Path (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- sc.fiji.snt.Path

All Implemented Interfaces:

Comparable<Path>
```
public class Path
extends Object
implements Comparable<Path>
```
This class represents a traced segment (i.e., a Path) in a reconstruction. It has methods to manipulate its points (nodes) with sup-pixel accuracy, including drawing them onto threePane-style canvases, etc.
Paths are non-branching sequences of adjacent points (including diagonals) in the image. Branches and joins are supported by attributes of paths that specify that they begin on (or end on) other paths.

In SNT, a Path can exist in two versions or flavors: itself and a fitted version generated by PathFitter. Because fitting may fail around certain nodes, the fitted version may have a different number of nodes relatively to its unfitted version

Field Summary

Fields
Modifier and Type	Field and Description
`protected PointInCanvas`	`canvasOffset`
`protected ArrayList<Path>`	`children`
`protected Path`	`fitted`
`protected Path`	`fittedVersionOf`
`protected boolean`	`invalid3DMesh`
`protected static int`	`noMoreThanOneEvery`
`protected double[]`	`precise_x_positions`
`protected double[]`	`precise_y_positions`
`protected double[]`	`precise_z_positions`
`protected double[]`	`radii`
`protected ArrayList<Path>`	`somehowJoins`
`protected String`	`spacing_units`
`protected Path`	`startJoins`
`protected PointInImage`	`startJoinsPoint`
`static int`	`SWC_APICAL_DENDRITE` Flag specifying the SWC type 'apical dendrite'.
`static String`	`SWC_APICAL_DENDRITE_LABEL` String representation of `SWC_APICAL_DENDRITE`
`static int`	`SWC_AXON` Flag specifying the SWC type 'axon'.
`static String`	`SWC_AXON_LABEL` String representation of `SWC_AXON`
`static int`	`SWC_CUSTOM` Flag specifying the SWC type 'custom'.
`static String`	`SWC_CUSTOM_LABEL` String representation of `SWC_CUSTOM`
`static int`	`SWC_DENDRITE` Flag specifying the SWC type '(basal) dendrite'.
`static String`	`SWC_DENDRITE_LABEL` String representation of `SWC_DENDRITE`
`static int`	`SWC_END_POINT` Deprecated.
`static String`	`SWC_END_POINT_LABEL` String representation of `SWC_END_POINT`
`static int`	`SWC_FORK_POINT` Deprecated.
`static String`	`SWC_FORK_POINT_LABEL` String representation of `SWC_FORK_POINT`
`static int`	`SWC_SOMA` Flag specifying the SWC type 'soma'.
`static String`	`SWC_SOMA_LABEL` String representation of `SWC_SOMA`
`static int`	`SWC_UNDEFINED` Flag specifying the SWC type 'undefined'.
`static String`	`SWC_UNDEFINED_LABEL` String representation of `SWC_UNDEFINED`
`protected double[]`	`tangents_x`
`protected double[]`	`tangents_y`
`protected double[]`	`tangents_z`
`protected double`	`x_spacing`
`protected double`	`y_spacing`
`protected double`	`z_spacing`

