Setters Methods#

Methods that modify values or properties of objects.

Total methods in this category: 268

Annotation3D #

setBoundingBoxColor(arg0)#

Determines whether the mesh bounding box should be displayed.

Signature: setBoundingBoxColor(ColorRGB) -> void

Parameters:

arg0 (Any): - the color of the mesh bounding box. If null, no bounding box is displayed

Returns: None

setColor(arg0, arg1)#

Script friendly method to assign a color to the annotation.

Signature: setColor(String, double) -> void

Parameters:

arg0 (str): - the color to render the imported file, either a 1) HTML color codes starting with hash (
arg1 (float): ), a color preset (“red”, “blue”, etc.), or integer triples of the form

Returns: None

setTransparency(arg0)#

Script friendly method to assign a transparency to the annotation.

Signature: setTransparency(double) -> void

Parameters:

arg0 (float): - the color transparency (in percentage)

Returns: None

setWireframeColor(arg0)#

Assigns a wireframe color to the annotation.

Signature: setWireframeColor(String) -> void

Parameters:

arg0 (str): - the wireframe color. Ignored if the annotation has no wireframe.

Returns: None

BiSearch #

addProgressListener(arg0)#

Signature: addProgressListener(SearchProgressCallback) -> void

Parameters:

arg0 (Any)

Returns: None

BiSearchNode #

setFFromGoal(arg0)#

Signature: setFFromGoal(double) -> void

Parameters:

arg0 (float)

Returns: None

setFFromStart(arg0)#

Signature: setFFromStart(double) -> void

Parameters:

arg0 (float)

Returns: None

setFrom(arg0, arg1, arg2, arg3)#

Signature: setFrom(double, double, BiSearchNode, boolean) -> void

Parameters:

arg0 (float)
arg1 (float)
arg2 (BiSearchNode)
arg3 (bool)

Returns: None

setFromGoal(arg0, arg1, arg2)#

Signature: setFromGoal(double, double, BiSearchNode) -> void

Parameters:

arg0 (float)
arg1 (float)
arg2 (BiSearchNode)

Returns: None

setFromStart(arg0, arg1, arg2)#

Signature: setFromStart(double, double, BiSearchNode) -> void

Parameters:

arg0 (float)
arg1 (float)
arg2 (BiSearchNode)

Returns: None

setGFromGoal(arg0)#

Signature: setGFromGoal(double) -> void

Parameters:

arg0 (float)

Returns: None

setGFromStart(arg0)#

Signature: setGFromStart(double) -> void

Parameters:

arg0 (float)

Returns: None

setHeapHandle(arg0, arg1)#

Signature: setHeapHandle(AddressableHeap$Handle, boolean) -> void

Parameters:

arg0 (Any)
arg1 (bool)

Returns: None

setHeapHandleFromGoal(arg0)#

Signature: setHeapHandleFromGoal(AddressableHeap$Handle) -> void

Parameters:

arg0 (Any)

Returns: None

setHeapHandleFromStart(arg0)#

Signature: setHeapHandleFromStart(AddressableHeap$Handle) -> void

Parameters:

arg0 (Any)

Returns: None

setPosition(arg0, arg1, arg2)#

Signature: setPosition(int, int, int) -> void

Parameters:

arg0 (int)
arg1 (int)
arg2 (int)

Returns: None

setPredecessorFromGoal(arg0)#

Signature: setPredecessorFromGoal(BiSearchNode) -> void

Parameters:

arg0 (BiSearchNode)

Returns: None

setPredecessorFromStart(arg0)#

Signature: setPredecessorFromStart(BiSearchNode) -> void

Parameters:

arg0 (BiSearchNode)

Returns: None

setState(arg0, arg1)#

Signature: setState(BiSearchNode$State, boolean) -> void

Parameters:

arg0 (Any)
arg1 (bool)

Returns: None

setStateFromGoal(arg0)#

Signature: setStateFromGoal(BiSearchNode$State) -> void

Parameters:

arg0 (Any)

Returns: None

setStateFromStart(arg0)#

Signature: setStateFromStart(BiSearchNode$State) -> void

Parameters:

arg0 (Any)

Returns: None

setX(arg0)#

Signature: setX(int) -> void

Parameters:

arg0 (int)

Returns: None

setY(arg0)#

Signature: setY(int) -> void

Parameters:

arg0 (int)

Returns: None

setZ(arg0)#

Signature: setZ(int) -> void

Parameters:

arg0 (int)

Returns: None

BoundingBox #

setDimensions(arg0, arg1, arg2)#

Sets the dimensions of this bounding box using uncalibrated (pixel) lengths.

Signature: setDimensions(long, long, long) -> void

Parameters:

arg0 (int): - the uncalibrated width
arg1 (int)
arg2 (int)

Returns: None

setOrigin(arg0)#

Sets the origin for this box, i.e., its (xMin, yMin, zMin) vertex.

Signature: setOrigin(PointInImage) -> void

Parameters:

arg0 (PointInImage): - the new origin

Returns: None

setOriginOpposite(arg0)#

Sets the origin opposite for this box, i.e., its (xMax, yMax, zMax) vertex.

Signature: setOriginOpposite(PointInImage) -> void

Parameters:

arg0 (PointInImage): - the new origin opposite.

Returns: None

setSpacing(arg0, arg1, arg2, arg3)#

Sets the voxel spacing.

