) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Sets the negative state of voxel column size.

setColSize(double) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Sets the size of a voxel along the column dimension.

setCompressionType(int) - Method in class edu.uthscsa.ric.volume.ImageType

Sets the compression type.

setConsole(ConsoleLogger) - Static method in class edu.uthscsa.ric.utilities.AppLogger

Set the ConsoleLogger to use.

setCoordinateSpace(int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Deprecated. 

setCurrentPosition(Coordinate) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Sets the current position.

setCurrentSeriesPoint(int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Sets the current series point.

setCurrentSeriesPoint(int) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Sets the current series point.

setCurrentVolumeIndex(int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Sets the current volume by index.

setCurrentVolumeManager(VolumeManager) - Method in interface edu.uthscsa.ric.mango.MangoContext

Sets the specified VolumeManager to be currently selected.

setCurrentVolumeManagerIndex(int) - Method in interface edu.uthscsa.ric.mango.MangoContext

Sets the VolumeManager at the specified index to be currently selected.

setDataScaleIntercepts(float[]) - Method in class edu.uthscsa.ric.volume.ImageRange

Sets the data scale intercepts.

setDataScaleSlopes(float[]) - Method in class edu.uthscsa.ric.volume.ImageRange

Sets the data scale slopes.

setDate(String) - Method in class edu.uthscsa.ric.volume.ImageDescription

Deprecated. 

setDescription(String) - Method in interface edu.uthscsa.ric.mango.ProgressMeter

Sets the text of the progress meter.

setDescription(String) - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Surface

Sets the surface description.

setDescription(String) - Method in class edu.uthscsa.ric.volume.ImageDescription

Sets the description.

setDicomItems(Map<Long, String>) - Method in class edu.uthscsa.ric.volume.ImageDescription

Sets a map of DICOM tag id to string value.

setDisplayMax(double) - Method in class edu.uthscsa.ric.volume.ImageRange

Sets the display max.

setDisplayMin(double) - Method in class edu.uthscsa.ric.volume.ImageRange

Sets the display min.

setDisplayRangeToImageRange(ImageVolume, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Sets the display range of the specified ImageVolume to its image min/max.

setEditableFieldValue(String, String, int) - Method in interface edu.uthscsa.ric.volume.EditableHeader

Sets a header field.

setFile(URI) - Method in class edu.uthscsa.ric.volume.ImageDescription

Sets the URI of this image.

setFlip(boolean) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

 

setForceLoadInThead(boolean) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Set to true to force loading this image in the current thread, instead of a background thread.

setGlobalDataScaleIntercept(int, float) - Method in class edu.uthscsa.ric.volume.ImageRange

Sets global data scale intercept.

setGlobalDataScaleSlope(int, float) - Method in class edu.uthscsa.ric.volume.ImageRange

Sets global data scale slope.

setHidden(boolean) - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Surface

Sets the surface visibility.

setHighlighted(boolean) - Method in interface edu.uthscsa.ric.roi.ROI

Sets the highlight state of this ROI.

setID(String) - Method in class edu.uthscsa.ric.volume.ImageDescription

Sets the scan ID.

setImageAsDirty() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Flag the image as dirty (needs to be saved).

setImageMax(double) - Method in class edu.uthscsa.ric.volume.ImageRange

Sets the image max.

setImageMaxOffset(long) - Method in class edu.uthscsa.ric.volume.ImageRange

Sets the offset of the maximum voxel.

setImageMin(double) - Method in class edu.uthscsa.ric.volume.ImageRange

Sets the image min.

setImageMinOffset(long) - Method in class edu.uthscsa.ric.volume.ImageRange

Sets the offset of the minimum voxel.

setImageOffset(int) - Method in class edu.uthscsa.ric.volume.ImageDimensions

Sets the image offset.

setImageOffsets(int[]) - Method in class edu.uthscsa.ric.volume.ImageDimensions

Sets an array of image offsets for multi-file images.

