OMEXMLService (Bio-Formats API)

All Superinterfaces:

loci.common.services.Service

All Known Implementing Classes:

OMEXMLServiceImpl
```
public interface OMEXMLService
extends loci.common.services.Service
```

Method Summary

All Methods Instance Methods Abstract 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 omexmlMeta, CoreMetadata core, int image)` 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(java.lang.String xml, MetadataStore dest)` Converts information from an OME-XML string (source) into a metadata store (destination).
`OMEXMLMetadata`	`createOMEXMLMetadata()` Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional `loci.formats.ome` package.
`OMEXMLMetadata`	`createOMEXMLMetadata(java.lang.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(java.lang.String xml, java.lang.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.
`ome.xml.model.OMEModelObject`	`createOMEXMLRoot(java.lang.String xml)` Constructs an OME root node.
`java.lang.String`	`getLatestVersion()` Retrieves the latest supported version of the OME-XML schema.
`Modulo`	`getModuloAlongC(OMEXMLMetadata omexmlMeta, int image)` Retrieve the ModuloAlongC annotation in the given Image in the given OME-XML metadata object.
`Modulo`	`getModuloAlongT(OMEXMLMetadata omexmlMeta, int image)` Retrieve the ModuloAlongT annotation in the given Image in the given OME-XML metadata object.
`Modulo`	`getModuloAlongZ(OMEXMLMetadata omexmlMeta, 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.
`java.lang.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.
`java.lang.String`	`getOMEXMLVersion(java.lang.Object o)` Gets the schema version for the given OME-XML metadata or root object (e.g., "2007-06" or "2003-FC").
`java.util.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(java.lang.Object o)` Checks whether the given object is an OME-XML metadata object.
`boolean`	`isOMEXMLRoot(java.lang.Object o)` Checks whether the given object is an OME-XML root object.
`void`	`populateOriginalMetadata(OMEXMLMetadata omexmlMeta, java.util.Hashtable<java.lang.String,java.lang.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, java.lang.String key, java.lang.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.
`java.lang.String`	`transformToLatestVersion(java.lang.String xml)` Transforms the given OME-XML string to the latest supported version of of the OME-XML schema.
`boolean`	`validateOMEXML(java.lang.String xml)` Attempts to validate the given OME-XML string using Java's XML validation facility.
`boolean`	`validateOMEXML(java.lang.String xml, boolean pixelsHack)` Attempts to validate the given OME-XML string using Java's XML validation facility.

- Method Detail
  - getLatestVersion
```
java.lang.String getLatestVersion()
```
    Retrieves the latest supported version of the OME-XML schema.
  - transformToLatestVersion
```
java.lang.String transformToLatestVersion(java.lang.String xml)
                                   throws loci.common.services.ServiceException
```
    Transforms the given OME-XML string to the latest supported version of of the OME-XML schema.
    
    Throws:
    
    loci.common.services.ServiceException
  - createOMEXMLMetadata
```
OMEXMLMetadata createOMEXMLMetadata()
                             throws loci.common.services.ServiceException
```
    Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package.
    
    Returns:
    
    A new instance of AbstractOMEXMLMetadata, or null if the class is not available.
    
    Throws:
    
    loci.common.services.ServiceException - If there is an error creating the OME-XML metadata object.
  - createOMEXMLMetadata
```
OMEXMLMetadata createOMEXMLMetadata(java.lang.String xml)
                             throws loci.common.services.ServiceException
```
    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.
    
    Returns:
    
    A new instance of AbstractOMEXMLMetadata, or null if the class is not available.
    
    Throws:
    
    loci.common.services.ServiceException - If there is an error creating the OME-XML metadata object.
  - createOMEXMLMetadata
```
OMEXMLMetadata createOMEXMLMetadata(java.lang.String xml,
                                    java.lang.String version)
                             throws loci.common.services.ServiceException
```
    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.
    
    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:
    
    loci.common.services.ServiceException - If there is an error creating the OME-XML metadata object.
  - createOMEXMLRoot
```
ome.xml.model.OMEModelObject createOMEXMLRoot(java.lang.String xml)
                                       throws loci.common.services.ServiceException
```
    Constructs an OME root node.
    
