Package loci.formats

Class MetadataTools

java.lang.Object

loci.formats.MetadataTools

public final class MetadataTools
extends Object

A utility class for working with metadata objects, including MetadataStore, MetadataRetrieve, and OME-XML strings. Most of the methods require the optional loci.formats.ome package, and optional ome-xml.jar library, to be present at runtime.

Field Summary

Fields

Modifier and Type	Field	Description
private static boolean	defaultDateEnabled
private static final org.slf4j.Logger	LOGGER

Constructor Summary

Constructors

Modifier	Constructor	Description
private	MetadataTools()

Method Summary

Modifier and Type	Method	Description
static String	createLSID(String type, int... indices)	Constructs an LSID, given the object type and indices.
static IMetadata	createOMEXMLMetadata()	Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package.
static ome.xml.model.enums.AcquisitionMode	getAcquisitionMode(String value)	Retrieves an AcquisitionMode enumeration value for the given String.
static ome.xml.model.enums.ArcType	getArcType(String value)	Retrieves an ArcType enumeration value for the given String.
static ome.xml.model.enums.Binning	getBinning(String value)	Retrieves an Binning enumeration value for the given String.
static ome.xml.model.enums.Compression	getCompression(String value)	Retrieves an Compression enumeration value for the given String.
static ome.xml.model.enums.ContrastMethod	getContrastMethod(String value)	Retrieves an ContrastMethod enumeration value for the given String.
static ome.xml.model.enums.Correction	getCorrection(String value)	Retrieves an Correction enumeration value for the given String.
static ome.xml.model.enums.DetectorType	getDetectorType(String value)	Retrieves an DetectorType enumeration value for the given String.
static ome.xml.model.enums.DimensionOrder	getDimensionOrder(String value)	Retrieves an DimensionOrder enumeration value for the given String.
static ome.xml.model.enums.ExperimentType	getExperimentType(String value)	Retrieves an ExperimentType enumeration value for the given String.
static ome.xml.model.enums.FilamentType	getFilamentType(String value)	Retrieves an FilamentType enumeration value for the given String.
static ome.xml.model.enums.FillRule	getFillRule(String value)	Retrieves an FillRule enumeration value for the given String.
static ome.xml.model.enums.FilterType	getFilterType(String value)	Retrieves an FilterType enumeration value for the given String.
static ome.xml.model.enums.FontFamily	getFontFamily(String value)	Retrieves an FontFamily enumeration value for the given String.
static ome.xml.model.enums.FontStyle	getFontStyle(String value)	Retrieves an FontStyle enumeration value for the given String.
static ome.xml.model.enums.IlluminationType	getIlluminationType(String value)	Retrieves an IlluminationType enumeration value for the given String.
static ome.xml.model.enums.Immersion	getImmersion(String value)	Retrieves an Immersion enumeration value for the given String.
static ome.xml.model.enums.LaserMedium	getLaserMedium(String value)	Retrieves an LaserMedium enumeration value for the given String.
static ome.xml.model.enums.LaserType	getLaserType(String value)	Retrieves an LaserType enumeration value for the given String.
static ome.xml.model.enums.Marker	getMarker(String value)	Retrieves an Marker enumeration value for the given String.
static ome.xml.model.enums.Medium	getMedium(String value)	Retrieves an Medium enumeration value for the given String.
static ome.xml.model.enums.MicrobeamManipulationType	getMicrobeamManipulationType(String value)	Retrieves an MicrobeamManipulationType enumeration value for the given String.
static ome.xml.model.enums.MicroscopeType	getMicroscopeType(String value)	Retrieves an MicroscopeType enumeration value for the given String.
static ome.xml.model.enums.NamingConvention	getNamingConvention(String value)	Retrieves an NamingConvention enumeration value for the given String.
static ome.xml.model.enums.PixelType	getPixelType(String value)	Retrieves an PixelType enumeration value for the given String.
static ome.xml.model.enums.Pulse	getPulse(String value)	Retrieves an Pulse enumeration value for the given String.
static String[]	keys(Hashtable<String,Object> meta)	Gets a sorted list of keys from the given hashtable.
static String	makeSaneDimensionOrder(String dimensionOrder)	Adjusts the given dimension order as needed so that it contains exactly one of each of the following characters: 'X', 'Y', 'Z', 'C', 'T'.
static void	merge(Map<String,Object> src, Map<String,Object> dest, String prefix)	Merges the given lists of metadata, prepending the specified prefix for the destination keys.
static void	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	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	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	populatePixels(MetadataStore store, IFormatReader r)	Populates the Pixels element of the given metadata store, using core metadata from the given reader.
static void	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	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	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	populatePixelsOnly(MetadataStore store, IFormatReader r)
static void	setDefaultCreationDate(MetadataStore store, String id, int series)	Sets a default creation date.
static void	setDefaultDateEnabled(boolean enabled)	Disables the setting of a default creation date.
static void	verifyMinimumPopulated(MetadataRetrieve src)	Checks whether the given metadata object has the minimum metadata populated to successfully describe an Image.
static void	verifyMinimumPopulated(MetadataRetrieve src, int n)	Checks whether the given metadata object has the minimum metadata populated to successfully describe the nth Image.

