public interface VolumeManager
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.
|
static final int FILTER_TYPE_SLICE
static final int FILTER_TYPE_TIME
static final int FILTER_TYPE_VOLUME
static final int INTERPOLATION_TYPE_LINEAR
static final int INTERPOLATION_TYPE_NN
static final int INTERPOLATION_TYPE_SINC
static final int RANK_TYPE_MAX
static final int RANK_TYPE_MEDIAN
static final int RANK_TYPE_MIN
static final int SELECTION_TYPE_ROI_INSIDE
static final int SELECTION_TYPE_ROI_OUTSIDE
static final int SELECTION_TYPE_SLICE
static final int SELECTION_TYPE_VOLUME
static final int SERIES_TYPE_MAX
static final int SERIES_TYPE_MEAN
static final int SERIES_TYPE_MIN
static final int SERIES_TYPE_STDEV
static final int SERIES_TYPE_SUM
static final int SLICE_DIRECTION_AXIAL
static final int SLICE_DIRECTION_CORONAL
static final int SLICE_DIRECTION_SAGITTAL
static final int SLICE_DIRECTION_TEMPORAL
static final int VIDEO_FORMAT_AVI_DIB
static final int VIDEO_FORMAT_AVI_MJPG
static final int VIDEO_FORMAT_AVI_PNG
static final int VIDEO_FORMAT_QUICKTIME_ANIMATION
static final int VIDEO_FORMAT_QUICKTIME_JPEG
static final int VIDEO_FORMAT_QUICKTIME_PNG
static final int VIDEO_FORMAT_QUICKTIME_RAW
static final int VIDEO_QUALITY_BEST
static final int VIDEO_QUALITY_FASTEST
static final int VIDEO_QUALITY_GOOD
void addBookmark(Coordinate coord, String label)
coord
- the bookmark coordinatelabel
- the bookmark labelvoid addMoreROIColors()
void addOverlay(String openLocation, boolean parametric)
openLocation
- the file locationparametric
- true to open both positives and negatives, false to only open positivesvoid addOverlayOnto(VolumeManager manager, String colorTable)
manager
- the other VolumeManagercolorTable
- the overlay color tablevoid addOverlayURL(String url)
url
- the URLvoid addSliceListener(SliceListener listener, int sliceDirection)
listener
- the SliceListener to addsliceDirection
- the slice directionvoid associatePluginWindow(String title, JFrame window)
title
- the title of this pluginwindow
- the windowProjectionManager buildProjection(int rankType, int sliceDirection, double resX, double resY, double resZ, int rotationAxis, int projectionQuality)
rankType
- the rank type (see ProjectionManager constants)sliceDirection
- the slice directionresX
- the X resolutionresY
- the Y resolutionresZ
- the Z resolutionrotationAxis
- the rotation axis (the ProjectionManager constants)projectionQuality
- the projection quality (see ProjectionManager constants)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)
threshold
- the build thresholdpercentMax
- true if the threshold values represent percent of image maximum, false if they refer to actual range valuesshrinkWrap
- true to use shrinkwrap, false otherwisemaximum
- true if the threshold represents a maximum, false otherwiseimageSmoothing
- true to use image smoothing, false otherwisewidth
- FWHM of the image smoothing filterkernelSize
- kernel size of the image smoothing filterresX
- the output X resolutionresY
- the output Y resolutionresZ
- the output Z resolutionsurfaceSmoothing
- true to use surface smoothing, false otherwisepointError
- the point error thresholdfeatureAngle
- the feature angle thresholditerations
- number of iterations of surface smoothingvoid captureLayout(String saveLocation, int rows, int columns, int startSlice, int skipSlices, boolean series, boolean useLabels, boolean useColorBars, boolean useText, String title, String footnote)
saveLocation
- the location to save the layout image filerows
- the number of layout rowscolumns
- the number of layout colsstartSlice
- the starting sliceskipSlices
- the number of slices to skip between each slice capturedseries
- true to capture along a series, false to capture along the current slice directionuseLabels
- true to embed slice labels, false otherwiseuseColorBars
