icy.sequence

Class MetaDataUtil

java.lang.Object

icy.sequence.MetaDataUtil

public class MetaDataUtil
extends java.lang.Object

Meta data utilities class.
Basically provide safe access to metadata.

Author:

Stephane

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	DEFAULT_CHANNEL_NAME

Constructor Summary

Constructors

Constructor and Description
MetaDataUtil()

Method Summary

Methods

Modifier and Type	Method and Description
static void	clean(ome.xml.meta.OMEXMLMetadata metaData) Cleanup the meta data (sometime we have empty data structure sitting there)
static void	clean(loci.formats.ome.OMEXMLMetadataImpl metaData) Deprecated. Use clean(OMEXMLMetadata) instead.
static void	cleanBinData(ome.xml.model.Image img) Clean BinData packet
static void	cleanPlanes(ome.xml.model.Image img) Clean plane(s) which are outside the pixel sizeC / sizeZ and sizeT.
static void	cleanTiffData(ome.xml.model.Image img) Clean TiffData packet
static loci.formats.ome.OMEXMLMetadataImpl	createDefaultMetadata(java.lang.String name) Deprecated. Use createMetadata(String) instead.
static ome.xml.meta.OMEXMLMetadata	createMetadata(java.lang.String name) Create and return a default (OME XML) Metadata object with default image name.
static ome.xml.meta.OMEXMLMetadata	createOMEMetadata(loci.formats.meta.MetadataRetrieve metadata, int series) Deprecated. Use OMEUtil.createOMEXMLMetadata(MetadataRetrieve, int)
static ome.xml.model.Channel	ensureChannel(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, int index) Deprecated. Use ensureChannel(OMEXMLMetadata, int, int) instead
static ome.xml.model.Channel	ensureChannel(ome.xml.meta.OMEXMLMetadata metaData, int series, int index) Ensure the channel at specified index exist for the specified image series.
static ome.xml.model.Channel	ensureChannel(ome.xml.model.Pixels pix, int index) Ensure the channel at specified index exist for the specified image series.
static ome.xml.model.Plane	ensurePlane(ome.xml.model.Pixels pix, int index) Ensure the plane at specified index exist for the specified Pixels object.
static ome.xml.model.Plane	ensurePlane(ome.xml.model.Pixels pix, int t, int z, int c) Ensure the plane at specified T, Z, C position exist for the specified Pixels object.
static ome.xml.model.Image	ensureSerie(ome.xml.model.OME ome, int index) Deprecated. Use ensureSeries(OME, int) instead
static ome.xml.model.Image	ensureSeries(ome.xml.model.OME ome, int index) Ensure the image series at specified index exist for the specified metaData description.
static ome.xml.meta.OMEXMLMetadata	generateMetaData(IcyBufferedImage image, boolean separateChannel) Generates Meta Data for the given BufferedImage.
static ome.xml.meta.OMEXMLMetadata	generateMetaData(int sizeX, int sizeY, int sizeC, DataType dataType, boolean separateChannel) Generates Meta Data for the given arguments.
static ome.xml.meta.OMEXMLMetadata	generateMetaData(int sizeX, int sizeY, int sizeC, int sizeZ, int sizeT, DataType dataType, boolean separateChannel) Generates meta data for the given image properties.
static ome.xml.meta.OMEXMLMetadata	generateMetaData(Sequence sequence, boolean separateChannel) Generates Meta Data for the given Sequence.
static ome.xml.meta.OMEXMLMetadata	generateMetaData(Sequence sequence, boolean useZ, boolean useT, boolean separateChannel) Deprecated. Use generateMetaData(Sequence, boolean) instead.
static ome.xml.meta.OMEXMLMetadata	generateMetaData(Sequence sequence, int sizeZ, int sizeT, boolean separateChannel) Deprecated. Use generateMetaData(Sequence, boolean) instead.
static ome.xml.model.Channel	getChannel(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, int index) Deprecated. Use getChannel(OMEXMLMetadata, int, int) instead
static ome.xml.model.Channel	getChannel(ome.xml.meta.OMEXMLMetadata metaData, int series, int index) Return channel object at specified index for the specified image series.
static java.awt.Color	getChannelColor(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, int channel) Deprecated. Use getChannelColor(OMEXMLMetadata, int, int) instead
static java.awt.Color	getChannelColor(ome.xml.meta.OMEXMLMetadata metaData, int series, int channel) Returns Color of specified channel image series.
static java.lang.String	getChannelName(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, int channel) Deprecated. Use getChannelName(OMEXMLMetadata, int, int) instead
static java.lang.String	getChannelName(ome.xml.meta.OMEXMLMetadata metaData, int series, int channel) Returns name of specified channel image series.
static long	getDataSize(ome.xml.meta.OMEXMLMetadata metaData, int series) Returns the total data size (in bytes) of the specified image series.
static long	getDataSize(ome.xml.meta.OMEXMLMetadata metaData, int series, int resolution) Returns the total data size (in bytes) of the specified image series for the given resolution (0 = full, 1 = 1/2, ...)
static long	getDataSize(ome.xml.meta.OMEXMLMetadata metaData, int series, int resolution, int sizeZ, int sizeT) Returns the total data size (in bytes) of the specified image series for the given resolution (0 = full, 1 = 1/2, ...) and size informations
static long	getDataSize(ome.xml.meta.OMEXMLMetadata metaData, int series, int resolution, int sizeZ, int sizeT, int sizeC) Returns the total data size (in bytes) of the specified image series for the given resolution (0 = full, 1 = 1/2, ...) and size informations
static DataType	getDataType(loci.formats.ome.OMEXMLMetadataImpl metaData, int series) Deprecated. Use getDataType(OMEXMLMetadata, int) instead
static DataType	getDataType(ome.xml.meta.OMEXMLMetadata metaData, int series) Returns the data type of the specified image series.
static java.lang.String	getDefaultChannelName(int channel) Get default name for specified channel.
static java.lang.String	getImageID(loci.formats.ome.OMEXMLMetadataImpl metaData, int series) Deprecated. Use getImageID(OMEXMLMetadata, int) instead
static java.lang.String	getImageID(ome.xml.meta.OMEXMLMetadata metaData, int series) Returns the id of the specified image series.
static java.lang.String	getName(loci.formats.ome.OMEXMLMetadataImpl metaData, int series) Deprecated. Use getName(OMEXMLMetadata, int) instead
static java.lang.String	getName(ome.xml.meta.OMEXMLMetadata metaData, int series) Returns the name of the specified image series.
static int	getNumChannel(loci.formats.ome.OMEXMLMetadataImpl metaData, int series) Deprecated. Use getNumChannel(OMEXMLMetadata, int) instead
static int	getNumChannel(ome.xml.meta.OMEXMLMetadata metaData, int series) Returns the number of channel for the specified image series in metaData description.
static int	getNumSerie(loci.formats.ome.OMEXMLMetadata metaData) Deprecated. Use getNumSeries(OMEXMLMetadata) instead
static int	getNumSerie(ome.xml.meta.OMEXMLMetadata metaData) Deprecated. Use getNumSeries(OMEXMLMetadata) instead
static int	getNumSerie(loci.formats.ome.OMEXMLMetadataImpl metaData) Deprecated. Use getNumSeries(OMEXMLMetadata) instead
static int	getNumSeries(ome.xml.meta.OMEXMLMetadata metaData) Returns the number of image series of the specified metaData description.
static ome.xml.model.OME	getOME(ome.xml.meta.OMEXMLMetadata metaData) Returns OME root element (create it if needed).
