I/O Operations Methods#

Methods that handle input/output operations, file loading, and data import/export.

Total methods in this category: 32

DefaultSearchNode#

asPath(arg0, arg1, arg2, arg3)#

Signature: asPath(double, double, double, String) -> Path

Parameters:

  • arg0 (float)

  • arg1 (float)

  • arg2 (float)

  • arg3 (str)

Returns: Path

asPathReversed(arg0, arg1, arg2, arg3)#

Signature: asPathReversed(double, double, double, String) -> Path

Parameters:

  • arg0 (float)

  • arg1 (float)

  • arg2 (float)

  • arg3 (str)

Returns: Path

Fill#

writeNodesXML(arg0)#

Signature: writeNodesXML(PrintWriter) -> void

Parameters:

  • arg0 (Any)

Returns: None

writeXML(arg0, arg1)#

Signature: writeXML(PrintWriter, int) -> void

Parameters:

  • arg0 (Any)

  • arg1 (int)

Returns: None

MouseLightLoader#

saveAsJSON(arg0)#

Convenience method to save JSON data to a local directory.

Signature: saveAsJSON(String) -> boolean

Parameters:

  • arg0 (str): - the output directory

Returns: (bool) true, if successful

saveAsSWC(arg0)#

Convenience method to save SWC data to a local directory.

Signature: saveAsSWC(String) -> boolean

Parameters:

  • arg0 (str): - the output directory

Returns: (bool) true, if successful

Path#

createPath()#

Returns a new Path with this Path’s attributes (e.g. spatial scale), but no nodes.

Signature: createPath() -> Path

Returns: (Path) the empty path

drawPathAsPoints(arg0, arg1, arg2, arg3, arg4, arg5, arg6)#

Signature: drawPathAsPoints(TracerCanvas, Graphics2D, Color, boolean, boolean, int, int) -> void

Parameters:

  • arg0 (Any)

  • arg1 (Any)

  • arg2 (Any)

  • arg3 (bool)

  • arg4 (bool)

  • arg5 (int)

  • arg6 (int)

Returns: None

PathAndFillManager#

deletePath(arg0)#

Deletes a path.

Signature: deletePath(int) -> boolean

Parameters:

  • arg0 (int): - the path to be deleted

Returns: (bool) true, if path was found and successfully deleted

deletePaths(arg0)#

Delete paths by position.

Signature: deletePaths([I) -> void

Parameters:

  • arg0 (Any): - the indices to be deleted

Returns: None

exportAllPathsAsSWC(arg0)#

Exports all as Paths as SWC file(s). Multiple files are created if multiple Trees exist.

Signature: exportAllPathsAsSWC(String) -> boolean

Parameters:

  • arg0 (str): - the file path (including common basename) for exported files. The

Returns: (bool) true, if successful

exportFillsAsCSV(arg0)#

Export fills as CSV.

Signature: exportFillsAsCSV(File) -> void

Parameters:

  • arg0 (str): - the output file

Returns: None

exportToCSV(arg0)#

Output some potentially useful information about all the Paths managed by this instance as a CSV (comma separated values) file.

Signature: exportToCSV(File) -> void

Parameters:

  • arg0 (str): - the output file

Returns: None

exportTree(arg0, arg1)#

Signature: exportTree(int, File) -> boolean

Parameters:

  • arg0 (int)

  • arg1 (str)

Returns: bool

static createFromFile(arg0, arg1)

Creates a PathAndFillManager instance from imported data

Signature: static createFromFile(String, [I) -> PathAndFillManager

Parameters:

  • arg0 (str): - the absolute path of the file to be imported as per load(String, int…)

  • arg1 (Any)

Returns: (Any) the PathAndFillManager instance, or null if file could not be imported

PathChangeListener#

pathChanged(arg0)#

Signature: pathChanged(PathChangeEvent) -> void

Parameters:

  • arg0 (Any)

Returns: None

PathFitter#

readPreferences()#

Signature: readPreferences() -> void

Returns: None

SNTService#

loadGraph(arg0)#

Signature: loadGraph(DirectedWeightedGraph) -> void

Parameters:

  • arg0 (DirectedWeightedGraph)

Returns: None

loadTracings(arg0)#

Loads the specified tracings file.

