Field Detail

• compressionOptions

  public static final String[] compressionOptions

Constructor Detail

• BigWarpToDeformationFieldPlugIn

  public BigWarpToDeformationFieldPlugIn()

Method Detail

• main

  public static void main(String[] args)

• runFromBigWarpInstance

  public <T> void runFromBigWarpInstance(LandmarkTableModel landmarkModel,
                                         List<SourceAndConverter<T>> sources,
                                         int[] targetSourceIndexList)

• run

  public void run(String arg)

  Specified by:

  run in interface ij.plugin.PlugIn

• toImagePlus

  public static ij.ImagePlus toImagePlus(LandmarkTableModel ltm,
                                         boolean ignoreAffine,
                                         long[] dims,
                                         double[] spacing,
                                         int nThreads)

• writeN5

  public static void writeN5(String n5BasePath,
                             LandmarkTableModel ltm,
                             long[] dims,
                             double[] spacing,
                             int[] spatialBlockSize,
                             org.janelia.saalfeldlab.n5.Compression compression,
                             int nThreads)
                      throws IOException,
                             org.janelia.saalfeldlab.n5.dataaccess.DataAccessException

  Throws:

  IOException

  org.janelia.saalfeldlab.n5.dataaccess.DataAccessException

• writeN5

  public static void writeN5(String n5BasePath,
                             String n5Dataset,
                             LandmarkTableModel ltm,
                             long[] dims,
                             double[] spacing,
                             int[] spatialBlockSize,
                             org.janelia.saalfeldlab.n5.Compression compression,
                             int nThreads)
                      throws IOException,
                             org.janelia.saalfeldlab.n5.dataaccess.DataAccessException

  Throws:

  IOException

  org.janelia.saalfeldlab.n5.dataaccess.DataAccessException

• toAffine

  public static AffineGet toAffine(ThinPlateR2LogRSplineKernelTransform tps)

• toFlatAffine

  public static double[] toFlatAffine(ThinPlateR2LogRSplineKernelTransform tps)

• dimensionsFromImagePlus

  public static long[] dimensionsFromImagePlus(ij.ImagePlus ref_imp)

• convertToDeformationField

  public static FloatImagePlus<FloatType> convertToDeformationField(long[] dims,
                                                                    RealTransform transform,
                                                                    AffineGet pixToPhysical,
                                                                    int nThreads)

• areTransformsTheSame

  public static boolean areTransformsTheSame(RealTransform xfm1,
                                             RealTransform xfm2,
                                             Interval itvl,
                                             double EPS)

• fromRealTransform

  public static <T extends RealType<T>> void fromRealTransform(RealTransform transform,
                                                               AffineGet pixelToPhysical,
                                                               RandomAccessibleInterval<T> deformationField)

  Converts a RealTransform into a deformation field. Writes the result into the passed RandomAccessibleInterval. If the transform has N source dimensions, then the deformation field must have at least N+1 dimensions where the last dimensions of of length at least N. A DeformationField creating with the resulting RandomAccessibleInterval will give the same results as the transform inside its Interval.

  Type Parameters:

  T - the type of the deformation field

  Parameters:

  transform - the RealTransform to convert

  pixelToPhysical - the transform from coordinates in the RandomAccessibleInterval to physical units

  deformationField - the RandomAccessibleInterval into which the displacement field will be written

• fromRealTransform

  public static <T extends RealType<T>> void fromRealTransform(RealTransform transform,
                                                               AffineGet pixelToPhysical,
                                                               RandomAccessibleInterval<T> deformationField,
                                                               int nThreads)

  Converts a RealTransform into a deformation field. Writes the result into the passed RandomAccessibleInterval. If the transform has N source dimensions, then the deformation field must have at least N+1 dimensions where the last dimensions of of length at least N. A DeformationField creating with the resulting RandomAccessibleInterval will give the same results as the transform inside its Interval.

  Type Parameters:

  T - the type of the deformation field

  Parameters:

  transform - the RealTransform to convert

  pixelToPhysical - the transform from coordinates in the RandomAccessibleInterval to physical units

  deformationField - the RandomAccessibleInterval into which the displacement field will be written

  nThreads - the number of threads