Field Detail

• statusService

  protected StatusService statusService

• legacyService

  protected LegacyService legacyService

• datasetIOService

  protected DatasetIOService datasetIOService

• convertService

  protected ConvertService convertService

• opService

  protected OpService opService

• lutService

  protected LUTService lutService

• verbose

  protected static boolean verbose

• MIN_SNAP_CURSOR_WINDOW_XY

  protected static final int MIN_SNAP_CURSOR_WINDOW_XY

  See Also:

  Constant Field Values

• MIN_SNAP_CURSOR_WINDOW_Z

  protected static final int MIN_SNAP_CURSOR_WINDOW_Z

  See Also:

  Constant Field Values

• MAX_SNAP_CURSOR_WINDOW_XY

  protected static final int MAX_SNAP_CURSOR_WINDOW_XY

  See Also:

  Constant Field Values

• MAX_SNAP_CURSOR_WINDOW_Z

  protected static final int MAX_SNAP_CURSOR_WINDOW_Z

  See Also:

  Constant Field Values

• startBallName

  protected static final String startBallName

  See Also:

  Constant Field Values

• targetBallName

  protected static final String targetBallName

  See Also:

  Constant Field Values

• ballRadiusMultiplier

  protected static final int ballRadiusMultiplier

  See Also:

  Constant Field Values

• univ

  protected Image3DUniverse univ

• use3DViewer

  protected boolean use3DViewer

• colorImage

  protected ij.ImagePlus colorImage

• DISPLAY_PATHS_SURFACE

  protected static final int DISPLAY_PATHS_SURFACE

  See Also:

  Constant Field Values

• DISPLAY_PATHS_LINES

  protected static final int DISPLAY_PATHS_LINES

  See Also:

  Constant Field Values

• DISPLAY_PATHS_LINES_AND_DISCS

  protected static final int DISPLAY_PATHS_LINES_AND_DISCS

  See Also:

