Quillot Mathias / Clustering

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bin/measures.py 3.18 KB
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60d1f63cd   Mathias Quillot   Script and lib th... 
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  '''
  This module is a part of my library. 
  It aims to compute some measures for clustering.
  '''
  
  import numpy as np
  
  def disequilibrium_(matrix1, matrix2, isGlobal=False, mod=None):
      '''
      Compute disequilibrium for all the clusters.
      The disequilibrium is compute from the difference
      between two clustering sets.
      isGlobal permet à l'utilisateur de choisir le dénominateur de
      la fonction : 
          - True : divise la valeur par le nombre d'élément du cluster
          - False : divise la valeur par le nombre d'élément total
  
      withPower permet à l'utilisateur de décider d'appliquer un carré 2 ou
      une valeur absolue.
      '''
  
      def divide_line(a, divider):
          '''
          Sub function used for dividing matrix by a vector line by line.
          '''
          return np.divide(a, divider, out=np.zeros_like(a), where=divider!=0)
  
      dividers1 = 0
      dividers2 = 0
  
      if isGlobal:
          dividers1 = matrix1.sum()
          dividers2 = matrix2.sum()
      else:
          dividers1 = matrix1.sum(axis=1)
          dividers2 = matrix2.sum(axis=1)
      
      matrix1_divided = np.apply_along_axis(divide_line, 0, np.asarray(matrix1, dtype=np.float), dividers1)
      
      matrix2_divided = np.apply_along_axis(divide_line, 0, np.asarray(matrix2, dtype=np.float), dividers2)
      
      diff = matrix1_divided - matrix2_divided
      
      mask = (matrix2==0) & (matrix1==0)
      result = diff
  
      if mod != None or mod == "":
          for word in mod.split(" "):
              if word == "power":
                  result = np.power(result,2)
              elif word == "human":
                  result = result * 100
              elif word == "abs":
                  result = np.absolute(result)    
              else:
                  raise Exception("Need to specify an accepted mod of the disequilibrium (\"power\", \"human\" or \"abs\"")
      return (mask, result)
  
  
  
  def disequilibrium_mean_by_cluster(mask, matrix):
      '''
      Mean of disequilibrium
      matrix is the disequilibrium calculated
      from number of occurences belonging to a class,
      for each cluster. 
      '''
      nb_k = len(matrix)
      results = np.zeros((nb_k))
      for i in range(nb_k):
          results[i] = matrix[i].sum() / mask[i].sum()
      return results
  
  
  def disequilibrium(matrix1, matrix2, isGlobal=False):
      '''
      Disequilibrium matrix
      And Disequilibrium value
      '''
      mask, result = disequilibrium_(matrix1, matrix2, isGlobal)
      result_human = result * 100
      result_power = np.power(result, 2)
  
      return (
          mask,
          result_human,
0b3071878   Mathias Quillot   normalize the glo... 
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          disequilibrium_mean_by_cluster(mask, result_power).sum()/matrix1.shape[0]
60d1f63cd   Mathias Quillot   Script and lib th... 
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      )
  
  
  def entropy(count_matrix):
      def divide_line(a, divider):
          '''
          Sub function used for dividing matrix by a vector line by line.
          '''
          return np.divide(a, divider, out=np.zeros_like(a), where=divider!=0)
  
      dividers = count_matrix.sum(axis=1)
  
      matrix_divided = np.apply_along_axis(divide_line, 0, np.asarray(count_matrix, dtype=np.float), dividers)
      
      result_matrix = -1 * matrix_divided * np.log2(matrix_divided, where=count_matrix != 0)
      result = result_matrix.sum(axis=1) * dividers / dividers.sum()
      result = result.sum()
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      return (result_matrix, result)