Package 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:
IMetadata, IPyramidStore, MetadataRetrieve, MetadataStore, OMEXMLMetadata, 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
    Description
    (package private) class 
    OMEPyramidStore.Resolution
     

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final String
    NAMESPACE
     
    private List<List<OMEPyramidStore.Resolution>>
    resolutions
     
    private boolean
    written
     

    Fields inherited from class ome.xml.meta.AbstractOMEXMLMetadata

    LOGGER, SCHEMA, XSI_NS

  • Constructor Summary

    Constructors
    Constructor
    Description
    OMEPyramidStore()
     

  • Method Summary

    Modifier and Type
    Method
    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.
    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.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

    Methods inherited from interface ome.xml.meta.OMEXMLMetadata

    resolveReferences

  • Field Details

  • Constructor Details

    • OMEPyramidStore

      public OMEPyramidStore()

  • Method Details

    • dumpXML

      public 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:

    • 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:

    • 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:
      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:
      IllegalArgumentException - if either index is invalid
      See Also:

    • 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

      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