Field Detail

• MEAN

  public static final String MEAN

  See Also:

  Constant Field Values

• MAX

  public static final String MAX

  See Also:

  Constant Field Values

• MAX_FITTED

  public static final String MAX_FITTED

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  Constant Field Values

• MAX_FITTED_RADIUS

  public static final String MAX_FITTED_RADIUS

  See Also:

  Constant Field Values

• POLY_FIT_DEGREE

  public static final String POLY_FIT_DEGREE

  See Also:

  Constant Field Values

• N_MAX

  public static final String N_MAX

  See Also:

  Constant Field Values

• SUM

  public static final String SUM

  See Also:

  Constant Field Values

• N_SECONDARY_MAX

  public static final String N_SECONDARY_MAX

  See Also:

  Constant Field Values

• DECAY

  public static final String DECAY

  See Also:

  Constant Field Values

Constructor Detail

• ShollAnalyzer

  public ShollAnalyzer(Tree tree)

  Instantiates a new Sholl analyzer using default settings, i.e., focused on Tree's root; using sampling step size of average inter-node distance; curve fitting enabled; and all other parameters left to defaults/auto-discovery.

  Parameters:

  tree - the Tree to be analyzed

Method Detail

• setPolynomialFitRange

  public void setPolynomialFitRange(int fromDegree,
                                    int toDegree)

  Sets the polynomial fit range for linear Sholl statistics.

  Parameters:

  fromDegree - the lowest degree to be considered. Set it to -1 to skip polynomial fit

  toDegree - the highest degree to be considered. Set it to -1 to skip polynomial fit

• setEnableCurveFitting

  public void setEnableCurveFitting(boolean enable)

  Sets whether curve fitting computations should be performed.

  Parameters:

  enable - if true polynomial and linear regression on normalized Sholl data will be performed. Enabling this option may adversely affect performance.

• getMetrics

  public static List<String> getMetrics()

• getSingleValueMetrics

  public Map<String,Number> getSingleValueMetrics()

• getMaximaRadii

  public ArrayList<Double> getMaximaRadii()

• getSecondaryMaxima

  public ArrayList<double[]> getSecondaryMaxima()

• getLinearStats

  public LinearProfileStats getLinearStats()

  Gets the LinearProfileStats associated with this analyzer. By default it is set to determine the polynomial of 'best-fit' (2-20 degree range.)

  Returns:

  the LinearProfileStats instance

• getNormStats

  public NormalizedProfileStats getNormStats()

  Gets the NormalizedProfileStats associated with this analyzer. By default it is set to determine the regression method of 'best-fit' (log-log or semi-log) using shell volume as normalizer (if Tree has a depth component) or shell area if Tree is 2D.

  Returns:

  the LinearProfileStats instance

• main

  public static void main(String[] args)
                   throws InterruptedException

  Throws:

  InterruptedException