Class: Cicada::P3DFitter

Inherits:
DistributionFitter show all
Defined in:
lib/cicada/fitting/p3d_fitter.rb

Overview

A distribution fitter that fits data to a P3D distribution.

Constant Summary collapse

REQUIRED_PARAMETERS =

parameters required by the methods in this class

[]
OPTIONAL_PARAMETERS =

parmeters used but not required in this class or only required for optional functionality

[:robust_p3d_fit_cutoff]

Instance Attribute Summary

Attributes inherited from DistributionFitter

#parameters

Instance Method Summary collapse

Methods inherited from DistributionFitter

#initialize

Constructor Details

This class inherits a constructor from Cicada::DistributionFitter

Instance Method Details

#fit(objects, diffs) ⇒ Array

Fits the P3D mean- and standard-deviation-like parameters to the data.

Parameters:

  • objects (Array<ImageObject>) —

    the image objects whose distances are being fit

  • diffs (Array<Numeric>) —

    the distances being fit

Returns:

  • (Array) —

    a two-element array containing the mean- and standard-deviation-like parameters.



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# File 'lib/cicada/fitting/p3d_fitter.rb', line 201

def fit(objects, diffs)

  of = P3DObjectiveFunction.new

  of.r = diffs

  tol = 1e-12

  nmm = Java::edu.stanford.cfuller.imageanalysistools.fitting.NelderMeadMinimizer.new(tol)

  initial_mean = Math.mean(diffs)

  initial_width = Math.std(diffs)

  starting_point = Java::org.apache.commons.math3.linear.ArrayRealVector.new(2, 0.0)

  starting_point.setEntry(0, initial_mean)
  starting_point.setEntry(1, initial_width)

  if @parameters[:robust_p3d_fit_cutoff] then
    
    of.min_prob= @parmaeters[:robust_p3d_fit_cutoff].to_f

  end

  nmm.optimize(of, starting_point).toArray.to_a

end