static ome.xml.model.OME	getOME(loci.formats.ome.OMEXMLMetadataImpl metaData) Deprecated. Use getOME(OMEXMLMetadata) instead
static ome.xml.model.Pixels	getPixels(ome.xml.model.OME ome, int index) Return pixels object at specified index for the specified metaData description.
static ome.xml.model.Pixels	getPixels(loci.formats.ome.OMEXMLMetadataImpl metaData, int index) Deprecated. Use getPixels(OMEXMLMetadata, int) instead
static ome.xml.model.Pixels	getPixels(ome.xml.meta.OMEXMLMetadata metaData, int index) Return pixels object at specified index for the specified metaData description.
static double	getPixelSizeX(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, double defaultValue) Deprecated. Use getPixelSizeX(OMEXMLMetadata, int, double) instead
static double	getPixelSizeX(ome.xml.meta.OMEXMLMetadata metaData, int series, double defaultValue) Returns X pixel size (in µm) of the specified image series.
static double	getPixelSizeY(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, double defaultValue) Deprecated. Use getPixelSizeY(OMEXMLMetadata, int, double) instead
static double	getPixelSizeY(ome.xml.meta.OMEXMLMetadata metaData, int series, double defaultValue) Returns Y pixel size (in µm) of the specified image series.
static double	getPixelSizeZ(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, double defaultValue) Deprecated. Use getPixelSizeZ(OMEXMLMetadata, int, double) instead
static double	getPixelSizeZ(ome.xml.meta.OMEXMLMetadata metaData, int series, double defaultValue) Returns Z pixel size (in µm) of the specified image series.
static ome.xml.model.Plane	getPlane(ome.xml.model.Pixels pix, int index)
static ome.xml.model.Plane	getPlane(ome.xml.model.Pixels pix, int t, int z, int c) Return plane object for the specified T, Z, C position.
static int	getPlaneIndex(ome.xml.model.Pixels pix, int t, int z, int c) Return plane index for the specified T, Z, C position.
static double	getPositionT(ome.xml.meta.OMEXMLMetadata metaData, int series, int t, int z, int c, double defaultValue) Deprecated. USe getPositionTOffset(OMEXMLMetadata, int, int, int, int, double) instead
static double	getPositionT(ome.xml.meta.OMEXMLMetadata metaData, int series, long defaultValue)
static double	getPositionTOffset(ome.xml.meta.OMEXMLMetadata metaData, int series, int t, int z, int c, double defaultValue) Returns the time position offset (in second) relative to first image for the image at the specified Z, T, C position.
static double	getPositionX(ome.xml.meta.OMEXMLMetadata metaData, int series, int t, int z, int c, double defaultValue) Returns the X field position (in µm) for the image at the specified Z, T, C position.
static double	getPositionY(ome.xml.meta.OMEXMLMetadata metaData, int series, int t, int z, int c, double defaultValue) Returns the Y field position (in µm) for the image at the specified Z, T, C position.
static double	getPositionZ(ome.xml.meta.OMEXMLMetadata metaData, int series, int t, int z, int c, double defaultValue) Returns the Z field position (in µm) for the image at the specified Z, T, C position.
static ome.xml.model.Image	getSerie(loci.formats.ome.OMEXMLMetadataImpl metaData, int index) Deprecated. Use getSeries(OMEXMLMetadata, int) instead
static ome.xml.model.Image	getSerie(ome.xml.meta.OMEXMLMetadata metaData, int index) Deprecated. Use getSeries(OMEXMLMetadata, int) instead
static ome.xml.model.Image	getSeries(ome.xml.meta.OMEXMLMetadata metaData, int index) Return image series object at specified index for the specified metaData description.
static int	getSizeC(loci.formats.ome.OMEXMLMetadataImpl metaData, int series) Deprecated. Use getSizeC(OMEXMLMetadata, int) instead
static int	getSizeC(ome.xml.meta.OMEXMLMetadata metaData, int series) Returns the number of channel (sizeC) of the specified image series.
static int	getSizeT(loci.formats.ome.OMEXMLMetadataImpl metaData, int series) Deprecated. Use getSizeT(OMEXMLMetadata, int) instead
static int	getSizeT(ome.xml.meta.OMEXMLMetadata metaData, int series) Returns the number of frame (sizeT) of the specified image series.
static int	getSizeX(loci.formats.ome.OMEXMLMetadataImpl metaData, int series) Deprecated. Use getSizeX(OMEXMLMetadata, int) instead
static int	getSizeX(ome.xml.meta.OMEXMLMetadata metaData, int series) Returns the width (sizeX) of the specified image series.
static int	getSizeY(loci.formats.ome.OMEXMLMetadataImpl metaData, int series) Deprecated. Use getSizeY(OMEXMLMetadata, int) instead
static int	getSizeY(ome.xml.meta.OMEXMLMetadata metaData, int series) Returns the height (sizeY) of the specified image series.
static int	getSizeZ(loci.formats.ome.OMEXMLMetadataImpl metaData, int series) Deprecated. Use getSizeZ(OMEXMLMetadata, int) instead
static int	getSizeZ(ome.xml.meta.OMEXMLMetadata metaData, int series) Returns the depth (sizeZ) of the specified image series.
static double	getTimeInterval(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, double defaultValue) Deprecated. Use getTimeInterval(OMEXMLMetadata, int, double) instead
static double	getTimeInterval(ome.xml.meta.OMEXMLMetadata metaData, int series, double defaultValue) Returns T time interval (in second) for the specified image series.
static double	getTimeIntervalFromTimePositions(loci.formats.ome.OMEXMLMetadataImpl metaData, int series) Deprecated. Use getTimeIntervalFromTimePositions(OMEXMLMetadata, int) instead
static double	getTimeIntervalFromTimePositions(ome.xml.meta.OMEXMLMetadata metaData, int series) Computes and returns the T time interval (in second) from internal time positions.
static double	getTimePosition(ome.xml.meta.OMEXMLMetadata metaData, int series, int t, int z, int c, double defaultValue) Deprecated. USe getPositionTOffset(OMEXMLMetadata, int, int, int, int, double) instead
static long	getTimeStamp(ome.xml.meta.OMEXMLMetadata metaData, int series, long defaultValue) Returns the time stamp (elapsed milliseconds from the Java epoch of 1970-01-01 T00:00:00Z) for the specified image.
static boolean	isEmpty(ome.xml.model.XMLAnnotation xmlAnnotation) Returns true if the specified XML annotation are empty.
static void	keepPlanes(ome.xml.model.Image img, int posT, int posZ, int posC) Keep only plane(s) at specified C, Z, T position from the given metadata.
static void	keepPlanes(ome.xml.meta.OMEXMLMetadata metadata, int series, int posT, int posZ, int posC) Keep only plane(s) at specified C, Z, T position from the given metadata.
static void	keepSinglePlane(ome.xml.model.Image img, int index) Keep only the specified plane metadata.
static void	keepSingleSerie(loci.formats.ome.OMEXMLMetadataImpl metaData, int num) Deprecated. Use keepSingleSerie(OMEXMLMetadata, int) instead
static void	keepSingleSerie(ome.xml.meta.OMEXMLMetadata metaData, int num) Keep only the specified image series.
static void	removeChannel(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, int index) Deprecated. Use removeChannel(OMEXMLMetadata, int, int) instead
static void	removeChannel(ome.xml.meta.OMEXMLMetadata metaData, int series, int index) Remove a channel for the specified image series.
static void	removeChannel(ome.xml.model.Pixels pix, int index) Remove a channel from the specified Pixels object.
static boolean	removePlane(ome.xml.model.Image img, int index) Remove the plane at specified position.
