DefaultOMEMetadataService (SCIFIO Javadocs 0-SNAPSHOT API)

java.lang.Object
- org.scijava.AbstractContextual
- - org.scijava.plugin.AbstractRichPlugin
  - - org.scijava.service.AbstractService
    - - io.scif.ome.services.DefaultOMEMetadataService

All Implemented Interfaces:

OMEMetadataService, SCIFIOService, Comparable<Prioritized>, Contextual, Disposable, Identifiable, Initializable, Locatable, Logged, HasPluginInfo, RichPlugin, SciJavaPlugin, Prioritized, Service, Versioned
```
public class DefaultOMEMetadataService
extends AbstractService
implements OMEMetadataService
```
Default implementation of OMEMetadataService.

Constructor Summary

Constructors
Constructor and Description

DefaultOMEMetadataService()

Constructors
Constructor and Description
`DefaultOMEMetadataService()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`String`	`createLSID(String type, int... indices)` Constructs an LSID, given the object type and indices.
`AxisType[]`	`findDimensionList(String dimensionOrder)` Converts the given String to a list of AxisTypes suitable for Metadata construction.
`String`	`findDimensionOrder(ImageMetadata imageMeta)` Extracts a standard 5-D dimension order from an N-dimensional ImageMetadata object.
`String`	`findDimensionOrder(Metadata meta, int imageIndex)` Extracts a standard 5-D dimension order from an N-dimensional ImageMetadata object.
`ome.xml.model.enums.Binning`	`getBinning(String value)` Retrieves an `Binning` enumeration value for the given String.
`ome.xml.model.enums.Correction`	`getCorrection(String value)` Retrieves an `Correction` enumeration value for the given String.
`ome.xml.model.enums.DetectorType`	`getDetectorType(String value)` Retrieves an `DetectorType` enumeration value for the given String.
`ome.xml.model.enums.ExperimentType`	`getExperimentType(String value)` Retrieves an `ExperimentType` enumeration value for the given String.
`ome.xml.model.enums.Immersion`	`getImmersion(String value)` Retrieves an `Immersion` enumeration value for the given String.
`ome.xml.model.enums.LaserMedium`	`getLaserMedium(String value)` Retrieves an `LaserMedium` enumeration value for the given String.
`ome.xml.model.enums.LaserType`	`getLaserType(String value)` Retrieves an `LaserType` enumeration value for the given String.
`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'.
`void`	`populateImageMetadata(MetadataRetrieve retrieve, int imageIndex, ImageMetadata iMeta)` Populates the provided ImageMetadata object using the specified image index into the MetadataRetrieve.
`void`	`populateMetadata(MetadataRetrieve retrieve, Metadata meta)` Uses the provided MetadataRetrieve to populate the format-agnostic image information in the provided Metadata object (that is, the ImageMetadata).
`void`	`populateMetadata(MetadataStore store, int imageIndex, String imageName, boolean littleEndian, String dimensionOrder, String pixelType, int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT, double calX, double calY, double calZ, double calC, double calT, int samplesPerPixel)` Populates the given `MetadataStore`, for the specified imageIndex, using the provided values.
`void`	`populateMetadata(MetadataStore store, int imageIndex, String imageName, ImageMetadata iMeta)` Populates the given `MetadataStore`, for the specified imageIndex, using the values from the provided `ImageMetadata`.
`void`	`populateMetadata(MetadataStore store, int imageIndex, String imageName, Metadata meta)` Populates the given `MetadataStore`, for the specified imageIndex, using the values from the provided `Metadata`.
`void`	`populateMetadata(MetadataStore store, String file, int imageIndex, String imageName, boolean littleEndian, String dimensionOrder, String pixelType, int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT, double calX, double calY, double calZ, double calC, double calT, int samplesPerPixel)` Populates the given `MetadataStore`, for the specified imageIndex, using the provided values.
`void`	`populatePixels(MetadataStore store, List<ImageMetadata> imageMeta, boolean doPlane, String imageName)` Populates the 'pixels' element of the given metadata store, using the provided `ImageMetadata`.
`void`	`populatePixels(MetadataStore store, Metadata meta)` Populates the 'pixels' element of the given metadata store, using core metadata from the given reader.
`void`	`populatePixels(MetadataStore store, Metadata meta, boolean doPlane)` Populates the 'pixels' element of the given metadata store, using core metadata from the given reader.
`void`	`populatePixels(MetadataStore store, Metadata meta, boolean doPlane, boolean doImageName)` Populates the 'pixels' element of the given metadata store, using core metadata from the given metadata.
`void`	`populatePixelsOnly(MetadataStore store, int imageIndex, boolean littleEndian, String dimensionOrder, String pixelType, int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT, double calX, double calY, double calZ, double calC, double calT, int samplesPerPixel)`
`void`	`populatePixelsOnly(MetadataStore store, Reader r)`
`void`	`setDefaultCreationDate(MetadataStore store, String id, int imageIndex)` Sets a default creation date.
`void`	`setDefaultDateEnabled(boolean enabled)` Disables the setting of a default creation date.
`void`	`verifyMinimumPopulated(MetadataRetrieve src)`
`void`	`verifyMinimumPopulated(MetadataRetrieve src, int n)`
`long[]`	`zctToArray(String order, int z, int c, int t)` Given a String dimension order, places the given z, c and t indices in the correct relative positions in a long array, which is returned.