Signature: loadTracings(String) -> void

Parameters:

  • arg0 (str): - either a “SWC”, “TRACES” or “JSON” file path. URLs defining remote files also supported. Null not allowed.

Returns: None

loadTree(arg0)#

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.

Signature: loadTree(Tree) -> void

Parameters:

  • arg0 (Tree): - the Tree to be loaded (null not allowed).

Returns: None

SNTTable#

static fromFile(arg0, arg1)

Script-friendly method for loading tabular data from a file/URL.

Signature: static fromFile(String, String) -> SNTTable

Parameters:

  • arg0 (str)

  • arg1 (str)

Returns: SNTTable

SNTUtils#

static downloadToTempFile(arg0)

Downloads a file from the specified URL to a temporary file

Signature: static downloadToTempFile(String) -> File

Parameters:

  • arg0 (str): - the URL of the file to download

Returns: (str) the downloaded file

static fileAvailable(arg0)

Signature: static fileAvailable(File) -> boolean

Parameters:

  • arg0 (str)

Returns: bool

static getReconstructionFiles(arg0, arg1)

Retrieves a list of reconstruction files stored in a common directory matching the specified criteria.

Signature: static getReconstructionFiles(File, String) -> File;

Parameters:

  • arg0 (str): - the directory containing the reconstruction files (.(e)swc, .traces, .json extension)

  • arg1 (str)

Returns: (Any) the array of files. An empty list is retrieved if dir is not a valid, readable directory.

static getUniquelySuffixedFile(arg0, arg1)

Signature: static getUniquelySuffixedFile(File, String) -> File

Parameters:

  • arg0 (str)

  • arg1 (str)

Returns: str

static getUniquelySuffixedTifFile(arg0)

Signature: static getUniquelySuffixedTifFile(File) -> File

Parameters:

  • arg0 (str)

Returns: str

static isReconstructionFile(arg0)

Signature: static isReconstructionFile(File) -> boolean

Parameters:

  • arg0 (str)

Returns: bool

static randomPaths()

Generates a list of random paths. Only useful for debugging purposes

Signature: static randomPaths() -> List

Returns: (List[Any]) the list of random Paths

SciViewSNT#

syncPathManagerList()#

(Re)loads the current list of Paths in the Path Manager list.

Signature: syncPathManagerList() -> boolean

Returns: (bool) true, if Path Manager list is not empty and synchronization was successful

Tree#

static fromFile(arg0)

Script-friendly method for loading a Tree from a reconstruction file.

Signature: static fromFile(String) -> Tree

Parameters:

  • arg0 (str): - the absolute path to the file (.Traces, (e)SWC or JSON) to be imported

Returns: (Tree) the Tree instance, or null if file could not be imported

Viewer3D#

loadMesh(arg0, arg1, arg2)#

Loads a Wavefront .OBJ file. Files should be loaded _before_ displaying the scene, otherwise, if the scene is already visible, validate() should be called to ensure all meshes are visible.

Signature: loadMesh(String, ColorRGB, double) -> OBJMesh

Parameters:

  • arg0 (str): - the absolute file path (or URL) of the file to be imported. The filename is used as unique identifier of the object (see setVisible(String, boolean))

  • arg1 (Any)

  • arg2 (float)

Returns: (Any) the loaded OBJ mesh

loadRefBrain(arg0)#

Loads the surface mesh of a supported reference brain/neuropil. Internet connection may be required.

Signature: loadRefBrain(String) -> OBJMesh

Parameters:

  • arg0 (str): - the reference brain to be loaded (case-insensitive). E.g., “zebrafish” (MP ZBA); “mouse” (Allen CCF); “JFRC2”, “JFRC3” “JFRC2018”, “FCWB”(adult), “L1”, “L3”, “VNC” (Drosophila)

Returns: (Any) a reference to the loaded mesh

Category index generated on 2026-01-02 23:09:09