Field Detail

• defaultSameModelTimePoints

  public static boolean defaultSameModelTimePoints

• defaultSameModelChannels

  public static boolean defaultSameModelChannels

• defaultSameModelIlluminations

  public static boolean defaultSameModelIlluminations

• defaultSameModelAngles

  public static boolean defaultSameModelAngles

• defaultModel

  public static int defaultModel

• defaultDefineAs

  public static int defaultDefineAs

• defaultApplyTo

  public static int defaultApplyTo

• applyToChoice

  public static String[] applyToChoice

• modelChoice

  public static String[] modelChoice

• defineAsChoice

  public static String[] defineAsChoice

• axesChoice

  public String[] axesChoice

• defaultAxis

  public static int[] defaultAxis

• defaultDegrees

  public static double[] defaultDegrees

• defaultModels

  public static ArrayList<double[]> defaultModels

Constructor Detail

• Apply_Transformation

  public Apply_Transformation()

Method Detail

• run

  public void run(String arg0)

  Specified by:

  run in interface ij.plugin.PlugIn

• queryParams

  public final ApplyParameters queryParams(SpimData data,
                                           List<ViewId> viewIds)

  Parameters:

  data -

  viewIds -

  Returns:

  - transformation model and explanation for each viewid, also sets global variables applyTo and minResolution

• queryBigDataViewer

  public Map<ViewDescription,Pair<double[],String>> queryBigDataViewer(SpimData data,
                                                                       List<ViewId> viewIds,
                                                                       ApplyParameters params)

• queryRotationAxis

  public Map<ViewDescription,Pair<double[],String>> queryRotationAxis(SpimData data,
                                                                      List<ViewId> viewIds,
                                                                      ApplyParameters params)

• queryString

  public Map<ViewDescription,Pair<double[],String>> queryString(SpimData data,
                                                                List<ViewId> viewIds,
                                                                ApplyParameters params)

• applyModels

  public void applyModels(SpimData spimData,
                          double minResolution,
                          int applyTo,
                          Map<ViewDescription,Pair<double[],String>> modelLinks)

• parseString

  protected static final double[] parseString(String entry,
                                              int numValues)

• preConcatenateTransform

  public static void preConcatenateTransform(SpimData spimData,
                                             ViewId viewId,
                                             AffineTransform3D model,
                                             String name)

• setModelToCalibration

  public static void setModelToCalibration(SpimData spimData,
                                           ViewId viewId,
                                           double minResolution)

• setModelToIdentity

  public static void setModelToIdentity(SpimData spimData,
                                        ViewId viewId)

• assembleAllMetaData

  public static double assembleAllMetaData(SequenceDescription sequenceDescription,
                                           Collection<? extends ViewId> viewIdsToProcess)

  Should be called before registration to make sure all metadata is right

  Returns:

  - minimal resolution in all dimensions

• applyAxis

  public static void applyAxis(SpimData data)

• main

  public static void main(String[] args)

  Parameters:

  args -