Constructor Summary

Constructors
Constructor and Description
`Path()` Instantiates a new path under default settings (isotropic 1um pixel spacing)
`Path(double x_spacing, double y_spacing, double z_spacing, String spacing_units)` Instantiates a new path.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`add(Path other)`
`protected Content`	`addAsLinesTo3DViewer(Image3DUniverse univ, Color3f c, ij.ImagePlus colorImage)` Deprecated.
`Content`	`addAsLinesTo3DViewer(Image3DUniverse univ, Color c, ij.ImagePlus colorImage)` Deprecated.
`protected void`	`addChangeListener(sc.fiji.snt.PathChangeListener listener)`
`Content`	`addDiscsTo3DViewer(Image3DUniverse univ, Color3f c, ij.ImagePlus colorImage)` Deprecated.
`Content`	`addDiscsTo3DViewer(Image3DUniverse univ, Color c, ij.ImagePlus colorImage)` Deprecated.
`void`	`addNode(PointInImage point)` Appends a node to this Path.
`void`	`addPointDouble(double x, double y, double z)`
`void`	`addTo3DViewer(Image3DUniverse univ, Color3f c, ij.ImagePlus colorImage)` Deprecated.
`void`	`addTo3DViewer(Image3DUniverse univ, Color c, ij.ImagePlus colorImage)` Deprecated.
`protected String`	`childrenAsString()`
`Path`	`clone()`
`Path`	`clone(boolean includeImmediateChildren)`
`int`	`compareTo(Path o)`
`boolean`	`contains(PointInImage pim)` Check whether this Path contains the specified point
`protected boolean`	`containsUnscaledNodesInViewPort(TracerCanvas canvas)`
`void`	`createCircles()`
`Path`	`createPath()` Returns a new Path with this Path's attributes (e.g.
`protected void`	`discardFit()`
`protected void`	`disconnectFromAll()`
`void`	`downsample(double maximumAllowedDeviation)`
`protected void`	`drawPathAsPoints(Graphics2D g2, TracerCanvas canvas, SNT snt)`
`void`	`drawPathAsPoints(TracerCanvas canvas, Graphics2D g, Color c, int plane, boolean highContrast, boolean drawDiameter)`
`void`	`drawPathAsPoints(TracerCanvas canvas, Graphics2D g2, Color c, int plane, boolean highContrast, boolean drawDiameter, int slice, int either_side)`
`protected void`	`drawPathAsPoints(TracerCanvas canvas, Graphics2D g, Color c, int plane, boolean drawDiameter, int slice, int either_side)`
`TreeSet<Integer>`	`findJunctionIndices()` Returns the indices of nodes which are indicated to be a join, either in this Path object, or any other that starts or ends on it.
`List<PointInImage>`	`findJunctions()` Returns the nodes which are indicated to be a join (junction/branch point), either in this Path object, or any other that starts or ends on it.
`double`	`getApproximatedVolume()` Returns an estimated volume of this path.
`ij.measure.Calibration`	`getCalibration()` Gets the spatial calibration of this Path.
`PointInCanvas`	`getCanvasOffset()` Returns the translation offset used to render this Path in a `TracerCanvas`.
`int`	`getChannel()` Gets the hyperstack channel associated with this Path.
`ArrayList<Path>`	`getChildren()`
`Color`	`getColor()` Gets the color of this Path
`ColorRGB`	`getColorRGB()` Gets the color of this Path
`double`	`getContraction()` Returns the ratio between the "Euclidean distance" of this path and its length.
`int`	`getEditableNodeIndex()` Gets the position of the node tagged as 'editable', if any.
`Path`	`getFitted()` Gets the fitted version ('flavor') of this Path.
`int`	`getFrame()` Gets the hyperstack frame position associated with this Path.
`int`	`getID()` Gets the identifier of this Path
`Set<PointInImage>`	`getJunctionNodes()` This is a version of `findJunctions()` ensuring that a junction node is only retrieved once even if multiple child paths are associated with it.
`double`	`getLength()` Gets the length of this Path
`double`	`getMeanRadius()` Gets the path mean radius.
`protected double`	`getMinimumSeparation()`
`String`	`getName()` Gets this Path's name.
`PointInImage`	`getNode(int pos)` Gets the node at the specified position.
`BrainAnnotation`	`getNodeAnnotation(int pos)` Returns the neuropil annotation associated with this node.
`Color`	`getNodeColor(int pos)` Gets the node color.
`Color[]`	`getNodeColors()` Gets the node colors.
`char`	`getNodeHemisphereFlag(int pos)` Returns the hemisphere flag associated with this node.
`int`	`getNodeIndex(PointInImage pim)` Gets the first node index associated with the specified image coordinates.
`double`	`getNodeRadius(int pos)` Gets the radius of the specified node.
`List<PointInImage>`	`getNodes()` Gets the nodes of this path.
`double`	`getNodeValue(int pos)` Returns the "value" property of this node.
`protected PointInImage`	`getNodeWithoutChecks(int pos)`
`int`	`getOrder()` Gets the "bifurcation" (branching) order of this Path.
`List<Point3f>`	`getPoint3fList()`
`protected void`	`getPointDouble(int i, double[] p)`
`protected PointInCanvas`	`getPointInCanvas(int node)`
`protected PointInCanvas`	`getPointInCanvas2D(int node, TracerCanvas canvas)`
`protected String`	`getRealLengthString()`
`Path`	`getSection(int startIndex, int endIndex)` Gets a section between two nodes of this Path.
`int`	`getSpineOrVaricosityCount()`
`Path`	`getStartJoins()`
`PointInImage`	`getStartJoinsPoint()`
`static Color`	`getSWCcolor(int swcType)` Gets the default SWC colors used by SNT.
`int`	`getSWCType()` Gets the SWC type.
`static String`	`getSWCtypeName(int type, boolean capitalized)` Gets the SWC type label associated with the specified type flag.
`static ArrayList<String>`	`getSWCtypeNames()` Gets the list of string representations of non-redundant SWC types (i.e., excluding `SWC_FORK_POINT_LABEL`, and `SWC_FORK_POINT_LABEL`
`static ArrayList<Integer>`	`getSWCtypes()` Gets the list of non-redundant SWC types (i.e., excluding the redundant types `SWC_FORK_POINT_LABEL`, and `SWC_FORK_POINT_LABEL`
`void`	`getTangent(int i, int pointsEitherSide, double[] result)`
`int`	`getTreeID()` Gets the identifier of the `Tree` associated to this Path (if any).
`String`	`getTreeLabel()`
`protected List<PointInCanvas>`	`getUnscaledNodesInViewPort(TracerCanvas canvas)`
`boolean`	`getUseFitted()` Gets whether the fitted 'flavor' of this Path is in use.
`int`	`getXUnscaled(int i)`
`double`	`getXUnscaledDouble(int i)`
`int`	`getYUnscaled(int i)`
`double`	`getYUnscaledDouble(int i)`
`int`	`getZUnscaled(int i)`
`double`	`getZUnscaledDouble(int i)`
`boolean`	`hasCustomColor()` Assesses whether a custom color has been assigned to this Path.
`boolean`	`hasNodeAnnotations()` Assesses whether the nodes of this path have been assigned `BrainAnnotation`s.
`boolean`	`hasNodeColors()` Assesses whether the nodes of this path have been assigned an array of colors
`boolean`	`hasNodeHemisphereFlags()` Assesses whether the nodes of this path have been assigned hemisphere flags.
`boolean`	`hasNodeValues()` Assesses whether the nodes of this path have been assigned an array of values
`boolean`	`hasRadii()` Checks whether the nodes of this path have been assigned defined thickness.
`protected int`	`indexNearestTo(double x, double y, double z)`
`int`	`indexNearestTo(double x, double y, double z, double within)` Gets the index of the closest node associated with the specified world coordinates.
`protected int`	`indexNearestToCanvasPosition2D(double xInCanvas, double yInCanvas, double withinPixels)`
`void`	`insertNode(int index, PointInImage point)` Inserts a node at a specified position.
`protected boolean`	`isBeingEdited()`
`boolean`	`isConnectedTo(Path other)`
`protected boolean`	`isEditableNodeLocked()`
`boolean`	`isFittedVersionOfAnotherPath()` Checks if this Path is a fitted version of another path.
`boolean`	`isPrimary()` Checks if this Path is root.
`boolean`	`isSelected()`
`protected PointInImage`	`lastPoint()`
`void`	`moveNode(int index, PointInImage destination)` Assigns a new location to the specified node.
`PointInImage`	`nearestNodeTo(PointInImage node, double within)` Gets the closest node associated with the specified node.
`protected static String`	`pathsToIDListString(ArrayList<Path> a)`
`protected void`	`rebuildConnectionsOfFittedVersion()`
`protected boolean`	`removeChangeListener(sc.fiji.snt.PathChangeListener listener)`
`void`	`removeFrom3DViewer(Image3DUniverse univ)`
`void`	`removeNode(int index)` Removes the specified node if this path has at least two nodes.
`protected void`	`replaceNodesWithFittedVersion()`
`void`	`resetColor()` Resets this path color, forcing SNT to render it under default settings.
`Path`	`reversed()`
`void`	`setCanvasOffset(PointInCanvas canvasOffset)` Specifies a translation offset when rendering this Path in a `TracerCanvas`.
`protected void`	`setChildren(Set<Path> pathsLeft)`
`void`	`setColor(Color color)` Sets this path color.
`void`	`setColor(ColorRGB color)` Sets this path color.
`void`	`setCTposition(int channel, int frame)` Sets the hyperstack position of this Path
`void`	`setEditableNode(int index)` Tags the specified point position as 'editable'.
`protected void`	`setEditableNodeLocked(boolean editableNodeLocked)`
`protected void`	`setFitted(Path p)`
`protected void`	`setFittedCircles(int nPoints, double[] tangents_x, double[] tangents_y, double[] tangents_z, double[] radii, double[] optimized_x, double[] optimized_y, double[] optimized_z)`
`void`	`setGuessedTangents(int pointsEitherSide)`
`protected void`	`setIDs(int pathID, int treeID)`
`protected void`	`setIsPrimary(boolean primary)`
`void`	`setName(String newName)` Sets this Path's name.
`void`	`setNodeAnnotation(BrainAnnotation annotation, int pos)` Assigns an annotation to an existing node.
`void`	`setNodeColor(Color color, int pos)` Sets the node color.
`void`	`setNodeColor(ColorRGB color, int pos)` Sets the node color.
`void`	`setNodeColors(Color[] colors)` Sets the node colors.
`void`	`setNodeHemisphere(char hemisphereFlag, int pos)` Assigns an hemisphere to an existing node.
`void`	`setNodeValue(double value, int pos)` Assigns the "value" property to this node.
`void`	`setNodeValues(double[] values)` Sets the path "values", the array containing the numeric property assigned to path nodes, typically voxel intensities.
`void`	`setOrder(int order)`
`void`	`setRadii(double[] radii)` Assigns radii to this Path
`void`	`setRadius(double r)` Assigns a fixed radius to all the nodes of this Path
`void`	`setRadius(double r, int index)`
`void`	`setSelected(boolean newSelectedStatus)`
`protected void`	`setSpacing(ij.measure.Calibration cal)`
`void`	`setSpineOrVaricosityCount(int newCount)`
`void`	`setStartJoin(Path other, PointInImage joinPoint)`
`void`	`setSWCType(int newSWCType)` Sets the SWC type.
`protected void`	`setSWCType(int newSWCType, boolean alsoSetInFittedVersion)`
`protected void`	`setTreeLabel(String treeLabel)`
`void`	`setUseFitted(boolean useFitted)` Sets whether the fitted flavor of this Path should be used.
`int`	`size()` Returns the number of nodes of this path
`protected String`	`somehowJoinsAsString()`
`protected void`	`stopBeingEdited()`
`String`	`toString()` This toString() method shows details of the path which is actually being displayed, not necessarily this path object.
`Path`	`transform(PathTransformer transformation, ij.ImagePlus template, ij.ImagePlus model)`
`protected void`	`unsetPrimaryForConnected(HashSet<Path> pathsExplored)`
`void`	`unsetStartJoin()`
`boolean`	`versionInUse()`