static boolean	removePlane(ome.xml.model.Image img, int t, int z, int c) Remove the plane at specified position.
static boolean	removePlane(loci.formats.ome.OMEXMLMetadataImpl metadata, int series, int t, int z, int c) Deprecated. Use removePlane(OMEXMLMetadata, int, int, int, int) instead
static boolean	removePlane(ome.xml.meta.OMEXMLMetadata metadata, int series, int t, int z, int c) Remove the plane at specified position.
static void	removePlanes(loci.formats.ome.OMEXMLMetadataImpl metadata, int series, int posT, int posZ, int posC) Deprecated. Use removePlanes(OMEXMLMetadata, int, int, int, int) instead
static void	removePlanes(ome.xml.meta.OMEXMLMetadata metadata, int series, int posT, int posZ, int posC) Remove planes at given position
static void	setChannelName(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, int channel, java.lang.String value) Deprecated. Use setChannelName(OMEXMLMetadata, int, int, String) instead
static void	setChannelName(ome.xml.meta.OMEXMLMetadata metaData, int series, int channel, java.lang.String value) Set name of specified channel image series.
static void	setDataType(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, DataType dataType) Deprecated. Use setDataType(OMEXMLMetadata, int, DataType) instead
static void	setDataType(ome.xml.meta.OMEXMLMetadata metaData, int series, DataType dataType) Sets the data type of the specified image series.
static void	setImageID(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, java.lang.String value) Deprecated. Use setImageID(OMEXMLMetadata, int, String) instead
static void	setImageID(ome.xml.meta.OMEXMLMetadata metaData, int series, java.lang.String value) Set the id of the specified image series.
static void	setMetaData(loci.formats.ome.OMEXMLMetadataImpl metadata, int sizeX, int sizeY, int sizeC, int sizeZ, int sizeT, DataType dataType, boolean separateChannel) Deprecated. Use setMetaData(OMEXMLMetadata, int, int, int, int, int, DataType, boolean) instead
static void	setMetaData(ome.xml.meta.OMEXMLMetadata metadata, int sizeX, int sizeY, int sizeC, int sizeZ, int sizeT, DataType dataType, boolean separateChannel) Set metadata object with the given image properties.
static void	setName(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, java.lang.String value) Deprecated. Use setName(OMEXMLMetadata, int, String) instead
static void	setName(ome.xml.meta.OMEXMLMetadata metaData, int series, java.lang.String value) Set the name of the specified image series.
static void	setNumChannel(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, int num) Deprecated. Use setNumChannel(OMEXMLMetadata, int, int) instead
static void	setNumChannel(ome.xml.meta.OMEXMLMetadata metaData, int series, int num) Set the number of channel for the specified image series in metaData description.
static void	setNumSerie(loci.formats.ome.OMEXMLMetadataImpl metaData, int num) Deprecated. Use setNumSerie(OMEXMLMetadata, int) instead
static void	setNumSerie(ome.xml.meta.OMEXMLMetadata metaData, int num) Deprecated. Use setNumSeries(OMEXMLMetadata, int) instead
static void	setNumSeries(ome.xml.meta.OMEXMLMetadata metaData, int num) Set the number of image series for the specified metaData description.
static void	setPixelSizeX(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, double value) Deprecated. Use setPixelSizeX(OMEXMLMetadata, int, double) instead
static void	setPixelSizeX(ome.xml.meta.OMEXMLMetadata metaData, int series, double value) Set X pixel size (in µm) of the specified image series.
static void	setPixelSizeY(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, double value) Deprecated. Use setPixelSizeY(OMEXMLMetadata, int, double) instead
static void	setPixelSizeY(ome.xml.meta.OMEXMLMetadata metaData, int series, double value) Set Y pixel size (in µm) of the specified image series.
static void	setPixelSizeZ(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, double value) Deprecated. Use setPixelSizeZ(OMEXMLMetadata, int, double) instead
static void	setPixelSizeZ(ome.xml.meta.OMEXMLMetadata metaData, int series, double value) Set Z pixel size (in µm) of the specified image series.
static void	setPositionT(ome.xml.meta.OMEXMLMetadata metaData, int series, long value) Same as setTimeStamp(OMEXMLMetadata, int, long)
static void	setPositionTOffset(ome.xml.meta.OMEXMLMetadata metaData, int series, int t, int z, int c, double value) Sets the time position offset (in second) relative to the first image for the image at the specified Z, T, C position.
static void	setPositionX(ome.xml.meta.OMEXMLMetadata metaData, int series, int t, int z, int c, double value) Sets the X field position (in µm) for the image at the specified Z, T, C position.
static void	setPositionY(ome.xml.meta.OMEXMLMetadata metaData, int series, int t, int z, int c, double value) Sets the Y field position (in µm) for the image at the specified Z, T, C position.
static void	setPositionZ(ome.xml.meta.OMEXMLMetadata metaData, int series, int t, int z, int c, double value) Sets the Z field position (in µm) for the image at the specified Z, T, C position.
static void	setSizeC(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, int sizeC) Deprecated. Use setSizeC(OMEXMLMetadata, int, int) instead
static void	setSizeC(ome.xml.meta.OMEXMLMetadata metaData, int series, int sizeC) Sets the number of channel (sizeC) of the specified image series (need to be >= 1).
static void	setSizeT(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, int sizeT) Deprecated. Use setSizeT(OMEXMLMetadata, int, int) instead
static void	setSizeT(ome.xml.meta.OMEXMLMetadata metaData, int series, int sizeT) Sets the number of frame (sizeT) of the specified image series (need to be >= 1).
static void	setSizeX(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, int sizeX) Deprecated. Use setSizeX(OMEXMLMetadata, int, int) instead
static void	setSizeX(ome.xml.meta.OMEXMLMetadata metaData, int series, int sizeX) Sets the width (sizeX) of the specified image series (need to be >= 1).
static void	setSizeY(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, int sizeY) Deprecated. Use setSizeY(OMEXMLMetadata, int, int) instead
static void	setSizeY(ome.xml.meta.OMEXMLMetadata metaData, int series, int sizeY) Sets the height (sizeY) of the specified image series (need to be >= 1).
static void	setSizeZ(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, int sizeZ) Deprecated. Use setSizeZ(OMEXMLMetadata, int, int) instead
static void	setSizeZ(ome.xml.meta.OMEXMLMetadata metaData, int series, int sizeZ) Sets the depth (sizeZ) of the specified image series (need to be >= 1).
static void	setTimeInterval(loci.formats.ome.OMEXMLMetadataImpl metaData, int series, double value) Deprecated. Use setTimeInterval(OMEXMLMetadata, int, double) instead
static void	setTimeInterval(ome.xml.meta.OMEXMLMetadata metaData, int series, double value) Set T time resolution (in second) of the specified image series.
static void	setTimeStamp(ome.xml.meta.OMEXMLMetadata metaData, int series, long value) Sets the time stamp (elapsed milliseconds from the Java epoch of 1970-01-01 T00:00:00Z) for the specified image.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_CHANNEL_NAME

