Constructor Detail

• Scripting

  public Scripting()

  Deprecated. 

Method Detail

• createSpimRegistrationSequence

  @Deprecated
  public static SpimRegistrationSequence createSpimRegistrationSequence(String huiskenExperimentXmlFile,
                                                                                    String channels,
                                                                                    String angles,
                                                                                    String timepoints,
                                                                                    int referenceTimePoint)
                                                                             throws ConfigurationParserException

  Deprecated. 
  Create a SpimRegistrationSequence based on a Huisken experiment xml file.

  Parameters:

  huiskenExperimentXmlFile - path of the experiment xml file.

  channels - String specifying the channels to include in the sequence. In the format used by the SPIMRegistration plugin. For single-channel sequence, set to null.

  angles - String specifying the angles to include in the sequence. In the format used by the SPIMRegistration plugin.

  timepoints - String specifying the timepoints to include in the sequence. In the format used by the SPIMRegistration plugin.

  referenceTimePoint - the reference timepoint (registrations relative to this timepoint are laoded), or -1, indicating to use individual (non-timelapse) view registrations.

  Returns:

  an initialized SpimRegistrationSequence sequence.

  Throws:

  ConfigurationParserException

• createSpimRegistrationSequence

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

  Deprecated. 
  Create a SpimRegistrationSequence based on a directory of image (.tif, .czi, etc...).

  Parameters:

  inputDirectory - path of image directory.

  inputFilePattern - pattern of the image file names In the format used by the SPIMRegistration plugin.

  channels - String specifying the channels to include in the sequence. In the format used by the SPIMRegistration plugin. For single-channel sequence, set to null.

  angles - String specifying the angles to include in the sequence. In the format used by the SPIMRegistration plugin.

  timepoints - String specifying the timepoints to include in the sequence. In the format used by the SPIMRegistration plugin.

  referenceTimePoint - the reference timepoint (registrations relative to this timepoint are laoded), or -1, indicating to use individual (non-timelapse) view registrations.

  overrideImageZStretching - whether the z-stretching of the images should be overridden. If false, the z-stretching is read from the image metadata.

  zStretching - z-stretching to use (if overrideImageZStretching == true).

  Returns:

  an initialized SpimRegistrationSequence sequence.

  Throws:

  ConfigurationParserException

• getFusionTransforms

  @Deprecated
  public static Map<Integer,AffineTransform3D> getFusionTransforms(SpimRegistrationSequence spimseq,
                                                                               int scale,
                                                                               int cropOffsetX,
                                                                               int cropOffsetY,
                                                                               int cropOffsetZ)

  Deprecated. 
  TODO

  Parameters:

  spimseq -

  scale -

  cropOffsetX -

  cropOffsetY -

  cropOffsetZ -

  Returns:

• createFusionResult

  @Deprecated
  public static FusionResult createFusionResult(SpimRegistrationSequence spimseq,
                                                            String filepath,
                                                            String filepattern,
                                                            int numSlices,
                                                            double sliceValueMin,
                                                            double sliceValueMax,
                                                            Map<Integer,AffineTransform3D> fusionTransforms)

  Deprecated. 
  TODO

  Parameters:

  spimseq -

  filepath -

  filepattern -

  numSlices -

  sliceValueMin -

  sliceValueMax -

  fusionTransforms -

  Returns:

• split

  @Deprecated
  public static ArrayList<Partition> split(SetupAggregator aggregator,
                                                       int timepointsPerPartition,
                                                       int setupsPerPartition,
                                                       String xmlFilename)

  Deprecated. 
  Split the sequence represented in aggregator into partitions.

  Parameters:

  aggregator - represents the full dataset.

  timepointsPerPartition - how many timepoints should each partition contain (if this is ≤0, put do not split timepoints across partitions).

  setupsPerPartition - how many setups should each partition contain (if this is ≤0, put do not split setups across partitions).

  xmlFilename - path to the xml file to which the sequence will be saved. This is used to generate paths for the partitions.

  Returns:

  list of partitions.

• example_main

  public static void example_main(String[] args)
                           throws Exception

  Deprecated. 

  Throws:

  Exception