PathAndFillManager

java.lang.Object
- org.xml.sax.helpers.DefaultHandler
- - sc.fiji.snt.PathAndFillManager

All Implemented Interfaces:

ij3d.UniverseListener, org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler
```
public class PathAndFillManager
extends org.xml.sax.helpers.DefaultHandler
implements ij3d.UniverseListener
```
The PathAndFillManager is responsible for importing, handling and managing of Paths and Fills. Typically, a PathAndFillManager is accessed from a SNT instance, but accessing a PathAndFillManager directly is useful for batch/headless operations.

Author:

Mark Longair, Tiago Ferreira

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

class PathAndFillManager.AllPointsIterator

Nested Classes
Modifier and Type	Class and Description
`class`	`PathAndFillManager.AllPointsIterator`

Constructor Summary

Constructors
Constructor and Description
`PathAndFillManager()` Instantiates a new PathAndFillManager using default values.
`PathAndFillManager(double x_spacing, double y_spacing, double z_spacing, java.lang.String spacing_units)` Instantiates a new PathAndFillManager imposing specified pixel dimensions, which may be required for pixel operations.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`addPath(Path p)` Adds a new path.
`void`	`addPathAndFillListener(sc.fiji.snt.PathAndFillListener listener)` Adds a PathAndFillListener.
`void`	`addTree(Tree tree)` Adds a `Tree`.
`java.util.Iterator<PointInImage>`	`allPointsIterator()`
`boolean`	`anySelected()` Checks whether at least one Path is currently selected in the UI.
`void`	`canvasResized()` Deprecated.
`void`	`clear()` Deletes all paths and fills.
`void`	`contentAdded(ij3d.Content c)` Deprecated.
`void`	`contentChanged(ij3d.Content c)` Deprecated.
`void`	`contentRemoved(ij3d.Content c)` Deprecated.
`void`	`contentSelected(ij3d.Content c)` Deprecated.
`static PathAndFillManager`	`createFromFile(java.lang.String filePath)` Creates a PathAndFillManager instance from imported data
`static PathAndFillManager`	`createFromNodes(java.util.Collection<SWCPoint> nodes)` Creates a PathAndFillManager instance from a collection of reconstruction nodes.
`boolean`	`deletePath(int index)` Deletes a Path by index
`boolean`	`deletePath(Path p)` Deletes a path.
`void`	`deletePaths(int[] indices)` Delete paths by position.
`void`	`downsampleAll(double maximumPermittedDistance)` Downsamples alls path using Ramer–Douglas–Peucker simplification.
`void`	`endElement(java.lang.String uri, java.lang.String localName, java.lang.String qName)`
`boolean`	`exportAllPathsAsSWC(java.lang.String baseFilename)` Exports all as Paths as SWC file(s).
`void`	`exportFillsAsCSV(java.io.File outputFile)` Export fills as CSV.
`void`	`exportToCSV(java.io.File outputFile)` Output some potentially useful information about all the Paths managed by this instance as a CSV (comma separated values) file.
`BoundingBox`	`getBoundingBox(boolean compute)` Returns the BoundingBox enclosing all nodes of all existing Paths.
`java.util.List<NearPoint>`	`getCorrespondences(PathAndFillManager other, double maxDistance)` For each point in this PathAndFillManager, find the corresponding point on the other one.
`Path`	`getPath(int i)` Returns the Path at the specified position in the PathAndFillManager list.
`Path`	`getPathFromID(int id)` Returns the Path with the specified id.
`Path`	`getPathFromName(java.lang.String name, boolean caseSensitive)` Returns the Path with the specified name.
`int`	`getPathIndex(Path p)` Gets the index of a Path
`java.util.ArrayList<Path>`	`getPaths()` Returns all the paths.
`java.util.ArrayList<Path>`	`getPathsFiltered()`
`Path[]`	`getPathsStructured()`
`Path[]`	`getPathsStructured(java.util.Collection<Path> paths)`
`SNT`	`getPlugin()` Gets the SNT instance.
`java.util.Set<Path>`	`getSelectedPaths()` Gets all paths selected in the GUI
`java.util.List<SWCPoint>`	`getSWCFor(java.util.Collection<Path> paths)` Gets the list of SWCPoints associated with a collection of Paths.
`java.util.Map<java.lang.String,Tree>`	`importNeurons(java.util.Map<java.lang.String,java.util.TreeSet<SWCPoint>> map, org.scijava.util.ColorRGB color, java.lang.String spatialUnit)` Import neuron(s) as a collection of reconstruction nodes (SWC points)
`boolean`	`importSWC(java.lang.String urlOrFilePath)` Imports an SWC file using default settings.
`boolean`	`importSWC(java.lang.String filePath, boolean assumeCoordinatesInVoxels, double xOffset, double yOffset, double zOffset, double xScale, double yScale, double zScale, boolean replaceAllPaths)` Imports an SWC file using advanced options.
`java.util.List<Tree>`	`importSWCs(java.util.Map<java.lang.String,java.lang.String> swcs, org.scijava.util.ColorRGB color)` Imports a group of SWC files (Remote URLs supported).
`boolean`	`isSelected(Path path)` Checks if a Path is currently selected in the GUI.
`boolean`	`load(java.lang.String filePath)` Imports a reconstruction file (any supported extension).
`NearPoint`	`nearestPointOnAnyPath(double x, double y, double z, double distanceLimit)`
`void`	`resetListeners(Path justAdded)`
`void`	`setHeadless(boolean headless)` Sets whether this PathAndFillManager instance should run headless.
`int`	`size()` Returns the number of Paths in the PathAndFillManager list.
`void`	`startElement(java.lang.String uri, java.lang.String localName, java.lang.String qName, org.xml.sax.Attributes attributes)`
`void`	`transformationFinished(org.scijava.java3d.View view)`
`void`	`transformationStarted(org.scijava.java3d.View view)`
`void`	`transformationUpdated(org.scijava.java3d.View view)`
`PathAndFillManager`	`transformPaths(PathTransformer transformation, ij.ImagePlus templateImage, ij.ImagePlus modelImage)`
`void`	`universeClosed()` Deprecated.