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - SWC_UNDEFINED
```
public static final int SWC_UNDEFINED
```
    Flag specifying the SWC type 'undefined'. @see Path#SWC_UNDEFINED_LABEL
    
    See Also:
    
    Constant Field Values
  - SWC_SOMA
```
public static final int SWC_SOMA
```
    Flag specifying the SWC type 'soma'. @see Path#SWC_SOMA_LABEL
    
    See Also:
    
    Constant Field Values
  - SWC_AXON
```
public static final int SWC_AXON
```
    Flag specifying the SWC type 'axon'. @see Path#SWC_AXON_LABEL
    
    See Also:
    
    Constant Field Values
  - SWC_DENDRITE
```
public static final int SWC_DENDRITE
```
    Flag specifying the SWC type '(basal) dendrite'. @see Path#SWC_DENDRITE_LABEL
    
    See Also:
    
    Constant Field Values
  - SWC_APICAL_DENDRITE
```
public static final int SWC_APICAL_DENDRITE
```
    Flag specifying the SWC type 'apical dendrite'. @see Path#SWC_APICAL_DENDRITE_LABEL
    
    See Also:
    
    Constant Field Values
  - SWC_FORK_POINT
```
@Deprecated
public static final int SWC_FORK_POINT
```
    Deprecated.
    
    Flag specifying the SWC type 'fork point' @see Path#SWC_FORK_POINT_LABEL
    
    See Also:
    
