MouseLightLoader (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- sc.fiji.snt.io.MouseLightLoader

```
public class MouseLightLoader
extends 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 String AXON
The Constant AXON.

static String DENDRITE
The Constant DENDRITE.

static String SOMA
The Constant SOMA.

Fields
Modifier and Type	Field and Description
`static String`	`AXON` The Constant AXON.
`static String`	`DENDRITE` The Constant DENDRITE.
`static String`	`SOMA` The Constant SOMA.

Constructor Summary

Constructors
Constructor and Description

MouseLightLoader(String id)
Instantiates a new loader.

Constructors
Constructor and Description
`MouseLightLoader(String id)` Instantiates a new loader.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static Map<String,TreeSet<SWCPoint>>`	`extractNodes(File jsonFile, String compartment)` Extracts reconstruction(s) from a JSON file.
`static Map<String,TreeSet<SWCPoint>>`	`extractNodes(InputStream stream, String compartment)`
`static Map<String,Tree>`	`extractTrees(File jsonFile, String compartment)` Extracts reconstruction(s) from a JSON file.
`static Map<String,Tree>`	`extractTrees(InputStream stream, String compartment)`
`static List<MouseLightLoader>`	`getAllLoaders()` Gets the loaders for all the cells publicly available in the MouseLight database.
`String`	`getDOI()`
`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.
`TreeSet<SWCPoint>`	`getNodes()` Extracts the nodes (single-point soma, axonal and dendritic arbor) of the loaded neuron.
`TreeSet<SWCPoint>`	`getNodes(String compartment)` Script-friendly method to extract the nodes of a cellular compartment.
`String`	`getSampleInfo()`
`AllenCompartment`	`getSomaCompartment()`
`SWCPoint`	`getSomaLocation()`
`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(String compartment)` Script-friendly method to extract a compartment as a collection of Paths.
`Tree`	`getTree(String compartment, 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(String... args)`
`boolean`	`save(File file)` Convenience method to save JSON data.
`boolean`	`save(String path)` Convenience method to save JSON data.
`boolean`	`saveAsJSON(String outputDirectory)` Convenience method to save JSON data to a local directory.
`boolean`	`saveAsSWC(String outputDirectory)` Convenience method to save SWC data to a local directory.

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

- Field Detail
  - AXON
```
public static final String AXON
```
    The Constant AXON.
    
    See Also:
    
    Constant Field Values
  - DENDRITE
```
public static final String DENDRITE
```
    The Constant DENDRITE.
    
    See Also:
    
    Constant Field Values
  - SOMA
```
public static final String SOMA
```
    The Constant SOMA.
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - MouseLightLoader
```
public MouseLightLoader(String id)
```
    Instantiates a new loader.
    
    Parameters:
    
    id - the neuron id (e.g., "AA0001"). Note that DOIs are not allowed
- Method Detail
  - getID
```
public String getID()
```
  - getDOI
```
public String getDOI()
```
  - getSampleInfo
```
public String getSampleInfo()
```
  - getNodes
```
public 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 TreeSet<SWCPoint> getNodes(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.
  - getSomaLocation
```
public SWCPoint getSomaLocation()
```
  - getSomaCompartment
```
public AllenCompartment getSomaCompartment()
```
  - extractTrees
```
public static Map<String,Tree> extractTrees(File jsonFile,
                                            String compartment)
                                     throws 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:
    
    FileNotFoundException - if file could not be retrieved
    
    See Also:
    
    extractNodesFromJSONObject(String, JSONObject)
  - extractTrees
```
public static Map<String,Tree> extractTrees(InputStream stream,
                                            String compartment)
```
  - extractNodes
```
public static Map<String,TreeSet<SWCPoint>> extractNodes(File jsonFile,
                                                         String compartment)
                                                  throws org.json.JSONException,
                                                         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:
    
    org.json.JSONException - if file is malformed
    
    FileNotFoundException - if file could not be retrieved
    
    See Also:
    
    extractTrees(File, String)
  - extractNodes
```
public static Map<String,TreeSet<SWCPoint>> extractNodes(InputStream stream,
                                                         String compartment)
                                                  throws org.json.JSONException
```
    Throws:
    
    org.json.JSONException
  - 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).
  - save
```
public boolean save(String path)
```
    Convenience method to save JSON data.
    
    Parameters:
    
    path - the absolute path to output directory/file
    
    Returns:
    
    true, if successful
    
    See Also:
    
    saveAsJSON(String)
  - save
```
public boolean save(File file)
```
    Convenience method to save JSON data.
    
    Parameters:
    
    file - the output directory or the output file
    
    Returns:
    
    true, if successful
    
    See Also:
    
    saveAsJSON(String)
  - 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 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(String outputDirectory)
                  throws IOException
```
    Convenience method to save SWC data to a local directory.
    
    Parameters:
    
    outputDirectory - the output directory
    
    Returns:
    
    true, if successful
    
    Throws:
    
    IOException - if an I/O exception occurred during saving
  - saveAsJSON
```
public boolean saveAsJSON(String outputDirectory)
                   throws IOException
```
    Convenience method to save JSON data to a local directory.
    
    Parameters:
    
    outputDirectory - the output directory
    
    Returns:
    
    true, if successful
    
    Throws:
    
    IOException - if an I/O exception occurred during saving
  - getTree
```
public Tree getTree(String compartment,
                    ColorRGB color)
             throws 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:
    
    IllegalArgumentException - if compartment is not recognized or retrieval of data for this neuron is not possible
  - getTree
```
public Tree getTree(String compartment)
             throws 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:
    
    IllegalArgumentException - if compartment is not recognized or retrieval of data for this neuron is not possible
  - getTree
```
public Tree getTree()
             throws 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:
    
    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.
  - getAllLoaders
```
public static List<MouseLightLoader> getAllLoaders()
                                            throws IllegalArgumentException
```
    Gets the loaders for all the cells publicly available in the MouseLight database.
    
    Returns:
    
    the list of loaders
    
    Throws:
    
    IllegalArgumentException - if the ML database could not be reached.
  - main
```
public static void main(String... args)
                 throws IOException
```
    Throws:
    
    IOException

Class MouseLightLoader

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

AXON

DENDRITE

SOMA

Constructor Detail

MouseLightLoader

Method Detail

getID

getDOI

getSampleInfo

getNodes

getNodes

getSomaLocation

getSomaCompartment

extractTrees

extractTrees

extractNodes

extractNodes

getJSON

save

save

idExists

getSWC

saveAsSWC

saveAsJSON

getTree

getTree

getTree

isDatabaseAvailable

getNeuronCount

getAllLoaders

main