setImageTrailer(int) - Method in class edu.uthscsa.ric.volume.ImageDimensions

Sets the number of bytes in the image trailer

setImageTypeDescription(String) - Method in class edu.uthscsa.ric.volume.ImageDescription

Sets the image type description.

setIndeterminateMode(boolean) - Method in interface edu.uthscsa.ric.mango.ProgressMeter

Sets the indeterminate state (progress meter with no current value).

setLabel(ROI, String) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Sets the label of the specified ROI.

setLabel(int, String) - Method in interface edu.uthscsa.ric.volume.LabelManager

Sets the specified label at the specified index.

setLabel(int, String, boolean) - Method in interface edu.uthscsa.ric.volume.LabelManager

Sets the specified label at the specified index.

setLabelData(byte[]) - Method in interface edu.uthscsa.ric.volume.LabelManager

Sets the label data.

setLighting(double, double, double, double, double) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Sets the lighting parameters.

setMaterial(Surface, int, boolean, boolean, boolean, int, double, double, double, double) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Sets the material parameters.

setMenuOption(String, boolean) - Method in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

Sets menu items (typically checkboxes).

setMenuOption(String, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Sets a menu option.

setMenuOption(String, boolean) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Sets menu items (typically checkboxes).

setMultisliceMode(boolean) - Method in interface edu.uthscsa.ric.mango.MangoContext

Sets ROI "multislice" mode.

setName(String) - Method in class edu.uthscsa.ric.volume.ImageDescription

Sets the scan name.

setNativeType(ImageType) - Method in class edu.uthscsa.ric.volume.ImageType

Set the native image type.

setNotes(String) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Sets the note of the base volume.

setOptions(String, double, double) - Method in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

Sets projection options.

setOptions(String) - Method in interface edu.uthscsa.ric.visualization.surface.io.SurfaceFormat

Sets the options.

setOrientationOption(ImageVolume, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Sets the orientation option (e.g., NIFTI s-form or q-form) of the currently selected ImageVolume.

setOrigin(Coordinate) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Sets the origin of the base volume.

setOrigin(Coordinate) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Sets the origin of this ImageVolume.

setPointHighlightState(Coordinate, Color, boolean) - Method in interface edu.uthscsa.ric.roi.ROIData

Sets the highlight state of a special point.

setRadiologicalMode(boolean) - Method in interface edu.uthscsa.ric.mango.MangoContext

Sets radiological display mode.

setRangeT(int, int) - Method in class edu.uthscsa.ric.volume.ImageBounds

Set series bounds.

setRangeX(int, int) - Method in class edu.uthscsa.ric.volume.ImageBounds

Set X bounds.

setRangeY(int, int) - Method in class edu.uthscsa.ric.volume.ImageBounds

Set Y bounds.

setRangeZ(int, int) - Method in class edu.uthscsa.ric.volume.ImageBounds

Set Z bounds.

setReadOnly(boolean) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Set this image as read-only.

setRGBBySample(boolean) - Method in class edu.uthscsa.ric.volume.ImageType

Sets whether RGB data is grouped by location or sample.

setRGBMode(boolean) - Method in class edu.uthscsa.ric.volume.ImageType

Set to true to interpret this RGB data as color rather than intensity

setRGBPalette(boolean) - Method in class edu.uthscsa.ric.volume.ImageType

Sets to true if this data uses a RGB palette.

setRoiColor(int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Sets the current ROI color.

setRowNegativeState(boolean) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Sets the negative state of voxel row size.

setRowSize(double) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Sets the size of a voxel along the row dimension.

setShapeHighlightState(int, Shape, boolean) - Method in interface edu.uthscsa.ric.roi.ROIData

Sets the highlight state of a special shape.

setSliceDirection(int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Sets the current slice direction.

setSliceNegativeState(boolean) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Sets the negative state of voxel slice size.

setSliceNumber(int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Sets the current slice number.

setSliceThickness(double) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Sets the size of a voxel along the slice dimension.

setSpatialUnit(int) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Sets the spatial unit of the voxel.

