loci.formats

Class MetadataTools

java.lang.Object

loci.formats.MetadataTools

public final class MetadataTools
extends Object

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

Source code:

Trac, Gitweb

Method Summary

Methods

Modifier and Type	Method and Description
static MetadataRetrieve	asRetrieve(MetadataStore meta) Deprecated. This method is not thread-safe; use OMEXMLService.asRetrieve(MetadataStore) instead.
static String	createLSID(String type, int... indices) Constructs an LSID, given the object type and indices.
static IMetadata	createOMEXMLMetadata() Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package.
static IMetadata	createOMEXMLMetadata(String xml) Deprecated. This method is not thread-safe; use OMEXMLService.createOMEXMLMetadata(String) instead.
static IMetadata	createOMEXMLMetadata(String xml, String version) Deprecated. This method is not thread-safe; use OMEXMLService.createOMEXMLMetadata(String, String) instead.
static Object	createOMEXMLRoot(String xml) Deprecated. This method is not thread-safe; use OMEXMLService.createOMEXMLRoot(String) instead.
static String	getLatestVersion() Deprecated. This method is not thread-safe; use OMEXMLService.getLatestVersion() instead.
static IMetadata	getOMEMetadata(MetadataRetrieve src) Deprecated. This method is not thread-safe; use OMEXMLService.getOMEMetadata(MetadataRetrieve) instead.
static String	getOMEXML(MetadataRetrieve src) Deprecated. This method is not thread-safe; use OMEXMLService.getOMEXML(MetadataRetrieve) instead.
static String	getOMEXMLVersion(Object o) Deprecated. This method is not thread-safe; use OMEXMLService.getOMEXMLVersion(Object) instead.
static boolean	isOMEXMLMetadata(Object o) Deprecated. This method is not thread-safe; use OMEXMLService.isOMEXMLMetadata(Object) instead.
static boolean	isOMEXMLRoot(Object o) Deprecated. This method is not thread-safe; use OMEXMLService.isOMEXMLRoot(Object) instead.
static String[]	keys(Hashtable<String,Object> meta) Gets a sorted list of keys from the given hashtable.
static String	makeSaneDimensionOrder(String dimensionOrder) Adjusts the given dimension order as needed so that it contains exactly one of each of the following characters: 'X', 'Y', 'Z', 'C', 'T'.
static void	merge(Map<String,Object> src, Map<String,Object> dest, String prefix) Merges the given lists of metadata, prepending the specified prefix for the destination keys.
static void	populateMetadata(MetadataStore store, int series, String imageName, boolean littleEndian, String dimensionOrder, String pixelType, int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT, int samplesPerPixel) Populates the given MetadataStore, for the specified series, using the provided values.
static void	populateMetadata(MetadataStore store, int series, String imageName, CoreMetadata coreMeta) Populates the given MetadataStore, for the specified series, using the values from the provided CoreMetadata.
static void	populateMetadata(MetadataStore store, String file, int series, String imageName, boolean littleEndian, String dimensionOrder, String pixelType, int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT, int samplesPerPixel) Populates the given MetadataStore, for the specified series, using the provided values.
static void	populatePixels(MetadataStore store, IFormatReader r) Populates the 'pixels' element of the given metadata store, using core metadata from the given reader.
static void	populatePixels(MetadataStore store, IFormatReader r, boolean doPlane) Populates the 'pixels' element of the given metadata store, using core metadata from the given reader.
static void	populatePixels(MetadataStore store, IFormatReader r, boolean doPlane, boolean doImageName) Populates the 'pixels' element of the given metadata store, using core metadata from the given reader.
static void	populatePixelsOnly(MetadataStore store, IFormatReader r)
static void	populatePixelsOnly(MetadataStore store, int series, boolean littleEndian, String dimensionOrder, String pixelType, int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT, int samplesPerPixel)
static void	setDefaultCreationDate(MetadataStore store, String id, int series) Sets a default creation date.
static void	setDefaultDateEnabled(boolean enabled) Disables the setting of a default creation date.
static boolean	validateOMEXML(String xml) Deprecated. This method is not thread-safe; use OMEXMLService.validateOMEXML(String) instead.
static boolean	validateOMEXML(String xml, boolean pixelsHack) Deprecated. This method is not thread-safe; use OMEXMLService.validateOMEXML(String, boolean) instead.
static void	verifyMinimumPopulated(MetadataRetrieve src) Checks whether the given metadata object has the minimum metadata populated to successfully describe an Image.
static void	verifyMinimumPopulated(MetadataRetrieve src, int n) Checks whether the given metadata object has the minimum metadata populated to successfully describe the nth Image.

