Tree (Fiji Javadocs 0-SNAPSHOT API)

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

All Implemented Interfaces:

TreeProperties
```
public class Tree
extends Object
implements TreeProperties
```
Utility class to access a Collection of Paths (typically a complete reconstruction) . A Tree is the preferred way to group, access and manipulate Paths that share something in common, specially when scripting SNT. Note that a "Tree" here is literally a collection of Paths. Very few restrictions are imposed on its topology, although it is generally assumed that the Collection of paths describes a single-rooted structure with no loops.

Author:

Tiago Ferreira, Cameron Arshadi

Field Summary

Fields
Modifier and Type Field and Description

static int X_AXIS

static int Y_AXIS

static int Z_AXIS
- Fields inherited from interface sc.fiji.snt.TreeProperties
  AXONAL, DENDRITIC, KEY_COLOR, KEY_COMPARTMENT, KEY_FRAME_POS, KEY_ID, KEY_IMG, KEY_IMG_CHANNEL, KEY_IMG_FRAME, KEY_LABEL, KEY_SOURCE, KEY_SPATIAL_UNIT, SOMATIC, UNSET

Fields
Modifier and Type	Field and Description
`static int`	`X_AXIS`
`static int`	`Y_AXIS`
`static int`	`Z_AXIS`

Constructor Summary

Constructors
Constructor and Description
`Tree()` Instantiates a new empty Tree.
`Tree(Collection<Path> paths)` Instantiates a new Tree from a set of paths.
`Tree(Collection<SWCPoint> nodes, String label)` Instantiates a Tree from a collection of reconstruction nodes.
`Tree(DirectedWeightedGraph graph, String label)`
`Tree(DirectedWeightedGraph graph, String label, boolean keepTreePathStructure)`
`Tree(String filename)` Instantiates a new tree from a SWC, TRACES or JSON file.
`Tree(String filename, int... swcTypes)` Instantiates a new tree from a filtered SWC, TRACES or JSON file.
`Tree(String filename, String compartment)` Instantiates a new tree from a SWC, TRACES or JSON file with filtering.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`add(Path p)` Adds a new Path to this Tree.
`void`	`applyCanvasOffset(double xOffset, double yOffset, double zOffset)` Specifies the offset to be used when rendering this Tree in a `TracerCanvas`.
`void`	`applyProperties(Tree tree)`
`void`	`assignImage(Dataset dataset)`
`void`	`assignImage(ij.ImagePlus imp)` Assigns the spatial calibration of an image to this Tree.
`static void`	`assignUniqueColors(Collection<Tree> trees)`
`void`	`assignValue(double value)` Assigns a numeric property to this Tree.
`Tree`	`clone()`
`void`	`downSample(double maximumAllowedDeviation)` Downsamples the tree.
`static Tree`	`fromFile(String filePath)` Script-friendly method for creating a Tree from a reconstruction file.
`Path`	`get(int index)` Returns the Path at the specified position.
`double`	`getApproximatedVolume()` Retrieves an approximate estimate of Tree's volume by approximating the volume of each path, and summing to total.
`double`	`getAssignedValue()` Retrieves the numeric property assigned to this Tree.
`BoundingBox`	`getBoundingBox()` Gets the bounding box associated with this tree.
`BoundingBox`	`getBoundingBox(boolean computeIfUnset)` Gets the bounding box associated with this tree.
`DirectedWeightedGraph`	`getGraph()` Assembles a DirectedGraph from this Tree.
`DirectedWeightedGraph`	`getGraph(boolean simplify)` Assembles a DirectedGraph from this Tree.
`ij.ImagePlus`	`getImpContainer(int multiDThreePaneView, int bitDepth)` Gets an empty image capable of holding the skeletonized version of this tree.
`String`	`getLabel()` Returns the identifying label of this tree.
`List<PointInImage>`	`getNodes()` Gets all the nodes (path points) forming this tree.
`List<SWCPoint>`	`getNodesAsSWCPoints()`
`Properties`	`getProperties()` Returns the Properties instance holding the persistent set of properties.
`PointInImage`	`getRoot()` Gets the first node of the main primary path of this tree