- true to embed color bars, false otherwiseuseText
- true to embed text, false otherwisetitle
- the layout titlefootnote
- the layout footnotevoid captureSnapshot(String saveLocation)
saveLocation
- the location to save the image filevoid captureVideoStart(String saveLocation, int videoFormat, int videoQuality, int fps, boolean animate)
saveLocation
- the location to save the video filevideoFormat
- the video format code (see constants)videoQuality
- the video quality code (see constants)fps
- the frames per secondanimate
- true to automatically animate the projection, false otherwisevoid captureVideoStop()
void continueScript()
void convertIndexToWorldCoordinate(Coordinate coor)
coor
- the index coordinatevoid convertWorldToIndexCoordinate(Coordinate coor)
coor
- the world coordinate@Deprecated void createWebpage(String saveLocation, String title, boolean useOverlays, boolean useAtlas, boolean useKioskMode, boolean outputSingleFile)
saveLocation
- the location to save the webpage filestitle
- the title of the webpageuseOverlays
- true to include overlay data in the webpage, false to only include the base volumeuseAtlas
- true to include atlas data in the webpage, false otherwiseuseKioskMode
- true to use "kiosk mode", false otherwiseoutputSingleFile
- true to output a single HTML file, false to output separate HTML, CSS, and JS filesvoid createWebpage(String saveLocation, String title, boolean useOverlays, boolean useAtlas, boolean useSurfaces, boolean useKioskMode, boolean outputSingleFile)
saveLocation
- the location to save the webpage filestitle
- the title of the webpageuseOverlays
- true to include overlay data in the webpage, false to only include the base volumeuseAtlas
- true to include atlas data in the webpage, false otherwiseuseSurfaces
- true to include surface data, false otherwiseuseKioskMode
- true to use "kiosk mode", false otherwiseoutputSingleFile
- true to output a single HTML file, false to output separate HTML, CSS, and JS filesboolean decrement(int direction)
direction
- the slice direction (see constants)void deleteROI(ROI roi)
roi
- the ROI to deletevoid disposeVolumeManager()
Point findGoodPluginWindowLocation(Dimension dimension)
dimension
- the size of the plugin windowvoid flipOrientation(ImageVolume volume, int sliceDirection)
volume
- the volume to flipsliceDirection
- the slice direction to flip about (see constants)ImageVolume getBaseVolume()
Coordinate getCurrentPosition()
ImageVolume getCurrentVolume()
Coordinate getCurrentWorldPosition()
JFrame getFrame()
Histogram getHistogramAnalysis()
URI getLoadedURI()
URI getLoadedURI(ImageVolume volume)
volume
- the ImageVolumeBufferedImage getMainImage()
BufferedImage getMainImage(boolean exclude)
exclude
- exclude non-image information (e.g., ROIs)BufferedImage getMainImage(BufferedImage bi, int slice)
bi
- the image in which to store the image (typical to call after calling the no-arg method first)slice
- the slice to renderBufferedImage getMainImage(BufferedImage bi, int slice, boolean exclude)
bi
- the image in which to store the image (typical to call after calling the no-arg method first)slice
- the slice to renderexclude
- exclude non-image information (e.g., ROIs)BufferedImage getMainImage(BufferedImage bi, int slice, int timeIndex, boolean exclude)
bi
- the image in which to store the image (typical to call after calling the no-arg method first)slice
- the slice to rendertimeIndex
- 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)String getManagerTitle()
@Deprecated MangoData getMangoData()
String getName(ImageVolume volume)
volume
- the ImageVolumeCoordinate getOrigin()
List<ImageVolume> getOverlays()
ProjectionManager getProjectionManager()
int getRoiColor()
ROIData getRoiData()
String getScriptObjectName()
int getSliceDirection()
int getSliceNumber()
SurfaceManager getSurfaceManager()
String getVersion()