setSpatialUnit(String) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Sets the spatial unit of the voxel.

setStudyDate(Date) - Method in class edu.uthscsa.ric.volume.ImageDescription

Sets the study date.

setTE1(double) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Sets the TE1.

setTE2(double) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Sets the TE2.

setTemporalUnit(int) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Sets the temporal unit of the voxel.

setTemporalUnit(String) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Sets the temporal unit of the voxel.

setThreshold(float) - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Surface

Sets the surface threshold.

setTiled(boolean) - Method in class edu.uthscsa.ric.volume.ImageDimensions

Set to true if the data is tiled.

setTime(String) - Method in class edu.uthscsa.ric.volume.ImageDescription

Deprecated. 

setTimepoints(int) - Method in class edu.uthscsa.ric.volume.ImageDimensions

Sets the number of timepoints in this image.

setTitle(String) - Method in class edu.uthscsa.ric.volume.ImageDescription

Sets a nice title for this image.

setTool(int) - Method in interface edu.uthscsa.ric.mango.MangoContext

Sets the current ROI tool (see tool code constants).

setToolRange(boolean, double, double, boolean) - Method in interface edu.uthscsa.ric.mango.MangoContext

Sets the ROI tool intensity range.

setToolRelativeRange(double) - Method in interface edu.uthscsa.ric.mango.MangoContext

Sets the ROI tool relative range (only applies to "magic wand" Add tool).

setTR(double) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Sets the TR.

setTransformMode(boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Sets the transform mode.

setUseROISeries(boolean) - Method in interface edu.uthscsa.ric.roi.ROIData

True to use a ROI series, false otherwise.

setUseTransform(boolean) - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Surface

Sets if the viewer transform is applied to the surface.

setValue(int) - Method in interface edu.uthscsa.ric.mango.ProgressMeter

Sets the current value of the meter.

setValues(Coordinate) - Method in class edu.uthscsa.ric.volume.Coordinate

Sets the values of this Coordinate to that of another Coordinate

setValues(double, double, double) - Method in class edu.uthscsa.ric.volume.Coordinate

Sets the values of this Coordinate.

setValues(double, double, double, int) - Method in class edu.uthscsa.ric.volume.Coordinate4D

Sets the values of this Coordinate4D.

setValues(int, int, int, int, int, int) - Method in class edu.uthscsa.ric.volume.ImageBounds

Set XYZ bounds.

setValues(int, int, int, int, int, int, int, int) - Method in class edu.uthscsa.ric.volume.ImageBounds

Set XYZT bounds.

setValues(ImageDimensions) - Method in class edu.uthscsa.ric.volume.ImageDimensions

Set the values of this ImageDimensions to that of another.

setValues(ImageDimensions, boolean) - Method in class edu.uthscsa.ric.volume.ImageDimensions

Set the values of this ImageDimensions to that of another.

setValues(ImageType) - Method in class edu.uthscsa.ric.volume.ImageType

Set the values of this ImageType to that of another.

setValues(VoxelDimensions) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Set the values of this VoxelDimensions to that of another.

setValues(VoxelDimensions, boolean) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Set the values of this VoxelDimensions to that of another.

setValuesRound(double, double, double) - Method in class edu.uthscsa.ric.volume.Coordinate

Sets the values of this Coordinate and rounds the integer values.

setVariableSpacing(float[]) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Sets an array of variable slice spacings.

setVariableTiming(float[]) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Sets an array of variable volume durations.

setVisible(boolean) - Method in interface edu.uthscsa.ric.visualization.surface.primitives.Shape

Sets the visibility of the shape.

setVolumeDisplayAlpha(ImageVolume, double) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Sets the alpha value of the specified ImageVolume.

setVolumeDisplayColorTable(ImageVolume, String) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Sets the color table of the specified ImageVolume.

setVolumeDisplayHidden(ImageVolume, boolean) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Sets the hidden state of the specified ImageVolume.

