Uses of Interface
loci.formats.meta.MetadataStore

Packages that use MetadataStore

Package	Description
loci.formats	Bio-Formats: a library for reading and writing popular microscopy file formats.
loci.formats.gui	Package containing Bio-Formats graphical user interface code.
loci.formats.in	Package containing Bio-Formats file format readers.
loci.formats.meta	Package containing core Bio-Formats metadata interfaces for the OME data model.
loci.formats.ome	Package containing Bio-Formats OME-related logic for OME-XML metadata, and database import, upload and download.
loci.formats.services
loci.plugins.util	Utility classes and methods for the Bio-Formats plugins for ImageJ.

Uses of MetadataStore in loci.formats

Fields in loci.formats declared as MetadataStore

Modifier and Type	Field and Description
protected MetadataStore	FormatReader.metadataStore Current metadata store.
private MetadataStore	Memoizer.replacementMetadataStore MetadataStore created internally.
private MetadataStore	FileStitcher.store
private MetadataStore	Memoizer.userMetadataStore MetadataStore set by the caller.

Methods in loci.formats that return MetadataStore

Modifier and Type	Method and Description
MetadataStore	Memoizer.getMetadataStore()
MetadataStore	FileStitcher.getMetadataStore()
MetadataStore	FormatReader.getMetadataStore()
MetadataStore	ReaderWrapper.getMetadataStore()
MetadataStore	IFormatReader.getMetadataStore() Retrieves the current metadata store for this reader.
MetadataStore	ImageReader.getMetadataStore()
protected MetadataStore	FormatReader.makeFilterMetadata() Return a properly configured loci.formats.meta.FilterMetadata.

Methods in loci.formats with parameters of type MetadataStore

Modifier and Type	Method and Description
static void	MetadataTools.populateMetadata(MetadataStore store, int series, String imageName, boolean littleEndian, String dimensionOrder, String pixelType, int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT, int samplesPerPixel) Populates the given MetadataStore, for the specified series, using the provided values.
static void	MetadataTools.populateMetadata(MetadataStore store, int series, String imageName, CoreMetadata coreMeta) Populates the given MetadataStore, for the specified series, using the values from the provided CoreMetadata.
static void	MetadataTools.populateMetadata(MetadataStore store, String file, int series, String imageName, boolean littleEndian, String dimensionOrder, String pixelType, int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT, int samplesPerPixel) Populates the given MetadataStore, for the specified series, using the provided values.
static void	MetadataTools.populatePixels(MetadataStore store, IFormatReader r) Populates the Pixels element of the given metadata store, using core metadata from the given reader.
static void	MetadataTools.populatePixels(MetadataStore store, IFormatReader r, boolean doPlane) Populates the Pixels element of the given metadata store, using core metadata from the given reader.
static void	MetadataTools.populatePixels(MetadataStore store, IFormatReader r, boolean doPlane, boolean doImageName) Populates the Pixels element of the given metadata store, using core metadata from the given reader.
static void	MetadataTools.populatePixelsOnly(MetadataStore store, IFormatReader r)
static void	MetadataTools.populatePixelsOnly(MetadataStore store, int series, boolean littleEndian, String dimensionOrder, String pixelType, int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT, int samplesPerPixel)
static void	MetadataTools.setDefaultCreationDate(MetadataStore store, String id, int series) Sets a default creation date.
void	Memoizer.setMetadataStore(MetadataStore store)
void	FileStitcher.setMetadataStore(MetadataStore store)
void	FormatReader.setMetadataStore(MetadataStore store)
void	ReaderWrapper.setMetadataStore(MetadataStore store)
void	IFormatReader.setMetadataStore(MetadataStore store) Sets the default metadata store for this reader.
void	ImageReader.setMetadataStore(MetadataStore store)
void	DelegateReader.setMetadataStore(MetadataStore store)

Uses of MetadataStore in loci.formats.gui

Fields in loci.formats.gui declared as MetadataStore

Modifier and Type	Field and Description
protected MetadataStore	ImageViewer.omeMeta Attached OME metadata store, if available.

