VolumeManager (Mango Plugin API)

```
public interface VolumeManager
```
This class manages ImageVolume data.

Author:

michaelmartinez

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`FILTER_TYPE_SLICE`
`static int`	`FILTER_TYPE_TIME`
`static int`	`FILTER_TYPE_VOLUME`
`static int`	`INTERPOLATION_TYPE_LINEAR`
`static int`	`INTERPOLATION_TYPE_NN`
`static int`	`INTERPOLATION_TYPE_SINC`
`static int`	`RANK_TYPE_MAX`
`static int`	`RANK_TYPE_MEDIAN`
`static int`	`RANK_TYPE_MIN`
`static int`	`SELECTION_TYPE_ROI_INSIDE`
`static int`	`SELECTION_TYPE_ROI_OUTSIDE`
`static int`	`SELECTION_TYPE_SLICE`
`static int`	`SELECTION_TYPE_VOLUME`
`static int`	`SERIES_TYPE_MAX`
`static int`	`SERIES_TYPE_MEAN`
`static int`	`SERIES_TYPE_MIN`
`static int`	`SERIES_TYPE_STDEV`
`static int`	`SERIES_TYPE_SUM`
`static int`	`SLICE_DIRECTION_AXIAL`
`static int`	`SLICE_DIRECTION_CORONAL`
`static int`	`SLICE_DIRECTION_SAGITTAL`
`static int`	`SLICE_DIRECTION_TEMPORAL`
`static int`	`VIDEO_FORMAT_AVI_DIB`
`static int`	`VIDEO_FORMAT_AVI_MJPG`
`static int`	`VIDEO_FORMAT_AVI_PNG`
`static int`	`VIDEO_FORMAT_QUICKTIME_ANIMATION`
`static int`	`VIDEO_FORMAT_QUICKTIME_JPEG`
`static int`	`VIDEO_FORMAT_QUICKTIME_PNG`
`static int`	`VIDEO_FORMAT_QUICKTIME_RAW`
`static int`	`VIDEO_QUALITY_BEST`
`static int`	`VIDEO_QUALITY_FASTEST`
`static int`	`VIDEO_QUALITY_GOOD`

