ome.xml.model

Class Pixels

java.lang.Object

ome.xml.model.AbstractOMEModelObject

ome.xml.model.Pixels

All Implemented Interfaces:

OMEModelObject

public class Pixels
extends AbstractOMEModelObject

Field Summary

Fields

Modifier and Type	Field and Description
static String	NAMESPACE

Constructor Summary

Constructors

Constructor and Description
Pixels() Default constructor.
Pixels(Element element, OMEModel model) Constructs Pixels recursively from an XML DOM tree.
Pixels(Pixels orig) Copy constructor.

Method Summary

Methods

Modifier and Type	Method and Description
void	addBinData(BinData binData)
void	addChannel(Channel channel)
void	addPlane(Plane plane)
void	addTiffData(TiffData tiffData)
Element	asXMLElement(Document document) Takes the entire object hierarchy and produces an XML DOM tree.
protected Element	asXMLElement(Document document, Element Pixels_element) Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.
List<BinData>	copyBinDataList()
List<Channel>	copyChannelList()
List<Annotation>	copyLinkedAnnotationList()
List<Plane>	copyPlaneList()
List<TiffData>	copyTiffDataList()
Boolean	getBigEndian()
BinData	getBinData(int index)
Channel	getChannel(int index)
DimensionOrder	getDimensionOrder()
String	getID()
Boolean	getInterleaved()
Annotation	getLinkedAnnotation(int index)
MetadataOnly	getMetadataOnly()
PositiveFloat	getPhysicalSizeX()
PositiveFloat	getPhysicalSizeY()
PositiveFloat	getPhysicalSizeZ()
Plane	getPlane(int index)
PositiveInteger	getSignificantBits()
PositiveInteger	getSizeC()
PositiveInteger	getSizeT()
PositiveInteger	getSizeX()
PositiveInteger	getSizeY()
PositiveInteger	getSizeZ()
TiffData	getTiffData(int index)
Double	getTimeIncrement()
PixelType	getType()
boolean	link(Reference reference, OMEModelObject o) Link a given OME model object to this model object.
boolean	linkAnnotation(Annotation o)
void	removeBinData(BinData binData)
void	removeChannel(Channel channel)
void	removePlane(Plane plane)
void	removeTiffData(TiffData tiffData)
void	setBigEndian(Boolean bigEndian)
BinData	setBinData(int index, BinData binData)
Channel	setChannel(int index, Channel channel)
void	setDimensionOrder(DimensionOrder dimensionOrder)
void	setID(String id)
void	setInterleaved(Boolean interleaved)
Annotation	setLinkedAnnotation(int index, Annotation o)
void	setMetadataOnly(MetadataOnly metadataOnly)
void	setPhysicalSizeX(PositiveFloat physicalSizeX)
void	setPhysicalSizeY(PositiveFloat physicalSizeY)
void	setPhysicalSizeZ(PositiveFloat physicalSizeZ)
Plane	setPlane(int index, Plane plane)
void	setSignificantBits(PositiveInteger significantBits)
void	setSizeC(PositiveInteger sizeC)
void	setSizeT(PositiveInteger sizeT)
void	setSizeX(PositiveInteger sizeX)
void	setSizeY(PositiveInteger sizeY)
void	setSizeZ(PositiveInteger sizeZ)
TiffData	setTiffData(int index, TiffData tiffData)
void	setTimeIncrement(Double timeIncrement)
void	setType(PixelType type)
int	sizeOfBinDataList()
int	sizeOfChannelList()
int	sizeOfLinkedAnnotationList()
int	sizeOfPlaneList()
int	sizeOfTiffDataList()
boolean	unlinkAnnotation(Annotation o)
void	update(Element element, OMEModel model) Updates Pixels recursively from an XML DOM tree.

Methods inherited from class ome.xml.model.AbstractOMEModelObject

getChildrenByTagName, stripNamespacePrefix

Methods inherited from class java.lang.Object

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

Field Detail

NAMESPACE

public static final String NAMESPACE

See Also:

Constant Field Values

Constructor Detail

Pixels

public Pixels()

Default constructor.

Pixels

public Pixels(Element element,
      OMEModel model)
       throws EnumerationException

Constructs Pixels recursively from an XML DOM tree.

Parameters:

element - Root of the XML DOM tree to construct a model object graph from.

model - Handler for the OME model which keeps track of instances and references seen during object population.

Throws:

EnumerationException - If there is an error instantiating an enumeration during model object creation.

Pixels

public Pixels(Pixels orig)

Copy constructor.

Method Detail

update

public void update(Element element,
          OMEModel model)
            throws EnumerationException

Updates Pixels recursively from an XML DOM tree. NOTE: No properties are removed, only added or updated.

Specified by:

update in interface OMEModelObject

Overrides:

update in class AbstractOMEModelObject

Parameters:

element - Root of the XML DOM tree to construct a model object graph from.

model - Handler for the OME model which keeps track of instances and references seen during object population.

Throws:

EnumerationException - If there is an error instantiating an enumeration during model object creation.

link

public boolean link(Reference reference,
           OMEModelObject o)

Description copied from interface: OMEModelObject

Link a given OME model object to this model object.

