Constructor Detail

• SpimRegistrationSequence

  public SpimRegistrationSequence(SPIMConfiguration conf)

  Deprecated. 

• SpimRegistrationSequence

  public SpimRegistrationSequence(String huiskenExperimentXmlFile,
                                  String channels,
                                  String angles,
                                  String timepoints,
                                  int referenceTimePoint)
                           throws ConfigurationParserException

  Deprecated. 

  Throws:

  ConfigurationParserException

• SpimRegistrationSequence

  public SpimRegistrationSequence(String inputDirectory,
                                  String inputFilePattern,
                                  String channels,
                                  String angles,
                                  String timepoints,
                                  int referenceTimePoint,
                                  boolean overrideImageZStretching,
                                  double zStretching)
                           throws ConfigurationParserException

  Deprecated. 

  Throws:

  ConfigurationParserException

Method Detail

• getSequenceDescription

  public SequenceDescriptionMinimal getSequenceDescription()

  Deprecated. 

• getViewRegistrations

  public ViewRegistrations getViewRegistrations()

  Deprecated. 

• createImageLoader

  protected static BasicImgLoader createImageLoader(SPIMConfiguration conf,
                                                    ArrayList<ViewSetup> setups)

  Deprecated. 

• initExperimentConfiguration

  protected static SPIMConfiguration initExperimentConfiguration(String inputDirectory,
                                                                 String inputFilePattern,
                                                                 String angles,
                                                                 String timepoints,
                                                                 int referenceTimePoint,
                                                                 boolean overrideImageZStretching,
                                                                 double zStretching)
                                                          throws ConfigurationParserException

  Deprecated. 
  Instantiate the SPIM configuration only with the necessary parameters

  Returns:

  Throws:

  ConfigurationParserException

• initExperimentConfiguration

  protected static SPIMConfiguration initExperimentConfiguration(String inputDirectory,
                                                                 String inputFilePattern,
                                                                 String channels,
                                                                 String angles,
                                                                 String timepoints,
                                                                 int referenceTimePoint,
                                                                 boolean overrideImageZStretching,
                                                                 double zStretching)
                                                          throws ConfigurationParserException

  Deprecated. 
  Instantiate the SPIM configuration only with the necessary parameters

  Returns:

  Throws:

  ConfigurationParserException

• createViewSetups

  protected static ArrayList<ViewSetup> createViewSetups(SPIMConfiguration conf)

  Deprecated. 

• createTimePoints

  protected static TimePoints createTimePoints(SPIMConfiguration conf)

  Deprecated. 

• getFusionTransforms

  public Map<Integer,AffineTransform3D> getFusionTransforms(int cropOffsetX,
                                                            int cropOffsetY,
                                                            int cropOffsetZ,
                                                            int scale)

  Deprecated. 

• getFusionBoundingBox

  protected static RealInterval getFusionBoundingBox(SPIMConfiguration conf,
                                                     int timepointId)

  Deprecated. 

• createViewRegistrations

  protected static ViewRegistrations createViewRegistrations(SPIMConfiguration conf,
                                                             ArrayList<ViewSetup> setups)

  Deprecated. 

• makeList

  protected static ArrayList<Integer> makeList(int[] ints)

  Deprecated. 

• getViewSetupId

  protected static int getViewSetupId(ArrayList<ViewSetup> setups,
                                      int angle,
                                      int illumination,
                                      int channel)

  Deprecated. 
  find ViewSetup index corresponding to given (angle, illumination, channel) triple.

  Returns:

  setup index or -1 if no corresponding setup was found.

• getConf

  public SPIMConfiguration getConf()

  Deprecated.