    Constant Field Values
  - SWC_END_POINT
```
@Deprecated
public static final int SWC_END_POINT
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - SWC_CUSTOM
```
public static final int SWC_CUSTOM
```
    Flag specifying the SWC type 'custom'. @see Path#SWC_CUSTOM_LABEL
    
    See Also:
    
    Constant Field Values
  - SWC_UNDEFINED_LABEL
```
public static final String SWC_UNDEFINED_LABEL
```
    String representation of SWC_UNDEFINED
    
    See Also:
    
    Constant Field Values
  - SWC_SOMA_LABEL
```
public static final String SWC_SOMA_LABEL
```
    String representation of SWC_SOMA
    
    See Also:
    
    Constant Field Values
  - SWC_AXON_LABEL
```
public static final String SWC_AXON_LABEL
```
    String representation of SWC_AXON
    
    See Also:
    
    Constant Field Values
  - SWC_DENDRITE_LABEL
```
public static final String SWC_DENDRITE_LABEL
```
    String representation of SWC_DENDRITE
    
    See Also:
    
    Constant Field Values
  - SWC_APICAL_DENDRITE_LABEL
```
public static final String SWC_APICAL_DENDRITE_LABEL
```
    String representation of SWC_APICAL_DENDRITE
    
    See Also:
    
    Constant Field Values
  - SWC_FORK_POINT_LABEL
```
public static final String SWC_FORK_POINT_LABEL
```
    String representation of SWC_FORK_POINT
    
    See Also:
    
    Constant Field Values
  - SWC_END_POINT_LABEL
```
public static final String SWC_END_POINT_LABEL
```
    String representation of SWC_END_POINT
    
    See Also:
    
    Constant Field Values
  - SWC_CUSTOM_LABEL
```
public static final String SWC_CUSTOM_LABEL
```
    String representation of SWC_CUSTOM
    
    See Also:
    
    Constant Field Values
  - noMoreThanOneEvery
```
protected static final int noMoreThanOneEvery
```
    See Also:
    
    Constant Field Values
  - precise_x_positions
```
protected double[] precise_x_positions
```
  - precise_y_positions
```
protected double[] precise_y_positions
```
  - precise_z_positions
```
protected double[] precise_z_positions
```
  - radii
```
protected double[] radii
```
  - tangents_x
```
protected double[] tangents_x
```
  - tangents_y
```
protected double[] tangents_y
```
  - tangents_z
```
protected double[] tangents_z
```
  - canvasOffset
```
protected PointInCanvas canvasOffset
```
  - x_spacing
```
protected double x_spacing
```
  - y_spacing
```
protected double y_spacing
```
  - z_spacing
```
protected double z_spacing
```
  - spacing_units
```
protected String spacing_units
```
  - startJoins
```
protected Path startJoins
```
  - startJoinsPoint
```
protected PointInImage startJoinsPoint
```
  - somehowJoins
```
protected ArrayList<Path> somehowJoins
```
  - children
```
protected ArrayList<Path> children
```
  - fitted
```
protected Path fitted
```
  - fittedVersionOf
```
protected Path fittedVersionOf
```
  - invalid3DMesh
```
protected boolean invalid3DMesh
```
- Constructor Detail
  - Path
```
public Path()
```
    Instantiates a new path under default settings (isotropic 1um pixel spacing)
  - Path
```
public Path(double x_spacing,
            double y_spacing,
            double z_spacing,
            String spacing_units)
```
    Instantiates a new path.
    
    Parameters:
    
    x_spacing - Pixel width in spacing_units
    
    y_spacing - Pixel height in spacing_units
    
    z_spacing - Pixel depth in spacing_units
    
    spacing_units - the length unit in physical world units (typically "um").
- Method Detail
  - compareTo
```
public int compareTo(Path o)
```
    Specified by:
    
    compareTo in interface Comparable<Path>
  - getID
```
public int getID()
```
    Gets the identifier of this Path
    
    Returns:
    
    the identifier
  - getTreeID
```
public int getTreeID()
```
    Gets the identifier of the Tree associated to this Path (if any).
    
    Returns:
    
    the Tree identifier
  - setIDs
```
protected void setIDs(int pathID,
                      int treeID)
```
  - setTreeLabel
```
protected void setTreeLabel(String treeLabel)
```
  - getTreeLabel
```
public String getTreeLabel()
```
  - setCanvasOffset
```
public void setCanvasOffset(PointInCanvas canvasOffset)
```
    Specifies a translation offset when rendering this Path in a TracerCanvas. Path coordinates remain unaltered.
    
    Parameters:
    
    canvasOffset - the x,y,z coordinates (pixel-based) specifying the translation offset
  - getCanvasOffset
```
public PointInCanvas getCanvasOffset()
```
    Returns the translation offset used to render this Path in a TracerCanvas.
    
    Returns:
    
    the rendering offset (in pixel coordinates)
  - getStartJoins
```
public Path getStartJoins()
```
  - getStartJoinsPoint
```
public PointInImage getStartJoinsPoint()
```
  - setName
```
public void setName(String newName)
```
    Sets this Path's name. Set it to null or "", to reset it to the default.
    
    Parameters:
    
    newName - the new name.
    
    See Also:
    
    getName()
  - getName
```
public String getName()
```
    Gets this Path's name.
    
    Returns:
    
    the name. If no name as been set, the default name is returned.
    
    See Also:
    
    setName(String)
  - pathsToIDListString
```
protected static String pathsToIDListString(ArrayList<Path> a)
```
  - somehowJoinsAsString
```
protected String somehowJoinsAsString()
```
  - childrenAsString
```
protected String childrenAsString()
```
  - setChildren
```
protected void setChildren(Set<Path> pathsLeft)
```
  - getContraction
```
public double getContraction()
```
    Returns the ratio between the "Euclidean distance" of this path and its length. The Euclidean distance of this path is defined as the distance between this Path's start and end point.
    
    Returns:
    
    the Contraction of this Path, or NaN if this Path has no length
  - getLength
```
public double getLength()
```
    Gets the length of this Path
    
    Returns:
    
    the length of this Path
  - getRealLengthString
```
protected String getRealLengthString()
```
  - createCircles
```
public void createCircles()
```
  - setIsPrimary
```
protected void setIsPrimary(boolean primary)
```
  - isPrimary
```
public boolean isPrimary()
```
    Checks if this Path is root.
    
    Returns:
    
    true, if is primary (root)
  - disconnectFromAll
```
protected void disconnectFromAll()
```
  - setStartJoin
```
public void setStartJoin(Path other,
                         PointInImage joinPoint)
```
  - replaceNodesWithFittedVersion
```
protected void replaceNodesWithFittedVersion()
```
  - rebuildConnectionsOfFittedVersion
```
protected void rebuildConnectionsOfFittedVersion()
