PathAndFillManager (Fiji Javadocs 0-SNAPSHOT API)

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

All Implemented Interfaces:

UniverseListener, ContentHandler, DTDHandler, EntityResolver, ErrorHandler
```
public class PathAndFillManager
extends DefaultHandler
implements 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, Cameron Arshadi

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`

Field Summary

Fields
Modifier and Type	Field and Description
`protected boolean`	`enableUIupdates`
`protected SNT`	`plugin`
`protected static int`	`TRACES_FILE_TYPE_COMPRESSED_XML`
`protected static int`	`TRACES_FILE_TYPE_ML_JSON`
`protected static int`	`TRACES_FILE_TYPE_SWC`
`protected static int`	`TRACES_FILE_TYPE_UNCOMPRESSED_XML`

Constructor Summary

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

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`protected void`	`addFill(Fill fill)`
`void`	`addPath(Path p)` Adds a new path.
`void`	`addPath(Path p, boolean retainTags)`
`void`	`addPath(Path p, boolean forceNewName, boolean forceNewId)`
`protected void`	`addPath(Path p, boolean forceNewName, boolean forceNewId, boolean assumeMaxUsedTreeID)`
`void`	`addPath(Path p, int id, int treeID)`
`void`	`addPathAndFillListener(sc.fiji.snt.PathAndFillListener listener)` Adds a PathAndFillListener.
`void`	`addTree(Tree tree)` Adds a `Tree`.
`protected boolean`	`allPathsShareSameSpatialCalibration()`
`Iterator<PointInImage>`	`allPointsIterator()`
`boolean`	`anySelected()` Checks whether at least one Path is currently selected in the UI.
`protected ij.measure.Calibration`	`assignSpatialSettings(Dataset dataset)`
`protected void`	`assignSpatialSettings(ij.ImagePlus imp)`
`void`	`canvasResized()` Deprecated.
`void`	`clear()` Deletes all paths and fills.
`void`	`contentAdded(Content c)` Deprecated.
`void`	`contentChanged(Content c)` Deprecated.
`void`	`contentRemoved(Content c)` Deprecated.
`void`	`contentSelected(Content c)` Deprecated.
`static PathAndFillManager`	`createFromFile(String filePath, int... swcTypes)` Creates a PathAndFillManager instance from imported data
`static PathAndFillManager`	`createFromGraph(DirectedWeightedGraph graph, boolean keepTreePathStructure)` Create a new PathAndFillManager instance from the graph.
`static PathAndFillManager`	`createFromNodes(Collection<SWCPoint> nodes)` Creates a PathAndFillManager instance from a collection of reconstruction nodes.
`protected void`	`deleteFills(int[] indices)`
`boolean`	`deletePath(int index)` Deletes a Path by index
`boolean`	`deletePath(Path p)` Deletes a path.
`boolean`	`deletePaths(Collection<Path> paths)` Deletes a collection of paths.
`void`	`deletePaths(int[] indices)` Delete paths by position.
`void`	`downsampleAll(double maximumPermittedDistance)` Downsamples alls path using Ramer–Douglas–Peucker simplification.
`void`	`endElement(String uri, String localName, String qName)`
`protected boolean`	`exportAllPathsAsSWC(Path[] primaryPaths, String baseFilename)`
`boolean`	`exportAllPathsAsSWC(String baseFilename)` Exports all as Paths as SWC file(s).
`protected boolean`	`exportConnectedStructureAsSWC(Path primaryPath, File swcFile)`
`void`	`exportFillsAsCSV(File outputFile)` Export fills as CSV.
`void`	`exportToCSV(File outputFile)` Output some potentially useful information about all the Paths managed by this instance as a CSV (comma separated values) file.
`boolean`	`exportTree(int treeIndex, File file)`
`protected void`	`flushSWCPoints(List<SWCPoint> swcPoints, PrintWriter pw)`
`protected List<Fill>`	`getAllFills()`
`protected List<Path>`	`getAllPathsRenderedInViewPort(TracerCanvas canvas)`
`BoundingBox`	`getBoundingBox(boolean compute)` Returns the BoundingBox enclosing all nodes of all existing Paths.
`List<NearPoint>`	`getCorrespondences(PathAndFillManager other, double maxDistance)` For each point in this PathAndFillManager, find the corresponding point on the other one.
`protected String`	`getDefaultName(Path p)`
`Map<Fill,FillerThread>`	`getLoadedFills()`
