Path

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

All Implemented Interfaces:

java.lang.Comparable<Path>
```
public class Path
extends java.lang.Object
implements java.lang.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
`static int`	`SWC_APICAL_DENDRITE` Flag specifying the SWC type 'apical dendrite'.
`static java.lang.String`	`SWC_APICAL_DENDRITE_LABEL` String representation of `SWC_APICAL_DENDRITE`
`static int`	`SWC_AXON` Flag specifying the SWC type 'axon'.
`static java.lang.String`	`SWC_AXON_LABEL` String representation of `SWC_AXON`
`static int`	`SWC_CUSTOM` Flag specifying the SWC type 'custom'.
`static java.lang.String`	`SWC_CUSTOM_LABEL` String representation of `SWC_CUSTOM`
`static int`	`SWC_DENDRITE` Flag specifying the SWC type '(basal) dendrite'.
`static java.lang.String`	`SWC_DENDRITE_LABEL` String representation of `SWC_DENDRITE`
`static int`	`SWC_END_POINT` Deprecated.
`static java.lang.String`	`SWC_END_POINT_LABEL` String representation of `SWC_END_POINT`
`static int`	`SWC_FORK_POINT` Deprecated.
`static java.lang.String`	`SWC_FORK_POINT_LABEL` String representation of `SWC_FORK_POINT`
`static int`	`SWC_SOMA` Flag specifying the SWC type 'soma'.
`static java.lang.String`	`SWC_SOMA_LABEL` String representation of `SWC_SOMA`
`static int`	`SWC_UNDEFINED` Flag specifying the SWC type 'undefined'.
`static java.lang.String`	`SWC_UNDEFINED_LABEL` String representation of `SWC_UNDEFINED`

Constructor Summary

Constructors
Constructor and Description

Path(double x_spacing, double y_spacing, double z_spacing, java.lang.String spacing_units)
Instantiates a new path.

Constructors
Constructor and Description
`Path(double x_spacing, double y_spacing, double z_spacing, java.lang.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
`ij3d.Content`	`addAsLinesTo3DViewer(ij3d.Image3DUniverse univ, java.awt.Color c, ij.ImagePlus colorImage)` Deprecated.
`ij3d.Content`	`addDiscsTo3DViewer(ij3d.Image3DUniverse univ, org.scijava.vecmath.Color3f c, ij.ImagePlus colorImage)` Deprecated.
`ij3d.Content`	`addDiscsTo3DViewer(ij3d.Image3DUniverse univ, java.awt.Color c, ij.ImagePlus colorImage)` Deprecated.
`void`	`addNode(PointInImage point)` Appends a node to this Path.
`void`	`addTo3DViewer(ij3d.Image3DUniverse univ, org.scijava.vecmath.Color3f c, ij.ImagePlus colorImage)` Deprecated.
`void`	`addTo3DViewer(ij3d.Image3DUniverse univ, java.awt.Color c, ij.ImagePlus colorImage)` Deprecated.
`Path`	`clone()`
`int`	`compareTo(Path o)`
`boolean`	`contains(PointInImage pim)` Check whether this Path contains the specified point
`void`	`downsample(double maximumAllowedDeviation)`
`void`	`drawPathAsPoints(sc.fiji.snt.TracerCanvas canvas, java.awt.Graphics2D g, java.awt.Color c, int plane, boolean highContrast, boolean drawDiameter)`
`void`	`drawPathAsPoints(sc.fiji.snt.TracerCanvas canvas, java.awt.Graphics2D g2, java.awt.Color c, int plane, boolean highContrast, boolean drawDiameter, int slice, int either_side)`
`java.util.TreeSet<java.lang.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.
`java.util.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.
`java.awt.Color`	`getColor()` Gets the color of this Path
`org.scijava.util.ColorRGB`	`getColorRGB()` Gets the color of this Path
`int`	`getEditableNodeIndex()` Gets the position of the node tagged as 'editable', if any.
`Path`	`getEndJoins()`
`PointInImage`	`getEndJoinsPoint()`
`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
`double`	`getLength()` Gets the length of this Path
`double`	`getMeanRadius()` Gets the path mean radius.