Methods inherited from class java.lang.Object

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

Method Detail

populatePixels

public static void populatePixels(MetadataStore store,
                  IFormatReader r)

Populates the 'pixels' element of the given metadata store, using core metadata from the given reader.

populatePixels

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

Populates the 'pixels' element of the given metadata store, using core metadata from the given reader. If the 'doPlane' flag is set, then the 'plane' elements will be populated as well.

populatePixels

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

Populates the 'pixels' element of the given metadata store, using core metadata from the given reader. If the 'doPlane' flag is set, then the 'plane' elements will be populated as well. If the 'doImageName' flag is set, then the image name will be populated as well. By default, 'doImageName' is true.

populateMetadata

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

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

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

populateMetadata

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

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

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

populateMetadata

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

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

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

populatePixelsOnly

public static void populatePixelsOnly(MetadataStore store,
                      IFormatReader r)

populatePixelsOnly

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

createLSID

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

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

verifyMinimumPopulated

public static void verifyMinimumPopulated(MetadataRetrieve src)
                                   throws FormatException

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

Throws:

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

verifyMinimumPopulated

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

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

Throws:

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

setDefaultDateEnabled

public static void setDefaultDateEnabled(boolean enabled)

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

Parameters:

enabled - See above.

See Also:

setDefaultCreationDate(MetadataStore, String, int)

setDefaultCreationDate

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

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

See Also:

setDefaultDateEnabled(boolean)

makeSaneDimensionOrder

public static String makeSaneDimensionOrder(String dimensionOrder)

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

keys

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

Gets a sorted list of keys from the given hashtable.

merge

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

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

asRetrieve

public static MetadataRetrieve asRetrieve(MetadataStore meta)

Deprecated. This method is not thread-safe; use OMEXMLService.asRetrieve(MetadataStore) instead.

getLatestVersion

public static String getLatestVersion()

Deprecated. This method is not thread-safe; use OMEXMLService.getLatestVersion() instead.

createOMEXMLMetadata

public static IMetadata createOMEXMLMetadata()

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

Returns:

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

createOMEXMLMetadata

public static IMetadata createOMEXMLMetadata(String xml)

Deprecated. This method is not thread-safe; use OMEXMLService.createOMEXMLMetadata(String) instead.

createOMEXMLMetadata

public static IMetadata createOMEXMLMetadata(String xml,
                             String version)

Deprecated. This method is not thread-safe; use OMEXMLService.createOMEXMLMetadata(String, String) instead.

createOMEXMLRoot

public static Object createOMEXMLRoot(String xml)

Deprecated. This method is not thread-safe; use OMEXMLService.createOMEXMLRoot(String) instead.

isOMEXMLMetadata

public static boolean isOMEXMLMetadata(Object o)

Deprecated. This method is not thread-safe; use OMEXMLService.isOMEXMLMetadata(Object) instead.

isOMEXMLRoot

public static boolean isOMEXMLRoot(Object o)

Deprecated. This method is not thread-safe; use OMEXMLService.isOMEXMLRoot(Object) instead.

getOMEXMLVersion

public static String getOMEXMLVersion(Object o)

Deprecated. This method is not thread-safe; use OMEXMLService.getOMEXMLVersion(Object) instead.

getOMEMetadata

public static IMetadata getOMEMetadata(MetadataRetrieve src)

Deprecated. This method is not thread-safe; use OMEXMLService.getOMEMetadata(MetadataRetrieve) instead.

getOMEXML

public static String getOMEXML(MetadataRetrieve src)

Deprecated. This method is not thread-safe; use OMEXMLService.getOMEXML(MetadataRetrieve) instead.

validateOMEXML

public static boolean validateOMEXML(String xml)

Deprecated. This method is not thread-safe; use OMEXMLService.validateOMEXML(String) instead.

validateOMEXML

public static boolean validateOMEXML(String xml,
                     boolean pixelsHack)

Deprecated. This method is not thread-safe; use OMEXMLService.validateOMEXML(String, boolean) instead.