`ij.ImagePlus`	`getSkeleton()` Retrieves the rasterized skeleton of this tree at 1:1 scaling.
`protected List<Object>`	`getSkeleton2()` Retrieves the rasterized skeleton of this tree at 1:1 scaling.
`ij.ImagePlus`	`getSkeleton2D()` Retrieves a 2D projection of the rasterized skeleton of this tree at 1:1 scaling.
`List<PointInImage>`	`getSomaNodes()` Gets the list of all nodes tagged as `Path.SWC_SOMA`.
`static Map<Integer,String>`	`getSWCTypeMap()` Returns the SWC Type flags used by SNT.
`Set<Integer>`	`getSWCTypes()` Extracts the SWC-type flags present in this Tree.
`int`	`indexOf(Path path)` Returns the index of the specified Path in this Tree.
`boolean`	`is3D()` Assesses whether this Tree has depth.
`boolean`	`isAnnotated()` Checks if the nodes of this Tree have been assigned `BrainAnnotation`s (neuropil labels).
`boolean`	`isEmpty()` Checks if this Tree is empty.
`ArrayList<Path>`	`list()` Gets all the paths from this tree.
`static List<Tree>`	`listFromDir(String dir)` Retrieves a list of `Tree`s from reconstruction files stored in a common directory.
`static List<Tree>`	`listFromDir(String dir, String pattern)` Retrieves a list of `Tree`s from reconstruction files stored in a common directory matching the specified criteria.
`static List<Tree>`	`listFromDir(String dir, String pattern, String... swcTypes)` Retrieves a list of `Tree`s from reconstruction files stored in a common directory matching the specified criteria.
`static Collection<Tree>`	`listFromFile(String tracesOrJsonFile)` Retrieves a list of `Tree`s from a single file.
`static void`	`main(String[] args)`
`boolean`	`merge(Tree tree)` Appends all paths of a specified `Tree` to this one.
`void`	`rebuildGraph()` Re-assembles the DirectedGraph object returned by `getGraph()` ensuring that no untracked changes exist.
`boolean`	`remove(Path p)` Removes a path from this tree.
`void`	`replaceAll(List<Path> paths)` Replaces all Paths in this Tree.
`void`	`rotate(int axis, double angle)` Rotates the tree.
`boolean`	`save(String filePath)` Saves this Tree to a .TRACES (XML, compressed) file.
`boolean`	`saveAsSWC(String filePath)` Saves this Tree to an SWC file.
`void`	`scale(double xScale, double yScale, double zScale)` Scales the tree by the specified factors.
`void`	`scale(double xScale, double yScale, double zScale, double radiusScale)` Scales the tree by the specified factors.
`void`	`setBoundingBox(BoundingBox box)` Associates a bounding box to this tree.
`void`	`setColor(ColorRGB color)` Assigns a color to all the paths in this tree.
`void`	`setColor(String color)` Assigns a color to all the paths in this tree.
`void`	`setColor(String color, double transparencyPercent)` Assigns a color to all the paths in this tree.
`void`	`setLabel(String label)` Sets an identifying label for this Tree.
`void`	`setRadii(double r)` Assigns a fixed radius to all the nodes in this tree.
`void`	`setSWCType(String type)` Assigns an SWC type label to all the Paths in this Tree.
`void`	`setType(int type)` Assigns an SWC type label to all the Paths in this Tree.
`void`	`show()`
`Viewer2D`	`show2D()`
`Viewer3D`	`show3D()`
`int`	`size()` Retrieves the number of paths in this tree.
`void`	`skeletonize(ij.ImagePlus destinationImp, int value)` Skeletonizes (rasterizes) this tree on the specified image using Bresenham’s Algorithm (3D).
`Tree`	`subTree(int... swcTypes)` Extracts the subset of paths matching the specified criteria.
`Tree`	`subTree(String... swcTypes)` Extracts the subset of paths matching the specified criteria (script friendly method)
`void`	`swapAxes(int axis1, int axis2)` Swaps the coordinates of two axes in this Tree.
`void`	`translate(double xOffset, double yOffset, double zOffset)` Translates the tree by the specified offset.

