Class: GenCurvefit

Inherits:
Object
  • Object
show all
Defined in:
lib/ms/curvefit/curve_fit_helper.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(pts_in, function = nil, paramsize = nil, mutation_limits = nil, popsize = 0, generations = nil) ⇒ GenCurvefit

Returns a new instance of GenCurvefit.



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# File 'lib/ms/curvefit/curve_fit_helper.rb', line 26

def initialize(pts_in,function = nil,paramsize = nil,mutation_limits = nil,popsize = 0,generations = nil)
  @pts_in = pts_in
  @function = function
  @paramsize = paramsize
  @mutation_limits = mutation_limits
  @popsize = popsize
  @generations = generations
  @population = []
  if @popsize != 0 and @paramsize != nil and @mutation_limits != nil and @function != nil
    init_population
  end
end

Instance Attribute Details

#function ⇒ Object (readonly)

Returns the value of attribute function.



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# File 'lib/ms/curvefit/curve_fit_helper.rb', line 39

def function
  @function
end

#generations ⇒ Object

Returns the value of attribute generations.



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# File 'lib/ms/curvefit/curve_fit_helper.rb', line 39

def generations
  @generations
end

#mutation_limits ⇒ Object

Returns the value of attribute mutation_limits.



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# File 'lib/ms/curvefit/curve_fit_helper.rb', line 39

def mutation_limits
  @mutation_limits
end

#paramsize ⇒ Object

Returns the value of attribute paramsize.



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# File 'lib/ms/curvefit/curve_fit_helper.rb', line 39

def paramsize
  @paramsize
end

#popsize ⇒ Object

Returns the value of attribute popsize.



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# File 'lib/ms/curvefit/curve_fit_helper.rb', line 39

def popsize
  @popsize
end

#population ⇒ Object

Returns the value of attribute population.



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# File 'lib/ms/curvefit/curve_fit_helper.rb', line 39

def population
  @population
end

Class Method Details

.normalize(arr) ⇒ Object 



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# File 'lib/ms/curvefit/curve_fit_helper.rb', line 80

def self.normalize(arr)
  max = arr.max
  arr.map!{|i| (i.to_f/max) * 100}
end

.smoothave(arr) ⇒ Object 



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# File 'lib/ms/curvefit/curve_fit_helper.rb', line 64

def self.smoothave(arr)
  smooth_ave = [nil,nil,nil]
  queue = []
  arr.each do |i|
    queue.push(i)
    if queue.size > 7
      queue.shift
    end
    smooth_ave<<queue.inject(:+)/queue.size if queue.size == 7
  end
  3.times do 
    smooth_ave<<nil
  end
  return smooth_ave
end

Instance Method Details

#fit ⇒ Object 



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# File 'lib/ms/curvefit/curve_fit_helper.rb', line 121

def fit
  prog = Progress.new("Generation")
  num = 0
  total = @generations
  step = total/100
  @generations.times do |i|
    if i > step * (num + 1)
	num = ((i/total.to_f)*100).to_i
	prog.update(num," #{i+1}:")
    end
    #Generate mutations
    index = rand(@popsize)
    clone = @population[index].clone
    mutate(clone)
    clone[@paramsize] = fitness(clone,@pts_in)

    if(clone.last < @population.last.last)
      @population[@population.size - (@paramsize-1)] = clone
    end
    #Re-sort
    @population = sort_by_fitness

    #Print best
    if i == @generations - 1
      @best = @population.first
    end
  end 
  prog.finish!
  return @best
end

#fitness(set, pts_in, plot = false) ⇒ Object 



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# File 'lib/ms/curvefit/curve_fit_helper.rb', line 106

def fitness(set,pts_in,plot = false)
  pts = []
  xs = pts_in.transpose[0]
  xs.each do |x|
    fit_pt = function.call(set,x)
    pts<<[x,fit_pt]
  end

  if plot
    return pts
  end

  return rmsd(pts_in,pts)
end

#init_population ⇒ Object 



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# File 'lib/ms/curvefit/curve_fit_helper.rb', line 42

def init_population
  @popsize.times do
    set = []
    @paramsize.times do |i|
      limits = @mutation_limits[i]
      set<<random_float(limits[0],limits[1])
    end
    set<<fitness(set,@pts_in)
    @population<<set
  end
end

#mutate(set) ⇒ Object 



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# File 'lib/ms/curvefit/curve_fit_helper.rb', line 58

def mutate(set)
  index = rand(set.size-1)
  limits = @mutation_limits[index]
  set[index] += random_float(limits[0],limits[1])
end

#plot(file, labels = nil) ⇒ Object 



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# File 'lib/ms/curvefit/curve_fit_helper.rb', line 152

def plot(file,labels = nil)
  pts = fitness(@best,@pts_in,true)
  Fit_plot.plot(@pts_in,pts,file,labels)
  puts "  Output File: #{file}"
end

#random_float(a, b) ⇒ Object 



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# File 'lib/ms/curvefit/curve_fit_helper.rb', line 89

def random_float(a,b)
  a = a.to_f
  b = b.to_f
  random = rand(2147483647.0) / 2147483647.0
  diff = b - a
  r = random * diff
  return a + r
end

#rmsd(v, w) ⇒ Object 



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# File 'lib/ms/curvefit/curve_fit_helper.rb', line 98

def rmsd(v,w)
  n = v.size
  sum = 0.0
  n.times{|i| sum += ((v[i][0]-w[i][0])**2.0 + (v[i][1]-w[i][1])**2.0) }
  return Math.sqrt( (1/n.to_f) * sum )
end

#set_fit_function(func) ⇒ Object 



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# File 'lib/ms/curvefit/curve_fit_helper.rb', line 54

def set_fit_function(func)
  @function = func
end

#sort_by_fitness ⇒ Object 



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# File 'lib/ms/curvefit/curve_fit_helper.rb', line 85

def sort_by_fitness
  @population.sort_by!{|set| set.last}     
end