sc.fiji.snt.io

Class MouseLightQuerier

java.lang.Object

sc.fiji.snt.io.MouseLightQuerier

public class MouseLightQuerier
extends java.lang.Object

Importer 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
MouseLightQuerier(java.lang.String id) Instantiates a new loader.

Method Summary

Modifier and Type	Method and Description
java.util.TreeSet<SWCPoint>	getAxonNodes() Extracts the nodes of the axonal arbor of loaded neuron.
org.json.JSONObject	getCompartment(java.lang.String structure) Gets a traced compartment of the loaded cell.
java.util.TreeSet<SWCPoint>	getDendriteNodes() Extracts the nodes of the dendritic arbor of loaded neuron.
static java.util.List<java.lang.String>	getIDs(AllenCompartment compartment) Gets the IDs of the cells publicly available in the MouseLight database having the soma associated with the specified compartment.
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 compartment.
SWCPoint	getSoma() Retrieves the soma (single-point representation) of the loaded neuron.
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)

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

MouseLightQuerier

public MouseLightQuerier(java.lang.String id)

Instantiates a new loader.

Parameters:

id - the neuron id (e.g., "AA0001") or DOI (e.g., "10.25378/janelia.5527672") of the neuron to be loaded

Method Detail

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

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

getCompartment

public org.json.JSONObject getCompartment(java.lang.String structure)
                                   throws java.lang.IllegalArgumentException

Gets a traced compartment of the loaded cell.

Parameters:

structure - either AXON or DENDRITE

Returns:

the specified compartment as a JSON object

Throws:

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

getNodes

public java.util.TreeSet<SWCPoint> getNodes()
                                     throws java.lang.IllegalArgumentException

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

Returns:

the list of nodes of the neuron as SWCPoints. Note that the first point in the set (the soma) has an SWC sample number of 0.

Throws:

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

getAxonNodes

public java.util.TreeSet<SWCPoint> getAxonNodes()
                                         throws java.lang.IllegalArgumentException

Extracts the nodes of the axonal arbor of loaded neuron.

Returns:

the list of nodes of the axonal arbor as SWCPoints

Throws:

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

getDendriteNodes

public java.util.TreeSet<SWCPoint> getDendriteNodes()
                                             throws java.lang.IllegalArgumentException

Extracts the nodes of the dendritic arbor of loaded neuron.

Returns:

the list of nodes of the dendritic arbor as SWCPoints

Throws:

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

getNodes

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

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

Parameters:

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

Returns:

the list of nodes of the neuron as SWCPoints. All nodes are retrieved if compartment was not recognized.

Throws:

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

getSoma

public SWCPoint getSoma()
                 throws java.lang.IllegalArgumentException

Retrieves the soma (single-point representation) of the loaded neuron.

Returns:

the soma as SWCPoint. Note that point has an SWC sample number of 0.

Throws:

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

getIDs

public static java.util.List<java.lang.String> getIDs(AllenCompartment compartment)

Gets the IDs of the cells publicly available in the MouseLight database having the soma associated with the specified compartment.

Returns:

the list of cell IDs associated with compartment or an empty list if no cells were found

main

public static void main(java.lang.String... args)