Signature: setSpacing(double, double, double, String) -> void

Parameters:

arg0 (float): - the ‘voxel width’ of the bounding box
arg1 (float)
arg2 (float)
arg3 (str)

Returns: None

setUnit(arg0)#

Sets the default length unit for voxel spacing (typically um, for SWC reconstructions)

Signature: setUnit(String) -> void

Parameters:

arg0 (str): - the new unit

Returns: None

ConvexHullAnalyzer #

setContext(arg0)#

Signature: setContext(Context) -> void

Parameters:

arg0 (Any)

Returns: None

setLabel(arg0)#

Sets the optional description for the analysis

Signature: setLabel(String) -> void

Parameters:

arg0 (str): - a string describing the analysis

Returns: None

DefaultSearchNode #

setFrom(arg0)#

Signature: setFrom(DefaultSearchNode) -> void

Parameters:

arg0 (Any)

Returns: None

setHandle(arg0)#

Signature: setHandle(AddressableHeap$Handle) -> void

Parameters:

arg0 (Any)

Returns: None

setPredecessor(arg0)#

Signature: setPredecessor(DefaultSearchNode) -> void

Parameters:

arg0 (Any)

Returns: None

Fill #

setMetric(arg0)#

Sets the cost metric for the filled structure.

Signature: setMetric(SNT$CostType) -> void

Parameters:

arg0 (Any): - the cost type to set

Returns: None

setSourcePaths(arg0)#

Sets the source paths for the filled structure using a set of paths.

Signature: setSourcePaths(Path;) -> void

Parameters:

arg0 (Any): - the set of new source paths

Returns: None

setSpacing(arg0, arg1, arg2, arg3)#

Signature: setSpacing(double, double, double, String) -> void

Parameters:

arg0 (float)
arg1 (float)
arg2 (float)
arg3 (str)

Returns: None

setThreshold(arg0)#

Sets the distance threshold for the filled structure.

Signature: setThreshold(double) -> void

Parameters:

arg0 (float): - the threshold value to set

Returns: None

FillerThread #

addNode(arg0, arg1)#

Signature: addNode(DefaultSearchNode, boolean) -> void

Parameters:

arg0 (Any)
arg1 (bool)

Returns: None

addProgressListener(arg0)#

Signature: addProgressListener(SearchProgressCallback) -> void

Parameters:

arg0 (Any)

Returns: None

setSourcePaths(arg0)#

Signature: setSourcePaths(Collection) -> void

Parameters:

arg0 (List[Any])

Returns: None

setStopAtThreshold(arg0)#

Whether to terminate the fill operation once all nodes less than or equal to the distance threshold have been explored. If false, the search will run until it has explored the entire image. The default is false.

Signature: setStopAtThreshold(boolean) -> void

Parameters:

arg0 (bool): -

Returns: None

setStoreExtraNodes(arg0)#

Whether to store above-threshold nodes in the Fill object. The default is true.

Signature: setStoreExtraNodes(boolean) -> void

Parameters:

arg0 (bool): -

Returns: None

setThreshold(arg0)#

Signature: setThreshold(double) -> void

Parameters:

arg0 (float)

Returns: None

Frangi #

setEnvironment(arg0)#

Signature: setEnvironment(OpEnvironment) -> void

Parameters:

arg0 (Any)

Returns: None

setInput(arg0)#

Signature: setInput(Object) -> void

Parameters:

arg0 (Any)

Returns: None

setOutput(arg0)#

Signature: setOutput(Object) -> void

Parameters:

arg0 (Any)

Returns: None

GroupedTreeStatistics #

addGroup(arg0, arg1, arg2)#

Adds a comparison group to the analysis queue.

Signature: addGroup(Collection, String, String;) -> void

Parameters:

arg0 (List[Any])
arg1 (str)
arg2 (Any)

Returns: None

setMinNBins(arg0)#

Sets the minimum number of bins when assembling histograms.

Signature: setMinNBins(int) -> void

Parameters:

arg0 (int): - the minimum number of bins.

Returns: None

InteractiveTracerCanvas #

addComponentListener(arg0)#

Signature: addComponentListener(ComponentListener) -> void

Parameters:

arg0 (Any)

Returns: None

addFocusListener(arg0)#

Signature: addFocusListener(FocusListener) -> void

Parameters:

arg0 (Any)

Returns: None

addHierarchyBoundsListener(arg0)#

Signature: addHierarchyBoundsListener(HierarchyBoundsListener) -> void

Parameters:

arg0 (Any)

Returns: None

addHierarchyListener(arg0)#

Signature: addHierarchyListener(HierarchyListener) -> void

Parameters:

arg0 (Any)

Returns: None

addInputMethodListener(arg0)#

Signature: addInputMethodListener(InputMethodListener) -> void

Parameters:

arg0 (Any)

Returns: None

addKeyListener(arg0)#

Signature: addKeyListener(KeyListener) -> void

Parameters:

arg0 (Any)

Returns: None

addMouseListener(arg0)#

Signature: addMouseListener(MouseListener) -> void

Parameters:

arg0 (Any)

Returns: None

addMouseMotionListener(arg0)#

Signature: addMouseMotionListener(MouseMotionListener) -> void

Parameters:

arg0 (Any)

Returns: None

addMouseWheelListener(arg0)#

Signature: addMouseWheelListener(MouseWheelListener) -> void

Parameters:

arg0 (Any)

Returns: None

addNotify()#

Signature: addNotify() -> void

Returns: None

addPropertyChangeListener(arg0)#

Signature: addPropertyChangeListener(PropertyChangeListener) -> void

Parameters:

arg0 (Any)

Returns: None

disableEvents(arg0)#

Signature: disableEvents(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

disablePopupMenu(arg0)#

Signature: disablePopupMenu(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

MultiTreeColorMapper #

setMinMax(arg0, arg1)#

Signature: setMinMax(double, double) -> void

Parameters:

arg0 (float)
arg1 (float)

Returns: None

setNaNColor(arg0)#

Signature: setNaNColor(Color) -> void

Parameters:

arg0 (Any)

Returns: None

MultiViewer2D #

setAxesVisible(arg0)#

Signature: setAxesVisible(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

setColorBarLegend(arg0, arg1, arg2)#

Signature: setColorBarLegend(String, double, double) -> void

Parameters:

arg0 (str)
arg1 (float)
arg2 (float)

Returns: None

setGridlinesVisible(arg0)#

Signature: setGridlinesVisible(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

setLayoutColumns(arg0)#

Signature: setLayoutColumns(int) -> void

Parameters:

arg0 (int)

Returns: None

setOutlineVisible(arg0)#

Signature: setOutlineVisible(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

setTitle(arg0)#

Sets the title of this Viewer’s frame.

