public class MetaDataUtil extends java.lang.Object
Modifier and Type | Field and Description |
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static java.lang.String |
DEFAULT_CHANNEL_NAME |
Constructor and Description |
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MetaDataUtil() |
Modifier and Type | Method and Description |
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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 serie)
Deprecated.
|
static ome.xml.model.Channel |
ensureChannel(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie,
int index)
Deprecated.
Use
ensureChannel(OMEXMLMetadata, int, int) instead |
static ome.xml.model.Channel |
ensureChannel(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
int index)
Ensure the channel at specified index exist for the specified image serie.
|
static ome.xml.model.Channel |
ensureChannel(ome.xml.model.Pixels pix,
int index)
Ensure the channel at specified index exist for the specified image serie.
|
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)
Ensure the image serie 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 serie,
int index)
Deprecated.
Use
getChannel(OMEXMLMetadata, int, int) instead |
static ome.xml.model.Channel |
getChannel(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
int index)
Return channel object at specified index for the specified image serie.
|
static java.awt.Color |
getChannelColor(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie,
int channel)
Deprecated.
Use
getChannelColor(OMEXMLMetadata, int, int) instead |
static java.awt.Color |
getChannelColor(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
int channel)
Returns Color of specified channel image serie.
|
static java.lang.String |
getChannelName(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie,
int channel)
Deprecated.
Use
getChannelName(OMEXMLMetadata, int, int) instead |
static java.lang.String |
getChannelName(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
int channel)
Returns name of specified channel image serie.
|
static long |
getDataSize(ome.xml.meta.OMEXMLMetadata metaData,
int serie)
Returns the total data size (in bytes) of the specified image serie.
|
static long |
getDataSize(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
int resolution)
Returns the total data size (in bytes) of the specified image serie
for the given resolution (0 = full, 1 = 1/2, ...)
|
static long |
getDataSize(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
int resolution,
int sizeZ,
int sizeT)
Returns the total data size (in bytes) of the specified image serie
for the given resolution (0 = full, 1 = 1/2, ...) and size informations
|
static long |
getDataSize(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
int resolution,
int sizeZ,
int sizeT,
int sizeC)
Returns the total data size (in bytes) of the specified image serie
for the given resolution (0 = full, 1 = 1/2, ...) and size informations
|
static DataType |
getDataType(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie)
Deprecated.
Use
getDataType(OMEXMLMetadata, int) instead |
static DataType |
getDataType(ome.xml.meta.OMEXMLMetadata metaData,
int serie)
Returns the data type of the specified image serie.
|
static java.lang.String |
getDefaultChannelName(int channel)
Get default name for specified channel.
|
static java.lang.String |
getImageID(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie)
Deprecated.
Use
getImageID(OMEXMLMetadata, int) instead |
static java.lang.String |
getImageID(ome.xml.meta.OMEXMLMetadata metaData,
int serie)
Returns the id of the specified image serie.
|
static java.lang.String |
getName(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie)
Deprecated.
Use
getName(OMEXMLMetadata, int) instead |
static java.lang.String |
getName(ome.xml.meta.OMEXMLMetadata metaData,
int serie)
Returns the name of the specified image serie.
|
static int |
getNumChannel(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie)
Deprecated.
Use
getNumChannel(OMEXMLMetadata, int) instead |
static int |
getNumChannel(ome.xml.meta.OMEXMLMetadata metaData,
int serie)
Returns the number of channel for the specified image serie in metaData description.
|
static int |
getNumSerie(ome.xml.meta.OMEXMLMetadata metaData)
Returns the number of image serie of the specified metaData description.
|
static int |
getNumSerie(loci.formats.ome.OMEXMLMetadataImpl metaData)
Deprecated.
Use
getNumSerie(OMEXMLMetadata) instead |
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 serie,
double defaultValue)
Deprecated.
Use
getPixelSizeX(OMEXMLMetadata, int, double) instead |
static double |
getPixelSizeX(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
double defaultValue)
Returns X pixel size (in µm) of the specified image serie.
|
static double |
getPixelSizeY(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie,
double defaultValue)
Deprecated.
