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annotate python/utils.py @ 672:5473b7460375

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moved and rationalized imports in modules
author Nicolas Saunier <nicolas.saunier@polymtl.ca>
date Tue, 26 May 2015 13:53:40 +0200
parents 849f5f8bf4b9
children 01b89182891a
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1 #! /usr/bin/env python
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2 ''' Generic utilities.'''
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4 import matplotlib.pyplot as plt
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5 from datetime import time, datetime
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6 from math import sqrt, ceil, floor
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7 from scipy.stats import kruskal, shapiro
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8 from numpy import zeros, array, exp, sum as npsum, arange, cumsum
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9
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10 datetimeFormat = "%Y-%m-%d %H:%M:%S"
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12 #########################
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13 # Enumerations
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14 #########################
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15
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16 def inverseEnumeration(l):
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17 'Returns the dictionary that provides for each element in the input list its index in the input list'
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18 result = {}
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19 for i,x in enumerate(l):
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20 result[x] = i
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21 return result
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22
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23 #########################
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24 # Simple statistics
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25 #########################
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27 def sampleSize(stdev, tolerance, percentConfidence, printLatex = False):
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28 from scipy.stats.distributions import norm
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29 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1)*100)/100. # 1.-(100-percentConfidence)/200.
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30 if printLatex:
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31 print('${0}^2\\frac{{{1}^2}}{{{2}^2}}$'.format(k, stdev, tolerance))
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32 return (k*stdev/tolerance)**2
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33
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34 def confidenceInterval(mean, stdev, nSamples, percentConfidence, trueStd = True, printLatex = False):
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35 '''if trueStd, use normal distribution, otherwise, Student
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36
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37 Use otherwise t.interval or norm.interval
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38 ex: norm.interval(0.95, loc = 0., scale = 2.3/sqrt(11))
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39 t.interval(0.95, 10, loc=1.2, scale = 2.3/sqrt(nSamples))
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40 loc is mean, scale is sigma/sqrt(n) (for Student, 10 is df)'''
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41 from scipy.stats.distributions import norm, t
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42 if trueStd:
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43 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1)*100)/100. # 1.-(100-percentConfidence)/200.
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44 else: # use Student
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45 k = round(t.ppf(0.5+percentConfidence/200., nSamples-1)*100)/100.
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46 e = k*stdev/sqrt(nSamples)
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47 if printLatex:
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48 print('${0} \pm {1}\\frac{{{2}}}{{\sqrt{{{3}}}}}$'.format(mean, k, stdev, nSamples))
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49 return mean-e, mean+e
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51 def computeChi2(expected, observed):
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52 '''Returns the Chi2 statistics'''
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53 result = 0.
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54 for e, o in zip(expected, observed):
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55 result += ((e-o)*(e-o))/e
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56 return result
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57
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58 class EmpiricalDistribution(object):
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59 def nSamples(self):
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60 return sum(self.counts)
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61
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62 def cumulativeDensityFunction(sample, normalized = False):
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63 '''Returns the cumulative density function of the sample of a random variable'''
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64 xaxis = sorted(sample)
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65 counts = arange(1,len(sample)+1) # dtype = float
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66 if normalized:
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67 counts /= float(len(sample))
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68 return xaxis, counts
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69
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70 class EmpiricalDiscreteDistribution(EmpiricalDistribution):
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71 '''Class to represent a sample of a distribution for a discrete random variable
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72 '''
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73 def __init__(self, categories, counts):
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74 self.categories = categories
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75 self.counts = counts
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76
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77 def mean(self):
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78 result = [float(x*y) for x,y in zip(self.categories, self.counts)]
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79 return npsum(result)/self.nSamples()
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80
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81 def var(self, mean = None):
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82 if not mean:
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83 m = self.mean()
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84 else:
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85 m = mean
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86 result = 0.
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87 squares = [float((x-m)*(x-m)*y) for x,y in zip(self.categories, self.counts)]
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88 return npsum(squares)/(self.nSamples()-1)
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89
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90 def referenceCounts(self, probability):
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91 '''probability is a function that returns the probability of the random variable for the category values'''
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92 refProba = [probability(c) for c in self.categories]
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93 refProba[-1] = 1-npsum(refProba[:-1])
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94 refCounts = [r*self.nSamples() for r in refProba]
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95 return refCounts, refProba
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96
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97 class EmpiricalContinuousDistribution(EmpiricalDistribution):
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98 '''Class to represent a sample of a distribution for a continuous random variable
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99 with the number of observations for each interval
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100 intervals (categories variable) are defined by their left limits, the last one being the right limit
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101 categories contain therefore one more element than the counts'''
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102 def __init__(self, categories, counts):
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103 # todo add samples for initialization and everything to None? (or setSamples?)
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104 self.categories = categories
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105 self.counts = counts
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106
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107 def mean(self):
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108 result = 0.
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109 for i in range(len(self.counts)-1):
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110 result += self.counts[i]*(self.categories[i]+self.categories[i+1])/2
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111 return result/self.nSamples()
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112
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113 def var(self, mean = None):
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114 if not mean:
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115 m = self.mean()
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116 else:
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117 m = mean
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118 result = 0.
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119 for i in range(len(self.counts)-1):
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120 mid = (self.categories[i]+self.categories[i+1])/2
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121 result += self.counts[i]*(mid - m)*(mid - m)
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122 return result/(self.nSamples()-1)
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123
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124 def referenceCounts(self, cdf):
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125 '''cdf is a cumulative distribution function
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126 returning the probability of the variable being less that x'''
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127 # refCumulativeCounts = [0]#[cdf(self.categories[0][0])]
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128 # for inter in self.categories:
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129 # refCumulativeCounts.append(cdf(inter[1]))
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130 refCumulativeCounts = [cdf(x) for x in self.categories[1:-1]]
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131
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132 refProba = [refCumulativeCounts[0]]
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parents: 32
diff changeset
133 for i in xrange(1,len(refCumulativeCounts)):
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parents: 32
diff changeset
134 refProba.append(refCumulativeCounts[i]-refCumulativeCounts[i-1])
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parents: 32
diff changeset
135 refProba.append(1-refCumulativeCounts[-1])
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parents: 32
diff changeset
136 refCounts = [p*self.nSamples() for p in refProba]
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parents: 32
diff changeset
137
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parents: 32
diff changeset
138 return refCounts, refProba
31
c000f37c316d moved tests to independent file, added chi2 computation
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parents: 29
diff changeset
139
77
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diff changeset
140 def printReferenceCounts(self, refCounts=None):
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parents: 76
diff changeset
141 if refCounts:
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parents: 76
diff changeset
142 ref = refCounts
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parents: 76
diff changeset
143 else:
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parents: 76
diff changeset
144 ref = self.referenceCounts
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parents: 76
diff changeset
145 for i in xrange(len(ref[0])):
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parents: 76
diff changeset
146 print('{0}-{1} & {2:0.3} & {3:0.3} \\\\'.format(self.categories[i],self.categories[i+1],ref[1][i], ref[0][i]))
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parents: 76
diff changeset
147
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parents: 76
diff changeset
148
31
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diff changeset
149 #########################
370
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parents: 369
diff changeset
150 # maths section
27
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diff changeset
151 #########################
24
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152
433
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diff changeset
153 # def kernelSmoothing(sampleX, X, Y, weightFunc, halfwidth):
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154 # '''Returns a smoothed weighted version of Y at the predefined values of sampleX
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diff changeset
155 # Sum_x weight(sample_x,x) * y(x)'''
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diff changeset
156 # from numpy import zeros, array
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diff changeset
157 # smoothed = zeros(len(sampleX))
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diff changeset
158 # for i,x in enumerate(sampleX):
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diff changeset
159 # weights = array([weightFunc(x,xx, halfwidth) for xx in X])
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diff changeset
160 # if sum(weights)>0:
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parents: 423
diff changeset
161 # smoothed[i] = sum(weights*Y)/sum(weights)
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parents: 423
diff changeset
162 # else:
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diff changeset
163 # smoothed[i] = 0
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diff changeset
164 # return smoothed
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165
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diff changeset
166 def kernelSmoothing(x, X, Y, weightFunc, halfwidth):
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diff changeset
167 '''Returns the smoothed estimate of (X,Y) at x
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diff changeset
168 Sum_x weight(sample_x,x) * y(x)'''
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diff changeset
169 weights = array([weightFunc(x,observedx, halfwidth) for observedx in X])
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diff changeset
170 if sum(weights)>0:
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parents: 423
diff changeset
171 return sum(weights*Y)/sum(weights)
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diff changeset
172 else:
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diff changeset
173 return 0
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parents: 423
diff changeset
174
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parents: 423
diff changeset
175 def uniform(center, x, halfwidth):
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parents: 423
diff changeset
176 if abs(center-x)<halfwidth:
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parents: 423
diff changeset
177 return 1.
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parents: 423
diff changeset
178 else:
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diff changeset
179 return 0.
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diff changeset
180
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diff changeset
181 def gaussian(center, x, halfwidth):
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diff changeset
182 return exp(-((center-x)/halfwidth)**2/2)
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parents: 423
diff changeset
183
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parents: 423
diff changeset
184 def epanechnikov(center, x, halfwidth):
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parents: 423
diff changeset
185 diff = abs(center-x)
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parents: 423
diff changeset
186 if diff<halfwidth:
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diff changeset
187 return 1.-(diff/halfwidth)**2
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parents: 423
diff changeset
188 else:
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diff changeset
189 return 0.
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diff changeset
190
434
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parents: 433
diff changeset
191 def triangular(center, x, halfwidth):
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parents: 433
diff changeset
192 diff = abs(center-x)
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parents: 433
diff changeset
193 if diff<halfwidth:
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parents: 433
diff changeset
194 return 1.-abs(diff/halfwidth)
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parents: 433
diff changeset
195 else:
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diff changeset
196 return 0.