public static final java.lang.String DEFAULT_CHANNEL_NAME

See Also:

Constant Field Values

Constructor Detail

MetaDataUtil

public MetaDataUtil()

Method Detail

getOME

public static ome.xml.model.OME getOME(ome.xml.meta.OMEXMLMetadata metaData)

Returns OME root element (create it if needed).

getOME

@Deprecated
public static ome.xml.model.OME getOME(loci.formats.ome.OMEXMLMetadataImpl metaData)

Deprecated. Use getOME(OMEXMLMetadata) instead

getNumSeries

public static int getNumSeries(ome.xml.meta.OMEXMLMetadata metaData)

Returns the number of image series of the specified metaData description.

getNumSerie

@Deprecated
public static int getNumSerie(loci.formats.ome.OMEXMLMetadata metaData)

Deprecated. Use getNumSeries(OMEXMLMetadata) instead

getNumSerie

@Deprecated
public static int getNumSerie(ome.xml.meta.OMEXMLMetadata metaData)

Deprecated. Use getNumSeries(OMEXMLMetadata) instead

getNumSerie

@Deprecated
public static int getNumSerie(loci.formats.ome.OMEXMLMetadataImpl metaData)

Deprecated. Use getNumSeries(OMEXMLMetadata) instead

getSeries

public static ome.xml.model.Image getSeries(ome.xml.meta.OMEXMLMetadata metaData,
                            int index)

Return image series object at specified index for the specified metaData description.

getSerie

@Deprecated
public static ome.xml.model.Image getSerie(ome.xml.meta.OMEXMLMetadata metaData,
                                      int index)

Deprecated. Use getSeries(OMEXMLMetadata, int) instead

getSerie

@Deprecated
public static ome.xml.model.Image getSerie(loci.formats.ome.OMEXMLMetadataImpl metaData,
                                      int index)

Deprecated. Use getSeries(OMEXMLMetadata, int) instead

ensureSeries

public static ome.xml.model.Image ensureSeries(ome.xml.model.OME ome,
                               int index)

Ensure the image series at specified index exist for the specified metaData description.

ensureSerie

@Deprecated
public static ome.xml.model.Image ensureSerie(ome.xml.model.OME ome,
                                         int index)

Deprecated. Use ensureSeries(OME, int) instead

setNumSeries

public static void setNumSeries(ome.xml.meta.OMEXMLMetadata metaData,
                int num)

Set the number of image series for the specified metaData description.

setNumSerie

@Deprecated
public static void setNumSerie(ome.xml.meta.OMEXMLMetadata metaData,
                          int num)

Deprecated. Use setNumSeries(OMEXMLMetadata, int) instead

setNumSerie

@Deprecated
public static void setNumSerie(loci.formats.ome.OMEXMLMetadataImpl metaData,
                          int num)

Deprecated. Use setNumSerie(OMEXMLMetadata, int) instead

getPixels

public static ome.xml.model.Pixels getPixels(ome.xml.model.OME ome,
                             int index)

Return pixels object at specified index for the specified metaData description.

getPixels

public static ome.xml.model.Pixels getPixels(ome.xml.meta.OMEXMLMetadata metaData,
                             int index)

Return pixels object at specified index for the specified metaData description.

getPixels

@Deprecated
public static ome.xml.model.Pixels getPixels(loci.formats.ome.OMEXMLMetadataImpl metaData,
                                        int index)

Deprecated. Use getPixels(OMEXMLMetadata, int) instead

getPlaneIndex

public static int getPlaneIndex(ome.xml.model.Pixels pix,
                int t,
                int z,
                int c)

Return plane index for the specified T, Z, C position.

getPlane

public static ome.xml.model.Plane getPlane(ome.xml.model.Pixels pix,
                           int index)

getPlane

public static ome.xml.model.Plane getPlane(ome.xml.model.Pixels pix,
                           int t,
                           int z,
                           int c)

Return plane object for the specified T, Z, C position.

ensurePlane

public static ome.xml.model.Plane ensurePlane(ome.xml.model.Pixels pix,
                              int index)

Ensure the plane at specified index exist for the specified Pixels object.

ensurePlane

public static ome.xml.model.Plane ensurePlane(ome.xml.model.Pixels pix,
                              int t,
                              int z,
                              int c)

Ensure the plane at specified T, Z, C position exist for the specified Pixels object.

removePlane

public static boolean removePlane(ome.xml.model.Image img,
                  int index)

Remove the plane at specified position.

