TubeTK/Documentation/SegmentConnectedComponentsUsingParzenPDFs

  Description: Given multiple, registered images and foreground and
  background masks, computes multivariate PDFs for inside and outside
  classes, and then performs competitive region growing.

USAGE:

  ./SegmentConnectedComponentsUsingParzenPDFs  [--returnparameterfile
                                       <std::string>]
                                       [--processinformationaddress
                                       <std::string>] [--xml] [--echo]
                                       [--saveClassPDFBase <std::string>]
                                       [--loadClassPDFBase <std::string>]
                                       [--saveClassProbabilityVolumeBase
                                       <std::string>]
                                       [--forceClassification]
                                       [--reclassifyNotObjectLabels]
                                       [--reclassifyObjectLabels]
                                       [--draft]
                                       [--histogramSmoothingStdDev
                                       <double>]
                                       [--probImageSmoothingStdDev
                                       <double>] [--objectPDFWeight
                                       <std::vector<double>>]
                                       [--dilateFirst]
                                       [--holeFillIterations <int>]
                                       [--erodeRadius <int>] [--voidId
                                       <int>] [--objectId
                                       <std::vector<int>>] [--inputVolume4
                                       <std::string>] [--inputVolume3
                                       <std::string>] [--inputVolume2
                                       <std::string>] [--] [--version]
                                       [-h] <std::string> <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)

  --saveClassPDFBase <std::string>
    Save images that represent probability density functions.

  --loadClassPDFBase <std::string>
    Load images that represent probability density functions.

  --saveClassProbabilityVolumeBase <std::string>
    Save images where each represents the probability of being a
    particular object at each voxel. Image files create =
    base.classNum.mha.

  --forceClassification
    Force classification using simple maximum likelihood. (default: 0)

  --reclassifyNotObjectLabels
    Perform classification on all non-void voxels. (default: 0)

  --reclassifyObjectLabels
    Perform classification on voxels within the object mask. (default: 0)

  --draft
    Generate draft results. (default: 0)

  --histogramSmoothingStdDev <double>
    Standard deviation of blur applied to convert the histogram to a
    probability density function estimate (default: 5)

  --probImageSmoothingStdDev <double>
    Standard deviation of blur applied to probability images prior to
    computing maximum likelihood of each class at each pixel (default: 1)

  --objectPDFWeight <std::vector<double>>
    Relative weight (multiplier) of each PDF. (default: 1)

  --dilateFirst
    Performs dilation then erosion (versus opposite order) to help fill-in
    sparse models. (default: 0)

  --holeFillIterations <int>
    Number of iterations for hole filling. (default: 1)

  --erodeRadius <int>
    Radius of noise to clip from edges. (default: 1)

  --voidId <int>
    Value that represents 'nothing' in the label map. (default: 0)

  --objectId <std::vector<int>>
    List of values that represent the objects in the label map. (default:
    255,127)

  --inputVolume4 <std::string>
    Input volume 4.

  --inputVolume3 <std::string>
    Input volume 3.

  --inputVolume2 <std::string>
    Input volume 2.

  --,  --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 1.

  <std::string>
    (required)  Label map that designates the object of interest and
    'other.'

  <std::string>
    (required)  Segmentation results.

  Author(s): Stephen R. Aylward (Kitware)

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