Uses of MetadataStore in loci.formats.in

Fields in loci.formats.in declared as MetadataStore

Modifier and Type	Field and Description
private MetadataStore	LeicaHandler.store
private MetadataStore	ZeissCZIReader.store
private MetadataStore	InCellReader.InCellHandler.store
private MetadataStore	CellH5Reader.store
private MetadataStore	FlexReader.FlexHandler.store

Methods in loci.formats.in that return MetadataStore

Modifier and Type	Method and Description
MetadataStore	FilePatternReader.getMetadataStore()
MetadataStore	OMETiffReader.getMetadataStoreForConversion() Deprecated. Use the general FormatReader.getMetadataStore() method.
MetadataStore	OMETiffReader.getMetadataStoreForDisplay() Deprecated. Use the general FormatReader.getMetadataStore() method.

Methods in loci.formats.in with parameters of type MetadataStore

Modifier and Type	Method and Description
private void	FakeReader.fillAcquisitionDate(MetadataStore store, String date, int imageIndex)
private void	FakeReader.fillAnnotations(MetadataStore store, int imageIndex)
private void	FakeReader.fillExposureTime(MetadataStore store)
protected void	ZeissZVIReader.fillMetadataPass1(MetadataStore store)
protected void	ZeissTIFFReader.fillMetadataPass1(MetadataStore store)
protected void	BaseZeissReader.fillMetadataPass1(MetadataStore store) Read and store basic dimensions in model
protected void	ZeissTIFFReader.fillMetadataPass2(MetadataStore store)
protected void	BaseZeissReader.fillMetadataPass2(MetadataStore store) Read and store basic dimensions in model
protected void	ZeissZVIReader.fillMetadataPass3(MetadataStore store)
protected void	BaseZeissReader.fillMetadataPass3(MetadataStore store) Read and store basic dimensions in model
protected void	BaseZeissReader.fillMetadataPass4(MetadataStore store) Read and store basic dimensions in model
protected void	ZeissZVIReader.fillMetadataPass5(MetadataStore store)
protected void	ZeissTIFFReader.fillMetadataPass5(MetadataStore store)
protected void	BaseZeissReader.fillMetadataPass5(MetadataStore store) Read and store basic dimensions in model
protected void	BaseZeissReader.fillMetadataPass6(MetadataStore store) Read and store basic dimensions in model
protected void	BaseZeissReader.fillMetadataPass7(MetadataStore store) Store basic dimensions in model
private void	FakeReader.fillPhysicalSizes(MetadataStore store)
private void	FakeReader.fillRegions(MetadataStore store, int imageIndex)
private void	FlexReader.groupFiles(String[] fileList, MetadataStore store)
private void	DeltavisionReader.parseDeconvolutionLog(MetadataStore store) Parse deconvolution output, if it exists.
private void	FlexReader.parseFlexFile(int currentWell, int wellRow, int wellCol, int field, boolean firstFile, MetadataStore store) Parses XML metadata from the Flex file corresponding to the given well.
private void	LeicaReader.parseInstrumentData(MetadataStore store, int blockNum)
private boolean	DeltavisionReader.parseLogFile(MetadataStore store) Extract metadata from associated log file, if it exists.
(package private) void	BaseZeissReader.parseMainTags(int image, MetadataStore store, ArrayList<BaseZeissReader.Tag> tags)