Returns:

true if the operation succeed, false otherwise

removePlane

public static boolean removePlane(ome.xml.model.Image img,
                  int t,
                  int z,
                  int c)

Remove the plane at specified position.

Returns:

true if the operation succeed, false otherwise

removePlane

public static boolean removePlane(ome.xml.meta.OMEXMLMetadata metadata,
                  int series,
                  int t,
                  int z,
                  int c)

Remove the plane at specified position.

Returns:

true if the operation succeed, false otherwise

removePlane

@Deprecated
public static boolean removePlane(loci.formats.ome.OMEXMLMetadataImpl metadata,
                             int series,
                             int t,
                             int z,
                             int c)

Deprecated. Use removePlane(OMEXMLMetadata, int, int, int, int) instead

removePlanes

public static void removePlanes(ome.xml.meta.OMEXMLMetadata metadata,
                int series,
                int posT,
                int posZ,
                int posC)

Remove planes at given position

Parameters:

posT - T position where we want to remove metadata (-1 for all)

posZ - Z position where we want to remove metadata (-1 for all)

posC - C position where we want to remove metadata (-1 for all)

removePlanes

@Deprecated
public static void removePlanes(loci.formats.ome.OMEXMLMetadataImpl metadata,
                           int series,
                           int posT,
                           int posZ,
                           int posC)

Deprecated. Use removePlanes(OMEXMLMetadata, int, int, int, int) instead

getDataType

public static DataType getDataType(ome.xml.meta.OMEXMLMetadata metaData,
                   int series)

Returns the data type of the specified image series.

getDataType

@Deprecated
public static DataType getDataType(loci.formats.ome.OMEXMLMetadataImpl metaData,
                              int series)

Deprecated. Use getDataType(OMEXMLMetadata, int) instead

getSizeX

public static int getSizeX(ome.xml.meta.OMEXMLMetadata metaData,
           int series)

Returns the width (sizeX) of the specified image series.

getSizeX

@Deprecated
public static int getSizeX(loci.formats.ome.OMEXMLMetadataImpl metaData,
                      int series)

Deprecated. Use getSizeX(OMEXMLMetadata, int) instead

getSizeY

public static int getSizeY(ome.xml.meta.OMEXMLMetadata metaData,
           int series)

Returns the height (sizeY) of the specified image series.

getSizeY

@Deprecated
public static int getSizeY(loci.formats.ome.OMEXMLMetadataImpl metaData,
                      int series)

Deprecated. Use getSizeY(OMEXMLMetadata, int) instead

getSizeC

public static int getSizeC(ome.xml.meta.OMEXMLMetadata metaData,
           int series)

Returns the number of channel (sizeC) of the specified image series.

getSizeC

@Deprecated
public static int getSizeC(loci.formats.ome.OMEXMLMetadataImpl metaData,
                      int series)

Deprecated. Use getSizeC(OMEXMLMetadata, int) instead

getSizeZ

public static int getSizeZ(ome.xml.meta.OMEXMLMetadata metaData,
           int series)

Returns the depth (sizeZ) of the specified image series.

getSizeZ

@Deprecated
public static int getSizeZ(loci.formats.ome.OMEXMLMetadataImpl metaData,
                      int series)

Deprecated. Use getSizeZ(OMEXMLMetadata, int) instead

getSizeT

public static int getSizeT(ome.xml.meta.OMEXMLMetadata metaData,
           int series)

Returns the number of frame (sizeT) of the specified image series.

getSizeT

@Deprecated
public static int getSizeT(loci.formats.ome.OMEXMLMetadataImpl metaData,
                      int series)

Deprecated. Use getSizeT(OMEXMLMetadata, int) instead

getDataSize

public static long getDataSize(ome.xml.meta.OMEXMLMetadata metaData,
               int series)

Returns the total data size (in bytes) of the specified image series.

getDataSize

public static long getDataSize(ome.xml.meta.OMEXMLMetadata metaData,
               int series,
               int resolution)

Returns the total data size (in bytes) of the specified image series for the given resolution (0 = full, 1 = 1/2, ...)

getDataSize

public static long getDataSize(ome.xml.meta.OMEXMLMetadata metaData,
               int series,
               int resolution,
               int sizeZ,
               int sizeT)

Returns the total data size (in bytes) of the specified image series for the given resolution (0 = full, 1 = 1/2, ...) and size informations

getDataSize

public static long getDataSize(ome.xml.meta.OMEXMLMetadata metaData,
               int series,
               int resolution,
               int sizeZ,
               int sizeT,
               int sizeC)

Returns the total data size (in bytes) of the specified image series for the given resolution (0 = full, 1 = 1/2, ...) and size informations

setDataType

public static void setDataType(ome.xml.meta.OMEXMLMetadata metaData,
               int series,
               DataType dataType)

Sets the data type of the specified image series.

setDataType

@Deprecated
public static void setDataType(loci.formats.ome.OMEXMLMetadataImpl metaData,
                          int series,
                          DataType dataType)

Deprecated. Use setDataType(OMEXMLMetadata, int, DataType) instead

setSizeX

public static void setSizeX(ome.xml.meta.OMEXMLMetadata metaData,
            int series,
            int sizeX)

Sets the width (sizeX) of the specified image series (need to be >= 1).

setSizeX

@Deprecated
public static void setSizeX(loci.formats.ome.OMEXMLMetadataImpl metaData,
                       int series,
                       int sizeX)

Deprecated. Use setSizeX(OMEXMLMetadata, int, int) instead

setSizeY

public static void setSizeY(ome.xml.meta.OMEXMLMetadata metaData,
            int series,
            int sizeY)

Sets the height (sizeY) of the specified image series (need to be >= 1).

setSizeY

@Deprecated
public static void setSizeY(loci.formats.ome.OMEXMLMetadataImpl metaData,
                       int series,
                       int sizeY)

Deprecated. Use setSizeY(OMEXMLMetadata, int, int) instead

setSizeC

public static void setSizeC(ome.xml.meta.OMEXMLMetadata metaData,
            int series,
            int sizeC)