`Path`	`getPath(int i)` Returns the Path at the specified position in the PathAndFillManager list.
`protected Path`	`getPathFrom3DViewerName(String name)`
`Path`	`getPathFromID(int id)` Returns the Path with the specified id.
`Path`	`getPathFromName(String name, boolean caseSensitive)` Returns the Path with the specified name.
`int`	`getPathIndex(Path p)` Gets the index of a Path.
`ArrayList<Path>`	`getPaths()` Returns all the paths.
`List<Path>`	`getPathsFiltered()` Returns the 'de facto' Paths.
`Collection<Path>`	`getPathsInROI(Roi roi)`
`Path[]`	`getPathsStructured()`
`Path[]`	`getPathsStructured(Collection<Path> paths)`
`SNT`	`getPlugin()` Gets the SNT instance.
`Set<Path>`	`getSelectedPaths()` Gets all paths selected in the GUI
`protected List<Path>`	`getSelectedPathsRenderedInViewPort(TracerCanvas canvas)`
`protected File`	`getSWCFileForIndex(String prefix, int index)`
`List<SWCPoint>`	`getSWCFor(Collection<Path> paths)`
`List<SWCPoint>`	`getSWCForOld(Collection<Path> paths)` Gets the list of SWCPoints associated with a collection of Paths.
`Collection<Tree>`	`getTrees()` Returns all the paths associated with this PathAndFillManager instance, grouped by Tree.
`protected List<Path>`	`getUnSelectedPathsRenderedInViewPort(TracerCanvas canvas)`
`protected int`	`guessTracesFileType(String filename)`
`protected void`	`importGraph(DirectedWeightedGraph graph)`
`protected void`	`importGraphWithPathStructure(DirectedWeightedGraph graph)`
`Map<String,Tree>`	`importNeurons(Map<String,TreeSet<SWCPoint>> map, ColorRGB color, String spatialUnit)` Import neuron(s) as a collection of reconstruction nodes (SWC points)
`protected boolean`	`importSWC(BufferedReader br, String descriptor, boolean assumeCoordinatesInVoxels, double xOffset, double yOffset, double zOffset, double xScale, double yScale, double zScale, boolean replaceAllPaths, int... swcTypes)` Imports SWC data with advanced settings.
`protected boolean`	`importSWC(String filePath, boolean ignoreCalibration)` Imports an SWC file.
`boolean`	`importSWC(String filePath, boolean assumeCoordinatesInVoxels, double xOffset, double yOffset, double zOffset, double xScale, double yScale, double zScale, boolean replaceAllPaths, int... swcTypes)` Imports an SWC file using advanced options.
`boolean`	`importSWC(String descriptor, String urlOrFilePath)` Imports an SWC file using default settings.
`List<Tree>`	`importSWCs(Map<String,String> swcs, 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(String filePath, int... swcTypes)` Imports a reconstruction file (any supported extension).
`protected boolean`	`loadCompressedXML(String filename)`
`boolean`	`loadGuessingType(String optionalDescription, InputStream is)`
`protected boolean`	`loadUncompressedXML(String filename, int... swcTypes)`
`protected boolean`	`multipleTreesExist()`
`NearPoint`	`nearestPointOnAnyPath(Collection<Path> paths, PointInCanvas pic, double distanceLimit)`
`protected NearPoint`	`nearestPointOnAnyPath(Collection<Path> paths, PointInImage pim, double distanceLimitSquared, boolean unScaledPositions)`
`NearPoint`	`nearestPointOnAnyPath(double x, double y, double z, double distanceLimit)`
`void`	`pathChanged(sc.fiji.snt.PathChangeEvent event)`
`protected void`	`rebuildRelationships()` Rebuild relationships.
`protected void`	`reloadFills(int[] selectedIndices)`
`protected void`	`resetIDs()`
`void`	`resetListeners(Path justAdded)`
`protected void`	`resetListeners(Path justAdded, boolean expandAll)`
`protected void`	`resetSpatialSettings(boolean alsoResetPaths)`
`protected boolean`	`savetoFileOrFileSeries(File file)`
`void`	`setHeadless(boolean headless)` Sets whether this PathAndFillManager instance should run headless.
`protected void`	`setSelected(Collection<Path> selectedPaths, Object sourceOfMessage)`
`int`	`size()` Returns the number of Paths in the PathAndFillManager list.
`void`	`startElement(String uri, String localName, String qName, Attributes attributes)`
`protected void`	`syncSpatialSettingsWithPlugin()`