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

Methods inherited from interface sc.fiji.snt.TreeProperties
getStandardizedCompartment

- Field Detail
  - X_AXIS
```
public static final int X_AXIS
```
    See Also:
    
    Constant Field Values
  - Y_AXIS
```
public static final int Y_AXIS
```
    See Also:
    
    Constant Field Values
  - Z_AXIS
```
public static final int Z_AXIS
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - Tree
```
public Tree()
```
    Instantiates a new empty Tree.
  - Tree
```
public Tree(Collection<Path> paths)
```
    Instantiates a new Tree from a set of paths.
    
    Parameters:
    
    paths - the Collection of paths forming this tree. Null not allowed. Note that when a Path has been fitted and Path.getUseFitted() is true, its fitted 'flavor' is used.
  - Tree
```
public Tree(Collection<SWCPoint> nodes,
            String label)
```
    Instantiates a Tree from a collection of reconstruction nodes.
    
    Parameters:
    
    nodes - the collection of reconstruction nodes. Nodes will be sorted by id and any duplicate entries pruned.
    
    label - the identifying label for this Tree.
  - Tree
```
public Tree(DirectedWeightedGraph graph,
            String label)
```
  - Tree
```
public Tree(DirectedWeightedGraph graph,
            String label,
            boolean keepTreePathStructure)
```
  - Tree
```
public Tree(String filename)
     throws IllegalArgumentException
```
    Instantiates a new tree from a SWC, TRACES or JSON file.
    
    Parameters:
    
    filename - the absolute file path of the imported file
    
    Throws:
    
    IllegalArgumentException - if file path is not valid
  - Tree
```
public Tree(String filename,
            String compartment)
     throws IllegalArgumentException
```
    Instantiates a new tree from a SWC, TRACES or JSON file with filtering.
    
    Parameters:
    
    filename - the absolute file path of the imported file
    
    compartment - A case insensitive string with at least 2 characters describing the sub-cellular compartment (axonal or dendritic) to be imported (e.g., 'axon', 'dendrites', 'axn', 'dnd', etc.). It is ignored if filename encodes a .TRACES file.
    
    Throws:
    
    IllegalArgumentException - if file path is not valid
  - Tree
```
public Tree(String filename,
            int... swcTypes)
     throws IllegalArgumentException
```
    Instantiates a new tree from a filtered SWC, TRACES or JSON file.
    
    Parameters:
    
    filename - the absolute file path of the imported file
    
    swcTypes - only paths matching the specified SWC type(s) (e.g., Path.SWC_AXON, Path.SWC_DENDRITE, etc.) will be imported. Ignored if filename encodes a .TRACES file.
    
    Throws:
    
    IllegalArgumentException - if file path is not valid
- Method Detail
  - add
```
public boolean add(Path p)
```
    Adds a new Path to this Tree.
    
    Parameters:
    
    p - the Path to be added
    
    Returns:
    
    true, if Path successful added
  - merge
```
public boolean merge(Tree tree)
```
    Appends all paths of a specified Tree to this one.
    
    Parameters:
    
    tree - the Tree to be merged
    
    Returns:
    
    true if this Tree changed as a result of the merge
  - replaceAll
```
public void replaceAll(List<Path> paths)
```
    Replaces all Paths in this Tree.
    
    Parameters:
    
    paths - the replacing Paths
  - get
```
public Path get(int index)
```
    Returns the Path at the specified position.
    
    Parameters:
    
    index - index of the element to return
    
    Returns:
    
    the element at the specified position
  - indexOf
```
public int indexOf(Path path)
```
    Returns the index of the specified Path in this Tree.
    
    Parameters:
    
    path - the Path to be searched for
    
    Returns:
    
    the path index, or -1 if it was not found
  - remove
```
public boolean remove(Path p)
```
    Removes a path from this tree.
    
    Parameters:
    
    p - the Path to be removed
    
    Returns:
    
    true if this tree contained p
  - list
```
public ArrayList<Path> list()
```
    Gets all the paths from this tree.
    
    Returns:
    
    the paths forming this tree
  - isEmpty
```
public boolean isEmpty()
```
    Checks if this Tree is empty.
    
    Returns:
    
    true if this tree contains no Paths, false otherwise
  - isAnnotated
```
public boolean isAnnotated()
```
    Checks if the nodes of this Tree have been assigned BrainAnnotations (neuropil labels).
    
    Returns:
    
    true if at least one node in the Tree has a valid annotation, false otherwise
