loci.formats.services

Class OMEXMLServiceImpl

java.lang.Object

loci.common.services.AbstractService

loci.formats.services.OMEXMLServiceImpl

All Implemented Interfaces:

Service, OMEXMLService

public class OMEXMLServiceImpl
extends AbstractService
implements OMEXMLService

Author:

callan

Field Summary

Fields

Modifier and Type	Field and Description
static String	LATEST_VERSION Latest OME-XML version namespace.
private static org.slf4j.Logger	LOGGER Logger for this class.
static String	NO_OME_XML_MSG
private static Templates	reorderXSLT Reordering stylesheet.
private static String	SCHEMA_PATH
private static Templates	update2003FC Stylesheets for updating from previous schema releases.
private static Templates	update200706
private static Templates	update200802
private static Templates	update200809
private static Templates	update200909
private static Templates	update201004
private static Templates	update201006
private static Templates	update201106
private static Templates	update201206
private static Templates	update201306
private static String	XSLT_2003FC
private static String	XSLT_200706
private static String	XSLT_200802
private static String	XSLT_200809
private static String	XSLT_200909
private static String	XSLT_201004
private static String	XSLT_201006
private static String	XSLT_201106
private static String	XSLT_201206
private static String	XSLT_201306
private static String	XSLT_PATH

Constructor Summary

Constructors

Constructor and Description
OMEXMLServiceImpl() Default constructor.

Method Summary

Methods

Modifier and Type	Method and Description
void	addMetadataOnly(OMEXMLMetadata omexmlMeta, int image) Insert a MetadataOnly element under the Image specified by 'index' in the given OME-XML metadata object.
void	addMetadataOnly(OMEXMLMetadata omexmlMeta, int image, boolean resolve) Insert a MetadataOnly element under the Image specified by 'index' in the given OME-XML metadata object.
void	addModuloAlong(OMEXMLMetadata meta, CoreMetadata core, int imageIdx) Adds ModuloAlong* annotations to the given OME-XML metadata object, using the given CoreMetadata object to determine modulo dimensions.
MetadataRetrieve	asRetrieve(MetadataStore meta) Gets the given MetadataStore object as a MetadataRetrieve.
MetadataStore	asStore(MetadataRetrieve meta) Gets the given MetadataRetrieve object as a MetadataStore.
void	convertMetadata(MetadataRetrieve src, MetadataStore dest) Copies information from a metadata retrieval object (source) into a metadata store (destination).
void	convertMetadata(String xml, MetadataStore dest) Converts information from an OME-XML string (source) into a metadata store (destination).
private void	createModulo(OMEXMLMetadata meta, Modulo modulo, StructuredAnnotations annotations, Image image, int imageIdx, int annotationIndex, int imageAnnotation) Create a ModuloAlong* annotation corresponding to the given Modulo.
OMEXMLMetadata	createOMEXMLMetadata() Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package.
OMEXMLMetadata	createOMEXMLMetadata(String xml) Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package, wrapping a DOM representation of the given OME-XML string.
OMEXMLMetadata	createOMEXMLMetadata(String xml, String version) Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package, wrapping a DOM representation of the given OME-XML string.
OMEModelObject	createOMEXMLRoot(String xml) Constructs an OME root node.
private OMEXMLMetadataRoot	createRoot(String xml) Constructs an OME root node.
boolean	equals(Node e1, Node e2) Compares two Elements for equality.
private Node	findChildWithID(Node root, String name, String id) Return the child node with specified value for the "ID" attribute.
private Node	findRootNode(Node child) Return the absolute root node for the specified child node.
String	getLatestVersion() Retrieves the latest supported version of the OME-XML schema.
private Modulo	getModuloAlong(OMEXMLMetadata omexml, String tag, int image) Create a Modulo corresponding to the given ModuloAlong* tag.
Modulo	getModuloAlongC(OMEXMLMetadata omexml, int image) Retrieve the ModuloAlongC annotation in the given Image in the given OME-XML metadata object.
Modulo	getModuloAlongT(OMEXMLMetadata omexml, int image) Retrieve the ModuloAlongT annotation in the given Image in the given OME-XML metadata object.
Modulo	getModuloAlongZ(OMEXMLMetadata omexml, int image) Retrieve the ModuloAlongZ annotation in the given Image in the given OME-XML metadata object.
OMEXMLMetadata	getOMEMetadata(MetadataRetrieve src) Returns a OMEXMLMetadata object with the same contents as the given MetadataRetrieve, converting it if necessary.
String	getOMEXML(MetadataRetrieve src) Extracts an OME-XML metadata string from the given metadata object, by converting to an OME-XML metadata object if necessary.
String	getOMEXMLVersion(Object o) Gets the schema version for the given OME-XML metadata or root object (e.g., "2007-06" or "2003-FC").
Hashtable	getOriginalMetadata(OMEXMLMetadata omexmlMeta) Parse any OriginalMetadata annotations from the given OME-XML metadata object and store them in a Hashtable.
boolean	isEqual(OMEXMLMetadata src1, OMEXMLMetadata src2) Determine whether or not two OMEXMLMetadata objects are equal.
boolean	isOMEXMLMetadata(Object o) Checks whether the given object is an OME-XML metadata object.
boolean	isOMEXMLRoot(Object o) Checks whether the given object is an OME-XML root object.
void	populateOriginalMetadata(OMEXMLMetadata omexmlMeta, Hashtable<String,Object> metadata) Adds the key/value pairs in the specified Hashtable as new OriginalMetadata annotations in the given OME-XML metadata object.
void	populateOriginalMetadata(OMEXMLMetadata omexmlMeta, String key, String value) Adds the specified key/value pair as a new OriginalMetadata node to the given OME-XML metadata object.
void	removeBinData(OMEXMLMetadata omexmlMeta) Remove all of the BinData elements from the given OME-XML metadata object.
void	removeChannels(OMEXMLMetadata omexmlMeta, int image, int sizeC) Remove all but the first sizeC valid Channel elements from the given OME-XML metadata object.
String	transformToLatestVersion(String xml) Transforms the given OME-XML string to the latest supported version of of the OME-XML schema.
boolean	validateOMEXML(String xml) Attempts to validate the given OME-XML string using Java's XML validation facility.
boolean	validateOMEXML(String xml, boolean pixelsHack) Attempts to validate the given OME-XML string using Java's XML validation facility.
private String	verifyOMENamespace(String xml) Ensures that an xmlns:ome element exists.