    Parameters:
    
    xml - String of XML to create the root node from.
    
    Returns:
    
    An ome.xml.model.OMEModelObject subclass root node.
    
    Throws:
    
    loci.common.services.ServiceException - If there is an error creating the OME-XML metadata object.
  - isOMEXMLMetadata
```
boolean isOMEXMLMetadata(java.lang.Object o)
```
    Checks whether the given object is an OME-XML metadata object.
    
    Returns:
    
    True if the object is an instance of OMEXMLMetadata.
  - isOMEXMLRoot
```
boolean isOMEXMLRoot(java.lang.Object o)
```
    Checks whether the given object is an OME-XML root object.
    
    Returns:
    
    True if the object is an instance of OME.
  - getOMEXMLVersion
```
java.lang.String getOMEXMLVersion(java.lang.Object o)
```
    Gets the schema version for the given OME-XML metadata or root object (e.g., "2007-06" or "2003-FC").
    
    Returns:
    
    OME-XML schema version, or null if the object is not an instance of OMEXMLMetadata.
  - getOMEMetadata
```
OMEXMLMetadata getOMEMetadata(MetadataRetrieve src)
                       throws loci.common.services.ServiceException
```
    Returns a OMEXMLMetadata object with the same contents as the given MetadataRetrieve, converting it if necessary.
    
    Throws:
    
    loci.common.services.ServiceException - If there is an error creating the OME-XML metadata object.
  - getOMEXML
```
java.lang.String getOMEXML(MetadataRetrieve src)
                    throws loci.common.services.ServiceException
```
    Extracts an OME-XML metadata string from the given metadata object, by converting to an OME-XML metadata object if necessary.
    
    Throws:
    
    loci.common.services.ServiceException - If there is an error creating the OME-XML metadata object.
  - validateOMEXML
```
boolean validateOMEXML(java.lang.String xml)
```
    Attempts to validate the given OME-XML string using Java's XML validation facility. Requires Java 1.5+.
    
    Parameters:
    
    xml - XML string to validate.
    
    Returns:
    
    true if the XML successfully validates.
  - validateOMEXML
```
boolean validateOMEXML(java.lang.String xml,
                       boolean pixelsHack)
```
    Attempts to validate the given OME-XML string using Java's XML validation facility. Requires Java 1.5+.
    
    Parameters:
    
    xml - XML string to validate.
    
    pixelsHack - Whether to ignore validation errors due to childless Pixels elements
    
    Returns:
    
    true if the XML successfully validates.
  - populateOriginalMetadata
```
void populateOriginalMetadata(OMEXMLMetadata omexmlMeta,
                              java.util.Hashtable<java.lang.String,java.lang.Object> metadata)
```
    Adds the key/value pairs in the specified Hashtable as new OriginalMetadata annotations in the given OME-XML metadata object.
    
    Parameters:
    
    omexmlMeta - An object of type OMEXMLMetadata.
    
    metadata - A hashtable containing metadata key/value pairs.
  - getModuloAlongZ
```
Modulo getModuloAlongZ(OMEXMLMetadata omexmlMeta,
                       int image)
```
    Retrieve the ModuloAlongZ annotation in the given Image in the given OME-XML metadata object. If no ModuloAlongZ annotation is present, return null.
    
    Parameters:
    
    omexmlMeta - An object of type OMEXMLMetadata
    
    image - the index of the Image to which the Annotation is linked
  - getModuloAlongC
```
Modulo getModuloAlongC(OMEXMLMetadata omexmlMeta,
                       int image)
```
    Retrieve the ModuloAlongC annotation in the given Image in the given OME-XML metadata object. If no ModuloAlongC annotation is present, return null.
    
    Parameters:
    
    omexmlMeta - An object of type OMEXMLMetadata
    
    image - the index of the Image to which the Annotation is linked
  - getModuloAlongT
```
Modulo getModuloAlongT(OMEXMLMetadata omexmlMeta,
                       int image)
```
    Retrieve the ModuloAlongT annotation in the given Image in the given OME-XML metadata object. If no ModuloAlongT annotation is present, return null.
    