  - downSample
```
public void downSample(double maximumAllowedDeviation)
```
    Downsamples the tree.
    
    Parameters:
    
    maximumAllowedDeviation - the maximum allowed distance between 'shaft' path nodes. Note that 1) upsampling is not supported, and 2) the position of nodes at branch points and tips remains unaltered during downsampling
    
    See Also:
    
    PathDownsampler
  - subTree
```
public Tree subTree(String... swcTypes)
```
    Extracts the subset of paths matching the specified criteria (script friendly method)
    
    Parameters:
    
    swcTypes - SWC type(s) a string with at least 2 characters describing the SWC type allowed in the subtree (e.g., 'soma', 'axn', or 'dendrite')
    
    Returns:
    
    the subset of paths matching the filtering criteria, or an empty Tree if no hits were retrieved
  - subTree
```
public Tree subTree(int... swcTypes)
```
    Extracts the subset of paths matching the specified criteria.
    
    Parameters:
    
    swcTypes - SWC type(s) (e.g., Path.SWC_AXON, Path.SWC_DENDRITE, etc.) allowed in the subtree
    
    Returns:
    
    the subset of paths matching the filtering criteria, or an empty Tree if no hits were retrieved
  - applyProperties
```
public void applyProperties(Tree tree)
```
  - setType
```
public void setType(int type)
```
    Assigns an SWC type label to all the Paths in this Tree.
    
    Parameters:
    
    type - the SWC type (e.g., Path.SWC_AXON, Path.SWC_DENDRITE, etc.)
  - setSWCType
```
public void setSWCType(String type)
```
    Assigns an SWC type label to all the Paths in this Tree.
    
    Parameters:
    
    type - the SWC type (e.g., "soma", "axon", "(basal) dendrite", "apical dendrite", etc.)
  - getSWCTypes
```
public Set<Integer> getSWCTypes()
```
    Extracts the SWC-type flags present in this Tree.
    
    Returns:
    
    the set of SWC type(s) (e.g., Path.SWC_AXON, Path.SWC_DENDRITE, etc.) present in the tree
  - show3D
```
public Viewer3D show3D()
```
  - show2D
```
public Viewer2D show2D()
```
  - show
```
public void show()
```
  - getSomaNodes
```
public List<PointInImage> getSomaNodes()
```
    Gets the list of all nodes tagged as Path.SWC_SOMA.
    
    Returns:
    
    the soma nodes or null if no Paths are tagged as soma.
    
    See Also:
    
    getRoot()
  - getRoot
```
public PointInImage getRoot()
```
    Gets the first node of the main primary path of this tree
    
    Returns:
    
    the root node, or null if the main primary path is undefined for this tree.
  - applyCanvasOffset
```
public void applyCanvasOffset(double xOffset,
                              double yOffset,
                              double zOffset)
```
    Specifies the offset to be used when rendering this Tree in a TracerCanvas. Path coordinates remain unaltered.
    
    Parameters:
    
    xOffset - the x offset (in pixels)
    
    yOffset - the y offset (in pixels)
    
    zOffset - the z offset (in pixels)
  - translate
```
public void translate(double xOffset,
                      double yOffset,
                      double zOffset)
```
    Translates the tree by the specified offset.
    
    Parameters:
    
    xOffset - the x offset
    
    yOffset - the y offset
    
    zOffset - the z offset
  - scale
```
public void scale(double xScale,
                  double yScale,
                  double zScale)
```
    Scales the tree by the specified factors.
    
    Parameters:
    
    xScale - the scaling factor for x coordinates
    
    yScale - the scaling factor for y coordinates
    
    zScale - the scaling factor for z coordinates
  - scale
```
public void scale(double xScale,
                  double yScale,
                  double zScale,
                  double radiusScale)
```
    Scales the tree by the specified factors.
    
    Parameters:
    
    xScale - the scaling factor for x coordinates
    
    yScale - the scaling factor for y coordinates
    
    zScale - the scaling factor for z coordinates
    
    radiusScale - the scaling factor for node radii.
  - rotate
```
public void rotate(int axis,
                   double angle)
```
    Rotates the tree.
    
    Parameters:
    
    axis - the rotation axis. Either X_AXIS, Y_AXIS, or Z_AXIS.
    
    angle - the rotation angle in degrees. Ignored if 0.
  - getNodes
```
public List<PointInImage> getNodes()
```
    Gets all the nodes (path points) forming this tree.
    
    Returns:
    
    the points
  - is3D
```
public boolean is3D()
             throws IllegalArgumentException
```
    Assesses whether this Tree has depth.
    
    Returns:
    