Signature: setTitle(String) -> void

Parameters:

arg0 (str): - the viewer’s title.

Returns: None

setXrange(arg0, arg1)#

Sets a manual range for the viewers’ X-axis. Calling setXrange(-1, -1) enables auto-range (the default). Must be called before Viewer is fully assembled.

Signature: setXrange(double, double) -> void

Parameters:

arg0 (float): - the lower-limit for the X-axis
arg1 (float)

Returns: None

setYrange(arg0, arg1)#

Sets a manual range for the viewers’ Y-axis. Calling setYrange(-1, -1) enables auto-range (the default). Must be called before Viewer is fully assembled.

Signature: setYrange(double, double) -> void

Parameters:

arg0 (float): - the lower-limit for the Y-axis
arg1 (float)

Returns: None

MultiViewer3D #

addColorBarLegend(arg0)#

Signature: addColorBarLegend(ColorMapper) -> void

Parameters:

arg0 (Any)

Returns: None

setAnimationEnabled(arg0)#

Signature: setAnimationEnabled(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

setGap(arg0)#

Signature: setGap(int) -> void

Parameters:

arg0 (int)

Returns: None

setLabels(arg0)#

Signature: setLabels(List) -> void

Parameters:

arg0 (List[Any])

Returns: None

setLayoutColumns(arg0)#

Signature: setLayoutColumns(int) -> void

Parameters:

arg0 (int)

Returns: None

setTitle(arg0)#

Sets the title of the Viewer’s frame.

Signature: setTitle(String) -> void

Parameters:

arg0 (str): - the viewer’s title.

Returns: None

setViewMode(arg0)#

Signature: setViewMode(Viewer3D$ViewMode) -> void

Parameters:

arg0 (Any)

Returns: None

NeuroMorphoLoader #

enableSourceVersion(arg0)#

Enables or disables the use of source version URLs.

Signature: enableSourceVersion(boolean) -> void

Parameters:

arg0 (bool): - true to enable source version URLs, false otherwise

Returns: None

NodeColorMapper #

setMinMax(arg0, arg1)#

Description copied from class: ColorMapper

Signature: setMinMax(double, double) -> void

Parameters:

arg0 (float): - the mapping lower bound (i.e., the highest measurement value for the LUT scale). It is automatically calculated (the default) when set to Double.NaN
arg1 (float)

Returns: None

setNaNColor(arg0)#

Signature: setNaNColor(Color) -> void

Parameters:

arg0 (Any)

Returns: None

NodeProfiler #

addInput(arg0, arg1)#

Signature: addInput(String, Class) -> MutableModuleItem

Parameters:

arg0 (str)
arg1 (type)

Returns: Any

addOutput(arg0)#

Signature: addOutput(ModuleItem) -> void

Parameters:

arg0 (Any)

Returns: None

removeInput(arg0)#

Signature: removeInput(ModuleItem) -> void

Parameters:

arg0 (Any)

Returns: None

removeOutput(arg0)#

Signature: removeOutput(ModuleItem) -> void

Parameters:

arg0 (Any)

Returns: None

setContext(arg0)#

Signature: setContext(Context) -> void

Parameters:

arg0 (Any)

Returns: None

setInput(arg0, arg1)#

Signature: setInput(String, Object) -> void

Parameters:

arg0 (str)
arg1 (Any)

Returns: None

setInputs(arg0)#

Signature: setInputs(Map) -> void

Parameters:

arg0 (Dict[str, Any])

Returns: None

setNodeStep(arg0)#

Signature: setNodeStep(int) -> void

Parameters:

arg0 (int): - sets the sampling frequency. I.e., if 10, each 10th node is sampled.

Returns: None

setOutput(arg0, arg1)#

Signature: setOutput(String, Object) -> void

Parameters:

arg0 (str)
arg1 (Any)

Returns: None

setOutputs(arg0)#

Signature: setOutputs(Map) -> void

Parameters:

arg0 (Dict[str, Any])

Returns: None

setRadius(arg0)#

Signature: setRadius(int) -> void

Parameters:

arg0 (int): - the radius (in pixels) of sampling shape

Returns: None

setResolved(arg0, arg1)#

Signature: setResolved(String, boolean) -> void

Parameters:

arg0 (str)
arg1 (bool)

Returns: None

setShape(arg0)#

Sets the shape of the iterating cursor.

Signature: setShape(ProfileProcessor$Shape) -> void

Parameters:

arg0 (Any): - A ProfileProcessor.Shape

Returns: None

NodeStatistics #

setLabel(arg0)#

Sets a descriptive label to this statistic analysis to be used in histograms, etc.

Signature: setLabel(String) -> void

Parameters:

arg0 (str): - the descriptive label

Returns: None

Path #

addNode(arg0)#

Appends a node to this Path.

Signature: addNode(PointInImage) -> void

Parameters:

arg0 (PointInImage): - the node to be inserted

Returns: None

addPointDouble(arg0, arg1, arg2)#

Signature: addPointDouble(double, double, double) -> void

Parameters:

arg0 (float)
arg1 (float)
arg2 (float)

Returns: None

PathAndFillManager #

addPath(arg0)#

Signature: addPath(Path) -> void

Parameters:

arg0 (Path)

Returns: None

addPathAndFillListener(arg0)#

Adds a PathAndFillListener. This is used by the interface to have changes in the path manager reported so that they can be reflected in the UI.

Signature: addPathAndFillListener(PathAndFillListener) -> void

Parameters:

arg0 (Any): - the listener

Returns: None

addTree(arg0, arg1)#

Adds a Tree. If an image is currently being traced, it is assumed it is large enough to contain the tree.

Signature: addTree(Tree, String) -> void

Parameters:

arg0 (Tree)
arg1 (str)

Returns: None

addTrees(arg0)#

Adds a collection of Trees.