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`addBookmark(Coordinate coord, String label)` Adds a bookmark.
`void`	`addMoreROIColors()` Adds more ROI colors (color count starts at 8, then 16, 32, 64).
`void`	`addOverlay(String openLocation, boolean parametric)` Adds an overlay.
`void`	`addOverlayOnto(VolumeManager manager, String colorTable)` Overlays the base volume onto another VolumeManager.
`void`	`addOverlayURL(String url)` Adds an overlay from a URL.
`void`	`addSliceListener(SliceListener listener, int sliceDirection)` Adds a slice listener, which will be notified anytime a slice's position has changed.
`void`	`associatePluginWindow(String title, JFrame window)` Associates a plugin window with this VolumeManager.
`ProjectionManager`	`buildProjection(int rankType, int sliceDirection, double resX, double resY, double resZ, int rotationAxis, int projectionQuality)` Creates a ProjectionManager.
`SurfaceManager`	`buildSurface(double threshold, boolean percentMax, boolean shrinkWrap, boolean maximum, boolean imageSmoothing, double width, int kernelSize, double resX, double resY, double resZ, boolean surfaceSmoothing, double pointError, double featureAngle, int iterations)` Creates a SurfaceManager.
`void`	`captureLayout(String saveLocation, int rows, int columns, int startSlice, int skipSlices, boolean series, boolean useLabels, boolean useColorBars, boolean useText, String title, String footnote)` Captures a multi-slice layout.
`void`	`captureSnapshot(String saveLocation)` Captures a single-slice.
`void`	`captureVideoStart(String saveLocation, int videoFormat, int videoQuality, int fps, boolean animate)` Starts video capture.
`void`	`captureVideoStop()` Stops the video capture.
`void`	`continueScript()` Continue a paused script.
`void`	`convertIndexToWorldCoordinate(Coordinate coor)` Converts index coordinate to world coordinate.
`void`	`convertWorldToIndexCoordinate(Coordinate coor)` Converts world coordinate to index coordinate.
`void`	`createWebpage(String saveLocation, String title, boolean useOverlays, boolean useAtlas, boolean useKioskMode, boolean outputSingleFile)` Deprecated.
`void`	`createWebpage(String saveLocation, String title, boolean useOverlays, boolean useAtlas, boolean useSurfaces, boolean useKioskMode, boolean outputSingleFile)` Creates a webpage.
`boolean`	`decrement(int direction)` Decrements the slice in the specified direction.
`void`	`deleteROI(ROI roi)` Deletes the specified ROI.
`void`	`disposeVolumeManager()` Call to remove this VolumeManager from the application.
`Point`	`findGoodPluginWindowLocation(Dimension dimension)` Returns a point to display a plugin window next to, but not in front of, the viewer window.
`void`	`flipOrientation(ImageVolume volume, int sliceDirection)` Flips the orientation of the data in the specified dimension.
`ImageVolume`	`getBaseVolume()` Returns the base volume.
`Coordinate`	`getCurrentPosition()` Returns the currently selected position.
`ImageVolume`	`getCurrentVolume()` Returns the currently selected volume.
`Coordinate`	`getCurrentWorldPosition()` Returns the currently selected position in world space.
`JFrame`	`getFrame()` Returns the parent window of this viewer.
`Histogram`	`getHistogramAnalysis()` Returns the result of the last Histogram analysis.
`URI`	`getLoadedURI()` Returns the URI of the file used to load the base volume of this viewer.
`URI`	`getLoadedURI(ImageVolume volume)` Returns the URI of the file used to load the specified volume.
`BufferedImage`	`getMainImage()` Returns a rendering of the main slice view.
`BufferedImage`	`getMainImage(boolean exclude)` Returns a rendering of the main slice view.
`BufferedImage`	`getMainImage(BufferedImage bi, int slice)` Returns a rendering of the main slice view.
`BufferedImage`	`getMainImage(BufferedImage bi, int slice, boolean exclude)` Returns a rendering of the main slice view.
`BufferedImage`	`getMainImage(BufferedImage bi, int slice, int timeIndex, boolean exclude)` Returns a rendering of the main slice view.
`String`	`getManagerTitle()` Returns a nicely formatted title for this VolumeManager
`MangoData`	`getMangoData()` Deprecated.
`String`	`getName(ImageVolume volume)` Returns a nice name for this volume;
`Coordinate`	`getOrigin()` Returns the origin of the base volume.
`List<ImageVolume>`	`getOverlays()` Returns a list of overlays volumes.
`ProjectionManager`	`getProjectionManager()` Returns the ProjectionManager.
`int`	`getRoiColor()` Returns the currently selected ROI color index.
`ROIData`	`getRoiData()` Returns a ROIData object.
`String`	`getScriptObjectName()` Returns the name reference of this viewer during the recording of a script.
`int`	`getSliceDirection()` Returns the currently selected slice direction.
`int`	`getSliceNumber()` Returns the currently selected slice number.
`SurfaceManager`	`getSurfaceManager()` Returns the SurfaceManager
`String`	`getVersion()` Returns the Mango version.
`ImageVolume`	`getVolume(int index)` Gets the ImageVolume at the specified index.
`double`	`getVolumeDisplayAlpha(ImageVolume volume)` Returns the screen display alpha value of the specified ImageVolume.
`String`	`getVolumeDisplayColorTable(ImageVolume volume)` Returns the screen display color table for the specified ImageVolume.
`double`	`getVolumeDisplayRangeMax(ImageVolume volume)` Returns the screen display range maximum for the specified ImageVolume.
`double`	`getVolumeDisplayRangeMin(ImageVolume volume)` Returns the screen display range minimum for the specified ImageVolume.
`int`	`getVolumeIndex(ImageVolume volume)` Returns the index of the specified volume.
`List<ImageVolume>`	`getVolumes()` Returns a list of all loaded ImageVolumes.
`boolean`	`increment(int direction)` Increments the slice in the specified direction.
`boolean`	`isCurrentVolumeOverlay()` Returns true if the currently selected volume is an overlay.
`boolean`	`isCurrentVolumeUsingTransform()` Returns true if the currently selected volume is using a transform.
`boolean`	`isMultiSliceMode()` Returns true if the application is in multi-slice ROI mode.
`boolean`	`isVolumeDisplayHidden(ImageVolume volume)` Returns true if the screen display of the specified ImageVolume is hidden
`boolean`	`isVolumeDisplayNegative(ImageVolume volume)` Returns true if the screen display range is negative.
`boolean`	`isVolumeOverlay(ImageVolume volume)` Returns true if the specified ImageVolume is an overlay.
`boolean`	`isVolumeUsingTransform(ImageVolume volume)` Returns true if the specified ImageVolume is using a transform.
`boolean`	`isWorldMode()` Returns true if the application is using world mode.
`void`	`loadROI(String openLocation)` Loads an ROI.
`void`	`loadROIURL(String url, boolean forceImport, boolean forceWorld)` Loads an ROI from a URL.
`SurfaceManager`	`loadSurface(String openLocation)` Loads a surface.
`void`	`logPoint(Coordinate coordinate, String description)` Logs a point in the All Results table.
`String`	`makeFilename(String ext)` Builds a filename based on the base volume with the specified extension.
`ImageVolume`	`makeNewVolume()` Creates a new ImageVolume.
`BufferedImage`	`makePluginOverlay(int sliceDirection)` Makes a static slice overlay for painting by a plugin.
`ProgressMeter`	`makeProgressMeter()` Creates a new ProgressMeter.
`void`	`pauseScriptForUserInput()` Pauses script execution.
`void`	`recordPluginAction(String pluginName, String... args)` Records a scripted plugin action.
`void`	`reload()` Reload this VolumeManager.
`void`	`removeAllOverlays()` Remove all overlays from this VolumeManager.
`void`	`removeOverlay(ImageVolume overlay)` Remove overlay from this VolumeManager.
`void`	`removePluginOverlay(BufferedImage pluginOverlay, int sliceDirection)` Remove a plugin overlay.
`void`	`removePluginOverlays()` Deprecated.
`void`	`removeSliceListener(SliceListener listener, int sliceDirection)` Removes a slice listener.
`void`	`runAddROI(Coordinate coordinate, double size, boolean sphere)` Adds ROI mask data in the currently selected ROI color at the specified location.
`void`	`runAddROISlice(int sliceDirection, Coordinate coordinate, double size, boolean circle)` Adds ROI mask data in the currently selected ROI color at the specified location.
`List<Analysis>`	`runAllSliceStats(int sliceDirection)` Runs slice statistics on all slices of the currently selected ImageVolume in the specified slice direction.
`List<Analysis>`	`runAllSliceStatsROI(int sliceDirection, long roiMask, boolean includePointsAndLines, boolean onlySelectedPoints, boolean onlySelectedLines)` Runs slice statistics on all ROI slices of the currently selected ImageVolume in the specified slice direction.
`List<Analysis>`	`runAllVolumeStats()` Runs volume statistics on all volumes in a series of the currently selected ImageVolume.
`List<Analysis>`	`runAllVolumeStatsROI(long roiMask, boolean includePointsAndLines, boolean onlySelectedPoints, boolean onlySelectedLines)` Runs volume statistics on all ROI volumes in a series of the currently selected ImageVolume.
`void`	`runCloseROI(long roiMask, int kernelSize)` Runs a close ROI operation.
`void`	`runCloseROISlice(int sliceDirection, int sliceNumber, long roiMask, int kernelSize)` Runs a close ROI slice operation.
`List<Cluster>`	`runClusterAnalysis(ImageVolume overlay, double threshold)` Runs a cluster analysis.
`List<Cluster>`	`runComponentAnalysisROI(int roiColorIndex)` Runs a ROI component anlaysis.
`void`	`runComponentSplitROI(int roiColorIndex, int voxelCountThreshold)` Splits ROI components into different colors [runComponentAnalysisROI() must precede this call].
`void`	`runConvexHull(ROI roi)` Runs a convex hull on the specified ROI.
`void`	`runConvexHullROI(long roiMask, int roiOutputColorIndex)` Runs convex hull on the specified ROI mask.
`void`	`runConvexHullROISlice(int sliceDirection, int sliceNumber, long roiMask, int roiOutputColorIndex)` Runs convex hull on the specified ROI mask.
`double[]`	`runCrosssectionMM(Line line, double step)` Runs a cross-section on the specified Line.
`double[]`	`runCrosssectionVoxels(Line line)` Runs a cross-section on the specified line.
`void`	`runDilateROI(long roiMask, int kernelSize)` Runs a dilate ROI operation.
`void`	`runDilateROISlice(int sliceDirection, int sliceNumber, long roiMask, int kernelSize)` Runs a dilate ROI slice operation.
`void`	`runErodeROI(long roiMask, int kernelSize)` Runs an erode ROI operation.
`void`	`runErodeROISlice(int sliceDirection, int sliceNumber, long roiMask, int kernelSize)` Runs a erode ROI slice operation.
`void`	`runFilter(String name)` Runs a filter.
`void`	`runGenerateClusterROI(ImageVolume overlay, int voxelCountThreshold)` Generate ROIs from clusters [runClusterAnalysis() must precede this call].
`void`	`runGenerateHistogramROI(Histogram hist)` Adds new ROI mask data for voxels included in this histogram.
`void`	`runGenerateHistogramROISlice(int sliceDirection, int sliceNumber, Histogram hist)` Adds new ROI mask data for voxels included in this histogram.
`void`	`runGenerateHistogramWithinROI(Histogram hist, long roiMask)` Adds new ROI mask data for voxels included in this histogram, but only within the specified ROI mask.
`void`	`runGenerateHistogramWithinROISlice(int sliceDirection, int sliceNumber, Histogram hist, long roiMask)` Adds new ROI mask data for voxels included in this histogram, but only within the specified ROI mask.
`void`	`runGenerateLogicalROI(List<ImageVolume> overlays)` Creates a ROI based on the intersection of a list of ImageVolumes.
`Histogram`	`runHistogram(int numBins, double min, double max, boolean excludeZero, boolean isIntegerMode)` Runs a histogram.
`Histogram`	`runHistogramROI(int numBins, double min, double max, long roiMask, boolean excludeZero, boolean integerMode)` Runs a histogram within a ROI mask.
`Analysis`	`runLogicalAnalysis(List<ImageVolume> overlays)` Runs statistics on the intersection of a list of ImageVolumes.
`void`	`runOpenROI(long roiMask, int kernelSize)` Runs an open ROI operation.
`void`	`runOpenROISlice(int sliceDirection, int sliceNumber, long roiMask, int kernelSize)` Runs an open ROI slice operation.
`VolumeManager`	`runOperation(String expression, int selectionArea, boolean outputNewImage, boolean allSeriesPoints, boolean roiSlicesOnly)` Runs an operation.
`void`	`runOperationROILogic(String expression, int roiOutputColorIndex)` Runs a ROI logic operation.
`VolumeManager`	`runOperationSeriesStatistic(int startingSeriesIndex, int endingSeriesIndex, int seriesGroupSize, int statisticType)` Runs a series operation.
`Object`	`runPlugin(String pluginName, String[] args)` Runs a plugin.
`void`	`runPropagateROISlice(int sliceDirection, int sliceNumber, int startSlice, int endSlice, long roiMask, int roiOutputColorIndex)` Propagates an ROI slice.
`boolean`	`runRangeToROI(double min, double max, boolean percentMax, boolean excludeZero, boolean makeSeriesROI, boolean seriesUsesDynamicThreshold)` Creates new ROI mask data based on a range.
`boolean`	`runRangeToROISlice(double min, double max, int sliceDirection, int sliceNumber, boolean percentMax, boolean excludeZero, boolean makeSeriesROI, boolean seriesUsesDynamicThreshold)` Creates new ROI mask data based on a range.
`void`	`runRankFilter(int kernelSize, int rankType, int filterType)` Runs a rank filter.
`void`	`runReflectROI(int sliceDirection, int axis, boolean vertical, boolean includePointsAndLines, boolean onlySelectedLines, boolean onlySelectedPoints)` Reflects a ROI.
`void`	`runReflectROISlice(int sliceDirection, int sliceNumber, int axis, boolean vertical, boolean includePointsAndLines, boolean onlySelectedLines, boolean onlySelectedPoints)`
`void`	`runScript(String scriptName)` Runs a script.
`List<Analysis>`	`runSeriesROI(ROI roi)` Runs statistics on a series ROI.
`Analysis`	`runSeriesStats()` Runs series statistics on the currently selected ImageVolume.
`List<Analysis>`	`runSeriesStatsROI(long roiMask, boolean includePointsAndLines, boolean onlySelectedPoints, boolean onlySelectedLines)` Runs ROI series statistics.
`void`	`runShrinkWrapROI(double threshold, long roiMask, int roiOutputColorIndex, boolean percentMax, boolean seriesUsesDynamicThreshold)` Shrink wraps (3D) a ROI mask.
`void`	`runShrinkWrapROI(long roiMask, int roiOutputColorIndex)` Shrink wraps (3D) a ROI mask.
`void`	`runShrinkWrapROIAllSlices(double threshold, int sliceDirection, long roiMask, int roiOutputColorIndex, boolean percentMax, boolean seriesUsesDynamicThreshold)` Shrink wraps (2D) a ROI mask in a specified slice direction.
`void`	`runShrinkWrapROIAllSlices(int sliceDirection, long roiMask, int roiOutputColorIndex)` Shrink wraps (2D) a ROI mask in a specified slice direction.
`void`	`runShrinkWrapROISlice(double threshold, int sliceDirection, int sliceNumber, long roiMask, int roiOutputColorIndex, boolean percentMax, boolean seriesUsesDynamicThreshold)` Shrink wraps (2D) a ROI mask in a specified slice direction.
`void`	`runShrinkWrapROISlice(int sliceDirection, int sliceNumber, long roiMask, int roiOutputColorIndex)` Shrink wraps (2D) a ROI mask in a specified slice direction.
`Analysis`	`runSliceStats(int sliceDirection, int sliceNumber)` Run statistics on a slice.
`List<Analysis>`	`runSliceStatsROI(int sliceDirection, int sliceNumber, long roiMask, boolean includePointsAndLines, boolean onlySelectedPoints, boolean onlySelectedLines)` Runs statistics on a ROI slice.
`void`	`runSmooth(ROI roi)` Smooths a ROI (only applies to Lines).
`Analysis`	`runStat(ROI roi)` Runs statistics on a specified ROI.
`void`	`runThresholdToConvexHullROI(double threshold, boolean percentMax, boolean excludeZero, boolean makeSeriesROI, boolean seriesUsesDynamicThreshold)` Adds new ROI mask data based on a threshold and in a convex hull.
`void`	`runThresholdToConvexHullROISlice(double threshold, int sliceDirection, int sliceNumber, boolean percentMax, boolean excludeZero, boolean makeSeriesROI, boolean seriesUsesDynamicThreshold)` Adds new ROI mask data based on a threshold and in a convex hull.
`boolean`	`runThresholdToROI(double threshold, boolean percentMax, boolean excludeZero, boolean makeSeriesROI, boolean seriesUsesDynamicThreshold)` Adds new ROI mask data based on a threshold.
`boolean`	`runThresholdToROISlice(double threshold, int sliceDirection, int sliceNumber, boolean percentMax, boolean excludeZero, boolean makeSeriesROI, boolean seriesUsesDynamicThreshold)` Adds new ROI mask data based on a threshold.
`boolean`	`runThresholdToShrinkWrapROI(double threshold, boolean percentMax, boolean excludeZero, boolean makeSeriesROI, boolean seriesUsesDynamicThreshold)` Adds new ROI mask data based on a threshold and shrink wrap (3D).
`boolean`	`runThresholdToShrinkWrapROIAllSlices(double threshold, int sliceDirection, boolean percentMax, boolean excludeZero, boolean makeSeriesROI, boolean seriesUsesDynamicThreshold)` Adds new ROI mask data based on a threshold and shrink wrap (2D).
`boolean`	`runThresholdToShrinkWrapROISlice(double threshold, int sliceDirection, int sliceNumber, boolean percentMax, boolean excludeZero, boolean makeSeriesROI, boolean seriesUsesDynamicThreshold)` Adds new ROI mask data based on a threshold and shrink wrap (2D).
`Analysis`	`runVolumeStats()` Runs volume statistics on the currently selected series point of the currently selected ImageVolume.
`List<Analysis>`	`runVolumeStatsROI(long roiMask, boolean includePointsAndLines, boolean onlySelectedPoints, boolean onlySelectedLines)` Runs volume ROI statistics.
`void`	`save()` Saves this VolumeManager.
`void`	`saveAs(String saveLocation, String headerFormat, int datatype, int numBytes, boolean littleEndian, boolean compress, int xMin, int xMax, int yMin, int yMax, int zMin, int zMax, int tMin, int tMax, double xSize, double ySize, double zSize, double tSize, String orientation, boolean applyTransform, boolean applyOverlay, boolean overlayThreshold, boolean overlayMix, int interpolation, boolean applyDataScales, boolean fitPrecision, boolean maintainZero)` Saves this VolumeManager.
`void`	`saveOverlays()` Saves overlays.
`void`	`saveROI(String saveLocation)` Saves ROI.
`void`	`saveSingleROI(String saveLocation, int index)` Saves a single ROI color.
`void`	`saveWithName(String saveLocation)` Saves this VolumeManager
`void`	`select(ROI roi, boolean select)` Selects or unselects a specified ROI.
`void`	`selectAll()` Selects all ROI masks, lines, and points.
`void`	`selectMenuOption(String name)` Selects a menu option.
`void`	`setCoordinateSpace(int index)` Deprecated.
`void`	`setCurrentPosition(Coordinate coordinate)` Sets the current position.
`void`	`setCurrentSeriesPoint(int seriesIndex)` Sets the current series point.
`void`	`setCurrentVolumeIndex(int index)` Sets the current volume by index.
`void`	`setDisplayRangeToImageRange(ImageVolume volume, boolean entireSeries)` Sets the display range of the specified ImageVolume to its image min/max.
`void`	`setLabel(ROI roi, String label)` Sets the label of the specified ROI.
`void`	`setMenuOption(String name, boolean value)` Sets a menu option.
`void`	`setNotes(String text)` Sets the note of the base volume.
`void`	`setOrientationOption(ImageVolume volume, int index)` Sets the orientation option (e.g., NIFTI s-form or q-form) of the currently selected ImageVolume.
`void`	`setOrigin(Coordinate coordinate)` Sets the origin of the base volume.
`void`	`setRoiColor(int color)` Sets the current ROI color.
`void`	`setSliceDirection(int sliceDirection)` Sets the current slice direction.
`boolean`	`setSliceNumber(int sliceNumber)` Sets the current slice number.
`void`	`setTransformMode(boolean transform)` Sets the transform mode.
`void`	`setVolumeDisplayAlpha(ImageVolume volume, double alpha)` Sets the alpha value of the specified ImageVolume.
`void`	`setVolumeDisplayColorTable(ImageVolume volume, String colorTable)` Sets the color table of the specified ImageVolume.
`void`	`setVolumeDisplayHidden(ImageVolume volume, boolean hidden)` Sets the hidden state of the specified ImageVolume.
`void`	`setVolumeDisplayIndex(ImageVolume volume, int index)` Sets the display index of the specified ImageVolume (cannot change base volume index).
`void`	`setVolumeDisplayRange(ImageVolume volume, double screenMin, double screenMax)` Sets the display range of the specified ImageVolume.
`void`	`setVoxelValue(Coordinate coordinate, int seriesIndex, double value)` Sets a voxel value at the specified coordinate.
`void`	`showErrorMessage(String message, String title)` Shows an error message.
`void`	`showWarningMessage(String message, String title)` Shows a warning message.
`String`	`toString()` Returns a string representation.
`void`	`transform(ImageVolume volume, double m00, double m01, double m02, double m03, double m10, double m11, double m12, double m13, double m20, double m21, double m22, double m23, double m30, double m31, double m32, double m33)` Transform the specified ImageVolume.
`void`	`updateViewer()` Redraws this VolumeManager.