Methods inherited from class org.scijava.service.AbstractService
getContext, setContext, toString

Methods inherited from class org.scijava.plugin.AbstractRichPlugin
getInfo, getPriority, setInfo, setPriority

Methods inherited from class org.scijava.AbstractContextual
context

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.scijava.service.Service
initialize, registerEventHandlers

Methods inherited from interface org.scijava.plugin.RichPlugin
getIdentifier, log

Methods inherited from interface org.scijava.Contextual
context, getContext, setContext

Methods inherited from interface org.scijava.Prioritized
compareTo, getPriority, setPriority

Methods inherited from interface org.scijava.plugin.HasPluginInfo
getInfo, setInfo

Methods inherited from interface org.scijava.Locatable
getLocation

Methods inherited from interface org.scijava.Versioned
getVersion

Methods inherited from interface org.scijava.Disposable
dispose

- Constructor Detail
  - DefaultOMEMetadataService
```
public DefaultOMEMetadataService()
```
- Method Detail
  - populatePixels
```
public void populatePixels(MetadataStore store,
                           Metadata meta)
```
    Description copied from interface: OMEMetadataService
    
    Populates the 'pixels' element of the given metadata store, using core metadata from the given reader.
    
    Specified by:
    
    populatePixels in interface OMEMetadataService
  - populatePixels
```
public void populatePixels(MetadataStore store,
                           Metadata meta,
                           boolean doPlane)
```
    Description copied from interface: OMEMetadataService
    
    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.
    
    Specified by:
    
    populatePixels in interface OMEMetadataService
  - populatePixels
```
public void populatePixels(MetadataStore store,
                           Metadata meta,
                           boolean doPlane,
                           boolean doImageName)
```
    Description copied from interface: OMEMetadataService
    
    Populates the 'pixels' element of the given metadata store, using core metadata from the given metadata. 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.
    
    Specified by:
    
    populatePixels in interface OMEMetadataService
  - populatePixels
```
public void populatePixels(MetadataStore store,
                           List<ImageMetadata> imageMeta,
                           boolean doPlane,
                           String imageName)
```
    Description copied from interface: OMEMetadataService
    
    Populates the 'pixels' element of the given metadata store, using the provided ImageMetadata. If the 'doPlane' flag is set, then the 'plane' elements will be populated as well. If the 'imageName' field is non-null, then the image name will be populated as well.
    
    Specified by:
    
    populatePixels in interface OMEMetadataService
  - populateMetadata
```
public void populateMetadata(MetadataStore store,
                             int imageIndex,
                             String imageName,
                             boolean littleEndian,
                             String dimensionOrder,
                             String pixelType,
                             int sizeX,
                             int sizeY,
                             int sizeZ,
                             int sizeC,
                             int sizeT,
                             double calX,
                             double calY,
                             double calZ,
                             double calC,
                             double calT,
                             int samplesPerPixel)
```
    Description copied from interface: OMEMetadataService
    
    Populates the given MetadataStore, for the specified imageIndex, 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).
    
    Specified by:
    
    populateMetadata in interface OMEMetadataService
  - populateMetadata
```
public void populateMetadata(MetadataStore store,
                             int imageIndex,
                             String imageName,
                             Metadata meta)
```
    Description copied from interface: OMEMetadataService
    
    Populates the given MetadataStore, for the specified imageIndex, using the values from the provided Metadata.
    After calling this method, the metadata store will be sufficiently populated for use with an IFormatWriter (assuming it is also a MetadataRetrieve).
    
    Specified by:
    
    populateMetadata in interface OMEMetadataService
  - populateMetadata
```
public void populateMetadata(MetadataStore store,
                             int imageIndex,
                             String imageName,
                             ImageMetadata iMeta)
```
    Description copied from interface: OMEMetadataService
    
    Populates the given MetadataStore, for the specified imageIndex, using the values from the provided ImageMetadata.
    After calling this method, the metadata store will be sufficiently populated for use with an IFormatWriter (assuming it is also a MetadataRetrieve).
    