`void`	`transformationFinished(View view)`
`void`	`transformationStarted(View view)`
`void`	`transformationUpdated(View view)`
`PathAndFillManager`	`transformPaths(PathTransformer transformation, ij.ImagePlus templateImage, ij.ImagePlus modelImage)`
`void`	`universeClosed()` Deprecated.
`protected void`	`update3DViewerContents()`
`protected void`	`updateBoundingBox()`
`protected boolean`	`usingNonPhysicalUnits()`
`protected void`	`writeXML(String fileName, boolean compress)`

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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - TRACES_FILE_TYPE_COMPRESSED_XML
```
protected static final int TRACES_FILE_TYPE_COMPRESSED_XML
```
    See Also:
    
    Constant Field Values
  - TRACES_FILE_TYPE_UNCOMPRESSED_XML
```
protected static final int TRACES_FILE_TYPE_UNCOMPRESSED_XML
```
    See Also:
    
    Constant Field Values
  - TRACES_FILE_TYPE_SWC
```
protected static final int TRACES_FILE_TYPE_SWC
```
    See Also:
    
    Constant Field Values
  - TRACES_FILE_TYPE_ML_JSON
```
protected static final int TRACES_FILE_TYPE_ML_JSON
```
    See Also:
    
    Constant Field Values
  - plugin
```
protected SNT plugin
```
  - enableUIupdates
```
protected boolean enableUIupdates
```
- Constructor Detail
  - PathAndFillManager
```
public PathAndFillManager()
```
    Instantiates a new PathAndFillManager using default values. Voxel dimensions are inferred from the first imported set of nodes.
  - PathAndFillManager
```
protected PathAndFillManager(SNT plugin)
```
  - PathAndFillManager
```
public PathAndFillManager(double x_spacing,
                          double y_spacing,
                          double z_spacing,
                          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
  - syncSpatialSettingsWithPlugin
```
protected void syncSpatialSettingsWithPlugin()
```
  - assignSpatialSettings
```
protected void assignSpatialSettings(ij.ImagePlus imp)
```
  - assignSpatialSettings
```
protected ij.measure.Calibration assignSpatialSettings(Dataset dataset)
```
  - resetSpatialSettings
```
protected void resetSpatialSettings(boolean alsoResetPaths)
```
  - rebuildRelationships
```
protected void rebuildRelationships()
```
    Rebuild relationships. Will wipe existing fitted flavors.
  - 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(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.
  - getPathFrom3DViewerName
```
protected Path getPathFrom3DViewerName(String name)
```
  - 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.
  - setSelected
```
protected void setSelected(Collection<Path> selectedPaths,
                           Object sourceOfMessage)
```
  - 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 Set<Path> getSelectedPaths()
```
    Gets all paths selected in the GUI
    
    Returns:
    
    the collection of selected paths
  - getPathsInROI
```
public Collection<Path> getPathsInROI(Roi roi)
```
  - anySelected
```
public boolean anySelected()
```
    Checks whether at least one Path is currently selected in the UI.
    
    Returns:
    
    true, if successful
  - getSWCFileForIndex
```
protected File getSWCFileForIndex(String prefix,
                                  int index)
```
  - exportAllPathsAsSWC
```
public boolean exportAllPathsAsSWC(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
  - exportTree
```
public boolean exportTree(int treeIndex,
                          File file)
```
  - savetoFileOrFileSeries
```
protected boolean savetoFileOrFileSeries(File file)
```
  - exportAllPathsAsSWC
```
protected boolean exportAllPathsAsSWC(Path[] primaryPaths,
                                      String baseFilename)
```
  - exportConnectedStructureAsSWC
```
protected boolean exportConnectedStructureAsSWC(Path primaryPath,
                                                File swcFile)
```
  - setHeadless
```
public void setHeadless(boolean headless)
```
    Sets whether this PathAndFillManager instance should run headless.
    