- Field Detail
  - FILTER_TYPE_SLICE
```
static final int FILTER_TYPE_SLICE
```
    See Also:
    Constant Field Values
  - FILTER_TYPE_TIME
```
static final int FILTER_TYPE_TIME
```
    See Also:
    Constant Field Values
  - FILTER_TYPE_VOLUME
```
static final int FILTER_TYPE_VOLUME
```
    See Also:
    Constant Field Values
  - INTERPOLATION_TYPE_LINEAR
```
static final int INTERPOLATION_TYPE_LINEAR
```
    See Also:
    Constant Field Values
  - INTERPOLATION_TYPE_NN
```
static final int INTERPOLATION_TYPE_NN
```
    See Also:
    Constant Field Values
  - INTERPOLATION_TYPE_SINC
```
static final int INTERPOLATION_TYPE_SINC
```
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    Constant Field Values
  - RANK_TYPE_MAX
```
static final int RANK_TYPE_MAX
```
    See Also:
    Constant Field Values
  - RANK_TYPE_MEDIAN
```
static final int RANK_TYPE_MEDIAN
```
    See Also:
    Constant Field Values
  - RANK_TYPE_MIN
```
static final int RANK_TYPE_MIN
```
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    Constant Field Values
  - SELECTION_TYPE_ROI_INSIDE
```
static final int SELECTION_TYPE_ROI_INSIDE
```
    See Also:
    Constant Field Values
  - SELECTION_TYPE_ROI_OUTSIDE
```
static final int SELECTION_TYPE_ROI_OUTSIDE
```
    See Also:
    Constant Field Values
  - SELECTION_TYPE_SLICE
```
static final int SELECTION_TYPE_SLICE
```
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    Constant Field Values
  - SELECTION_TYPE_VOLUME
```
static final int SELECTION_TYPE_VOLUME
```
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    Constant Field Values
  - SERIES_TYPE_MAX
```
static final int SERIES_TYPE_MAX
```
    See Also:
    Constant Field Values
  - SERIES_TYPE_MEAN
```
static final int SERIES_TYPE_MEAN
```
    See Also:
    Constant Field Values
  - SERIES_TYPE_MIN
```
static final int SERIES_TYPE_MIN
```
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    Constant Field Values
  - SERIES_TYPE_STDEV
```
static final int SERIES_TYPE_STDEV
```
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    Constant Field Values
  - SERIES_TYPE_SUM
```
static final int SERIES_TYPE_SUM
```
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    Constant Field Values
  - SLICE_DIRECTION_AXIAL
```
static final int SLICE_DIRECTION_AXIAL
```
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    Constant Field Values
  - SLICE_DIRECTION_CORONAL
```
static final int SLICE_DIRECTION_CORONAL
```
    See Also:
    Constant Field Values
  - SLICE_DIRECTION_SAGITTAL
```
static final int SLICE_DIRECTION_SAGITTAL
```
    See Also:
    Constant Field Values
  - SLICE_DIRECTION_TEMPORAL
```
static final int SLICE_DIRECTION_TEMPORAL
```
    See Also:
    Constant Field Values
  - VIDEO_FORMAT_AVI_DIB
```
static final int VIDEO_FORMAT_AVI_DIB
```
    See Also:
    Constant Field Values
  - VIDEO_FORMAT_AVI_MJPG
```
static final int VIDEO_FORMAT_AVI_MJPG
```
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    Constant Field Values
  - VIDEO_FORMAT_AVI_PNG
```
static final int VIDEO_FORMAT_AVI_PNG
```
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    Constant Field Values
  - VIDEO_FORMAT_QUICKTIME_ANIMATION
```
static final int VIDEO_FORMAT_QUICKTIME_ANIMATION
```
    See Also:
    Constant Field Values
  - VIDEO_FORMAT_QUICKTIME_JPEG
```
static final int VIDEO_FORMAT_QUICKTIME_JPEG
```
    See Also:
    Constant Field Values
  - VIDEO_FORMAT_QUICKTIME_PNG
```
static final int VIDEO_FORMAT_QUICKTIME_PNG
```
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    Constant Field Values
  - VIDEO_FORMAT_QUICKTIME_RAW
```
static final int VIDEO_FORMAT_QUICKTIME_RAW
```
    See Also:
    Constant Field Values
  - VIDEO_QUALITY_BEST
```
static final int VIDEO_QUALITY_BEST
```
    See Also:
    Constant Field Values
  - VIDEO_QUALITY_FASTEST
```
static final int VIDEO_QUALITY_FASTEST
```
    See Also:
    Constant Field Values
  - VIDEO_QUALITY_GOOD
```
static final int VIDEO_QUALITY_GOOD
```
    See Also:
    Constant Field Values
- Method Detail
  - addBookmark
```
void addBookmark(Coordinate coord,
               String label)
```
    Adds a bookmark.
    
    Parameters:
    coord - the bookmark coordinate
    label - the bookmark label
  - addMoreROIColors
```
void addMoreROIColors()
```
    Adds more ROI colors (color count starts at 8, then 16, 32, 64).
  - addOverlay
```
void addOverlay(String openLocation,
              boolean parametric)
```
    Adds an overlay.
    
    Parameters:
    openLocation - the file location
    parametric - true to open both positives and negatives, false to only open positives
  - addOverlayOnto
```
void addOverlayOnto(VolumeManager manager,
                  String colorTable)
```
    Overlays the base volume onto another VolumeManager.
    
    Parameters:
    manager - the other VolumeManager
    colorTable - the overlay color table
  - addOverlayURL
```
void addOverlayURL(String url)
```
    Adds an overlay from a URL.
    
    Parameters:
    url - the URL
  - addSliceListener
```
void addSliceListener(SliceListener listener,
                    int sliceDirection)
```
    Adds a slice listener, which will be notified anytime a slice's position has changed.
    
    Parameters:
    listener - the SliceListener to add
    sliceDirection - the slice direction
  - associatePluginWindow
```
void associatePluginWindow(String title,
                         JFrame window)
```
    Associates a plugin window with this VolumeManager.
    
    Parameters:
    title - the title of this plugin
    window - the window
  - buildProjection
```
ProjectionManager buildProjection(int rankType,
                                int sliceDirection,
                                double resX,
                                double resY,
                                double resZ,
                                int rotationAxis,
                                int projectionQuality)
```
    Creates a ProjectionManager.
    
    Parameters:
    rankType - the rank type (see ProjectionManager constants)
    sliceDirection - the slice direction
    resX - the X resolution
    resY - the Y resolution
    resZ - the Z resolution
    rotationAxis - the rotation axis (the ProjectionManager constants)
    projectionQuality - the projection quality (see ProjectionManager constants)
    
    Returns:
    the ProjectionManager
  - buildSurface
```
SurfaceManager buildSurface(double threshold,
                          boolean percentMax,
                          boolean shrinkWrap,
                          boolean maximum,
                          boolean imageSmoothing,
                          double width,
                          int kernelSize,
                          double resX,
                          double resY,
                          double resZ,
                          boolean surfaceSmoothing,
                          double pointError,
                          double featureAngle,
                          int iterations)
```
    Creates a SurfaceManager.
    
    Parameters:
    threshold - the build threshold
    percentMax - true if the threshold values represent percent of image maximum, false if they refer to actual range values
    shrinkWrap - true to use shrinkwrap, false otherwise
    maximum - true if the threshold represents a maximum, false otherwise
    imageSmoothing - true to use image smoothing, false otherwise
    width - FWHM of the image smoothing filter
    kernelSize - kernel size of the image smoothing filter
    resX - the output X resolution
    resY - the output Y resolution
    resZ - the output Z resolution
    surfaceSmoothing - true to use surface smoothing, false otherwise
    pointError - the point error threshold
    featureAngle - the feature angle threshold
    iterations - number of iterations of surface smoothing
    
    Returns:
    the SurfaceManager
  - captureLayout
```
void captureLayout(String saveLocation,
                 int rows,
                 int columns,
                 int startSlice,
                 int skipSlices,
                 boolean series,
                 boolean useLabels,
                 boolean useColorBars,
                 boolean useText,
                 String title,
                 String footnote)
```
    Captures a multi-slice layout.
    
