loci.formats.ome

Class OMEPyramidStore

java.lang.Object

ome.xml.meta.AbstractOMEXMLMetadata

ome.xml.meta.OMEXMLMetadataImpl

loci.formats.ome.OMEXMLMetadataImpl

loci.formats.ome.OMEPyramidStore

All Implemented Interfaces:

IPyramidStore, ome.xml.meta.BaseMetadata, ome.xml.meta.IMetadata, ome.xml.meta.MetadataRetrieve, ome.xml.meta.MetadataStore, ome.xml.meta.OMEXMLMetadata

public class OMEPyramidStore
extends OMEXMLMetadataImpl
implements IPyramidStore

Extension of OMEXMLMetadataImpl that allows for pyramid resolution storage and retrieval.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	OMEPyramidStore.Resolution

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	NAMESPACE
private java.util.List<java.util.List<OMEPyramidStore.Resolution>>	resolutions
private boolean	written

Fields inherited from class ome.xml.meta.AbstractOMEXMLMetadata

LOGGER, SCHEMA, XSI_NS

Constructor Summary

Constructors

Constructor and Description
OMEPyramidStore()

Method Summary

Modifier and Type	Method and Description
private void	checkImageIndex(int image) Verify that the given index is non-negative and less than the Image count.
private void	checkResolutionIndex(int image, int res) Verify that the given image and resolution indices are valid.
java.lang.String	dumpXML()
int	getResolutionCount(int image) Retrieve the number of pyramid resolutions defined for the given Image.
ome.xml.model.primitives.PositiveInteger	getResolutionSizeX(int image, int resolution) Retrieve the image width in pixels of the given pyramid resolution.
ome.xml.model.primitives.PositiveInteger	getResolutionSizeY(int image, int resolution) Retrieve the image height in pixels of the given pyramid resolution.
private void	insertResolution(OMEPyramidStore.Resolution r, int image, int res) Store the given Resolution object at the given indices.
private OMEPyramidStore.Resolution	lookupResolution(int image, int res) Find the Resolution object for the given indices.
private OMEPyramidStore.Resolution	lookupResolution(int image, int res, boolean insert) Find the Resolution object for the given indices.
void	setResolutionSizeX(ome.xml.model.primitives.PositiveInteger sizeX, int image, int resolution) Define the image width in pixels of the given pyramid resolution.
void	setResolutionSizeY(ome.xml.model.primitives.PositiveInteger sizeY, int image, int resolution) Define the image height in pixels of the given pyramid resolution.
void	setRoot(ome.xml.meta.MetadataRoot root)

