Method Detail

• chooseFile

  public static File chooseFile()

  Prompts the user to choose a file.

• initializeReader

  public static IFormatReader initializeReader(File file)
                                        throws FormatException,
                                               IOException

  Throws:

  FormatException

  IOException

• getFirstCalibration

  public static ij.measure.Calibration getFirstCalibration(IMetadata meta)

  Creates a Calibration object using the first valid physical sizes X, Y and Z across all series in the provided Metadata. These values can be used to standardize the height and width of coordinates when combining multiple series (e.g. for coordinates generatead by readCoords(IMetadata)).

• readCoords

  public static List<Pt> readCoords(IMetadata meta)

  Generates a list of coordinates from all series described by the provided IMetadata object. Each coordinate consists of a stage position and physical extents. Stage positions are in uncalibrated units, while dimension lengths are standardized to the first valid calibration values found in the provided IMetadata (as calibration can differ between series). For a compatible Calibration object, use getFirstCalibration(IMetadata).

• sizeX

  public static Integer sizeX(IMetadata meta,
                              int i)

• sizeY

  public static Integer sizeY(IMetadata meta,
                              int i)

• sizeZ

  public static Integer sizeZ(IMetadata meta,
                              int i)

• posX

  public static Double posX(IMetadata meta,
                            int i,
                            int p)

• posY

  public static Double posY(IMetadata meta,
                            int i,
                            int p)

• posZ

  public static Double posZ(IMetadata meta,
                            int i,
                            int p)

• physicalSizeX

  public static Double physicalSizeX(IMetadata meta,
                                     int i)

• physicalSizeY

  public static Double physicalSizeY(IMetadata meta,
                                     int i)

• physicalSizeZ

  public static Double physicalSizeZ(IMetadata meta,
                                     int i)

• physicalSizeX

  public static double physicalSizeX(IMetadata meta,
                                     int i,
                                     double defaultValue)

• physicalSizeY

  public static double physicalSizeY(IMetadata meta,
                                     int i,
                                     double defaultValue)

• physicalSizeZ

  public static double physicalSizeZ(IMetadata meta,
                                     int i,
                                     double defaultValue)

• stageLabelX

  public static Double stageLabelX(IMetadata meta,
                                   int i)

• stageLabelY

  public static Double stageLabelY(IMetadata meta,
                                   int i)

• stageLabelZ

  public static Double stageLabelZ(IMetadata meta,
                                   int i)

• rawValue

  public static Double rawValue(ome.units.quantity.Length l)

• rawValue

  public static double rawValue(ome.units.quantity.Length l,
                                double defaultValue)

• micronValue

  public static Double micronValue(ome.units.quantity.Length l)

• micronValue

  public static double micronValue(ome.units.quantity.Length l,
                                   double defaultValue)

• value

  public static double value(Double d,
                             double defaultValue)

• value

  public static Integer value(ome.xml.model.primitives.PositiveInteger pi)