Use
getPixelSizeY(OMEXMLMetadata, int, double) instead |
static double |
getPixelSizeY(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
double defaultValue)
Returns Y pixel size (in µm) of the specified image serie.
|
static double |
getPixelSizeZ(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie,
double defaultValue)
Deprecated.
Use
getPixelSizeZ(OMEXMLMetadata, int, double) instead |
static double |
getPixelSizeZ(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
double defaultValue)
Returns Z pixel size (in µm) of the specified image serie.
|
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 |
getPositionX(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
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 serie,
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 serie,
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
getSerie(OMEXMLMetadata, int) instead |
static ome.xml.model.Image |
getSerie(ome.xml.meta.OMEXMLMetadata metaData,
int index)
Return image serie object at specified index for the specified metaData description.
|
static int |
getSizeC(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie)
Deprecated.
Use
getSizeC(OMEXMLMetadata, int) instead |
static int |
getSizeC(ome.xml.meta.OMEXMLMetadata metaData,
int serie)
Returns the number of channel (sizeC) of the specified image serie.
|
static int |
getSizeT(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie)
Deprecated.
Use
getSizeT(OMEXMLMetadata, int) instead |
static int |
getSizeT(ome.xml.meta.OMEXMLMetadata metaData,
int serie)
Returns the number of frame (sizeT) of the specified image serie.
|
static int |
getSizeX(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie)
Deprecated.
Use
getSizeX(OMEXMLMetadata, int) instead |
static int |
getSizeX(ome.xml.meta.OMEXMLMetadata metaData,
int serie)
Returns the width (sizeX) of the specified image serie.
|
static int |
getSizeY(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie)
Deprecated.
Use
getSizeY(OMEXMLMetadata, int) instead |
static int |
getSizeY(ome.xml.meta.OMEXMLMetadata metaData,
int serie)
Returns the height (sizeY) of the specified image serie.
|
static int |
getSizeZ(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie)
Deprecated.
Use
getSizeZ(OMEXMLMetadata, int) instead |
static int |
getSizeZ(ome.xml.meta.OMEXMLMetadata metaData,
int serie)
Returns the depth (sizeZ) of the specified image serie.
|
static double |
getTimeInterval(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie,
double defaultValue)
Deprecated.
Use
getTimeInterval(OMEXMLMetadata, int, double) instead |
static double |
getTimeInterval(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
double defaultValue)
Returns T time interval (in second) for the specified image serie.
|
static double |
getTimeIntervalFromTimePositions(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie)
Deprecated.
|
static double |
getTimeIntervalFromTimePositions(ome.xml.meta.OMEXMLMetadata metaData,
int serie)
Computes and returns the T time interval (in second) from internal time positions.
|
static double |
getTimePosition(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
int t,
int z,
int c,
double defaultValue)
Returns the time position (in second) for the image at the specified Z, T, C position.
|
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 serie,
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 serie.
|
static void |
removeChannel(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie,
int index)
Deprecated.
Use
removeChannel(OMEXMLMetadata, int, int) instead |
static void |
removeChannel(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
int index)
Remove a channel for the specified image serie.
|
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 serie,
int t,
int z,
int c)
Deprecated.
Use
removePlane(OMEXMLMetadata, int, int, int, int) instead |
static boolean |
removePlane(ome.xml.meta.OMEXMLMetadata metadata,
int serie,
int t,
int z,
int c)
Remove the plane at specified position.
|
static void |
removePlanes(loci.formats.ome.OMEXMLMetadataImpl metadata,
int serie,
int posT,
int posZ,
int posC)
Deprecated.
Use
removePlanes(OMEXMLMetadata, int, int, int, int) instead |
static void |
removePlanes(ome.xml.meta.OMEXMLMetadata metadata,
int serie,
int posT,
int posZ,
int posC)
Remove planes at given position
|
static void |
setChannelName(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie,
int channel,
java.lang.String value)
Deprecated.
Use
setChannelName(OMEXMLMetadata, int, int, String) instead |
static void |
setChannelName(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
int channel,
java.lang.String value)
Set name of specified channel image serie.
|
static void |
setDataType(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie,
DataType dataType)
Deprecated.
