Constructor Detail

• SpimData2

  public SpimData2(File basePath,
                   SequenceDescription sequenceDescription,
                   ViewRegistrations viewRegistrations,
                   ViewInterestPoints viewsInterestPoints,
                   BoundingBoxes boundingBoxes)

• SpimData2

  protected SpimData2()

Method Detail

• getViewInterestPoints

  public ViewInterestPoints getViewInterestPoints()

• getBoundingBoxes

  public BoundingBoxes getBoundingBoxes()

• setViewsInterestPoints

  protected void setViewsInterestPoints(ViewInterestPoints viewsInterestPoints)

• setBoundingBoxes

  protected void setBoundingBoxes(BoundingBoxes boundingBoxes)

• getViewId

  public static ViewId getViewId(SequenceDescription seqDesc,
                                 TimePoint t,
                                 Channel c,
                                 Angle a,
                                 Illumination i)

  Parameters:

  seqDesc -

  t -

  c -

  a -

  i -

  Returns:

  - the ViewId that fits to timepoint, angle, channel & illumination by ID (or null if it does not exist)

• getViewSetup

  public static ViewSetup getViewSetup(List<? extends ViewSetup> list,
                                       Channel c,
                                       Angle a,
                                       Illumination i)

• getAllViewSetupsSorted

  public static ArrayList<ViewSetup> getAllViewSetupsSorted(SpimData data,
                                                            List<? extends ViewId> viewIds)

• getAllViewIdsSorted

  public static ArrayList<ViewId> getAllViewIdsSorted(SpimData data,
                                                      List<? extends ViewSetup> setups,
                                                      List<? extends TimePoint> tps)

• getAllAnglesForChannelTimepointSorted

  public static ArrayList<Angle> getAllAnglesForChannelTimepointSorted(SpimData data,
                                                                       Collection<? extends ViewId> viewIds,
                                                                       Channel c,
                                                                       TimePoint t)

• getAllAnglesSorted

  public static ArrayList<Angle> getAllAnglesSorted(SpimData data,
                                                    Collection<? extends ViewId> viewIds)

• getAllIlluminationsForChannelTimepointSorted

  public static ArrayList<Illumination> getAllIlluminationsForChannelTimepointSorted(SpimData data,
                                                                                     Collection<? extends ViewId> viewIds,
                                                                                     Channel c,
                                                                                     TimePoint t)

• getAllIlluminationsSorted

  public static ArrayList<Illumination> getAllIlluminationsSorted(SpimData data,
                                                                  Collection<? extends ViewId> viewIds)

• getAllChannelsSorted

  public static ArrayList<Channel> getAllChannelsSorted(SpimData data,
                                                        Collection<? extends ViewId> viewIds)

• getAllViewIdsForChannelSorted

  public static ArrayList<ViewDescription> getAllViewIdsForChannelSorted(SpimData data,
                                                                         Collection<? extends ViewId> viewIds,
                                                                         Channel channel)

• getAllViewIdsForChannelTimePointSorted

  public static ArrayList<ViewDescription> getAllViewIdsForChannelTimePointSorted(SpimData data,
                                                                                  Collection<? extends ViewId> viewIds,
                                                                                  Channel channel,
                                                                                  TimePoint timePoint)

• getAllViewIdsForTimePointSorted

  public static ArrayList<ViewDescription> getAllViewIdsForTimePointSorted(SpimData data,
                                                                           Collection<? extends ViewId> viewIds,
                                                                           TimePoint timepoint)

• getAllViewSetups

  public static ArrayList<ViewSetup> getAllViewSetups(Collection<? extends ViewDescription> vds)

• getAllTimePointsSorted

  public static ArrayList<TimePoint> getAllTimePointsSorted(SpimData data,
                                                            Collection<? extends ViewId> viewIds)

• getAllTimePointsSorted

  public static ArrayList<TimePoint> getAllTimePointsSorted(Collection<? extends ViewDescription> vds)

• saveXML

  public static String saveXML(SpimData2 data,
                               String xmlFileName,
                               String clusterExtension)