Methods inherited from class org.xml.sax.helpers.DefaultHandler
characters, endDocument, endPrefixMapping, error, fatalError, ignorableWhitespace, notationDecl, processingInstruction, resolveEntity, setDocumentLocator, skippedEntity, startDocument, startPrefixMapping, unparsedEntityDecl, warning

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

- Constructor Detail
  - PathAndFillManager
```
public PathAndFillManager()
```
    Instantiates a new PathAndFillManager using default values. Voxel dimensions are inferred from the first imported set of nodes.
  - PathAndFillManager
```
public PathAndFillManager(double x_spacing,
                          double y_spacing,
                          double z_spacing,
                          java.lang.String spacing_units)
```
    Instantiates a new PathAndFillManager imposing specified pixel dimensions, which may be required for pixel operations. New Paths created under this instance, will adopt the specified spacing details.
    
    Parameters:
    
    x_spacing - the 'voxel width'
    
    y_spacing - the 'voxel height'
    
    z_spacing - the 'voxel depth'
    
    spacing_units - the spacing units (e.g., 'um', 'mm)
- Method Detail
  - size
```
public int size()
```
    Returns the number of Paths in the PathAndFillManager list.
    
    Returns:
    
    the the number of Paths
  - addPathAndFillListener
```
public void addPathAndFillListener(sc.fiji.snt.PathAndFillListener listener)
```
    Adds a PathAndFillListener. This is used by the interface to have changes in the path manager reported so that they can be reflected in the UI.
    
    Parameters:
    
    listener - the listener
  - getPath
```
public Path getPath(int i)
```
    Returns the Path at the specified position in the PathAndFillManager list.
    
    Parameters:
    
    i - the index of the Path
    
    Returns:
    
    the Path at the specified index
  - getPathFromName
```
public Path getPathFromName(java.lang.String name,
                            boolean caseSensitive)
```
    Returns the Path with the specified name.
    
    Parameters:
    
    name - the name of the Path to be retrieved
    
    caseSensitive - If true, case considerations are ignored
    
    Returns:
    
    the Path with the specified name, or null if name was not found.
  - getPathFromID
```
public Path getPathFromID(int id)
```
    Returns the Path with the specified id.
    
    Parameters:
    
    id - the id of the Path to be retrieved
    
    Returns:
    
    the Path with the specified id, or null if id was not found.
  - isSelected
```
public boolean isSelected(Path path)
```
    Checks if a Path is currently selected in the GUI.
    
    Parameters:
    
    path - the path to be checked
    
    Returns:
    
    true, if is selected
  - getSelectedPaths
```
public java.util.Set<Path> getSelectedPaths()
```
    Gets all paths selected in the GUI
    
    Returns:
    
    the collection of selected paths
  - anySelected
```
public boolean anySelected()
```
    Checks whether at least one Path is currently selected in the UI.
    