    Parameters:
    saveLocation - the location to save the layout image file
    rows - the number of layout rows
    columns - the number of layout cols
    startSlice - the starting slice
    skipSlices - the number of slices to skip between each slice captured
    series - true to capture along a series, false to capture along the current slice direction
    useLabels - true to embed slice labels, false otherwise
    useColorBars - true to embed color bars, false otherwise
    useText - true to embed text, false otherwise
    title - the layout title
    footnote - the layout footnote
  - captureSnapshot
```
void captureSnapshot(String saveLocation)
```
    Captures a single-slice.
    
    Parameters:
    saveLocation - the location to save the image file
  - captureVideoStart
```
void captureVideoStart(String saveLocation,
                     int videoFormat,
                     int videoQuality,
                     int fps,
                     boolean animate)
```
    Starts video capture.
    
    Parameters:
    saveLocation - the location to save the video file
    videoFormat - the video format code (see constants)
    videoQuality - the video quality code (see constants)
    fps - the frames per second
    animate - true to automatically animate the projection, false otherwise
  - captureVideoStop
```
void captureVideoStop()
```
    Stops the video capture.
  - continueScript
```
void continueScript()
```
    Continue a paused script.
  - convertIndexToWorldCoordinate
```
void convertIndexToWorldCoordinate(Coordinate coor)
```
    Converts index coordinate to world coordinate.
    
    Parameters:
    coor - the index coordinate
  - convertWorldToIndexCoordinate
```
void convertWorldToIndexCoordinate(Coordinate coor)
```
    Converts world coordinate to index coordinate.
    
    Parameters:
    coor - the world coordinate
  - createWebpage
```
@Deprecated
void createWebpage(String saveLocation,
                            String title,
                            boolean useOverlays,
                            boolean useAtlas,
                            boolean useKioskMode,
                            boolean outputSingleFile)
```
    Deprecated.
    
    Creates a webpage.
    
    Parameters:
    saveLocation - the location to save the webpage files
    title - the title of the webpage
    useOverlays - true to include overlay data in the webpage, false to only include the base volume
    useAtlas - true to include atlas data in the webpage, false otherwise
    useKioskMode - true to use "kiosk mode", false otherwise
    outputSingleFile - true to output a single HTML file, false to output separate HTML, CSS, and JS files
  - createWebpage
```
void createWebpage(String saveLocation,
                 String title,
                 boolean useOverlays,
                 boolean useAtlas,
                 boolean useSurfaces,
                 boolean useKioskMode,
                 boolean outputSingleFile)
```
    Creates a webpage.
    
    Parameters:
    saveLocation - the location to save the webpage files
    title - the title of the webpage
    useOverlays - true to include overlay data in the webpage, false to only include the base volume
    useAtlas - true to include atlas data in the webpage, false otherwise
    useSurfaces - true to include surface data, false otherwise
    useKioskMode - true to use "kiosk mode", false otherwise
    outputSingleFile - true to output a single HTML file, false to output separate HTML, CSS, and JS files
  - decrement
```
boolean decrement(int direction)
```
    Decrements the slice in the specified direction.
    
    Parameters:
    direction - the slice direction (see constants)
    
    Returns:
    true if the slice was able to be decremented in that direction, false otherwise
  - deleteROI
```
void deleteROI(ROI roi)
```
    Deletes the specified ROI.
    
    Parameters:
    roi - the ROI to delete
  - disposeVolumeManager
```
void disposeVolumeManager()
```
    Call to remove this VolumeManager from the application.
  - findGoodPluginWindowLocation
```
Point findGoodPluginWindowLocation(Dimension dimension)
```
    Returns a point to display a plugin window next to, but not in front of, the viewer window.
    
    Parameters:
    dimension - the size of the plugin window
    
    Returns:
    the point to display the plugin window
  - flipOrientation
```
void flipOrientation(ImageVolume volume,
                   int sliceDirection)
```
    Flips the orientation of the data in the specified dimension.
    
    Parameters:
    volume - the volume to flip
    sliceDirection - the slice direction to flip about (see constants)
  - getBaseVolume
```
ImageVolume getBaseVolume()
```
    Returns the base volume.
    
    Returns:
    the base volume
  - getCurrentPosition
```
Coordinate getCurrentPosition()
```
    Returns the currently selected position.
    
    Returns:
    the currently selected position
  - getCurrentVolume
```
ImageVolume getCurrentVolume()
```
    Returns the currently selected volume.
    
    Returns:
    the currently selected volume
  - getCurrentWorldPosition
```
Coordinate getCurrentWorldPosition()
```
    Returns the currently selected position in world space.
    
    Returns:
    the currently selected position in world space
  - getFrame
```
JFrame getFrame()
```
    Returns the parent window of this viewer.
    
    Returns:
    the parent window of this viewer
  - getHistogramAnalysis
```
Histogram getHistogramAnalysis()
```
    Returns the result of the last Histogram analysis.
    
    Returns:
    the result of the last Histogram
  - getLoadedURI
```
URI getLoadedURI()
```
    Returns the URI of the file used to load the base volume of this viewer.
    
    Returns:
    the URI
  - getLoadedURI
```
URI getLoadedURI(ImageVolume volume)
```
    Returns the URI of the file used to load the specified volume.
    
    Parameters:
    volume - the ImageVolume
    
    Returns:
    the URI
  - getMainImage
```
BufferedImage getMainImage()
```
    Returns a rendering of the main slice view. If operating in a new thread, you may want to call setStopPaintingState() and setNavigationDisabledState() first. If several slices are needed, successive calls can use getMainImage(BufferedImage bi, int slice).
    
    Returns:
    the rendered image
  - getMainImage
```
BufferedImage getMainImage(boolean exclude)
```
    Returns a rendering of the main slice view. If operating in a new thread, you may want to call setStopPaintingState() and setNavigationDisabledState() first. If several slices are needed, successive calls can use getMainImage(BufferedImage bi, int slice, boolean exclude).
    
    Parameters:
    exclude - exclude non-image information (e.g., ROIs)
    
    Returns:
    the rendered image
  - getMainImage
```
BufferedImage getMainImage(BufferedImage bi,
                         int slice)
```
    Returns a rendering of the main slice view.
    
    Parameters:
    bi - the image in which to store the image (typical to call after calling the no-arg method first)
    slice - the slice to render
    
    Returns:
    the rendered image
  - getMainImage
```
BufferedImage getMainImage(BufferedImage bi,
                         int slice,
                         boolean exclude)
```
    Returns a rendering of the main slice view.
    
    Parameters:
    bi - the image in which to store the image (typical to call after calling the no-arg method first)
    slice - the slice to render
    exclude - exclude non-image information (e.g., ROIs)
    
    Returns:
    the rendered image
  - getMainImage
```
BufferedImage getMainImage(BufferedImage bi,
                         int slice,
                         int timeIndex,
                         boolean exclude)
```
    Returns a rendering of the main slice view.
    
    Parameters:
    bi - the image in which to store the image (typical to call after calling the no-arg method first)
    slice - the slice to render
    timeIndex - the timepoint to render (note, you must manually set the timepoint back to the correct position after this method is called)
    exclude - exclude non-image information (e.g., ROIs)
    
    Returns:
    the rendered image
  - getManagerTitle
```
String getManagerTitle()
```
    Returns a nicely formatted title for this VolumeManager
    
    Returns:
    a nicely formatted title for this VolumeManager
  - getMangoData
```
@Deprecated
MangoData getMangoData()
```
    Deprecated.
    
    Returns a MangoData object.
    
    Returns:
    a MangoData object
  - getName
```
String getName(ImageVolume volume)
```
    Returns a nice name for this volume;
    
    Parameters:
    volume - the ImageVolume
    
    Returns:
    the nice name
  - getOrigin
```
Coordinate getOrigin()
```
    Returns the origin of the base volume.
    
    Returns:
    the origin of the base volume
  - getOverlays
```
List<ImageVolume> getOverlays()
```
    Returns a list of overlays volumes.
    
    Returns:
    a list of overlay volumes
  - getProjectionManager
```
ProjectionManager getProjectionManager()
```
    Returns the ProjectionManager.
    
    Returns:
    the ProjectionManager
  - getRoiColor
```
int getRoiColor()
```
    Returns the currently selected ROI color index.
    
    Returns:
    the currently selected ROI color index
  - getRoiData
```
ROIData getRoiData()
```
    Returns a ROIData object.
    
    Returns:
    a ROIData object
  - getScriptObjectName
```
String getScriptObjectName()
```
    Returns the name reference of this viewer during the recording of a script.
    
    Returns:
    the name reference of this viewer
  - getSliceDirection
```
int getSliceDirection()
```
    Returns the currently selected slice direction.
    
    Returns:
    the currently selected slice direction
  - getSliceNumber
```
int getSliceNumber()
```
    Returns the currently selected slice number.
    
    Returns:
    the currently selected slice number
  - getSurfaceManager
```
SurfaceManager getSurfaceManager()
```
    Returns the SurfaceManager
    
    Returns:
    the SurfaceManager
  - getVersion
```
String getVersion()
```
    Returns the Mango version.
    
    Returns:
    the Mango version
  - getVolume
```
ImageVolume getVolume(int index)
```
    Gets the ImageVolume at the specified index.
    
    Parameters:
    index - the index
    
    Returns:
    the ImageVolume
  - getVolumeDisplayAlpha
```
double getVolumeDisplayAlpha(ImageVolume volume)
```
    Returns the screen display alpha value of the specified ImageVolume.
    
    Parameters:
    volume - the ImageVolume
    
    Returns:
    the screen display alpha value
  - getVolumeDisplayColorTable
```
String getVolumeDisplayColorTable(ImageVolume volume)
```
    Returns the screen display color table for the specified ImageVolume.
    
    Parameters:
    volume - the ImageVolume
    
    Returns:
    the screen display color table
  - getVolumeDisplayRangeMax
```
double getVolumeDisplayRangeMax(ImageVolume volume)
```
    Returns the screen display range maximum for the specified ImageVolume.
    
    Parameters:
    volume - the ImageVolume
    
    Returns:
    the screen display range maximum
  - getVolumeDisplayRangeMin
```
double getVolumeDisplayRangeMin(ImageVolume volume)
```
    Returns the screen display range minimum for the specified ImageVolume.
    
    Parameters:
    volume - the ImageVolume
    
    Returns:
    the screen display range minimum
  - getVolumeIndex
```
int getVolumeIndex(ImageVolume volume)
```
    Returns the index of the specified volume.
    