    Parameters:
    
    headless - true to activate headless calls, otherwise false
  - flushSWCPoints
```
protected void flushSWCPoints(List<SWCPoint> swcPoints,
                              PrintWriter pw)
```
  - usingNonPhysicalUnits
```
protected boolean usingNonPhysicalUnits()
```
  - updateBoundingBox
```
protected void updateBoundingBox()
```
  - 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.
  - allPathsShareSameSpatialCalibration
```
protected boolean allPathsShareSameSpatialCalibration()
```
  - getPathsStructured
```
public Path[] getPathsStructured()
```
  - getTrees
```
public Collection<Tree> getTrees()
```
    Returns all the paths associated with this PathAndFillManager instance, grouped by Tree.
    
    Returns:
    
    the Trees associated with this PathAndFillManager instance
  - multipleTreesExist
```
protected boolean multipleTreesExist()
```
  - getPathsStructured
```
public Path[] getPathsStructured(Collection<Path> paths)
```
  - getSWCFor
```
public List<SWCPoint> getSWCFor(Collection<Path> paths)
                         throws sc.fiji.snt.SWCExportException
```
    Throws:
    
    sc.fiji.snt.SWCExportException
  - getSWCForOld
```
public List<SWCPoint> getSWCForOld(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)
```
  - resetListeners
```
protected void resetListeners(Path justAdded,
                              boolean expandAll)
```
  - 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
  - addPath
```
public void addPath(Path p,
                    boolean retainTags)
```
  - addPath
```
public void addPath(Path p,
                    boolean forceNewName,
                    boolean forceNewId)
```
  - addPath
```
protected void addPath(Path p,
                       boolean forceNewName,
                       boolean forceNewId,
                       boolean assumeMaxUsedTreeID)
```
  - addPath
```
public void addPath(Path p,
                    int id,
                    int treeID)
```
  - getDefaultName
```
protected String getDefaultName(Path p)
```
  - 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)
```
    Deletes a path.
    
    Parameters:
    
    p - the path to be deleted
    
    Returns:
    
    true, if path was found and successfully deleted
  - deletePaths
```
public boolean deletePaths(Collection<Path> paths)
```
    Deletes a collection of paths. If present, the UI is only updated once operation completes.
    
    Parameters:
    
    paths - the collection to be deleted
    
    Returns:
    
    true, if all Paths in the collection were found and successfully deleted
  - 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
  - addFill
```
protected void addFill(Fill fill)
```
  - deleteFills
```
protected void deleteFills(int[] indices)
```
  - getLoadedFills
```
public Map<Fill,FillerThread> getLoadedFills()
```
  - reloadFills
```
protected void reloadFills(int[] selectedIndices)
```
  - writeXML
```
protected void writeXML(String fileName,
                        boolean compress)
                 throws IOException
```
    Throws:
    
    IOException
  - startElement
```
public void startElement(String uri,
                         String localName,
                         String qName,
                         Attributes attributes)
                  throws sc.fiji.snt.TracesFileFormatException
```
    Specified by:
    
    startElement in interface ContentHandler
    
    Overrides:
    
    startElement in class DefaultHandler
    
    Throws:
    
    sc.fiji.snt.TracesFileFormatException
  - endElement
```
public void endElement(String uri,
                       String localName,
                       String qName)
                throws sc.fiji.snt.TracesFileFormatException
```
    Specified by:
    
    endElement in interface ContentHandler
    
    Overrides:
    
    endElement in class DefaultHandler
    
    Throws:
    
    sc.fiji.snt.TracesFileFormatException
  - createFromFile
```
public static PathAndFillManager createFromFile(String filePath,
                                                int... swcTypes)
```
    Creates a PathAndFillManager instance from imported data
    
    Parameters:
    
    filePath - the absolute path of the file to be imported as per load(String, int...)
    
    Returns:
    
    the PathAndFillManager instance, or null if file could not be imported
  - createFromNodes
```
public static PathAndFillManager createFromNodes(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
  - createFromGraph
```
public static PathAndFillManager createFromGraph(DirectedWeightedGraph graph,
                                                 boolean keepTreePathStructure)
```
    Create a new PathAndFillManager instance from the graph.
    