Signature: addTrees(Collection) -> void

Parameters:

arg0 (List[Any]): - the collection of trees to be added

Returns: None

PathFitter #

setCrossSectionRadius(arg0)#

Sets the max radius (side search) for constraining the fit.

Signature: setCrossSectionRadius(double) -> void

Parameters:

arg0 (float): - the new maximum radius

Returns: None

setImage(arg0)#

Sets the target image

Signature: setImage(RandomAccessibleInterval) -> void

Parameters:

arg0 (Any): - the Image containing the signal to which the fit will be performed

Returns: None

setNodeRadiusFallback(arg0)#

Signature: setNodeRadiusFallback(int) -> void

Parameters:

arg0 (int)

Returns: None

setProgressCallback(arg0, arg1)#

Signature: setProgressCallback(int, MultiTaskProgress) -> void

Parameters:

arg0 (int)
arg1 (Any)

Returns: None

setReplaceNodes(arg0)#

Sets whether fitting should occur “in place”.

Signature: setReplaceNodes(boolean) -> void

Parameters:

arg0 (bool): - If true, the nodes of the input Path will be replaced by those of the fitted result. If false, the fitted result is kept as a separated Path linked to the input as per Path.getFitted(). Note that in the latter case, some topological operations (e.g., forking) performed on the fitted result may not percolate to the non-fitted Path.

Returns: None

setScope(arg0)#

Sets the fitting scope.

Signature: setScope(int) -> void

Parameters:

arg0 (int): - Either RADII, MIDPOINTS, or RADII_AND_MIDPOINTS

Returns: None

setShowAnnotatedView(arg0)#

Sets whether an interactive image of the result should be displayed.

Signature: setShowAnnotatedView(boolean) -> void

Parameters:

arg0 (bool): - If true, an interactive stack (cross-section view) of the fit is displayed. Note that this is probably only useful if SNT’s UI is visible and functional.

Returns: None

PathManagerUI #

addComponentListener(arg0)#

Signature: addComponentListener(ComponentListener) -> void

Parameters:

arg0 (Any)

Returns: None

addContainerListener(arg0)#

Signature: addContainerListener(ContainerListener) -> void

Parameters:

arg0 (Any)

Returns: None

addFocusListener(arg0)#

Signature: addFocusListener(FocusListener) -> void

Parameters:

arg0 (Any)

Returns: None

addHierarchyBoundsListener(arg0)#

Signature: addHierarchyBoundsListener(HierarchyBoundsListener) -> void

Parameters:

arg0 (Any)

Returns: None

addHierarchyListener(arg0)#

Signature: addHierarchyListener(HierarchyListener) -> void

Parameters:

arg0 (Any)

Returns: None

addInputMethodListener(arg0)#

Signature: addInputMethodListener(InputMethodListener) -> void

Parameters:

arg0 (Any)

Returns: None

addKeyListener(arg0)#

Signature: addKeyListener(KeyListener) -> void

Parameters:

arg0 (Any)

Returns: None

addMouseListener(arg0)#

Signature: addMouseListener(MouseListener) -> void

Parameters:

arg0 (Any)

Returns: None

addMouseMotionListener(arg0)#

Signature: addMouseMotionListener(MouseMotionListener) -> void

Parameters:

arg0 (Any)

Returns: None

addMouseWheelListener(arg0)#

Signature: addMouseWheelListener(MouseWheelListener) -> void

Parameters:

arg0 (Any)

Returns: None

addNotify()#

Signature: addNotify() -> void

Returns: None

addPropertyChangeListener(arg0)#

Signature: addPropertyChangeListener(PropertyChangeListener) -> void

Parameters:

arg0 (Any)

Returns: None

addWindowFocusListener(arg0)#

Signature: addWindowFocusListener(WindowFocusListener) -> void

Parameters:

arg0 (Any)

Returns: None

addWindowListener(arg0)#

Signature: addWindowListener(WindowListener) -> void

Parameters:

arg0 (Any)

Returns: None

addWindowStateListener(arg0)#

Signature: addWindowStateListener(WindowStateListener) -> void

Parameters:

arg0 (Any)

Returns: None

clearSelection()#

Clears the current path selection.

Signature: clearSelection() -> void

Returns: None

PathProfiler #

addInput(arg0, arg1)#

Signature: addInput(String, Class) -> MutableModuleItem

Parameters:

arg0 (str)
arg1 (type)

Returns: Any

addOutput(arg0)#

Signature: addOutput(ModuleItem) -> void

Parameters:

arg0 (Any)

Returns: None

removeInput(arg0)#

Signature: removeInput(ModuleItem) -> void

Parameters:

arg0 (Any)

Returns: None

removeOutput(arg0)#

Signature: removeOutput(ModuleItem) -> void

Parameters:

arg0 (Any)

Returns: None

setContext(arg0)#

Signature: setContext(Context) -> void

Parameters:

arg0 (Any)

Returns: None

setInput(arg0, arg1)#

Signature: setInput(String, Object) -> void

Parameters:

arg0 (str): - Either ProfileProcessor.Shape
arg1 (Any)

Returns: None

setInputs(arg0)#

Signature: setInputs(Map) -> void

Parameters:

arg0 (Dict[str, Any])

Returns: None

setMetric(arg0)#

Signature: setMetric(ProfileProcessor$Metric) -> void

Parameters:

arg0 (Any)

Returns: None

setNodeIndicesAsDistances(arg0)#

Sets whether the profile abscissae should be reported in real-word units (the default) or node indices (zero-based). Must be called before calling getValues(Path), getPlot() or getXYPlot().

Signature: setNodeIndicesAsDistances(boolean) -> void

Parameters:

arg0 (bool): - If true, distances will be reported as indices.