Methods inherited from class loci.common.services.AbstractService

checkClassDependency

Methods inherited from class java.lang.Object

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

Field Detail

LATEST_VERSION

public static final String LATEST_VERSION

Latest OME-XML version namespace.

See Also:

Constant Field Values

NO_OME_XML_MSG

public static final String NO_OME_XML_MSG

See Also:

Constant Field Values

LOGGER

private static final org.slf4j.Logger LOGGER

Logger for this class.

XSLT_PATH

private static final String XSLT_PATH

See Also:

Constant Field Values

XSLT_2003FC

private static final String XSLT_2003FC

See Also:

Constant Field Values

XSLT_200706

private static final String XSLT_200706

See Also:

Constant Field Values

XSLT_200802

private static final String XSLT_200802

See Also:

Constant Field Values

XSLT_200809

private static final String XSLT_200809

See Also:

Constant Field Values

XSLT_200909

private static final String XSLT_200909

See Also:

Constant Field Values

XSLT_201004

private static final String XSLT_201004

See Also:

Constant Field Values

XSLT_201006

private static final String XSLT_201006

See Also:

Constant Field Values

XSLT_201106

private static final String XSLT_201106

See Also:

Constant Field Values

XSLT_201206

private static final String XSLT_201206

See Also:

Constant Field Values

XSLT_201306

private static final String XSLT_201306

See Also:

Constant Field Values

reorderXSLT

private static Templates reorderXSLT

Reordering stylesheet.

update2003FC

private static Templates update2003FC

Stylesheets for updating from previous schema releases.

update200706

private static Templates update200706

update200802

private static Templates update200802

update200809

private static Templates update200809

update200909

private static Templates update200909

update201004

private static Templates update201004

update201006

private static Templates update201006

update201106

private static Templates update201106

update201206

private static Templates update201206

update201306

private static Templates update201306

SCHEMA_PATH

private static final String SCHEMA_PATH

See Also:

Constant Field Values

Constructor Detail

OMEXMLServiceImpl

public OMEXMLServiceImpl()

Default constructor.