Methods inherited from class java.lang.Object

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

Field Details

LOGGER

private static final org.slf4j.Logger LOGGER

defaultDateEnabled

private static boolean defaultDateEnabled

Constructor Details

MetadataTools

private MetadataTools()

Method Details

populatePixels

public static void populatePixels(MetadataStore store,
 IFormatReader r)

Populates the Pixels element of the given metadata store, using core metadata from the given reader. Delegate to populatePixels(MetadataStore, IFormatReader, boolean, boolean) with doPlane set to false and doImageName set to true.

Parameters:

store - The metadata store whose Pixels should be populated

r - The format reader whose core metadata should be used

populatePixels

public static void populatePixels(MetadataStore store,
 IFormatReader r,
 boolean doPlane)

Populates the Pixels element of the given metadata store, using core metadata from the given reader. If the doPlane flag is set, then the Plane elements will be populated as well. Delegates to populatePixels(MetadataStore, IFormatReader, boolean, boolean) with doImageName set to true.

Parameters:

store - The metadata store whose Pixels should be populated

r - The format reader whose core metadata should be used

doPlane - Specifies whether Plane elements should be populated

populatePixels

public static void 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. If the doPlane flag is set, then the Plane elements will be populated as well. If the doImageName flag is set, then the image name will be populated as well.

Parameters:

store - The metadata store whose Pixels should be populated

r - The format reader whose core metadata should be used

doPlane - Specifies whether Plane elements should be populated

doImageName - Specifies whether the Image name should be populated

populateMetadata

public static void populateMetadata(MetadataStore store,
 int series,
 String imageName,
 CoreMetadata coreMeta)

Populates the given MetadataStore, for the specified series, using the values from the provided CoreMetadata.

After calling this method, the metadata store will be sufficiently populated for use with an IFormatWriter (assuming it is also a MetadataRetrieve).

populateMetadata

public static void 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.

After calling this method, the metadata store will be sufficiently populated for use with an IFormatWriter (assuming it is also a MetadataRetrieve).

populateMetadata

public static void 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.

After calling this method, the metadata store will be sufficiently populated for use with an IFormatWriter (assuming it is also a MetadataRetrieve).

populatePixelsOnly

public static void populatePixelsOnly(MetadataStore store,
 IFormatReader r)

populatePixelsOnly

public static void populatePixelsOnly(MetadataStore store,
 int series,
 boolean littleEndian,
 String dimensionOrder,
 String pixelType,
 int sizeX,
 int sizeY,
 int sizeZ,
 int sizeC,
 int sizeT,
 int samplesPerPixel)

createLSID

public static String createLSID(String type,
 int... indices)

Constructs an LSID, given the object type and indices. For example, if the arguments are "Detector", 1, and 0, the LSID will be "Detector:1:0".

verifyMinimumPopulated

public static void verifyMinimumPopulated(MetadataRetrieve src)
                                   throws FormatException

Checks whether the given metadata object has the minimum metadata populated to successfully describe an Image.

Throws:

FormatException - if there is a missing metadata field, or the metadata object is uninitialized

verifyMinimumPopulated

public static void verifyMinimumPopulated(MetadataRetrieve src,
 int n)
                                   throws FormatException

Checks whether the given metadata object has the minimum metadata populated to successfully describe the nth Image.

Throws:

FormatException - if there is a missing metadata field, or the metadata object is uninitialized

setDefaultDateEnabled

public static void setDefaultDateEnabled(boolean enabled)

Disables the setting of a default creation date. By default, missing creation dates will be replaced with the corresponding file's last modification date, or the current time if the modification date is not available. Calling this method with the 'enabled' parameter set to 'false' causes missing creation dates to be left as null.

Parameters:

enabled - See above.

See Also:

• setDefaultCreationDate(MetadataStore, String, int)

setDefaultCreationDate

public static void setDefaultCreationDate(MetadataStore store,
 String id,
 int series)

Sets a default creation date. If the named file exists, then the creation date is set to the file's last modification date. Otherwise, it is set to the current date.