setVolumeDisplayIndex(ImageVolume, int) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Sets the display index of the specified ImageVolume (cannot change base volume index).

setVolumeDisplayRange(ImageVolume, double, double) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Sets the display range of the specified ImageVolume.

setVoxelValue(Coordinate, int, double) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Sets a voxel value at the specified coordinate.

setWorldMode(boolean) - Method in interface edu.uthscsa.ric.mango.MangoContext

Sets "world space" mode.

setX(int) - Method in class edu.uthscsa.ric.volume.ImageDimensions

Sets the X dimension.

setXSize(double) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Sets the size of a voxel along the X dimension.

setY(int) - Method in class edu.uthscsa.ric.volume.ImageDimensions

Sets the Y dimension.

setYSize(double) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Sets the size of a voxel along the Y dimension.

setZ(int) - Method in class edu.uthscsa.ric.volume.ImageDimensions

Sets the Z dimension.

setZSize(double) - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Sets the size of a voxel along the Z dimension.

Shape - Interface in edu.uthscsa.ric.visualization.surface.primitives

A Shape represents a surface line or point.

showErrorMessage(String, String) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Shows an error message.

showWarningMessage(String, String) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Shows a warning message.

SLATE_INDEX - Static variable in interface edu.uthscsa.ric.roi.ROIData

Deprecated.

SLATE_MASK - Static variable in interface edu.uthscsa.ric.roi.ROIData

Deprecated.

SLICE_DIRECTION_AXIAL - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

SLICE_DIRECTION_AXIAL - Static variable in interface edu.uthscsa.ric.roi.ROIData

 

SLICE_DIRECTION_AXIAL - Static variable in class edu.uthscsa.ric.volume.ImageDimensions

 

SLICE_DIRECTION_CORONAL - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

SLICE_DIRECTION_CORONAL - Static variable in interface edu.uthscsa.ric.roi.ROIData

 

SLICE_DIRECTION_CORONAL - Static variable in class edu.uthscsa.ric.volume.ImageDimensions

 

SLICE_DIRECTION_SAGITTAL - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

SLICE_DIRECTION_SAGITTAL - Static variable in interface edu.uthscsa.ric.roi.ROIData

 

SLICE_DIRECTION_SAGITTAL - Static variable in class edu.uthscsa.ric.volume.ImageDimensions

 

SLICE_DIRECTION_TEMPORAL - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

start(int, int, int) - Method in interface edu.uthscsa.ric.mango.ProgressMeter

Starts the progress meter.

start(int, int, int, boolean) - Method in interface edu.uthscsa.ric.mango.ProgressMeter

Starts the progress meter.

Surface - Interface in edu.uthscsa.ric.visualization.surface.primitives

A surface.

SurfaceFormat - Interface in edu.uthscsa.ric.visualization.surface.io

A class that implements SurfaceFormat can be registered with Mango to extend the number of surface formats supported.

SurfaceFormatException - Exception in edu.uthscsa.ric.visualization.surface.io

 

SurfaceFormatException(String) - Constructor for exception edu.uthscsa.ric.visualization.surface.io.SurfaceFormatException

Constructor

SurfaceFormatException(Throwable) - Constructor for exception edu.uthscsa.ric.visualization.surface.io.SurfaceFormatException

Constructor.

SurfaceManager - Interface in edu.uthscsa.ric.mango.viewersurface

Manages surface data.

SurfacePlugin - Interface in edu.uthscsa.ric.visualization.surface

A class which implements SurfacePlugin can be registered with Mango and have access to surface-related data.

surfaceToShape(Shape, Shape) - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Adds a line along the surface bewteen two shapes.