  Constant Field Values

• cursorSnapWindowXY

  protected volatile int cursorSnapWindowXY

• cursorSnapWindowZ

  protected volatile int cursorSnapWindowZ

• autoCanvasActivation

  protected volatile boolean autoCanvasActivation

• panMode

  protected volatile boolean panMode

• snapCursor

  protected volatile boolean snapCursor

• unsavedPaths

  protected volatile boolean unsavedPaths

• showOnlySelectedPaths

  protected volatile boolean showOnlySelectedPaths

• showOnlyActiveCTposPaths

  protected volatile boolean showOnlyActiveCTposPaths

• activateFinishedPath

  protected volatile boolean activateFinishedPath

• requireShiftToFork

  protected volatile boolean requireShiftToFork

• width

  protected int width

• height

  protected int height

• depth

  protected int depth

• imageType

  protected int imageType

• x_spacing

  protected double x_spacing

• y_spacing

  protected double y_spacing

• z_spacing

  protected double z_spacing

• spacing_units

  protected String spacing_units

• channel

  protected int channel

• frame

  protected int frame

• filterType

  protected SNT.FilterType filterType

• searchImageType

  protected SNT.SearchImageType searchImageType

• isUseSubVolumeStats

  protected volatile boolean isUseSubVolumeStats

• oneMinusErfZFudge

  protected volatile double oneMinusErfZFudge

• doSearchOnSecondaryData

  protected boolean doSearchOnSecondaryData

• secondaryData

  protected RandomAccessibleInterval secondaryData

• secondaryImageFile

  protected File secondaryImageFile

• tubularGeodesicsTracingEnabled

  protected boolean tubularGeodesicsTracingEnabled

• tubularGeodesicsThread

  protected TubularGeodesicsTracer tubularGeodesicsThread

• last_start_point_x

  protected double last_start_point_x

• last_start_point_y

  protected double last_start_point_y

• last_start_point_z

  protected double last_start_point_z

• temporaryPath

  protected Path temporaryPath

• currentPath

  protected Path currentPath

• ui

  protected SNTUI ui

• tracingHalted

  protected volatile boolean tracingHalted

• DEFAULT_DESELECTED_COLOR

  protected static final Color DEFAULT_DESELECTED_COLOR

• DEFAULT_SELECTED_COLOR3F

  protected static final Color3f DEFAULT_SELECTED_COLOR3F

• DEFAULT_DESELECTED_COLOR3F

  protected static final Color3f DEFAULT_DESELECTED_COLOR3F

• selectedColor3f

  protected Color3f selectedColor3f

• deselectedColor3f

  protected Color3f deselectedColor3f

• selectedColor

  protected Color selectedColor

• deselectedColor

  protected Color deselectedColor

• displayCustomPathColors

  protected boolean displayCustomPathColors

• listeners

  protected List<SNTListener> listeners

• drawDiametersXY

  protected boolean drawDiametersXY

Constructor Detail

• SNT

  public SNT(Context context,
             ij.ImagePlus sourceImage)
      throws IllegalArgumentException

  Instantiates SNT in 'Tracing Mode'.

  Parameters:

  context - the SciJava application context providing the services required by the class

  sourceImage - the source image

  Throws:

  IllegalArgumentException - If sourceImage is of type 'RGB'

• SNT

  public SNT(Context context,
             PathAndFillManager pathAndFillManager)

  Instantiates SNT in 'Analysis Mode'

  Parameters:

  context - the SciJava application context providing the services required by the class

  pathAndFillManager - The PathAndFillManager instance to be associated with the plugin

Method Detail

• rebuildDisplayCanvases

  public void rebuildDisplayCanvases()
                              throws IllegalArgumentException

  Rebuilds display canvases, i.e., the placeholder canvases used when no valid image data exists (a single-canvas is rebuilt if only the XY view is active).

  Useful when multiple files are imported and imported paths 'fall off' the dimensions of current canvas(es). If there is not enough memory to accommodate enlarged dimensions, the resulting canvas will be a 2D image.

  Throws:

  IllegalArgumentException - if valid image data exists

• updateDisplayCanvases

  public void updateDisplayCanvases()

  Rebuilds display canvas(es) to ensure all paths are contained in the image. Does nothing if placeholder canvas(es) are not being used.

  See Also:

  rebuildDisplayCanvases()

• accessToValidImageData

  public boolean accessToValidImageData()

• isDisplayCanvas

  protected boolean isDisplayCanvas(ij.ImagePlus imp)

• initialize

  public void initialize(ij.ImagePlus imp)

  Overrides:

  initialize in class MultiDThreePanes

• initialize

  public void initialize(boolean singlePane,
                         int channel,
                         int frame)

  Initializes the plugin by assembling all the required tracing views

  Parameters:

  singlePane - if true only the XY view will be generated, if false XY, ZY, XZ views are created

  channel - the channel to be traced. Ignored when no valid image data exists.

  frame - the frame to be traced. Ignored when no valid image data exists.

• reloadImage

  public void reloadImage(int channel,
                          int frame)

• rebuildZYXZpanes

  public void rebuildZYXZpanes()

• startUI

  public void startUI()

• loadTracings

  public void loadTracings(File file)

• isChangesUnsaved

  protected boolean isChangesUnsaved()

• getPathAndFillManager

  public PathAndFillManager getPathAndFillManager()

• getXYCanvas

  protected sc.fiji.snt.InteractiveTracerCanvas getXYCanvas()

• getXZCanvas

  protected sc.fiji.snt.InteractiveTracerCanvas getXZCanvas()

• getZYCanvas

  protected sc.fiji.snt.InteractiveTracerCanvas getZYCanvas()

• getDataset

  public Dataset getDataset()

• getImagePlus

  public ij.ImagePlus getImagePlus()

• getImpDiagonalLength

  protected double getImpDiagonalLength(boolean scaled,
                                        boolean xyOnly)

• createCanvas

  public sc.fiji.snt.InteractiveTracerCanvas createCanvas(ij.ImagePlus imagePlus,
                                                          int plane)

  Overrides:

  createCanvas in class MultiDThreePanes

• cancelSearch

  public void cancelSearch(boolean cancelFillToo)

• threadStatus

  public void threadStatus(SearchInterface source,
                           int status)

  Specified by:

  threadStatus in interface SearchProgressCallback

• changeUIState

  public void changeUIState(int newState)

• getUIState

  protected int getUIState()