Method Detail

getLatestVersion

public String getLatestVersion()

Description copied from interface: OMEXMLService

Retrieves the latest supported version of the OME-XML schema.

Specified by:

getLatestVersion in interface OMEXMLService

See Also:

OMEXMLService.getLatestVersion()

transformToLatestVersion

public String transformToLatestVersion(String xml)
                                throws ServiceException

Description copied from interface: OMEXMLService

Transforms the given OME-XML string to the latest supported version of of the OME-XML schema.

Specified by:

transformToLatestVersion in interface OMEXMLService

Throws:

ServiceException

See Also:

OMEXMLService.transformToLatestVersion(String)

createOMEXMLMetadata

public OMEXMLMetadata createOMEXMLMetadata()
                                    throws ServiceException

Description copied from interface: OMEXMLService

Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package.

Specified by:

createOMEXMLMetadata in interface OMEXMLService

Returns:

A new instance of AbstractOMEXMLMetadata, or null if the class is not available.

Throws:

ServiceException - If there is an error creating the OME-XML metadata object.

See Also:

OMEXMLService.createOMEXMLMetadata()

createOMEXMLMetadata

public OMEXMLMetadata createOMEXMLMetadata(String xml)
                                    throws ServiceException

Description copied from interface: OMEXMLService

Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package, wrapping a DOM representation of the given OME-XML string.

Specified by:

createOMEXMLMetadata in interface OMEXMLService

Returns:

A new instance of AbstractOMEXMLMetadata, or null if the class is not available.

Throws:

ServiceException - If there is an error creating the OME-XML metadata object.

See Also:

OMEXMLService.createOMEXMLMetadata(java.lang.String)

createOMEXMLMetadata

public OMEXMLMetadata createOMEXMLMetadata(String xml,
                                  String version)
                                    throws ServiceException

Description copied from interface: OMEXMLService

Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package, wrapping a DOM representation of the given OME-XML string.

Specified by:

createOMEXMLMetadata in interface OMEXMLService

Parameters:

xml - The OME-XML string to use for initial population of the metadata object.

version - The OME-XML version to use (e.g., "2003-FC" or "2007-06"). If the xml and version parameters are both null, the newest version is used.

Returns:

A new instance of AbstractOMEXMLMetadata, or null if the class is not available.

Throws:

ServiceException - If there is an error creating the OME-XML metadata object.

See Also:

OMEXMLService.createOMEXMLMetadata(java.lang.String, java.lang.String)

createOMEXMLRoot

public OMEModelObject createOMEXMLRoot(String xml)
                                throws ServiceException

Description copied from interface: OMEXMLService

Constructs an OME root node.

Specified by:

createOMEXMLRoot in interface OMEXMLService

Parameters:

xml - String of XML to create the root node from.

Returns:

An ome.xml.model.OMEModelObject subclass root node.

Throws:

ServiceException - If there is an error creating the OME-XML metadata object.

See Also:

OMEXMLService.createOMEXMLRoot(java.lang.String)

isOMEXMLMetadata

public boolean isOMEXMLMetadata(Object o)

Description copied from interface: OMEXMLService

Checks whether the given object is an OME-XML metadata object.

Specified by:

isOMEXMLMetadata in interface OMEXMLService

Returns:

True if the object is an instance of OMEXMLMetadata.

See Also:

OMEXMLService.isOMEXMLMetadata(java.lang.Object)

isOMEXMLRoot

public boolean isOMEXMLRoot(Object o)

Description copied from interface: OMEXMLService

Checks whether the given object is an OME-XML root object.

Specified by:

isOMEXMLRoot in interface OMEXMLService

Returns:

True if the object is an instance of OME.

