sc.fiji.snt.io

Class MouseLightLoader

java.lang.Object

sc.fiji.snt.io.MouseLightLoader

public class MouseLightLoader
extends java.lang.Object

Methods for retrieving reconstructions from MouseLight's online database at ml-neuronbrowser.janelia.org *

Author:

Tiago Ferreira

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	AXON The Constant AXON.
static java.lang.String	DENDRITE The Constant DENDRITE.
static java.lang.String	SOMA The Constant SOMA.

Constructor Summary

Constructors

Constructor and Description
MouseLightLoader(java.lang.String id) Instantiates a new loader.

Method Summary

Modifier and Type	Method and Description
static java.util.Map<java.lang.String,java.util.TreeSet<SWCPoint>>	extractNodes(java.io.File jsonFile, java.lang.String compartment) Extracts reconstruction(s) from a JSON file.
static java.util.Map<java.lang.String,Tree>	extractTrees(java.io.File jsonFile, java.lang.String compartment) Extracts reconstruction(s) from a JSON file.
java.util.List<java.lang.String>	getAllNeuronIDs() Gets the IDs of all the cells publicly available in the MouseLight database.
java.lang.String	getID()
org.json.JSONObject	getJSON() Gets all the data associated with this reconstruction as a JSON object.
static int	getNeuronCount() Gets the number of cells publicly available in the MouseLight database.
java.util.TreeSet<SWCPoint>	getNodes() Extracts the nodes (single-point soma, axonal and dendritic arbor) of the loaded neuron.
java.util.TreeSet<SWCPoint>	getNodes(java.lang.String compartment) Script-friendly method to extract the nodes of a cellular compartment.
java.lang.String	getSWC() Gets all the data associated with this reconstruction in the SWC format.
Tree	getTree() Script-friendly method to extract the entire neuron as a collection of Paths.
Tree	getTree(java.lang.String compartment) Script-friendly method to extract a compartment as a collection of Paths.
Tree	getTree(java.lang.String compartment, org.scijava.util.ColorRGB color) Extracts a cell compartment as a collection of Paths.
boolean	idExists() Checks whether the neuron to be loaded was found in the database.
static boolean	isDatabaseAvailable() Checks whether a connection to the MouseLight database can be established.
static void	main(java.lang.String... args)
boolean	saveAsJSON(java.lang.String outputDirectory) Convenience method to save JSON data to a local directory.
boolean	saveAsSWC(java.lang.String outputDirectory) Convenience method to save SWC data to a local directory.

Methods inherited from class java.lang.Object

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

Field Detail

AXON

public static final java.lang.String AXON

The Constant AXON.

See Also:

Constant Field Values

DENDRITE

public static final java.lang.String DENDRITE

The Constant DENDRITE.

See Also:

Constant Field Values

SOMA

public static final java.lang.String SOMA

The Constant SOMA.

See Also:

Constant Field Values

Constructor Detail

MouseLightLoader

public MouseLightLoader(java.lang.String id)

Instantiates a new loader.

Parameters:

id - the neuron id (e.g., "AA0001"). Note that DOIs are not allowed

Method Detail

getID

public java.lang.String getID()

getNodes

public java.util.TreeSet<SWCPoint> getNodes()

Extracts the nodes (single-point soma, axonal and dendritic arbor) of the loaded neuron.

Returns:

the list of nodes of the neuron as SWCPoints.

getNodes

public java.util.TreeSet<SWCPoint> getNodes(java.lang.String compartment)

Script-friendly method to extract the nodes of a cellular compartment.

Parameters:

compartment - 'soma', 'axon', 'dendrite', 'all' (case insensitive). All nodes are retrieved if compartment is not recognized

Returns:

the set of nodes of the neuron as SWCPoints.

extractTrees

public static java.util.Map<java.lang.String,Tree> extractTrees(java.io.File jsonFile,
                                                                java.lang.String compartment)
                                                         throws java.io.FileNotFoundException

Extracts reconstruction(s) from a JSON file.