Use
setDataType(OMEXMLMetadata, int, DataType) instead |
static void |
setDataType(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
DataType dataType)
Sets the data type of the specified image serie.
|
static void |
setImageID(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie,
java.lang.String value)
Deprecated.
Use
setImageID(OMEXMLMetadata, int, String) instead |
static void |
setImageID(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
java.lang.String value)
Set the id of the specified image serie.
|
static void |
setMetaData(loci.formats.ome.OMEXMLMetadataImpl metadata,
int sizeX,
int sizeY,
int sizeC,
int sizeZ,
int sizeT,
DataType dataType,
boolean separateChannel)
Deprecated.
|
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 serie,
java.lang.String value)
Deprecated.
Use
setName(OMEXMLMetadata, int, String) instead |
static void |
setName(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
java.lang.String value)
Set the name of the specified image serie.
|
static void |
setNumChannel(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie,
int num)
Deprecated.
Use
setNumChannel(OMEXMLMetadata, int, int) instead |
static void |
setNumChannel(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
int num)
Set the number of channel for the specified image serie 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)
Set the number of image serie for the specified metaData description.
|
static void |
setPixelSizeX(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie,
double value)
Deprecated.
Use
setPixelSizeX(OMEXMLMetadata, int, double) instead |
static void |
setPixelSizeX(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
double value)
Set X pixel size (in µm) of the specified image serie.
|
static void |
setPixelSizeY(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie,
double value)
Deprecated.
Use
setPixelSizeY(OMEXMLMetadata, int, double) instead |
static void |
setPixelSizeY(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
double value)
Set Y pixel size (in µm) of the specified image serie.
|
static void |
setPixelSizeZ(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie,
double value)
Deprecated.
Use
setPixelSizeZ(OMEXMLMetadata, int, double) instead |
static void |
setPixelSizeZ(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
double value)
Set Z pixel size (in µm) of the specified image serie.
|
static void |
setPositionX(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
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 serie,
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 serie,
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 serie,
int sizeC)
Deprecated.
Use
setSizeC(OMEXMLMetadata, int, int) instead |
static void |
setSizeC(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
int sizeC)
Sets the number of channel (sizeC) of the specified image serie (need to be >= 1).
|
static void |
setSizeT(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie,
int sizeT)
Deprecated.
Use
setSizeT(OMEXMLMetadata, int, int) instead |
static void |
setSizeT(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
int sizeT)
Sets the number of frame (sizeT) of the specified image serie (need to be >= 1).
|
static void |
setSizeX(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie,
int sizeX)
Deprecated.
Use
setSizeX(OMEXMLMetadata, int, int) instead |
static void |
setSizeX(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
int sizeX)
Sets the width (sizeX) of the specified image serie (need to be >= 1).
|
static void |
setSizeY(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie,
int sizeY)
Deprecated.
Use
setSizeY(OMEXMLMetadata, int, int) instead |
static void |
setSizeY(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
int sizeY)
Sets the height (sizeY) of the specified image serie (need to be >= 1).
|
static void |
setSizeZ(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie,
int sizeZ)
Deprecated.
Use
setSizeZ(OMEXMLMetadata, int, int) instead |
static void |
setSizeZ(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
int sizeZ)
Sets the depth (sizeZ) of the specified image serie (need to be >= 1).
|
static void |
setTimeInterval(loci.formats.ome.OMEXMLMetadataImpl metaData,
int serie,
double value)
Deprecated.
