Field Detail

• minInlierFactor

  public static float minInlierFactor

• preAlignTiles

  public static boolean preAlignTiles

Constructor Detail

• BeadRegistration

  public BeadRegistration(ViewStructure viewStructure)

  Instantiates the object with a certain ViewStructure it is working on when using non-static method calls

  Parameters:

  viewStructure - - the ViewStructure to work on

Method Detail

• getViewStructure

  public ViewStructure getViewStructure()

  The ViewStructure this BeadRegistration is working with

  Returns:

  - the associated ViewStructure

• registerViews

  public TileConfigurationSPIM registerViews()

  Registers the current ViewStructure, see registerViews(ViewStructure)

• registerViews

  public TileConfigurationSPIM registerViews(boolean resetW)

  Registers the current ViewStructure, see registerViews(ViewStructure)

• registerViewStructure

  public void registerViewStructure(ViewStructure template)

  Registers the template ViewStructure to the ViewStructure of this BeadRegistration object, see registerViewStructure(ViewStructure, ViewStructure)

• registerViewStructure

  public static void registerViewStructure(ViewStructure reference,
                                           ViewStructure template)

  Registers the ViewDataBeads of the template ViewStructure to the ViewDataBeads of the reference ViewStructure. All tiles of the reference ViewStructure are therefore fixed during the registration. The SPIMConfiguration and GlobalErrorStatistics are taken from the template ViewStructure, the debuglevel is the highest of template and reference.

  Parameters:

  reference - - the reference ViewStructure

  template - - the template ViewStructure

• registerViews

  public static TileConfigurationSPIM registerViews(ViewStructure viewStructure)

• registerViews

  public static TileConfigurationSPIM registerViews(ViewStructure viewStructure,
                                                    boolean resetW)

  Registers all ViewDataBeads within a given ViewStructure, taking the first view as fixed Tile Registration works without z-scaling, it has to be concatenated afterwards if wanted

  Parameters:

  viewStructure - - The ViewStructure to register

• computeErrors

  public static void computeErrors(ArrayList<ViewDataBeads> views,
                                   TileConfigurationSPIM tc)

• optimizeTiles

  public static TileConfigurationSPIM optimizeTiles(ArrayList<ViewDataBeads> views,
                                                    GlobalErrorStatistics errorStatistics,
                                                    int debugLevel)

• optimizeTiles

  public static TileConfigurationSPIM optimizeTiles(ArrayList<ViewDataBeads> views,
                                                    int numFixed,
                                                    GlobalErrorStatistics errorStatistics,
                                                    int debugLevel)

• concatenateAxialScaling

  public static void concatenateAxialScaling(AbstractAffineModel3D model,
                                             double zStretching)

• concatenateAxialScaling

  public static void concatenateAxialScaling(ViewDataBeads view,
                                             int debugLevel)

• concatenateAxialScaling

  public static void concatenateAxialScaling(ArrayList<ViewDataBeads> views,
                                             int debugLevel)