public final class MetadataTools extends Object
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.Modifier and Type | Field and Description |
---|---|
private static boolean |
defaultDateEnabled |
private static org.slf4j.Logger |
LOGGER |
Modifier | Constructor and Description |
---|---|
private |
MetadataTools() |
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.
|
private static final org.slf4j.Logger LOGGER
private static boolean defaultDateEnabled
public static void populatePixels(MetadataStore store, IFormatReader r)
populatePixels(MetadataStore, IFormatReader, boolean, boolean)
with doPlane
set to false
and doImageName
set to
true
.store
- The metadata store whose Pixels should be populatedr
- The format reader whose core metadata should be usedpublic static void populatePixels(MetadataStore store, IFormatReader r, boolean doPlane)
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
.store
- The metadata store whose Pixels should be populatedr
- The format reader whose core metadata should be useddoPlane
- Specifies whether Plane elements should be populatedpublic static void populatePixels(MetadataStore store, IFormatReader r, boolean doPlane, boolean doImageName)
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.store
- The metadata store whose Pixels should be populatedr
- The format reader whose core metadata should be useddoPlane
- Specifies whether Plane elements should be populateddoImageName
- Specifies whether the Image name should be populatedpublic static void populateMetadata(MetadataStore store, int series, String imageName, CoreMetadata coreMeta)
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
).
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)
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
).
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)
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
).
public static void populatePixelsOnly(MetadataStore store, IFormatReader r)
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)
public static String createLSID(String type, int... indices)
public static void verifyMinimumPopulated(MetadataRetrieve src) throws FormatException
FormatException
- if there is a missing metadata field,
or the metadata object is uninitializedpublic static void verifyMinimumPopulated(MetadataRetrieve src, int n) throws FormatException
FormatException
- if there is a missing metadata field,
or the metadata object is uninitializedpublic static void setDefaultDateEnabled(boolean enabled)
enabled
- See above.setDefaultCreationDate(MetadataStore, String, int)
public static void setDefaultCreationDate(MetadataStore store, String id, int series)
setDefaultDateEnabled(boolean)
public static String makeSaneDimensionOrder(String dimensionOrder)
public static String[] keys(Hashtable<String,Object> meta)
public static void merge(Map<String,Object> src, Map<String,Object> dest, String prefix)
public static IMetadata createOMEXMLMetadata()
loci.formats.ome
package.AbstractOMEXMLMetadata
,
or null if one cannot be created.Copyright © 2016 Open Microscopy Environment