Constructor Detail

• ExportSpimData2HDF5

  public ExportSpimData2HDF5()

Method Detail

• finish

  public boolean finish()

  Description copied from interface: ImgExport
  Called last when the fusion is finished (e.g. to write the XML)

  Specified by:

  finish in interface ImgExport

  Returns:

  - true if the spimdata was modified, otherwise false

• setXMLData

  public void setXMLData(List<TimePoint> newTimepoints,
                         List<ViewSetup> newViewSetups)

  Specified by:

  setXMLData in interface ImgExport

• queryParameters

  public boolean queryParameters(SpimData2 spimData,
                                 boolean is16bit)

  Description copied from interface: ImgExport
  Query the necessary parameters for the fusion (new dialog has to be made)

  Specified by:

  queryParameters in interface ImgExport

  Returns:

• initSpimData

  protected static Pair<SpimData2,HashMap<ViewId,Partition>> initSpimData(List<TimePoint> newTimepoints,
                                                                          List<ViewSetup> newViewSetups,
                                                                          Generic_Resave_HDF5.Parameters params,
                                                                          Map<Integer,ExportMipmapInfo> perSetupExportMipmapInfo)

• exportImage

  public <T extends RealType<T> & NativeType<T>> boolean exportImage(RandomAccessibleInterval<T> img,
                                                                     BoundingBoxGUI bb,
                                                                     TimePoint tp,
                                                                     ViewSetup vs)

  Description copied from interface: ImgExport
  Exports the image (min and max intensity will be computed)

  Specified by:

  exportImage in interface ImgExport

  Parameters:

  img - - Note, in rare cases this can be null (i.e. do nothing)

  bb - - the bounding box used to fuse this image

  tp - - the current (new) timepoint

  vs - - the current (new) viewsetup

• updateAndGetMinMax

  public static <T extends RealType<T>> double[] updateAndGetMinMax(RandomAccessibleInterval<T> img,
                                                                    Generic_Resave_HDF5.Parameters params)

• convert

  public static <T extends RealType<T>> RandomAccessibleInterval<UnsignedShortType> convert(RandomAccessibleInterval<T> img,
                                                                                            Generic_Resave_HDF5.Parameters params)

• exportImage

  public <T extends RealType<T> & NativeType<T>> boolean exportImage(RandomAccessibleInterval<T> img,
                                                                     BoundingBoxGUI bb,
                                                                     TimePoint tp,
                                                                     ViewSetup vs,
                                                                     double min,
                                                                     double max)

  Description copied from interface: ImgExport
  Exports the image using a predefined min/max

  Specified by:

  exportImage in interface ImgExport

  Parameters:

  img - - Note, in rare cases this can be null (i.e. do nothing)

  bb - - the bounding box used to fuse this image

  tp - - the current (new) timepoint

  vs - - the current (new) viewsetup

  min - - define min intensity of this image

  max - - define max intensity of this image

• queryAdditionalParameters

  public void queryAdditionalParameters(GenericDialog gd,
                                        SpimData2 spimData)

  Description copied from interface: ImgExport
  Query additional parameters within the bounding box dialog

  Specified by:

  queryAdditionalParameters in interface ImgExport

• parseAdditionalParameters

  public boolean parseAdditionalParameters(GenericDialog gd,
                                           SpimData2 spimData)

  Description copied from interface: ImgExport
  Parse the additional parameters added before within the bounding box dialog

  Specified by:

  parseAdditionalParameters in interface ImgExport

  Returns:

• newInstance

  public ImgExport newInstance()

  Specified by:

  newInstance in interface ImgExport

• getDescription

  public String getDescription()

  Specified by:

  getDescription in interface ImgExport

  Returns:

  - to be displayed in the generic dialog