`java.lang.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.
`java.awt.Color`	`getNodeColor(int pos)` Gets the node color.
`java.awt.Color[]`	`getNodeColors()` Gets the node colors.
`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.
`double`	`getNodeValue(int pos)` Returns the "value" property of this node.
`int`	`getOrder()` Gets the branching order of this Path
`java.util.List<org.scijava.vecmath.Point3f>`	`getPoint3fList()`
`Path`	`getSection(int startIndex, int endIndex)` Gets a section between two nodes of this Path.
`Path`	`getStartJoins()`
`PointInImage`	`getStartJoinsPoint()`
`static java.awt.Color`	`getSWCcolor(int swcType)` Gets the default SWC colors used by SNT.
`int`	`getSWCType()` Gets the SWC type.
`static java.lang.String`	`getSWCtypeName(int type, boolean capitalized)` Gets the SWC type label associated with the specified type flag.
`static java.util.ArrayList<java.lang.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 java.util.ArrayList<java.lang.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`
`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, or its nodes have been assigned an array of colors
`boolean`	`hasNodeAnnotations()` Assesses whether the nodes of this path have been assigned an array of annotations
`boolean`	`hasNodeColors()` Assesses whether the nodes of this path have been assigned an array of colors
`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.
`int`	`indexNearestTo(double x, double y, double z, double within)` Gets the index of the closest node associated with the specified world coordinates.
`void`	`insertNode(int index, PointInImage point)` Inserts a node at a specified position.
`boolean`	`isFittedVersionOfAnotherPath()` Checks if this Path is a fitted version of another path.
`boolean`	`isPrimary()` Checks if this Path is root.
`boolean`	`isSelected()`
`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.
`java.lang.String`	`realToString()`
`void`	`removeFrom3DViewer(ij3d.Image3DUniverse univ)`
`void`	`removeNode(int index)` Removes the specified node if this path has at least two nodes.
`void`	`setCanvasOffset(PointInCanvas canvasOffset)` Specifies a translation offset when rendering this Path in a `TracerCanvas`.
`void`	`setColor(java.awt.Color color)` Sets this path color.
`void`	`setColorRGB(org.scijava.util.ColorRGB colorRGB)` 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'.
`void`	`setEndJoin(Path other, PointInImage joinPoint)`
`void`	`setName(java.lang.String newName)` Sets this Path's name.
`void`	`setNodeAnnotation(BrainAnnotation annotation, int pos)` Assigns an annotation to an existing node.
`void`	`setNodeColor(java.awt.Color color, int pos)` Sets the node color.
`void`	`setNodeColors(java.awt.Color[] colors)` Sets the node colors.
`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`	`setRadii(double[] radii)` Assigns radii to this Path
`void`	`setRadius(double r)` Assigns a fixed radius to all the nodes of this Path
`void`	`setSelected(boolean newSelectedStatus)`
`void`	`setStartJoin(Path other, PointInImage joinPoint)`
`void`	`setSWCType(int newSWCType)` Sets the SWC type.
`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
`java.lang.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)`
`void`	`unsetEndJoin()`
`void`	`unsetStartJoin()`
`boolean`	`versionInUse()`

Methods inherited from class java.lang.Object
equals, 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 java.lang.String SWC_UNDEFINED_LABEL
```
    String representation of SWC_UNDEFINED
    