Use
setTimeInterval(OMEXMLMetadata, int, double) instead |
static void |
setTimeInterval(ome.xml.meta.OMEXMLMetadata metaData,
int serie,
double value)
Set T time resolution (in second) of the specified image serie.
|
public static final java.lang.String DEFAULT_CHANNEL_NAME
public MetaDataUtil()
public static ome.xml.model.OME getOME(ome.xml.meta.OMEXMLMetadata metaData)
@Deprecated public static ome.xml.model.OME getOME(loci.formats.ome.OMEXMLMetadataImpl metaData)
getOME(OMEXMLMetadata)
insteadpublic static int getNumSerie(ome.xml.meta.OMEXMLMetadata metaData)
@Deprecated public static int getNumSerie(loci.formats.ome.OMEXMLMetadataImpl metaData)
getNumSerie(OMEXMLMetadata)
insteadpublic static ome.xml.model.Image getSerie(ome.xml.meta.OMEXMLMetadata metaData, int index)
@Deprecated public static ome.xml.model.Image getSerie(loci.formats.ome.OMEXMLMetadataImpl metaData, int index)
getSerie(OMEXMLMetadata, int)
insteadpublic static ome.xml.model.Image ensureSerie(ome.xml.model.OME ome, int index)
public static void setNumSerie(ome.xml.meta.OMEXMLMetadata metaData, int num)
@Deprecated public static void setNumSerie(loci.formats.ome.OMEXMLMetadataImpl metaData, int num)
setNumSerie(OMEXMLMetadata, int)
insteadpublic static ome.xml.model.Pixels getPixels(ome.xml.model.OME ome, int index)
public static ome.xml.model.Pixels getPixels(ome.xml.meta.OMEXMLMetadata metaData, int index)
@Deprecated public static ome.xml.model.Pixels getPixels(loci.formats.ome.OMEXMLMetadataImpl metaData, int index)
getPixels(OMEXMLMetadata, int)
insteadpublic static int getPlaneIndex(ome.xml.model.Pixels pix, int t, int z, int c)
public static ome.xml.model.Plane getPlane(ome.xml.model.Pixels pix, int index)
public static ome.xml.model.Plane getPlane(ome.xml.model.Pixels pix, int t, int z, int c)
public static ome.xml.model.Plane ensurePlane(ome.xml.model.Pixels pix, int index)
public static ome.xml.model.Plane ensurePlane(ome.xml.model.Pixels pix, int t, int z, int c)
public static boolean removePlane(ome.xml.model.Image img, int index)
true
if the operation succeed, false
otherwisepublic static boolean removePlane(ome.xml.model.Image img, int t, int z, int c)
true
if the operation succeed, false
otherwisepublic static boolean removePlane(ome.xml.meta.OMEXMLMetadata metadata, int serie, int t, int z, int c)
true
if the operation succeed, false
otherwise@Deprecated public static boolean removePlane(loci.formats.ome.OMEXMLMetadataImpl metadata, int serie, int t, int z, int c)
removePlane(OMEXMLMetadata, int, int, int, int)
insteadpublic static void removePlanes(ome.xml.meta.OMEXMLMetadata metadata, int serie, int posT, int posZ, int posC)
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)@Deprecated public static void removePlanes(loci.formats.ome.OMEXMLMetadataImpl metadata, int serie, int posT, int posZ, int posC)
removePlanes(OMEXMLMetadata, int, int, int, int)
insteadpublic static DataType getDataType(ome.xml.meta.OMEXMLMetadata metaData, int serie)
@Deprecated public static DataType getDataType(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie)
getDataType(OMEXMLMetadata, int)
insteadpublic static int getSizeX(ome.xml.meta.OMEXMLMetadata metaData, int serie)
@Deprecated public static int getSizeX(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie)
getSizeX(OMEXMLMetadata, int)
insteadpublic static int getSizeY(ome.xml.meta.OMEXMLMetadata metaData, int serie)
@Deprecated public static int getSizeY(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie)
getSizeY(OMEXMLMetadata, int)
insteadpublic static int getSizeC(ome.xml.meta.OMEXMLMetadata metaData, int serie)
@Deprecated public static int getSizeC(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie)
getSizeC(OMEXMLMetadata, int)
insteadpublic static int getSizeZ(ome.xml.meta.OMEXMLMetadata metaData, int serie)
@Deprecated public static int getSizeZ(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie)
getSizeZ(OMEXMLMetadata, int)
insteadpublic static int getSizeT(ome.xml.meta.OMEXMLMetadata metaData, int serie)
@Deprecated public static int getSizeT(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie)