Sets the number of channel (sizeC) of the specified image series (need to be >= 1).

setSizeC

@Deprecated
public static void setSizeC(loci.formats.ome.OMEXMLMetadataImpl metaData,
                       int series,
                       int sizeC)

Deprecated. Use setSizeC(OMEXMLMetadata, int, int) instead

setSizeZ

public static void setSizeZ(ome.xml.meta.OMEXMLMetadata metaData,
            int series,
            int sizeZ)

Sets the depth (sizeZ) of the specified image series (need to be >= 1).

setSizeZ

@Deprecated
public static void setSizeZ(loci.formats.ome.OMEXMLMetadataImpl metaData,
                       int series,
                       int sizeZ)

Deprecated. Use setSizeZ(OMEXMLMetadata, int, int) instead

setSizeT

public static void setSizeT(ome.xml.meta.OMEXMLMetadata metaData,
            int series,
            int sizeT)

Sets the number of frame (sizeT) of the specified image series (need to be >= 1).

setSizeT

@Deprecated
public static void setSizeT(loci.formats.ome.OMEXMLMetadataImpl metaData,
                       int series,
                       int sizeT)

Deprecated. Use setSizeT(OMEXMLMetadata, int, int) instead

getImageID

public static java.lang.String getImageID(ome.xml.meta.OMEXMLMetadata metaData,
                          int series)

Returns the id of the specified image series.

getImageID

@Deprecated
public static java.lang.String getImageID(loci.formats.ome.OMEXMLMetadataImpl metaData,
                                     int series)

Deprecated. Use getImageID(OMEXMLMetadata, int) instead

setImageID

public static void setImageID(ome.xml.meta.OMEXMLMetadata metaData,
              int series,
              java.lang.String value)

Set the id of the specified image series.

setImageID

@Deprecated
public static void setImageID(loci.formats.ome.OMEXMLMetadataImpl metaData,
                         int series,
                         java.lang.String value)

Deprecated. Use setImageID(OMEXMLMetadata, int, String) instead

getName

public static java.lang.String getName(ome.xml.meta.OMEXMLMetadata metaData,
                       int series)

Returns the name of the specified image series.

getName

@Deprecated
public static java.lang.String getName(loci.formats.ome.OMEXMLMetadataImpl metaData,
                                  int series)

Deprecated. Use getName(OMEXMLMetadata, int) instead

setName

public static void setName(ome.xml.meta.OMEXMLMetadata metaData,
           int series,
           java.lang.String value)

Set the name of the specified image series.

setName

@Deprecated
public static void setName(loci.formats.ome.OMEXMLMetadataImpl metaData,
                      int series,
                      java.lang.String value)

Deprecated. Use setName(OMEXMLMetadata, int, String) instead

getPixelSizeX

public static double getPixelSizeX(ome.xml.meta.OMEXMLMetadata metaData,
                   int series,
                   double defaultValue)

Returns X pixel size (in µm) of the specified image series.

getPixelSizeX

@Deprecated
public static double getPixelSizeX(loci.formats.ome.OMEXMLMetadataImpl metaData,
                              int series,
                              double defaultValue)

Deprecated. Use getPixelSizeX(OMEXMLMetadata, int, double) instead

getPixelSizeY

public static double getPixelSizeY(ome.xml.meta.OMEXMLMetadata metaData,
                   int series,
                   double defaultValue)

Returns Y pixel size (in µm) of the specified image series.

getPixelSizeY

@Deprecated
public static double getPixelSizeY(loci.formats.ome.OMEXMLMetadataImpl metaData,
                              int series,
                              double defaultValue)

Deprecated. Use getPixelSizeY(OMEXMLMetadata, int, double) instead

getPixelSizeZ

public static double getPixelSizeZ(ome.xml.meta.OMEXMLMetadata metaData,
                   int series,
                   double defaultValue)

Returns Z pixel size (in µm) of the specified image series.

getPixelSizeZ

@Deprecated
public static double getPixelSizeZ(loci.formats.ome.OMEXMLMetadataImpl metaData,
                              int series,
                              double defaultValue)

Deprecated. Use getPixelSizeZ(OMEXMLMetadata, int, double) instead

getTimeIntervalFromTimePositions

public static double getTimeIntervalFromTimePositions(ome.xml.meta.OMEXMLMetadata metaData,
                                      int series)

Computes and returns the T time interval (in second) from internal time positions.
If there is no internal time positions 0d is returned.

getTimeIntervalFromTimePositions

@Deprecated
public static double getTimeIntervalFromTimePositions(loci.formats.ome.OMEXMLMetadataImpl metaData,
                                                 int series)

Deprecated. Use getTimeIntervalFromTimePositions(OMEXMLMetadata, int) instead

getTimeInterval

public static double getTimeInterval(ome.xml.meta.OMEXMLMetadata metaData,
                     int series,
                     double defaultValue)

Returns T time interval (in second) for the specified image series.

getTimeInterval

@Deprecated
public static double getTimeInterval(loci.formats.ome.OMEXMLMetadataImpl metaData,
                                int series,
                                double defaultValue)

Deprecated. Use getTimeInterval(OMEXMLMetadata, int, double) instead

setPixelSizeX

public static void setPixelSizeX(ome.xml.meta.OMEXMLMetadata metaData,
                 int series,
                 double value)

Set X pixel size (in µm) of the specified image series.

setPixelSizeX

@Deprecated
public static void setPixelSizeX(loci.formats.ome.OMEXMLMetadataImpl metaData,
                            int series,
                            double value)

Deprecated. Use setPixelSizeX(OMEXMLMetadata, int, double) instead

setPixelSizeY

public static void setPixelSizeY(ome.xml.meta.OMEXMLMetadata metaData,
                 int series,
                 double value)

Set Y pixel size (in µm) of the specified image series.

setPixelSizeY

@Deprecated
public static void setPixelSizeY(loci.formats.ome.OMEXMLMetadataImpl metaData,
                            int series,
                            double value)

Deprecated. Use setPixelSizeY(OMEXMLMetadata, int, double) instead

setPixelSizeZ

public static void setPixelSizeZ(ome.xml.meta.OMEXMLMetadata metaData,
                 int series,
                 double value)

Set Z pixel size (in µm) of the specified image series.

setPixelSizeZ

@Deprecated
public static void setPixelSizeZ(loci.formats.ome.OMEXMLMetadataImpl metaData,
                            int series,
                            double value)