T

TIME_FORMAT - Variable in class edu.uthscsa.ric.volume.ImageDescription

 

TOOL_MODE_ADD_POINT - Static variable in interface edu.uthscsa.ric.mango.MangoContext

 

TOOL_MODE_ADD_REGION - Static variable in interface edu.uthscsa.ric.mango.MangoContext

 

TOOL_MODE_DRAW_ELLIPSE - Static variable in interface edu.uthscsa.ric.mango.MangoContext

 

TOOL_MODE_DRAW_RECT - Static variable in interface edu.uthscsa.ric.mango.MangoContext

 

TOOL_MODE_NAV - Static variable in interface edu.uthscsa.ric.mango.MangoContext

 

TOOL_MODE_PAINT_ELLIPSE_EDIT - Static variable in interface edu.uthscsa.ric.mango.MangoContext

 

TOOL_MODE_PAINT_ELLIPSE_ERASE - Static variable in interface edu.uthscsa.ric.mango.MangoContext

 

TOOL_MODE_PAINT_ELLIPSE_PAINT - Static variable in interface edu.uthscsa.ric.mango.MangoContext

 

TOOL_MODE_PAINT_RECT_EDIT - Static variable in interface edu.uthscsa.ric.mango.MangoContext

 

TOOL_MODE_PAINT_RECT_ERASE - Static variable in interface edu.uthscsa.ric.mango.MangoContext

 

TOOL_MODE_PAINT_RECT_PAINT - Static variable in interface edu.uthscsa.ric.mango.MangoContext

 

TOOL_MODE_TRACE_LINE - Static variable in interface edu.uthscsa.ric.mango.MangoContext

 

TOOL_MODE_TRACE_REGION - Static variable in interface edu.uthscsa.ric.mango.MangoContext

 

TOOL_MODE_WAND_COPY - Static variable in interface edu.uthscsa.ric.mango.MangoContext

 

TOOL_MODE_WAND_DILATE_ERODE - Static variable in interface edu.uthscsa.ric.mango.MangoContext

 

TOOL_MODE_WAND_PRESERVE - Static variable in interface edu.uthscsa.ric.mango.MangoContext

 

TOOL_MODE_WAND_REMOVE - Static variable in interface edu.uthscsa.ric.mango.MangoContext

 

toString() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Returns a string representation.

toString() - Method in interface edu.uthscsa.ric.roi.ROI

Returns a string representation of this ROI.

toString() - Method in class edu.uthscsa.ric.volume.Coordinate

Returns a string representation of this object.

toString() - Method in class edu.uthscsa.ric.volume.Coordinate4D

Returns a string representation of this object.

toString() - Method in class edu.uthscsa.ric.volume.EditableHeader.CodeOption

Returns a string representation.

toString() - Method in class edu.uthscsa.ric.volume.ImageBounds

Returns a string representation of this object.

toString() - Method in class edu.uthscsa.ric.volume.ImageDescription

Returns a string representation of this object.

toString() - Method in class edu.uthscsa.ric.volume.ImageDimensions

Returns a string representation of this object.

toString() - Method in class edu.uthscsa.ric.volume.ImageRange

Returns a string representation of this object.

toString() - Method in class edu.uthscsa.ric.volume.ImageType

Returns a string representation of this object.

toString() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Returns a string representation of this ImageVolume.

toString() - Method in interface edu.uthscsa.ric.volume.ReadableHeader

Returns a formatted text representation of the image header (such as would be displayed in the 'Image Info' window).

toString() - Method in class edu.uthscsa.ric.volume.VoxelDimensions

Returns a string representation of this object.

transform(ImageVolume, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double) - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Transform the specified ImageVolume.

transform(Coordinate) - Method in interface edu.uthscsa.ric.volume.ImageTransform

Transforms the coordinate.

transformNative(Coordinate) - Method in interface edu.uthscsa.ric.volume.ImageTransform

Transforms the coordinate.