See Also:

OMEXMLService.isOMEXMLRoot(java.lang.Object)

createRoot

private OMEXMLMetadataRoot createRoot(String xml)
                               throws ServiceException

Constructs an OME root node. NOTE: This method is mostly here to ensure type safety of return values as instances of service dependency classes should not leak out of the interface.

Parameters:

xml - String of XML to create the root node from.

Returns:

An ome.xml.model.OMEModelObject subclass root node.

Throws:

IOException - If there is an error reading from the string.

SAXException - If there is an error parsing the XML.

ParserConfigurationException - If there is an error preparing the parsing infrastructure.

ServiceException

getOMEXMLVersion

public String getOMEXMLVersion(Object o)

Description copied from interface: OMEXMLService

Gets the schema version for the given OME-XML metadata or root object (e.g., "2007-06" or "2003-FC").

Specified by:

getOMEXMLVersion in interface OMEXMLService

Returns:

OME-XML schema version, or null if the object is not an instance of OMEXMLMetadata.

See Also:

OMEXMLService.getOMEXMLVersion(java.lang.Object)

getOMEMetadata

public OMEXMLMetadata getOMEMetadata(MetadataRetrieve src)
                              throws ServiceException

Description copied from interface: OMEXMLService

Returns a OMEXMLMetadata object with the same contents as the given MetadataRetrieve, converting it if necessary.

Specified by:

getOMEMetadata in interface OMEXMLService

Throws:

ServiceException - If there is an error creating the OME-XML metadata object.

See Also:

OMEXMLService.getOMEMetadata(loci.formats.meta.MetadataRetrieve)

getOMEXML

public String getOMEXML(MetadataRetrieve src)
                 throws ServiceException

Description copied from interface: OMEXMLService

Extracts an OME-XML metadata string from the given metadata object, by converting to an OME-XML metadata object if necessary.

Specified by:

getOMEXML in interface OMEXMLService

Throws:

ServiceException - If there is an error creating the OME-XML metadata object.

See Also:

OMEXMLService.getOMEXML(loci.formats.meta.MetadataRetrieve)

validateOMEXML

public boolean validateOMEXML(String xml)

Description copied from interface: OMEXMLService

Attempts to validate the given OME-XML string using Java's XML validation facility. Requires Java 1.5+.

Specified by:

validateOMEXML in interface OMEXMLService

Parameters:

xml - XML string to validate.

Returns:

true if the XML successfully validates.

See Also:

OMEXMLService.validateOMEXML(java.lang.String)

validateOMEXML

public boolean validateOMEXML(String xml,
                     boolean pixelsHack)

Description copied from interface: OMEXMLService

Attempts to validate the given OME-XML string using Java's XML validation facility. Requires Java 1.5+.

Specified by:

validateOMEXML in interface OMEXMLService

Parameters:

xml - XML string to validate.

pixelsHack - Whether to ignore validation errors due to childless Pixels elements

Returns:

true if the XML successfully validates.

See Also:

OMEXMLService.validateOMEXML(java.lang.String, boolean)

getModuloAlongZ

public Modulo getModuloAlongZ(OMEXMLMetadata omexml,
                     int image)

Description copied from interface: OMEXMLService

Retrieve the ModuloAlongZ annotation in the given Image in the given OME-XML metadata object. If no ModuloAlongZ annotation is present, return null.

Specified by:

getModuloAlongZ in interface OMEXMLService

Parameters:

omexml - An object of type OMEXMLMetadata

image - the index of the Image to which the Annotation is linked

See Also:

OMEXMLService.getModuloAlongZ(OMEXMLMetadata, int)

getModuloAlongC

public Modulo getModuloAlongC(OMEXMLMetadata omexml,
                     int image)

Description copied from interface: OMEXMLService

Retrieve the ModuloAlongC annotation in the given Image in the given OME-XML metadata object. If no ModuloAlongC annotation is present, return null.

Specified by:

getModuloAlongC in interface OMEXMLService

Parameters:

omexml - An object of type OMEXMLMetadata

image - the index of the Image to which the Annotation is linked

See Also:

OMEXMLService.getModuloAlongC(OMEXMLMetadata, int)

getModuloAlongT

public Modulo getModuloAlongT(OMEXMLMetadata omexml,
                     int image)

Description copied from interface: OMEXMLService

Retrieve the ModuloAlongT annotation in the given Image in the given OME-XML metadata object. If no ModuloAlongT annotation is present, return null.