Deprecated. Use setPixelSizeZ(OMEXMLMetadata, int, double) instead

setTimeInterval

public static void setTimeInterval(ome.xml.meta.OMEXMLMetadata metaData,
                   int series,
                   double value)

Set T time resolution (in second) of the specified image series.

setTimeInterval

@Deprecated
public static void setTimeInterval(loci.formats.ome.OMEXMLMetadataImpl metaData,
                              int series,
                              double value)

Deprecated. Use setTimeInterval(OMEXMLMetadata, int, double) instead

getPositionX

public static double getPositionX(ome.xml.meta.OMEXMLMetadata metaData,
                  int series,
                  int t,
                  int z,
                  int c,
                  double defaultValue)

Returns the X field position (in µm) for the image at the specified Z, T, C position.

getPositionY

public static double getPositionY(ome.xml.meta.OMEXMLMetadata metaData,
                  int series,
                  int t,
                  int z,
                  int c,
                  double defaultValue)

Returns the Y field position (in µm) for the image at the specified Z, T, C position.

getPositionZ

public static double getPositionZ(ome.xml.meta.OMEXMLMetadata metaData,
                  int series,
                  int t,
                  int z,
                  int c,
                  double defaultValue)

Returns the Z field position (in µm) for the image at the specified Z, T, C position.

getPositionT

public static double getPositionT(ome.xml.meta.OMEXMLMetadata metaData,
                  int series,
                  long defaultValue)

getTimeStamp

public static long getTimeStamp(ome.xml.meta.OMEXMLMetadata metaData,
                int series,
                long defaultValue)

Returns the time stamp (elapsed milliseconds from the Java epoch of 1970-01-01 T00:00:00Z) for the specified image.

getPositionTOffset

public static double getPositionTOffset(ome.xml.meta.OMEXMLMetadata metaData,
                        int series,
                        int t,
                        int z,
                        int c,
                        double defaultValue)

Returns the time position offset (in second) relative to first image for the image at the specified Z, T, C position.

getPositionT

@Deprecated
public static double getPositionT(ome.xml.meta.OMEXMLMetadata metaData,
                             int series,
                             int t,
                             int z,
                             int c,
                             double defaultValue)

Deprecated. USe getPositionTOffset(OMEXMLMetadata, int, int, int, int, double) instead

getTimePosition

@Deprecated
public static double getTimePosition(ome.xml.meta.OMEXMLMetadata metaData,
                                int series,
                                int t,
                                int z,
                                int c,
                                double defaultValue)

Deprecated. USe getPositionTOffset(OMEXMLMetadata, int, int, int, int, double) instead

setPositionX

public static void setPositionX(ome.xml.meta.OMEXMLMetadata metaData,
                int series,
                int t,
                int z,
                int c,
                double value)

Sets the X field position (in µm) for the image at the specified Z, T, C position.

setPositionY

public static void setPositionY(ome.xml.meta.OMEXMLMetadata metaData,
                int series,
                int t,
                int z,
                int c,
                double value)

Sets the Y field position (in µm) for the image at the specified Z, T, C position.

setPositionZ

public static void setPositionZ(ome.xml.meta.OMEXMLMetadata metaData,
                int series,
                int t,
                int z,
                int c,
                double value)

Sets the Z field position (in µm) for the image at the specified Z, T, C position.

setPositionT

public static void setPositionT(ome.xml.meta.OMEXMLMetadata metaData,
                int series,
                long value)

Same as setTimeStamp(OMEXMLMetadata, int, long)

setTimeStamp

public static void setTimeStamp(ome.xml.meta.OMEXMLMetadata metaData,
                int series,
                long value)

Sets the time stamp (elapsed milliseconds from the Java epoch of 1970-01-01 T00:00:00Z) for the specified image.

setPositionTOffset

public static void setPositionTOffset(ome.xml.meta.OMEXMLMetadata metaData,
                      int series,
                      int t,
                      int z,
                      int c,
                      double value)

Sets the time position offset (in second) relative to the first image for the image at the specified Z, T, C position.

getDefaultChannelName

public static java.lang.String getDefaultChannelName(int channel)

Get default name for specified channel.

getNumChannel

public static int getNumChannel(ome.xml.meta.OMEXMLMetadata metaData,
                int series)

Returns the number of channel for the specified image series in metaData description.

getNumChannel

@Deprecated
public static int getNumChannel(loci.formats.ome.OMEXMLMetadataImpl metaData,
                           int series)

Deprecated. Use getNumChannel(OMEXMLMetadata, int) instead

getChannel

public static ome.xml.model.Channel getChannel(ome.xml.meta.OMEXMLMetadata metaData,
                               int series,
                               int index)

Return channel object at specified index for the specified image series.

getChannel

@Deprecated
public static ome.xml.model.Channel getChannel(loci.formats.ome.OMEXMLMetadataImpl metaData,
                                          int series,
                                          int index)

Deprecated. Use getChannel(OMEXMLMetadata, int, int) instead

ensureChannel

public static ome.xml.model.Channel ensureChannel(ome.xml.meta.OMEXMLMetadata metaData,
                                  int series,
                                  int index)

Ensure the channel at specified index exist for the specified image series.

ensureChannel

@Deprecated
public static ome.xml.model.Channel ensureChannel(loci.formats.ome.OMEXMLMetadataImpl metaData,
                                             int series,
                                             int index)

Deprecated. Use ensureChannel(OMEXMLMetadata, int, int) instead

ensureChannel

public static ome.xml.model.Channel ensureChannel(ome.xml.model.Pixels pix,
                                  int index)

Ensure the channel at specified index exist for the specified image series.

removeChannel

public static void removeChannel(ome.xml.meta.OMEXMLMetadata metaData,
                 int series,
                 int index)

Remove a channel for the specified image series.

removeChannel

@Deprecated
public static void removeChannel(loci.formats.ome.OMEXMLMetadataImpl metaData,
                            int series,
                            int index)

Deprecated. Use removeChannel(OMEXMLMetadata, int, int) instead

removeChannel

public static void removeChannel(ome.xml.model.Pixels pix,
                 int index)

Remove a channel from the specified Pixels object.

setNumChannel

public static void setNumChannel(ome.xml.meta.OMEXMLMetadata metaData,
                 int series,
                 int num)

Set the number of channel for the specified image series in metaData description.
This is different from getSizeC(OMEXMLMetadata, int).

setNumChannel

@Deprecated
public static void setNumChannel(loci.formats.ome.OMEXMLMetadataImpl metaData,
                            int series,
                            int num)