• saveFill

  protected void saveFill()

• discardFill

  protected void discardFill()

• stopFilling

  protected void stopFilling()

• startFilling

  protected void startFilling()

• addListener

  public void addListener(SNTListener listener)

• notifyListeners

  public void notifyListeners(SNTEvent event)

• anyListeners

  protected boolean anyListeners()

• finished

  public void finished(SearchInterface source,
                       boolean success)

  Specified by:

  finished in interface SearchProgressCallback

• pointsInSearch

  public void pointsInSearch(SearchInterface source,
                             long inOpen,
                             long inClosed)

  Specified by:

  pointsInSearch in interface SearchProgressCallback

• justDisplayNearSlices

  public void justDisplayNearSlices(boolean value,
                                    int eitherSide)

• uiReadyForModeChange

  protected boolean uiReadyForModeChange()

• getEditingPath

  protected Path getEditingPath()

• getPreviousEditingPath

  protected Path getPreviousEditingPath()

• getEditingNode

  protected int getEditingNode()

• editModeAllowed

  public boolean editModeAllowed()

  Assesses if activation of 'Edit Mode' is possible.

  Returns:

  true, if possible, false otherwise

• editModeAllowed

  protected boolean editModeAllowed(boolean warnUserIfNot)

• setEditingPath

  protected void setEditingPath(Path path)

• detectEditingPath

  protected void detectEditingPath()

• getSingleSelectedPath

  protected Path getSingleSelectedPath()

• enableEditMode

  protected void enableEditMode(boolean enable)

• pause

  protected void pause(boolean pause,
                       boolean hideSideViewsOnPause)

• pauseTracing

  protected void pauseTracing(boolean pause,
                              boolean validateChange)

• isEditModeEnabled

  protected boolean isEditModeEnabled()

• updateCursor

  protected void updateCursor(double new_x,
                              double new_y,
                              double new_z)

• loadLabelsFile

  public void loadLabelsFile(String path)

• loadTracesFile

  protected void loadTracesFile(File file)

  Assumes UI is available

• loadSWCFile

  protected void loadSWCFile(File file)

  Assumes UI is available

• mouseMovedTo

  public void mouseMovedTo(double x_in_pane,
                           double y_in_pane,
                           int in_plane,
                           boolean sync_panes_modifier_down,
                           boolean join_modifier_down)

• setTemporaryPath

  public void setTemporaryPath(Path path)

• setCurrentPath

  public void setCurrentPath(Path path)

• getCurrentPath

  public Path getCurrentPath()

• setPathUnfinished

  protected void setPathUnfinished(boolean unfinished)

• makePathVolume

  public ij.ImagePlus makePathVolume(Collection<Path> paths)

• makePathVolume

  public ij.ImagePlus makePathVolume()

• confirmTemporary

  public void confirmTemporary(boolean updateTracingViewers)

• cancelTemporary

  public void cancelTemporary()

• cancelPath

  public void cancelPath()

  Cancels the temporary path.

• startHessian

  @Deprecated
  public void startHessian(String image,
                                       double sigma,
                                       double max,
                                       boolean wait)

  Deprecated. 
  Constructs and enables a lazy instance of a Tubeness filter. The image is filtered locally during path searches. Filtered data is stored in a disk cache when memory runs full. This method is slated for redesign.

  Parameters:

  image - the image to filter, either "primary" or "secondary".

  sigma - the scale parameter for the Tubeness filter, in physical units.

  max - the maximum pixel intensity in the Tubeness image beyond which the cost function of the A* search is minimized.

  wait - this parameter does nothing.

• startHessian

  public <T extends RealType<T>> void startHessian(String image,
                                                   String filter,
                                                   double[] scales,
                                                   String strategy,
                                                   int nThreads)

  Constructs and enables an instance of a hessian eigenvalue filter. If the strategy is "preprocess", the entire filtered image, including intensity statistics, are pre-computed and stored in memory. If the strategy is "lazy", the image is filtered and measured locally during path searches, and filtered data is stored in a disk cache when memory runs full. If you are tracing over a large image or if you are in a memory-limited environment, you should choose "lazy".