    true, if is 3D
    
    Throws:
    
    IllegalArgumentException - if tree is empty
  - setBoundingBox
```
public void setBoundingBox(BoundingBox box)
```
    Associates a bounding box to this tree.
    
    Parameters:
    
    box - the BoundingBox, typically referring to the image associated with this tree
  - getBoundingBox
```
public BoundingBox getBoundingBox()
```
    Gets the bounding box associated with this tree.
    
    Returns:
    
    the BoundingBox. It will be computed if no boundaries have been set.
  - getBoundingBox
```
public BoundingBox getBoundingBox(boolean computeIfUnset)
```
    Gets the bounding box associated with this tree.
    
    Parameters:
    
    computeIfUnset - if true no BoundingBox has been explicitly set, and, a BoundingBox will be compute from all the nodes of this Tree
    
    Returns:
    
    the BoundingBox
  - getImpContainer
```
public ij.ImagePlus getImpContainer(int multiDThreePaneView,
                                    int bitDepth)
```
    Gets an empty image capable of holding the skeletonized version of this tree.
    
    Parameters:
    
    multiDThreePaneView - the pane flag indicating the SNT view for this image e.g., MultiDThreePanes.XY_PLANE
    
    bitDepth - 8, 16 or 32 (float)
    
    Returns:
    
    the empty ImagePlus container
  - skeletonize
```
public void skeletonize(ij.ImagePlus destinationImp,
                        int value)
                 throws IllegalArgumentException
```
    Skeletonizes (rasterizes) this tree on the specified image using Bresenham’s Algorithm (3D).
    
    Parameters:
    
    destinationImp - the destination image (16-bit). It is assumed that the image dimensions are suitable, and that the spatial calibration of the image is compatible with that of this tree. Out of bound locations will be silently ignored.
    
    value - the pixel intensity of the skeleton
    
    Throws:
    
    IllegalArgumentException - If image is not 16-bit grayscale (unsigned)
  - getSkeleton
```
public ij.ImagePlus getSkeleton()
```
    Retrieves the rasterized skeleton of this tree at 1:1 scaling.
    
    Returns:
    
    the skeletonized 8-bit binary image: (skeleton: 255, background: 0).
    
    See Also:
    
    skeletonize(ImagePlus, int)
  - getSkeleton2
```
protected List<Object> getSkeleton2()
```
    Retrieves the rasterized skeleton of this tree at 1:1 scaling.
    
    Returns:
    
    the skeletonized 8-bit binary image: (skeleton: 255, background: 0).
    
    See Also:
    
    skeletonize(ImagePlus, int)
  - getSkeleton2D
```
public ij.ImagePlus getSkeleton2D()
```
    Retrieves a 2D projection of the rasterized skeleton of this tree at 1:1 scaling.
    
    Returns:
    
    the skeletonized 8-bit binary image: (skeleton: 255, background: 0).
    
    See Also:
    
    getSkeleton()
  - size
```
public int size()
```
    Retrieves the number of paths in this tree.
    
    Returns:
    
    Returns the number of paths in this tree.
  - setColor
```
public void setColor(ColorRGB color)
```
    Assigns a color to all the paths in this tree. Note that assigning a non-null color will remove node colors from Paths.
    
    Parameters:
    
    color - the color to be applied.
    
    See Also:
    
    Path.hasNodeColors()
  - setColor
```
public void setColor(String color)
```
    Assigns a color to all the paths in this tree. Note that assigning a non-null color will remove node colors from Paths.
    
    Parameters:
    
    color - the color to be applied, either a 1) HTML color codes starting with hash (#), a color preset ("red", "blue", etc.), or integer triples of the form r,g,b and range [0, 255]
  - setColor
```
public void setColor(String color,
                     double transparencyPercent)
```
    Assigns a color to all the paths in this tree. Note that assigning a non-null color will remove node colors from Paths.
    
    Parameters:
    
    color - the color to be applied, either a 1) HTML color codes starting with hash (#), a color preset ("red", "blue", etc.), or integer triples of the form r,g,b and range [0, 255]
    
    transparencyPercent - the color transparency (in percentage)
  - setRadii
```
public void setRadii(double r)
```
    Assigns a fixed radius to all the nodes in this tree.
    
    Parameters:
    
    r - the radius to be assigned. Setting it to 0 or Double.NaN removes the radius attribute from the Tree
  - getProperties
```
public Properties getProperties()
```
    Returns the Properties instance holding the persistent set of properties. Useful to associate metadata to this tree. E.g.
```
 
