SNTService (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- org.scijava.AbstractContextual
- - org.scijava.plugin.AbstractRichPlugin
  - - org.scijava.service.AbstractService
    - - sc.fiji.snt.SNTService

All Implemented Interfaces:

Comparable<Prioritized>, ImageJService, Contextual, Disposable, Identifiable, Initializable, Locatable, Logged, HasPluginInfo, RichPlugin, SciJavaPlugin, Prioritized, Service, Versioned
```
public class SNTService
extends AbstractService
implements ImageJService
```
Service for accessing and scripting the active instance of SNT.

Author:

Tiago Ferreira, Kyle Harrington

Constructor Summary

Constructors
Constructor and Description

SNTService()

Constructors
Constructor and Description
`SNTService()`

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`assignValues(boolean selectedPathsOnly)` Assigns pixel intensities at each Path node, storing them as Path values.
`ij.ImagePlus`	`captureView(String view, boolean project)` Retrieves a WYSIWYG 'snapshot' of a tracing canvas.
`ij.ImagePlus`	`captureView(String view, ColorRGB backgroundColor)` Retrieves a WYSIWYG 'snapshot' of a tracing canvas without voxel data.
`ij.ImagePlus`	`demoImage(String img)` Returns one of the demo images bundled with SNT image associated with the demo (fractal) tree.
`Tree`	`demoTree()` Deprecated.
`Tree`	`demoTree(String tree)` Returns a demo tree.
`ij.ImagePlus`	`demoTreeImage()` Deprecated.
`List<Tree>`	`demoTrees()` Returns a collection of four demo reconstructions (dendrites from pyramidal cells from the MouseLight database).
`protected List<Tree>`	`demoTreesSWC()`
`void`	`dispose()` Quits SNT.
`TreeAnalyzer`	`getAnalyzer(boolean selectedPathsOnly)` Returns a `TreeAnalyzer` instance constructed from current Paths.
`SciViewSNT`	`getOrCreateSciViewSNT()`
`PathAndFillManager`	`getPathAndFillManager()` Returns the `PathAndFillManager` associated with the current SNT instance.
`List<Path>`	`getPaths()` Gets the paths currently listed in the Path Manager
`SNT`	`getPlugin()` Returns a reference to the active `SNT` plugin.
`Viewer3D`	`getRecViewer()` Returns a reference to the active Reconstruction Viewer (either stand-alone or SNT-associated instance).
`Viewer3D`	`getRecViewer(int id)` Returns a reference to an opened Reconstruction Viewer (standalone instance).
`SciViewSNT`	`getSciViewSNT()`
`Collection<Path>`	`getSelectedPaths()` Gets the paths currently selected in the Path Manager list.
`TreeStatistics`	`getStatistics(boolean selectedPathsOnly)` Returns a `TreeStatistics` instance constructed from current Paths.
`SNTTable`	`getTable()` Returns a reference to SNT's main table of measurements.
`Tree`	`getTree()` Gets the collection of paths listed in the Path Manager as a `Tree` object.
`Tree`	`getTree(boolean selectedPathsOnly)` Gets the collection of paths listed in the Path Manager as a `Tree` object.
`SNTUI`	`getUI()` Returns a reference to SNT's UI.
`SNT`	`initialize(boolean startUI)` Initializes SNT.
`SNT`	`initialize(ij.ImagePlus imp, boolean startUI)` Initializes SNT.
`SNT`	`initialize(String imagePath, boolean startUI)` Initializes SNT.
`boolean`	`isActive()` Gets whether SNT is running.
`void`	`loadGraph(DirectedWeightedGraph graph)`
`void`	`loadTracings(String filePathOrURL)` Loads the specified tracings file.
`void`	`loadTree(Tree tree)` Loads the specified tree.
`Viewer3D`	`newRecViewer(boolean guiControls)` Instantiates a new standalone Reconstruction Viewer.
`boolean`	`save(String filePath)` Saves all the existing paths to a file.
`void`	`updateViewers()` Script-friendly method for updating (refreshing) all viewers currently in use by SNT.

