ome.xml.model

Class Image

java.lang.Object

ome.xml.model.AbstractOMEModelObject

ome.xml.model.Image

All Implemented Interfaces:

OMEModelObject

public class Image
extends AbstractOMEModelObject

Field Summary

Fields

Modifier and Type	Field and Description
private Timestamp	acquisitionDate
private List<Annotation>	annotationLinks
private List<Dataset>	datasetLinks
private String	description
private Experiment	experiment
private Experimenter	experimenter
private ExperimenterGroup	experimenterGroup
private String	id
private ImagingEnvironment	imagingEnvironment
private Instrument	instrument
private static org.slf4j.Logger	LOGGER Logger for this class.
private List<MicrobeamManipulation>	microbeamManipulationLinks
private String	name
static String	NAMESPACE
private ObjectiveSettings	objectiveSettings
private Pixels	pixels
private List<ROI>	roiLinks
private StageLabel	stageLabel
private List<WellSample>	wellSamples

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
Element	asXMLElement(Document document) Takes the entire object hierarchy and produces an XML DOM tree.
protected Element	asXMLElement(Document document, Element Image_element) Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.
List<Annotation>	copyLinkedAnnotationList()
List<Dataset>	copyLinkedDatasetList()
List<MicrobeamManipulation>	copyLinkedMicrobeamManipulationList()
List<ROI>	copyLinkedROIList()
List<WellSample>	copyLinkedWellSampleList()
Timestamp	getAcquisitionDate()
String	getDescription()
String	getID()
ImagingEnvironment	getImagingEnvironment()
Annotation	getLinkedAnnotation(int index)
Dataset	getLinkedDataset(int index)
Experiment	getLinkedExperiment()
Experimenter	getLinkedExperimenter()
ExperimenterGroup	getLinkedExperimenterGroup()
Instrument	getLinkedInstrument()
MicrobeamManipulation	getLinkedMicrobeamManipulation(int index)
ROI	getLinkedROI(int index)
WellSample	getLinkedWellSample(int index)
String	getName()
ObjectiveSettings	getObjectiveSettings()
Pixels	getPixels()
StageLabel	getStageLabel()
boolean	link(Reference reference, OMEModelObject o) Link a given OME model object to this model object.
boolean	linkAnnotation(Annotation o)
boolean	linkDataset(Dataset o)
void	linkExperiment(Experiment o)
void	linkExperimenter(Experimenter o)
void	linkExperimenterGroup(ExperimenterGroup o)
void	linkInstrument(Instrument o)
boolean	linkMicrobeamManipulation(MicrobeamManipulation o)
boolean	linkROI(ROI o)
boolean	linkWellSample(WellSample o)
void	setAcquisitionDate(Timestamp acquisitionDate)
void	setDescription(String description)
void	setID(String id)
void	setImagingEnvironment(ImagingEnvironment imagingEnvironment)
Annotation	setLinkedAnnotation(int index, Annotation o)
Dataset	setLinkedDataset(int index, Dataset o)
MicrobeamManipulation	setLinkedMicrobeamManipulation(int index, MicrobeamManipulation o)
ROI	setLinkedROI(int index, ROI o)
WellSample	setLinkedWellSample(int index, WellSample o)
void	setName(String name)
void	setObjectiveSettings(ObjectiveSettings objectiveSettings)
void	setPixels(Pixels pixels)
void	setStageLabel(StageLabel stageLabel)
int	sizeOfLinkedAnnotationList()
int	sizeOfLinkedDatasetList()
int	sizeOfLinkedMicrobeamManipulationList()
int	sizeOfLinkedROIList()
int	sizeOfLinkedWellSampleList()
boolean	unlinkAnnotation(Annotation o)
boolean	unlinkDataset(Dataset o)
void	unlinkExperiment(Experiment o)
void	unlinkExperimenter(Experimenter o)
void	unlinkExperimenterGroup(ExperimenterGroup o)
void	unlinkInstrument(Instrument o)
boolean	unlinkMicrobeamManipulation(MicrobeamManipulation o)
boolean	unlinkROI(ROI o)
boolean	unlinkWellSample(WellSample o)
void	update(Element element, OMEModel model) Updates Image 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

LOGGER

private static final org.slf4j.Logger LOGGER

Logger for this class.

id

private String id

name

private String name

acquisitionDate

private Timestamp acquisitionDate

experimenter

private Experimenter experimenter

description

private String description

experiment

private Experiment experiment

experimenterGroup

private ExperimenterGroup experimenterGroup

instrument

private Instrument instrument

objectiveSettings

private ObjectiveSettings objectiveSettings

imagingEnvironment

private ImagingEnvironment imagingEnvironment

stageLabel

private StageLabel stageLabel

pixels

private Pixels pixels

roiLinks

private List<ROI> roiLinks

microbeamManipulationLinks

private List<MicrobeamManipulation> microbeamManipulationLinks

annotationLinks

private List<Annotation> annotationLinks

datasetLinks

private List<Dataset> datasetLinks

wellSamples

private List<WellSample> wellSamples

Constructor Detail

Image

public Image()

Default constructor.