    Parameters:
    volume - the ImageVolume
    
    Returns:
    the index
  - getVolumes
```
List<ImageVolume> getVolumes()
```
    Returns a list of all loaded ImageVolumes.
    
    Returns:
    a list of all loaded ImageVolumes
  - increment
```
boolean increment(int direction)
```
    Increments the slice in the specified direction.
    
    Parameters:
    direction - the slice direction (see constants)
    
    Returns:
    true if the slice was able to be incremented in that direction, false otherwise
  - isCurrentVolumeOverlay
```
boolean isCurrentVolumeOverlay()
```
    Returns true if the currently selected volume is an overlay.
    
    Returns:
    true if the currently selected volume is an overlay, false if it is the base volume
  - isCurrentVolumeUsingTransform
```
boolean isCurrentVolumeUsingTransform()
```
    Returns true if the currently selected volume is using a transform.
    
    Returns:
    true if the currently selected volume is using a transform.
  - isMultiSliceMode
```
boolean isMultiSliceMode()
```
    Returns true if the application is in multi-slice ROI mode.
    
    Returns:
    true if the application is in multi-slice ROI mode, false otherwise
  - isVolumeDisplayHidden
```
boolean isVolumeDisplayHidden(ImageVolume volume)
```
    Returns true if the screen display of the specified ImageVolume is hidden
    
    Parameters:
    volume - the ImageVolume
    
    Returns:
    true if the screen display is hidden, false if it is shown
  - isVolumeDisplayNegative
```
boolean isVolumeDisplayNegative(ImageVolume volume)
```
    Returns true if the screen display range is negative.
    
    Parameters:
    volume - the ImageVolume
    
    Returns:
    true of the screen display range is negative
  - isVolumeOverlay
```
boolean isVolumeOverlay(ImageVolume volume)
```
    Returns true if the specified ImageVolume is an overlay.
    
    Parameters:
    volume - the ImageVolume
    
    Returns:
    true if the specified ImageVolume is an overlay, false otherwise
  - isVolumeUsingTransform
```
boolean isVolumeUsingTransform(ImageVolume volume)
```
    Returns true if the specified ImageVolume is using a transform.
    
    Parameters:
    volume - the ImageVolume
    
    Returns:
    true if the specified ImageVolume is using a transform, false otherwise
  - isWorldMode
```
boolean isWorldMode()
```
    Returns true if the application is using world mode.
    
    Returns:
    true if the application is using world mode
  - loadROI
```
void loadROI(String openLocation)
```
    Loads an ROI.
    
    Parameters:
    openLocation - the location of the file to load
  - loadROIURL
```
void loadROIURL(String url,
              boolean forceImport,
              boolean forceWorld)
```
    Loads an ROI from a URL.
    
    Parameters:
    url - the URL
    forceImport - true to force loading this in import mode, false otherwise
    forceWorld - true to force loading this in world mode, false otherwise
  - loadSurface
```
SurfaceManager loadSurface(String openLocation)
```
    Loads a surface.
    
    Parameters:
    openLocation - the location of the file to load
    
    Returns:
    the SurfaceManager
  - logPoint
```
void logPoint(Coordinate coordinate,
            String description)
```
    Logs a point in the All Results table.
    
    Parameters:
    coordinate - the coordinate to log
    description - a label for the point
  - makeFilename
```
String makeFilename(String ext)
```
    Builds a filename based on the base volume with the specified extension.
    
    Parameters:
    ext - the extension
    
    Returns:
    a filename
  - makeNewVolume
```
ImageVolume makeNewVolume()
```
    Creates a new ImageVolume.
    
    Returns:
    a new ImageVolume
  - makePluginOverlay
```
BufferedImage makePluginOverlay(int sliceDirection)
```
    Makes a static slice overlay for painting by a plugin.
    
    Parameters:
    sliceDirection - slice direction of the main slice view
    
    Returns:
    the overlay data as an ARGB BufferedImage
  - makeProgressMeter
```
ProgressMeter makeProgressMeter()
```
    Creates a new ProgressMeter.
    
    Returns:
    a new ProgressMeter
  - pauseScriptForUserInput
```
void pauseScriptForUserInput()
```
    Pauses script execution.
  - recordPluginAction
```
void recordPluginAction(String pluginName,
                      String... args)
```
    Records a scripted plugin action.
    
    Parameters:
    pluginName - the plugin name
    args - the arguments
  - reload
```
void reload()
```
    Reload this VolumeManager.
  - removeAllOverlays
```
void removeAllOverlays()
```
    Remove all overlays from this VolumeManager.
  - removeOverlay
```
void removeOverlay(ImageVolume overlay)
```
    Remove overlay from this VolumeManager.
    
    Parameters:
    overlay - the volume to remove
  - removePluginOverlays
```
@Deprecated
void removePluginOverlays()
```
    Deprecated.
    
    Removes all plugin overlays.
  - removePluginOverlay
```
void removePluginOverlay(BufferedImage pluginOverlay,
                       int sliceDirection)
```
    Remove a plugin overlay.
    
    Parameters:
    pluginOverlay - the BufferedImage to remove
    sliceDirection - the slice direction
  - removeSliceListener
```
void removeSliceListener(SliceListener listener,
                       int sliceDirection)
```
    Removes a slice listener.
    
    Parameters:
    listener - the SliceListener to remove
    sliceDirection - the slice direction
  - runAddROI
```
void runAddROI(Coordinate coordinate,
             double size,
             boolean sphere)
```
    Adds ROI mask data in the currently selected ROI color at the specified location.
    
    Parameters:
    coordinate - the center of the new ROI mask data
    size - the size in mm
    sphere - true to add a sphere, false to add a cube
  - runAddROISlice
```
void runAddROISlice(int sliceDirection,
                  Coordinate coordinate,
                  double size,
                  boolean circle)
```
    Adds ROI mask data in the currently selected ROI color at the specified location.
    
    Parameters:
    sliceDirection - the slice direction on which to add the new ROI data
    coordinate - the center of the new ROI mask data
    size - the size in mm
    circle - true to add a circle, false to add a square
  - runAllSliceStats
```
List<Analysis> runAllSliceStats(int sliceDirection)
```
    Runs slice statistics on all slices of the currently selected ImageVolume in the specified slice direction.
    
    Parameters:
    sliceDirection - the slice direction
    
    Returns:
    a list of Analyses
  - runAllSliceStatsROI
```
List<Analysis> runAllSliceStatsROI(int sliceDirection,
                                 long roiMask,
                                 boolean includePointsAndLines,
                                 boolean onlySelectedPoints,
                                 boolean onlySelectedLines)
```
    Runs slice statistics on all ROI slices of the currently selected ImageVolume in the specified slice direction.
    
    Parameters:
    sliceDirection - the slice direction
    roiMask - the mask of the ROIs to include
    includePointsAndLines - true to also analyze points and lines
    onlySelectedPoints - true to only analyze selected points
    onlySelectedLines - true to only analyze selected lines
    
    Returns:
    a list of Analyses
  - runAllVolumeStats
```
List<Analysis> runAllVolumeStats()
```
    Runs volume statistics on all volumes in a series of the currently selected ImageVolume.
    
    Returns:
    a list of Analyses
  - runAllVolumeStatsROI
```
List<Analysis> runAllVolumeStatsROI(long roiMask,
                                  boolean includePointsAndLines,
                                  boolean onlySelectedPoints,
                                  boolean onlySelectedLines)
```
    Runs volume statistics on all ROI volumes in a series of the currently selected ImageVolume.
    
    Parameters:
    roiMask - the mask of ROIs to include
    includePointsAndLines - true to also analyze points and lines
    onlySelectedPoints - true to only analyze selected points
    onlySelectedLines - true to only analyze selected lines
    
    Returns:
    a list of Analyses
  - runCloseROI
```
void runCloseROI(long roiMask,
               int kernelSize)
```
    Runs a close ROI operation.
    
    Parameters:
    roiMask - the mask of ROIs to include
    kernelSize - the kernel size
  - runCloseROISlice
```
void runCloseROISlice(int sliceDirection,
                    int sliceNumber,
                    long roiMask,
                    int kernelSize)
```
    Runs a close ROI slice operation.
    
    Parameters:
    sliceDirection - the slice direction
    sliceNumber - the slice number
    roiMask - the mask of the ROIs to include
    kernelSize - the kernel size
  - runClusterAnalysis
```
List<Cluster> runClusterAnalysis(ImageVolume overlay,
                               double threshold)
```
    Runs a cluster analysis.
    
    Parameters:
    overlay - the ImageVolume to analyze
    threshold - the threshold
    
    Returns:
    a list of Clusters
  - runComponentAnalysisROI
```
List<Cluster> runComponentAnalysisROI(int roiColorIndex)
```
    Runs a ROI component anlaysis.
    
    Parameters:
    roiColorIndex - the ROI color index
    
    Returns:
    a list of Clusters
  - runComponentSplitROI
```
void runComponentSplitROI(int roiColorIndex,
                        int voxelCountThreshold)
```
    Splits ROI components into different colors [runComponentAnalysisROI() must precede this call].
    
    Parameters:
    roiColorIndex - the ROI color index
    voxelCountThreshold - the minimum number of voxels a component must contain in order to include in the split
  - runConvexHull
```
void runConvexHull(ROI roi)
```
    Runs a convex hull on the specified ROI.
    
    Parameters:
    roi - the ROI
  - runConvexHullROI
```
void runConvexHullROI(long roiMask,
                    int roiOutputColorIndex)
```
    Runs convex hull on the specified ROI mask.
    
    Parameters:
    roiMask - the ROI mask to include
    roiOutputColorIndex - the output ROI color index
  - runConvexHullROISlice
```
void runConvexHullROISlice(int sliceDirection,
                         int sliceNumber,
                         long roiMask,
                         int roiOutputColorIndex)
```
    Runs convex hull on the specified ROI mask.
    
    Parameters:
    sliceDirection - the slice direction
    sliceNumber - the slice number
    roiMask - the ROI mask to include
    roiOutputColorIndex - the output ROI color index
  - runCrosssectionMM
```
double[] runCrosssectionMM(Line line,
                         double step)
```
    Runs a cross-section on the specified Line.
    
    Parameters:
    line - the Line
    step - the interpolation interval
    
    Returns:
    an array of values at the interpolated points
  - runCrosssectionVoxels
```
double[] runCrosssectionVoxels(Line line)
```
    Runs a cross-section on the specified line.
    
    Parameters:
    line - the Line
    
    Returns:
    an array of value of all intersected voxels
  - runDilateROI
```
void runDilateROI(long roiMask,
                int kernelSize)
```
    Runs a dilate ROI operation.
    
