Method Detail

• blockMean

  protected static float blockMean(ij.process.FloatProcessor fp,
                                   int tx,
                                   int ty,
                                   int blockWidth,
                                   int blockHeight)

  Estimate the mean intensity of a block.

  Note:

  Make sure that the block is fully contained in the image, this will not be checked by the method for efficiency reasons.

  Parameters:

  fp -

  tx -

  ty -

  blockWidth -

  blockHeight -

  Returns:

• blockVariance

  protected static float blockVariance(ij.process.FloatProcessor fp,
                                       int tx,
                                       int ty,
                                       int blockWidth,
                                       int blockHeight,
                                       float mean)

  Estimate the intensity variance of a block.

  Note:

  Make sure that the block is fully contained in the image, this will not be checked by the method for efficiency reasons.

  Parameters:

  fp -

  tx -

  ty -

  blockWidth -

  blockHeight -

  Returns:

• matchByMinimalSquareDifference

  public static void matchByMinimalSquareDifference(ij.process.FloatProcessor source,
                                                    ij.process.FloatProcessor target,
                                                    InvertibleCoordinateTransform transform,
                                                    int blockRadiusX,
                                                    int blockRadiusY,
                                                    int searchRadiusX,
                                                    int searchRadiusY,
                                                    Collection<? extends Point> sourcePoints,
                                                    Collection<PointMatch> sourceMatches)

  Estimate point correspondences for a Collection of Points among two images that are approximately related by an InvertibleCoordinateTransform using the square difference of pixel intensities as a similarity measure.

  Parameters:

  source -

  target -

  transform - transfers source into target approximately

  blockRadiusX - horizontal radius of a block

  blockRadiusY - vertical radius of a block

  searchRadiusX - horizontal search radius

  searchRadiusY - vertical search radius

  sourcePoints -

  sourceMatches -

• matchByMaximalPMCC

  protected static void matchByMaximalPMCC(ij.process.FloatProcessor source,
                                           ij.process.FloatProcessor target,
                                           int blockRadiusX,
                                           int blockRadiusY,
                                           int searchRadiusX,
                                           int searchRadiusY,
                                           float minR,
                                           float rod,
                                           float maxCurvature,
                                           Collection<PointMatch> query,
                                           Collection<PointMatch> results)
                                    throws InterruptedException,
                                           ExecutionException

  Throws:

  InterruptedException

  ExecutionException

• matchByMaximalPMCC

  public static void matchByMaximalPMCC(ij.process.FloatProcessor source,
                                        ij.process.FloatProcessor target,
                                        ij.process.FloatProcessor sourceMask,
                                        ij.process.FloatProcessor targetMask,
                                        double scale,
                                        CoordinateTransform transform,
                                        int blockRadiusX,
                                        int blockRadiusY,
                                        int searchRadiusX,
                                        int searchRadiusY,
                                        float minR,
                                        float rod,
                                        float maxCurvature,
                                        Collection<? extends Point> sourcePoints,
                                        Collection<PointMatch> sourceMatches,
                                        ErrorStatistic observer)
                                 throws InterruptedException,
                                        ExecutionException

  Estimate point correspondences for a Collection of Points among two images that are approximately related by an InvertibleCoordinateTransform using the Pearson product-moment correlation coefficient (PMCC) r of pixel intensities as similarity measure. Only correspondence candidates with r >= a given threshold are accepted.

  Parameters:

  source -

  target -

  sourceMask -

  targetMask -

  scale - [0,1]

  transform - transfers source into target approximately

  blockRadiusX - horizontal radius of a block

  blockRadiusY - vertical radius of a block

  searchRadiusX - horizontal search radius

  searchRadiusY - vertical search radius

  minR - minimal accepted Cross-Correlation coefficient

  rod -

  sourcePoints -

  sourceMatches -

  observer -

  Throws:

  InterruptedException

  ExecutionException

• matchByMaximalPMCCFromPreScaledImages

  public static void matchByMaximalPMCCFromPreScaledImages(ij.process.FloatProcessor source_scaled,
                                                           ij.process.FloatProcessor target_scaled,
                                                           double scale,
                                                           int blockRadiusX,
                                                           int blockRadiusY,
                                                           int searchRadiusX,
                                                           int searchRadiusY,
                                                           float minR,
                                                           float rod,
                                                           float maxCurvature,
                                                           Collection<? extends Point> sourcePoints,
                                                           Collection<PointMatch> sourceMatches)
                                                    throws InterruptedException,
                                                           ExecutionException

