Method Detail

• populatePixels

  void populatePixels(MetadataStore store,
                      Metadata meta)

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

• populatePixels

  void populatePixels(MetadataStore store,
                      Metadata meta,
                      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

  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. 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.

• populatePixels

  void populatePixels(MetadataStore store,
                      List<ImageMetadata> imageMeta,
                      boolean doPlane,
                      String imageName)

  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.

• populateMetadata

  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 claY,
                        double calZ,
                        double calC,
                        double calT,
                        int samplesPerPixel)

  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).

• populateMetadata

  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.

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

• populateMetadata

  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.

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

• populateMetadata

  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 claY,
                        double calZ,
                        double calC,
                        double calT,
                        int samplesPerPixel)

  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).

• populatePixelsOnly

  void populatePixelsOnly(MetadataStore store,
                          Reader r)

• populatePixelsOnly

  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 claY,
                          double calZ,
                          double calC,
                          double calT,
                          int samplesPerPixel)

• setDefaultDateEnabled

  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

  void setDefaultCreationDate(MetadataStore store,
                              String id,
                              int imageIndex)

  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)

• verifyMinimumPopulated

  void verifyMinimumPopulated(MetadataRetrieve src)
                       throws FormatException

  Throws:

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

• verifyMinimumPopulated

  void verifyMinimumPopulated(MetadataRetrieve src,
                              int n)
                       throws FormatException

  Throws:

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

• findDimensionOrder

  String findDimensionOrder(Metadata meta,
                            int imageIndex)

  Extracts a standard 5-D dimension order from an N-dimensional ImageMetadata object.

• findDimensionOrder

  String findDimensionOrder(ImageMetadata imageMeta)

  Extracts a standard 5-D dimension order from an N-dimensional ImageMetadata object.

• findDimensionList

  AxisType[] findDimensionList(String dimensionOrder)

  Converts the given String to a list of AxisTypes suitable for Metadata construction.

• zctToArray

  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.

• makeSaneDimensionOrder

  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'.

• createLSID

  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".

• getExperimentType

  ome.xml.model.enums.ExperimentType getExperimentType(String value)
                                                throws FormatException

  Retrieves an ExperimentType enumeration value for the given String.

  Throws:

  FormatException - if an appropriate enumeration value is not found.

• getLaserType

  ome.xml.model.enums.LaserType getLaserType(String value)
                                      throws FormatException

  Retrieves an LaserType enumeration value for the given String.

  Throws:

  FormatException - if an appropriate enumeration value is not found.

• getLaserMedium

  ome.xml.model.enums.LaserMedium getLaserMedium(String value)
                                          throws FormatException

  Retrieves an LaserMedium enumeration value for the given String.

  Throws:

  FormatException - if an appropriate enumeration value is not found.

• getImmersion

  ome.xml.model.enums.Immersion getImmersion(String value)
                                      throws FormatException

  Retrieves an Immersion enumeration value for the given String.

  Throws:

  FormatException - if an appropriate enumeration value is not found.

• getCorrection

  ome.xml.model.enums.Correction getCorrection(String value)
                                        throws FormatException

  Retrieves an Correction enumeration value for the given String.

  Throws:

  FormatException - if an appropriate enumeration value is not found.

• getDetectorType

  ome.xml.model.enums.DetectorType getDetectorType(String value)
                                            throws FormatException

  Retrieves an DetectorType enumeration value for the given String.

  Throws:

  FormatException - if an appropriate enumeration value is not found.

• getBinning

  ome.xml.model.enums.Binning getBinning(String value)
                                  throws FormatException

  Retrieves an Binning enumeration value for the given String.

  Throws:

  FormatException - if an appropriate enumeration value is not found.

• populateMetadata

  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).

• populateImageMetadata

  void populateImageMetadata(MetadataRetrieve retrieve,
                             int imageIndex,
                             ImageMetadata iMeta)

  Populates the provided ImageMetadata object using the specified image index into the MetadataRetrieve.