void	MIASReader.parseMasks(MetadataStore overlayStore) Parse masks into a separate overlay-specific MetadataStore.
private int	MIASReader.parseMasks(MetadataStore store, int series, int roi, String overlayTiff) Parse Mask ROIs from the given TIFF and place them in the given MetadataStore.
private boolean	BioRadReader.parseNotes(MetadataStore store)
protected void	ZeissLSMReader.parseOverlays(int series, long data, String suffix, MetadataStore store) Parses overlay-related fields.
private int	FV1000Reader.parseROIFile(String filename, MetadataStore store, int nextROI, int plane)
private void	ZeissZVIReader.parseROIs(int imageNum, String name, MetadataStore store) Parse ROI data from the given RandomAccessInputStream and store it in the given MetadataStore.
private void	TrestleReader.parseROIs(MetadataStore store)
private void	BDReader.parseROIs(MetadataStore store)
private void	ZeissZVIReader.parseTags(int image, String file, MetadataStore store) Parse all of the tags in a stream.
private void	IPLabReader.parseTags(MetadataStore store)
private void	MIASReader.parseTemplateFile(MetadataStore store) Parse metadata from the Nugenesistemplate.txt file.
private void	CellWorxReader.parseWellLogFile(int wellIndex, MetadataStore store) Parse metadata from a well log file.
boolean	MIASReader.populateMaskPixels(int imageIndex, int roiIndex, int shapeIndex, MetadataStore store) Populate the MaskPixels.BinData attribute for the Mask identified by the given Image index, ROI index, and Shape index.
private void	FlexReader.populateMetadataStore(MetadataStore store)
private void	FV1000Reader.populateMetadataStore(MetadataStore store, String path)
protected void	ZeissLSMReader.populateMetadataStore(ZeissLSMReader.SubBlock block, MetadataStore store, int series)
private void	TiffReader.populateMetadataStoreImageJ(MetadataStore store) Checks the original metadata table for ImageJ-specific information to propagate into the metadata store.
private void	DeltavisionReader.populateObjective(MetadataStore store, int lensID) Populate an Objective based upon the lens ID.
private void	HitachiReader.populateOMEMetadata(IniTable image, MetadataStore store)
private void	MIASReader.populateROI(List<String> columns, String[] data, int series, int roi, int time, int z, MetadataStore store)
private void	SPEReader.populateRoiMetaData(MetadataStore store) Reads and populates ROI Meta Data values.
void	ND2Handler.populateROIs(MetadataStore store)
private int	FakeReader.populateSPW(MetadataStore store, int screens, int plates, int rows, int cols, int fields, int acqs, boolean withMicrobeam)
private void	KodakReader.readExtraMetadata(MetadataStore store)
private void	KodakReader.readFileInfoMetadata(MetadataStore store)
private void	DeltavisionReader.readWavelength(int channel, MetadataStore store)
void	FilePatternReader.setMetadataStore(MetadataStore store)
void	LeicaHandler.ROI.storeROI(MetadataStore store, int series, int roi)
void	LIFReader.ROI.storeROI(MetadataStore store, int series, int roi, int roiIndex)
protected void	BaseZeissReader.storeROIs(MetadataStore store) Store basic dimensions in model