ImageVolume getVolume(int index)
index
- the indexdouble getVolumeDisplayAlpha(ImageVolume volume)
volume
- the ImageVolumeString getVolumeDisplayColorTable(ImageVolume volume)
volume
- the ImageVolumedouble getVolumeDisplayRangeMax(ImageVolume volume)
volume
- the ImageVolumedouble getVolumeDisplayRangeMin(ImageVolume volume)
volume
- the ImageVolumeint getVolumeIndex(ImageVolume volume)
volume
- the ImageVolumeList<ImageVolume> getVolumes()
boolean increment(int direction)
direction
- the slice direction (see constants)boolean isCurrentVolumeOverlay()
boolean isCurrentVolumeUsingTransform()
boolean isMultiSliceMode()
boolean isVolumeDisplayHidden(ImageVolume volume)
volume
- the ImageVolumeboolean isVolumeDisplayNegative(ImageVolume volume)
volume
- the ImageVolumeboolean isVolumeOverlay(ImageVolume volume)
volume
- the ImageVolumeboolean isVolumeUsingTransform(ImageVolume volume)
volume
- the ImageVolumeboolean isWorldMode()
void loadROI(String openLocation)
openLocation
- the location of the file to loadvoid loadROIURL(String url, boolean forceImport, boolean forceWorld)
url
- the URLforceImport
- true to force loading this in import mode, false otherwiseforceWorld
- true to force loading this in world mode, false otherwiseSurfaceManager loadSurface(String openLocation)
openLocation
- the location of the file to loadvoid logPoint(Coordinate coordinate, String description)
coordinate
- the coordinate to logdescription
- a label for the pointString makeFilename(String ext)
ext
- the extensionImageVolume makeNewVolume()
BufferedImage makePluginOverlay(int sliceDirection)
sliceDirection
- slice direction of the main slice viewProgressMeter makeProgressMeter()
void pauseScriptForUserInput()
void recordPluginAction(String pluginName, String... args)
pluginName
- the plugin nameargs
- the argumentsvoid reload()
void removeAllOverlays()
void removeOverlay(ImageVolume overlay)
overlay
- the volume to remove@Deprecated void removePluginOverlays()
void removePluginOverlay(BufferedImage pluginOverlay, int sliceDirection)
pluginOverlay
- the BufferedImage to removesliceDirection
- the slice directionvoid removeSliceListener(SliceListener listener, int sliceDirection)
listener
- the SliceListener to removesliceDirection
- the slice directionvoid runAddROI(Coordinate coordinate, double size, boolean sphere)
coordinate
- the center of the new ROI mask datasize
- the size in mmsphere
- true to add a sphere, false to add a cubevoid runAddROISlice(int sliceDirection, Coordinate coordinate, double size, boolean circle)
sliceDirection
- the slice direction on which to add the new ROI datacoordinate
- the center of the new ROI mask datasize
- the size in mmcircle
- true to add a circle, false to add a squareList<Analysis> runAllSliceStats(int sliceDirection)
sliceDirection
- the slice directionList<Analysis> runAllSliceStatsROI(int sliceDirection, long roiMask, boolean includePointsAndLines, boolean onlySelectedPoints, boolean onlySelectedLines)
sliceDirection
- the slice directionroiMask
- the mask of the ROIs to includeincludePointsAndLines
- true to also analyze points and linesonlySelectedPoints
- true to only analyze selected pointsonlySelectedLines
- true to only analyze selected linesList<Analysis> runAllVolumeStats()
List<Analysis> runAllVolumeStatsROI(long roiMask, boolean includePointsAndLines, boolean onlySelectedPoints, boolean onlySelectedLines)
roiMask
- the mask of ROIs to includeincludePointsAndLines
- true to also analyze points and linesonlySelectedPoints
- true to only analyze selected pointsonlySelectedLines
- true to only analyze selected linesvoid runCloseROI(long roiMask, int kernelSize)
roiMask
- the mask of ROIs to includekernelSize
- the kernel sizevoid runCloseROISlice(int sliceDirection, int sliceNumber, long roiMask, int kernelSize)
sliceDirection
- the slice directionsliceNumber