    Parameters:
    roiMask - the ROI mask to include
    kernelSize - the kernel size
  - runDilateROISlice
```
void runDilateROISlice(int sliceDirection,
                     int sliceNumber,
                     long roiMask,
                     int kernelSize)
```
    Runs a dilate ROI slice operation.
    
    Parameters:
    sliceDirection - the slice direction
    sliceNumber - the slice number
    roiMask - the ROI mask to include
    kernelSize - the kernel size
  - runErodeROI
```
void runErodeROI(long roiMask,
               int kernelSize)
```
    Runs an erode ROI operation.
    
    Parameters:
    roiMask - the ROI mask to include
    kernelSize - the kernel size
  - runErodeROISlice
```
void runErodeROISlice(int sliceDirection,
                    int sliceNumber,
                    long roiMask,
                    int kernelSize)
```
    Runs a erode ROI slice operation.
    
    Parameters:
    sliceDirection - the slice direction
    sliceNumber - the slice number
    roiMask - the ROI mask to include
    kernelSize - the kernel size
  - runFilter
```
void runFilter(String name)
```
    Runs a filter.
    
    Parameters:
    name - the name of the filter
  - runGenerateClusterROI
```
void runGenerateClusterROI(ImageVolume overlay,
                         int voxelCountThreshold)
```
    Generate ROIs from clusters [runClusterAnalysis() must precede this call].
    
    Parameters:
    overlay - the overlay ImageVolume
    voxelCountThreshold - the minimum number of voxels a component must contain in order to include in the split
  - runGenerateHistogramROI
```
void runGenerateHistogramROI(Histogram hist)
```
    Adds new ROI mask data for voxels included in this histogram.
    
    Parameters:
    hist - the Histogram
  - runGenerateHistogramROISlice
```
void runGenerateHistogramROISlice(int sliceDirection,
                                int sliceNumber,
                                Histogram hist)
```
    Adds new ROI mask data for voxels included in this histogram.
    
    Parameters:
    sliceDirection - the slice direction
    sliceNumber - the slice number
    hist - the Histogram
  - runGenerateHistogramWithinROI
```
void runGenerateHistogramWithinROI(Histogram hist,
                                 long roiMask)
```
    Adds new ROI mask data for voxels included in this histogram, but only within the specified ROI mask.
    
    Parameters:
    hist - the Histogram
    roiMask - the ROI mask to include
  - runGenerateHistogramWithinROISlice
```
void runGenerateHistogramWithinROISlice(int sliceDirection,
                                      int sliceNumber,
                                      Histogram hist,
                                      long roiMask)
```
    Adds new ROI mask data for voxels included in this histogram, but only within the specified ROI mask.
    
    Parameters:
    sliceDirection - the slice direction
    sliceNumber - the slice number
    hist - the Histogram
    roiMask - the ROI mask to include
  - runGenerateLogicalROI
```
void runGenerateLogicalROI(List<ImageVolume> overlays)
```
    Creates a ROI based on the intersection of a list of ImageVolumes.
    
    Parameters:
    overlays - a list of ImageVolumes
  - runHistogram
```
Histogram runHistogram(int numBins,
                     double min,
                     double max,
                     boolean excludeZero,
                     boolean isIntegerMode)
```
    Runs a histogram.
    
    Parameters:
    numBins - the number of histogram bins
    min - the histogram bin range min
    max - the histogram bin range max
    excludeZero - true to exclude voxel value zero counts, false to include zeros
    isIntegerMode - true to create equal size bins when working with integer data (may automatically change numBins)
    
    Returns:
    the Histogram
  - runHistogramROI
```
Histogram runHistogramROI(int numBins,
                        double min,
                        double max,
                        long roiMask,
                        boolean excludeZero,
                        boolean integerMode)
```
    Runs a histogram within a ROI mask.
    
    Parameters:
    numBins - the number of histogram bins
    min - the histogram bin range min
    max - the histogram bin range max
    roiMask - the ROI mask to include
    excludeZero - true to exclude voxel value zero counts, false to include zeros
    integerMode - true to create equal size bins when working with integer data (may automatically change numBins)
    
    Returns:
    the Histogram
  - runLogicalAnalysis
```
Analysis runLogicalAnalysis(List<ImageVolume> overlays)
```
    Runs statistics on the intersection of a list of ImageVolumes.
    
    Parameters:
    overlays - a list of ImageVolumes
  - runOpenROI
```
void runOpenROI(long roiMask,
              int kernelSize)
```
    Runs an open ROI operation.
    
    Parameters:
    roiMask - the ROI mask to include
    kernelSize - the kernel size
  - runOpenROISlice
```
void runOpenROISlice(int sliceDirection,
                   int sliceNumber,
                   long roiMask,
                   int kernelSize)
```
    Runs an open ROI slice operation.
    
    Parameters:
    sliceDirection - the slice direction
    sliceNumber - the slice number
    roiMask - the ROI mask to include
    kernelSize - the kernel size
  - runOperation
```
VolumeManager runOperation(String expression,
                         int selectionArea,
                         boolean outputNewImage,
                         boolean allSeriesPoints,
                         boolean roiSlicesOnly)
```
    Runs an operation.
    
    Parameters:
    expression - the expression, where "this" refers to the base volume (e.g., "this + 1" would add one to every voxel in the image)
    selectionArea - the selection area (see constants)
    outputNewImage - true to output a new image, false to output into the existing image
    allSeriesPoints - true to process all series points, alse to process only the current series point
    roiSlicesOnly - true to process only those slices that contain ROI data, false to process all slices
    
    Returns:
    the output VolumeManager
  - runOperationROILogic
```
void runOperationROILogic(String expression,
                        int roiOutputColorIndex)
```
    Runs a ROI logic operation.
    
    Parameters:
    expression - the expression
    roiOutputColorIndex - the output ROI color index
  - runOperationSeriesStatistic
```
VolumeManager runOperationSeriesStatistic(int startingSeriesIndex,
                                        int endingSeriesIndex,
                                        int seriesGroupSize,
                                        int statisticType)
```
    Runs a series operation.
    
    Parameters:
    startingSeriesIndex - the starting series index
    endingSeriesIndex - the ending series index
    seriesGroupSize - the series group size (e.g., 10 series points with a group size of 5 would produce a new series with 2 points)
    statisticType - the series statistic type (see constants)
    
    Returns:
    the output VolumeManager
  - runPlugin
```
Object runPlugin(String pluginName,
               String[] args)
```
    Runs a plugin.
    
    Parameters:
    pluginName - the plugin name
    args - the arguments
    
    Returns:
    returns an optional data object
  - runPropagateROISlice
```
void runPropagateROISlice(int sliceDirection,
                        int sliceNumber,
                        int startSlice,
                        int endSlice,
                        long roiMask,
                        int roiOutputColorIndex)
```
    Propagates an ROI slice.
    
    Parameters:
    sliceDirection - the slice direction of the slice to propagate
    sliceNumber - the slice number of the slice propagate
    startSlice - the starting slice of the propagate range
    endSlice - the ending slice of the propagate range
    roiMask - the ROI mask to include
    roiOutputColorIndex - the output ROI color index
  - runRangeToROI
```
boolean runRangeToROI(double min,
                    double max,
                    boolean percentMax,
                    boolean excludeZero,
                    boolean makeSeriesROI,
                    boolean seriesUsesDynamicThreshold)
```
    Creates new ROI mask data based on a range.
    
    Parameters:
    min - the range minimum
    max - the range maximum
    percentMax - true if the min/max values represent percent of image maximum, false if they refer to actual range values
    excludeZero - true to exclude zero from calculation
    makeSeriesROI - true to make a series ROI
    seriesUsesDynamicThreshold - true only if percentMax is also true, in which case percent max is determined for each series point individually
    
    Returns:
    true if new ROI mask data was added, false otherwise
  - runRangeToROISlice
```
boolean runRangeToROISlice(double min,
                         double max,
                         int sliceDirection,
                         int sliceNumber,
                         boolean percentMax,
                         boolean excludeZero,
                         boolean makeSeriesROI,
                         boolean seriesUsesDynamicThreshold)
```
    Creates new ROI mask data based on a range.
    
    Parameters:
    min - the range minimum
    max - the range maximum
    sliceDirection - the slice direction
    sliceNumber - the slice number
    percentMax - true if the min/max values represent percent of image maximum, false if they refer to actual range values
    excludeZero - true to exclude zero from calculation
    makeSeriesROI - true to make a series ROI
    seriesUsesDynamicThreshold - true only if percentMax is also true, in which case percent max is determined for each series point individually
    
    Returns:
    true if new ROI mask data was added, false otherwise
  - runRankFilter
```
void runRankFilter(int kernelSize,
                 int rankType,
                 int filterType)
```
    Runs a rank filter.
    
    Parameters:
    kernelSize - the kernel size
    rankType - the rank type (see contants)
    filterType - the filter type (see constants)
  - runReflectROI
```
void runReflectROI(int sliceDirection,
                 int axis,
                 boolean vertical,
                 boolean includePointsAndLines,
                 boolean onlySelectedLines,
                 boolean onlySelectedPoints)
```
    Reflects a ROI.
    
    Parameters:
    sliceDirection - the slice direction
    axis - the axis of reflection (slice number)
    vertical - true to reflect vertically, false horizontally
    includePointsAndLines - true to reflect points and lines, false otherwise
    onlySelectedLines - true to reflect only selected lines, false otherwise
    onlySelectedPoints - true to reflect only selected points, false otherwise
  - runReflectROISlice
```
void runReflectROISlice(int sliceDirection,
                      int sliceNumber,
                      int axis,
                      boolean vertical,
                      boolean includePointsAndLines,
                      boolean onlySelectedLines,
                      boolean onlySelectedPoints)
```
    Parameters:
    sliceDirection -
    sliceNumber -
    axis -
    vertical -
    includePointsAndLines -
    onlySelectedLines -
    onlySelectedPoints -
  - runScript
```
void runScript(String scriptName)
```
    Runs a script.
    
    Parameters:
    scriptName - the script name
  - runSeriesROI
```
List<Analysis> runSeriesROI(ROI roi)
```
    Runs statistics on a series ROI.
    
    Parameters:
    roi - the ROI
    
    Returns:
    a list of Analyses
  - runSeriesStats
```
Analysis runSeriesStats()
```
    Runs series statistics on the currently selected ImageVolume.
    
    Returns:
    a series statistic
  - runSeriesStatsROI
```
List<Analysis> runSeriesStatsROI(long roiMask,
                               boolean includePointsAndLines,
                               boolean onlySelectedPoints,
                               boolean onlySelectedLines)
```
    Runs ROI series statistics.
    