Specified by:

getModuloAlongT in interface OMEXMLService

Parameters:

omexml - An object of type OMEXMLMetadata

image - the index of the Image to which the Annotation is linked

See Also:

OMEXMLService.getModuloAlongT(OMEXMLMetadata, int)

getModuloAlong

private Modulo getModuloAlong(OMEXMLMetadata omexml,
                    String tag,
                    int image)

Create a Modulo corresponding to the given ModuloAlong* tag.

Parameters:

omexml - the OMEXMLMetadata from which to retrieve the ModuloAlong* tag

tag - the tag name (e.g. "ModuloAlongC")

image - the Image index within the OMEXMLMetadata

Returns:

the corresponding Modulo object

getOriginalMetadata

public Hashtable getOriginalMetadata(OMEXMLMetadata omexmlMeta)

Description copied from interface: OMEXMLService

Parse any OriginalMetadata annotations from the given OME-XML metadata object and store them in a Hashtable.

Specified by:

getOriginalMetadata in interface OMEXMLService

Parameters:

omexmlMeta - An object of type OMEXMLMetadata.

See Also:

OMEXMLService.getOriginalMetadata(loci.formats.ome.OMEXMLMetadata)

populateOriginalMetadata

public void populateOriginalMetadata(OMEXMLMetadata omexmlMeta,
                            Hashtable<String,Object> metadata)

Description copied from interface: OMEXMLService

Adds the key/value pairs in the specified Hashtable as new OriginalMetadata annotations in the given OME-XML metadata object.

Specified by:

populateOriginalMetadata in interface OMEXMLService

Parameters:

omexmlMeta - An object of type OMEXMLMetadata.

metadata - A hashtable containing metadata key/value pairs.

See Also:

OMEXMLService.populateOriginalMetadata(loci.formats.ome.OMEXMLMetadata, Hashtable)

populateOriginalMetadata

public void populateOriginalMetadata(OMEXMLMetadata omexmlMeta,
                            String key,
                            String value)

Description copied from interface: OMEXMLService

Adds the specified key/value pair as a new OriginalMetadata node to the given OME-XML metadata object.

Specified by:

populateOriginalMetadata in interface OMEXMLService

Parameters:

omexmlMeta - An object of type OMEXMLMetadata.

key - Metadata key to populate.

value - Metadata value corresponding to the specified key.

See Also:

OMEXMLService.populateOriginalMetadata(loci.formats.ome.OMEXMLMetadata, java.lang.String, java.lang.String)

convertMetadata

public void convertMetadata(String xml,
                   MetadataStore dest)
                     throws ServiceException

Description copied from interface: OMEXMLService

Converts information from an OME-XML string (source) into a metadata store (destination).

Specified by:

convertMetadata in interface OMEXMLService

Throws:

ServiceException - If there is an error creating the OME-XML metadata object.

See Also:

OMEXMLService.convertMetadata(java.lang.String, loci.formats.meta.MetadataStore)

convertMetadata

public void convertMetadata(MetadataRetrieve src,
                   MetadataStore dest)

Description copied from interface: OMEXMLService

Copies information from a metadata retrieval object (source) into a metadata store (destination).

Specified by:

convertMetadata in interface OMEXMLService

See Also:

OMEXMLService.convertMetadata(loci.formats.meta.MetadataRetrieve, loci.formats.meta.MetadataStore)

removeBinData

public void removeBinData(OMEXMLMetadata omexmlMeta)

Description copied from interface: OMEXMLService

Remove all of the BinData elements from the given OME-XML metadata object.

Specified by:

removeBinData in interface OMEXMLService

See Also:

OMEXMLService.removeBinData(OMEXMLMetadata)

removeChannels

public void removeChannels(OMEXMLMetadata omexmlMeta,
                  int image,
                  int sizeC)

Description copied from interface: OMEXMLService

Remove all but the first sizeC valid Channel elements from the given OME-XML metadata object.