Methods inherited from class ome.xml.meta.OMEXMLMetadataImpl

createRoot, getArcAnnotationRef, getArcID, getArcLotNumber, getArcManufacturer, getArcModel, getArcPower, getArcSerialNumber, getArcType, getBinaryFileBinData, getBinaryFileBinDataBigEndian, getBinaryFileBinDataCompression, getBinaryFileBinDataLength, getBinaryFileFileName, getBinaryFileMIMEType, getBinaryFileSize, getBinaryOnlyMetadataFile, getBinaryOnlyUUID, getBooleanAnnotationAnnotationCount, getBooleanAnnotationAnnotationRef, getBooleanAnnotationAnnotator, getBooleanAnnotationCount, getBooleanAnnotationDescription, getBooleanAnnotationID, getBooleanAnnotationNamespace, getBooleanAnnotationValue, getChannelAcquisitionMode, getChannelAnnotationRef, getChannelAnnotationRefCount, getChannelColor, getChannelContrastMethod, getChannelCount, getChannelEmissionWavelength, getChannelExcitationWavelength, getChannelFilterSetRef, getChannelFluor, getChannelID, getChannelIlluminationType, getChannelLightSourceSettingsAttenuation, getChannelLightSourceSettingsID, getChannelLightSourceSettingsWavelength, getChannelName, getChannelNDFilter, getChannelPinholeSize, getChannelPockelCellSetting, getChannelSamplesPerPixel, getCommentAnnotationAnnotationCount, getCommentAnnotationAnnotationRef, getCommentAnnotationAnnotator, getCommentAnnotationCount, getCommentAnnotationDescription, getCommentAnnotationID, getCommentAnnotationNamespace, getCommentAnnotationValue, getCreator, getDatasetAnnotationRef, getDatasetAnnotationRefCount, getDatasetCount, getDatasetDescription, getDatasetExperimenterGroupRef, getDatasetExperimenterRef, getDatasetID, getDatasetImageRef, getDatasetImageRefCount, getDatasetName, getDatasetRefCount, getDetectorAmplificationGain, getDetectorAnnotationRef, getDetectorAnnotationRefCount, getDetectorCount, getDetectorGain, getDetectorID, getDetectorLotNumber, getDetectorManufacturer, getDetectorModel, getDetectorOffset, getDetectorSerialNumber, getDetectorSettingsBinning, getDetectorSettingsGain, getDetectorSettingsID, getDetectorSettingsIntegration, getDetectorSettingsOffset, getDetectorSettingsReadOutRate, getDetectorSettingsVoltage, getDetectorSettingsZoom, getDetectorType, getDetectorVoltage, getDetectorZoom, getDichroicAnnotationRef, getDichroicAnnotationRefCount, getDichroicCount, getDichroicID, getDichroicLotNumber, getDichroicManufacturer, getDichroicModel, getDichroicSerialNumber, getDoubleAnnotationAnnotationCount, getDoubleAnnotationAnnotationRef, getDoubleAnnotationAnnotator, getDoubleAnnotationCount, getDoubleAnnotationDescription, getDoubleAnnotationID, getDoubleAnnotationNamespace, getDoubleAnnotationValue, getEllipseAnnotationRef, getEllipseFillColor, getEllipseFillRule, getEllipseFontFamily, getEllipseFontSize, getEllipseFontStyle, getEllipseID, getEllipseLocked, getEllipseRadiusX, getEllipseRadiusY, getEllipseStrokeColor, getEllipseStrokeDashArray, getEllipseStrokeWidth, getEllipseText, getEllipseTheC, getEllipseTheT, getEllipseTheZ, getEllipseTransform, getEllipseX, getEllipseY, getExperimentCount, getExperimentDescription, getExperimenterAnnotationRef, getExperimenterAnnotationRefCount, getExperimenterCount, getExperimenterEmail, getExperimenterFirstName, getExperimenterGroupAnnotationRef, getExperimenterGroupAnnotationRefCount, getExperimenterGroupCount, getExperimenterGroupDescription, getExperimenterGroupExperimenterRef, getExperimenterGroupExperimenterRefCount, getExperimenterGroupID, getExperimenterGroupLeader, getExperimenterGroupName, getExperimenterID, getExperimenterInstitution, getExperimenterLastName, getExperimenterMiddleName, getExperimenterUserName, getExperimentExperimenterRef, getExperimentID, getExperimentType, getFilamentAnnotationRef, getFilamentID, getFilamentLotNumber, getFilamentManufacturer, getFilamentModel, getFilamentPower, getFilamentSerialNumber, getFilamentType, getFileAnnotationAnnotationCount, getFileAnnotationAnnotationRef, getFileAnnotationAnnotator, getFileAnnotationCount, getFileAnnotationDescription, getFileAnnotationID, getFileAnnotationNamespace, getFilterAnnotationRef, getFilterAnnotationRefCount, getFilterCount, getFilterFilterWheel, getFilterID, getFilterLotNumber, getFilterManufacturer, getFilterModel, getFilterSerialNumber, getFilterSetCount, getFilterSetDichroicRef, getFilterSetEmissionFilterRef, getFilterSetEmissionFilterRefCount, getFilterSetExcitationFilterRef, getFilterSetExcitationFilterRefCount, getFilterSetID, getFilterSetLotNumber, getFilterSetManufacturer, getFilterSetModel, getFilterSetSerialNumber, getFilterType, getFolderAnnotationRef, getFolderAnnotationRefCount, getFolderCount, getFolderDescription, getFolderFolderRef, getFolderID, getFolderImageRef, getFolderImageRefCount, getFolderName, getFolderRefCount, getFolderROIRef, getFolderROIRefCount, getGenericExcitationSourceAnnotationRef, getGenericExcitationSourceID, getGenericExcitationSourceLotNumber, getGenericExcitationSourceManufacturer, getGenericExcitationSourceMap, getGenericExcitationSourceModel, getGenericExcitationSourcePower, getGenericExcitationSourceSerialNumber, getImageAcquisitionDate, getImageAnnotationRef, getImageAnnotationRefCount, getImageCount, getImageDescription, getImageExperimenterGroupRef, getImageExperimenterRef, getImageExperimentRef, getImageID, getImageInstrumentRef, getImageMicrobeamManipulationRef, getImageName, getImageROIRef, getImageROIRefCount, getImagingEnvironmentAirPressure, getImagingEnvironmentCO2Percent, getImagingEnvironmentHumidity, getImagingEnvironmentMap, getImagingEnvironmentTemperature, getInstrumentAnnotationRef, getInstrumentAnnotationRefCount, getInstrumentCount, getInstrumentID, getLabelAnnotationRef, getLabelFillColor, getLabelFillRule, getLabelFontFamily, getLabelFontSize, getLabelFontStyle, getLabelID, getLabelLocked, getLabelStrokeColor, getLabelStrokeDashArray, getLabelStrokeWidth, getLabelText, getLabelTheC, getLabelTheT, getLabelTheZ, getLabelTransform, getLabelX, getLabelY, getLaserAnnotationRef, getLaserFrequencyMultiplication, getLaserID, getLaserLaserMedium, getLaserLotNumber, getLaserManufacturer, getLaserModel, getLaserPockelCell, getLaserPower, getLaserPulse, getLaserPump, getLaserRepetitionRate, getLaserSerialNumber, getLaserTuneable, getLaserType, getLaserWavelength, getLeaderCount, getLightEmittingDiodeAnnotationRef, getLightEmittingDiodeID, getLightEmittingDiodeLotNumber, getLightEmittingDiodeManufacturer, getLightEmittingDiodeModel, getLightEmittingDiodePower, getLightEmittingDiodeSerialNumber, getLightPathAnnotationRef, getLightPathAnnotationRefCount, getLightPathDichroicRef, getLightPathEmissionFilterRef, getLightPathEmissionFilterRefCount, getLightPathExcitationFilterRef, getLightPathExcitationFilterRefCount, getLightSourceAnnotationRefCount, getLightSourceCount, getLightSourceType, getLineAnnotationRef, getLineFillColor, getLineFillRule, getLineFontFamily, getLineFontSize, getLineFontStyle, getLineID, getLineLocked, getLineMarkerEnd, getLineMarkerStart, getLineStrokeColor, getLineStrokeDashArray, getLineStrokeWidth, getLineText, getLineTheC, getLineTheT, getLineTheZ, getLineTransform, getLineX1, getLineX2, getLineY1, getLineY2, getListAnnotationAnnotationCount, getListAnnotationAnnotationRef, getListAnnotationAnnotator, getListAnnotationCount, getListAnnotationDescription, getListAnnotationID, getListAnnotationNamespace, getLongAnnotationAnnotationCount, getLongAnnotationAnnotationRef, getLongAnnotationAnnotator, getLongAnnotationCount, getLongAnnotationDescription, getLongAnnotationID, getLongAnnotationNamespace, getLongAnnotationValue, getMapAnnotationAnnotationCount, getMapAnnotationAnnotationRef, getMapAnnotationAnnotator, getMapAnnotationCount, getMapAnnotationDescription, getMapAnnotationID, getMapAnnotationNamespace, getMapAnnotationValue, getMaskAnnotationRef, getMaskBinData, getMaskBinDataBigEndian, getMaskBinDataCompression, getMaskBinDataLength, getMaskFillColor, getMaskFillRule, getMaskFontFamily, getMaskFontSize, getMaskFontStyle, getMaskHeight, getMaskID, getMaskLocked, getMaskStrokeColor, getMaskStrokeDashArray, getMaskStrokeWidth, getMaskText, getMaskTheC, getMaskTheT, getMaskTheZ, getMaskTransform, getMaskWidth, getMaskX, getMaskY, getMicrobeamManipulationCount, getMicrobeamManipulationDescription, getMicrobeamManipulationExperimenterRef, getMicrobeamManipulationID, getMicrobeamManipulationLightSourceSettingsAttenuation, getMicrobeamManipulationLightSourceSettingsCount, getMicrobeamManipulationLightSourceSettingsID, getMicrobeamManipulationLightSourceSettingsWavelength, getMicrobeamManipulationRefCount, getMicrobeamManipulationROIRef, getMicrobeamManipulationROIRefCount, getMicrobeamManipulationType, getMicroscopeLotNumber, getMicroscopeManufacturer, getMicroscopeModel, getMicroscopeSerialNumber, getMicroscopeType, getObjectiveAnnotationRef, getObjectiveAnnotationRefCount, getObjectiveCalibratedMagnification, getObjectiveCorrection, getObjectiveCount, getObjectiveID, getObjectiveImmersion, getObjectiveIris, getObjectiveLensNA, getObjectiveLotNumber, getObjectiveManufacturer, getObjectiveModel, getObjectiveNominalMagnification, getObjectiveSerialNumber, getObjectiveSettingsCorrectionCollar, getObjectiveSettingsID, getObjectiveSettingsMedium, getObjectiveSettingsRefractiveIndex, getObjectiveWorkingDistance, getPixelsBigEndian, getPixelsBinData, getPixelsBinDataBigEndian, getPixelsBinDataCompression, getPixelsBinDataCount, getPixelsBinDataLength, getPixelsDimensionOrder, getPixelsID, getPixelsInterleaved, getPixelsPhysicalSizeX, getPixelsPhysicalSizeY, getPixelsPhysicalSizeZ, getPixelsSignificantBits, getPixelsSizeC, getPixelsSizeT, getPixelsSizeX, getPixelsSizeY, getPixelsSizeZ, getPixelsTimeIncrement, getPixelsType, getPlaneAnnotationRef, getPlaneAnnotationRefCount, getPlaneCount, getPlaneDeltaT, getPlaneExposureTime, getPlaneHashSHA1, getPlanePositionX, getPlanePositionY, getPlanePositionZ, getPlaneTheC, getPlaneTheT, getPlaneTheZ, getPlateAcquisitionAnnotationRef, getPlateAcquisitionAnnotationRefCount, getPlateAcquisitionCount, getPlateAcquisitionDescription, getPlateAcquisitionEndTime, getPlateAcquisitionID, getPlateAcquisitionMaximumFieldCount, getPlateAcquisitionName, getPlateAcquisitionStartTime, getPlateAcquisitionWellSampleRef, getPlateAnnotationRef, getPlateAnnotationRefCount, getPlateColumnNamingConvention, getPlateColumns, getPlateCount, getPlateDescription, getPlateExternalIdentifier, getPlateFieldIndex, getPlateID, getPlateName, getPlateRefCount, getPlateRowNamingConvention, getPlateRows, getPlateStatus, getPlateWellOriginX, getPlateWellOriginY, getPointAnnotationRef, getPointFillColor, getPointFillRule, getPointFontFamily, getPointFontSize, getPointFontStyle, getPointID, getPointLocked, getPointStrokeColor, getPointStrokeDashArray, getPointStrokeWidth, getPointText, getPointTheC, getPointTheT, getPointTheZ, getPointTransform, getPointX, getPointY, getPolygonAnnotationRef, getPolygonFillColor, getPolygonFillRule, getPolygonFontFamily, getPolygonFontSize, getPolygonFontStyle, getPolygonID, getPolygonLocked, getPolygonPoints, getPolygonStrokeColor, getPolygonStrokeDashArray, getPolygonStrokeWidth, getPolygonText, getPolygonTheC, getPolygonTheT, getPolygonTheZ, getPolygonTransform, getPolylineAnnotationRef, getPolylineFillColor, getPolylineFillRule, getPolylineFontFamily, getPolylineFontSize, getPolylineFontStyle, getPolylineID, getPolylineLocked, getPolylineMarkerEnd, getPolylineMarkerStart, getPolylinePoints, getPolylineStrokeColor, getPolylineStrokeDashArray, getPolylineStrokeWidth, getPolylineText, getPolylineTheC, getPolylineTheT, getPolylineTheZ, getPolylineTransform, getProjectAnnotationRef, getProjectAnnotationRefCount, getProjectCount, getProjectDatasetRef, getProjectDescription, getProjectExperimenterGroupRef, getProjectExperimenterRef, getProjectID, getProjectName, getReagentAnnotationRef, getReagentAnnotationRefCount, getReagentCount, getReagentDescription, getReagentID, getReagentName, getReagentReagentIdentifier, getRectangleAnnotationRef, getRectangleFillColor, getRectangleFillRule, getRectangleFontFamily, getRectangleFontSize, getRectangleFontStyle, getRectangleHeight, getRectangleID, getRectangleLocked, getRectangleStrokeColor, getRectangleStrokeDashArray, getRectangleStrokeWidth, getRectangleText, getRectangleTheC, getRectangleTheT, getRectangleTheZ, getRectangleTransform, getRectangleWidth, getRectangleX, getRectangleY, getRightsRightsHeld, getRightsRightsHolder, getROIAnnotationRef, getROIAnnotationRefCount, getROICount, getROIDescription, getROIID, getROIName, getRoot, getScreenAnnotationRef, getScreenAnnotationRefCount, getScreenCount, getScreenDescription, getScreenID, getScreenName, getScreenPlateRef, getScreenProtocolDescription, getScreenProtocolIdentifier, getScreenReagentSetDescription, getScreenReagentSetIdentifier, getScreenType, getShapeAnnotationRefCount, getShapeCount, getShapeType, getStageLabelName, getStageLabelX, getStageLabelY, getStageLabelZ, getTagAnnotationAnnotationCount, getTagAnnotationAnnotationRef, getTagAnnotationAnnotator, getTagAnnotationCount, getTagAnnotationDescription, getTagAnnotationID, getTagAnnotationNamespace, getTagAnnotationValue, getTermAnnotationAnnotationCount, getTermAnnotationAnnotationRef, getTermAnnotationAnnotator, getTermAnnotationCount, getTermAnnotationDescription, getTermAnnotationID, getTermAnnotationNamespace, getTermAnnotationValue, getTiffDataCount, getTiffDataFirstC, getTiffDataFirstT, getTiffDataFirstZ, getTiffDataIFD, getTiffDataPlaneCount, getTimestampAnnotationAnnotationCount, getTimestampAnnotationAnnotationRef, getTimestampAnnotationAnnotator, getTimestampAnnotationCount, getTimestampAnnotationDescription, getTimestampAnnotationID, getTimestampAnnotationNamespace, getTimestampAnnotationValue, getTransmittanceRangeCutIn, getTransmittanceRangeCutInTolerance, getTransmittanceRangeCutOut, getTransmittanceRangeCutOutTolerance, getTransmittanceRangeTransmittance, getUUID, getUUIDFileName, getUUIDValue, getWellAnnotationRef, getWellAnnotationRefCount, getWellColor, getWellColumn, getWellCount, getWellExternalDescription, getWellExternalIdentifier, getWellID, getWellReagentRef, getWellRow, getWellSampleCount, getWellSampleID, getWellSampleImageRef, getWellSampleIndex, getWellSamplePositionX, getWellSamplePositionY, getWellSampleRefCount, getWellSampleTimepoint, getWellType, getXMLAnnotationAnnotationCount, getXMLAnnotationAnnotationRef, getXMLAnnotationAnnotator, getXMLAnnotationCount, getXMLAnnotationDescription, getXMLAnnotationID, getXMLAnnotationNamespace, getXMLAnnotationValue, resolveReferences, setArcAnnotationRef, setArcID, setArcLotNumber, setArcManufacturer, setArcModel, setArcPower, setArcSerialNumber, setArcType, setBinaryFileBinData, setBinaryFileBinDataBigEndian, setBinaryFileBinDataCompression, setBinaryFileBinDataLength, setBinaryFileFileName, setBinaryFileMIMEType, setBinaryFileSize, setBinaryOnlyMetadataFile, setBinaryOnlyUUID, setBooleanAnnotationAnnotationRef, setBooleanAnnotationAnnotator, setBooleanAnnotationDescription, setBooleanAnnotationID, setBooleanAnnotationNamespace, setBooleanAnnotationValue, setChannelAcquisitionMode, setChannelAnnotationRef, setChannelColor, setChannelContrastMethod, setChannelEmissionWavelength, setChannelExcitationWavelength, setChannelFilterSetRef, setChannelFluor, setChannelID, setChannelIlluminationType, setChannelLightSourceSettingsAttenuation, setChannelLightSourceSettingsID, setChannelLightSourceSettingsWavelength, setChannelName, setChannelNDFilter, setChannelPinholeSize, setChannelPockelCellSetting, setChannelSamplesPerPixel, setCommentAnnotationAnnotationRef, setCommentAnnotationAnnotator, setCommentAnnotationDescription, setCommentAnnotationID, setCommentAnnotationNamespace, setCommentAnnotationValue, setCreator, setDatasetAnnotationRef, setDatasetDescription, setDatasetExperimenterGroupRef, setDatasetExperimenterRef, setDatasetID, setDatasetImageRef, setDatasetName, setDetectorAmplificationGain, setDetectorAnnotationRef, setDetectorGain, setDetectorID, setDetectorLotNumber, setDetectorManufacturer, setDetectorModel, setDetectorOffset, setDetectorSerialNumber, setDetectorSettingsBinning, setDetectorSettingsGain, setDetectorSettingsID, setDetectorSettingsIntegration, setDetectorSettingsOffset, setDetectorSettingsReadOutRate, setDetectorSettingsVoltage, setDetectorSettingsZoom, setDetectorType, setDetectorVoltage, setDetectorZoom, setDichroicAnnotationRef, setDichroicID, setDichroicLotNumber, setDichroicManufacturer, setDichroicModel, setDichroicSerialNumber, setDoubleAnnotationAnnotationRef, setDoubleAnnotationAnnotator, setDoubleAnnotationDescription, setDoubleAnnotationID, setDoubleAnnotationNamespace, setDoubleAnnotationValue, setEllipseAnnotationRef, setEllipseFillColor, setEllipseFillRule, setEllipseFontFamily, setEllipseFontSize, setEllipseFontStyle, setEllipseID, setEllipseLocked, setEllipseRadiusX, setEllipseRadiusY, setEllipseStrokeColor, setEllipseStrokeDashArray, setEllipseStrokeWidth, setEllipseText, setEllipseTheC, setEllipseTheT, setEllipseTheZ, setEllipseTransform, setEllipseX, setEllipseY, setExperimentDescription, setExperimenterAnnotationRef, setExperimenterEmail, setExperimenterFirstName, setExperimenterGroupAnnotationRef, setExperimenterGroupDescription, setExperimenterGroupExperimenterRef, setExperimenterGroupID, setExperimenterGroupLeader, setExperimenterGroupName, setExperimenterID, setExperimenterInstitution, setExperimenterLastName, setExperimenterMiddleName, setExperimenterUserName, setExperimentExperimenterRef, setExperimentID, setExperimentType, setFilamentAnnotationRef, setFilamentID, setFilamentLotNumber, setFilamentManufacturer, setFilamentModel, setFilamentPower, setFilamentSerialNumber, setFilamentType, setFileAnnotationAnnotationRef, setFileAnnotationAnnotator, setFileAnnotationDescription, setFileAnnotationID, setFileAnnotationNamespace, setFilterAnnotationRef, setFilterFilterWheel, setFilterID, setFilterLotNumber, setFilterManufacturer, setFilterModel, setFilterSerialNumber, setFilterSetDichroicRef, setFilterSetEmissionFilterRef, setFilterSetExcitationFilterRef, setFilterSetID, setFilterSetLotNumber, setFilterSetManufacturer, setFilterSetModel, setFilterSetSerialNumber, setFilterType, setFolderAnnotationRef, setFolderDescription, setFolderFolderRef, setFolderID, setFolderImageRef, setFolderName, setFolderROIRef, setGenericExcitationSourceAnnotationRef, setGenericExcitationSourceID, setGenericExcitationSourceLotNumber, setGenericExcitationSourceManufacturer, setGenericExcitationSourceMap, setGenericExcitationSourceModel, setGenericExcitationSourcePower, setGenericExcitationSourceSerialNumber, setImageAcquisitionDate, setImageAnnotationRef, setImageDescription, setImageExperimenterGroupRef, setImageExperimenterRef, setImageExperimentRef, setImageID, setImageInstrumentRef, setImageMicrobeamManipulationRef, setImageName, setImageROIRef, setImagingEnvironmentAirPressure, setImagingEnvironmentCO2Percent, setImagingEnvironmentHumidity, setImagingEnvironmentMap, setImagingEnvironmentTemperature, setInstrumentAnnotationRef, setInstrumentID, setLabelAnnotationRef, setLabelFillColor, setLabelFillRule, setLabelFontFamily, setLabelFontSize, setLabelFontStyle, setLabelID, setLabelLocked, setLabelStrokeColor, setLabelStrokeDashArray, setLabelStrokeWidth, setLabelText, setLabelTheC, setLabelTheT, setLabelTheZ, setLabelTransform, setLabelX, setLabelY, setLaserAnnotationRef, setLaserFrequencyMultiplication, setLaserID, setLaserLaserMedium, setLaserLotNumber, setLaserManufacturer, setLaserModel, setLaserPockelCell, setLaserPower, setLaserPulse, setLaserPump, setLaserRepetitionRate, setLaserSerialNumber, setLaserTuneable, setLaserType, setLaserWavelength, setLightEmittingDiodeAnnotationRef, setLightEmittingDiodeID, setLightEmittingDiodeLotNumber, setLightEmittingDiodeManufacturer, setLightEmittingDiodeModel, setLightEmittingDiodePower, setLightEmittingDiodeSerialNumber, setLightPathAnnotationRef, setLightPathDichroicRef, setLightPathEmissionFilterRef, setLightPathExcitationFilterRef, setLineAnnotationRef, setLineFillColor, setLineFillRule, setLineFontFamily, setLineFontSize, setLineFontStyle, setLineID, setLineLocked, setLineMarkerEnd, setLineMarkerStart, setLineStrokeColor, setLineStrokeDashArray, setLineStrokeWidth, setLineText, setLineTheC, setLineTheT, setLineTheZ, setLineTransform, setLineX1, setLineX2, setLineY1, setLineY2, setListAnnotationAnnotationRef, setListAnnotationAnnotator, setListAnnotationDescription, setListAnnotationID, setListAnnotationNamespace, setLongAnnotationAnnotationRef, setLongAnnotationAnnotator, setLongAnnotationDescription, setLongAnnotationID, setLongAnnotationNamespace, setLongAnnotationValue, setMapAnnotationAnnotationRef, setMapAnnotationAnnotator, setMapAnnotationDescription, setMapAnnotationID, setMapAnnotationNamespace, setMapAnnotationValue, setMaskAnnotationRef, setMaskBinData, setMaskBinDataBigEndian, setMaskBinDataCompression, setMaskBinDataLength, setMaskFillColor, setMaskFillRule, setMaskFontFamily, setMaskFontSize, setMaskFontStyle, setMaskHeight, setMaskID, setMaskLocked, setMaskStrokeColor, setMaskStrokeDashArray, setMaskStrokeWidth, setMaskText, setMaskTheC, setMaskTheT, setMaskTheZ, setMaskTransform, setMaskWidth, setMaskX, setMaskY, setMicrobeamManipulationDescription, setMicrobeamManipulationExperimenterRef, setMicrobeamManipulationID, setMicrobeamManipulationLightSourceSettingsAttenuation, setMicrobeamManipulationLightSourceSettingsID, setMicrobeamManipulationLightSourceSettingsWavelength, setMicrobeamManipulationROIRef, setMicrobeamManipulationType, setMicroscopeLotNumber, setMicroscopeManufacturer, setMicroscopeModel, setMicroscopeSerialNumber, setMicroscopeType, setObjectiveAnnotationRef, setObjectiveCalibratedMagnification, setObjectiveCorrection, setObjectiveID, setObjectiveImmersion, setObjectiveIris, setObjectiveLensNA, setObjectiveLotNumber, setObjectiveManufacturer, setObjectiveModel, setObjectiveNominalMagnification, setObjectiveSerialNumber, setObjectiveSettingsCorrectionCollar, setObjectiveSettingsID, setObjectiveSettingsMedium, setObjectiveSettingsRefractiveIndex, setObjectiveWorkingDistance, setPixelsBigEndian, setPixelsBinData, setPixelsBinDataBigEndian, setPixelsBinDataCompression, setPixelsBinDataLength, setPixelsDimensionOrder, setPixelsID, setPixelsInterleaved, setPixelsPhysicalSizeX, setPixelsPhysicalSizeY, setPixelsPhysicalSizeZ, setPixelsSignificantBits, setPixelsSizeC, setPixelsSizeT, setPixelsSizeX, setPixelsSizeY, setPixelsSizeZ, setPixelsTimeIncrement, setPixelsType, setPlaneAnnotationRef, setPlaneDeltaT, setPlaneExposureTime, setPlaneHashSHA1, setPlanePositionX, setPlanePositionY, setPlanePositionZ, setPlaneTheC, setPlaneTheT, setPlaneTheZ, setPlateAcquisitionAnnotationRef, setPlateAcquisitionDescription, setPlateAcquisitionEndTime, setPlateAcquisitionID, setPlateAcquisitionMaximumFieldCount, setPlateAcquisitionName, setPlateAcquisitionStartTime, setPlateAcquisitionWellSampleRef, setPlateAnnotationRef, setPlateColumnNamingConvention, setPlateColumns, setPlateDescription, setPlateExternalIdentifier, setPlateFieldIndex, setPlateID, setPlateName, setPlateRowNamingConvention, setPlateRows, setPlateStatus, setPlateWellOriginX, setPlateWellOriginY, setPointAnnotationRef, setPointFillColor, setPointFillRule, setPointFontFamily, setPointFontSize, setPointFontStyle, setPointID, setPointLocked, setPointStrokeColor, setPointStrokeDashArray, setPointStrokeWidth, setPointText, setPointTheC, setPointTheT, setPointTheZ, setPointTransform, setPointX, setPointY, setPolygonAnnotationRef, setPolygonFillColor, setPolygonFillRule, setPolygonFontFamily, setPolygonFontSize, setPolygonFontStyle, setPolygonID, setPolygonLocked, setPolygonPoints, setPolygonStrokeColor, setPolygonStrokeDashArray, setPolygonStrokeWidth, setPolygonText, setPolygonTheC, setPolygonTheT, setPolygonTheZ, setPolygonTransform, setPolylineAnnotationRef, setPolylineFillColor, setPolylineFillRule, setPolylineFontFamily, setPolylineFontSize, setPolylineFontStyle, setPolylineID, setPolylineLocked, setPolylineMarkerEnd, setPolylineMarkerStart, setPolylinePoints, setPolylineStrokeColor, setPolylineStrokeDashArray, setPolylineStrokeWidth, setPolylineText, setPolylineTheC, setPolylineTheT, setPolylineTheZ, setPolylineTransform, setProjectAnnotationRef, setProjectDatasetRef, setProjectDescription, setProjectExperimenterGroupRef, setProjectExperimenterRef, setProjectID, setProjectName, setReagentAnnotationRef, setReagentDescription, setReagentID, setReagentName, setReagentReagentIdentifier, setRectangleAnnotationRef, setRectangleFillColor, setRectangleFillRule, setRectangleFontFamily, setRectangleFontSize, setRectangleFontStyle, setRectangleHeight, setRectangleID, setRectangleLocked, setRectangleStrokeColor, setRectangleStrokeDashArray, setRectangleStrokeWidth, setRectangleText, setRectangleTheC, setRectangleTheT, setRectangleTheZ, setRectangleTransform, setRectangleWidth, setRectangleX, setRectangleY, setRightsRightsHeld, setRightsRightsHolder, setROIAnnotationRef, setROIDescription, setROIID, setROIName, setScreenAnnotationRef, setScreenDescription, setScreenID, setScreenName, setScreenPlateRef, setScreenProtocolDescription, setScreenProtocolIdentifier, setScreenReagentSetDescription, setScreenReagentSetIdentifier, setScreenType, setStageLabelName, setStageLabelX, setStageLabelY, setStageLabelZ, setTagAnnotationAnnotationRef, setTagAnnotationAnnotator, setTagAnnotationDescription, setTagAnnotationID, setTagAnnotationNamespace, setTagAnnotationValue, setTermAnnotationAnnotationRef, setTermAnnotationAnnotator, setTermAnnotationDescription, setTermAnnotationID, setTermAnnotationNamespace, setTermAnnotationValue, setTiffDataFirstC, setTiffDataFirstT, setTiffDataFirstZ, setTiffDataIFD, setTiffDataPlaneCount, setTimestampAnnotationAnnotationRef, setTimestampAnnotationAnnotator, setTimestampAnnotationDescription, setTimestampAnnotationID, setTimestampAnnotationNamespace, setTimestampAnnotationValue, setTransmittanceRangeCutIn, setTransmittanceRangeCutInTolerance, setTransmittanceRangeCutOut, setTransmittanceRangeCutOutTolerance, setTransmittanceRangeTransmittance, setUUID, setUUIDFileName, setUUIDValue, setWellAnnotationRef, setWellColor, setWellColumn, setWellExternalDescription, setWellExternalIdentifier, setWellID, setWellReagentRef, setWellRow, setWellSampleID, setWellSampleImageRef, setWellSampleIndex, setWellSamplePositionX, setWellSamplePositionY, setWellSampleTimepoint, setWellType, setXMLAnnotationAnnotationRef, setXMLAnnotationAnnotator, setXMLAnnotationDescription, setXMLAnnotationID, setXMLAnnotationNamespace, setXMLAnnotationValue