getSizeT(OMEXMLMetadata, int)
insteadpublic static long getDataSize(ome.xml.meta.OMEXMLMetadata metaData, int serie)
public static long getDataSize(ome.xml.meta.OMEXMLMetadata metaData, int serie, int resolution)
public static long getDataSize(ome.xml.meta.OMEXMLMetadata metaData, int serie, int resolution, int sizeZ, int sizeT)
public static long getDataSize(ome.xml.meta.OMEXMLMetadata metaData, int serie, int resolution, int sizeZ, int sizeT, int sizeC)
public static void setDataType(ome.xml.meta.OMEXMLMetadata metaData, int serie, DataType dataType)
@Deprecated public static void setDataType(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, DataType dataType)
setDataType(OMEXMLMetadata, int, DataType)
insteadpublic static void setSizeX(ome.xml.meta.OMEXMLMetadata metaData, int serie, int sizeX)
@Deprecated public static void setSizeX(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, int sizeX)
setSizeX(OMEXMLMetadata, int, int)
insteadpublic static void setSizeY(ome.xml.meta.OMEXMLMetadata metaData, int serie, int sizeY)
@Deprecated public static void setSizeY(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, int sizeY)
setSizeY(OMEXMLMetadata, int, int)
insteadpublic static void setSizeC(ome.xml.meta.OMEXMLMetadata metaData, int serie, int sizeC)
@Deprecated public static void setSizeC(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, int sizeC)
setSizeC(OMEXMLMetadata, int, int)
insteadpublic static void setSizeZ(ome.xml.meta.OMEXMLMetadata metaData, int serie, int sizeZ)
@Deprecated public static void setSizeZ(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, int sizeZ)
setSizeZ(OMEXMLMetadata, int, int)
insteadpublic static void setSizeT(ome.xml.meta.OMEXMLMetadata metaData, int serie, int sizeT)
@Deprecated public static void setSizeT(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, int sizeT)
setSizeT(OMEXMLMetadata, int, int)
insteadpublic static java.lang.String getImageID(ome.xml.meta.OMEXMLMetadata metaData, int serie)
@Deprecated public static java.lang.String getImageID(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie)
getImageID(OMEXMLMetadata, int)
insteadpublic static void setImageID(ome.xml.meta.OMEXMLMetadata metaData, int serie, java.lang.String value)
@Deprecated public static void setImageID(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, java.lang.String value)
setImageID(OMEXMLMetadata, int, String)
insteadpublic static java.lang.String getName(ome.xml.meta.OMEXMLMetadata metaData, int serie)
@Deprecated public static java.lang.String getName(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie)
getName(OMEXMLMetadata, int)
insteadpublic static void setName(ome.xml.meta.OMEXMLMetadata metaData, int serie, java.lang.String value)
@Deprecated public static void setName(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, java.lang.String value)
setName(OMEXMLMetadata, int, String)
insteadpublic static double getPixelSizeX(ome.xml.meta.OMEXMLMetadata metaData, int serie, double defaultValue)
@Deprecated public static double getPixelSizeX(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, double defaultValue)
getPixelSizeX(OMEXMLMetadata, int, double)
insteadpublic static double getPixelSizeY(ome.xml.meta.OMEXMLMetadata metaData, int serie, double defaultValue)
@Deprecated public static double getPixelSizeY(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, double defaultValue)
getPixelSizeY(OMEXMLMetadata, int, double)
insteadpublic static double getPixelSizeZ(ome.xml.meta.OMEXMLMetadata metaData, int serie, double defaultValue)
@Deprecated public static double getPixelSizeZ(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, double defaultValue)
getPixelSizeZ(OMEXMLMetadata, int, double)
insteadpublic static double getTimeIntervalFromTimePositions(ome.xml.meta.OMEXMLMetadata metaData, int serie)
0d
is returned.@Deprecated public static double getTimeIntervalFromTimePositions(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie)
getTimeIntervalFromTimePositions(OMEXMLMetadata, int)
insteadpublic static double getTimeInterval(ome.xml.meta.OMEXMLMetadata metaData, int serie, double defaultValue)
