Field Detail

• VoxelSize

  public static float VoxelSize

• editSeamCellOutput

  public static final java.lang.String editSeamCellOutput

• namedSeamCellOutput

  public static final java.lang.String namedSeamCellOutput

• autoLatticeGenerationOutput

  public static final java.lang.String autoLatticeGenerationOutput

• editLatticeOutput

  public static final java.lang.String editLatticeOutput

• integratedAnnotationOutput

  public static final java.lang.String integratedAnnotationOutput

• straightenedLattice

  public static final java.lang.String straightenedLattice

• straightenedAnnotations

  public static final java.lang.String straightenedAnnotations

• neuriteOutput

  public static final java.lang.String neuriteOutput

• imageName

  private java.lang.String imageName

• wormImage

  private ModelImage wormImage

• outputDirectory

  private java.lang.String outputDirectory

• outputImagesDirectory

  private java.lang.String outputImagesDirectory

Constructor Detail

• WormData

  public WormData​(ModelImage image)

Method Detail

• getOutputDirectory

  public static java.lang.String getOutputDirectory​(ModelImage image)

• integratedExists

  public static boolean integratedExists​(java.lang.String outputDirectory)

• getIntegratedMarkerAnnotationsPath

  public static java.lang.String getIntegratedMarkerAnnotationsPath​(java.lang.String outputDirectory)

• getStraightAnnotationsPath

  public static java.lang.String getStraightAnnotationsPath​(java.lang.String outputDirectory)

• getIntegratedMarkerAnnotations

  public static VOI getIntegratedMarkerAnnotations​(java.lang.String outputDirectory)

• openStraightAnnotations

  public static void openStraightAnnotations​(java.lang.String dir,
                                             ModelImage image)

• readStraightLattice

  public static VOIVector readStraightLattice​(java.lang.String outputDirectory)

• readFinalLattice

  public VOIVector readFinalLattice()

• readFinalLattice

  private VOIVector readFinalLattice​(boolean convertLegacyXML)

• readFinalLattice

  public static VOIVector readFinalLattice​(java.lang.String outputDirectory,
                                           boolean convertLegacyXML,
                                           ModelImage image)

• readLegacyLattice

  private static VOIVector readLegacyLattice​(java.lang.String fileName,
                                             ModelImage wormImage)

• checkSeamCells

  private static boolean checkSeamCells​(java.lang.String outputDirectory)

• saveIntegratedMarkerAnnotations

  public static void saveIntegratedMarkerAnnotations​(java.lang.String outputDirectory,
                                                     VOI annotations)

• saveSeamAnnotations

  public static void saveSeamAnnotations​(java.lang.String outputDirectory,
                                         VOI annotations,
                                         boolean rename,
                                         boolean checkImage)

• checkParentDir

  private void checkParentDir​(java.lang.String parentDir)

  Creates the parent directory for the output images and data created by worm segmentation and untwisting:

  Parameters:

  parentDir -