Constructor Detail

• InterestPointRegistration

  public InterestPointRegistration(SpimData2 spimData,
                                   List<ViewId> viewIdsToProcess,
                                   List<ChannelProcess> channelsToProcess)

  Instantiate the interest point registration. It is performed for a spimdata object on a subset of angles, channels, illuminations and timepoints. Each channel is linked to a certain type of detections (e.g. beads, nuclei), hence the ChannelProcess object.

  Parameters:

  spimData -

  viewIdsToProcess - - which view id's to register

  channelsToProcess - - which Channel uses which label for registration

Method Detail

• addQuery

  public abstract void addQuery(GenericDialog gd,
                                Interest_Point_Registration.RegistrationType registrationType)

  adds the questions this registration wants to ask

  Parameters:

  gd -

  registrationType - - which kind of registration

• parseDialog

  public abstract boolean parseDialog(GenericDialog gd,
                                      Interest_Point_Registration.RegistrationType registrationType)

  queries the questions asked before

  Parameters:

  gd -

  registrationType - - which kind of timeseries registration

  Returns:

• newInstance

  public abstract InterestPointRegistration newInstance(SpimData2 spimData,
                                                        List<ViewId> viewIdsToProcess,
                                                        List<ChannelProcess> channelsToProcess)

  Returns:

  - a new instance without any special properties

• getDescription

  public abstract String getDescription()

  Returns:

  - to be displayed in the generic dialog

• pairwiseMatchingInstance

  protected abstract Callable<PairwiseMatch> pairwiseMatchingInstance(PairwiseMatch pair,
                                                                      String description)

  Parameters:

  pair - - which pair to compare

  description - - a description String which pairs are compared

  Returns:

  - the object that will perform a pairwise matching and can return a result

• getTransformationModel

  protected abstract TransformationModel getTransformationModel()

  Returns:

  - the transformation model to be used for the global optimization, and in most cases also for RANSAC

• runGlobalOpt

  protected final boolean runGlobalOpt(GlobalOptimizationSubset subset,
                                       GlobalOptimizationType registrationType)

  Run the global optimization on the subset

  Parameters:

  subset -

  registrationType -

  Returns:

  - true if the global optimization could be run successfully, otherwise false (XML will not be saved if false)

• getSpimData

  protected SpimData2 getSpimData()

• getViewIdsToProcess

  public List<ViewId> getViewIdsToProcess()

• getChannelsToProcess

  public List<ChannelProcess> getChannelsToProcess()

• getStatistics

  public List<List<PairwiseMatch>> getStatistics()

• register

  public boolean register(GlobalOptimizationType registrationType,
                          boolean save,
                          boolean collectStatistics)

  Registers all timepoints. No matter which matching is done it is always the same principle. First all pairwise correspondences are established, and then a global optimization is computed. The global optimization can is done in subsets, where the number of subsets >= 1.

  Parameters:

  registrationType - - which kind of registration

  save - - if you want to save the correspondence files

  Returns: