public class OMEUtil extends java.lang.Object
Constructor and Description |
---|
OMEUtil() |
Modifier and Type | Method and Description |
---|---|
static loci.formats.ome.OMEXMLMetadataImpl |
createOMEMetadata()
Create a new empty OME Metadata object.
|
static loci.formats.ome.OMEXMLMetadataImpl |
createOMEMetadata(loci.formats.meta.MetadataRetrieve metadata)
Create a new OME Metadata object from the specified Metadata object.
|
static loci.formats.ome.OMEXMLMetadataImpl |
createOMEMetadata(loci.formats.meta.MetadataRetrieve metadata,
int serie)
Create a new single serie OME Metadata object from the specified Metadata object.
|
static loci.formats.ome.OMEXMLMetadata |
generateMetaData(IcyBufferedImage image,
boolean separateChannel)
Deprecated.
|
static loci.formats.ome.OMEXMLMetadata |
generateMetaData(int sizeX,
int sizeY,
int sizeC,
DataType dataType,
boolean separateChannel)
Deprecated.
|
static loci.formats.ome.OMEXMLMetadata |
generateMetaData(int sizeX,
int sizeY,
int sizeC,
int sizeZ,
int sizeT,
DataType dataType,
boolean separateChannel)
Deprecated.
|
static loci.formats.ome.OMEXMLMetadataImpl |
generateMetaData(loci.formats.ome.OMEXMLMetadataImpl metadata,
int sizeX,
int sizeY,
int sizeC,
int sizeZ,
int sizeT,
DataType dataType,
boolean separateChannel)
Deprecated.
|
static loci.formats.ome.OMEXMLMetadata |
generateMetaData(Sequence sequence,
boolean separateChannel)
Deprecated.
Use
MetaDataUtil.generateMetaData(Sequence, boolean) instead. |
static loci.formats.ome.OMEXMLMetadata |
generateMetaData(Sequence sequence,
boolean useZ,
boolean useT,
boolean separateChannel)
Deprecated.
|
static loci.formats.ome.OMEXMLMetadata |
generateMetaData(Sequence sequence,
int sizeZ,
int sizeT,
boolean separateChannel)
Deprecated.
|
static java.awt.Color |
getJavaColor(ome.xml.model.primitives.Color value)
Return a java Color object from a OME Color object
|
static ome.units.quantity.Length |
getLength(double value)
Return a Length object representing the specified value (in µm)
|
static ome.xml.model.primitives.Color |
getOMEColor(java.awt.Color value)
Return a OME Color object from a java Color object
|
static loci.formats.ome.OMEXMLMetadataImpl |
getOMEMetadata(loci.formats.meta.MetadataRetrieve metadata)
Convert the specified Metadata object to OME Metadata.
|
static ome.xml.model.primitives.PositiveFloat |
getPositiveFloat(double value)
Return a PositiveFloat object representing the specified value
|
static ome.xml.model.primitives.PositiveInteger |
getPositiveInteger(int value)
Return a PositiveInteger object representing the specified value
|
static ome.units.quantity.Time |
getTime(double value)
Return a Time object representing the specified value (in second)
|
static double |
getValue(ome.units.quantity.Length obj,
double defaultValue)
Convert specified Length to double value in µm (for backward compatibility).
|
static double |
getValue(ome.xml.model.primitives.PositiveFloat obj,
double defaultValue)
Safe float evaluation from PositiveFloat object.
|
static double |
getValue(ome.xml.model.primitives.PositiveFloat obj,
double defaultValue,
boolean allowInfinite)
Safe float evaluation from PositiveFloat object.
|
static int |
getValue(ome.xml.model.primitives.PositiveInteger obj,
int defaultValue)
Safe integer evaluation from PositiveInteger object.
|
static double |
getValue(ome.units.quantity.Time obj,
double defaultValue)
Convert specified Time to double value in second (for backward compatibility).
|
static org.w3c.dom.Document |
getXMLDocument(loci.formats.meta.MetadataRetrieve metadata)
Return a XML document from the specified Metadata object
|
static boolean |
reportLociError(java.lang.String fileName,
java.lang.String errorMessage)
Report and upload the specified filename to LOCI team.