- the slice numberroiMask
- the mask of the ROIs to includekernelSize
- the kernel sizeList<Cluster> runClusterAnalysis(ImageVolume overlay, double threshold)
overlay
- the ImageVolume to analyzethreshold
- the thresholdList<Cluster> runComponentAnalysisROI(int roiColorIndex)
roiColorIndex
- the ROI color indexvoid runComponentSplitROI(int roiColorIndex, int voxelCountThreshold)
roiColorIndex
- the ROI color indexvoxelCountThreshold
- the minimum number of voxels a component must contain in order to include in the splitvoid runConvexHull(ROI roi)
roi
- the ROIvoid runConvexHullROI(long roiMask, int roiOutputColorIndex)
roiMask
- the ROI mask to includeroiOutputColorIndex
- the output ROI color indexvoid runConvexHullROISlice(int sliceDirection, int sliceNumber, long roiMask, int roiOutputColorIndex)
sliceDirection
- the slice directionsliceNumber
- the slice numberroiMask
- the ROI mask to includeroiOutputColorIndex
- the output ROI color indexdouble[] runCrosssectionMM(Line line, double step)
line
- the Linestep
- the interpolation intervaldouble[] runCrosssectionVoxels(Line line)
line
- the Linevoid runDilateROI(long roiMask, int kernelSize)
roiMask
- the ROI mask to includekernelSize
- the kernel sizevoid runDilateROISlice(int sliceDirection, int sliceNumber, long roiMask, int kernelSize)
sliceDirection
- the slice directionsliceNumber
- the slice numberroiMask
- the ROI mask to includekernelSize
- the kernel sizevoid runErodeROI(long roiMask, int kernelSize)
roiMask
- the ROI mask to includekernelSize
- the kernel sizevoid runErodeROISlice(int sliceDirection, int sliceNumber, long roiMask, int kernelSize)
sliceDirection
- the slice directionsliceNumber
- the slice numberroiMask
- the ROI mask to includekernelSize
- the kernel sizevoid runFilter(String name)
name
- the name of the filtervoid runGenerateClusterROI(ImageVolume overlay, int voxelCountThreshold)
overlay
- the overlay ImageVolumevoxelCountThreshold
- the minimum number of voxels a component must contain in order to include in the splitvoid runGenerateHistogramROI(Histogram hist)
hist
- the Histogramvoid runGenerateHistogramROISlice(int sliceDirection, int sliceNumber, Histogram hist)
sliceDirection
- the slice directionsliceNumber
- the slice numberhist
- the Histogramvoid runGenerateHistogramWithinROI(Histogram hist, long roiMask)
hist
- the HistogramroiMask
- the ROI mask to includevoid runGenerateHistogramWithinROISlice(int sliceDirection, int sliceNumber, Histogram hist, long roiMask)
sliceDirection
- the slice directionsliceNumber
- the slice numberhist
- the HistogramroiMask
- the ROI mask to includevoid runGenerateLogicalROI(List<ImageVolume> overlays)
overlays
- a list of ImageVolumesHistogram runHistogram(int numBins, double min, double max, boolean excludeZero, boolean isIntegerMode)
numBins
- the number of histogram binsmin
- the histogram bin range minmax
- the histogram bin range maxexcludeZero
- true to exclude voxel value zero counts, false to include zerosisIntegerMode
- true to create equal size bins when working with integer data (may automatically change numBins)Histogram runHistogramROI(int numBins, double min, double max, long roiMask, boolean excludeZero, boolean integerMode)
numBins
- the number of histogram binsmin
- the histogram bin range minmax
- the histogram bin range maxroiMask
- the ROI mask to includeexcludeZero
- true to exclude voxel value zero counts, false to include zerosintegerMode
- true to create equal size bins when working with integer data (may automatically change numBins)Analysis runLogicalAnalysis(List<ImageVolume> overlays)
overlays
- a list of ImageVolumesvoid runOpenROI(long roiMask, int kernelSize)
roiMask
- the ROI mask to includekernelSize
- the kernel sizevoid runOpenROISlice(int sliceDirection, int sliceNumber, long roiMask, int kernelSize)
sliceDirection
- the slice directionsliceNumber