 getProperties().setProperty(Tree.KEY_SPATIAL_UNIT, "um");
 String unit = getProperties().getProperty(Tree.KEY_SPATIAL_UNIT);
 getProperties().setProperty(Tree.KEY_COMPARTMENT, Tree.DENDRITIC);
 
 
```
    Returns:
    
    the Properties instance
  - setLabel
```
public void setLabel(String label)
```
    Sets an identifying label for this Tree.
    
    Parameters:
    
    label - the identifying string
  - getLabel
```
public String getLabel()
```
    Returns the identifying label of this tree. When importing files, the label typically defaults to the imported filename,
    
    Returns:
    
    the Tree label (or null) if none has been set.
  - getNodesAsSWCPoints
```
public List<SWCPoint> getNodesAsSWCPoints()
                                   throws IllegalArgumentException
```
    Throws:
    
    IllegalArgumentException
  - getGraph
```
public DirectedWeightedGraph getGraph()
                               throws IllegalArgumentException
```
    Assembles a DirectedGraph from this Tree.
    
    Returns:
    
    the Tree's graph with edge weights corresponding to inter-node distances
    
    Throws:
    
    IllegalArgumentException - if tree contains multiple roots or loops
  - rebuildGraph
```
public void rebuildGraph()
```
    Re-assembles the DirectedGraph object returned by getGraph() ensuring that no untracked changes exist. Usually, calling this method is not necessary since most changes to this Tree percolate to its graph representation.
  - getGraph
```
public DirectedWeightedGraph getGraph(boolean simplify)
                               throws IllegalArgumentException
```
    Assembles a DirectedGraph from this Tree.
    
    Parameters:
    
    simplify - if true, graph will be simplified so that Tree is only represented by root, branch-points and tips.
    
    Returns:
    
    the Tree's graph with edge weights corresponding to branch lengths
    
    Throws:
    
    IllegalArgumentException - if tree contains multiple roots or loops
  - fromFile
```
public static Tree fromFile(String filePath)
```
    Script-friendly method for creating a Tree from a reconstruction file.
    
    Parameters:
    
    filePath - the absolute path to the file (.Traces, (e)SWC or JSON) to be imported
    
    Returns:
    
    the Tree instance, or null if file could not be imported
  - listFromFile
```
public static Collection<Tree> listFromFile(String tracesOrJsonFile)
                                     throws IllegalArgumentException
```
    Retrieves a list of Trees from a single file.
    
    Parameters:
    
    tracesOrJsonFile - the file containing the reconstructions (typically a .traces or .json extension). A directory is also supported.
    
    Returns:
    
    the collection of imported Trees. An empty list is retrieved if tracesOrJsonFile is not a valid, readable file.
    
    Throws:
    
    IllegalArgumentException
  - listFromDir
```
public static List<Tree> listFromDir(String dir)
```
    Retrieves a list of Trees from reconstruction files stored in a common directory.
    
    Parameters:
    
    dir - the directory containg the reconstruction files (.(e)swc, .traces, .json extension)
    
    Returns:
    
    the list of imported Trees. An empty list is retrieved if dir is not a valid, readable directory.
  - listFromDir
```
public static List<Tree> listFromDir(String dir,
                                     String pattern)
```
    Retrieves a list of Trees from reconstruction files stored in a common directory matching the specified criteria.
    
    Parameters:
    
    dir - the directory containing the reconstruction files (.(e)swc, .traces, .json extension)
    
    pattern - the filename substring (case sensitive) to be matched. Only filenames containing pattern will be imported from the directory. null allowed.
    
    Returns:
    
    the list of imported Trees. An empty list is retrieved if dir is not a valid, readable directory.
  - listFromDir
```
public static List<Tree> listFromDir(String dir,
                                     String pattern,
                                     String... swcTypes)
```
    Retrieves a list of Trees from reconstruction files stored in a common directory matching the specified criteria.
    
    Parameters:
    
    dir - the directory containing the reconstruction files (.(e)swc, .traces, .json extension)
    