@Deprecated public static double getTimeInterval(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, double defaultValue)
getTimeInterval(OMEXMLMetadata, int, double)
insteadpublic static void setPixelSizeX(ome.xml.meta.OMEXMLMetadata metaData, int serie, double value)
@Deprecated public static void setPixelSizeX(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, double value)
setPixelSizeX(OMEXMLMetadata, int, double)
insteadpublic static void setPixelSizeY(ome.xml.meta.OMEXMLMetadata metaData, int serie, double value)
@Deprecated public static void setPixelSizeY(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, double value)
setPixelSizeY(OMEXMLMetadata, int, double)
insteadpublic static void setPixelSizeZ(ome.xml.meta.OMEXMLMetadata metaData, int serie, double value)
@Deprecated public static void setPixelSizeZ(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, double value)
setPixelSizeZ(OMEXMLMetadata, int, double)
insteadpublic static void setTimeInterval(ome.xml.meta.OMEXMLMetadata metaData, int serie, double value)
@Deprecated public static void setTimeInterval(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, double value)
setTimeInterval(OMEXMLMetadata, int, double)
insteadpublic static double getPositionX(ome.xml.meta.OMEXMLMetadata metaData, int serie, int t, int z, int c, double defaultValue)
public static double getPositionY(ome.xml.meta.OMEXMLMetadata metaData, int serie, int t, int z, int c, double defaultValue)
public static double getPositionZ(ome.xml.meta.OMEXMLMetadata metaData, int serie, int t, int z, int c, double defaultValue)
public static double getTimePosition(ome.xml.meta.OMEXMLMetadata metaData, int serie, int t, int z, int c, double defaultValue)
public static void setPositionX(ome.xml.meta.OMEXMLMetadata metaData, int serie, int t, int z, int c, double value)
public static void setPositionY(ome.xml.meta.OMEXMLMetadata metaData, int serie, int t, int z, int c, double value)
public static void setPositionZ(ome.xml.meta.OMEXMLMetadata metaData, int serie, int t, int z, int c, double value)
public static java.lang.String getDefaultChannelName(int channel)
public static int getNumChannel(ome.xml.meta.OMEXMLMetadata metaData, int serie)
@Deprecated public static int getNumChannel(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie)
getNumChannel(OMEXMLMetadata, int)
insteadpublic static ome.xml.model.Channel getChannel(ome.xml.meta.OMEXMLMetadata metaData, int serie, int index)
@Deprecated public static ome.xml.model.Channel getChannel(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, int index)
getChannel(OMEXMLMetadata, int, int)
insteadpublic static ome.xml.model.Channel ensureChannel(ome.xml.meta.OMEXMLMetadata metaData, int serie, int index)
@Deprecated public static ome.xml.model.Channel ensureChannel(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, int index)
ensureChannel(OMEXMLMetadata, int, int)
insteadpublic static ome.xml.model.Channel ensureChannel(ome.xml.model.Pixels pix, int index)
public static void removeChannel(ome.xml.meta.OMEXMLMetadata metaData, int serie, int index)
@Deprecated public static void removeChannel(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, int index)
removeChannel(OMEXMLMetadata, int, int)
insteadpublic static void removeChannel(ome.xml.model.Pixels pix, int index)
public static void setNumChannel(ome.xml.meta.OMEXMLMetadata metaData, int serie, int num)
getSizeC(OMEXMLMetadata, int)
.@Deprecated public static void setNumChannel(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, int num)
setNumChannel(OMEXMLMetadata, int, int)
insteadpublic static java.lang.String getChannelName(ome.xml.meta.OMEXMLMetadata metaData, int serie, int channel)
@Deprecated public static java.lang.String getChannelName(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, int channel)
getChannelName(OMEXMLMetadata, int, int)
insteadpublic static void setChannelName(ome.xml.meta.OMEXMLMetadata metaData, int serie, int channel, java.lang.String value)
@Deprecated public static void setChannelName(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, int channel, java.lang.String value)