- the slice numberroiMask
- the ROI mask to includekernelSize
- the kernel sizeVolumeManager runOperation(String expression, int selectionArea, boolean outputNewImage, boolean allSeriesPoints, boolean roiSlicesOnly)
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 imageallSeriesPoints
- true to process all series points, alse to process only the current series pointroiSlicesOnly
- true to process only those slices that contain ROI data, false to process all slicesvoid runOperationROILogic(String expression, int roiOutputColorIndex)
expression
- the expressionroiOutputColorIndex
- the output ROI color indexVolumeManager runOperationSeriesStatistic(int startingSeriesIndex, int endingSeriesIndex, int seriesGroupSize, int statisticType)
startingSeriesIndex
- the starting series indexendingSeriesIndex
- the ending series indexseriesGroupSize
- 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)Object runPlugin(String pluginName, String[] args)
pluginName
- the plugin nameargs
- the argumentsvoid runPropagateROISlice(int sliceDirection, int sliceNumber, int startSlice, int endSlice, long roiMask, int roiOutputColorIndex)
sliceDirection
- the slice direction of the slice to propagatesliceNumber
- the slice number of the slice propagatestartSlice
- the starting slice of the propagate rangeendSlice
- the ending slice of the propagate rangeroiMask
- the ROI mask to includeroiOutputColorIndex
- the output ROI color indexboolean runRangeToROI(double min, double max, boolean percentMax, boolean excludeZero, boolean makeSeriesROI, boolean seriesUsesDynamicThreshold)
min
- the range minimummax
- the range maximumpercentMax
- true if the min/max values represent percent of image maximum, false if they refer to actual range valuesexcludeZero
- true to exclude zero from calculationmakeSeriesROI
- true to make a series ROIseriesUsesDynamicThreshold
- true only if percentMax is also true, in which case percent max is determined for each series point individuallyboolean runRangeToROISlice(double min, double max, int sliceDirection, int sliceNumber, boolean percentMax, boolean excludeZero, boolean makeSeriesROI, boolean seriesUsesDynamicThreshold)
min
- the range minimummax
- the range maximumsliceDirection
- the slice directionsliceNumber
- the slice numberpercentMax
- true if the min/max values represent percent of image maximum, false if they refer to actual range valuesexcludeZero
- true to exclude zero from calculationmakeSeriesROI
- true to make a series ROIseriesUsesDynamicThreshold
- true only if percentMax is also true, in which case percent max is determined for each series point individuallyvoid runRankFilter(int kernelSize, int rankType, int filterType)
kernelSize
- the kernel sizerankType
- the rank type (see contants)filterType
- the filter type (see constants)void runReflectROI(int sliceDirection, int axis, boolean vertical, boolean includePointsAndLines, boolean onlySelectedLines, boolean onlySelectedPoints)
sliceDirection
- the slice directionaxis
- the axis of reflection (slice number)vertical
- true to reflect vertically, false horizontallyincludePointsAndLines
- true to reflect points and lines, false otherwiseonlySelectedLines
- true to reflect only selected lines, false otherwiseonlySelectedPoints
- true to reflect only selected points, false otherwisevoid runReflectROISlice(int sliceDirection, int sliceNumber, int axis, boolean vertical, boolean includePointsAndLines, boolean onlySelectedLines, boolean onlySelectedPoints)
sliceDirection
- sliceNumber
- axis
- vertical
- includePointsAndLines
- onlySelectedLines
- onlySelectedPoints
- void runScript(String scriptName)
scriptName
- the script nameList<Analysis> runSeriesROI(ROI roi)
roi
- the ROIAnalysis runSeriesStats()
List<Analysis> runSeriesStatsROI(long roiMask, boolean includePointsAndLines, boolean onlySelectedPoints, boolean onlySelectedLines)
