ome.formats

Class OMEROMetadataStore

java.lang.Object

ome.formats.OMEROMetadataStore

public class OMEROMetadataStore
extends Object

An OMERO metadata store. This particular metadata store requires the user to be logged into OMERO prior to use with the #login() method. While attempts have been made to allow the caller to switch back and forth between Images and Pixels during metadata population it is strongly encouraged that at least Images and Pixels are populated in ascending order. For example: Image_1 --> Pixels_1, Pixels_2 followed by Image_2 --> Pixels_1, Pixels2, Pixels_3.

Author:

Brian W. Loranger brain at lifesci.dundee.ac.uk, Chris Allan callan at blackcat.ca

Constructor Summary

Constructors

Constructor and Description
OMEROMetadataStore() Empty constructor for testing purposes.
OMEROMetadataStore(ServiceFactory factory, SqlAction sql) Creates a new instance.

Method Summary

Methods

Modifier and Type	Method and Description
void	checkAndCollapseGraph() Checks the entire object graph for sections that may be collapsed if the data is derived from a Plate.
void	createRoot()
IObject	getObjectByLSID(LSID lsid) Retrieves an object from the internal object graph by LSID.
void	populateMinMax(double[][][] imageChannelGlobalMinMax) Synchronize the minimum and maximum intensity values with those specified by the client and save them in the DB.
List<Pixels>	saveToDB(FilesetJobLink link) Saves the current object graph to the database.
void	updateObject(String lsid, IObject sourceObject, Map<String,Integer> indexes) Updates a given model object in our object graph.
void	updateReferences(Map<String,String[]> referenceCache) Updates our object graph references.

Methods inherited from class java.lang.Object

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

Constructor Detail

OMEROMetadataStore

public OMEROMetadataStore()

Empty constructor for testing purposes.

OMEROMetadataStore

public OMEROMetadataStore(ServiceFactory factory,
                  SqlAction sql)
                   throws Exception

Creates a new instance.

Parameters:

factory - a non-null, active ServiceFactory

Throws:

MetadataStoreException - if the factory is null or there is another error instantiating required services.

Exception

Method Detail

updateObject

public void updateObject(String lsid,
                IObject sourceObject,
                Map<String,Integer> indexes)

Updates a given model object in our object graph.

Parameters:

lsid - LSID of model object.

sourceObject - Model object itself.

indexes - Any indexes that should are used to describe the model object's graph location.

updateReferences

public void updateReferences(Map<String,String[]> referenceCache)

Updates our object graph references.

Parameters:

referenceCache - Client side LSID reference cache.

getObjectByLSID

public IObject getObjectByLSID(LSID lsid)

Retrieves an object from the internal object graph by LSID.

Parameters:

lsid - LSID of the object.

Returns:

See above. null if the object is not in the internal LSID map.

createRoot

public void createRoot()

checkAndCollapseGraph

public void checkAndCollapseGraph()

Checks the entire object graph for sections that may be collapsed if the data is derived from a Plate. Collapsible points:

• Image --> ObjectiveSettings
• Image --> Channel --> LogicalChannel --> LightSettings
• Image --> Channel --> LogicalChannel --> LightPath
• Image --> Channel --> LogicalChannel --> DetectorSettings

saveToDB

public List<Pixels> saveToDB(FilesetJobLink link)

Saves the current object graph to the database.

Returns:

List of the Pixels objects with their attached object graphs that have been saved.

populateMinMax

public void populateMinMax(double[][][] imageChannelGlobalMinMax)

Synchronize the minimum and maximum intensity values with those specified by the client and save them in the DB.

Parameters:

imageChannelGlobalMinMax - Minimums and maximums to update.