  Type Parameters:

  T -

  Parameters:

  image - the image to filter, either "primary" or "secondary".

  filter - the hessian filter type, either "tubeness" or "frangi"

  scales - the scale parameters for the Hessian filter, in physical units. Computation time increases linearly with the number of scales.

  strategy - either "lazy" or "preprocess"

  nThreads - number of threads to use in the computation

• startHessian

  public <T extends RealType<T>> void startHessian(String image,
                                                   String filter,
                                                   double[] scales,
                                                   double min,
                                                   double max,
                                                   String strategy,
                                                   int nThreads)

  Constructs and enables an instance of a hessian eigenvalue filter. If the strategy is "preprocess", the entire filtered image is pre-computed and stored in memory. If the strategy is "lazy", the image is filtered locally during path searches, and filtered data is stored in a disk cache when memory runs full. If you are tracing over a large image or if you are in a memory-limited environment, you should choose "lazy".

  Type Parameters:

  T -

  Parameters:

  image - the image to filter, either "primary" or "secondary".

  filter - the hessian filter type, either "tubeness" or "frangi"

  scales - the scale parameters for the Hessian filter, in physical units. Computation time increases linearly with the number of scales.

  min - the minimum pixel intensity in the filtered image beyond which the cost function of the A* search is maximized.

  max - the maximum pixel intensity in the filtered image beyond which the cost function of the A* search is minimized.

  strategy - either "lazy" or "preprocess"

  nThreads - number of threads to use in the computation

• autoTrace

  public Path autoTrace(SNTPoint start,
                        SNTPoint end,
                        PointInImage forkPoint)

  Automatically traces a path from a point A to a point B. See autoTrace(List, PointInImage) for details.

  Parameters:

  start - the PointInImage the starting point of the path

  end - the PointInImage the terminal point of the path

  forkPoint - the PointInImage fork point of the parent Path from which the searched path should branch off, or null if the the path should not have any parent.

  Returns:

  the path a reference to the computed path.

  See Also:

  autoTrace(List, PointInImage)

• autoTrace

  public Path autoTrace(SNTPoint start,
                        SNTPoint end,
                        PointInImage forkPoint,
                        boolean headless)

• autoTrace

  public Path autoTrace(List<SNTPoint> pointList,
                        PointInImage forkPoint)

  Automatically traces a path from a list of points and adds it to the active PathAndFillManager instance. Note that this method still requires SNT's UI. For headless auto-tracing have a look at TracerThread.

  SNT's UI will remain blocked in "search mode" until the Path computation completes. Tracing occurs through the active SearchInterface selected in the UI, i.e., TracerThread (the default A* search), TubularGeodesicsTracer, etc.

  All input PointInImage must be specified in real world coordinates.

  Parameters:

  pointList - the list of PointInImage containing the nodes to be used as target goals during the search. If the search cannot converge into a target point, such point is omitted from path, if Successful, target point will be included in the final path. the final path. The first point in the list is the start of the path, the last its terminus. Null objects not allowed.

  forkPoint - the PointInImage fork point of the parent Path from which the searched path should branch off, or null if the the path should not have any parent.

  Returns:

  the path a reference to the computed path. It is added to the Path Manager list.If a path cannot be fully computed from the specified list of points, a single-point path is generated.

• autoTrace

  public Path autoTrace(List<SNTPoint> pointList,
                        PointInImage forkPoint,
                        boolean headless)

• replaceCurrentPath

  protected void replaceCurrentPath(Path path)

• finishedPath

  protected void finishedPath()

• clickForTrace

  protected void clickForTrace(Point3d p,
                               boolean join)

• clickForTrace

  protected void clickForTrace(double world_x,
                               double world_y,
                               double world_z,
                               boolean join)

• clickForTrace

  protected void clickForTrace(double x_in_pane_precise,
                               double y_in_pane_precise,
                               int plane,
                               boolean join)

• setFillThresholdFrom

  public void setFillThresholdFrom(double world_x,
                                   double world_y,
                                   double world_z)

• setFillThreshold

  public void setFillThreshold(double distance)
                        throws IllegalArgumentException

  Sets the fill threshold distance. Typically, this value is set before a filling operation as a starting value for the FillerThread.