roiMask
- the ROI mask to includeincludePointsAndLines
- true to also run stats on lines and points, false otherwiseonlySelectedPoints
- true to run stats on only selected points, false otherwiseonlySelectedLines
- true to run stats on only selected lines, false otherwisevoid runShrinkWrapROI(double threshold, long roiMask, int roiOutputColorIndex, boolean percentMax, boolean seriesUsesDynamicThreshold)
threshold
- the thresholdroiMask
- the roiMask to includeroiOutputColorIndex
- the output ROI color indexpercentMax
- true if the threshold represents percent of image maximum, false if they refer to actual range valuesseriesUsesDynamicThreshold
- true only if percentMax is also true, in which case percent max is determined for each series point individuallyvoid runShrinkWrapROI(long roiMask, int roiOutputColorIndex)
roiMask
- the roiMask to includeroiOutputColorIndex
- the output ROI color indexvoid runShrinkWrapROIAllSlices(double threshold, int sliceDirection, long roiMask, int roiOutputColorIndex, boolean percentMax, boolean seriesUsesDynamicThreshold)
threshold
- the thresholdsliceDirection
- the slice directionroiMask
- the ROI mask to includeroiOutputColorIndex
- the output ROI color indexpercentMax
- true if the threshold represents percent of image maximum, false if they refer to actual range valuesseriesUsesDynamicThreshold
- true only if percentMax is also true, in which case percent max is determined for each series point individuallyvoid runShrinkWrapROIAllSlices(int sliceDirection, long roiMask, int roiOutputColorIndex)
sliceDirection
- the slice directionroiMask
- the ROI mask to includeroiOutputColorIndex
- the output ROI color indexvoid runShrinkWrapROISlice(double threshold, int sliceDirection, int sliceNumber, long roiMask, int roiOutputColorIndex, boolean percentMax, boolean seriesUsesDynamicThreshold)
threshold
- the thresholdsliceDirection
- the slice directionsliceNumber
- the slice numberroiMask
- the ROI mask to includeroiOutputColorIndex
- the output ROI color indexpercentMax
- true if the threshold represents percent of image maximum, false if they refer to actual range valuesseriesUsesDynamicThreshold
- true only if percentMax is also true, in which case percent max is determined for each series point individuallyvoid runShrinkWrapROISlice(int sliceDirection, int sliceNumber, long roiMask, int roiOutputColorIndex)
sliceDirection
- the slice directionsliceNumber
- the slice numberroiMask
- the ROI mask to includeroiOutputColorIndex
- the output ROI color indexAnalysis runSliceStats(int sliceDirection, int sliceNumber)
sliceDirection
- the slice directionsliceNumber
- the slice numberList<Analysis> runSliceStatsROI(int sliceDirection, int sliceNumber, long roiMask, boolean includePointsAndLines, boolean onlySelectedPoints, boolean onlySelectedLines)
sliceDirection
- the slice directionsliceNumber
- the slice numberroiMask
- the ROI mask to includeincludePointsAndLines
- true to include points and lines, false otherwiseonlySelectedPoints
- true to include only selected pointsonlySelectedLines
- true to include only selected linesvoid runSmooth(ROI roi)
roi
- the ROI to smoothAnalysis runStat(ROI roi)
roi
- the ROIvoid runThresholdToConvexHullROI(double threshold, boolean percentMax, boolean excludeZero, boolean makeSeriesROI, boolean seriesUsesDynamicThreshold)
threshold
- the thresholdpercentMax
- true if the threshold represents percent of image maximum, false if they refer to actual range valuesexcludeZero
- true to exclude zero from calculationmakeSeriesROI
- true to make a series ROIseriesUsesDynamicThreshold
- true only if percentMax is also true, in which case percent max is determined for each series point individuallyvoid runThresholdToConvexHullROISlice(double threshold, int sliceDirection, int sliceNumber, boolean percentMax, boolean excludeZero, boolean makeSeriesROI, boolean seriesUsesDynamicThreshold)