TYPE_CLUSTER - Static variable in interface edu.uthscsa.ric.volume.Analysis

 

TYPE_LINE - Static variable in interface edu.uthscsa.ric.volume.Analysis

 

TYPE_LOGICAL - Static variable in interface edu.uthscsa.ric.volume.Analysis

 

TYPE_POINT - Static variable in interface edu.uthscsa.ric.volume.Analysis

 

TYPE_SLICE - Static variable in interface edu.uthscsa.ric.volume.Analysis

 

TYPE_SURFACE - Static variable in interface edu.uthscsa.ric.volume.Analysis

 

TYPE_TIMESERIES - Static variable in interface edu.uthscsa.ric.volume.Analysis

 

TYPE_VOLUME - Static variable in interface edu.uthscsa.ric.volume.Analysis

 

U

UNIT_STRING - Static variable in class edu.uthscsa.ric.volume.VoxelDimensions

 

UNITS_HZ - Static variable in class edu.uthscsa.ric.volume.VoxelDimensions

 

UNITS_METER - Static variable in class edu.uthscsa.ric.volume.VoxelDimensions

 

UNITS_MICRON - Static variable in class edu.uthscsa.ric.volume.VoxelDimensions

 

UNITS_MM - Static variable in class edu.uthscsa.ric.volume.VoxelDimensions

 

UNITS_MSEC - Static variable in class edu.uthscsa.ric.volume.VoxelDimensions

 

UNITS_PPM - Static variable in class edu.uthscsa.ric.volume.VoxelDimensions

 

UNITS_RADS - Static variable in class edu.uthscsa.ric.volume.VoxelDimensions

 

UNITS_SEC - Static variable in class edu.uthscsa.ric.volume.VoxelDimensions

 

UNITS_UNKNOWN - Static variable in class edu.uthscsa.ric.volume.VoxelDimensions

 

UNITS_USEC - Static variable in class edu.uthscsa.ric.volume.VoxelDimensions

 

updateSurface() - Method in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

Redraws the surface view.

updateTransform(double[][]) - Method in interface edu.uthscsa.ric.volume.ImageTransform

Update the transform.

updateViewer() - Method in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

Redraws this VolumeManager.

updateViewers() - Method in interface edu.uthscsa.ric.mango.MangoContext

Redraws all the VolumeManagers.

V

valuesHaveBeenSet() - Method in class edu.uthscsa.ric.volume.ImageBounds

Returns true if setValues() has been called.

VIDEO_FORMAT_AVI_DIB - Static variable in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

 

VIDEO_FORMAT_AVI_DIB - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

VIDEO_FORMAT_AVI_DIB - Static variable in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

 

VIDEO_FORMAT_AVI_MJPG - Static variable in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

 

VIDEO_FORMAT_AVI_MJPG - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

VIDEO_FORMAT_AVI_MJPG - Static variable in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

 

VIDEO_FORMAT_AVI_PNG - Static variable in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

 

VIDEO_FORMAT_AVI_PNG - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

VIDEO_FORMAT_AVI_PNG - Static variable in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

 

VIDEO_FORMAT_QUICKTIME_ANIMATION - Static variable in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

 

VIDEO_FORMAT_QUICKTIME_ANIMATION - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

VIDEO_FORMAT_QUICKTIME_ANIMATION - Static variable in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

 

VIDEO_FORMAT_QUICKTIME_JPEG - Static variable in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

 

VIDEO_FORMAT_QUICKTIME_JPEG - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

VIDEO_FORMAT_QUICKTIME_JPEG - Static variable in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

 

VIDEO_FORMAT_QUICKTIME_PNG - Static variable in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

 

VIDEO_FORMAT_QUICKTIME_PNG - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

VIDEO_FORMAT_QUICKTIME_PNG - Static variable in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

 

VIDEO_FORMAT_QUICKTIME_RAW - Static variable in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

 

VIDEO_FORMAT_QUICKTIME_RAW - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

VIDEO_FORMAT_QUICKTIME_RAW - Static variable in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

 

VIDEO_QUALITY_BEST - Static variable in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

 

VIDEO_QUALITY_BEST - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

VIDEO_QUALITY_BEST - Static variable in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

 

VIDEO_QUALITY_FASTEST - Static variable in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

 

VIDEO_QUALITY_FASTEST - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

VIDEO_QUALITY_FASTEST - Static variable in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

 

VIDEO_QUALITY_GOOD - Static variable in interface edu.uthscsa.ric.mango.viewerprojection.ProjectionManager

 

VIDEO_QUALITY_GOOD - Static variable in interface edu.uthscsa.ric.mango.viewerslice.VolumeManager

 

VIDEO_QUALITY_GOOD - Static variable in interface edu.uthscsa.ric.mango.viewersurface.SurfaceManager

 

VolumeIOException - Exception in edu.uthscsa.ric.volume

An exception thrown when something goes wrong while reading or writing an image, not specifically associated with the header.