    Specified by:
    
    populateMetadata in interface OMEMetadataService
  - populateMetadata
```
public void populateMetadata(MetadataStore store,
                             String file,
                             int imageIndex,
                             String imageName,
                             boolean littleEndian,
                             String dimensionOrder,
                             String pixelType,
                             int sizeX,
                             int sizeY,
                             int sizeZ,
                             int sizeC,
                             int sizeT,
                             double calX,
                             double calY,
                             double calZ,
                             double calC,
                             double calT,
                             int samplesPerPixel)
```
    Description copied from interface: OMEMetadataService
    
    Populates the given MetadataStore, for the specified imageIndex, 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).
    
    Specified by:
    
    populateMetadata in interface OMEMetadataService
  - populatePixelsOnly
```
public void populatePixelsOnly(MetadataStore store,
                               Reader r)
```
    Specified by:
    
    populatePixelsOnly in interface OMEMetadataService
  - populatePixelsOnly
```
public void populatePixelsOnly(MetadataStore store,
                               int imageIndex,
                               boolean littleEndian,
                               String dimensionOrder,
                               String pixelType,
                               int sizeX,
                               int sizeY,
                               int sizeZ,
                               int sizeC,
                               int sizeT,
                               double calX,
                               double calY,
                               double calZ,
                               double calC,
                               double calT,
                               int samplesPerPixel)
```
    Specified by:
    
    populatePixelsOnly in interface OMEMetadataService
  - setDefaultDateEnabled
```
public void setDefaultDateEnabled(boolean enabled)
```
    Description copied from interface: OMEMetadataService
    
    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.
    
    Specified by:
    
    setDefaultDateEnabled in interface OMEMetadataService
    
    Parameters:
    
    enabled - See above.
    
    See Also:
    
    OMEMetadataService.setDefaultCreationDate(MetadataStore, String, int)
  - setDefaultCreationDate
```
public void setDefaultCreationDate(MetadataStore store,
                                   String id,
                                   int imageIndex)
```
    Description copied from interface: OMEMetadataService
    
    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.
    
    Specified by:
    
    setDefaultCreationDate in interface OMEMetadataService
    
    See Also:
    
    OMEMetadataService.setDefaultDateEnabled(boolean)
  - verifyMinimumPopulated
```
public void verifyMinimumPopulated(MetadataRetrieve src)
                            throws FormatException
```
    Specified by:
    
    verifyMinimumPopulated in interface OMEMetadataService
    
    Throws:
    
    FormatException - if there is a missing metadata field, or the metadata object is uninitialized
  - verifyMinimumPopulated
```
public void verifyMinimumPopulated(MetadataRetrieve src,
                                   int n)
                            throws FormatException
```
    Specified by:
    
    verifyMinimumPopulated in interface OMEMetadataService
    
    Throws:
    
    FormatException - if there is a missing metadata field, or the metadata object is uninitialized
  - findDimensionOrder
```
public String findDimensionOrder(Metadata meta,
                                 int imageIndex)
```
    Description copied from interface: OMEMetadataService
    
    Extracts a standard 5-D dimension order from an N-dimensional ImageMetadata object.
    
    Specified by:
    
    findDimensionOrder in interface OMEMetadataService
  - findDimensionOrder
```
public String findDimensionOrder(ImageMetadata imageMeta)
```
    Description copied from interface: OMEMetadataService
    
    Extracts a standard 5-D dimension order from an N-dimensional ImageMetadata object.
    
    Specified by:
    
    findDimensionOrder in interface OMEMetadataService
  - findDimensionList
```
public AxisType[] findDimensionList(String dimensionOrder)
```
    Description copied from interface: OMEMetadataService
    
    Converts the given String to a list of AxisTypes suitable for Metadata construction.
    
    Specified by:
    
    findDimensionList in interface OMEMetadataService
  - zctToArray
```
public long[] zctToArray(String order,
                         int z,
                         int c,
                         int t)
```
    Description copied from interface: OMEMetadataService
    
    Given a String dimension order, places the given z, c and t indices in the correct relative positions in a long array, which is returned.
    
    Specified by:
    
    zctToArray in interface OMEMetadataService
  - makeSaneDimensionOrder
```
public String makeSaneDimensionOrder(String dimensionOrder)
```
    Description copied from interface: OMEMetadataService
    
    Adjusts the given dimension order as needed so that it contains exactly one of each of the following characters: 'X', 'Y', 'Z', 'C', 'T'.
    
    Specified by:
    
    makeSaneDimensionOrder in interface OMEMetadataService
  - createLSID
```
public String createLSID(String type,
                         int... indices)
```
    Description copied from interface: OMEMetadataService
    
    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".
    
    Specified by:
    
    createLSID in interface OMEMetadataService
  - getExperimentType
```
public ome.xml.model.enums.ExperimentType getExperimentType(String value)
                                                     throws FormatException
```
    Description copied from interface: OMEMetadataService
    
    Retrieves an ExperimentType enumeration value for the given String.
    