Methods inherited from class ome.xml.meta.AbstractOMEXMLMetadata

createNewDocument

Methods inherited from class java.lang.Object

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

Methods inherited from interface ome.xml.meta.OMEXMLMetadata

resolveReferences

Methods inherited from interface ome.xml.meta.MetadataRetrieve

getArcAnnotationRef, getArcID, getArcLotNumber, getArcManufacturer, getArcModel, getArcPower, getArcSerialNumber, getArcType, getBinaryFileBinData, getBinaryFileBinDataBigEndian, getBinaryFileBinDataCompression, getBinaryFileBinDataLength, getBinaryFileFileName, getBinaryFileMIMEType, getBinaryFileSize, getBinaryOnlyMetadataFile, getBinaryOnlyUUID, getBooleanAnnotationAnnotationCount, getBooleanAnnotationAnnotationRef, getBooleanAnnotationAnnotator, getBooleanAnnotationCount, getBooleanAnnotationDescription, getBooleanAnnotationID, getBooleanAnnotationNamespace, getBooleanAnnotationValue, getChannelAcquisitionMode, getChannelAnnotationRef, getChannelAnnotationRefCount, getChannelColor, getChannelContrastMethod, getChannelCount, getChannelEmissionWavelength, getChannelExcitationWavelength, getChannelFilterSetRef, getChannelFluor, getChannelID, getChannelIlluminationType, getChannelLightSourceSettingsAttenuation, getChannelLightSourceSettingsID, getChannelLightSourceSettingsWavelength, getChannelName, getChannelNDFilter, getChannelPinholeSize, getChannelPockelCellSetting, getChannelSamplesPerPixel, getCommentAnnotationAnnotationCount, getCommentAnnotationAnnotationRef, getCommentAnnotationAnnotator, getCommentAnnotationCount, getCommentAnnotationDescription, getCommentAnnotationID, getCommentAnnotationNamespace, getCommentAnnotationValue, getCreator, getDatasetAnnotationRef, getDatasetAnnotationRefCount, getDatasetCount, getDatasetDescription, getDatasetExperimenterGroupRef, getDatasetExperimenterRef, getDatasetID, getDatasetImageRef, getDatasetImageRefCount, getDatasetName, getDatasetRefCount, getDetectorAmplificationGain, getDetectorAnnotationRef, getDetectorAnnotationRefCount, getDetectorCount, getDetectorGain, getDetectorID, getDetectorLotNumber, getDetectorManufacturer, getDetectorModel, getDetectorOffset, getDetectorSerialNumber, getDetectorSettingsBinning, getDetectorSettingsGain, getDetectorSettingsID, getDetectorSettingsIntegration, getDetectorSettingsOffset, getDetectorSettingsReadOutRate, getDetectorSettingsVoltage, getDetectorSettingsZoom, getDetectorType, getDetectorVoltage, getDetectorZoom, getDichroicAnnotationRef, getDichroicAnnotationRefCount, getDichroicCount, getDichroicID, getDichroicLotNumber, getDichroicManufacturer, getDichroicModel, getDichroicSerialNumber, getDoubleAnnotationAnnotationCount, getDoubleAnnotationAnnotationRef, getDoubleAnnotationAnnotator, getDoubleAnnotationCount, getDoubleAnnotationDescription, getDoubleAnnotationID, getDoubleAnnotationNamespace, getDoubleAnnotationValue, getEllipseAnnotationRef, getEllipseFillColor, getEllipseFillRule, getEllipseFontFamily, getEllipseFontSize, getEllipseFontStyle, getEllipseID, getEllipseLocked, getEllipseRadiusX, getEllipseRadiusY, getEllipseStrokeColor, getEllipseStrokeDashArray, getEllipseStrokeWidth, getEllipseText, getEllipseTheC, getEllipseTheT, getEllipseTheZ, getEllipseTransform, getEllipseX, getEllipseY, getExperimentCount, getExperimentDescription, getExperimenterAnnotationRef, getExperimenterAnnotationRefCount, getExperimenterCount, getExperimenterEmail, getExperimenterFirstName, getExperimenterGroupAnnotationRef, getExperimenterGroupAnnotationRefCount, getExperimenterGroupCount, getExperimenterGroupDescription, getExperimenterGroupExperimenterRef, getExperimenterGroupExperimenterRefCount, getExperimenterGroupID, getExperimenterGroupLeader, getExperimenterGroupName, getExperimenterID, getExperimenterInstitution, getExperimenterLastName, getExperimenterMiddleName, getExperimenterUserName, getExperimentExperimenterRef, getExperimentID, getExperimentType, getFilamentAnnotationRef, getFilamentID, getFilamentLotNumber, getFilamentManufacturer, getFilamentModel, getFilamentPower, getFilamentSerialNumber, getFilamentType, getFileAnnotationAnnotationCount, getFileAnnotationAnnotationRef, getFileAnnotationAnnotator, getFileAnnotationCount, getFileAnnotationDescription, getFileAnnotationID, getFileAnnotationNamespace, getFilterAnnotationRef, getFilterAnnotationRefCount, getFilterCount, getFilterFilterWheel, getFilterID, getFilterLotNumber, getFilterManufacturer, getFilterModel, getFilterSerialNumber, getFilterSetCount, getFilterSetDichroicRef, getFilterSetEmissionFilterRef, getFilterSetEmissionFilterRefCount, getFilterSetExcitationFilterRef, getFilterSetExcitationFilterRefCount, getFilterSetID, getFilterSetLotNumber, getFilterSetManufacturer, getFilterSetModel, getFilterSetSerialNumber, getFilterType, getFolderAnnotationRef, getFolderAnnotationRefCount, getFolderCount, getFolderDescription, getFolderFolderRef, getFolderID, getFolderImageRef, getFolderImageRefCount, getFolderName, getFolderRefCount, getFolderROIRef, getFolderROIRefCount, getGenericExcitationSourceAnnotationRef, getGenericExcitationSourceID, getGenericExcitationSourceLotNumber, getGenericExcitationSourceManufacturer, getGenericExcitationSourceMap, getGenericExcitationSourceModel, getGenericExcitationSourcePower, getGenericExcitationSourceSerialNumber, getImageAcquisitionDate, getImageAnnotationRef, getImageAnnotationRefCount, getImageCount, getImageDescription, getImageExperimenterGroupRef, getImageExperimenterRef, getImageExperimentRef, getImageID, getImageInstrumentRef, getImageMicrobeamManipulationRef, getImageName, getImageROIRef, getImageROIRefCount, getImagingEnvironmentAirPressure, getImagingEnvironmentCO2Percent, getImagingEnvironmentHumidity, getImagingEnvironmentMap, getImagingEnvironmentTemperature, getInstrumentAnnotationRef, getInstrumentAnnotationRefCount, getInstrumentCount, getInstrumentID, getLabelAnnotationRef, getLabelFillColor, getLabelFillRule, getLabelFontFamily, getLabelFontSize, getLabelFontStyle, getLabelID, getLabelLocked, getLabelStrokeColor, getLabelStrokeDashArray, getLabelStrokeWidth, getLabelText, getLabelTheC, getLabelTheT, getLabelTheZ, getLabelTransform, getLabelX, getLabelY, getLaserAnnotationRef, getLaserFrequencyMultiplication, getLaserID, getLaserLaserMedium, getLaserLotNumber, getLaserManufacturer, getLaserModel, getLaserPockelCell, getLaserPower, getLaserPulse, getLaserPump, getLaserRepetitionRate, getLaserSerialNumber, getLaserTuneable, getLaserType, getLaserWavelength, getLeaderCount, getLightEmittingDiodeAnnotationRef, getLightEmittingDiodeID, getLightEmittingDiodeLotNumber, getLightEmittingDiodeManufacturer, getLightEmittingDiodeModel, getLightEmittingDiodePower, getLightEmittingDiodeSerialNumber, getLightPathAnnotationRef, getLightPathAnnotationRefCount, getLightPathDichroicRef, getLightPathEmissionFilterRef, getLightPathEmissionFilterRefCount, getLightPathExcitationFilterRef, getLightPathExcitationFilterRefCount, getLightSourceAnnotationRefCount, getLightSourceCount, getLightSourceType, getLineAnnotationRef, getLineFillColor, getLineFillRule, getLineFontFamily, getLineFontSize, getLineFontStyle, getLineID, getLineLocked, getLineMarkerEnd, getLineMarkerStart, getLineStrokeColor, getLineStrokeDashArray, getLineStrokeWidth, getLineText, getLineTheC, getLineTheT, getLineTheZ, getLineTransform, getLineX1, getLineX2, getLineY1, getLineY2, getListAnnotationAnnotationCount, getListAnnotationAnnotationRef, getListAnnotationAnnotator, getListAnnotationCount, getListAnnotationDescription, getListAnnotationID, getListAnnotationNamespace, getLongAnnotationAnnotationCount, getLongAnnotationAnnotationRef, getLongAnnotationAnnotator, getLongAnnotationCount, getLongAnnotationDescription, getLongAnnotationID, getLongAnnotationNamespace, getLongAnnotationValue, getMapAnnotationAnnotationCount, getMapAnnotationAnnotationRef, getMapAnnotationAnnotator, getMapAnnotationCount, getMapAnnotationDescription, getMapAnnotationID, getMapAnnotationNamespace, getMapAnnotationValue, getMaskAnnotationRef, getMaskBinData, getMaskBinDataBigEndian, getMaskBinDataCompression, getMaskBinDataLength, getMaskFillColor, getMaskFillRule, getMaskFontFamily, getMaskFontSize, getMaskFontStyle, getMaskHeight, getMaskID, getMaskLocked, getMaskStrokeColor, getMaskStrokeDashArray, getMaskStrokeWidth, getMaskText, getMaskTheC, getMaskTheT, getMaskTheZ, getMaskTransform, getMaskWidth, getMaskX, getMaskY, getMicrobeamManipulationCount, getMicrobeamManipulationDescription, getMicrobeamManipulationExperimenterRef, getMicrobeamManipulationID, getMicrobeamManipulationLightSourceSettingsAttenuation, getMicrobeamManipulationLightSourceSettingsCount, getMicrobeamManipulationLightSourceSettingsID, getMicrobeamManipulationLightSourceSettingsWavelength, getMicrobeamManipulationRefCount, getMicrobeamManipulationROIRef, getMicrobeamManipulationROIRefCount, getMicrobeamManipulationType, getMicroscopeLotNumber, getMicroscopeManufacturer, getMicroscopeModel, getMicroscopeSerialNumber, getMicroscopeType, getObjectiveAnnotationRef, getObjectiveAnnotationRefCount, getObjectiveCalibratedMagnification, getObjectiveCorrection, getObjectiveCount, getObjectiveID, getObjectiveImmersion, getObjectiveIris, getObjectiveLensNA, getObjectiveLotNumber, getObjectiveManufacturer, getObjectiveModel, getObjectiveNominalMagnification, getObjectiveSerialNumber, getObjectiveSettingsCorrectionCollar, getObjectiveSettingsID, getObjectiveSettingsMedium, getObjectiveSettingsRefractiveIndex, getObjectiveWorkingDistance, getPixelsBigEndian, getPixelsBinData, getPixelsBinDataBigEndian, getPixelsBinDataCompression, getPixelsBinDataCount, getPixelsBinDataLength, getPixelsDimensionOrder, getPixelsID, getPixelsInterleaved, getPixelsPhysicalSizeX, getPixelsPhysicalSizeY, getPixelsPhysicalSizeZ, getPixelsSignificantBits, getPixelsSizeC, getPixelsSizeT, getPixelsSizeX, getPixelsSizeY, getPixelsSizeZ, getPixelsTimeIncrement, getPixelsType, getPlaneAnnotationRef, getPlaneAnnotationRefCount, getPlaneCount, getPlaneDeltaT, getPlaneExposureTime, getPlaneHashSHA1, getPlanePositionX, getPlanePositionY, getPlanePositionZ, getPlaneTheC, getPlaneTheT, getPlaneTheZ, getPlateAcquisitionAnnotationRef, getPlateAcquisitionAnnotationRefCount, getPlateAcquisitionCount, getPlateAcquisitionDescription, getPlateAcquisitionEndTime, getPlateAcquisitionID, getPlateAcquisitionMaximumFieldCount, getPlateAcquisitionName, getPlateAcquisitionStartTime, getPlateAcquisitionWellSampleRef, getPlateAnnotationRef, getPlateAnnotationRefCount, getPlateColumnNamingConvention, getPlateColumns, getPlateCount, getPlateDescription, getPlateExternalIdentifier, getPlateFieldIndex, getPlateID, getPlateName, getPlateRefCount, getPlateRowNamingConvention, getPlateRows, getPlateStatus, getPlateWellOriginX, getPlateWellOriginY, getPointAnnotationRef, getPointFillColor, getPointFillRule, getPointFontFamily, getPointFontSize, getPointFontStyle, getPointID, getPointLocked, getPointStrokeColor, getPointStrokeDashArray, getPointStrokeWidth, getPointText, getPointTheC, getPointTheT, getPointTheZ, getPointTransform, getPointX, getPointY, getPolygonAnnotationRef, getPolygonFillColor, getPolygonFillRule, getPolygonFontFamily, getPolygonFontSize, getPolygonFontStyle, getPolygonID, getPolygonLocked, getPolygonPoints, getPolygonStrokeColor, getPolygonStrokeDashArray, getPolygonStrokeWidth, getPolygonText, getPolygonTheC, getPolygonTheT, getPolygonTheZ, getPolygonTransform, getPolylineAnnotationRef, getPolylineFillColor, getPolylineFillRule, getPolylineFontFamily, getPolylineFontSize, getPolylineFontStyle, getPolylineID, getPolylineLocked, getPolylineMarkerEnd, getPolylineMarkerStart, getPolylinePoints, getPolylineStrokeColor, getPolylineStrokeDashArray, getPolylineStrokeWidth, getPolylineText, getPolylineTheC, getPolylineTheT, getPolylineTheZ, getPolylineTransform, getProjectAnnotationRef, getProjectAnnotationRefCount, getProjectCount, getProjectDatasetRef, getProjectDescription, getProjectExperimenterGroupRef, getProjectExperimenterRef, getProjectID, getProjectName, getReagentAnnotationRef, getReagentAnnotationRefCount, getReagentCount, getReagentDescription, getReagentID, getReagentName, getReagentReagentIdentifier, getRectangleAnnotationRef, getRectangleFillColor, getRectangleFillRule, getRectangleFontFamily, getRectangleFontSize, getRectangleFontStyle, getRectangleHeight, getRectangleID, getRectangleLocked, getRectangleStrokeColor, getRectangleStrokeDashArray, getRectangleStrokeWidth, getRectangleText, getRectangleTheC, getRectangleTheT, getRectangleTheZ, getRectangleTransform, getRectangleWidth, getRectangleX, getRectangleY, getRightsRightsHeld, getRightsRightsHolder, getROIAnnotationRef, getROIAnnotationRefCount, getROICount, getROIDescription, getROIID, getROIName, getScreenAnnotationRef, getScreenAnnotationRefCount, getScreenCount, getScreenDescription, getScreenID, getScreenName, getScreenPlateRef, getScreenProtocolDescription, getScreenProtocolIdentifier, getScreenReagentSetDescription, getScreenReagentSetIdentifier, getScreenType, getShapeAnnotationRefCount, getShapeCount, getShapeType, getStageLabelName, getStageLabelX, getStageLabelY, getStageLabelZ, getTagAnnotationAnnotationCount, getTagAnnotationAnnotationRef, getTagAnnotationAnnotator, getTagAnnotationCount, getTagAnnotationDescription, getTagAnnotationID, getTagAnnotationNamespace, getTagAnnotationValue, getTermAnnotationAnnotationCount, getTermAnnotationAnnotationRef, getTermAnnotationAnnotator, getTermAnnotationCount, getTermAnnotationDescription, getTermAnnotationID, getTermAnnotationNamespace, getTermAnnotationValue, getTiffDataCount, getTiffDataFirstC, getTiffDataFirstT, getTiffDataFirstZ, getTiffDataIFD, getTiffDataPlaneCount, getTimestampAnnotationAnnotationCount, getTimestampAnnotationAnnotationRef, getTimestampAnnotationAnnotator, getTimestampAnnotationCount, getTimestampAnnotationDescription, getTimestampAnnotationID, getTimestampAnnotationNamespace, getTimestampAnnotationValue, getTransmittanceRangeCutIn, getTransmittanceRangeCutInTolerance, getTransmittanceRangeCutOut, getTransmittanceRangeCutOutTolerance, getTransmittanceRangeTransmittance, getUUID, getUUIDFileName, getUUIDValue, getWellAnnotationRef, getWellAnnotationRefCount, getWellColor, getWellColumn, getWellCount, getWellExternalDescription, getWellExternalIdentifier, getWellID, getWellReagentRef, getWellRow, getWellSampleCount, getWellSampleID, getWellSampleImageRef, getWellSampleIndex, getWellSamplePositionX, getWellSamplePositionY, getWellSampleRefCount, getWellSampleTimepoint, getWellType, getXMLAnnotationAnnotationCount, getXMLAnnotationAnnotationRef, getXMLAnnotationAnnotator, getXMLAnnotationCount, getXMLAnnotationDescription, getXMLAnnotationID, getXMLAnnotationNamespace, getXMLAnnotationValue