|
public OMEUtil()
public static int getValue(ome.xml.model.primitives.PositiveInteger obj, int defaultValue)
public static double getValue(ome.xml.model.primitives.PositiveFloat obj, double defaultValue, boolean allowInfinite)
defaultValue
if obj
is null or equal to infinite with
allowInfinite
set to false.public static double getValue(ome.xml.model.primitives.PositiveFloat obj, double defaultValue)
public static double getValue(ome.units.quantity.Length obj, double defaultValue)
null
.public static double getValue(ome.units.quantity.Time obj, double defaultValue)
null
.public static ome.xml.model.primitives.PositiveFloat getPositiveFloat(double value)
public static ome.xml.model.primitives.PositiveInteger getPositiveInteger(int value)
public static ome.units.quantity.Length getLength(double value)
public static ome.units.quantity.Time getTime(double value)
public static java.awt.Color getJavaColor(ome.xml.model.primitives.Color value)
public static ome.xml.model.primitives.Color getOMEColor(java.awt.Color value)
public static loci.formats.ome.OMEXMLMetadataImpl createOMEMetadata()
public static loci.formats.ome.OMEXMLMetadataImpl createOMEMetadata(loci.formats.meta.MetadataRetrieve metadata)
public static loci.formats.ome.OMEXMLMetadataImpl createOMEMetadata(loci.formats.meta.MetadataRetrieve metadata, int serie)
serie
- Index of the serie we want to keep.public static loci.formats.ome.OMEXMLMetadataImpl getOMEMetadata(loci.formats.meta.MetadataRetrieve metadata)
public static org.w3c.dom.Document getXMLDocument(loci.formats.meta.MetadataRetrieve metadata)
@Deprecated public static loci.formats.ome.OMEXMLMetadataImpl generateMetaData(loci.formats.ome.OMEXMLMetadataImpl metadata, int sizeX, int sizeY, int sizeC, int sizeZ, int sizeT, DataType dataType, boolean separateChannel) throws loci.common.services.ServiceException
MetaDataUtil.setMetaData(OMEXMLMetadataImpl, int, int, int, int, int, DataType, boolean)
instead.loci.common.services.ServiceException
@Deprecated public static loci.formats.ome.OMEXMLMetadata generateMetaData(int sizeX, int sizeY, int sizeC, int sizeZ, int sizeT, DataType dataType, boolean separateChannel) throws loci.common.services.ServiceException
MetaDataUtil.generateMetaData(int, int, int, int, int, DataType, boolean)
instead.loci.common.services.ServiceException
@Deprecated public static loci.formats.ome.OMEXMLMetadata generateMetaData(int sizeX, int sizeY, int sizeC, DataType dataType, boolean separateChannel) throws loci.common.services.ServiceException
MetaDataUtil.generateMetaData(int, int, int, DataType, boolean)
instead.loci.common.services.ServiceException
@Deprecated public static loci.formats.ome.OMEXMLMetadata generateMetaData(IcyBufferedImage image, boolean separateChannel) throws loci.common.services.ServiceException
MetaDataUtil.generateMetaData(IcyBufferedImage, boolean)
instead.loci.common.services.ServiceException
@Deprecated public static loci.formats.ome.OMEXMLMetadata generateMetaData(Sequence sequence, boolean useZ, boolean useT, boolean separateChannel) throws loci.common.services.ServiceException
MetaDataUtil.generateMetaData(Sequence, boolean, boolean, boolean)
instead.loci.common.services.ServiceException
@Deprecated public static loci.formats.ome.OMEXMLMetadata generateMetaData(Sequence sequence, int sizeZ, int sizeT, boolean separateChannel) throws loci.common.services.ServiceException
MetaDataUtil.generateMetaData(Sequence, int, int, boolean)
instead.loci.common.services.ServiceException
@Deprecated public static loci.formats.ome.OMEXMLMetadata generateMetaData(Sequence sequence, boolean separateChannel) throws loci.common.services.ServiceException
MetaDataUtil.generateMetaData(Sequence, boolean)
instead.loci.common.services.ServiceException
public static boolean reportLociError(java.lang.String fileName, java.lang.String errorMessage)