Methods inherited from class org.scijava.service.AbstractService
getContext, setContext, toString

Methods inherited from class org.scijava.plugin.AbstractRichPlugin
getInfo, getPriority, setInfo, setPriority

Methods inherited from class org.scijava.AbstractContextual
context

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

Methods inherited from interface org.scijava.service.Service
initialize, registerEventHandlers

Methods inherited from interface org.scijava.plugin.RichPlugin
getIdentifier, log

Methods inherited from interface org.scijava.Contextual
context, getContext, setContext

Methods inherited from interface org.scijava.Prioritized
compareTo, getPriority, setPriority

Methods inherited from interface org.scijava.plugin.HasPluginInfo
getInfo, setInfo

Methods inherited from interface org.scijava.Locatable
getLocation

Methods inherited from interface org.scijava.Versioned
getVersion

- Constructor Detail
  - SNTService
```
public SNTService()
```
- Method Detail
  - isActive
```
public boolean isActive()
```
    Gets whether SNT is running.
    
    Returns:
    
    true if this SNTService is active, tied to the active instance of SNT
  - assignValues
```
public void assignValues(boolean selectedPathsOnly)
                  throws UnsupportedOperationException,
                         IllegalArgumentException
```
    Assigns pixel intensities at each Path node, storing them as Path values. Assigned intensities are those of the channel and time point currently being traced. Assumes SNT has been initialized with a valid image.
    
    Parameters:
    
    selectedPathsOnly - If true, only selected paths will be assigned values, otherwise voxel intensities will be assigned to all paths
    
    Throws:
    
    UnsupportedOperationException - if SNT is not running
    
    IllegalArgumentException - If valid imaged data is not available
    
    See Also:
    
    PathProfiler, Path.setNodeValues(double[])
  - initialize
```
public SNT initialize(boolean startUI)
```
    Initializes SNT. Since no image is specified, tracing functions are disabled.
    
    Parameters:
    
    startUI - Whether SNT's UI should also be initialized;
    
    Returns:
    
    the SNT instance.
  - initialize
```
public SNT initialize(String imagePath,
                      boolean startUI)
```
    Initializes SNT.
    
    Parameters:
    
    imagePath - the image to be traced. If "demo" (case insensitive), SNT is initialized using the demoTreeImage(). If empty or null and SNT's UI is available an "Open" dialog prompt is displayed. URL's supported.
    
    startUI - Whether SNT's UI should also be initialized;
    
    Returns:
    
    the SNT instance.
  - initialize
```
public SNT initialize(ij.ImagePlus imp,
                      boolean startUI)
```
    Initializes SNT.
    
    Parameters:
    
    imp - the image to be traced (null not allowed)
    
    startUI - Whether SNT's UI should also be initialized;
    
    Returns:
    
    the SNT instance.
  - getPlugin
```
public SNT getPlugin()
```
    Returns a reference to the active SNT plugin.
    
    Returns:
    
    the SNT instance
  - loadTracings
```
public void loadTracings(String filePathOrURL)
                  throws UnsupportedOperationException,
                         IOException
```
    Loads the specified tracings file.
    
    Parameters:
    
    filePathOrURL - either a "SWC", "TRACES" or "JSON" file path. URLs defining remote files also supported.. Null not allowed.
    
    Throws:
    
    UnsupportedOperationException - if SNT is not running
    
    IOException - if data cannot be imported
  - loadTree
```
public void loadTree(Tree tree)
              throws UnsupportedOperationException
```
    Loads the specified tree. Note that if SNT has not been properly initialized, spatial calibration mismatches may occur. In that case, assign the spatial calibration of the image to {#@code Tree} using Tree.assignImage(ImagePlus), before loading it.
    
    Parameters:
    
    tree - the Tree to be loaded (null not allowed).
    
    Throws:
    
    UnsupportedOperationException - if SNT is not running
  - loadGraph
```
public void loadGraph(DirectedWeightedGraph graph)
               throws UnsupportedOperationException
```
    Throws:
    
    UnsupportedOperationException
  - save
```
public boolean save(String filePath)
```
    Saves all the existing paths to a file.
    
    Parameters:
    
    filePath - the saving output file path. If filePath ends in ".swc" (case insensitive), an SWC file is created, otherwise a "traces" file is created. If empty and a GUI exists, a save prompt is displayed.
    
    Returns:
    
    true, if paths exist and file was successfully written.
    
    Throws:
    
    UnsupportedOperationException - if SNT is not running
  - getSelectedPaths
```
public Collection<Path> getSelectedPaths()
```
    Gets the paths currently selected in the Path Manager list.
    
