OMEXMLServiceImpl (Bio-Formats API)

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 XMLTools.SchemaReader`	`SCHEMA_CLASSPATH_READER` Finds OME-XML schema definitions in specifications.jar.
`private static String`	`SCHEMA_PATH`
`private static Pattern`	`SCHEMA_URL_PATTERN` The pattern of system ID URLs for OME-XML schema definitions.
`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 Templates`	`update201501`
`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_201501`
`private static String`	`XSLT_PATH`

Constructor Summary

Constructors
Constructor and Description

OMEXMLServiceImpl()
Default constructor.

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.
`void`	`removeTiffData(OMEXMLMetadata omexmlMeta)` Remove all of the TiffData 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
  - XSLT_201501
```
private static final String XSLT_201501
```
    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
```
  - update201501
```
private static Templates update201501
```
  - SCHEMA_PATH
```
private static final String SCHEMA_PATH
```
    See Also:
    Constant Field Values
  - SCHEMA_URL_PATTERN
```
private static final Pattern SCHEMA_URL_PATTERN
```
    The pattern of system ID URLs for OME-XML schema definitions.
  - SCHEMA_CLASSPATH_READER
```
private static final XMLTools.SchemaReader SCHEMA_CLASSPATH_READER
```
    Finds OME-XML schema definitions in specifications.jar.
- 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)
  - removeTiffData
```
public void removeTiffData(OMEXMLMetadata omexmlMeta)
```
    Description copied from interface: OMEXMLService
    
    Remove all of the TiffData elements from the given OME-XML metadata object.
    
    Specified by:
    
    removeTiffData in interface OMEXMLService
    
    See Also:
    OMEXMLService.removeTiffData(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.

Class OMEXMLServiceImpl

Field Summary

Constructor Summary

Method Summary

Methods inherited from class loci.common.services.AbstractService

Methods inherited from class java.lang.Object

Field Detail

LATEST_VERSION

NO_OME_XML_MSG

LOGGER

XSLT_PATH

XSLT_2003FC

XSLT_200706

XSLT_200802

XSLT_200809

XSLT_200909

XSLT_201004

XSLT_201006

XSLT_201106

XSLT_201206

XSLT_201306

XSLT_201501

reorderXSLT

update2003FC

update200706

update200802

update200809

update200909

update201004

update201006

update201106

update201206

update201306

update201501

SCHEMA_PATH

SCHEMA_URL_PATTERN

SCHEMA_CLASSPATH_READER

Constructor Detail

OMEXMLServiceImpl

Method Detail

getLatestVersion

transformToLatestVersion

createOMEXMLMetadata

createOMEXMLMetadata

createOMEXMLMetadata

createOMEXMLRoot

isOMEXMLMetadata

isOMEXMLRoot

createRoot

getOMEXMLVersion

getOMEMetadata

getOMEXML

validateOMEXML

validateOMEXML

getModuloAlongZ

getModuloAlongC

getModuloAlongT

getModuloAlong

getOriginalMetadata

populateOriginalMetadata

populateOriginalMetadata

convertMetadata

convertMetadata

removeBinData

removeTiffData

removeChannels

addMetadataOnly

addMetadataOnly

isEqual

addModuloAlong

createModulo

asStore

asRetrieve

verifyOMENamespace

equals

findRootNode

findChildWithID