Methods inherited from interface ome.xml.meta.MetadataStore

createRoot, getRoot, setArcAnnotationRef, setArcID, setArcLotNumber, setArcManufacturer, setArcModel, setArcPower, setArcSerialNumber, setArcType, setBinaryFileBinData, setBinaryFileBinDataBigEndian, setBinaryFileBinDataCompression, setBinaryFileBinDataLength, setBinaryFileFileName, setBinaryFileMIMEType, setBinaryFileSize, setBinaryOnlyMetadataFile, setBinaryOnlyUUID, setBooleanAnnotationAnnotationRef, setBooleanAnnotationAnnotator, setBooleanAnnotationDescription, setBooleanAnnotationID, setBooleanAnnotationNamespace, setBooleanAnnotationValue, setChannelAcquisitionMode, setChannelAnnotationRef, setChannelColor, setChannelContrastMethod, setChannelEmissionWavelength, setChannelExcitationWavelength, setChannelFilterSetRef, setChannelFluor, setChannelID, setChannelIlluminationType, setChannelLightSourceSettingsAttenuation, setChannelLightSourceSettingsID, setChannelLightSourceSettingsWavelength, setChannelName, setChannelNDFilter, setChannelPinholeSize, setChannelPockelCellSetting, setChannelSamplesPerPixel, setCommentAnnotationAnnotationRef, setCommentAnnotationAnnotator, setCommentAnnotationDescription, setCommentAnnotationID, setCommentAnnotationNamespace, setCommentAnnotationValue, setCreator, setDatasetAnnotationRef, setDatasetDescription, setDatasetExperimenterGroupRef, setDatasetExperimenterRef, setDatasetID, setDatasetImageRef, setDatasetName, setDetectorAmplificationGain, setDetectorAnnotationRef, setDetectorGain, setDetectorID, setDetectorLotNumber, setDetectorManufacturer, setDetectorModel, setDetectorOffset, setDetectorSerialNumber, setDetectorSettingsBinning, setDetectorSettingsGain, setDetectorSettingsID, setDetectorSettingsIntegration, setDetectorSettingsOffset, setDetectorSettingsReadOutRate, setDetectorSettingsVoltage, setDetectorSettingsZoom, setDetectorType, setDetectorVoltage, setDetectorZoom, setDichroicAnnotationRef, setDichroicID, setDichroicLotNumber, setDichroicManufacturer, setDichroicModel, setDichroicSerialNumber, setDoubleAnnotationAnnotationRef, setDoubleAnnotationAnnotator, setDoubleAnnotationDescription, setDoubleAnnotationID, setDoubleAnnotationNamespace, setDoubleAnnotationValue, setEllipseAnnotationRef, setEllipseFillColor, setEllipseFillRule, setEllipseFontFamily, setEllipseFontSize, setEllipseFontStyle, setEllipseID, setEllipseLocked, setEllipseRadiusX, setEllipseRadiusY, setEllipseStrokeColor, setEllipseStrokeDashArray, setEllipseStrokeWidth, setEllipseText, setEllipseTheC, setEllipseTheT, setEllipseTheZ, setEllipseTransform, setEllipseX, setEllipseY, setExperimentDescription, setExperimenterAnnotationRef, setExperimenterEmail, setExperimenterFirstName, setExperimenterGroupAnnotationRef, setExperimenterGroupDescription, setExperimenterGroupExperimenterRef, setExperimenterGroupID, setExperimenterGroupLeader, setExperimenterGroupName, setExperimenterID, setExperimenterInstitution, setExperimenterLastName, setExperimenterMiddleName, setExperimenterUserName, setExperimentExperimenterRef, setExperimentID, setExperimentType, setFilamentAnnotationRef, setFilamentID, setFilamentLotNumber, setFilamentManufacturer, setFilamentModel, setFilamentPower, setFilamentSerialNumber, setFilamentType, setFileAnnotationAnnotationRef, setFileAnnotationAnnotator, setFileAnnotationDescription, setFileAnnotationID, setFileAnnotationNamespace, setFilterAnnotationRef, setFilterFilterWheel, setFilterID, setFilterLotNumber, setFilterManufacturer, setFilterModel, setFilterSerialNumber, setFilterSetDichroicRef, setFilterSetEmissionFilterRef, setFilterSetExcitationFilterRef, setFilterSetID, setFilterSetLotNumber, setFilterSetManufacturer, setFilterSetModel, setFilterSetSerialNumber, setFilterType, setFolderAnnotationRef, setFolderDescription, setFolderFolderRef, setFolderID, setFolderImageRef, setFolderName, setFolderROIRef, setGenericExcitationSourceAnnotationRef, setGenericExcitationSourceID, setGenericExcitationSourceLotNumber, setGenericExcitationSourceManufacturer, setGenericExcitationSourceMap, setGenericExcitationSourceModel, setGenericExcitationSourcePower, setGenericExcitationSourceSerialNumber, setImageAcquisitionDate, setImageAnnotationRef, setImageDescription, setImageExperimenterGroupRef, setImageExperimenterRef, setImageExperimentRef, setImageID, setImageInstrumentRef, setImageMicrobeamManipulationRef, setImageName, setImageROIRef, setImagingEnvironmentAirPressure, setImagingEnvironmentCO2Percent, setImagingEnvironmentHumidity, setImagingEnvironmentMap, setImagingEnvironmentTemperature, setInstrumentAnnotationRef, setInstrumentID, setLabelAnnotationRef, setLabelFillColor, setLabelFillRule, setLabelFontFamily, setLabelFontSize, setLabelFontStyle, setLabelID, setLabelLocked, setLabelStrokeColor, setLabelStrokeDashArray, setLabelStrokeWidth, setLabelText, setLabelTheC, setLabelTheT, setLabelTheZ, setLabelTransform, setLabelX, setLabelY, setLaserAnnotationRef, setLaserFrequencyMultiplication, setLaserID, setLaserLaserMedium, setLaserLotNumber, setLaserManufacturer, setLaserModel, setLaserPockelCell, setLaserPower, setLaserPulse, setLaserPump, setLaserRepetitionRate, setLaserSerialNumber, setLaserTuneable, setLaserType, setLaserWavelength, setLightEmittingDiodeAnnotationRef, setLightEmittingDiodeID, setLightEmittingDiodeLotNumber, setLightEmittingDiodeManufacturer, setLightEmittingDiodeModel, setLightEmittingDiodePower, setLightEmittingDiodeSerialNumber, setLightPathAnnotationRef, setLightPathDichroicRef, setLightPathEmissionFilterRef, setLightPathExcitationFilterRef, setLineAnnotationRef, setLineFillColor, setLineFillRule, setLineFontFamily, setLineFontSize, setLineFontStyle, setLineID, setLineLocked, setLineMarkerEnd, setLineMarkerStart, setLineStrokeColor, setLineStrokeDashArray, setLineStrokeWidth, setLineText, setLineTheC, setLineTheT, setLineTheZ, setLineTransform, setLineX1, setLineX2, setLineY1, setLineY2, setListAnnotationAnnotationRef, setListAnnotationAnnotator, setListAnnotationDescription, setListAnnotationID, setListAnnotationNamespace, setLongAnnotationAnnotationRef, setLongAnnotationAnnotator, setLongAnnotationDescription, setLongAnnotationID, setLongAnnotationNamespace, setLongAnnotationValue, setMapAnnotationAnnotationRef, setMapAnnotationAnnotator, setMapAnnotationDescription, setMapAnnotationID, setMapAnnotationNamespace, setMapAnnotationValue, setMaskAnnotationRef, setMaskBinData, setMaskBinDataBigEndian, setMaskBinDataCompression, setMaskBinDataLength, setMaskFillColor, setMaskFillRule, setMaskFontFamily, setMaskFontSize, setMaskFontStyle, setMaskHeight, setMaskID, setMaskLocked, setMaskStrokeColor, setMaskStrokeDashArray, setMaskStrokeWidth, setMaskText, setMaskTheC, setMaskTheT, setMaskTheZ, setMaskTransform, setMaskWidth, setMaskX, setMaskY, setMicrobeamManipulationDescription, setMicrobeamManipulationExperimenterRef, setMicrobeamManipulationID, setMicrobeamManipulationLightSourceSettingsAttenuation, setMicrobeamManipulationLightSourceSettingsID, setMicrobeamManipulationLightSourceSettingsWavelength, setMicrobeamManipulationROIRef, setMicrobeamManipulationType, setMicroscopeLotNumber, setMicroscopeManufacturer, setMicroscopeModel, setMicroscopeSerialNumber, setMicroscopeType, setObjectiveAnnotationRef, setObjectiveCalibratedMagnification, setObjectiveCorrection, setObjectiveID, setObjectiveImmersion, setObjectiveIris, setObjectiveLensNA, setObjectiveLotNumber, setObjectiveManufacturer, setObjectiveModel, setObjectiveNominalMagnification, setObjectiveSerialNumber, setObjectiveSettingsCorrectionCollar, setObjectiveSettingsID, setObjectiveSettingsMedium, setObjectiveSettingsRefractiveIndex, setObjectiveWorkingDistance, setPixelsBigEndian, setPixelsBinData, setPixelsBinDataBigEndian, setPixelsBinDataCompression, setPixelsBinDataLength, setPixelsDimensionOrder, setPixelsID, setPixelsInterleaved, setPixelsPhysicalSizeX, setPixelsPhysicalSizeY, setPixelsPhysicalSizeZ, setPixelsSignificantBits, setPixelsSizeC, setPixelsSizeT, setPixelsSizeX, setPixelsSizeY, setPixelsSizeZ, setPixelsTimeIncrement, setPixelsType, setPlaneAnnotationRef, setPlaneDeltaT, setPlaneExposureTime, setPlaneHashSHA1, setPlanePositionX, setPlanePositionY, setPlanePositionZ, setPlaneTheC, setPlaneTheT, setPlaneTheZ, setPlateAcquisitionAnnotationRef, setPlateAcquisitionDescription, setPlateAcquisitionEndTime, setPlateAcquisitionID, setPlateAcquisitionMaximumFieldCount, setPlateAcquisitionName, setPlateAcquisitionStartTime, setPlateAcquisitionWellSampleRef, setPlateAnnotationRef, setPlateColumnNamingConvention, setPlateColumns, setPlateDescription, setPlateExternalIdentifier, setPlateFieldIndex, setPlateID, setPlateName, setPlateRowNamingConvention, setPlateRows, setPlateStatus, setPlateWellOriginX, setPlateWellOriginY, setPointAnnotationRef, setPointFillColor, setPointFillRule, setPointFontFamily, setPointFontSize, setPointFontStyle, setPointID, setPointLocked, setPointStrokeColor, setPointStrokeDashArray, setPointStrokeWidth, setPointText, setPointTheC, setPointTheT, setPointTheZ, setPointTransform, setPointX, setPointY, setPolygonAnnotationRef, setPolygonFillColor, setPolygonFillRule, setPolygonFontFamily, setPolygonFontSize, setPolygonFontStyle, setPolygonID, setPolygonLocked, setPolygonPoints, setPolygonStrokeColor, setPolygonStrokeDashArray, setPolygonStrokeWidth, setPolygonText, setPolygonTheC, setPolygonTheT, setPolygonTheZ, setPolygonTransform, setPolylineAnnotationRef, setPolylineFillColor, setPolylineFillRule, setPolylineFontFamily, setPolylineFontSize, setPolylineFontStyle, setPolylineID, setPolylineLocked, setPolylineMarkerEnd, setPolylineMarkerStart, setPolylinePoints, setPolylineStrokeColor, setPolylineStrokeDashArray, setPolylineStrokeWidth, setPolylineText, setPolylineTheC, setPolylineTheT, setPolylineTheZ, setPolylineTransform, setProjectAnnotationRef, setProjectDatasetRef, setProjectDescription, setProjectExperimenterGroupRef, setProjectExperimenterRef, setProjectID, setProjectName, setReagentAnnotationRef, setReagentDescription, setReagentID, setReagentName, setReagentReagentIdentifier, setRectangleAnnotationRef, setRectangleFillColor, setRectangleFillRule, setRectangleFontFamily, setRectangleFontSize, setRectangleFontStyle, setRectangleHeight, setRectangleID, setRectangleLocked, setRectangleStrokeColor, setRectangleStrokeDashArray, setRectangleStrokeWidth, setRectangleText, setRectangleTheC, setRectangleTheT, setRectangleTheZ, setRectangleTransform, setRectangleWidth, setRectangleX, setRectangleY, setRightsRightsHeld, setRightsRightsHolder, setROIAnnotationRef, setROIDescription, setROIID, setROIName, setScreenAnnotationRef, setScreenDescription, setScreenID, setScreenName, setScreenPlateRef, setScreenProtocolDescription, setScreenProtocolIdentifier, setScreenReagentSetDescription, setScreenReagentSetIdentifier, setScreenType, setStageLabelName, setStageLabelX, setStageLabelY, setStageLabelZ, setTagAnnotationAnnotationRef, setTagAnnotationAnnotator, setTagAnnotationDescription, setTagAnnotationID, setTagAnnotationNamespace, setTagAnnotationValue, setTermAnnotationAnnotationRef, setTermAnnotationAnnotator, setTermAnnotationDescription, setTermAnnotationID, setTermAnnotationNamespace, setTermAnnotationValue, setTiffDataFirstC, setTiffDataFirstT, setTiffDataFirstZ, setTiffDataIFD, setTiffDataPlaneCount, setTimestampAnnotationAnnotationRef, setTimestampAnnotationAnnotator, setTimestampAnnotationDescription, setTimestampAnnotationID, setTimestampAnnotationNamespace, setTimestampAnnotationValue, setTransmittanceRangeCutIn, setTransmittanceRangeCutInTolerance, setTransmittanceRangeCutOut, setTransmittanceRangeCutOutTolerance, setTransmittanceRangeTransmittance, setUUID, setUUIDFileName, setUUIDValue, setWellAnnotationRef, setWellColor, setWellColumn, setWellExternalDescription, setWellExternalIdentifier, setWellID, setWellReagentRef, setWellRow, setWellSampleID, setWellSampleImageRef, setWellSampleIndex, setWellSamplePositionX, setWellSamplePositionY, setWellSampleTimepoint, setWellType, setXMLAnnotationAnnotationRef, setXMLAnnotationAnnotator, setXMLAnnotationDescription, setXMLAnnotationID, setXMLAnnotationNamespace, setXMLAnnotationValue