    Returns:
    
    the paths currently selected, or null if no selection exists
    
    Throws:
    
    UnsupportedOperationException - if SNT is not running
    
    See Also:
    
    getTree(boolean)
  - getPaths
```
public List<Path> getPaths()
```
    Gets the paths currently listed in the Path Manager
    
    Returns:
    
    all the listed paths, or null if the Path Manager is empty
    
    Throws:
    
    UnsupportedOperationException - if SNT is not running
    
    See Also:
    
    getTree(boolean)
  - getTree
```
public Tree getTree(boolean selectedPathsOnly)
```
    Gets the collection of paths listed in the Path Manager as a Tree object.
    
    Parameters:
    
    selectedPathsOnly - If true, only selected paths are retrieved
    
    Returns:
    
    the Tree holding the Path collection
    
    Throws:
    
    UnsupportedOperationException - if SNT is not running
  - getTree
```
public Tree getTree()
```
    Gets the collection of paths listed in the Path Manager as a Tree object.
    
    Returns:
    
    the Tree holding the Path collection
    
    Throws:
    
    UnsupportedOperationException - if SNT is not running
  - getAnalyzer
```
public TreeAnalyzer getAnalyzer(boolean selectedPathsOnly)
```
    Returns a TreeAnalyzer instance constructed from current Paths.
    
    Parameters:
    
    selectedPathsOnly - If true only selected paths will be considered
    
    Returns:
    
    the TreeAnalyzer instance
    
    Throws:
    
    UnsupportedOperationException - if SNT is not running
  - getStatistics
```
public TreeStatistics getStatistics(boolean selectedPathsOnly)
```
    Returns a TreeStatistics instance constructed from current Paths.
    
    Parameters:
    
    selectedPathsOnly - If true only selected paths will be considered
    
    Returns:
    
    the TreeStatistics instance
    
    Throws:
    
    UnsupportedOperationException - if SNT is not running
  - getPathAndFillManager
```
public PathAndFillManager getPathAndFillManager()
```
    Returns the PathAndFillManager associated with the current SNT instance.
    
    Returns:
    
    the PathAndFillManager instance
    
    Throws:
    
    UnsupportedOperationException - if no SNT instance exists.
  - updateViewers
```
public void updateViewers()
```
    Script-friendly method for updating (refreshing) all viewers currently in use by SNT. Does nothing if no SNT instance exists.
  - getUI
```
public SNTUI getUI()
```
    Returns a reference to SNT's UI.
    
    Returns:
    
    the SNTUI window, or null if SNT is not running, or is running without GUI
  - getRecViewer
```
public Viewer3D getRecViewer()
```
    Returns a reference to the active Reconstruction Viewer (either stand-alone or SNT-associated instance). A new instance is retrieved if none exists.
    
    Returns:
    
    The active Viewer3D instance. For stand-alone viewers, this is typically the viewer that is frontmost or the last initiated viewer.
  - getRecViewer
```
public Viewer3D getRecViewer(int id)
```
    Returns a reference to an opened Reconstruction Viewer (standalone instance). *
    
    Parameters:
    
    id - the unique numeric ID of the Reconstruction Viewer to be retrieved (as used by the "Script This Viewer" command, and typically displayed in the Viewer's window title)
    
    Returns:
    
    The standalone Viewer3D instance, or null if id was not recognized
  - newRecViewer
```
public Viewer3D newRecViewer(boolean guiControls)
```
    Instantiates a new standalone Reconstruction Viewer.
    
    Returns:
    
    The standalone Viewer3D instance
  - getOrCreateSciViewSNT
```
public SciViewSNT getOrCreateSciViewSNT()
                                 throws NoClassDefFoundError
```
    Throws:
    
    NoClassDefFoundError
  - getSciViewSNT
```
public SciViewSNT getSciViewSNT()
                         throws UnsupportedOperationException,
                                NoClassDefFoundError
```
    Throws:
    
    UnsupportedOperationException
    
    NoClassDefFoundError
  - getTable
```
public SNTTable getTable()
```
    Returns a reference to SNT's main table of measurements.
    
    Returns:
    
    SNT measurements table (a DefaultGenericTable)
    
    Throws:
    
    UnsupportedOperationException - if SNT is not running
  - demoTree
```
@Deprecated
public Tree demoTree()
```
    Deprecated.
    
    Returns a toy reconstruction (fractal tree).
    
    Returns:
    
    a reference to the loaded tree, or null if data could no be retrieved
    
    See Also:
    
    demoTreeImage()
  - demoTree
```
public Tree demoTree(String tree)
```
    Returns a demo tree.
    