Returns: None

setOutput(arg0, arg1)#

Signature: setOutput(String, Object) -> void

Parameters:

arg0 (str)
arg1 (Any)

Returns: None

setOutputs(arg0)#

Signature: setOutputs(Map) -> void

Parameters:

arg0 (Dict[str, Any])

Returns: None

setRadius(arg0)#

Signature: setRadius(int) -> void

Parameters:

arg0 (int)

Returns: None

PathResult #

setErrorMessage(arg0)#

Signature: setErrorMessage(String) -> void

Parameters:

arg0 (str)

Returns: None

setPath(arg0)#

Signature: setPath([F) -> void

Parameters:

arg0 (Any)

Returns: None

setSuccess(arg0)#

Signature: setSuccess(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

PathStraightener #

setWidth(arg0)#

Sets the width of the straightened path image.

Signature: setWidth(int) -> void

Parameters:

arg0 (int): - the width in pixels

Returns: None

PointInImage #

setAnnotation(arg0)#

Description copied from interface: SNTPoint

Signature: setAnnotation(BrainAnnotation) -> void

Parameters:

arg0 (Any): - the annotation to be assigned to this point

Returns: None

setHemisphere(arg0)#

Signature: setHemisphere(char) -> void

Parameters:

arg0 (str)

Returns: None

setPath(arg0)#

Associates a Path with this node

Signature: setPath(Path) -> void

Parameters:

arg0 (Path): - the Path to be associated with this node

Returns: None

SNT #

addFillerThread(arg0)#

Signature: addFillerThread(FillerThread) -> void

Parameters:

arg0 (FillerThread)

Returns: None

addListener(arg0)#

Signature: addListener(SNTListener) -> void

Parameters:

arg0 (Any)

Returns: None

disableEventsAllPanes(arg0)#

Description copied from interface: PaneOwner

Signature: disableEventsAllPanes(boolean) -> void

Parameters:

arg0 (bool): - the current progress value

Returns: None

disableZoomAllPanes(arg0)#

Signature: disableZoomAllPanes(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

enableAstar(arg0)#

Toggles the A* search algorithm (enabled by default)

Signature: enableAstar(boolean) -> void

Parameters:

arg0 (bool): - true to enable A* search, false otherwise

Returns: None

enableAutoActivation(arg0)#

Signature: enableAutoActivation(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

enableAutoSelectionOfFinishedPath(arg0)#

Signature: enableAutoSelectionOfFinishedPath(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

enableSecondaryLayerTracing(arg0)#

Signature: enableSecondaryLayerTracing(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

enableSnapCursor(arg0)#

Enables SNT’s XYZ snap cursor feature. Does nothing if no image data is available or currently loaded image is binary

Signature: enableSnapCursor(boolean) -> void

Parameters:

arg0 (bool): - whether cursor snapping should be enabled

Returns: None

SNTChart #

addAncestorListener(arg0)#

Signature: addAncestorListener(AncestorListener) -> void

Parameters:

arg0 (Any)

Returns: None

addChartMouseListener(arg0)#

Signature: addChartMouseListener(ChartMouseListener) -> void

Parameters:

arg0 (Any)

Returns: None

addColorBarLegend(arg0, arg1, arg2, arg3, arg4)#

Adds a color bar legend (LUT ramp).

Signature: addColorBarLegend(String, ColorTable, double, double, int) -> void

Parameters:

arg0 (str): - the color bar label
arg1 (Any)
arg2 (float)
arg3 (float)
arg4 (int)

Returns: None

addComponentListener(arg0)#

Signature: addComponentListener(ComponentListener) -> void

Parameters:

arg0 (Any)

Returns: None

addContainerListener(arg0)#

Signature: addContainerListener(ContainerListener) -> void

Parameters:

arg0 (Any)

Returns: None

addFocusListener(arg0)#

Signature: addFocusListener(FocusListener) -> void

Parameters:

arg0 (Any)

Returns: None

addHierarchyBoundsListener(arg0)#

Signature: addHierarchyBoundsListener(HierarchyBoundsListener) -> void

Parameters:

arg0 (Any)

Returns: None

addHierarchyListener(arg0)#

Signature: addHierarchyListener(HierarchyListener) -> void

Parameters:

arg0 (Any)

Returns: None

addInputMethodListener(arg0)#

Signature: addInputMethodListener(InputMethodListener) -> void

Parameters:

arg0 (Any)

Returns: None

addKeyListener(arg0)#

Signature: addKeyListener(KeyListener) -> void

Parameters:

arg0 (Any)

Returns: None

addMouseListener(arg0)#

Signature: addMouseListener(MouseListener) -> void

Parameters:

arg0 (Any)

Returns: None

addMouseMotionListener(arg0)#

Signature: addMouseMotionListener(MouseMotionListener) -> void

Parameters:

arg0 (Any)

Returns: None

addMouseWheelListener(arg0)#

Signature: addMouseWheelListener(MouseWheelListener) -> void

Parameters:

arg0 (Any)

Returns: None

addNotify()#

Signature: addNotify() -> void

Returns: None

addOverlay(arg0)#

Signature: addOverlay(Overlay) -> void

Parameters:

arg0 (Any)

Returns: None

addPolygon(arg0, arg1, arg2)#

Signature: addPolygon(Polygon2D, String, String) -> void

Parameters:

arg0 (Any)
arg1 (str)
arg2 (str)

Returns: None

addPropertyChangeListener(arg0, arg1)#

Signature: addPropertyChangeListener(String, PropertyChangeListener) -> void

Parameters:

arg0 (str)
arg1 (Any)

Returns: None

addVetoableChangeListener(arg0)#

Signature: addVetoableChangeListener(VetoableChangeListener) -> void

Parameters:

arg0 (Any)

Returns: None

SNTColor #

setAWTColor(arg0)#

Re-assigns an AWT color.

Signature: setAWTColor(Color) -> void

Parameters:

arg0 (Any): - the new color

Returns: None

setSWCType(arg0)#

Re-assigns a SWC type integer flag

Signature: setSWCType(int) -> void

Parameters:

arg0 (int): - the new SWC type

Returns: None

SNTPoint #

setAnnotation(arg0)#

Assigns a neuropil annotation (e.g., atlas compartment) to this point.