setChannelName(OMEXMLMetadata, int, int, String)
insteadpublic static java.awt.Color getChannelColor(ome.xml.meta.OMEXMLMetadata metaData, int serie, int channel)
@Deprecated public static java.awt.Color getChannelColor(loci.formats.ome.OMEXMLMetadataImpl metaData, int serie, int channel)
getChannelColor(OMEXMLMetadata, int, int)
insteadpublic static ome.xml.meta.OMEXMLMetadata createMetadata(java.lang.String name)
@Deprecated public static loci.formats.ome.OMEXMLMetadataImpl createDefaultMetadata(java.lang.String name)
createMetadata(String)
instead.@Deprecated public static ome.xml.meta.OMEXMLMetadata createOMEMetadata(loci.formats.meta.MetadataRetrieve metadata, int serie)
OMEUtil.createOMEXMLMetadata(MetadataRetrieve, int)
public static void setMetaData(ome.xml.meta.OMEXMLMetadata metadata, int sizeX, int sizeY, int sizeC, int sizeZ, int sizeT, DataType dataType, boolean separateChannel) throws loci.common.services.ServiceException
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.loci.common.services.ServiceException
@Deprecated public static void setMetaData(loci.formats.ome.OMEXMLMetadataImpl metadata, int sizeX, int sizeY, int sizeC, int sizeZ, int sizeT, DataType dataType, boolean separateChannel) throws loci.common.services.ServiceException
setMetaData(OMEXMLMetadata, int, int, int, int, int, DataType, boolean)
insteadloci.common.services.ServiceException
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
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.loci.common.services.ServiceException
public static ome.xml.meta.OMEXMLMetadata generateMetaData(int sizeX, int sizeY, int sizeC, DataType dataType, boolean separateChannel) throws loci.common.services.ServiceException
loci.common.services.ServiceException
setMetaData(OMEXMLMetadata, int, int, int, int, int, DataType, boolean)
public static ome.xml.meta.OMEXMLMetadata generateMetaData(IcyBufferedImage image, boolean separateChannel) throws loci.common.services.ServiceException
loci.common.services.ServiceException
setMetaData(OMEXMLMetadata, int, int, int, int, int, DataType, boolean)
@Deprecated public static ome.xml.meta.OMEXMLMetadata generateMetaData(Sequence sequence, boolean useZ, boolean useT, boolean separateChannel) throws loci.common.services.ServiceException
generateMetaData(Sequence, boolean)
instead.loci.common.services.ServiceException
@Deprecated public static ome.xml.meta.OMEXMLMetadata generateMetaData(Sequence sequence, int sizeZ, int sizeT, boolean separateChannel) throws loci.common.services.ServiceException
generateMetaData(Sequence, boolean)
instead.loci.common.services.ServiceException
public static ome.xml.meta.OMEXMLMetadata generateMetaData(Sequence sequence, boolean separateChannel) throws loci.common.services.ServiceException
loci.common.services.ServiceException
setMetaData(OMEXMLMetadata, int, int, int, int, int, DataType, boolean)
public static void keepSingleSerie(ome.xml.meta.OMEXMLMetadata metaData, int num)
public static void keepSinglePlane(ome.xml.model.Image img, int index)
@Deprecated public static void keepSingleSerie(loci.formats.ome.OMEXMLMetadataImpl metaData, int num)
keepSingleSerie(OMEXMLMetadata, int)
insteadpublic static void keepPlanes(ome.xml.model.Image img, int posT, int posZ, int posC)
img
- image metadata to clean plane fromposT
- 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)public static void keepPlanes(ome.xml.meta.OMEXMLMetadata metadata, int serie, int posT, int posZ, int posC)
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)public static void cleanPlanes(ome.xml.model.Image img)
img
- image metadata to clean plane frompublic static void cleanTiffData(ome.xml.model.Image img)
img
- image metadata to clean TiffData frompublic static void cleanBinData(ome.xml.model.Image img)
img
- image metadata to clean BinData frompublic static void clean(ome.xml.meta.OMEXMLMetadata metaData)
@Deprecated public static void clean(loci.formats.ome.OMEXMLMetadataImpl metaData)
clean(OMEXMLMetadata)
instead.public static boolean isEmpty(ome.xml.model.XMLAnnotation xmlAnnotation)
true
if the specified XML annotation are empty.