    Returns:
    
    true, if successful
  - exportAllPathsAsSWC
```
public boolean exportAllPathsAsSWC(java.lang.String baseFilename)
```
    Exports all as Paths as SWC file(s). Multiple files are created if multiple Trees exist.
    
    Parameters:
    
    baseFilename - the file path (including common basename) for exported files. The .swc extension can be omitted. Each traced structure will be saved into a dedicated file using a 3-digits identifier. E.g., if only a single structure exists, specifying /path/to/results, generates a /path/to/results-000.swc file.
    
    Returns:
    
    true, if successful
  - setHeadless
```
public void setHeadless(boolean headless)
```
    Sets whether this PathAndFillManager instance should run headless.
    
    Parameters:
    
    headless - true to activate headless calls, otherwise false
  - getBoundingBox
```
public BoundingBox getBoundingBox(boolean compute)
```
    Returns the BoundingBox enclosing all nodes of all existing Paths.
    
    Parameters:
    
    compute - If true, BoundingBox dimensions will be computed for all the existing Paths. If false, the last computed BoundingBox will be returned. Also, if BoundingBox is not scaled, its spacing will be computed from the smallest inter-node distance of an arbitrary ' large' Path. Computations of Path boundaries typically occur during import operations.
    
    Returns:
    
    the BoundingBox enclosing existing nodes, or an 'empty' BoundingBox if no computation of boundaries has not yet occurred. Output is never null.
  - getPathsStructured
```
public Path[] getPathsStructured()
```
  - getPathsStructured
```
public Path[] getPathsStructured(java.util.Collection<Path> paths)
```
  - getSWCFor
```
public java.util.List<SWCPoint> getSWCFor(java.util.Collection<Path> paths)
                                   throws sc.fiji.snt.SWCExportException
```
    Gets the list of SWCPoints associated with a collection of Paths.
    
    Parameters:
    
    paths - the paths from which to retrieve the list
    
    Returns:
    
    the list of SWCPoints, corresponding to all the nodes of paths
    
    Throws:
    
    sc.fiji.snt.SWCExportException - if list could not be retrieved
  - resetListeners
```
public void resetListeners(Path justAdded)
```
  - addTree
```
public void addTree(Tree tree)
```
    Adds a Tree.
    
    Parameters:
    
    tree - the collection of paths to be added
  - addPath
```
public void addPath(Path p)
```
    Adds a new path.
    
    Parameters:
    
    p - the Path to be added
  - deletePath
```
public boolean deletePath(int index)
```
    Deletes a Path by index
    
    Parameters:
    
    index - the index (zero-based) of the Path to be deleted
    
    Returns:
    
    true, if index is valid and Path was successfully deleted
  - deletePath
```
public boolean deletePath(Path p)
                   throws java.lang.IllegalArgumentException
```
    Deletes a path.
    
    Parameters:
    
    p - the path to be deleted
    
    Returns:
    
    true, if path was found and successfully deleted
    
    Throws:
    
    java.lang.IllegalArgumentException
  - getPathIndex
```
public int getPathIndex(Path p)
```
    Gets the index of a Path
    
    Parameters:
    
    p - the Path for which the index should be retrieved
    
    Returns:
    
    the path index, or -1 if p was not found
  - deletePaths
```
public void deletePaths(int[] indices)
```
    Delete paths by position.
    
    Parameters:
    
    indices - the indices to be deleted
  - startElement
```
public void startElement(java.lang.String uri,
                         java.lang.String localName,
                         java.lang.String qName,
                         org.xml.sax.Attributes attributes)
                  throws sc.fiji.snt.TracesFileFormatException
```
    Specified by:
    
    startElement in interface org.xml.sax.ContentHandler
    
    Overrides:
    
    startElement in class org.xml.sax.helpers.DefaultHandler
    
    Throws:
    
    sc.fiji.snt.TracesFileFormatException
  - endElement
```
public void endElement(java.lang.String uri,
                       java.lang.String localName,
                       java.lang.String qName)
                throws sc.fiji.snt.TracesFileFormatException
```
    Specified by:
    
    endElement in interface org.xml.sax.ContentHandler
    
    Overrides:
    
    endElement in class org.xml.sax.helpers.DefaultHandler
    
    Throws:
    
    sc.fiji.snt.TracesFileFormatException
  - createFromFile
```
public static PathAndFillManager createFromFile(java.lang.String filePath)
```
    Creates a PathAndFillManager instance from imported data
    
    Parameters:
    
    filePath - the absolute path of the file to be imported as per load(String)
    
    Returns:
    
    the PathAndFillManager instance, or null if file could not be imported
  - createFromNodes
```
public static PathAndFillManager createFromNodes(java.util.Collection<SWCPoint> nodes)
```
    Creates a PathAndFillManager instance from a collection of reconstruction nodes.
    