Specified by:

link in interface OMEModelObject

Overrides:

link in class AbstractOMEModelObject

Parameters:

reference - The type qualifier for the reference. This should be the corresponding reference type for o. If, for example, o is of type Image, reference MUST be of type ImageRef.

o - Model object to link to.

Returns:

true if this model object was able to handle the reference, false otherwise.

getSizeT

public PositiveInteger getSizeT()

setSizeT

public void setSizeT(PositiveInteger sizeT)

getDimensionOrder

public DimensionOrder getDimensionOrder()

setDimensionOrder

public void setDimensionOrder(DimensionOrder dimensionOrder)

getTimeIncrement

public Double getTimeIncrement()

setTimeIncrement

public void setTimeIncrement(Double timeIncrement)

getPhysicalSizeY

public PositiveFloat getPhysicalSizeY()

setPhysicalSizeY

public void setPhysicalSizeY(PositiveFloat physicalSizeY)

getPhysicalSizeX

public PositiveFloat getPhysicalSizeX()

setPhysicalSizeX

public void setPhysicalSizeX(PositiveFloat physicalSizeX)

getPhysicalSizeZ

public PositiveFloat getPhysicalSizeZ()

setPhysicalSizeZ

public void setPhysicalSizeZ(PositiveFloat physicalSizeZ)

getSizeX

public PositiveInteger getSizeX()

setSizeX

public void setSizeX(PositiveInteger sizeX)

getSizeY

public PositiveInteger getSizeY()

setSizeY

public void setSizeY(PositiveInteger sizeY)

getSizeZ

public PositiveInteger getSizeZ()

setSizeZ

public void setSizeZ(PositiveInteger sizeZ)

getBigEndian

public Boolean getBigEndian()

setBigEndian

public void setBigEndian(Boolean bigEndian)

getSignificantBits

public PositiveInteger getSignificantBits()

setSignificantBits

public void setSignificantBits(PositiveInteger significantBits)

getSizeC

public PositiveInteger getSizeC()

setSizeC

public void setSizeC(PositiveInteger sizeC)

getType

public PixelType getType()

setType

public void setType(PixelType type)

getID

public String getID()

setID

public void setID(String id)

getInterleaved

public Boolean getInterleaved()

setInterleaved

public void setInterleaved(Boolean interleaved)

sizeOfChannelList

public int sizeOfChannelList()

copyChannelList

public List<Channel> copyChannelList()

getChannel

public Channel getChannel(int index)

setChannel

public Channel setChannel(int index,
                 Channel channel)

addChannel

public void addChannel(Channel channel)

removeChannel

public void removeChannel(Channel channel)

sizeOfBinDataList

public int sizeOfBinDataList()

copyBinDataList

public List<BinData> copyBinDataList()

getBinData

public BinData getBinData(int index)

setBinData

public BinData setBinData(int index,
                 BinData binData)

addBinData

public void addBinData(BinData binData)

removeBinData

public void removeBinData(BinData binData)

sizeOfTiffDataList

public int sizeOfTiffDataList()

copyTiffDataList

public List<TiffData> copyTiffDataList()

getTiffData

public TiffData getTiffData(int index)

setTiffData

public TiffData setTiffData(int index,
                   TiffData tiffData)

addTiffData

public void addTiffData(TiffData tiffData)

removeTiffData

public void removeTiffData(TiffData tiffData)

getMetadataOnly

public MetadataOnly getMetadataOnly()

setMetadataOnly

public void setMetadataOnly(MetadataOnly metadataOnly)

sizeOfPlaneList

public int sizeOfPlaneList()

copyPlaneList

public List<Plane> copyPlaneList()

getPlane

public Plane getPlane(int index)

setPlane

public Plane setPlane(int index,
             Plane plane)

addPlane

public void addPlane(Plane plane)

removePlane

public void removePlane(Plane plane)

sizeOfLinkedAnnotationList

public int sizeOfLinkedAnnotationList()

copyLinkedAnnotationList

public List<Annotation> copyLinkedAnnotationList()

getLinkedAnnotation

public Annotation getLinkedAnnotation(int index)

setLinkedAnnotation

public Annotation setLinkedAnnotation(int index,
                             Annotation o)

linkAnnotation

public boolean linkAnnotation(Annotation o)

unlinkAnnotation

public boolean unlinkAnnotation(Annotation o)

asXMLElement

public Element asXMLElement(Document document)

Description copied from interface: OMEModelObject

Takes the entire object hierarchy and produces an XML DOM tree.

Specified by:

asXMLElement in interface OMEModelObject

Specified by:

asXMLElement in class AbstractOMEModelObject

Parameters:

document - Destination document for element creation, etc.

Returns:

XML DOM tree root element for this model object.

asXMLElement

protected Element asXMLElement(Document document,
                   Element Pixels_element)

Description copied from class: AbstractOMEModelObject

Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.

Overrides:

asXMLElement in class AbstractOMEModelObject

Parameters:

document - Destination document for element creation, etc.

Pixels_element - Element from the subclass. If null a new element will be created of this class.

Returns:

element populated with properties from this class.