    Parameters:
    
    graph - The input graph
    
    keepTreePathStructure - Whether to maintain the path hierarchy of the Tree backing the input graph. If this is set to true, the graph must have been created from operations on at least one Tree. Note that even if the graph is backed by a Tree, this may not always be possible. For instance, consider the case where two graphs oriented in opposing directions are merged at an edge. One graph will need to be re-oriented, which will change the Path hierarchy of the result.
  - importGraph
```
protected void importGraph(DirectedWeightedGraph graph)
```
  - importGraphWithPathStructure
```
protected void importGraphWithPathStructure(DirectedWeightedGraph graph)
```
  - clear
```
public void clear()
```
    Deletes all paths and fills.
  - resetIDs
```
protected void resetIDs()
```
  - importSWC
```
public boolean importSWC(String descriptor,
                         String urlOrFilePath)
```
    Imports an SWC file using default settings.
    
    Parameters:
    
    descriptor - the identifier for the imported data
    
    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)
  - importSWCs
```
public List<Tree> importSWCs(Map<String,String> swcs,
                             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)
  - importSWC
```
protected boolean importSWC(BufferedReader br,
                            String descriptor,
                            boolean assumeCoordinatesInVoxels,
                            double xOffset,
                            double yOffset,
                            double zOffset,
                            double xScale,
                            double yScale,
                            double zScale,
                            boolean replaceAllPaths,
                            int... swcTypes)
```
    Imports SWC data with advanced settings. The SWC format is described in PMID 9821633 and e.g., neuromorpho.org It is named after the initials of Stockley, Wheal, and Cole, who earlier developed a pioneer system for morphometric reconstructions (PMID 8321013).
    Annoyingly, While the SWC specification details the usage of of world coordinates in microns, some published SWC files have adopted image (pixel) coordinates, which is inappropriate and less useful (an example of the latter seems to part of the DIADEM Challenge data set). In addition, it's not clear what the "radius" column is meant to mean in such files.
    
    Parameters:
    
    descriptor - the label describing the Tree associated with the data
    
    br - the character stream containing the data
    
    assumeCoordinatesInVoxels - If true, the SWC coordinates are assumed to be in image coordinates ("pixels"). Note that in this case, radii will be scaled by the minimum voxel separation. This workaround seems to be required to properly import unscaled files
    
    xOffset - the offset to be applied to all X coordinates. May be useful to import data obtained from multiple "un-stitched" fields of view. Default is 0.
    
    yOffset - the offset to be applied to all Y coordinates. May be useful to import data obtained from multiple "un-stitched" fields of view. Default is 0.
    
    zOffset - the offset to be applied to all Z coordinates. May be useful to import data obtained from multiple "un-stitched" fields of view. Default is 0.
    
    xScale - the scaling factor for all X coordinates. Useful to import data onto downsampled images. Default is 1.
    
    yScale - the scaling factor for all Y coordinates. Useful to import data onto downsampled images. Default is 1.
    
    zScale - the scaling factor for all Z coordinates. Useful to import data onto downsampled images. Default is 1.
    
    replaceAllPaths - If true, all existing Paths will be deleted before the import. Default is false.
    
    Returns:
    
    true, if import was successful
  - importNeurons
```
public Map<String,Tree> importNeurons(Map<String,TreeSet<SWCPoint>> map,
                                      ColorRGB color,
                                      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
```
protected boolean importSWC(String filePath,
                            boolean ignoreCalibration)
```
    Imports an SWC file.
    