    Parameters:
    
    nodes - the collection of reconstruction nodes. Nodes will be sorted by id and any duplicate entries pruned.
    
    Returns:
    
    the PathAndFillManager instance, or null if file could not be imported
  - clear
```
public void clear()
```
    Deletes all paths and fills.
  - importSWC
```
public boolean importSWC(java.lang.String urlOrFilePath)
```
    Imports an SWC file using default settings.
    
    Parameters:
    
    urlOrFilePath - the URL pointing to the SWC file or the absolute file path of a local file. Note that with URLs, https may not be supported.
    
    Returns:
    
    true, if import was successful
    
    See Also:
    
    NeuroMorphoLoader, importSWC(String, boolean), importSWC(BufferedReader, boolean, double, double, double, double, double, double, boolean)
  - importSWCs
```
public java.util.List<Tree> importSWCs(java.util.Map<java.lang.String,java.lang.String> swcs,
                                       org.scijava.util.ColorRGB color)
```
    Imports a group of SWC files (Remote URLs supported).
    
    Parameters:
    
    swcs - the HashMap containing the absolute file paths (or URLs) of files to be imported as values and a file descriptor as keys.
    
    color - the color to be applied to imported Paths. If null, paths from each file will assigned unique colors
    
    Returns:
    
    the List of imported Trees labeled after the file descriptor. The returned list will not contain null elements: If a file was not successfully imported an empty Tree will be generated
    
    See Also:
    
    Tree.isEmpty(), Tree.getLabel(), SNTColor.getDistinctColors(int)
  - importNeurons
```
public java.util.Map<java.lang.String,Tree> importNeurons(java.util.Map<java.lang.String,java.util.TreeSet<SWCPoint>> map,
                                                          org.scijava.util.ColorRGB color,
                                                          java.lang.String spatialUnit)
```
    Import neuron(s) as a collection of reconstruction nodes (SWC points)
    
    Parameters:
    
    map - the input map of reconstruction nodes
    
    color - the color to be applied to imported Paths. If null, paths from each ID will assigned unique colors
    
    spatialUnit - the spatial unit (um, mm, etc) associated with imported nodes. If null, "um" are assumed
    
    Returns:
    
    the map mapping imported ids to imported Trees. A null Tree will be assigned if a morphology could not be imported
    
    See Also:
    
    SNTColor.getDistinctColors(int)
  - importSWC
```
public boolean importSWC(java.lang.String filePath,
                         boolean assumeCoordinatesInVoxels,
                         double xOffset,
                         double yOffset,
                         double zOffset,
                         double xScale,
                         double yScale,
                         double zScale,
                         boolean replaceAllPaths)
```
    Imports an SWC file using advanced options.
    
    Parameters:
    
    filePath - the absolute file path to the imported file
    
    assumeCoordinatesInVoxels - see importSWC(BufferedReader, boolean, double, double, double, double, double, double, boolean)
    
    xOffset - see importSWC(BufferedReader, boolean, double, double, double, double, double, double, boolean)
    
    yOffset - see importSWC(BufferedReader, boolean, double, double, double, double, double, double, boolean)
    
    zOffset - see importSWC(BufferedReader, boolean, double, double, double, double, double, double, boolean)
    
    xScale - see importSWC(BufferedReader, boolean, double, double, double, double, double, double, boolean)
    
    yScale - see importSWC(BufferedReader, boolean, double, double, double, double, double, double, boolean)
    
    zScale - see importSWC(BufferedReader, boolean, double, double, double, double, double, double, boolean)
    
    replaceAllPaths - see importSWC(BufferedReader, boolean, double, double, double, double, double, double, boolean)
    
    Returns:
    
    true, if import was successful
  - load
```
public boolean load(java.lang.String filePath)
```
    Imports a reconstruction file (any supported extension).
    
    Parameters:
    
    filePath - the absolute path to the file (.Traces, SWC or JSON) to be imported
    
    Returns:
    
    true, if successful
  - getPaths
```
public java.util.ArrayList<Path> getPaths()
```
    Returns all the paths.
    