Field Detail

NAMESPACE

public static final java.lang.String NAMESPACE

See Also:

Constant Field Values

resolutions

private java.util.List<java.util.List<OMEPyramidStore.Resolution>> resolutions

written

private boolean written

Constructor Detail

OMEPyramidStore

public OMEPyramidStore()

Method Detail

dumpXML

public java.lang.String dumpXML()

Specified by:

dumpXML in interface ome.xml.meta.OMEXMLMetadata

Overrides:

dumpXML in class ome.xml.meta.OMEXMLMetadataImpl

setRoot

public void setRoot(ome.xml.meta.MetadataRoot root)

Specified by:

setRoot in interface ome.xml.meta.MetadataStore

Overrides:

setRoot in class ome.xml.meta.OMEXMLMetadataImpl

setResolutionSizeX

public void setResolutionSizeX(ome.xml.model.primitives.PositiveInteger sizeX,
                               int image,
                               int resolution)

Description copied from interface: IPyramidStore

Define the image width in pixels of the given pyramid resolution. Both width and height must be defined for each desired resolution.

Specified by:

setResolutionSizeX in interface IPyramidStore

Parameters:

sizeX - the image width in pixels

image - the Image (series) index

resolution - the resolution index; expected to be greater than 0 as the largest resolution is defined by the Image itself.

See Also:

IPyramidStore.setResolutionSizeY(PositiveInteger, int, int)

setResolutionSizeY

public void setResolutionSizeY(ome.xml.model.primitives.PositiveInteger sizeY,
                               int image,
                               int resolution)

Description copied from interface: IPyramidStore

Define the image height in pixels of the given pyramid resolution. Both width and height must be defined for each desired resolution.

Specified by:

setResolutionSizeY in interface IPyramidStore

Parameters:

sizeY - the image height in pixels

image - the Image (series) index

resolution - the resolution index; expected to be greater than 0 as the largest resolution is defined by the Image itself.

See Also:

IPyramidStore.setResolutionSizeX(PositiveInteger, int, int)

getResolutionCount

public int getResolutionCount(int image)

Description copied from interface: IPyramidStore

Retrieve the number of pyramid resolutions defined for the given Image.

Specified by:

getResolutionCount in interface IPyramidStore

Parameters:

image - the Image (series) index

Returns:

the number of valid pyramid resolutions, including the largest resolution; expected to be positive if the Image index is valid.

getResolutionSizeX

public ome.xml.model.primitives.PositiveInteger getResolutionSizeX(int image,
                                                                   int resolution)

Description copied from interface: IPyramidStore

Retrieve the image width in pixels of the given pyramid resolution.

Specified by:

getResolutionSizeX in interface IPyramidStore

Parameters:

image - the Image (series) index

resolution - the resolution index; expected to be greater than 0 as the largest resolution is defined by the Image itself.

Returns:

the width in pixels, or null if either index is invalid

getResolutionSizeY

public ome.xml.model.primitives.PositiveInteger getResolutionSizeY(int image,
                                                                   int resolution)

Description copied from interface: IPyramidStore

Retrieve the image height in pixels of the given pyramid resolution.

Specified by:

getResolutionSizeY in interface IPyramidStore

Parameters:

image - the Image (series) index

resolution - the resolution index; expected to be greater than 0 as the largest resolution is defined by the Image itself.

Returns:

the height in pixels, or null if either index is invalid

checkImageIndex

private void checkImageIndex(int image)

Verify that the given index is non-negative and less than the Image count.

Parameters:

image - the index to check

Throws:

java.lang.IllegalArgumentException - if the index is invalid

checkResolutionIndex

private void checkResolutionIndex(int image,
                                  int res)

Verify that the given image and resolution indices are valid.

Parameters:

image - the Image index to check

res - the resolution index to check

Throws:

java.lang.IllegalArgumentException - if either index is invalid

See Also:

checkImageIndex(int)

lookupResolution

private OMEPyramidStore.Resolution lookupResolution(int image,
                                                    int res)

Find the Resolution object for the given indices.

Parameters:

image - the Image index

res - the resolution index

Returns:

the corresponding Resolution object, or null if one does not exist

See Also:

lookupResolution(int, int, boolean)

lookupResolution

private OMEPyramidStore.Resolution lookupResolution(int image,
                                                    int res,
                                                    boolean insert)

Find the Resolution object for the given indices. If 'insert' is true, then a Resolution will be created if one does not exist.

Parameters:

image - the Image index

res - the resolution index

insert - true if a Resolution should be created

Returns:

the corresponding Resolution object, or null if one does not exist and 'insert' is false

insertResolution

private void insertResolution(OMEPyramidStore.Resolution r,
                              int image,
                              int res)

Store the given Resolution object at the given indices.

Parameters:

r - the Resolution object to store

image - the Image index

res - the resolution index