icy.util

Class OMEUtil

java.lang.Object

icy.util.OMEUtil

public class OMEUtil
extends java.lang.Object

Author:

Stephane

Constructor Summary

Constructors

Constructor and Description
OMEUtil()

Method Summary

Methods

Modifier and Type	Method and Description
static loci.formats.ome.OMEXMLMetadataImpl	createOMEMetadata() Deprecated. Use createOMEXMLMetadata() instead
static loci.formats.ome.OMEXMLMetadataImpl	createOMEMetadata(loci.formats.meta.MetadataRetrieve metadata) Deprecated. Use createOMEXMLMetadata(MetadataRetrieve) instead
static loci.formats.ome.OMEXMLMetadataImpl	createOMEMetadata(loci.formats.meta.MetadataRetrieve metadata, int serie) Deprecated. Use createOMEXMLMetadata(MetadataRetrieve,int) instead
static ome.xml.meta.OMEXMLMetadata	createOMEXMLMetadata() Create a new empty OME Metadata object.
static ome.xml.meta.OMEXMLMetadata	createOMEXMLMetadata(ome.xml.meta.MetadataRetrieve metadata) Create a new OME Metadata object from the specified Metadata object.
static ome.xml.meta.OMEXMLMetadata	createOMEXMLMetadata(ome.xml.meta.MetadataRetrieve metadata, int serie) Create a new single serie OME Metadata object from the specified Metadata object.
static ome.xml.meta.OMEXMLMetadata	generateMetaData(IcyBufferedImage image, boolean separateChannel) Deprecated. Use MetaDataUtil.generateMetaData(IcyBufferedImage, boolean) instead.
static ome.xml.meta.OMEXMLMetadata	generateMetaData(int sizeX, int sizeY, int sizeC, DataType dataType, boolean separateChannel) Deprecated. Use MetaDataUtil.generateMetaData(int, int, int, DataType, boolean) instead.
static ome.xml.meta.OMEXMLMetadata	generateMetaData(int sizeX, int sizeY, int sizeC, int sizeZ, int sizeT, DataType dataType, boolean separateChannel) Deprecated. Uses MetaDataUtil.generateMetaData(int, int, int, int, int, DataType, boolean) instead.
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. Uses MetaDataUtil.setMetaData(OMEXMLMetadata, int, int, int, int, int, DataType, boolean) instead.
static ome.xml.meta.OMEXMLMetadata	generateMetaData(Sequence sequence, boolean separateChannel) Deprecated. Use MetaDataUtil.generateMetaData(Sequence, boolean) instead.
static ome.xml.meta.OMEXMLMetadata	generateMetaData(Sequence sequence, boolean useZ, boolean useT, boolean separateChannel) Deprecated. Use MetaDataUtil.generateMetaData(Sequence, boolean) instead.
static ome.xml.meta.OMEXMLMetadata	generateMetaData(Sequence sequence, int sizeZ, int sizeT, boolean separateChannel) Deprecated. Use MetaDataUtil.generateMetaData(Sequence, boolean) instead.
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.NonNegativeInteger	getNonNegativeInteger(int value) Return a NonNegativeInteger object representing the specified value
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) Deprecated. Use getOMEXMLMetadata(MetadataRetrieve) instead
static ome.xml.meta.OMEXMLMetadata	getOMEXMLMetadata(ome.xml.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 int	getValue(ome.xml.model.primitives.NonNegativeInteger obj, int defaultValue) Safe integer evaluation from NonNegativeInteger object.
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) Deprecated. Use getXMLDocument(OMEXMLMetadata) instead
static org.w3c.dom.Document	getXMLDocument(ome.xml.meta.OMEXMLMetadata 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.

Methods inherited from class java.lang.Object

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

Constructor Detail

OMEUtil

public OMEUtil()

Method Detail

getValue

public static int getValue(ome.xml.model.primitives.PositiveInteger obj,
           int defaultValue)

Safe integer evaluation from PositiveInteger object.
Return defaultValue if specified object is null.

getValue

public static int getValue(ome.xml.model.primitives.NonNegativeInteger obj,
           int defaultValue)

Safe integer evaluation from NonNegativeInteger object.
Return defaultValue if specified object is null.

getValue

public static double getValue(ome.xml.model.primitives.PositiveFloat obj,
              double defaultValue,
              boolean allowInfinite)

Safe float evaluation from PositiveFloat object.
Return defaultValue if obj is null or equal to infinite with allowInfinite set to false.

getValue

public static double getValue(ome.xml.model.primitives.PositiveFloat obj,
              double defaultValue)

Safe float evaluation from PositiveFloat object.
Return defaultValue if specified object is null.

getValue

public static double getValue(ome.units.quantity.Length obj,
              double defaultValue)

Convert specified Length to double value in µm (for backward compatibility).
Return defaultValue if specified object is null.

getValue

public static double getValue(ome.units.quantity.Time obj,
              double defaultValue)

Convert specified Time to double value in second (for backward compatibility).
Return defaultValue if specified object is null.

getPositiveFloat

public static ome.xml.model.primitives.PositiveFloat getPositiveFloat(double value)

Return a PositiveFloat object representing the specified value

getPositiveInteger

public static ome.xml.model.primitives.PositiveInteger getPositiveInteger(int value)

Return a PositiveInteger object representing the specified value

getNonNegativeInteger

public static ome.xml.model.primitives.NonNegativeInteger getNonNegativeInteger(int value)