Signature: setAnnotation(BrainAnnotation) -> void

Parameters:

arg0 (Any): - the annotation to be assigned to this point

Returns: None

setHemisphere(arg0)#

Signature: setHemisphere(char) -> void

Parameters:

arg0 (str)

Returns: None

SNTService #

setContext(arg0)#

Signature: setContext(Context) -> void

Parameters:

arg0 (Any)

Returns: None

setInfo(arg0)#

Signature: setInfo(PluginInfo) -> void

Parameters:

arg0 (Any)

Returns: None

setPriority(arg0)#

Signature: setPriority(double) -> void

Parameters:

arg0 (float)

Returns: None

SNTTable #

addAll(arg0)#

Signature: addAll(Collection) -> boolean

Parameters:

arg0 (List[Any])

Returns: bool

addColumn(arg0, arg1)#

Signature: addColumn(String, [D) -> void

Parameters:

arg0 (str)
arg1 (Any)

Returns: None

addFirst(arg0)#

Sets a SciJava context to this table.

Signature: addFirst(Object) -> void

Parameters:

arg0 (Any): - the SciJava application context

Returns: None

addGenericColumn(arg0, arg1)#

Signature: addGenericColumn(String, Collection) -> void

Parameters:

arg0 (str)
arg1 (List[Any])

Returns: None

addLast(arg0)#

Signature: addLast(Object) -> void

Parameters:

arg0 (Any)

Returns: None

SNTUI #

addComponentListener(arg0)#

Signature: addComponentListener(ComponentListener) -> void

Parameters:

arg0 (Any)

Returns: None

addContainerListener(arg0)#

Signature: addContainerListener(ContainerListener) -> void

Parameters:

arg0 (Any)

Returns: None

addFocusListener(arg0)#

Signature: addFocusListener(FocusListener) -> void

Parameters:

arg0 (Any)

Returns: None

addHierarchyBoundsListener(arg0)#

Signature: addHierarchyBoundsListener(HierarchyBoundsListener) -> void

Parameters:

arg0 (Any)

Returns: None

addHierarchyListener(arg0)#

Signature: addHierarchyListener(HierarchyListener) -> void

Parameters:

arg0 (Any)

Returns: None

addInputMethodListener(arg0)#

Signature: addInputMethodListener(InputMethodListener) -> void

Parameters:

arg0 (Any)

Returns: None

addKeyListener(arg0)#

Signature: addKeyListener(KeyListener) -> void

Parameters:

arg0 (Any)

Returns: None

addMouseListener(arg0)#

Signature: addMouseListener(MouseListener) -> void

Parameters:

arg0 (Any)

Returns: None

addMouseMotionListener(arg0)#

Signature: addMouseMotionListener(MouseMotionListener) -> void

Parameters:

arg0 (Any)

Returns: None

addMouseWheelListener(arg0)#

Signature: addMouseWheelListener(MouseWheelListener) -> void

Parameters:

arg0 (Any)

Returns: None

addNotify()#

Signature: addNotify() -> void

Returns: None

addPropertyChangeListener(arg0)#

Signature: addPropertyChangeListener(PropertyChangeListener) -> void

Parameters:

arg0 (Any)

Returns: None

addWindowFocusListener(arg0)#

Signature: addWindowFocusListener(WindowFocusListener) -> void

Parameters:

arg0 (Any)

Returns: None

addWindowListener(arg0)#

Signature: addWindowListener(WindowListener) -> void

Parameters:

arg0 (Any)

Returns: None

addWindowStateListener(arg0)#

Signature: addWindowStateListener(WindowStateListener) -> void

Parameters:

arg0 (Any)

Returns: None

SWCPoint #

setAnnotation(arg0)#

Description copied from interface: SNTPoint

Signature: setAnnotation(BrainAnnotation) -> void

Parameters:

arg0 (Any): - the annotation to be assigned to this point

Returns: None

setColor(arg0)#

Sets the color of this point.

Signature: setColor(Color) -> void

Parameters:

arg0 (Any): - the color to set

Returns: None

setHemisphere(arg0)#

Signature: setHemisphere(char) -> void

Parameters:

arg0 (str)

Returns: None

setPath(arg0)#

Signature: setPath(Path) -> void

Parameters:

arg0 (Path)

Returns: None

setPrevious(arg0)#

Sets the preceding node in the reconstruction

Signature: setPrevious(SWCPoint) -> void

Parameters:

arg0 (SWCPoint): - the previous node preceding this one

Returns: None

setTags(arg0)#

Sets the tags associated with this point.

Signature: setTags(String) -> void

Parameters:

arg0 (str): - the tags string

Returns: None

SciViewSNT #

addTree(arg0)#

Adds a tree to the associated SciView instance. A new SciView instance is automatically instantiated if setSciView(SciView) has not been called.

Signature: addTree(Tree) -> void

Parameters:

arg0 (Tree): - the Tree to be added. The Tree’s label will be used as identifier. It is expected to be unique when rendering multiple Trees, if not (or no label exists) a unique label will be generated.

Returns: None

removeTree(arg0)#

Removes the specified Tree.

Signature: removeTree(Tree) -> boolean

Parameters:

arg0 (Tree): - the tree previously added to SciView using addTree(Tree)

Returns: (bool) true, if tree was successfully removed.

setSciView(arg0)#

Sets the SciView to be used.

Signature: setSciView(SciView) -> void

Parameters:

arg0 (Any): - the SciView instance. Null allowed.

Returns: None

SearchThread #

addNode(arg0, arg1)#

Signature: addNode(DefaultSearchNode, boolean) -> void

Parameters:

arg0 (Any)
arg1 (bool)

Returns: None

addProgressListener(arg0)#

Signature: addProgressListener(SearchProgressCallback) -> void

Parameters:

arg0 (Any)

Returns: None

ShollAnalyzer #

setEnableCurveFitting(arg0)#

Sets whether curve fitting computations should be performed.

