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.

Field Summary

Fields

Modifier and Type	Field and Description
private static boolean	defaultDateEnabled
private static org.slf4j.Logger	LOGGER

Constructor Summary

Constructors

Modifier	Constructor and Description
private	MetadataTools()

Method Summary

Methods

Modifier and Type	Method and Description
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 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 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

Field Detail

LOGGER

private static final org.slf4j.Logger LOGGER

defaultDateEnabled

private static boolean defaultDateEnabled

Constructor Detail

MetadataTools

private MetadataTools()

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. Delegate to populatePixels(MetadataStore, IFormatReader, boolean, boolean) with doPlane set to false and doImageName set to true.

Parameters:

store - The metadata store whose Pixels should be populated

r - The format reader whose core metadata should be used

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. Delegates to populatePixels(MetadataStore, IFormatReader, boolean, boolean) with doImageName set to true.

Parameters:

store - The metadata store whose Pixels should be populated

r - The format reader whose core metadata should be used

doPlane - Specifies whether Plane elements should be populated

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.

Parameters:

store - The metadata store whose Pixels should be populated

r - The format reader whose core metadata should be used

doPlane - Specifies whether Plane elements should be populated

doImageName - Specifies whether the Image name should be populated

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.

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.