    See Also:
    
    Constant Field Values
  - SWC_SOMA_LABEL
```
public static final java.lang.String SWC_SOMA_LABEL
```
    String representation of SWC_SOMA
    
    See Also:
    
    Constant Field Values
  - SWC_AXON_LABEL
```
public static final java.lang.String SWC_AXON_LABEL
```
    String representation of SWC_AXON
    
    See Also:
    
    Constant Field Values
  - SWC_DENDRITE_LABEL
```
public static final java.lang.String SWC_DENDRITE_LABEL
```
    String representation of SWC_DENDRITE
    
    See Also:
    
    Constant Field Values
  - SWC_APICAL_DENDRITE_LABEL
```
public static final java.lang.String SWC_APICAL_DENDRITE_LABEL
```
    String representation of SWC_APICAL_DENDRITE
    
    See Also:
    
    Constant Field Values
  - SWC_FORK_POINT_LABEL
```
public static final java.lang.String SWC_FORK_POINT_LABEL
```
    String representation of SWC_FORK_POINT
    
    See Also:
    
    Constant Field Values
  - SWC_END_POINT_LABEL
```
public static final java.lang.String SWC_END_POINT_LABEL
```
    String representation of SWC_END_POINT
    
    See Also:
    
    Constant Field Values
  - SWC_CUSTOM_LABEL
```
public static final java.lang.String SWC_CUSTOM_LABEL
```
    String representation of SWC_CUSTOM
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - Path
```
public Path(double x_spacing,
            double y_spacing,
            double z_spacing,
            java.lang.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 java.lang.Comparable<Path>
  - getID
```
public int getID()
```
    Gets the identifier of this Path
    
    Returns:
    
    the identifier
  - 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()
```
  - getEndJoins
```
public Path getEndJoins()
```
  - getEndJoinsPoint
```
public PointInImage getEndJoinsPoint()
```
  - setName
```
public void setName(java.lang.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 java.lang.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)
  - getLength
```
public double getLength()
```
    Gets the length of this Path
    
    Returns:
    
    the length of this Path
  - isPrimary
```
public boolean isPrimary()
```
    Checks if this Path is root.
    
    Returns:
    
    true, if is primary (root)
  - setStartJoin
```
public void setStartJoin(Path other,
                         PointInImage joinPoint)
```
  - setEndJoin
```
public void setEndJoin(Path other,
                       PointInImage joinPoint)
```
  - unsetStartJoin
```
public void unsetStartJoin()
```
  - unsetEndJoin
```
public void unsetEndJoin()
```
  - size
```
public int size()
```
    Returns the number of nodes of this path
    
    Returns:
    
    the size, i.e., number of nodes
  - getNode
```
public PointInImage getNode(int pos)
                     throws java.lang.IndexOutOfBoundsException
```
    Gets the node at the specified position.
    
    Parameters:
    
    pos - the position index (0-based)
    
    Returns:
    
    the node
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if position is out-of-range
  - 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:
    
    java.lang.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:
    
    java.lang.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:
    
    java.lang.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.
  - 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
  - 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.
  - clone
```
public Path clone()
```
    Overrides:
    
    clone in class java.lang.Object
  - getCalibration
```
public ij.measure.Calibration getCalibration()
```
    Gets the spatial calibration of this Path.
    
    Returns:
    
    the calibration details associated with this Path
  - addNode
```
public void addNode(PointInImage point)
```
    Appends a node to this Path.
    
    Parameters:
    
    point - the node to be inserted
  - drawPathAsPoints
```
public void drawPathAsPoints(sc.fiji.snt.TracerCanvas canvas,
                             java.awt.Graphics2D g,
                             java.awt.Color c,
                             int plane,
                             boolean highContrast,
                             boolean drawDiameter)
```
  - drawPathAsPoints
```
public void drawPathAsPoints(sc.fiji.snt.TracerCanvas canvas,
                             java.awt.Graphics2D g2,
                             java.awt.Color c,
                             int plane,
                             boolean highContrast,
                             boolean drawDiameter,
                             int slice,
                             int either_side)
```
  - setNodeColors
```
public void setNodeColors(java.awt.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 java.awt.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 java.awt.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(java.awt.Color 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
  - 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:
    
    PointInImage.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 an array of annotations
    
    Returns:
    
    true, if successful
    
    See Also:
    
    PointInImage.getAnnotation()
  - getColor
```
public java.awt.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 org.scijava.util.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(java.awt.Color color)
```
    Sets this path color.
    
    Parameters:
    
    color - the path color. Set it to null, to have SNT rendered using default settings.
  - setColorRGB
```
public void setColorRGB(org.scijava.util.ColorRGB colorRGB)
```
    Sets this path color.
    