Signature: setEnableCurveFitting(boolean) -> void

Parameters:

arg0 (bool): - if

Returns: None

setPolynomialFitRange(arg0, arg1)#

Sets the polynomial fit range for linear Sholl statistics.

Signature: setPolynomialFitRange(int, int) -> void

Parameters:

arg0 (int): - the lowest degree to be considered. Set it to -1 to skip polynomial fit
arg1 (int)

Returns: None

SkeletonConverter #

setConnectComponents(arg0)#: Sets whether to connect nearby skeleton components.

Controls whether disconnected skeleton components should be connected if they are within the maximum connection distance.

Signature: setConnectComponents(boolean) -> void

Parameters:

arg0 (bool): - true to connect components, false otherwise

Returns: None

setLengthThreshold(arg0)#: Sets the minimum component length necessary to avoid pruning. This value is only used if pruneByLength is true.

Specifies the minimum length below which skeleton components will be pruned from the result. Negative values are set to 0.

Signature: setLengthThreshold(double) -> void

Parameters:

arg0 (float): - the minimum length threshold

Returns: None

setMaxConnectDist(arg0)#: Sets the maximum distance for connecting skeleton components.

Specifies the maximum distance within which disconnected skeleton components will be connected. Values ≤ 0 are set to Double.MIN_VALUE.

Signature: setMaxConnectDist(double) -> void

Parameters:

arg0 (float): - the maximum connection distance

Returns: None

setOrigIP(arg0)#: Sets the original ImagePlus to be used during voxel-based loop pruning. See AnalyzeSkeleton documentation

Specifies the original (non-skeletonized) image to be used during skeleton analysis for additional processing options.

Signature: setOrigIP(ImagePlus) -> void

Parameters:

arg0 (Any): - the original ImagePlus

Returns: None

setPruneEnds(arg0)#: Sets whether to prune end branches during skeleton analysis.

Controls whether terminal branches should be pruned during the skeleton analysis process.

Signature: setPruneEnds(boolean) -> void

Parameters:

arg0 (bool): - true to prune end branches, false otherwise

Returns: None

setPruneMode(arg0)#

Sets the loop pruning strategy. See AnalyzeSkeleton documentation

Signature: setPruneMode(int) -> void

Parameters:

arg0 (int): - the loop prune strategy, e.g., SHORTEST_BRANCH, LOWEST_INTENSITY_BRANCH or LOWEST_INTENSITY_VOXEL

Returns: None

setRootRoi(arg0, arg1)#

Sets the Roi enclosing the nodes to be set as root(s) in the final graphs. Must be called before retrieval of any converted data.

Signature: setRootRoi(Roi, int) -> void

Parameters:

arg0 (Any): - The area enclosing the components defining the root(s) of the skeletonized structures. Typically this will correspond to an area ROI delineating the soma. Note that by default ImageJ ROIs do not carry depth information, so if you would like to restrain the delineation to a single plane, be sure to call
arg1 (int): beforehand.

Returns: None

setShortestPath(arg0)#

Sets whether to calculate the longest shortest-path in the skeleton result.

Signature: setShortestPath(boolean) -> void

Parameters:

arg0 (bool): - true to calculate shortest paths, false otherwise

Returns: None

setSilent(arg0)#: Sets whether to run skeleton analysis in silent mode.

Setting this to false will display both the tagged skeleton image and the shortest path image (if the shortest path calculation is enabled).

Signature: setSilent(boolean) -> void

Parameters:

arg0 (bool): - true for silent operation, false for debug output

Returns: None

setVerbose(arg0)#: Sets whether to run skeleton analysis in verbose mode.

Controls whether the skeleton analysis should provide detailed output messages during processing.

Signature: setVerbose(boolean) -> void

Parameters:

arg0 (bool): - true for verbose output, false for normal output

Returns: None

TracerCanvas #

addComponentListener(arg0)#

Signature: addComponentListener(ComponentListener) -> void

Parameters:

arg0 (Any)

Returns: None

addFocusListener(arg0)#

Signature: addFocusListener(FocusListener) -> void

Parameters:

arg0 (Any)

Returns: None

addHierarchyBoundsListener(arg0)#

Signature: addHierarchyBoundsListener(HierarchyBoundsListener) -> void

Parameters:

arg0 (Any)

Returns: None

addHierarchyListener(arg0)#

Signature: addHierarchyListener(HierarchyListener) -> void

Parameters:

arg0 (Any)

Returns: None

addInputMethodListener(arg0)#

Signature: addInputMethodListener(InputMethodListener) -> void

Parameters:

arg0 (Any)

Returns: None

addKeyListener(arg0)#

Signature: addKeyListener(KeyListener) -> void

Parameters:

arg0 (Any)

Returns: None

addMouseListener(arg0)#

Signature: addMouseListener(MouseListener) -> void

Parameters:

arg0 (Any)

Returns: None

addMouseMotionListener(arg0)#

Signature: addMouseMotionListener(MouseMotionListener) -> void

Parameters:

arg0 (Any)

Returns: None

addMouseWheelListener(arg0)#

Signature: addMouseWheelListener(MouseWheelListener) -> void

Parameters:

arg0 (Any)

Returns: None

addNotify()#

Signature: addNotify() -> void

Returns: None

addPropertyChangeListener(arg0)#

Signature: addPropertyChangeListener(PropertyChangeListener) -> void

Parameters:

arg0 (Any)

Returns: None

disableEvents(arg0)#

Signature: disableEvents(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

disablePopupMenu(arg0)#

Signature: disablePopupMenu(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

TracerThread #

addNode(arg0, arg1)#

Signature: addNode(DefaultSearchNode, boolean) -> void

Parameters:

arg0 (Any)
arg1 (bool)

Returns: None

addProgressListener(arg0)#

Signature: addProgressListener(SearchProgressCallback) -> void

Parameters:

arg0 (Any)