Image

public Image(Element element,
     OMEModel model)
      throws EnumerationException

Constructs Image 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.

Image

public Image(Image orig)

Copy constructor.

Method Detail

update

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

Updates Image 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.

getID

public String getID()

setID

public void setID(String id)

getName

public String getName()

setName

public void setName(String name)

getAcquisitionDate

public Timestamp getAcquisitionDate()

setAcquisitionDate

public void setAcquisitionDate(Timestamp acquisitionDate)

getLinkedExperimenter

public Experimenter getLinkedExperimenter()

linkExperimenter

public void linkExperimenter(Experimenter o)

unlinkExperimenter

public void unlinkExperimenter(Experimenter o)

getDescription

public String getDescription()

setDescription

public void setDescription(String description)

getLinkedExperiment

public Experiment getLinkedExperiment()

linkExperiment

public void linkExperiment(Experiment o)

unlinkExperiment

public void unlinkExperiment(Experiment o)

getLinkedExperimenterGroup

public ExperimenterGroup getLinkedExperimenterGroup()

linkExperimenterGroup

public void linkExperimenterGroup(ExperimenterGroup o)

unlinkExperimenterGroup

public void unlinkExperimenterGroup(ExperimenterGroup o)

getLinkedInstrument

public Instrument getLinkedInstrument()

linkInstrument

public void linkInstrument(Instrument o)

unlinkInstrument

public void unlinkInstrument(Instrument o)

getObjectiveSettings

public ObjectiveSettings getObjectiveSettings()

setObjectiveSettings

public void setObjectiveSettings(ObjectiveSettings objectiveSettings)

getImagingEnvironment

public ImagingEnvironment getImagingEnvironment()

setImagingEnvironment

public void setImagingEnvironment(ImagingEnvironment imagingEnvironment)

getStageLabel

public StageLabel getStageLabel()

setStageLabel

public void setStageLabel(StageLabel stageLabel)

getPixels

public Pixels getPixels()

setPixels

public void setPixels(Pixels pixels)

sizeOfLinkedROIList

public int sizeOfLinkedROIList()

copyLinkedROIList

public List<ROI> copyLinkedROIList()

getLinkedROI

public ROI getLinkedROI(int index)

setLinkedROI

public ROI setLinkedROI(int index,
               ROI o)

linkROI

public boolean linkROI(ROI o)

unlinkROI

public boolean unlinkROI(ROI o)

sizeOfLinkedMicrobeamManipulationList

public int sizeOfLinkedMicrobeamManipulationList()

copyLinkedMicrobeamManipulationList

public List<MicrobeamManipulation> copyLinkedMicrobeamManipulationList()

getLinkedMicrobeamManipulation

public MicrobeamManipulation getLinkedMicrobeamManipulation(int index)

setLinkedMicrobeamManipulation

public MicrobeamManipulation setLinkedMicrobeamManipulation(int index,
                                                   MicrobeamManipulation o)

linkMicrobeamManipulation

public boolean linkMicrobeamManipulation(MicrobeamManipulation o)

unlinkMicrobeamManipulation

public boolean unlinkMicrobeamManipulation(MicrobeamManipulation o)

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)

sizeOfLinkedDatasetList

public int sizeOfLinkedDatasetList()

copyLinkedDatasetList

public List<Dataset> copyLinkedDatasetList()

getLinkedDataset

public Dataset getLinkedDataset(int index)

setLinkedDataset

public Dataset setLinkedDataset(int index,
                       Dataset o)

linkDataset

public boolean linkDataset(Dataset o)

unlinkDataset

public boolean unlinkDataset(Dataset o)

sizeOfLinkedWellSampleList

public int sizeOfLinkedWellSampleList()

copyLinkedWellSampleList

public List<WellSample> copyLinkedWellSampleList()

getLinkedWellSample

public WellSample getLinkedWellSample(int index)

setLinkedWellSample

public WellSample setLinkedWellSample(int index,
                             WellSample o)

linkWellSample

public boolean linkWellSample(WellSample o)

unlinkWellSample

public boolean unlinkWellSample(WellSample 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 Image_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.

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

Returns:

element populated with properties from this class.