```
  - unsetStartJoin
```
public void unsetStartJoin()
```
  - getMinimumSeparation
```
protected double getMinimumSeparation()
```
  - size
```
public int size()
```
    Returns the number of nodes of this path
    
    Returns:
    
    the size, i.e., number of nodes
  - getPointDouble
```
protected void getPointDouble(int i,
                              double[] p)
```
  - getNode
```
public PointInImage getNode(int pos)
                     throws IndexOutOfBoundsException
```
    Gets the node at the specified position.
    
    Parameters:
    
    pos - the position index (0-based). NB: You can use -1 to retrieve the last node in the Path
    
    Returns:
    
    the node
    
    Throws:
    
    IndexOutOfBoundsException - if position is out-of-range
  - getNodes
```
public List<PointInImage> getNodes()
```
    Gets the nodes of this path.
    
    Returns:
    
    the list of nodes that form this path
  - getNodeWithoutChecks
```
protected PointInImage getNodeWithoutChecks(int pos)
```
  - getPointInCanvas
```
protected PointInCanvas getPointInCanvas(int node)
```
  - getPointInCanvas2D
```
protected PointInCanvas getPointInCanvas2D(int node,
                                           TracerCanvas canvas)
```
  - getUnscaledNodesInViewPort
```
protected List<PointInCanvas> getUnscaledNodesInViewPort(TracerCanvas canvas)
```
  - containsUnscaledNodesInViewPort
```
protected boolean containsUnscaledNodesInViewPort(TracerCanvas canvas)
```
  - contains
```
public boolean contains(PointInImage pim)
```
    Check whether this Path contains the specified point
    
    Parameters:
    
    pim - the PointInImage node
    
    Returns:
    
    true, if successful
  - insertNode
```
public void insertNode(int index,
                       PointInImage point)
```
    Inserts a node at a specified position.
    
    Parameters:
    
    index - the (zero-based) index of the position of the new node
    
    point - the node to be inserted
    
    Throws:
    
    IllegalArgumentException - if index is out-of-range
  - removeNode
```
public void removeNode(int index)
```
    Removes the specified node if this path has at least two nodes. Does nothing if this is a single point path.
    
    Parameters:
    
    index - the zero-based index of the node to be removed
    
    Throws:
    
    IllegalArgumentException - if index is out-of-range
  - moveNode
```
public void moveNode(int index,
                     PointInImage destination)
```
    Assigns a new location to the specified node.
    
    Parameters:
    
    index - the zero-based index of the node to be modified
    
    destination - the new node location
    
    Throws:
    
    IllegalArgumentException - if index is out-of-range
  - getNodeIndex
```
public int getNodeIndex(PointInImage pim)
```
    Gets the first node index associated with the specified image coordinates. Returns -1 if no such node was found.
    
    Parameters:
    
    pim - the image position (calibrated coordinates)
    
    Returns:
    
    the index of the first node occurrence or -1 if there is no such occurrence
  - nearestNodeTo
```
public PointInImage nearestNodeTo(PointInImage node,
                                  double within)
```
    Gets the closest node associated with the specified node.
    
    Parameters:
    
    node - location to be searched for
    
    within - sets the search sensitivity. E.g., Setting it to Double.MAX_VALUE (or the image's largest dimension) will always return a valid node.
    
    Returns:
    
    the closest node to the specified one or null if no such node was found.
  - indexNearestTo
```
public int indexNearestTo(double x,
                          double y,
                          double z,
                          double within)
```
    Gets the index of the closest node associated with the specified world coordinates.
    
    Parameters:
    
    x - the x-coordinates (spatially calibrated image units)
    
    y - the y-coordinates (spatially calibrated image units)
    
    z - the z-coordinates (spatially calibrated image units)
    
    within - sets the search sensitivity. E.g., Setting it to Double.MAX_VALUE (or the image's largest dimension) will always return a valid index.
    
    Returns:
    
    the index of the closest node to the specified coordinates. Returns -1 if no such node was found.
  - indexNearestToCanvasPosition2D
```
protected int indexNearestToCanvasPosition2D(double xInCanvas,
                                             double yInCanvas,
                                             double withinPixels)
```
  - indexNearestTo
```
protected int indexNearestTo(double x,
                             double y,
                             double z)
```
  - getEditableNodeIndex
```
public int getEditableNodeIndex()
```
    Gets the position of the node tagged as 'editable', if any.
    
    Returns:
    
    the index of the point currently tagged as editable, or -1 if no such point exists
  - setEditableNode
```
public void setEditableNode(int index)
```
    Tags the specified point position as 'editable'.
    
    Parameters:
    
    index - the index of the point to be tagged. Set it to -1 to for no tagging
  - isBeingEdited
```
protected boolean isBeingEdited()
```
  - stopBeingEdited
```
protected void stopBeingEdited()
```
  - isEditableNodeLocked
```
protected boolean isEditableNodeLocked()
```
  - setEditableNodeLocked
```
protected void setEditableNodeLocked(boolean editableNodeLocked)
```
  - getXUnscaled
```
public int getXUnscaled(int i)
```
  - getYUnscaled
```
public int getYUnscaled(int i)
```
  - getZUnscaled
```
public int getZUnscaled(int i)
```
  - getXUnscaledDouble
```
public double getXUnscaledDouble(int i)
```
  - getYUnscaledDouble
```
public double getYUnscaledDouble(int i)
```
  - getZUnscaledDouble
```
public double getZUnscaledDouble(int i)
```
  - getSection
```
public Path getSection(int startIndex,
                       int endIndex)
```
    Gets a section between two nodes of this Path.
    
    Parameters:
    
    startIndex - the node index defining the first node of the section
    
    endIndex - the node index defining the last node of the section
    
    Returns:
    
    the section. Note that the sectioned Path will share of all of this Path's properties but will not contain any information on junction points or connectivity to other Paths.
  - createPath
```
public Path createPath()
```
    Returns a new Path with this Path's attributes (e.g. spatial scale), but no nodes.
    
    Returns:
    
    the empty path
  - setSpacing
