TubeTK/Documentation/EnhanceCoherenceAndEdgesUsingDiffusion

  Description: Continuous switch between edge enhancing anisotropic
  diffusion (for homogeneous regions and plate-like structures) and
  coherence enhancing anisotropic diffusion (for tube-like structures and
  small spherical structures). Implemented as described in Mendrik et al.,
  Noise reduction in computed tomography scans using 3-D anisotropic
  diffusion with continuous switch, IEEE Transactions on Medical Imaging,
  28(10), pp. 1585-1594, 2009.

USAGE:

  ./EnhanceCoherenceAndEdgesUsingDiffusion  [--returnparameterfile
                                       <std::string>]
                                       [--processinformationaddress
                                       <std::string>] [--xml] [--echo] [-n
                                       <int>] [-t <double>] [-y <double>]
                                       [-a <double>] [-c <double>] [-e
                                       <double>] [-s <double>] [--]
                                       [--version] [-h] <std::string>
                                       <std::string>

Where:

  --returnparameterfile <std::string>
    Filename in which to write simple return parameters (int, float,
    int-vector, etc.) as opposed to bulk return parameters (image,
    geometry, transform, measurement, table).

  --processinformationaddress <std::string>
    Address of a structure to store process information (progress, abort,
    etc.). (default: 0)

  --xml
    Produce xml description of command line arguments (default: 0)

  --echo
    Echo the command line arguments (default: 0)

  -n <int>,  --numIterations <int>
    Number of iterations used in optimization. (default: 1)

  -t <double>,  --timeStep <double>
    Time step used in optimization. (default: 0.11)

  -y <double>,  --hybridContrast <double>
    Contrast of small structures and tubes to be filtered with coherence
    enhancing diffusion (CED). If set too low, noise in homogeneous
    regions will look like valid contrast and may be filtered with CED,
    instead of edge enhancing diffusion (EED). If set too high, only small
    structures and tubes with high contrast will be filtered with CED,
    while lower-contrast small structures and tubes will be filtered with
    EED. (default: 30)

  -a <double>,  --alpha <double>
    Regularization parameter to ensure that the diffusion tensor matrix is
    positive definite and to prevent division by zero (used by both the
    coherence enhancing diffusion and the continuous switch). Should be
    set to something very small. (default: 0.001)

  -c <double>,  --CEDContrast <double>
    Ratio between the second and third eigenvalues that indicates a
    tube-like structure (used by the coherence enhancing diffusion). If
    set too low, small spherical structures will not be preserved. If set
    too high, tubular structures will not be filtered. (default: 30)

  -e <double>,  --EEDContrast <double>
    Contrast of edges, as opposed to noise (used by the edge enhancing
    diffusion). If set too low, noise will not be filtered. If set too
    high, plate-like structures will not be preserved. (default: 20)

  -s <double>,  --scale <double>
    Scale at which first derivatives are calculated when determining the
    structure tensor and gradient magnitude. If set too low, filter will
    be overly sensitive to noise. If set too high, small structures will
    not be well preserved. (default: 1)

  --,  --ignore_rest
    Ignores the rest of the labeled arguments following this flag.

  --version
    Displays version information and exits.

  -h,  --help
    Displays usage information and exits.

  <std::string>
    (required)  Input volume.

  <std::string>
    (required)  Output volume.

  Author(s): Danielle F. Pace, Andinet Enquobahrie, Hua Yang, Stephen R.
  Aylward (Kitware)

  Acknowledgements: This work is part of the TubeTK project at Kitware.