  Parameters:

  distance - the new threshold distance. Set it to -1 to use SNT's default.

  Throws:

  IllegalArgumentException - If distance is not a valid positive value

• setStoreExtraFillNodes

  public void setStoreExtraFillNodes(boolean storeExtraFillNodes)

• setStopFillAtThreshold

  public void setStopFillAtThreshold(boolean stopFillAtThreshold)

• addSphere

  protected void addSphere(String name,
                           double x,
                           double y,
                           double z,
                           Color color,
                           double radius)

• removeSphere

  protected void removeSphere(String name)

• startSholl

  protected void startSholl(PointInImage centerScaled)

• getFilledBinaryImp

  public ij.ImagePlus getFilledBinaryImp()

• getFilledImp

  public <T extends RealType<T>> ij.ImagePlus getFilledImp()

• getFilledDistanceImp

  public ij.ImagePlus getFilledDistanceImp()

• getFilledLabelImp

  public <T extends IntegerType<T>> ij.ImagePlus getFilledLabelImp()

• guessResamplingFactor

  protected int guessResamplingFactor()

• isUIready

  protected boolean isUIready()

• addFillerThread

  public void addFillerThread(FillerThread filler)

• initPathsToFill

  public void initPathsToFill(Set<Path> fromPaths)

• setFillTransparent

  protected void setFillTransparent(boolean transparent)

• getMinimumSeparation

  public double getMinimumSeparation()

• getAverageSeparation

  public double getAverageSeparation()

• getLoadedDataAsImp

  public <T extends RealType<T>> ij.ImagePlus getLoadedDataAsImp()

  Retrieves the pixel data of the main image currently loaded in memory as an ImagePlus object. Returned image is always a single channel image.

  Returns:

  the loaded data corresponding to the C,T position currently being traced, or null if no image data has been loaded into memory.

• getLoadedData

  public <T extends RealType<T>> RandomAccessibleInterval<T> getLoadedData()

• getFilteredImageFile

  protected File getFilteredImageFile()

  Returns the file of the 'secondary image', if any.

  Returns:

  the secondary image file, or null if no file has been set

• isSecondaryDataAvailable

  public boolean isSecondaryDataAvailable()

  Assesses if the 'secondary image' has been loaded into memory. Note that while some tracer Threads will load the image into memory, others may waive the loading to third party libraries

  Returns:

  true, if image has been loaded into memory.

• isSecondaryImageFileLoaded

  public boolean isSecondaryImageFileLoaded()

• inputImageLoaded

  protected boolean inputImageLoaded()

• isTracingOnSecondaryImageAvailable

  protected boolean isTracingOnSecondaryImageAvailable()

• setSecondaryImage

  public void setSecondaryImage(File file)

  Specifies the 'secondary image' to be used during a tracing session.

  Parameters:

  file - The file containing the 'secondary image'

• loadSecondaryImage

  public void loadSecondaryImage(File file)
                          throws IOException,
                                 IllegalArgumentException

  Loads the 'secondary image' specified by setSecondaryImage(File) into memory as 32-bit data.

  Parameters:

  file - The file to be loaded

  Throws:

  IOException - If image could not be loaded

  IllegalArgumentException - if dimensions are unexpected, or image type is not supported

  See Also:

  isSecondaryDataAvailable(), getSecondaryDataAsImp()

• loadSecondaryImage

  public void loadSecondaryImage(ij.ImagePlus imp)
                          throws IllegalArgumentException

  Throws:

  IllegalArgumentException

• loadSecondaryImage

  public <T extends RealType<T>> void loadSecondaryImage(RandomAccessibleInterval<T> img,
                                                         boolean computeStatistics)

• setSecondaryImageMinMax

  public void setSecondaryImageMinMax(double min,
                                      double max)

• getSecondaryImageMinMax

  public double[] getSecondaryImageMinMax()

• loadSecondaryImage

  protected void loadSecondaryImage(ij.ImagePlus imp,
                                    boolean changeUIState)

• loadSecondaryImage

  protected <T extends RealType<T>> void loadSecondaryImage(RandomAccessibleInterval<T> img,
                                                            boolean changeUIState,
                                                            boolean computeStatistics)

• enableSecondaryLayerTracing

  public void enableSecondaryLayerTracing(boolean enable)

• flushSecondaryData

  public void flushSecondaryData()

• getSecondaryDataAsImp

  public <T extends NumericType<T>> ij.ImagePlus getSecondaryDataAsImp()

  Retrieves the 'secondary image' data currently loaded in memory as an ImagePlus object. Returned image is always of 32-bit type.