```
protected void setSpacing(ij.measure.Calibration cal)
```
  - clone
```
public Path clone()
```
    Overrides:
    
    clone in class Object
  - clone
```
public Path clone(boolean includeImmediateChildren)
```
  - getChildren
```
public ArrayList<Path> getChildren()
```
  - getCalibration
```
public ij.measure.Calibration getCalibration()
```
    Gets the spatial calibration of this Path.
    
    Returns:
    
    the calibration details associated with this Path
  - lastPoint
```
protected PointInImage lastPoint()
```
  - add
```
public void add(Path other)
```
  - unsetPrimaryForConnected
```
protected void unsetPrimaryForConnected(HashSet<Path> pathsExplored)
```
  - reversed
```
public Path reversed()
```
  - addNode
```
public void addNode(PointInImage point)
```
    Appends a node to this Path.
    
    Parameters:
    
    point - the node to be inserted
  - addPointDouble
```
public void addPointDouble(double x,
                           double y,
                           double z)
```
  - drawPathAsPoints
```
public void drawPathAsPoints(TracerCanvas canvas,
                             Graphics2D g,
                             Color c,
                             int plane,
                             boolean highContrast,
                             boolean drawDiameter)
```
  - drawPathAsPoints
```
protected void drawPathAsPoints(TracerCanvas canvas,
                                Graphics2D g,
                                Color c,
                                int plane,
                                boolean drawDiameter,
                                int slice,
                                int either_side)
```
  - drawPathAsPoints
```
protected void drawPathAsPoints(Graphics2D g2,
                                TracerCanvas canvas,
                                SNT snt)
```
  - drawPathAsPoints
```
public void drawPathAsPoints(TracerCanvas canvas,
                             Graphics2D g2,
                             Color c,
                             int plane,
                             boolean highContrast,
                             boolean drawDiameter,
                             int slice,
                             int either_side)
```
  - setNodeColors
```
public void setNodeColors(Color[] colors)
```
    Sets the node colors.
    
    Parameters:
    
    colors - the colors used to render the nodes of this. If null (the default) all nodes are rendered using the Path color.
  - getNodeColors
```
public Color[] getNodeColors()
```
    Gets the node colors.
    
    Returns:
    
    the colors used to render the nodes of this path, or null if nodes are rendered using the Path color
  - getNodeColor
```
public Color getNodeColor(int pos)
```
    Gets the node color.
    
    Parameters:
    
    pos - the node position
    
    Returns:
    
    the node color, or null if no color nodes have been assigned to this path
  - setNodeColor
```
public void setNodeColor(Color color,
                         int pos)
```
    Sets the node color.
    
    Parameters:
    
    color - the node color
    
    pos - the node position
  - setNodeColor
```
public void setNodeColor(ColorRGB color,
                         int pos)
```
    Sets the node color.
    
    Parameters:
    
    color - the node color
    
    pos - the node position
  - setNodeValue
```
public void setNodeValue(double value,
                         int pos)
```
    Assigns the "value" property to this node.
    
    Parameters:
    
    value - the node value
    
    pos - the node position
    
    See Also:
    
    PathProfiler.assignValues()
  - setNodeAnnotation
```
public void setNodeAnnotation(BrainAnnotation annotation,
                              int pos)
```
    Assigns an annotation to an existing node.
    
    Parameters:
    
    annotation - the node annotation
    
    pos - the node position
  - setNodeHemisphere
```
public void setNodeHemisphere(char hemisphereFlag,
                              int pos)
```
    Assigns an hemisphere to an existing node.
    
    Parameters:
    
    hemisphereFlag - the node hemisphere flag.
    
    pos - the node position
  - getNodeValue
```
public double getNodeValue(int pos)
```
    Returns the "value" property of this node.
    
    Parameters:
    
    pos - the node position
    
    Returns:
    
    the value property of this node
    
    See Also:
    
    PathProfiler.assignValues(), PointInImage.v
  - getNodeAnnotation
```
public BrainAnnotation getNodeAnnotation(int pos)
```
    Returns the neuropil annotation associated with this node.
    
    Parameters:
    
    pos - the node position
    
    Returns:
    
    the annotation of this node,
    
    See Also:
    
    SNTPoint.getAnnotation()
  - getNodeHemisphereFlag
```
public char getNodeHemisphereFlag(int pos)
```
    Returns the hemisphere flag associated with this node.
    
    Parameters:
    
    pos - the node position
    
    Returns:
    
    the flag associated with this node, either BrainAnnotation.LEFT_HEMISPHERE, BrainAnnotation.RIGHT_HEMISPHERE, or BrainAnnotation.ANY_HEMISPHERE
    
    See Also:
    
    SNTPoint.getAnnotation()
  - setNodeValues
```
public void setNodeValues(double[] values)
```
    Sets the path "values", the array containing the numeric property assigned to path nodes, typically voxel intensities.
    
    Parameters:
    
    values - the new node values
    
    See Also:
    
    PointInImage.v, PathProfiler.assignValues()
  - hasNodeValues
```
public boolean hasNodeValues()
```
    Assesses whether the nodes of this path have been assigned an array of values
    
    Returns:
    
    true, if successful
    
    See Also:
    
    PointInImage.v, PathProfiler.assignValues()
  - hasNodeAnnotations
```
public boolean hasNodeAnnotations()
```
    Assesses whether the nodes of this path have been assigned BrainAnnotations.
    
    Returns:
    
    true, if successful
    
    See Also:
    
    SNTPoint.getAnnotation()
  - hasNodeHemisphereFlags
```
public boolean hasNodeHemisphereFlags()
```
    Assesses whether the nodes of this path have been assigned hemisphere flags.
    
    Returns:
    
    true, if successful
    
    See Also:
    
    SNTPoint.getHemisphere()
  - getColor
```
public Color getColor()
```
    Gets the color of this Path
    
    Returns:
    
    the color, or null if no color has been assigned to this Path
    
    See Also:
    
    hasCustomColor, hasNodeColors()
  - getColorRGB
```
public ColorRGB getColorRGB()
```
    Gets the color of this Path
    
    Returns:
    
