Jenks natural breaks classification

gistfile1.py

# code from http://danieljlewis.org/files/2010/06/Jenks.pdf
# described at http://danieljlewis.org/2010/06/07/jenks-natural-breaks-algorithm-in-python/

def getJenksBreaks( dataList, numClass ):
  dataList.sort()
  mat1 = []
  for i in range(0,len(dataList)+1):
    temp = []
    for j in range(0,numClass+1):
      temp.append(0)
    mat1.append(temp)
  mat2 = []
  for i in range(0,len(dataList)+1):
    temp = []
    for j in range(0,numClass+1):
      temp.append(0)
    mat2.append(temp)
  for i in range(1,numClass+1):
    mat1[1][i] = 1
    mat2[1][i] = 0
    for j in range(2,len(dataList)+1):
      mat2[j][i] = float('inf')
  v = 0.0
  for l in range(2,len(dataList)+1):
    s1 = 0.0
    s2 = 0.0
    w = 0.0
    for m in range(1,l+1):
      i3 = l - m + 1
      val = float(dataList[i3-1])
      s2 += val * val
      s1 += val
      w += 1
      v = s2 - (s1 * s1) / w
      i4 = i3 - 1
      if i4 != 0:
        for j in range(2,numClass+1):
          if mat2[l][j] >= (v + mat2[i4][j - 1]):
            mat1[l][j] = i3
            mat2[l][j] = v + mat2[i4][j - 1]
    mat1[l][1] = 1
    mat2[l][1] = v
  k = len(dataList)
  kclass = []
  for i in range(0,numClass+1):
    kclass.append(0)
  kclass[numClass] = float(dataList[len(dataList) - 1])
  countNum = numClass
  while countNum >= 2:#print "rank = " + str(mat1[k][countNum])
    id = int((mat1[k][countNum]) - 2)
    #print "val = " + str(dataList[id])
    kclass[countNum - 1] = dataList[id]
    k = int((mat1[k][countNum] - 1))
    countNum -= 1
  return kclass
  
def getGVF( dataList, numClass ):
  """
  The Goodness of Variance Fit (GVF) is found by taking the 
  difference between the squared deviations
  from the array mean (SDAM) and the squared deviations from the 
  class means (SDCM), and dividing by the SDAM
  """
  breaks = getJenksBreaks(dataList, numClass)
  dataList.sort()
  listMean = sum(dataList)/len(dataList)
  print listMean
  SDAM = 0.0
  for i in range(0,len(dataList)):
    sqDev = (dataList[i] - listMean)**2
    SDAM += sqDev
  SDCM = 0.0
  for i in range(0,numClass):
    if breaks[i] == 0:
      classStart = 0
    else:
      classStart = dataList.index(breaks[i])
      classStart += 1
    classEnd = dataList.index(breaks[i+1])
    classList = dataList[classStart:classEnd+1]
    classMean = sum(classList)/len(classList)
    print classMean
    preSDCM = 0.0
    for j in range(0,len(classList)):
      sqDev2 = (classList[j] - classMean)**2
      preSDCM += sqDev2
    SDCM += preSDCM
  return (SDAM - SDCM)/SDAM
  
# written by Drew
# used after running getJenksBreaks()
def classify(value, breaks):
  for i in range(1, len(breaks)):
    if value < breaks[i]:
      return i
  return len(breaks) - 1

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