  Returns:

  the loaded data or null if no image has been loaded.

  See Also:

  isSecondaryDataAvailable(), loadSecondaryImage(ImagePlus), loadSecondaryImage(File)

• getSecondaryData

  public <T extends RealType<T>> RandomAccessibleInterval<T> getSecondaryData()

• getPrefs

  public SNTPrefs getPrefs()

• proportionDone

  public void proportionDone(double proportion)

  Specified by:

  proportionDone in interface HessianGenerationCallback

• showCorrespondencesTo

  @Deprecated
  public void showCorrespondencesTo(File tracesFile,
                                                Color c,
                                                double maxDistance)

  Deprecated. 

• setShowOnlySelectedPaths

  protected void setShowOnlySelectedPaths(boolean showOnlySelectedPaths,
                                          boolean updateGUI)

• setShowOnlyActiveCTposPaths

  protected void setShowOnlyActiveCTposPaths(boolean showOnlyActiveCTposPaths,
                                             boolean updateGUI)

• setShowOnlySelectedPaths

  public void setShowOnlySelectedPaths(boolean showOnlySelectedPaths)

• getImagePlus

  public ij.ImagePlus getImagePlus(int pane)

  Gets the Image associated with a view pane.

  Parameters:

  pane - the flag specifying the view either MultiDThreePanes.XY_PLANE, MultiDThreePanes.XZ_PLANE or MultiDThreePanes.ZY_PLANE.

  Returns:

  the image associate with the specified view, or null if the view is not available

• getMainImagePlusWithoutChecks

  protected ij.ImagePlus getMainImagePlusWithoutChecks()

• error

  protected void error(String msg)

• showMessage

  protected void showMessage(String msg,
                             String title)

• getActiveWindow

  protected Component getActiveWindow()

• isOnlySelectedPathsVisible

  public boolean isOnlySelectedPathsVisible()

• updateTracingViewers

  protected void updateTracingViewers(boolean includeLegacy3Dviewer)

• updateNonTracingViewers

  protected void updateNonTracingViewers()

• updateAllViewers

  public void updateAllViewers()

• get3DUniverse

  @Deprecated
  protected Image3DUniverse get3DUniverse()

  Deprecated. 
  Gets the instance of the legacy 3D viewer universe. Note that the legacy 3D viewer is now deprecated.

  Returns:

  the a reference to the 3DUniverse or null if no universe has been set

• set3DUniverse

  protected void set3DUniverse(Image3DUniverse universe)

• updateImageContent

  @Deprecated
  protected void updateImageContent(int resamplingFactor)

  Deprecated. 

• setSelectedColor

  protected void setSelectedColor(Color newColor)

• setDeselectedColor

  protected void setDeselectedColor(Color newColor)

• setColorImage

  @Deprecated
  protected void setColorImage(ij.ImagePlus newColorImage)

  Deprecated. 

• setPaths3DDisplay

  @Deprecated
  protected void setPaths3DDisplay(int paths3DDisplay)

  Deprecated. 

• getPaths3DDisplay

  @Deprecated
  protected int getPaths3DDisplay()

  Deprecated. 

• selectPath

  public void selectPath(Path p,
                         boolean addToExistingSelection)

• getSelectedPaths

  public Collection<Path> getSelectedPaths()

• setPathList

  public void setPathList(List<Path> pathList,
                          Path justAdded,
                          boolean expandAll)

• setFillList

  public void setFillList(List<Fill> fillList)

• setSelectedPaths

  public void setSelectedPaths(Collection<Path> selectedPathsSet,
                               Object source)

• findSnappingPointInXView

  protected void findSnappingPointInXView(double x_in_pane,
                                          double y_in_pane,
                                          double[] point)

• clickAtMaxPoint

  protected void clickAtMaxPoint(int x_in_pane,
                                 int y_in_pane,
                                 int plane)

• clickAtMaxPoint

  protected void clickAtMaxPoint(int x_in_pane,
                                 int y_in_pane,
                                 int plane,
                                 boolean join)

• showMIPOverlays

  public void showMIPOverlays(double opacity)

  Overlays a semi-transparent MIP (8-bit scaled) of the data being traced over the tracing canvas(es). Does nothing if image is 2D. Note that with multidimensional images, only the C,T position being traced is projected.