See Also:

• setDefaultDateEnabled(boolean)

makeSaneDimensionOrder

public static String makeSaneDimensionOrder(String dimensionOrder)

Adjusts the given dimension order as needed so that it contains exactly one of each of the following characters: 'X', 'Y', 'Z', 'C', 'T'.

keys

public static String[] keys(Hashtable<String,Object> meta)

Gets a sorted list of keys from the given hashtable.

merge

public static void merge(Map<String,Object> src,
 Map<String,Object> dest,
 String prefix)

Merges the given lists of metadata, prepending the specified prefix for the destination keys.

createOMEXMLMetadata

public static IMetadata createOMEXMLMetadata()

Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package.

Returns:

A new instance of AbstractOMEXMLMetadata, or null if one cannot be created.

getAcquisitionMode

public static ome.xml.model.enums.AcquisitionMode getAcquisitionMode(String value)
                                                              throws FormatException

Retrieves an AcquisitionMode enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getArcType

public static ome.xml.model.enums.ArcType getArcType(String value)
                                              throws FormatException

Retrieves an ArcType enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getBinning

public static ome.xml.model.enums.Binning getBinning(String value)
                                              throws FormatException

Retrieves an Binning enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getCompression

public static ome.xml.model.enums.Compression getCompression(String value)
                                                      throws FormatException

Retrieves an Compression enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getContrastMethod

public static ome.xml.model.enums.ContrastMethod getContrastMethod(String value)
                                                            throws FormatException

Retrieves an ContrastMethod enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getCorrection

public static ome.xml.model.enums.Correction getCorrection(String value)
                                                    throws FormatException

Retrieves an Correction enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getDetectorType

public static ome.xml.model.enums.DetectorType getDetectorType(String value)
                                                        throws FormatException

Retrieves an DetectorType enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getDimensionOrder

public static ome.xml.model.enums.DimensionOrder getDimensionOrder(String value)
                                                            throws FormatException

Retrieves an DimensionOrder enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getExperimentType

public static ome.xml.model.enums.ExperimentType getExperimentType(String value)
                                                            throws FormatException

Retrieves an ExperimentType enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getFilamentType

public static ome.xml.model.enums.FilamentType getFilamentType(String value)
                                                        throws FormatException

Retrieves an FilamentType enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getFillRule

public static ome.xml.model.enums.FillRule getFillRule(String value)
                                                throws FormatException

Retrieves an FillRule enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getFilterType

public static ome.xml.model.enums.FilterType getFilterType(String value)
                                                    throws FormatException

Retrieves an FilterType enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getFontFamily

public static ome.xml.model.enums.FontFamily getFontFamily(String value)
                                                    throws FormatException

Retrieves an FontFamily enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getFontStyle

public static ome.xml.model.enums.FontStyle getFontStyle(String value)
                                                  throws FormatException

Retrieves an FontStyle enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getIlluminationType

public static ome.xml.model.enums.IlluminationType getIlluminationType(String value)
                                                                throws FormatException

Retrieves an IlluminationType enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getImmersion

public static ome.xml.model.enums.Immersion getImmersion(String value)
                                                  throws FormatException

Retrieves an Immersion enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getLaserMedium

public static ome.xml.model.enums.LaserMedium getLaserMedium(String value)
                                                      throws FormatException

Retrieves an LaserMedium enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getLaserType

public static ome.xml.model.enums.LaserType getLaserType(String value)
                                                  throws FormatException

Retrieves an LaserType enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getMarker

public static ome.xml.model.enums.Marker getMarker(String value)
                                            throws FormatException

Retrieves an Marker enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getMedium

public static ome.xml.model.enums.Medium getMedium(String value)
                                            throws FormatException

Retrieves an Medium enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getMicrobeamManipulationType

public static ome.xml.model.enums.MicrobeamManipulationType getMicrobeamManipulationType(String value)
                                                                                  throws FormatException

Retrieves an MicrobeamManipulationType enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getMicroscopeType

public static ome.xml.model.enums.MicroscopeType getMicroscopeType(String value)
                                                            throws FormatException

Retrieves an MicroscopeType enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getNamingConvention

public static ome.xml.model.enums.NamingConvention getNamingConvention(String value)
                                                                throws FormatException

Retrieves an NamingConvention enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getPixelType

public static ome.xml.model.enums.PixelType getPixelType(String value)
                                                  throws FormatException

Retrieves an PixelType enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException

getPulse

public static ome.xml.model.enums.Pulse getPulse(String value)
                                          throws FormatException

Retrieves an Pulse enumeration value for the given String.

Throws:

ome.xml.model.enums.EnumerationException - if an appropriate enumeration value is not found.

FormatException