Specified by:

removeChannels in interface OMEXMLService

See Also:

OMEXMLService.removeChannels(OMEXMLMetadata, int, int)

addMetadataOnly

public void addMetadataOnly(OMEXMLMetadata omexmlMeta,
                   int image)

Description copied from interface: OMEXMLService

Insert a MetadataOnly element under the Image specified by 'index' in the given OME-XML metadata object.

Specified by:

addMetadataOnly in interface OMEXMLService

See Also:

OMEXMLService.addMetadataOnly(OMEXMLMetadata, int)

addMetadataOnly

public void addMetadataOnly(OMEXMLMetadata omexmlMeta,
                   int image,
                   boolean resolve)

Description copied from interface: OMEXMLService

Insert a MetadataOnly element under the Image specified by 'index' in the given OME-XML metadata object. If the 'resolve' flag is set, references in the OME-XML metadata object will be resolved before the new element is inserted.

Specified by:

addMetadataOnly in interface OMEXMLService

See Also:

OMEXMLService.addMetadataOnly(OMEXMLMetadata, int, boolean)

isEqual

public boolean isEqual(OMEXMLMetadata src1,
              OMEXMLMetadata src2)

Description copied from interface: OMEXMLService

Determine whether or not two OMEXMLMetadata objects are equal. Equality is defined as: * having the same object graph (without regard to specific ID values) * having the exact same attribute values on every node (with the exception of 'ID' attributes) Note that StructuredAnnotations are ignored, i.e. the two OMEXMLMetadata objects may have wildly different things under StructuredAnnotations and still be considered equal.

Specified by:

isEqual in interface OMEXMLService

See Also:

OMEXMLService.isEqual(OMEXMLMetadata, OMEXMLMetadata)

addModuloAlong

public void addModuloAlong(OMEXMLMetadata meta,
                  CoreMetadata core,
                  int imageIdx)

Description copied from interface: OMEXMLService

Adds ModuloAlong* annotations to the given OME-XML metadata object, using the given CoreMetadata object to determine modulo dimensions.

Specified by:

addModuloAlong in interface OMEXMLService

Parameters:

meta - An object of type OMEXMLMetadata

core - A fully populated object of type CoreMetadata

imageIdx - Index of the Image to which the annotation should be linked.

createModulo

private void createModulo(OMEXMLMetadata meta,
                Modulo modulo,
                StructuredAnnotations annotations,
                Image image,
                int imageIdx,
                int annotationIndex,
                int imageAnnotation)

Create a ModuloAlong* annotation corresponding to the given Modulo.

Parameters:

meta - the OMEXMLMetadata in which to create the annotation

modulo - the Modulo object that contains the annotation data

annotations - the list of existing annotations

image - the Image to which the new annotation should be linked

imageIdx - the index of the Image

annotationIndex - the index to be assigned to the new annotation

imageAnnotation - the index to be assigned to the new annotation link

asStore

public MetadataStore asStore(MetadataRetrieve meta)

Description copied from interface: OMEXMLService

Gets the given MetadataRetrieve object as a MetadataStore. Returns null if the object is incompatible and cannot be casted.

Specified by:

asStore in interface OMEXMLService

See Also:

OMEXMLService.asStore(loci.formats.meta.MetadataRetrieve)

asRetrieve

public MetadataRetrieve asRetrieve(MetadataStore meta)

Description copied from interface: OMEXMLService

Gets the given MetadataStore object as a MetadataRetrieve. Returns null if the object is incompatible and cannot be casted.

Specified by:

asRetrieve in interface OMEXMLService

See Also:

OMEXMLService.asRetrieve(loci.formats.meta.MetadataStore)

verifyOMENamespace

private String verifyOMENamespace(String xml)

Ensures that an xmlns:ome element exists.

equals

public boolean equals(Node e1,
             Node e2)

Compares two Elements for equality.

findRootNode

private Node findRootNode(Node child)

Return the absolute root node for the specified child node.

findChildWithID

private Node findChildWithID(Node root,
                   String name,
                   String id)

Return the child node with specified value for the "ID" attribute.