Return a NonNegativeInteger object representing the specified value

getLength

public static ome.units.quantity.Length getLength(double value)

Return a Length object representing the specified value (in µm)

getTime

public static ome.units.quantity.Time getTime(double value)

Return a Time object representing the specified value (in second)

getJavaColor

public static java.awt.Color getJavaColor(ome.xml.model.primitives.Color value)

Return a java Color object from a OME Color object

getOMEColor

public static ome.xml.model.primitives.Color getOMEColor(java.awt.Color value)

Return a OME Color object from a java Color object

createOMEXMLMetadata

public static ome.xml.meta.OMEXMLMetadata createOMEXMLMetadata()

Create a new empty OME Metadata object.

createOMEMetadata

@Deprecated
public static loci.formats.ome.OMEXMLMetadataImpl createOMEMetadata()

Deprecated. Use createOMEXMLMetadata() instead

createOMEXMLMetadata

public static ome.xml.meta.OMEXMLMetadata createOMEXMLMetadata(ome.xml.meta.MetadataRetrieve metadata)

Create a new OME Metadata object from the specified Metadata object.

createOMEMetadata

@Deprecated
public static loci.formats.ome.OMEXMLMetadataImpl createOMEMetadata(loci.formats.meta.MetadataRetrieve metadata)

Deprecated. Use createOMEXMLMetadata(MetadataRetrieve) instead

createOMEXMLMetadata

public static ome.xml.meta.OMEXMLMetadata createOMEXMLMetadata(ome.xml.meta.MetadataRetrieve metadata,
                                               int serie)

Create a new single serie OME Metadata object from the specified Metadata object.

Parameters:

serie - Index of the serie we want to keep.

createOMEMetadata

@Deprecated
public static loci.formats.ome.OMEXMLMetadataImpl createOMEMetadata(loci.formats.meta.MetadataRetrieve metadata,
                                                               int serie)

Deprecated. Use createOMEXMLMetadata(MetadataRetrieve,int) instead

getOMEXMLMetadata

public static ome.xml.meta.OMEXMLMetadata getOMEXMLMetadata(ome.xml.meta.MetadataRetrieve metadata)

Convert the specified Metadata object to OME Metadata.
If the specified Metadata is already OME no conversion is done.

getOMEMetadata

@Deprecated
public static loci.formats.ome.OMEXMLMetadataImpl getOMEMetadata(loci.formats.meta.MetadataRetrieve metadata)

Deprecated. Use getOMEXMLMetadata(MetadataRetrieve) instead

getXMLDocument

public static org.w3c.dom.Document getXMLDocument(ome.xml.meta.OMEXMLMetadata metadata)

Return a XML document from the specified Metadata object

getXMLDocument

@Deprecated
public static org.w3c.dom.Document getXMLDocument(loci.formats.meta.MetadataRetrieve metadata)

Deprecated. Use getXMLDocument(OMEXMLMetadata) instead

generateMetaData

@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)

Deprecated. Uses MetaDataUtil.setMetaData(OMEXMLMetadata, int, int, int, int, int, DataType, boolean) instead.

generateMetaData

@Deprecated
public static ome.xml.meta.OMEXMLMetadata generateMetaData(int sizeX,
                                                      int sizeY,
                                                      int sizeC,
                                                      int sizeZ,
                                                      int sizeT,
                                                      DataType dataType,
                                                      boolean separateChannel)
                                                    throws loci.common.services.ServiceException

Deprecated. Uses MetaDataUtil.generateMetaData(int, int, int, int, int, DataType, boolean) instead.

Throws:

loci.common.services.ServiceException

generateMetaData

@Deprecated
public static ome.xml.meta.OMEXMLMetadata generateMetaData(int sizeX,
                                                      int sizeY,
                                                      int sizeC,
                                                      DataType dataType,
                                                      boolean separateChannel)
                                                    throws loci.common.services.ServiceException

Deprecated. Use MetaDataUtil.generateMetaData(int, int, int, DataType, boolean) instead.

Throws:

loci.common.services.ServiceException

generateMetaData

@Deprecated
public static ome.xml.meta.OMEXMLMetadata generateMetaData(IcyBufferedImage image,
                                                      boolean separateChannel)
                                                    throws loci.common.services.ServiceException

Deprecated. Use MetaDataUtil.generateMetaData(IcyBufferedImage, boolean) instead.

Throws:

loci.common.services.ServiceException

generateMetaData

@Deprecated
public static ome.xml.meta.OMEXMLMetadata generateMetaData(Sequence sequence,
                                                      boolean useZ,
                                                      boolean useT,
                                                      boolean separateChannel)

Deprecated. Use MetaDataUtil.generateMetaData(Sequence, boolean) instead.

generateMetaData

@Deprecated
public static ome.xml.meta.OMEXMLMetadata generateMetaData(Sequence sequence,
                                                      int sizeZ,
                                                      int sizeT,
                                                      boolean separateChannel)

Deprecated. Use MetaDataUtil.generateMetaData(Sequence, boolean) instead.

generateMetaData

@Deprecated
public static ome.xml.meta.OMEXMLMetadata generateMetaData(Sequence sequence,
                                                      boolean separateChannel)

Deprecated. Use MetaDataUtil.generateMetaData(Sequence, boolean) instead.

reportLociError

public static boolean reportLociError(java.lang.String fileName,
                      java.lang.String errorMessage)

Report and upload the specified filename to LOCI team.