Constructors in loci.formats.in with parameters of type MetadataStore

Constructor and Description
FlexReader.FlexHandler(List<String> names, List<String> factors, MetadataStore store, boolean populateCore, int well, int thisField)
InCellReader.InCellHandler(MetadataStore store)
LeicaHandler(MetadataStore store, MetadataLevel level)

Uses of MetadataStore in loci.formats.meta

Subinterfaces of MetadataStore in loci.formats.meta

Modifier and Type	Interface and Description
interface	IMetadata

Methods in loci.formats.meta with parameters of type MetadataStore

Modifier and Type	Method and Description
private static void	MetadataConverter.convertBooleanAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all BooleanAnnotation attributes.
private static void	MetadataConverter.convertCommentAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all CommentAnnotation attributes.
private static void	MetadataConverter.convertDatasets(MetadataRetrieve src, MetadataStore dest) Convert all Dataset attributes.
private static void	MetadataConverter.convertDoubleAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all DoubleAnnotation attributes.
private static void	MetadataConverter.convertExperimenterGroups(MetadataRetrieve src, MetadataStore dest) Convert all ExperimenterGroup attributes.
private static void	MetadataConverter.convertExperimenters(MetadataRetrieve src, MetadataStore dest) Convert all Experimenter attributes.
private static void	MetadataConverter.convertExperiments(MetadataRetrieve src, MetadataStore dest) Convert all Experiment attributes.
private static void	MetadataConverter.convertFileAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all FileAnnotation attributes.
private static void	MetadataConverter.convertFolders(MetadataRetrieve src, MetadataStore dest) Convert all Folder attributes.
private static void	MetadataConverter.convertImages(MetadataRetrieve src, MetadataStore dest, List<String> lightSourceIds) Convert all Image attributes.
private static List<String>	MetadataConverter.convertInstruments(MetadataRetrieve src, MetadataStore dest) Convert all Instrument attributes.
private static void	MetadataConverter.convertLightSources(MetadataRetrieve src, MetadataStore dest, int instrumentIndex, List<String> lightSourceIds) Convert all LightSource attributes for the given instrument.
private static void	MetadataConverter.convertListAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all ListAnnotation attributes.
private static void	MetadataConverter.convertLongAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all LongAnnotation attributes.
private static void	MetadataConverter.convertMapAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all MapAnnotation attributes.
static void	MetadataConverter.convertMetadata(MetadataRetrieve src, MetadataStore dest) Copies information from a metadata retrieval object (source) into a metadata store (destination).
private static void	MetadataConverter.convertPlates(MetadataRetrieve src, MetadataStore dest) Convert all Plate attributes.
private static void	MetadataConverter.convertProjects(MetadataRetrieve src, MetadataStore dest) Convert all Project attributes.
private static void	MetadataConverter.convertROIs(MetadataRetrieve src, MetadataStore dest) Convert all ROI attributes.
private static void	MetadataConverter.convertRootAttributes(MetadataRetrieve src, MetadataStore dest) Convert all top-level attributes.
private static void	MetadataConverter.convertScreens(MetadataRetrieve src, MetadataStore dest) Convert all Screen attributes.
private static void	MetadataConverter.convertTagAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all TagAnnotation attributes.
private static void	MetadataConverter.convertTermAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all TermAnnotation attributes.
private static void	MetadataConverter.convertTimestampAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all TimestampAnnotation attributes.
private static void	MetadataConverter.convertXMLAnnotations(MetadataRetrieve src, MetadataStore dest) Convert all XMLAnnotation attributes.

Constructors in loci.formats.meta with parameters of type MetadataStore

Constructor and Description
FilterMetadata(MetadataStore store, boolean filter)

Uses of MetadataStore in loci.formats.ome

Subinterfaces of MetadataStore in loci.formats.ome

Modifier and Type	Interface and Description
interface	OMEXMLMetadata

Uses of MetadataStore in loci.formats.services

Methods in loci.formats.services that return MetadataStore

Modifier and Type	Method and Description
MetadataStore	OMEXMLService.asStore(MetadataRetrieve meta) Gets the given MetadataRetrieve object as a MetadataStore.
MetadataStore	OMEXMLServiceImpl.asStore(MetadataRetrieve meta)

Methods in loci.formats.services with parameters of type MetadataStore

Modifier and Type	Method and Description
MetadataRetrieve	OMEXMLService.asRetrieve(MetadataStore meta) Gets the given MetadataStore object as a MetadataRetrieve.
MetadataRetrieve	OMEXMLServiceImpl.asRetrieve(MetadataStore meta)
void	OMEXMLService.convertMetadata(MetadataRetrieve src, MetadataStore dest) Copies information from a metadata retrieval object (source) into a metadata store (destination).
void	OMEXMLServiceImpl.convertMetadata(MetadataRetrieve src, MetadataStore dest)
void	OMEXMLService.convertMetadata(String xml, MetadataStore dest) Converts information from an OME-XML string (source) into a metadata store (destination).
void	OMEXMLServiceImpl.convertMetadata(String xml, MetadataStore dest)

Uses of MetadataStore in loci.plugins.util

Methods in loci.plugins.util with parameters of type MetadataStore

Modifier and Type	Method and Description
static void	ROIHandler.saveROIs(MetadataStore store) Save ROIs in the ROI manager to the given MetadataStore.
private static void	ROIHandler.storeLine(ij.gui.Line roi, MetadataStore store, int roiNum, int shape, int c, int z, int t) Stores the Line ROI into the specified metadata store.
private static void	ROIHandler.storeOval(ij.gui.OvalRoi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t) Stores the Oval ROI into the specified metadata store.
private static void	ROIHandler.storePoint(ij.gui.PointRoi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t) Stores the Point ROI into the specified metadata store.
private static void	ROIHandler.storePolygon(ij.gui.PolygonRoi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t) Stores the Polygon ROI into the specified metadata store.
private static void	ROIHandler.storeRectangle(ij.gui.Roi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t) Stores the Rectangle ROI into the specified metadata store.
private static void	ROIHandler.storeText(ij.gui.TextRoi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t) Stores the text ROI into the metadata stored.