    Returns:
    
    the paths associated with this PathAndFillManager instance.
  - getPathsFiltered
```
public java.util.ArrayList<Path> getPathsFiltered()
```
  - transformationStarted
```
public void transformationStarted(org.scijava.java3d.View view)
```
    Specified by:
    
    transformationStarted in interface ij3d.UniverseListener
  - transformationUpdated
```
public void transformationUpdated(org.scijava.java3d.View view)
```
    Specified by:
    
    transformationUpdated in interface ij3d.UniverseListener
  - transformationFinished
```
public void transformationFinished(org.scijava.java3d.View view)
```
    Specified by:
    
    transformationFinished in interface ij3d.UniverseListener
  - contentAdded
```
@Deprecated
public void contentAdded(ij3d.Content c)
```
    Deprecated.
    
    Specified by:
    
    contentAdded in interface ij3d.UniverseListener
  - contentRemoved
```
@Deprecated
public void contentRemoved(ij3d.Content c)
```
    Deprecated.
    
    Specified by:
    
    contentRemoved in interface ij3d.UniverseListener
  - contentChanged
```
@Deprecated
public void contentChanged(ij3d.Content c)
```
    Deprecated.
    
    Specified by:
    
    contentChanged in interface ij3d.UniverseListener
  - contentSelected
```
@Deprecated
public void contentSelected(ij3d.Content c)
```
    Deprecated.
    
    Specified by:
    
    contentSelected in interface ij3d.UniverseListener
  - canvasResized
```
@Deprecated
public void canvasResized()
```
    Deprecated.
    
    Specified by:
    
    canvasResized in interface ij3d.UniverseListener
  - universeClosed
```
@Deprecated
public void universeClosed()
```
    Deprecated.
    
    Specified by:
    
    universeClosed in interface ij3d.UniverseListener
  - nearestPointOnAnyPath
```
public NearPoint nearestPointOnAnyPath(double x,
                                       double y,
                                       double z,
                                       double distanceLimit)
```
  - allPointsIterator
```
public java.util.Iterator<PointInImage> allPointsIterator()
```
  - getCorrespondences
```
public java.util.List<NearPoint> getCorrespondences(PathAndFillManager other,
                                                    double maxDistance)
```
    For each point in this PathAndFillManager, find the corresponding point on the other one. If there's no corresponding one, include a null instead. *
    
    Parameters:
    
    other - the other PathAndFillManager holding the corresponding Paths
    
    maxDistance - the distance limit below which the NearPoint is considered
    
    Returns:
    
    the cloud of NearPoint correspondences
  - exportFillsAsCSV
```
public void exportFillsAsCSV(java.io.File outputFile)
                      throws java.io.IOException
```
    Export fills as CSV.
    
    Parameters:
    
    outputFile - the output file
    
    Throws:
    
    java.io.IOException - Signals that an I/O exception has occurred.
  - exportToCSV
```
public void exportToCSV(java.io.File outputFile)
                 throws java.io.IOException
```
    Output some potentially useful information about all the Paths managed by this instance as a CSV (comma separated values) file.
    
    Parameters:
    
    outputFile - the output file
    
    Throws:
    
    java.io.IOException - if data could not be stored
  - transformPaths
```
public PathAndFillManager transformPaths(PathTransformer transformation,
                                         ij.ImagePlus templateImage,
                                         ij.ImagePlus modelImage)
```
  - downsampleAll
```
public void downsampleAll(double maximumPermittedDistance)
```
    Downsamples alls path using Ramer–Douglas–Peucker simplification. Downsampling occurs only between branch points and terminal points.
    
    Parameters:
    
    maximumPermittedDistance - the maximum permitted distance between nodes.
  - getPlugin
```
public SNT getPlugin()
```
    Gets the SNT instance.
    
    Returns:
    
    the SNT instance associated with this PathManager (if any)

Class PathAndFillManager

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class org.xml.sax.helpers.DefaultHandler

Methods inherited from class java.lang.Object

Constructor Detail

PathAndFillManager

PathAndFillManager

Method Detail

size

addPathAndFillListener

getPath

getPathFromName

getPathFromID

isSelected

getSelectedPaths

anySelected

exportAllPathsAsSWC

setHeadless

getBoundingBox

getPathsStructured

getPathsStructured

getSWCFor

resetListeners

addTree

addPath

deletePath

deletePath

getPathIndex

deletePaths

startElement

endElement

createFromFile

createFromNodes

clear

importSWC

importSWCs

importNeurons

importSWC

load

getPaths

getPathsFiltered

transformationStarted

transformationUpdated

transformationFinished

contentAdded

contentRemoved

contentChanged

contentSelected

canvasResized

universeClosed

nearestPointOnAnyPath

allPointsIterator

getCorrespondences

exportFillsAsCSV

exportToCSV

transformPaths

downsampleAll

getPlugin