    Parameters:
    roiMask - the ROI mask to include
    includePointsAndLines - true to also run stats on lines and points, false otherwise
    onlySelectedPoints - true to run stats on only selected points, false otherwise
    onlySelectedLines - true to run stats on only selected lines, false otherwise
    
    Returns:
    a list of Analyses
  - runShrinkWrapROI
```
void runShrinkWrapROI(double threshold,
                    long roiMask,
                    int roiOutputColorIndex,
                    boolean percentMax,
                    boolean seriesUsesDynamicThreshold)
```
    Shrink wraps (3D) a ROI mask.
    
    Parameters:
    threshold - the threshold
    roiMask - the roiMask to include
    roiOutputColorIndex - the output ROI color index
    percentMax - true if the threshold represents percent of image maximum, false if they refer to actual range values
    seriesUsesDynamicThreshold - true only if percentMax is also true, in which case percent max is determined for each series point individually
  - runShrinkWrapROI
```
void runShrinkWrapROI(long roiMask,
                    int roiOutputColorIndex)
```
    Shrink wraps (3D) a ROI mask.
    
    Parameters:
    roiMask - the roiMask to include
    roiOutputColorIndex - the output ROI color index
  - runShrinkWrapROIAllSlices
```
void runShrinkWrapROIAllSlices(double threshold,
                             int sliceDirection,
                             long roiMask,
                             int roiOutputColorIndex,
                             boolean percentMax,
                             boolean seriesUsesDynamicThreshold)
```
    Shrink wraps (2D) a ROI mask in a specified slice direction.
    
    Parameters:
    threshold - the threshold
    sliceDirection - the slice direction
    roiMask - the ROI mask to include
    roiOutputColorIndex - the output ROI color index
    percentMax - true if the threshold represents percent of image maximum, false if they refer to actual range values
    seriesUsesDynamicThreshold - true only if percentMax is also true, in which case percent max is determined for each series point individually
  - runShrinkWrapROIAllSlices
```
void runShrinkWrapROIAllSlices(int sliceDirection,
                             long roiMask,
                             int roiOutputColorIndex)
```
    Shrink wraps (2D) a ROI mask in a specified slice direction.
    
    Parameters:
    sliceDirection - the slice direction
    roiMask - the ROI mask to include
    roiOutputColorIndex - the output ROI color index
  - runShrinkWrapROISlice
```
void runShrinkWrapROISlice(double threshold,
                         int sliceDirection,
                         int sliceNumber,
                         long roiMask,
                         int roiOutputColorIndex,
                         boolean percentMax,
                         boolean seriesUsesDynamicThreshold)
```
    Shrink wraps (2D) a ROI mask in a specified slice direction.
    
    Parameters:
    threshold - the threshold
    sliceDirection - the slice direction
    sliceNumber - the slice number
    roiMask - the ROI mask to include
    roiOutputColorIndex - the output ROI color index
    percentMax - true if the threshold represents percent of image maximum, false if they refer to actual range values
    seriesUsesDynamicThreshold - true only if percentMax is also true, in which case percent max is determined for each series point individually
  - runShrinkWrapROISlice
```
void runShrinkWrapROISlice(int sliceDirection,
                         int sliceNumber,
                         long roiMask,
                         int roiOutputColorIndex)
```
    Shrink wraps (2D) a ROI mask in a specified slice direction.
    
    Parameters:
    sliceDirection - the slice direction
    sliceNumber - the slice number
    roiMask - the ROI mask to include
    roiOutputColorIndex - the output ROI color index
  - runSliceStats
```
Analysis runSliceStats(int sliceDirection,
                     int sliceNumber)
```
    Run statistics on a slice.
    
    Parameters:
    sliceDirection - the slice direction
    sliceNumber - the slice number
    
    Returns:
    the slice stat
  - runSliceStatsROI
```
List<Analysis> runSliceStatsROI(int sliceDirection,
                              int sliceNumber,
                              long roiMask,
                              boolean includePointsAndLines,
                              boolean onlySelectedPoints,
                              boolean onlySelectedLines)
```
    Runs statistics on a ROI slice.
    
    Parameters:
    sliceDirection - the slice direction
    sliceNumber - the slice number
    roiMask - the ROI mask to include
    includePointsAndLines - true to include points and lines, false otherwise
    onlySelectedPoints - true to include only selected points
    onlySelectedLines - true to include only selected lines
    
    Returns:
    a list of Analyses
  - runSmooth
```
void runSmooth(ROI roi)
```
    Smooths a ROI (only applies to Lines).
    
    Parameters:
    roi - the ROI to smooth
  - runStat
```
Analysis runStat(ROI roi)
```
    Runs statistics on a specified ROI.
    
    Parameters:
    roi - the ROI
    
    Returns:
    the stat
  - runThresholdToConvexHullROI
```
void runThresholdToConvexHullROI(double threshold,
                               boolean percentMax,
                               boolean excludeZero,
                               boolean makeSeriesROI,
                               boolean seriesUsesDynamicThreshold)
```
    Adds new ROI mask data based on a threshold and in a convex hull.
    
    Parameters:
    threshold - the threshold
    percentMax - true if the threshold represents percent of image maximum, false if they refer to actual range values
    excludeZero - true to exclude zero from calculation
    makeSeriesROI - true to make a series ROI
    seriesUsesDynamicThreshold - true only if percentMax is also true, in which case percent max is determined for each series point individually
  - runThresholdToConvexHullROISlice
```
void runThresholdToConvexHullROISlice(double threshold,
                                    int sliceDirection,
                                    int sliceNumber,
                                    boolean percentMax,
                                    boolean excludeZero,
                                    boolean makeSeriesROI,
                                    boolean seriesUsesDynamicThreshold)
```
    Adds new ROI mask data based on a threshold and in a convex hull.
    
    Parameters:
    threshold - the threshold
    sliceDirection - the slice direction
    sliceNumber - the slice number
    percentMax - true if the threshold represents percent of image maximum, false if they refer to actual range values
    excludeZero - true to exclude zero from calculation
    makeSeriesROI - true to make a series ROI
    seriesUsesDynamicThreshold - true only if percentMax is also true, in which case percent max is determined for each series point individually
  - runThresholdToROI
```
boolean runThresholdToROI(double threshold,
                        boolean percentMax,
                        boolean excludeZero,
                        boolean makeSeriesROI,
                        boolean seriesUsesDynamicThreshold)
```
    Adds new ROI mask data based on a threshold.
    
    Parameters:
    threshold - the threshold
    percentMax - true if the threshold represents percent of image maximum, false if they refer to actual range values
    excludeZero - true to exclude zero from calculation
    makeSeriesROI - true to make a series ROI
    seriesUsesDynamicThreshold - true only if percentMax is also true, in which case percent max is determined for each series point individually
    
    Returns:
    true if new ROI mask data was added, false otherwise
  - runThresholdToROISlice
```
boolean runThresholdToROISlice(double threshold,
                             int sliceDirection,
                             int sliceNumber,
                             boolean percentMax,
                             boolean excludeZero,
                             boolean makeSeriesROI,
                             boolean seriesUsesDynamicThreshold)
```
    Adds new ROI mask data based on a threshold.
    
    Parameters:
    threshold - the threshold
    sliceDirection - the slice direction
    sliceNumber - the slice number
    percentMax - true if the threshold represents percent of image maximum, false if they refer to actual range values
    excludeZero - true to exclude zero from calculation
    makeSeriesROI - true to make a series ROI
    seriesUsesDynamicThreshold - true only if percentMax is also true, in which case percent max is determined for each series point individually
    
    Returns:
    true if new ROI mask data was added, false otherwise
  - runThresholdToShrinkWrapROI
```
boolean runThresholdToShrinkWrapROI(double threshold,
                                  boolean percentMax,
                                  boolean excludeZero,
                                  boolean makeSeriesROI,
                                  boolean seriesUsesDynamicThreshold)
```
    Adds new ROI mask data based on a threshold and shrink wrap (3D).
    
    Parameters:
    threshold - the threshold
    percentMax - true if the threshold represents percent of image maximum, false if they refer to actual range values
    excludeZero - true to exclude zero from calculation
    makeSeriesROI - true to make a series ROI
    seriesUsesDynamicThreshold - true only if percentMax is also true, in which case percent max is determined for each series point individually
    
    Returns:
    true if new ROI mask data was added, false otherwise
  - runThresholdToShrinkWrapROIAllSlices
```
boolean runThresholdToShrinkWrapROIAllSlices(double threshold,
                                           int sliceDirection,
                                           boolean percentMax,
                                           boolean excludeZero,
                                           boolean makeSeriesROI,
                                           boolean seriesUsesDynamicThreshold)
```
    Adds new ROI mask data based on a threshold and shrink wrap (2D).
    
    Parameters:
    threshold - the threshold
    sliceDirection - the slice direction
    percentMax - true if the threshold represents percent of image maximum, false if they refer to actual range values
    excludeZero - true to exclude zero from calculation
    makeSeriesROI - true to make a series ROI
    seriesUsesDynamicThreshold - true only if percentMax is also true, in which case percent max is determined for each series point individually
    
    Returns:
    true if new ROI mask data was added, false otherwise
  - runThresholdToShrinkWrapROISlice
```
boolean runThresholdToShrinkWrapROISlice(double threshold,
                                       int sliceDirection,
                                       int sliceNumber,
                                       boolean percentMax,
                                       boolean excludeZero,
                                       boolean makeSeriesROI,
                                       boolean seriesUsesDynamicThreshold)
```
    Adds new ROI mask data based on a threshold and shrink wrap (2D).
    
    Parameters:
    threshold - the threshold
    sliceDirection - the slice direction
    sliceNumber - the slice number
    percentMax - true if the threshold represents percent of image maximum, false if they refer to actual range values
    excludeZero - true to exclude zero from calculation
    makeSeriesROI - true to make a series ROI
    seriesUsesDynamicThreshold - true only if percentMax is also true, in which case percent max is determined for each series point individually
    
    Returns:
    true if new ROI mask data was added, false otherwise
  - runVolumeStats
```
Analysis runVolumeStats()
```
    Runs volume statistics on the currently selected series point of the currently selected ImageVolume.
    
    Returns:
    the volume stat
  - runVolumeStatsROI
```
List<Analysis> runVolumeStatsROI(long roiMask,
                               boolean includePointsAndLines,
                               boolean onlySelectedPoints,
                               boolean onlySelectedLines)
```
    Runs volume ROI statistics.
    