    pattern - the filename substring (case sensitive) to be matched. Only filenames containing pattern will be imported from the directory. null allowed.
    
    swcTypes - SWC type(s) a string with at least 2 characters describing the SWC type allowed in the subtree (e.g., 'soma', 'axn', or 'dendrite'). Ignored when null
    
    Returns:
    
    the list of imported Trees. An empty list is retrieved if dir is not a valid, readable directory.
  - getSWCTypeMap
```
public static Map<Integer,String> getSWCTypeMap()
```
    Returns the SWC Type flags used by SNT.
    
    Returns:
    
    the map mapping swct type flags (e.g., Path.SWC_AXON, Path.SWC_DENDRITE, etc.) and their respective labels
  - saveAsSWC
```
public boolean saveAsSWC(String filePath)
```
    Saves this Tree to an SWC file.
    
    Parameters:
    
    filePath - the absolute path of the output file. .swc is automatically appended if filePath does not include an extension. If a label has been assigned, filePath can also be a directory. If this Tree contains multiple roots, each rooted structure will be saved on a series of files with 3-digit identifiers appended to the specified file path (e.g., -000.swc, -001.swc, etc).
    
    Returns:
    
    true, if file successfully saved.
    
    See Also:
    
    setLabel(String)
  - save
```
public boolean save(String filePath)
```
    Saves this Tree to a .TRACES (XML, compressed) file.
    
    Parameters:
    
    filePath - the absolute path of the output file. .traces is automatically appended if filePath does not include an extension. If a label has been assigned, filePath can also be a directory.
    
    Returns:
    
    true, if file successfully saved.
    
    See Also:
    
    setLabel(String)
  - assignValue
```
public void assignValue(double value)
```
    Assigns a numeric property to this Tree.
    
    Parameters:
    
    value - the value to be assigned to this Tree.
    
    See Also:
    
    getAssignedValue()
  - getApproximatedVolume
```
public double getApproximatedVolume()
```
    Retrieves an approximate estimate of Tree's volume by approximating the volume of each path, and summing to total. THe volume of each path is computed assuming the volume of each of inter-node segment to be that of a truncated cone (Frustum).
    
    Returns:
    
    the approximate volume or 9 if this Tree's paths have no radius information
    
    See Also:
    
    Path.getApproximatedVolume()
  - getAssignedValue
```
public double getAssignedValue()
```
    Retrieves the numeric property assigned to this Tree.
    
    Returns:
    
    the assigned value.
    
    See Also:
    
    assignValue(double)
  - clone
```
public Tree clone()
```
    Overrides:
    
    clone in class Object
  - assignUniqueColors
```
public static void assignUniqueColors(Collection<Tree> trees)
```
  - assignImage
```
public void assignImage(ij.ImagePlus imp)
```
    Assigns the spatial calibration of an image to this Tree.
    
    Parameters:
    
    imp - the image providing the spatial calibration. Null allowed.
  - assignImage
```
public void assignImage(Dataset dataset)
```
  - swapAxes
```
public void swapAxes(int axis1,
                     int axis2)
```
    Swaps the coordinates of two axes in this Tree.
    
    Parameters:
    
    axis1 - the first axis. Either X_AXIS, Y_AXIS, or Z_AXIS
    
    axis2 - the second axis. Either X_AXIS, Y_AXIS, or Z_AXIS
  - main
```
public static void main(String[] args)
```

Class Tree

Field Summary

Fields inherited from interface sc.fiji.snt.TreeProperties

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface sc.fiji.snt.TreeProperties

Field Detail

X_AXIS

Y_AXIS

Z_AXIS

Constructor Detail

Tree

Tree

Tree

Tree

Tree

Tree

Tree

Tree

Method Detail

add

merge

replaceAll

get

indexOf

remove

list

isEmpty

isAnnotated

downSample

subTree

subTree

applyProperties

setType

setSWCType

getSWCTypes

show3D

show2D

show

getSomaNodes

getRoot

applyCanvasOffset

translate

scale

scale

rotate

getNodes

is3D

setBoundingBox

getBoundingBox

getBoundingBox

getImpContainer

skeletonize

getSkeleton

getSkeleton2

getSkeleton2D

size

setColor

setColor

setColor

setRadii

getProperties

setLabel

getLabel

getNodesAsSWCPoints

getGraph

rebuildGraph

getGraph

fromFile

listFromFile

listFromDir

listFromDir

listFromDir

getSWCTypeMap

saveAsSWC

save

assignValue

getApproximatedVolume

getAssignedValue