    Parameters:
    
    tree - a string describing the type of demo tree. Either 'fractal' for the L-system toy neuron, 'pyramidal' for the dendritic arbor of mouse pyramidal cell (MouseLight's cell AA0001), or 'OP1'for the DIADEM OP_1 reconstruction.
    
    See Also:
    
    demoImage(String), demoTrees()
  - demoTreeImage
```
@Deprecated
public ij.ImagePlus demoTreeImage()
```
    Deprecated.
    
    Returns the image associated with the demo (fractal) tree.
    
    Returns:
    
    a reference to the image tree, or null if data could no be retrieved
    
    See Also:
    
    demoTree()
  - demoImage
```
public ij.ImagePlus demoImage(String img)
```
    Returns one of the demo images bundled with SNT image associated with the demo (fractal) tree.
    
    Parameters:
    
    img - a string describing the type of demo image. Either 'fractal' for the L-system toy neuron or 'ddaC' for the C4 ddaC drosophila neuron, a demo image initially distributed with the Sholl plugin.
    
    Returns:
    
    the demo image, or null if data could no be retrieved
    
    See Also:
    
    demoTree(String)
  - demoTrees
```
public List<Tree> demoTrees()
```
    Returns a collection of four demo reconstructions (dendrites from pyramidal cells from the MouseLight database). NB: Data is cached locally. No internet connection required.
    
    Returns:
    
    the list of Trees, corresponding to the dendritic arbors of cells "AA0001", "AA0002", "AA0003", "AA0004" (MouseLight database IDs).
  - demoTreesSWC
```
protected List<Tree> demoTreesSWC()
```
  - captureView
```
public ij.ImagePlus captureView(String view,
                                boolean project)
```
    Retrieves a WYSIWYG 'snapshot' of a tracing canvas.
    
    Parameters:
    
    view - A case-insensitive string specifying the canvas to be captured. Either "xy" (or "main"), "xz", "zy" or "3d" (for legacy's 3D Viewer).
    
    project - whether the snapshot of 3D image stacks should include its projection (MIP), or just the current plane
    
    Returns:
    
    the snapshot capture of the canvas as an RGB image
    
    Throws:
    
    UnsupportedOperationException - if SNT is not running
    
    IllegalArgumentException - if view is not a recognized option
  - captureView
```
public ij.ImagePlus captureView(String view,
                                ColorRGB backgroundColor)
                         throws IllegalArgumentException
```
    Retrieves a WYSIWYG 'snapshot' of a tracing canvas without voxel data.
    
    Parameters:
    
    view - A case-insensitive string specifying the canvas to be captured. Either "xy" (or "main"), "xz", "zy" or "3d" (for legacy's 3D Viewer).
    
    backgroundColor - the background color of the canvas (string, hex, or html)
    
    Returns:
    
    the snapshot capture of the canvas as an RGB image
    
    Throws:
    
    UnsupportedOperationException - if SNT is not running
    
    IllegalArgumentException - if view or backgroundColor are not recognized
  - dispose
```
public void dispose()
```
    Quits SNT. Does nothing if SNT is currently not running.
    
    Specified by:
    
    dispose in interface Disposable

Class SNTService

Constructor Summary

Method Summary

Methods inherited from class org.scijava.service.AbstractService

Methods inherited from class org.scijava.plugin.AbstractRichPlugin

Methods inherited from class org.scijava.AbstractContextual

Methods inherited from class java.lang.Object

Methods inherited from interface org.scijava.service.Service

Methods inherited from interface org.scijava.plugin.RichPlugin

Methods inherited from interface org.scijava.Contextual

Methods inherited from interface org.scijava.Prioritized

Methods inherited from interface org.scijava.plugin.HasPluginInfo

Methods inherited from interface org.scijava.Locatable

Methods inherited from interface org.scijava.Versioned

Constructor Detail

SNTService

Method Detail

isActive

assignValues

initialize

initialize

initialize

getPlugin

loadTracings

loadTree

loadGraph

save

getSelectedPaths

getPaths

getTree

getTree

getAnalyzer

getStatistics

getPathAndFillManager

updateViewers

getUI

getRecViewer

getRecViewer

newRecViewer

getOrCreateSciViewSNT

getSciViewSNT

getTable

demoTree

demoTree

demoTreeImage

demoImage

demoTrees

demoTreesSWC

captureView

captureView

dispose