    Parameters:
    
    colorRGB - the path color. Set it to null, to have SNT rendered using default settings.
  - hasCustomColor
```
public boolean hasCustomColor()
```
    Assesses whether a custom color has been assigned to this Path, or its nodes have been assigned an array of colors
    
    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 java.awt.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
  - setUseFitted
```
public void setUseFitted(boolean useFitted)
                  throws java.lang.IllegalArgumentException
```
    Sets whether the fitted flavor of this Path should be used.
    
    Parameters:
    
    useFitted - the new use fitted
    
    Throws:
    
    java.lang.IllegalArgumentException - if this Path has not been fitted
  - 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
  - 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
  - getSWCtypeNames
```
public static java.util.ArrayList<java.lang.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 java.util.ArrayList<java.lang.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 java.lang.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
  - realToString
```
public java.lang.String realToString()
```
  - toString
```
public java.lang.String toString()
```
    This toString() method shows details of the path which is actually being displayed, not necessarily this path object. FIXME: this is probably horribly confusing.
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    
    the string
  - setSWCType
```
public void setSWCType(int newSWCType)
```
    Sets the SWC type.
    
    Parameters:
    
    newSWCType - the new SWC type
  - getSWCType
```
public int getSWCType()
```
    Gets the SWC type.
    
    Returns:
    
    the SWC type
  - getOrder
```
public int getOrder()
```
    Gets the branching order of this Path
    
    Returns:
    
    the branching order (reverse Horton-Strahler order) of this path or A primary path is always of order 1.
  - removeFrom3DViewer
```
public void removeFrom3DViewer(ij3d.Image3DUniverse univ)
```
  - getPoint3fList
```
public java.util.List<org.scijava.vecmath.Point3f> getPoint3fList()
```
  - addAsLinesTo3DViewer
```
@Deprecated
public ij3d.Content addAsLinesTo3DViewer(ij3d.Image3DUniverse univ,
                                                     java.awt.Color c,
                                                     ij.ImagePlus colorImage)
```
    Deprecated.
  - addDiscsTo3DViewer
```
@Deprecated
public ij3d.Content addDiscsTo3DViewer(ij3d.Image3DUniverse univ,
                                                   java.awt.Color c,
                                                   ij.ImagePlus colorImage)
```
    Deprecated.
  - addDiscsTo3DViewer
```
@Deprecated
public ij3d.Content addDiscsTo3DViewer(ij3d.Image3DUniverse univ,
                                                   org.scijava.vecmath.Color3f c,
                                                   ij.ImagePlus colorImage)
```
    Deprecated.
  - addTo3DViewer
```
@Deprecated
public void addTo3DViewer(ij3d.Image3DUniverse univ,
                                      java.awt.Color c,
                                      ij.ImagePlus colorImage)
```
    Deprecated.
  - addTo3DViewer
```
@Deprecated
public void addTo3DViewer(ij3d.Image3DUniverse univ,
                                      org.scijava.vecmath.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 -1 if this Path has no radii
    
    See Also:
    
    hasRadii()
  - transform
```
public Path transform(PathTransformer transformation,
                      ij.ImagePlus template,
                      ij.ImagePlus model)
```
  - findJunctions
```
public java.util.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()
  - findJunctionIndices
```
public java.util.TreeSet<java.lang.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()
  - 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
  - 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)

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

Constructor Detail

Path

Method Detail

compareTo

getID

setCanvasOffset

getCanvasOffset

getStartJoins

getStartJoinsPoint

getEndJoins

getEndJoinsPoint

setName

getName

getLength

isPrimary

setStartJoin

setEndJoin

unsetStartJoin

unsetEndJoin

size

getNode

contains

insertNode

removeNode

moveNode

getNodeIndex

nearestNodeTo

indexNearestTo

getEditableNodeIndex

setEditableNode

getXUnscaled

getYUnscaled

getZUnscaled

getXUnscaledDouble

getYUnscaledDouble

getZUnscaledDouble

getSection

clone

getCalibration

addNode

drawPathAsPoints

drawPathAsPoints

setNodeColors

getNodeColors

getNodeColor

setNodeColor

setNodeValue

setNodeAnnotation

getNodeValue

getNodeAnnotation

setNodeValues

hasNodeValues

hasNodeAnnotations

getColor

getColorRGB

setColor

setColorRGB

hasCustomColor