    the color, or null if no color has been assigned to this Path
    
    See Also:
    
    hasCustomColor, hasNodeColors()
  - setColor
```
public void setColor(Color color)
```
    Sets this path color.
    
    Parameters:
    
    color - the path color. Set it to null, to have SNT render this Path using default settings. You may need to cast the null reference to Color to avoid ambiguous method overload
  - setColor
```
public void setColor(ColorRGB color)
```
    Sets this path color.
    
    Parameters:
    
    color - the path color. Set it to null, to have SNT render this Path using default settings. You may need to cast the null reference to ColorRGB to avoid ambiguous method overload
  - resetColor
```
public void resetColor()
```
    Resets this path color, forcing SNT to render it under default settings.
  - hasCustomColor
```
public boolean hasCustomColor()
```
    Assesses whether a custom color has been assigned to this Path.
    
    Returns:
    
    true, if successful
    
    See Also:
    
    hasNodeColors()
  - hasNodeColors
```
public boolean hasNodeColors()
```
    Assesses whether the nodes of this path have been assigned an array of colors
    
    Returns:
    
    true, if successful
    
    See Also:
    
    getNodeColors()
  - getSWCcolor
```
public static Color getSWCcolor(int swcType)
```
    Gets the default SWC colors used by SNT.
    
    Parameters:
    
    swcType - the SEC type (e.g., SWC_AXON, SWC_DENDRITE, etc.)
    
    Returns:
    
    the SWC color
  - isFittedVersionOfAnotherPath
```
public boolean isFittedVersionOfAnotherPath()
```
    Checks if this Path is a fitted version of another path.
    
    Returns:
    
    true, if it is a fitted version of another path
  - setFitted
```
protected void setFitted(Path p)
```
  - setUseFitted
```
public void setUseFitted(boolean useFitted)
                  throws IllegalArgumentException
```
    Sets whether the fitted flavor of this Path should be used.
    
    Parameters:
    
    useFitted - the new use fitted
    
    Throws:
    
    IllegalArgumentException - if this Path has not been fitted
  - discardFit
```
protected void discardFit()
```
  - getUseFitted
```
public boolean getUseFitted()
```
    Gets whether the fitted 'flavor' of this Path is in use.
    
    Returns:
    
    true, if the fitted version of this Path is in use, otherwise false
  - getSpineOrVaricosityCount
```
public int getSpineOrVaricosityCount()
```
  - setSpineOrVaricosityCount
```
public void setSpineOrVaricosityCount(int newCount)
```
  - getChannel
```
public int getChannel()
```
    Gets the hyperstack channel associated with this Path.
    
    Returns:
    
    the channel position of this path (1-based index). Note that if the channel associated with a path is not known, it is assumed to be 1;
  - getFrame
```
public int getFrame()
```
    Gets the hyperstack frame position associated with this Path.
    
    Returns:
    
    the frame position of this path (1-based index). Note that if the frame associated with a path is not known, it is assumed to be 1;
  - setCTposition
```
public void setCTposition(int channel,
                          int frame)
```
    Sets the hyperstack position of this Path
    
    Parameters:
    
    channel - the channel (one-based index)
    
    frame - the frame (one-based index)
  - getFitted
```
public Path getFitted()
```
    Gets the fitted version ('flavor') of this Path.
    
    Returns:
    
    the fitted version, or null if this Path has not been fitted
  - setGuessedTangents
```
public void setGuessedTangents(int pointsEitherSide)
```
  - getTangent
```
public void getTangent(int i,
                       int pointsEitherSide,
                       double[] result)
```
  - getSWCtypeNames
```
public static ArrayList<String> getSWCtypeNames()
```
    Gets the list of string representations of non-redundant SWC types (i.e., excluding SWC_FORK_POINT_LABEL, and SWC_FORK_POINT_LABEL
    
    Returns:
    
    the list of SWC type names
  - getSWCtypes
```
public static ArrayList<Integer> getSWCtypes()
```
    Gets the list of non-redundant SWC types (i.e., excluding the redundant types SWC_FORK_POINT_LABEL, and SWC_FORK_POINT_LABEL
    
    Returns:
    
    the list of SWC type flags
  - getSWCtypeName
```
public static String getSWCtypeName(int type,
                                    boolean capitalized)
```
    Gets the SWC type label associated with the specified type flag. SNT follows the specification detailed at neuronland
    
    Parameters:
    
    type - the SWC type flag
    
    capitalized - whether output String should be capitalized
    
    Returns:
    
    the respective label, or SWC_UNDEFINED_LABEL if flag was not recognized
  - getMeanRadius
```
public double getMeanRadius()
```
    Gets the path mean radius.
    
    Returns:
    
    the average radius of the path, or zero if path has no defined thickness
    
    See Also:
    
    hasRadii()
  - getNodeRadius
```
public double getNodeRadius(int pos)
```
    Gets the radius of the specified node.
    
    Parameters:
    
    pos - the node position
    
    Returns:
    
    the radius at the specified position, or zero if path has no defined thickness
  - hasRadii
```
public boolean hasRadii()
```
    Checks whether the nodes of this path have been assigned defined thickness.
    
    Returns:
    
    true, if the points defining with this path are associated with a list of radii
  - setFittedCircles
```
protected void setFittedCircles(int nPoints,
                                double[] tangents_x,
                                double[] tangents_y,
                                double[] tangents_z,
                                double[] radii,
                                double[] optimized_x,
                                double[] optimized_y,
                                double[] optimized_z)
```
  - toString
```
public String toString()
```
    This toString() method shows details of the path which is actually being displayed, not necessarily this path object.
    
    Overrides:
    
    toString in class Object
    
    Returns:
    
    the string
  - setSWCType
```
public void setSWCType(int newSWCType)
```
    Sets the SWC type.
    
    Parameters:
    
    newSWCType - the new SWC type
  - setSWCType
```
protected void setSWCType(int newSWCType,
                          boolean alsoSetInFittedVersion)
```
  - getSWCType
```
public int getSWCType()
```
    Gets the SWC type.
    
    Returns:
    
    the SWC type
  - getOrder
```
public int getOrder()