Parameters:

jsonFile - the JSON file to be parsed

compartment - 'soma', 'axon', 'dendrite', 'all' (case insensitive). All nodes are retrieved if compartment is not recognized

Returns:

the map containing the reconstruction nodes as Trees

Throws:

java.io.FileNotFoundException - if file could not be retrieved

See Also:

extractNodesFromJSONObject(String, JSONObject)

extractNodes

public static java.util.Map<java.lang.String,java.util.TreeSet<SWCPoint>> extractNodes(java.io.File jsonFile,
                                                                                       java.lang.String compartment)
                                                                                throws java.io.FileNotFoundException

Extracts reconstruction(s) from a JSON file.

Parameters:

jsonFile - the JSON file to be parsed

compartment - 'soma', 'axon', 'dendrite', 'all' (case insensitive). All nodes are retrieved if compartment is not recognized

Returns:

the map containing the reconstruction nodes as SWCPoints

Throws:

java.io.FileNotFoundException - if file could not be retrieved

See Also:

extractTrees(File, String)

getJSON

public org.json.JSONObject getJSON()

Gets all the data associated with this reconstruction as a JSON object.

Returns:

the JSON data (null if data could not be retrieved).

idExists

public boolean idExists()

Checks whether the neuron to be loaded was found in the database.

Returns:

true, if the neuron id specified in the constructor was found in the database

getSWC

public java.lang.String getSWC()

Gets all the data associated with this reconstruction in the SWC format.

Returns:

the SWC data (null if data could not be retrieved).

saveAsSWC

public boolean saveAsSWC(java.lang.String outputDirectory)
                  throws java.io.IOException

Convenience method to save SWC data to a local directory.

Parameters:

outputDirectory - the output directory

Returns:

true, if successful

Throws:

java.io.IOException - if an I/O exception occurred during saving

saveAsJSON

public boolean saveAsJSON(java.lang.String outputDirectory)
                   throws java.io.IOException

Convenience method to save JSON data to a local directory.

Parameters:

outputDirectory - the output directory

Returns:

true, if successful

Throws:

java.io.IOException - if an I/O exception occurred during saving

getTree

public Tree getTree(java.lang.String compartment,
                    org.scijava.util.ColorRGB color)
             throws java.lang.IllegalArgumentException

Extracts a cell compartment as a collection of Paths.

Parameters:

compartment - 'soma', 'axon', 'dendrite', 'all' (case insensitive)

color - the color to be applied to the Tree. Null not expected.

Returns:

the compartment as a Tree, or null if data could not be retrieved

Throws:

java.lang.IllegalArgumentException - if compartment is not recognized or retrieval of data for this neuron is not possible

getTree

public Tree getTree(java.lang.String compartment)
             throws java.lang.IllegalArgumentException

Script-friendly method to extract a compartment as a collection of Paths.

Parameters:

compartment - 'soma', 'axon', 'dendrite', 'all' (case insensitive)

Returns:

the compartment as a Tree, or null if data could not be retrieved

Throws:

java.lang.IllegalArgumentException - if compartment is not recognized or retrieval of data for this neuron is not possible

getTree

public Tree getTree()
             throws java.lang.IllegalArgumentException

Script-friendly method to extract the entire neuron as a collection of Paths.

Returns:

the neuron as a Tree, or null if data could not be retrieved

Throws:

java.lang.IllegalArgumentException - if retrieval of data for this neuron is not possible

isDatabaseAvailable

public static boolean isDatabaseAvailable()

Checks whether a connection to the MouseLight database can be established.

Returns:

true, if an HHTP connection could be established

getNeuronCount

public static int getNeuronCount()

Gets the number of cells publicly available in the MouseLight database.

Returns:

the number of available cells, or -1 if the database could not be reached.

getAllNeuronIDs

public java.util.List<java.lang.String> getAllNeuronIDs()

Gets the IDs of all the cells publicly available in the MouseLight database.

Returns:

the list of cell IDs or an empty list if no database could not be reached.

main

public static void main(java.lang.String... args)
                 throws java.io.IOException

Throws:

java.io.IOException