threshold
- the thresholdsliceDirection
- the slice directionsliceNumber
- the slice numberpercentMax
- true if the threshold represents percent of image maximum, false if they refer to actual range valuesexcludeZero
- true to exclude zero from calculationmakeSeriesROI
- true to make a series ROIseriesUsesDynamicThreshold
- true only if percentMax is also true, in which case percent max is determined for each series point individuallyboolean runThresholdToROI(double threshold, boolean percentMax, boolean excludeZero, boolean makeSeriesROI, boolean seriesUsesDynamicThreshold)
threshold
- the thresholdpercentMax
- true if the threshold represents percent of image maximum, false if they refer to actual range valuesexcludeZero
- true to exclude zero from calculationmakeSeriesROI
- true to make a series ROIseriesUsesDynamicThreshold
- true only if percentMax is also true, in which case percent max is determined for each series point individuallyboolean runThresholdToROISlice(double threshold, int sliceDirection, int sliceNumber, boolean percentMax, boolean excludeZero, boolean makeSeriesROI, boolean seriesUsesDynamicThreshold)
threshold
- the thresholdsliceDirection
- the slice directionsliceNumber
- the slice numberpercentMax
- true if the threshold represents percent of image maximum, false if they refer to actual range valuesexcludeZero
- true to exclude zero from calculationmakeSeriesROI
- true to make a series ROIseriesUsesDynamicThreshold
- true only if percentMax is also true, in which case percent max is determined for each series point individuallyboolean runThresholdToShrinkWrapROI(double threshold, boolean percentMax, boolean excludeZero, boolean makeSeriesROI, boolean seriesUsesDynamicThreshold)
threshold
- the thresholdpercentMax
- true if the threshold represents percent of image maximum, false if they refer to actual range valuesexcludeZero
- true to exclude zero from calculationmakeSeriesROI
- true to make a series ROIseriesUsesDynamicThreshold
- true only if percentMax is also true, in which case percent max is determined for each series point individuallyboolean runThresholdToShrinkWrapROIAllSlices(double threshold, int sliceDirection, boolean percentMax, boolean excludeZero, boolean makeSeriesROI, boolean seriesUsesDynamicThreshold)
threshold
- the thresholdsliceDirection
- the slice directionpercentMax
- true if the threshold represents percent of image maximum, false if they refer to actual range valuesexcludeZero
- true to exclude zero from calculationmakeSeriesROI
- true to make a series ROIseriesUsesDynamicThreshold
- true only if percentMax is also true, in which case percent max is determined for each series point individuallyboolean runThresholdToShrinkWrapROISlice(double threshold, int sliceDirection, int sliceNumber, boolean percentMax, boolean excludeZero, boolean makeSeriesROI, boolean seriesUsesDynamicThreshold)
threshold
- the thresholdsliceDirection
- the slice directionsliceNumber
- the slice numberpercentMax
- true if the threshold represents percent of image maximum, false if they refer to actual range valuesexcludeZero
- true to exclude zero from calculationmakeSeriesROI
- true to make a series ROIseriesUsesDynamicThreshold
- true only if percentMax is also true, in which case percent max is determined for each series point individuallyAnalysis runVolumeStats()
List<Analysis> runVolumeStatsROI(long roiMask, boolean includePointsAndLines, boolean onlySelectedPoints, boolean onlySelectedLines)
roiMask
- the ROI mask to includeincludePointsAndLines
- true to include points and lines, false otherwiseonlySelectedPoints
- true to include selected pointsonlySelectedLines
- true to include selected linesvoid save()
void saveWithName(String saveLocation)
saveLocation