```
    Gets the "bifurcation" (branching) order of this Path. If registered in the GUI, this would correspond to the level of this Path in PathManagerUI's JTree: E.g., a Path connected to a primary Path (order 1) will be assigned order 2, etc.. N.B.: Albeit related to reverse Horton-Strahler classification, Path ordering is formally distinct, as it classifies Paths instead of branches.
    
    Returns:
    
    the order of this path. A primary path is always of order 1.
    
    See Also:
    
    StrahlerAnalyzer
  - setOrder
```
public void setOrder(int order)
```
  - removeFrom3DViewer
```
public void removeFrom3DViewer(Image3DUniverse univ)
```
  - getPoint3fList
```
public List<Point3f> getPoint3fList()
```
  - addAsLinesTo3DViewer
```
@Deprecated
public Content addAsLinesTo3DViewer(Image3DUniverse univ,
                                                Color c,
                                                ij.ImagePlus colorImage)
```
    Deprecated.
  - addAsLinesTo3DViewer
```
@Deprecated
protected Content addAsLinesTo3DViewer(Image3DUniverse univ,
                                                   Color3f c,
                                                   ij.ImagePlus colorImage)
```
    Deprecated.
  - addDiscsTo3DViewer
```
@Deprecated
public Content addDiscsTo3DViewer(Image3DUniverse univ,
                                              Color c,
                                              ij.ImagePlus colorImage)
```
    Deprecated.
  - addDiscsTo3DViewer
```
@Deprecated
public Content addDiscsTo3DViewer(Image3DUniverse univ,
                                              Color3f c,
                                              ij.ImagePlus colorImage)
```
    Deprecated.
  - addTo3DViewer
```
@Deprecated
public void addTo3DViewer(Image3DUniverse univ,
                                      Color c,
                                      ij.ImagePlus colorImage)
```
    Deprecated.
  - addTo3DViewer
```
@Deprecated
public void addTo3DViewer(Image3DUniverse univ,
                                      Color3f c,
                                      ij.ImagePlus colorImage)
```
    Deprecated.
  - setSelected
```
public void setSelected(boolean newSelectedStatus)
```
  - isSelected
```
public boolean isSelected()
```
  - versionInUse
```
public boolean versionInUse()
```
  - getApproximatedVolume
```
public double getApproximatedVolume()
```
    Returns an estimated volume of this path.
    The most accurate volume of each path segment would be the volume of a convex hull of two arbitrarily oriented and sized circles in space. This is tough to work out analytically, and this precision isn't really warranted given the errors introduced in the fitting process, the tracing in the first place, etc. So, this method produces an approximate volume assuming that the volume of each of these parts is that of a truncated cone (Frustum) , with circles of the same size (i.e., as if the circles had simply been reoriented to be parallel and have a common normal vector)
    
    For more accurate measurements of the volumes of a neuron, you should use the filling interface.
    
    Returns:
    
    the approximate fitted volume (in physical units), or 0 if this Path has no radii
    
    See Also:
    
    hasRadii()
  - transform
```
public Path transform(PathTransformer transformation,
                      ij.ImagePlus template,
                      ij.ImagePlus model)
```
  - findJunctions
```
public List<PointInImage> findJunctions()
```
    Returns the nodes which are indicated to be a join (junction/branch point), either in this Path object, or any other that starts or ends on it.
    
    Returns:
    
    the list of nodes as PointInImage objects
    
    See Also:
    
    findJunctionIndices(), getJunctionNodes()
  - getJunctionNodes
```
public Set<PointInImage> getJunctionNodes()
```
    This is a version of findJunctions() ensuring that a junction node is only retrieved once even if multiple child paths are associated with it.
    
    Returns:
    
    the junction nodes
    
    See Also:
    
    findJunctionIndices()
  - findJunctionIndices
```
public TreeSet<Integer> findJunctionIndices()
```
    Returns the indices of nodes which are indicated to be a join, either in this Path object, or any other that starts or ends on it.
    
    Returns:
    
    the indices of junction nodes, naturally sorted
    
    See Also:
    
    findJunctions(), getJunctionNodes()
  - downsample
```
public void downsample(double maximumAllowedDeviation)
```
  - setRadius
```
public void setRadius(double r)
```
    Assigns a fixed radius to all the nodes of this Path
    
    Parameters:
    
    r - the radius to be assigned. Setting it to 0 or Double.NaN removes the radius attribute from the Path
  - setRadius
```
public void setRadius(double r,
                      int index)
```
  - setRadii
```
public void setRadii(double[] radii)
```
    Assigns radii to this Path
    
    Parameters:
    
    radii - the radii array. Setting it null removes the radius attribute from the Path
    
    See Also:
    
    setRadius(double)
  - isConnectedTo
```
public boolean isConnectedTo(Path other)
```
  - addChangeListener
```
protected void addChangeListener(sc.fiji.snt.PathChangeListener listener)
```
  - removeChangeListener
```
protected boolean removeChangeListener(sc.fiji.snt.PathChangeListener listener)
```

Class Path

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

SWC_UNDEFINED

SWC_SOMA

SWC_AXON

SWC_DENDRITE

SWC_APICAL_DENDRITE

SWC_FORK_POINT

SWC_END_POINT

SWC_CUSTOM

SWC_UNDEFINED_LABEL

SWC_SOMA_LABEL

SWC_AXON_LABEL

SWC_DENDRITE_LABEL

SWC_APICAL_DENDRITE_LABEL

SWC_FORK_POINT_LABEL

SWC_END_POINT_LABEL

SWC_CUSTOM_LABEL

noMoreThanOneEvery

precise_x_positions

precise_y_positions

precise_z_positions

radii

tangents_x

tangents_y

tangents_z

canvasOffset

x_spacing

y_spacing

z_spacing

spacing_units

startJoins

startJoinsPoint

somehowJoins

children

fitted

fittedVersionOf

invalid3DMesh

Constructor Detail

Path

Path

Method Detail

compareTo

getID

getTreeID

setIDs

setTreeLabel

getTreeLabel

setCanvasOffset

getCanvasOffset

getStartJoins

getStartJoinsPoint

setName

getName

pathsToIDListString

somehowJoinsAsString

childrenAsString

setChildren

getContraction

getLength

getRealLengthString

createCircles

setIsPrimary

isPrimary

disconnectFromAll

setStartJoin

replaceNodesWithFittedVersion

rebuildConnectionsOfFittedVersion

unsetStartJoin

getMinimumSeparation

size

getPointDouble

getNode

getNodes

getNodeWithoutChecks

getPointInCanvas