  Estimate point correspondences for a Collection of Points among two images that are approximately related by an InvertibleCoordinateTransform using the Pearson product-moment correlation coefficient (PMCC) r of pixel intensities as similarity measure. Only correspondence candidates with r >= a given threshold are accepted. Similar to matchByMaximalPMCC(FloatProcessor, FloatProcessor, FloatProcessor, FloatProcessor, double, CoordinateTransform, int, int, int, int, float, float, float, Collection, Collection, ErrorStatistic) but: 1. With its FloatProcessor images already scaled down to scale and already with their contrast normalized, and their masks applied if any. That is, images provided as arguments source_scaled and target_scaled are expected to have been pre-processed with Filter.createDownsampled(FloatProcessor, double, float, float) and with Util.normalizeContrast(FloatProcessor), and with mapAndMask(ImageProcessor, ImageProcessor, ImageProcessor, CoordinateTransform) to set pixels outside the mask to Float.NaN. 2. Without a transform, i.e., assumes images are almost registered already. These modifications are a performance optimization, by preventing the Gaussian blurring of images multiple times when e.g. comparing a section with its adjacent, its 2nd adjacent, etc., and also by preventing unnecessary repeats of image duplication, contrast normalization, and mask application.

  Parameters:

  source_scaled -

  target_scaled -

  scale - [0,1]

  blockRadiusX - horizontal radius of a block

  blockRadiusY - vertical radius of a block

  searchRadiusX - horizontal search radius

  searchRadiusY - vertical search radius

  minR - minimal accepted Cross-Correlation coefficient

  rod -

  sourcePoints -

  sourceMatches -

  Throws:

  InterruptedException

  ExecutionException

• matchByMaximalPMCC

  public static void matchByMaximalPMCC(ij.process.FloatProcessor source,
                                        ij.process.FloatProcessor target,
                                        ij.process.FloatProcessor sourceMask,
                                        ij.process.FloatProcessor targetMask,
                                        float scale,
                                        CoordinateTransform transform,
                                        int blockRadiusX,
                                        int blockRadiusY,
                                        int searchRadiusX,
                                        int searchRadiusY,
                                        Collection<? extends Point> sourcePoints,
                                        Collection<PointMatch> sourceMatches,
                                        ErrorStatistic observer)
                                 throws InterruptedException,
                                        ExecutionException

  Estimate point correspondences for a Collection of Points among two images that are approximately related by an InvertibleCoordinateTransform using the Pearson product-moment correlation coefficient (PMCC) r of pixel intensities as similarity measure. Only correspondence candidates with r >= a given threshold are accepted.

  Parameters:

  source -

  target -

  sourceMask -

  targetMask -

  scale - [0,1]

  transform - transfers source into target approximately

  blockRadiusX - horizontal radius of a block

  blockRadiusY - vertical radius of a block

  searchRadiusX - horizontal search radius

  searchRadiusY - vertical search radius

  sourcePoints -

  sourceMatches -

  observer -

  Throws:

  InterruptedException

  ExecutionException

• findMatches

  public static void findMatches(ij.process.FloatProcessor source,
                                 ij.process.FloatProcessor target,
                                 ij.process.FloatProcessor sourceMask,
                                 ij.process.FloatProcessor targetMask,
                                 Model<?> initialModel,
                                 Class<? extends AbstractAffineModel2D<?>> localModelClass,
                                 float maxEpsilon,
                                 float maxScale,
                                 float minR,
                                 float rodR,
                                 float maxCurvatureR,
                                 int meshResolution,
                                 float alpha,
                                 Collection<PointMatch> sourceMatches)
                          throws InterruptedException,
                                 ExecutionException

  Throws:

  InterruptedException

  ExecutionException

• illustrateMatches

  public static Shape illustrateMatches(Collection<PointMatch> matches)

  Create a Shape that illustrates a Collection of PointMatches.

  Returns:

  the illustration