- the location of the file to save tovoid 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)
saveLocation
- the location of the file to save toheaderFormat
- 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 ordercompress
- true to compress (not applicable to all header types)xMin
- x minimum boundsxMax
- x maximum boundsyMin
- y minimum boundsyMax
- y maximum boundszMin
- z minimum boundszMax
- z maximum boundstMin
- t minimum boundstMax
- t maximum boundsxSize
- x voxel sizeySize
- y voxel sizezSize
- z voxel sizetSize
- 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 otherwiseapplyOverlay
- true to save the currently selected overlay ImageVoluem, false to save the base volumeoverlayThreshold
- true to apply a threshold to the saved overlayoverlayMix
- 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 scalesfitPrecision
- true to fit the image data to the bounds of the datatypemaintainZero
- true to use data scale slope, but not data scale intercept (i.e., intercept = 0)void saveOverlays()
void saveROI(String saveLocation)
saveLocation
- the file location to savevoid saveSingleROI(String saveLocation, int index)
saveLocation
- the file location to saveindex
- the roi color indexvoid select(ROI roi, boolean select)
roi
- the ROIselect
- true to select, false to unselectvoid selectAll()
void selectMenuOption(String name)
name
- the menu option name@Deprecated void setCoordinateSpace(int index)
index
- the coordinate space indexvoid setOrientationOption(ImageVolume volume, int index)
volume
- the image volumeindex
- the orientation option indexvoid setCurrentPosition(Coordinate coordinate)
coordinate
- the new positionvoid setCurrentSeriesPoint(int seriesIndex)
seriesIndex
- the new series pointvoid setCurrentVolumeIndex(int index)
index
- the volume indexvoid setDisplayRangeToImageRange(ImageVolume volume, boolean entireSeries)
volume
- the ImageVolumeentireSeries
- true to use the min/max of the entire series, false to use the current series pointvoid setLabel(ROI roi, String label)
roi
- the ROIlabel
- the labelvoid setMenuOption(String name, boolean value)
name
- the menu optionvalue
- the menu option valuevoid setNotes(String text)
text
- the note textvoid setOrigin(Coordinate coordinate)
coordinate
- the new originvoid setRoiColor(int color)
color
- the ROI color indexvoid setSliceDirection(int sliceDirection)
sliceDirection
- the slice directionboolean setSliceNumber(int sliceNumber)
sliceNumber
- the slice numbervoid setTransformMode(boolean transform)
transform
- true to turn on transform, false to turn off transformvoid setVolumeDisplayAlpha(ImageVolume volume, double alpha)
volume
- the ImageVolumealpha
- the alpha value (0 to 1)void setVolumeDisplayColorTable(ImageVolume volume, String colorTable)
volume
- the ImageVolumecolorTable
- the color table namevoid setVolumeDisplayHidden(ImageVolume volume, boolean hidden)
volume
- the ImageVolumehidden
- true to hide the volume, false to display itvoid setVolumeDisplayIndex(ImageVolume volume, int index)
volume
- the ImageVolumeindex
- the new indexvoid setVolumeDisplayRange(ImageVolume volume, double screenMin, double screenMax)
volume
- the ImageVolumescreenMin
- the new display range minimumscreenMax
- the new display range maximumvoid setVoxelValue(Coordinate coordinate, int seriesIndex, double value)
coordinate
- the coordinateseriesIndex
- the series pointvalue
- the new valuevoid showErrorMessage(String message, String title)
message
- the message texttitle
- the message titlevoid showWarningMessage(String message, String title)
message
- the message texttitle
- the message titleString toString()
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)
volume
- the ImageVolumem00
- m00m01
- m01m02
- m02m03
- m03m10
- m10m11
- m11m12
- m12m13
- m13m20
- m20m21
- m21m22
- m22m23
- m23m30
- m30m31
- m31m32
- m32m33
- m33void updateViewer()