    Parameters:
    roiMask - the ROI mask to include
    includePointsAndLines - true to include points and lines, false otherwise
    onlySelectedPoints - true to include selected points
    onlySelectedLines - true to include selected lines
    
    Returns:
    a list of Analyses
  - save
```
void save()
```
    Saves this VolumeManager.
  - saveWithName
```
void saveWithName(String saveLocation)
```
    Saves this VolumeManager
    
    Parameters:
    saveLocation - the location of the file to save to
  - saveAs
```
void saveAs(String saveLocation,
          String headerFormat,
          int datatype,
          int numBytes,
          boolean littleEndian,
          boolean compress,
          int xMin,
          int xMax,
          int yMin,
          int yMax,
          int zMin,
          int zMax,
          int tMin,
          int tMax,
          double xSize,
          double ySize,
          double zSize,
          double tSize,
          String orientation,
          boolean applyTransform,
          boolean applyOverlay,
          boolean overlayThreshold,
          boolean overlayMix,
          int interpolation,
          boolean applyDataScales,
          boolean fitPrecision,
          boolean maintainZero)
```
    Saves this VolumeManager.
    
    Parameters:
    saveLocation - the location of the file to save to
    headerFormat - the header format (see ImageVolume constants)
    datatype - (see ImageType constants)
    numBytes - the number of bytes per voxel (1, 2, or 4 are supported)
    littleEndian - true to save multi-byte data in little endian byte order, false to use big endian byte order
    compress - true to compress (not applicable to all header types)
    xMin - x minimum bounds
    xMax - x maximum bounds
    yMin - y minimum bounds
    yMax - y maximum bounds
    zMin - z minimum bounds
    zMax - z maximum bounds
    tMin - t minimum bounds
    tMax - t maximum bounds
    xSize - x voxel size
    ySize - y voxel size
    zSize - z voxel size
    tSize - t size ratio (if old size is 2 and new size is .5, then this value should be .25)
    orientation - the orientation (e.g., "XYZ+--")
    applyTransform - true to apply the transform when saving, false otherwise
    applyOverlay - true to save the currently selected overlay ImageVoluem, false to save the base volume
    overlayThreshold - true to apply a threshold to the saved overlay
    overlayMix - true to save both the base volume and overlay volumes in the same image (i.e., needs a split color table)
    interpolation - the interpolation code (see constants)
    applyDataScales - true to apply data scales
    fitPrecision - true to fit the image data to the bounds of the datatype
    maintainZero - true to use data scale slope, but not data scale intercept (i.e., intercept = 0)
  - saveOverlays
```
void saveOverlays()
```
    Saves overlays.
  - saveROI
```
void saveROI(String saveLocation)
```
    Saves ROI.
    
    Parameters:
    saveLocation - the file location to save
  - saveSingleROI
```
void saveSingleROI(String saveLocation,
                 int index)
```
    Saves a single ROI color.
    
    Parameters:
    saveLocation - the file location to save
    index - the roi color index
  - select
```
void select(ROI roi,
          boolean select)
```
    Selects or unselects a specified ROI.
    
    Parameters:
    roi - the ROI
    select - true to select, false to unselect
  - selectAll
```
void selectAll()
```
    Selects all ROI masks, lines, and points.
  - selectMenuOption
```
void selectMenuOption(String name)
```
    Selects a menu option.
    
    Parameters:
    name - the menu option name
  - setCoordinateSpace
```
@Deprecated
void setCoordinateSpace(int index)
```
    Deprecated.
    
    Sets the coordinate space of the currently selected ImageVolume.
    
    Parameters:
    index - the coordinate space index
  - setOrientationOption
```
void setOrientationOption(ImageVolume volume,
                        int index)
```
    Sets the orientation option (e.g., NIFTI s-form or q-form) of the currently selected ImageVolume.
    
    Parameters:
    volume - the image volume
    index - the orientation option index
  - setCurrentPosition
```
void setCurrentPosition(Coordinate coordinate)
```
    Sets the current position.
    
    Parameters:
    coordinate - the new position
  - setCurrentSeriesPoint
```
void setCurrentSeriesPoint(int seriesIndex)
```
    Sets the current series point.
    
    Parameters:
    seriesIndex - the new series point
  - setCurrentVolumeIndex
```
void setCurrentVolumeIndex(int index)
```
    Sets the current volume by index.
    
    Parameters:
    index - the volume index
  - setDisplayRangeToImageRange
```
void setDisplayRangeToImageRange(ImageVolume volume,
                               boolean entireSeries)
```
    Sets the display range of the specified ImageVolume to its image min/max.
    
    Parameters:
    volume - the ImageVolume
    entireSeries - true to use the min/max of the entire series, false to use the current series point
  - setLabel
```
void setLabel(ROI roi,
            String label)
```
    Sets the label of the specified ROI.
    
    Parameters:
    roi - the ROI
    label - the label
  - setMenuOption
```
void setMenuOption(String name,
                 boolean value)
```
    Sets a menu option.
    
    Parameters:
    name - the menu option
    value - the menu option value
  - setNotes
```
void setNotes(String text)
```
    Sets the note of the base volume.
    
    Parameters:
    text - the note text
  - setOrigin
```
void setOrigin(Coordinate coordinate)
```
    Sets the origin of the base volume.
    
    Parameters:
    coordinate - the new origin
  - setRoiColor
```
void setRoiColor(int color)
```
    Sets the current ROI color.
    
    Parameters:
    color - the ROI color index
  - setSliceDirection
```
void setSliceDirection(int sliceDirection)
```
    Sets the current slice direction.
    
    Parameters:
    sliceDirection - the slice direction
  - setSliceNumber
```
boolean setSliceNumber(int sliceNumber)
```
    Sets the current slice number.
    
    Parameters:
    sliceNumber - the slice number
    
    Returns:
    true if the change in slice number was successful, false otherwise
  - setTransformMode
```
void setTransformMode(boolean transform)
```
    Sets the transform mode.
    
    Parameters:
    transform - true to turn on transform, false to turn off transform
  - setVolumeDisplayAlpha
```
void setVolumeDisplayAlpha(ImageVolume volume,
                         double alpha)
```
    Sets the alpha value of the specified ImageVolume.
    
    Parameters:
    volume - the ImageVolume
    alpha - the alpha value (0 to 1)
  - setVolumeDisplayColorTable
```
void setVolumeDisplayColorTable(ImageVolume volume,
                              String colorTable)
```
    Sets the color table of the specified ImageVolume.
    
    Parameters:
    volume - the ImageVolume
    colorTable - the color table name
  - setVolumeDisplayHidden
```
void setVolumeDisplayHidden(ImageVolume volume,
                          boolean hidden)
```
    Sets the hidden state of the specified ImageVolume.
    
    Parameters:
    volume - the ImageVolume
    hidden - true to hide the volume, false to display it
  - setVolumeDisplayIndex
```
void setVolumeDisplayIndex(ImageVolume volume,
                         int index)
```
    Sets the display index of the specified ImageVolume (cannot change base volume index).
    
    Parameters:
    volume - the ImageVolume
    index - the new index
  - setVolumeDisplayRange
```
void setVolumeDisplayRange(ImageVolume volume,
                         double screenMin,
                         double screenMax)
```
    Sets the display range of the specified ImageVolume.
    
    Parameters:
    volume - the ImageVolume
    screenMin - the new display range minimum
    screenMax - the new display range maximum
  - setVoxelValue
```
void setVoxelValue(Coordinate coordinate,
                 int seriesIndex,
                 double value)
```
    Sets a voxel value at the specified coordinate.
    
    Parameters:
    coordinate - the coordinate
    seriesIndex - the series point
    value - the new value
  - showErrorMessage
```
void showErrorMessage(String message,
                    String title)
```
    Shows an error message.
    
    Parameters:
    message - the message text
    title - the message title
  - showWarningMessage
```
void showWarningMessage(String message,
                      String title)
```
    Shows a warning message.
    
    Parameters:
    message - the message text
    title - the message title
  - toString
```
String toString()
```
    Returns a string representation.
    
    Overrides:
    
    toString in class Object
    
    Returns:
    a string representation
  - transform
```
void transform(ImageVolume volume,
             double m00,
             double m01,
             double m02,
             double m03,
             double m10,
             double m11,
             double m12,
             double m13,
             double m20,
             double m21,
             double m22,
             double m23,
             double m30,
             double m31,
             double m32,
             double m33)
```
    Transform the specified ImageVolume.
    
    Parameters:
    volume - the ImageVolume
    m00 - m00
    m01 - m01
    m02 - m02
    m03 - m03
    m10 - m10
    m11 - m11
    m12 - m12
    m13 - m13
    m20 - m20
    m21 - m21
    m22 - m22
    m23 - m23
    m30 - m30
    m31 - m31
    m32 - m32
    m33 - m33
  - updateViewer
```
void updateViewer()
```
    Redraws this VolumeManager.

Interface VolumeManager

Field Summary

Method Summary

Field Detail

FILTER_TYPE_SLICE

FILTER_TYPE_TIME

FILTER_TYPE_VOLUME

INTERPOLATION_TYPE_LINEAR

INTERPOLATION_TYPE_NN

INTERPOLATION_TYPE_SINC

RANK_TYPE_MAX

RANK_TYPE_MEDIAN

RANK_TYPE_MIN

SELECTION_TYPE_ROI_INSIDE

SELECTION_TYPE_ROI_OUTSIDE

SELECTION_TYPE_SLICE

SELECTION_TYPE_VOLUME

SERIES_TYPE_MAX

SERIES_TYPE_MEAN

SERIES_TYPE_MIN

SERIES_TYPE_STDEV

SERIES_TYPE_SUM

SLICE_DIRECTION_AXIAL

SLICE_DIRECTION_CORONAL

SLICE_DIRECTION_SAGITTAL

SLICE_DIRECTION_TEMPORAL

VIDEO_FORMAT_AVI_DIB

VIDEO_FORMAT_AVI_MJPG

VIDEO_FORMAT_AVI_PNG

VIDEO_FORMAT_QUICKTIME_ANIMATION

VIDEO_FORMAT_QUICKTIME_JPEG

VIDEO_FORMAT_QUICKTIME_PNG

VIDEO_FORMAT_QUICKTIME_RAW

VIDEO_QUALITY_BEST

VIDEO_QUALITY_FASTEST

VIDEO_QUALITY_GOOD

Method Detail

addBookmark

addMoreROIColors

addOverlay

addOverlayOnto

addOverlayURL

addSliceListener

associatePluginWindow

buildProjection

buildSurface

captureLayout

captureSnapshot

captureVideoStart

captureVideoStop

continueScript

convertIndexToWorldCoordinate

convertWorldToIndexCoordinate

createWebpage

createWebpage

decrement

deleteROI

disposeVolumeManager

findGoodPluginWindowLocation

flipOrientation

getBaseVolume

getCurrentPosition

getCurrentVolume

getCurrentWorldPosition

getFrame

getHistogramAnalysis

getLoadedURI

getLoadedURI

getMainImage

getMainImage

getMainImage

getMainImage

getMainImage

getManagerTitle

getMangoData

getName

getOrigin

getOverlays

getProjectionManager

getRoiColor