Returns: None

TreeColorMapper #

setMinMax(arg0, arg1)#

Signature: setMinMax(double, double) -> void

Parameters:

arg0 (float)
arg1 (float)

Returns: None

setNaNColor(arg0)#

Signature: setNaNColor(Color) -> void

Parameters:

arg0 (Any)

Returns: None

Tubeness #

setEnvironment(arg0)#

Signature: setEnvironment(OpEnvironment) -> void

Parameters:

arg0 (Any)

Returns: None

setInput(arg0)#

Signature: setInput(Object) -> void

Parameters:

arg0 (Any)

Returns: None

setOutput(arg0)#

Signature: setOutput(Object) -> void

Parameters:

arg0 (Any)

Returns: None

Viewer2D #

addColorBarLegend(arg0, arg1, arg2)#

Adds a color bar legend (LUT ramp) to the viewer. Does nothing if no measurement mapping occurred successfully. Note that when performing mapping to different measurements, the legend reflects only the last mapped measurement.

Signature: addColorBarLegend(ColorTable, double, double) -> void

Parameters:

arg0 (Any)
arg1 (float)
arg2 (float)

Returns: None

addNodes(arg0)#

Signature: addNodes(Map) -> void

Parameters:

arg0 (Dict[str, Any])

Returns: None

addPolygon(arg0, arg1)#

Signature: addPolygon(Polygon2D, String) -> void

Parameters:

arg0 (Any)
arg1 (str)

Returns: None

setAxesVisible(arg0)#

Signature: setAxesVisible(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

setDefaultColor(arg0)#

Sets the default (fallback) color for plotting paths.

Signature: setDefaultColor(ColorRGB) -> void

Parameters:

arg0 (Any): - null not allowed

Returns: None

setEqualizeAxes(arg0)#: /** Sets whether the axes should be equalized (same scale).

When enabled, both X and Y axes will use the same scale to maintain equal aspect ratio. When disabled, each axis maximizes its range.

Signature: setEqualizeAxes(boolean) -> void

Parameters:

arg0 (bool): - true to equalize axes, false otherwise

Returns: None

setGridlinesVisible(arg0)#

Signature: setGridlinesVisible(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

setMinMax(arg0, arg1)#

Signature: setMinMax(double, double) -> void

Parameters:

arg0 (float)
arg1 (float)

Returns: None

setNaNColor(arg0)#

Signature: setNaNColor(Color) -> void

Parameters:

arg0 (Any)

Returns: None

setOutlineVisible(arg0)#

Signature: setOutlineVisible(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

setTitle(arg0)#

Sets the plot display title.

Signature: setTitle(String) -> void

Parameters:

arg0 (str): - the new title

Returns: None

setXrange(arg0, arg1)#

Sets a manual range for the viewers’ X-axis. Calling setXrange(-1, -1) enables auto-range (the default). Must be called before Viewer is fully assembled.

Signature: setXrange(double, double) -> void

Parameters:

arg0 (float): - the lower-limit for the X-axis
arg1 (float)

Returns: None

setYrange(arg0, arg1)#

Sets a manual range for the viewers’ Y-axis. Calling setYrange(-1, -1) enables auto-range (the default). Must be called before Viewer is fully assembled.

Signature: setYrange(double, double) -> void

Parameters:

arg0 (float): - the lower-limit for the Y-axis
arg1 (float)

Returns: None

Viewer3D #

addColorBarLegend(arg0)#

Adds a color bar legend (LUT ramp).

Signature: addColorBarLegend(ColorMapper) -> void

Parameters:

arg0 (Any): - the color table

Returns: None

addLabel(arg0)#

Adds an annotation label to the scene.

Signature: addLabel(String) -> void

Parameters:

arg0 (str): - the annotation text

Returns: None

addMesh(arg0)#

Loads a Wavefront .OBJ file. Should be called before_ displaying the scene, otherwise, if the scene is already visible, validate() should be called to ensure all meshes are visible.

Signature: addMesh(OBJMesh) -> boolean

Parameters:

arg0 (Any): - the mesh to be loaded

Returns: (bool) true, if successful

addTree(arg0)#

Adds a tree to this viewer. Note that calling updateView() may be required to ensure that the current View’s bounding box includes the added Tree.

Signature: addTree(Tree) -> void

Parameters:

arg0 (Tree): - the Tree to be added. The Tree’s label will be used as identifier. It is expected to be unique when rendering multiple Trees, if not (or no label exists) a unique label will be generated.

Returns: None

WekaModelLoader #

addInput(arg0, arg1)#

Signature: addInput(String, Class) -> MutableModuleItem

Parameters:

arg0 (str)
arg1 (type)

Returns: Any

addOutput(arg0)#

Signature: addOutput(ModuleItem) -> void

Parameters:

arg0 (Any)

Returns: None

removeInput(arg0)#

Signature: removeInput(ModuleItem) -> void

Parameters:

arg0 (Any)

Returns: None

removeOutput(arg0)#

Signature: removeOutput(ModuleItem) -> void

Parameters:

arg0 (Any)

Returns: None

setContext(arg0)#

Signature: setContext(Context) -> void

Parameters:

arg0 (Any)

Returns: None

setInput(arg0, arg1)#

Signature: setInput(String, Object) -> void

Parameters:

arg0 (str)
arg1 (Any)

Returns: None

setInputs(arg0)#

Signature: setInputs(Map) -> void

Parameters:

arg0 (Dict[str, Any])

Returns: None

setOutput(arg0, arg1)#

Signature: setOutput(String, Object) -> void

Parameters:

arg0 (str)
arg1 (Any)

Returns: None

setOutputs(arg0)#

Signature: setOutputs(Map) -> void

Parameters:

arg0 (Dict[str, Any])

Returns: None

setResolved(arg0, arg1)#

Signature: setResolved(String, boolean) -> void

Parameters:

arg0 (str)
arg1 (bool)

Returns: None

Category index generated on 2026-01-02 23:09:09