Deprecated. Use setNumChannel(OMEXMLMetadata, int, int) instead

getChannelName

public static java.lang.String getChannelName(ome.xml.meta.OMEXMLMetadata metaData,
                              int series,
                              int channel)

Returns name of specified channel image series.

getChannelName

@Deprecated
public static java.lang.String getChannelName(loci.formats.ome.OMEXMLMetadataImpl metaData,
                                         int series,
                                         int channel)

Deprecated. Use getChannelName(OMEXMLMetadata, int, int) instead

setChannelName

public static void setChannelName(ome.xml.meta.OMEXMLMetadata metaData,
                  int series,
                  int channel,
                  java.lang.String value)

Set name of specified channel image series.

setChannelName

@Deprecated
public static void setChannelName(loci.formats.ome.OMEXMLMetadataImpl metaData,
                             int series,
                             int channel,
                             java.lang.String value)

Deprecated. Use setChannelName(OMEXMLMetadata, int, int, String) instead

getChannelColor

public static java.awt.Color getChannelColor(ome.xml.meta.OMEXMLMetadata metaData,
                             int series,
                             int channel)

Returns Color of specified channel image series.

getChannelColor

@Deprecated
public static java.awt.Color getChannelColor(loci.formats.ome.OMEXMLMetadataImpl metaData,
                                        int series,
                                        int channel)

Deprecated. Use getChannelColor(OMEXMLMetadata, int, int) instead

createMetadata

public static ome.xml.meta.OMEXMLMetadata createMetadata(java.lang.String name)

Create and return a default (OME XML) Metadata object with default image name.

createDefaultMetadata

@Deprecated
public static loci.formats.ome.OMEXMLMetadataImpl createDefaultMetadata(java.lang.String name)

Deprecated. Use createMetadata(String) instead.

createOMEMetadata

@Deprecated
public static ome.xml.meta.OMEXMLMetadata createOMEMetadata(loci.formats.meta.MetadataRetrieve metadata,
                                                       int series)

Deprecated. Use OMEUtil.createOMEXMLMetadata(MetadataRetrieve, int)

setMetaData

public static void setMetaData(ome.xml.meta.OMEXMLMetadata metadata,
               int sizeX,
               int sizeY,
               int sizeC,
               int sizeZ,
               int sizeT,
               DataType dataType,
               boolean separateChannel)

Set metadata object with the given image properties.

Parameters:

metadata - metadata object to fill.

sizeX - width in pixels (need to be >= 1)

sizeY - height in pixels (need to be >= 1)

sizeC - number of channel (need to be >= 1)

sizeZ - number of Z slices (need to be >= 1)

sizeT - number of T frames (need to be >= 1)

dataType - data type.

separateChannel - true if we want channel data to be separated.

setMetaData

@Deprecated
public static void setMetaData(loci.formats.ome.OMEXMLMetadataImpl metadata,
                          int sizeX,
                          int sizeY,
                          int sizeC,
                          int sizeZ,
                          int sizeT,
                          DataType dataType,
                          boolean separateChannel)

Deprecated. Use setMetaData(OMEXMLMetadata, int, int, int, int, int, DataType, boolean) instead

generateMetaData

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

Generates meta data for the given image properties.

Parameters:

sizeX - width in pixels.

sizeY - height in pixels.

sizeC - number of channel.

sizeZ - number of Z slices.

sizeT - number of T frames.

dataType - data type.

separateChannel - true if we want channel data to be separated.

Returns:

OMEXMLMetadata

Throws:

loci.common.services.ServiceException

generateMetaData

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

Generates Meta Data for the given arguments.

Throws:

loci.common.services.ServiceException

See Also:

setMetaData(OMEXMLMetadata, int, int, int, int, int, DataType, boolean)

generateMetaData

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

Generates Meta Data for the given BufferedImage.

Throws:

loci.common.services.ServiceException

See Also:

setMetaData(OMEXMLMetadata, int, int, int, int, int, DataType, boolean)

generateMetaData

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

Deprecated. Use generateMetaData(Sequence, boolean) instead.

generateMetaData

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

Deprecated. Use generateMetaData(Sequence, boolean) instead.

generateMetaData

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

Generates Meta Data for the given Sequence.

See Also:

setMetaData(OMEXMLMetadata, int, int, int, int, int, DataType, boolean)

keepSingleSerie

public static void keepSingleSerie(ome.xml.meta.OMEXMLMetadata metaData,
                   int num)

Keep only the specified image series.

keepSinglePlane

public static void keepSinglePlane(ome.xml.model.Image img,
                   int index)

Keep only the specified plane metadata.

keepSingleSerie

@Deprecated
public static void keepSingleSerie(loci.formats.ome.OMEXMLMetadataImpl metaData,
                              int num)

Deprecated. Use keepSingleSerie(OMEXMLMetadata, int) instead

keepPlanes

public static void keepPlanes(ome.xml.model.Image img,
              int posT,
              int posZ,
              int posC)

Keep only plane(s) at specified C, Z, T position from the given metadata.

Parameters:

img - image metadata to clean plane from

posT - keep Plane at given T position (-1 to keep all)

posZ - keep Plane at given Z position (-1 to keep all)

posC - keep Plane at given C position (-1 to keep all)

keepPlanes

public static void keepPlanes(ome.xml.meta.OMEXMLMetadata metadata,
              int series,
              int posT,
              int posZ,
              int posC)

Keep only plane(s) at specified C, Z, T position from the given metadata.

Parameters:

posT - keep Plane at given T position (-1 to keep all)

posZ - keep Plane at given Z position (-1 to keep all)

posC - keep Plane at given C position (-1 to keep all)

cleanPlanes

public static void cleanPlanes(ome.xml.model.Image img)

Clean plane(s) which are outside the pixel sizeC / sizeZ and sizeT.

Parameters:

img - image metadata to clean plane from

cleanTiffData

public static void cleanTiffData(ome.xml.model.Image img)

Clean TiffData packet

Parameters:

img - image metadata to clean TiffData from

cleanBinData

public static void cleanBinData(ome.xml.model.Image img)

Clean BinData packet

Parameters:

img - image metadata to clean BinData from

clean

public static void clean(ome.xml.meta.OMEXMLMetadata metaData)

Cleanup the meta data (sometime we have empty data structure sitting there)

clean

@Deprecated
public static void clean(loci.formats.ome.OMEXMLMetadataImpl metaData)

Deprecated. Use clean(OMEXMLMetadata) instead.

isEmpty

public static boolean isEmpty(ome.xml.model.XMLAnnotation xmlAnnotation)

Returns true if the specified XML annotation are empty.