    Parameters:
    
    filePath - the absolute path of the file to be imported
    
    ignoreCalibration - the ignore calibration
    
    Returns:
    
    true, if import was successful
  - importSWC
```
public boolean importSWC(String filePath,
                         boolean assumeCoordinatesInVoxels,
                         double xOffset,
                         double yOffset,
                         double zOffset,
                         double xScale,
                         double yScale,
                         double zScale,
                         boolean replaceAllPaths,
                         int... swcTypes)
```
    Imports an SWC file using advanced options.
    
    Parameters:
    
    filePath - the absolute file path to the imported file
    
    assumeCoordinatesInVoxels - If true, the SWC coordinates are assumed to be in image coordinates ("pixels"). Note that in this case, radii will be scaled by the minimum voxel separation. This workaround seems to be required to properly import unscaled files
    
    xOffset - the offset to be applied to all X coordinates. May be useful to import data obtained from multiple "un-stitched" fields of view. Default is 0.
    
    yOffset - the offset to be applied to all Y coordinates. May be useful to import data obtained from multiple "un-stitched" fields of view. Default is 0.
    
    zOffset - the offset to be applied to all Z coordinates. May be useful to import data obtained from multiple "un-stitched" fields of view. Default is 0.
    
    xScale - the scaling factor for all X coordinates. Useful to import data onto downsampled images. Default is 1.
    
    yScale - the scaling factor for all Y coordinates. Useful to import data onto downsampled images. Default is 1.
    
    zScale - the scaling factor for all Z coordinates. Useful to import data onto downsampled images. Default is 1.
    
    replaceAllPaths - If true, all existing Paths will be deleted before the import.
    
    Returns:
    
    true, if import was successful
  - guessTracesFileType
```
protected int guessTracesFileType(String filename)
```
  - loadCompressedXML
```
protected boolean loadCompressedXML(String filename)
```
  - loadUncompressedXML
```
protected boolean loadUncompressedXML(String filename,
                                      int... swcTypes)
```
  - load
```
public boolean load(String filePath,
                    int... swcTypes)
```
    Imports a reconstruction file (any supported extension).
    
    Parameters:
    
    filePath - the absolute path to the file (.Traces, SWC or JSON) to be imported
    
    swcTypes - (Optional) The SWC type(s) (e.g., Path.SWC_AXON, Path.SWC_DENDRITE, etc.) to be considered in the import. Ignored if filePath encodes a .TRACES file.
    
    Returns:
    
    true, if successful
  - loadGuessingType
```
public boolean loadGuessingType(String optionalDescription,
                                InputStream is)
                         throws IOException
```
    Throws:
    
    IOException
  - getPaths
```
public ArrayList<Path> getPaths()
```
    Returns all the paths.
    
    Returns:
    
    the paths associated with this PathAndFillManager instance.
  - getPathsFiltered
```
public List<Path> getPathsFiltered()
```
    Returns the 'de facto' Paths.
    
    Returns:
    
    the paths associated with this PathAndFillManager instance excluding those that are null or fitted version of o paths.
  - transformationStarted
```
public void transformationStarted(View view)
```
    Specified by:
    
    transformationStarted in interface UniverseListener
  - transformationUpdated
```
public void transformationUpdated(View view)
```
    Specified by:
    
    transformationUpdated in interface UniverseListener
  - transformationFinished
```
public void transformationFinished(View view)
```
    Specified by:
    
    transformationFinished in interface UniverseListener
  - contentAdded
```
@Deprecated
public void contentAdded(Content c)
```
    Deprecated.
    
    Specified by:
    
    contentAdded in interface UniverseListener
  - contentRemoved
```
@Deprecated
public void contentRemoved(Content c)
```
    Deprecated.
    