    Specified by:
    
    getExperimentType in interface OMEMetadataService
    
    Throws:
    
    FormatException - if an appropriate enumeration value is not found.
  - getLaserType
```
public ome.xml.model.enums.LaserType getLaserType(String value)
                                           throws FormatException
```
    Description copied from interface: OMEMetadataService
    
    Retrieves an LaserType enumeration value for the given String.
    
    Specified by:
    
    getLaserType in interface OMEMetadataService
    
    Throws:
    
    FormatException - if an appropriate enumeration value is not found.
  - getLaserMedium
```
public ome.xml.model.enums.LaserMedium getLaserMedium(String value)
                                               throws FormatException
```
    Description copied from interface: OMEMetadataService
    
    Retrieves an LaserMedium enumeration value for the given String.
    
    Specified by:
    
    getLaserMedium in interface OMEMetadataService
    
    Throws:
    
    FormatException - if an appropriate enumeration value is not found.
  - getImmersion
```
public ome.xml.model.enums.Immersion getImmersion(String value)
                                           throws FormatException
```
    Description copied from interface: OMEMetadataService
    
    Retrieves an Immersion enumeration value for the given String.
    
    Specified by:
    
    getImmersion in interface OMEMetadataService
    
    Throws:
    
    FormatException - if an appropriate enumeration value is not found.
  - getCorrection
```
public ome.xml.model.enums.Correction getCorrection(String value)
                                             throws FormatException
```
    Description copied from interface: OMEMetadataService
    
    Retrieves an Correction enumeration value for the given String.
    
    Specified by:
    
    getCorrection in interface OMEMetadataService
    
    Throws:
    
    FormatException - if an appropriate enumeration value is not found.
  - getDetectorType
```
public ome.xml.model.enums.DetectorType getDetectorType(String value)
                                                 throws FormatException
```
    Description copied from interface: OMEMetadataService
    
    Retrieves an DetectorType enumeration value for the given String.
    
    Specified by:
    
    getDetectorType in interface OMEMetadataService
    
    Throws:
    
    FormatException - if an appropriate enumeration value is not found.
  - getBinning
```
public ome.xml.model.enums.Binning getBinning(String value)
                                       throws FormatException
```
    Description copied from interface: OMEMetadataService
    
    Retrieves an Binning enumeration value for the given String.
    
    Specified by:
    
    getBinning in interface OMEMetadataService
    
    Throws:
    
    FormatException - if an appropriate enumeration value is not found.
  - populateMetadata
```
public void populateMetadata(MetadataRetrieve retrieve,
                             Metadata meta)
```
    Description copied from interface: OMEMetadataService
    
    Uses the provided MetadataRetrieve to populate the format-agnostic image information in the provided Metadata object (that is, the ImageMetadata).
    
    Specified by:
    
    populateMetadata in interface OMEMetadataService
  - populateImageMetadata
```
public void populateImageMetadata(MetadataRetrieve retrieve,
                                  int imageIndex,
                                  ImageMetadata iMeta)
```
    Description copied from interface: OMEMetadataService
    
    Populates the provided ImageMetadata object using the specified image index into the MetadataRetrieve.
    
    Specified by:
    
    populateImageMetadata in interface OMEMetadataService

Class DefaultOMEMetadataService

Constructor Summary

Method Summary

Methods inherited from class org.scijava.service.AbstractService

Methods inherited from class org.scijava.plugin.AbstractRichPlugin

Methods inherited from class org.scijava.AbstractContextual

Methods inherited from class java.lang.Object

Methods inherited from interface org.scijava.service.Service

Methods inherited from interface org.scijava.plugin.RichPlugin

Methods inherited from interface org.scijava.Contextual

Methods inherited from interface org.scijava.Prioritized

Methods inherited from interface org.scijava.plugin.HasPluginInfo

Methods inherited from interface org.scijava.Locatable

Methods inherited from interface org.scijava.Versioned

Methods inherited from interface org.scijava.Disposable

Constructor Detail

DefaultOMEMetadataService

Method Detail

populatePixels

populatePixels

populatePixels

populatePixels

populateMetadata

populateMetadata

populateMetadata

populateMetadata

populatePixelsOnly

populatePixelsOnly

setDefaultDateEnabled

setDefaultCreationDate

verifyMinimumPopulated

verifyMinimumPopulated

findDimensionOrder

findDimensionOrder

findDimensionList

zctToArray

makeSaneDimensionOrder

createLSID

getExperimentType

getLaserType

getLaserMedium

getImmersion

getCorrection

getDetectorType

getBinning

populateMetadata

populateImageMetadata