VolumeIOException() - Constructor for exception edu.uthscsa.ric.volume.VolumeIOException

Default constructor.

VolumeIOException(Exception) - Constructor for exception edu.uthscsa.ric.volume.VolumeIOException

Constructor.

VolumeIOException(String) - Constructor for exception edu.uthscsa.ric.volume.VolumeIOException

Constructor.

VolumeManager - Interface in edu.uthscsa.ric.mango.viewerslice

This class manages ImageVolume data.

volumeOperationCompleted() - Method in interface edu.uthscsa.ric.volume.ImageVolume

Notifies volume that an image operation has been performed.

volumeOperationCompleted(String) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Notifies volume that an image operation has been performed.

VoxelDimensions - Class in edu.uthscsa.ric.volume

VoxelDimensions contains information related to voxel size in column/row/slice and x/y/z orientations, as well as temporal resolution and units.

VoxelDimensions(double, double, double, double) - Constructor for class edu.uthscsa.ric.volume.VoxelDimensions

The only class constructor.

W

warn(String) - Static method in class edu.uthscsa.ric.utilities.AppLogger

Log warning.

warn(Throwable) - Static method in class edu.uthscsa.ric.utilities.AppLogger

Log warning.

willWriteImage() - Method in interface edu.uthscsa.ric.volume.WritableHeader

If for some reason the application should not attempt to write the image (i.e., the image is not stored as contiguous data), then this method should return true.

WritableHeader - Interface in edu.uthscsa.ric.volume

A class that implements WritableHeader can be registered with Mango to extend the types of image header formats that can be written.

writeFilesAs(File, int, String, ImageType, boolean, boolean) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Deprecated. 

writeFilesAs(File, String, ImageType, String, boolean, boolean) - Method in interface edu.uthscsa.ric.volume.ImageVolume

Write file.

writeHeader() - Method in interface edu.uthscsa.ric.volume.EditableHeader

Write out the header.

writeHeader(ImageDimensions, VoxelDimensions, ImageType, ImageRange, ImageDescription, boolean, Coordinate, String, ImageTransform[], File, File, ByteBuffer[], File) - Method in interface edu.uthscsa.ric.volume.WritableHeader

Writes the header.

writeSeriesHeaders(ImageDimensions, VoxelDimensions, ImageType, ImageRange, ImageDescription, boolean, Coordinate, String, ImageTransform[], File, File, ByteBuffer[], File) - Method in interface edu.uthscsa.ric.volume.WritableHeader

Writes a series of headers.

writeSurfaceFile(File, Surface[], Shape[], SurfaceController) - Method in interface edu.uthscsa.ric.visualization.surface.io.SurfaceFormat

Deprecated. 

X

xDbl - Variable in class edu.uthscsa.ric.volume.Coordinate

 

xInt - Variable in class edu.uthscsa.ric.volume.Coordinate

 

Y

yDbl - Variable in class edu.uthscsa.ric.volume.Coordinate

 

YELLOW_INDEX - Static variable in interface edu.uthscsa.ric.roi.ROIData

Deprecated.

YELLOW_MASK - Static variable in interface edu.uthscsa.ric.roi.ROIData

Deprecated.

yInt - Variable in class edu.uthscsa.ric.volume.Coordinate

 

Z

zDbl - Variable in class edu.uthscsa.ric.volume.Coordinate

 

zInt - Variable in class edu.uthscsa.ric.volume.Coordinate