    Specified by:
    
    contentRemoved in interface UniverseListener
  - contentChanged
```
@Deprecated
public void contentChanged(Content c)
```
    Deprecated.
    
    Specified by:
    
    contentChanged in interface UniverseListener
  - contentSelected
```
@Deprecated
public void contentSelected(Content c)
```
    Deprecated.
    
    Specified by:
    
    contentSelected in interface UniverseListener
  - canvasResized
```
@Deprecated
public void canvasResized()
```
    Deprecated.
    
    Specified by:
    
    canvasResized in interface UniverseListener
  - universeClosed
```
@Deprecated
public void universeClosed()
```
    Deprecated.
    
    Specified by:
    
    universeClosed in interface UniverseListener
  - nearestPointOnAnyPath
```
public NearPoint nearestPointOnAnyPath(double x,
                                       double y,
                                       double z,
                                       double distanceLimit)
```
  - getAllPathsRenderedInViewPort
```
protected List<Path> getAllPathsRenderedInViewPort(TracerCanvas canvas)
```
  - getSelectedPathsRenderedInViewPort
```
protected List<Path> getSelectedPathsRenderedInViewPort(TracerCanvas canvas)
```
  - getUnSelectedPathsRenderedInViewPort
```
protected List<Path> getUnSelectedPathsRenderedInViewPort(TracerCanvas canvas)
```
  - nearestPointOnAnyPath
```
public NearPoint nearestPointOnAnyPath(Collection<Path> paths,
                                       PointInCanvas pic,
                                       double distanceLimit)
```
  - nearestPointOnAnyPath
```
protected NearPoint nearestPointOnAnyPath(Collection<Path> paths,
                                          PointInImage pim,
                                          double distanceLimitSquared,
                                          boolean unScaledPositions)
```
  - allPointsIterator
```
public Iterator<PointInImage> allPointsIterator()
```
  - getCorrespondences
```
public 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
  - getAllFills
```
protected List<Fill> getAllFills()
```
  - exportFillsAsCSV
```
public void exportFillsAsCSV(File outputFile)
                      throws IOException
```
    Export fills as CSV.
    
    Parameters:
    
    outputFile - the output file
    
    Throws:
    
    IOException - Signals that an I/O exception has occurred.
  - exportToCSV
```
public void exportToCSV(File outputFile)
                 throws 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:
    
    IOException - if data could not be stored
  - update3DViewerContents
```
protected void update3DViewerContents()
```
  - 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)
  - pathChanged
```
public void pathChanged(sc.fiji.snt.PathChangeEvent event)
```

Class PathAndFillManager

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Detail

TRACES_FILE_TYPE_COMPRESSED_XML

TRACES_FILE_TYPE_UNCOMPRESSED_XML

TRACES_FILE_TYPE_SWC

TRACES_FILE_TYPE_ML_JSON

plugin

enableUIupdates

Constructor Detail

PathAndFillManager

PathAndFillManager

PathAndFillManager

Method Detail

syncSpatialSettingsWithPlugin

assignSpatialSettings

assignSpatialSettings

resetSpatialSettings

rebuildRelationships

size

addPathAndFillListener

getPath

getPathFromName

getPathFrom3DViewerName

getPathFromID

setSelected

isSelected

getSelectedPaths

getPathsInROI

anySelected

getSWCFileForIndex

exportAllPathsAsSWC

exportTree

savetoFileOrFileSeries

exportAllPathsAsSWC

exportConnectedStructureAsSWC

setHeadless

flushSWCPoints

usingNonPhysicalUnits

updateBoundingBox

getBoundingBox

allPathsShareSameSpatialCalibration

getPathsStructured

getTrees

multipleTreesExist

getPathsStructured

getSWCFor

getSWCForOld

resetListeners

resetListeners

addTree

addPath

addPath

addPath

addPath

addPath

getDefaultName

deletePath

deletePath

deletePaths

getPathIndex

deletePaths

addFill

deleteFills

getLoadedFills

reloadFills

writeXML

startElement

endElement

createFromFile

createFromNodes

createFromGraph

importGraph

importGraphWithPathStructure

clear