    Parameters:
    
    omexmlMeta - An object of type OMEXMLMetadata
    
    image - the index of the Image to which the Annotation is linked
  - getOriginalMetadata
```
java.util.Hashtable getOriginalMetadata(OMEXMLMetadata omexmlMeta)
```
    Parse any OriginalMetadata annotations from the given OME-XML metadata object and store them in a Hashtable.
    
    Parameters:
    
    omexmlMeta - An object of type OMEXMLMetadata.
  - populateOriginalMetadata
```
void populateOriginalMetadata(OMEXMLMetadata omexmlMeta,
                              java.lang.String key,
                              java.lang.String value)
```
    Adds the specified key/value pair as a new OriginalMetadata node to the given OME-XML metadata object.
    
    Parameters:
    
    omexmlMeta - An object of type OMEXMLMetadata.
    
    key - Metadata key to populate.
    
    value - Metadata value corresponding to the specified key.
  - addModuloAlong
```
void addModuloAlong(OMEXMLMetadata omexmlMeta,
                    CoreMetadata core,
                    int image)
```
    Adds ModuloAlong* annotations to the given OME-XML metadata object, using the given CoreMetadata object to determine modulo dimensions.
    
    Parameters:
    
    omexmlMeta - An object of type OMEXMLMetadata
    
    core - A fully populated object of type CoreMetadata
    
    image - Index of the Image to which the annotation should be linked.
  - convertMetadata
```
void convertMetadata(java.lang.String xml,
                     MetadataStore dest)
              throws loci.common.services.ServiceException
```
    Converts information from an OME-XML string (source) into a metadata store (destination).
    
    Throws:
    
    loci.common.services.ServiceException - If there is an error creating the OME-XML metadata object.
  - convertMetadata
```
void convertMetadata(MetadataRetrieve src,
                     MetadataStore dest)
```
    Copies information from a metadata retrieval object (source) into a metadata store (destination).
  - removeBinData
```
void removeBinData(OMEXMLMetadata omexmlMeta)
```
    Remove all of the BinData elements from the given OME-XML metadata object.
  - removeTiffData
```
void removeTiffData(OMEXMLMetadata omexmlMeta)
```
    Remove all of the TiffData elements from the given OME-XML metadata object.
  - removeChannels
```
void removeChannels(OMEXMLMetadata omexmlMeta,
                    int image,
                    int sizeC)
```
    Remove all but the first sizeC valid Channel elements from the given OME-XML metadata object.
  - addMetadataOnly
```
void addMetadataOnly(OMEXMLMetadata omexmlMeta,
                     int image)
```
    Insert a MetadataOnly element under the Image specified by 'index' in the given OME-XML metadata object.
  - addMetadataOnly
```
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. If the 'resolve' flag is set, references in the OME-XML metadata object will be resolved before the new element is inserted.
  - isEqual
```
boolean isEqual(OMEXMLMetadata src1,
                OMEXMLMetadata src2)
```
    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.
  - asStore
```
MetadataStore asStore(MetadataRetrieve meta)
```
    Gets the given MetadataRetrieve object as a MetadataStore. Returns null if the object is incompatible and cannot be casted.
  - asRetrieve
```
MetadataRetrieve asRetrieve(MetadataStore meta)
```
    Gets the given MetadataStore object as a MetadataRetrieve. Returns null if the object is incompatible and cannot be casted.

Interface OMEXMLService

Method Summary

Method Detail

getLatestVersion

transformToLatestVersion

createOMEXMLMetadata

createOMEXMLMetadata

createOMEXMLMetadata

createOMEXMLRoot

isOMEXMLMetadata

isOMEXMLRoot

getOMEXMLVersion

getOMEMetadata

getOMEXML

validateOMEXML

validateOMEXML

populateOriginalMetadata

getModuloAlongZ

getModuloAlongC

getModuloAlongT

getOriginalMetadata

populateOriginalMetadata

addModuloAlong

convertMetadata

convertMetadata

removeBinData

removeTiffData

removeChannels

addMetadataOnly

addMetadataOnly

isEqual

asStore

asRetrieve