  Parameters:

  opacity - (alpha), in the range 0.0-1.0, where 0.0 is none (fully transparent) and 1.0 is fully opaque. Setting opacity to zero clears previous MIPs.

• showMIPOverlays

  protected void showMIPOverlays(boolean filteredData,
                                 double opacity)

• discreteMsg

  protected void discreteMsg(String msg)

• getConfirmation

  protected boolean getConfirmation(String msg,
                                    String title)

• toggleSnapCursor

  protected void toggleSnapCursor()

• enableSnapCursor

  public void enableSnapCursor(boolean enable)

  Enables SNT's XYZ snap cursor feature. Does nothing if no image data is available

  Parameters:

  enable - whether cursor snapping should be enabled

• enableAutoActivation

  public void enableAutoActivation(boolean enable)

• enableAutoSelectionOfFinishedPath

  public void enableAutoSelectionOfFinishedPath(boolean enable)

• isTracingOnSecondaryImageActive

  protected boolean isTracingOnSecondaryImageActive()

• enableAstar

  public void enableAstar(boolean enable)

  Toggles the A* search algorithm (enabled by default)

  Parameters:

  enable - true to enable A* search, false otherwise

• isAstarEnabled

  public boolean isAstarEnabled()

  Checks if A* search is enabled

  Returns:

  true, if A* search is enabled, otherwise false

• is2D

  public boolean is2D()

  Returns:

  true if the image currently loaded does not have a depth (Z) dimension

• setDrawDiametersXY

  public void setDrawDiametersXY(boolean draw)

• getDrawDiametersXY

  public boolean getDrawDiametersXY()

• closeAndResetAllPanes

  public void closeAndResetAllPanes()

  Overrides:

  closeAndResetAllPanes in class MultiDThreePanes

• getContext

  public Context getContext()

• getUI

  public SNTUI getUI()

  Gets the main UI.

  Returns:

  the main dialog of SNT's UI

• showStatus

  public void showStatus(int progress,
                         int maximum,
                         String status)

  Specified by:

  showStatus in interface PaneOwner

  Overrides:

  showStatus in class MultiDThreePanes

• getOneMinusErfZFudge

  protected double getOneMinusErfZFudge()

• getStats

  public ij.process.ImageStatistics getStats()

• getStatsSecondary

  public ij.process.ImageStatistics getStatsSecondary()

• setUseSubVolumeStats

  public void setUseSubVolumeStats(boolean useSubVolumeStatistics)

• getUseSubVolumeStats

  public boolean getUseSubVolumeStats()

• getSearchType

  public SNT.SearchType getSearchType()

• setSearchType

  public void setSearchType(SNT.SearchType searchType)

• getCostType

  public SNT.CostType getCostType()

• setCostType

  public void setCostType(SNT.CostType costType)

• getHeuristicType

  public SNT.HeuristicType getHeuristicType()

• setHeuristicType

  public void setHeuristicType(SNT.HeuristicType heuristicType)

• getSearchImageType

  public SNT.SearchImageType getSearchImageType()

• setSearchImageType

  public void setSearchImageType(SNT.SearchImageType searchImageType)

• getFilterType

  public SNT.FilterType getFilterType()

• setFilterType

  public void setFilterType(SNT.FilterType filterType)

• getWidth

  public int getWidth()

• getHeight

  public int getHeight()

• getDepth

  public int getDepth()

• getPixelWidth

  public double getPixelWidth()

• getPixelHeight

  public double getPixelHeight()

• getPixelDepth

  public double getPixelDepth()

• getSpacingUnits

  public String getSpacingUnits()

• getChannel

  public int getChannel()

• getFrame

  public int getFrame()