433
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parents: 423
diff changeset
197
518
0c86c73f3c09 median smoothing
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parents: 511
diff changeset
198 def medianSmoothing(x, X, Y, halfwidth):
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parents: 511
diff changeset
199 '''Returns the media of Y's corresponding to X's in the interval [x-halfwidth, x+halfwidth]'''
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parents: 511
diff changeset
200 from numpy import median
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parents: 511
diff changeset
201 return median([y for observedx, y in zip(X,Y) if abs(x-observedx)<halfwidth])
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parents: 511
diff changeset
202
521
3707eeb20f25 changed argMaxDict name to argmaxDict
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parents: 518
diff changeset
203 def argmaxDict(d):
561
ee45c6eb6d49 added Mohamed Gomaa Mohamed function to smooth object trajectories
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parents: 553
diff changeset
204 return max(d, key=d.get)
279
3af4c267a7bf generic simple LCSS
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parents: 276
diff changeset
205
395
6fba1ab040f1 minor modification to framestotime
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parents: 391
diff changeset
206 def framesToTime(nFrames, frameRate, initialTime = time()):
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parents: 391
diff changeset
207 '''returns a datetime.time for the time in hour, minutes and seconds
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parents: 391
diff changeset
208 initialTime is a datetime.time'''
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parents: 391
diff changeset
209 seconds = int(floor(float(nFrames)/float(frameRate))+initialTime.hour*3600+initialTime.minute*60+initialTime.second)
261
4aa792cb0fa9 changing framesToTime to return a datetime.time
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 248
diff changeset
210 h = int(floor(seconds/3600.))
248
571ba5ed22e2 added utils for bus processing
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parents: 241
diff changeset
211 seconds = seconds - h*3600
261
4aa792cb0fa9 changing framesToTime to return a datetime.time
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 248
diff changeset
212 m = int(floor(seconds/60))
248
571ba5ed22e2 added utils for bus processing
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parents: 241
diff changeset
213 seconds = seconds - m*60
262
a048066bd20f correcting bug in framesToTime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 261
diff changeset
214 return time(h, m, seconds)
248
571ba5ed22e2 added utils for bus processing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 241
diff changeset
215
381
387cc0142211 script to replay event annotations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 376
diff changeset
216 def timeToFrames(t, frameRate):
387cc0142211 script to replay event annotations
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parents: 376
diff changeset
217 return frameRate*(t.hour*3600+t.minute*60+t.second)
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parents: 376
diff changeset
218
241
ee1caff48b03 added function to sort to list of paired data X,Y
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
219 def sortXY(X,Y):
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parents: 235
diff changeset
220 'returns the sorted (x, Y(x)) sorted on X'
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
221 D = {}
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
222 for x, y in zip(X,Y):
ee1caff48b03 added function to sort to list of paired data X,Y
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parents: 235
diff changeset
223 D[x]=y
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
224 xsorted = sorted(D.keys())
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parents: 235
diff changeset
225 return xsorted, [D[x] for x in xsorted]
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parents: 235
diff changeset
226
32
48e56179c39e added ceil function
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parents: 31
diff changeset
227 def ceilDecimals(v, nDecimals):
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parents: 31
diff changeset
228 '''Rounds the number at the nth decimal
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parents: 31
diff changeset
229 eg 1.23 at 0 decimal is 2, at 1 decimal is 1.3'''
670
f72ed51c6b65 corrected other missing imports
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parents: 669
diff changeset
230 tens = 10**nDecimals
32
48e56179c39e added ceil function
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parents: 31
diff changeset
231 return ceil(v*tens)/tens
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parents: 31
diff changeset
232
152
74b1fc68d4df re-organized code to avoid cyclic python module dependencies
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 116
diff changeset
233 def inBetween(bound1, bound2, x):
569
0057c04f94d5 work in progress on intersections (for PET)
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parents: 561
diff changeset
234 return bound1 <= x <= bound2 or bound2 <= x <= bound1
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
235
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
236 def pointDistanceL2(x1,y1,x2,y2):
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
237 ''' Compute point-to-point distance (L2 norm, ie Euclidean distance)'''
0057c04f94d5 work in progress on intersections (for PET)
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parents: 561
diff changeset
238 return sqrt((x2-x1)**2+(y2-y1)**2)
24
6fb59cfb201e first version of segmentIntersection
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parents: 19
diff changeset
239
6fb59cfb201e first version of segmentIntersection
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parents: 19
diff changeset
240 def crossProduct(l1, l2):
6fb59cfb201e first version of segmentIntersection
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parents: 19
diff changeset
241 return l1[0]*l2[1]-l1[1]*l2[0]
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parents: 19
diff changeset
242
574
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
243 def cat_mvgavg(cat_list, halfWidth):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
244 ''' Return a list of categories/values smoothed according to a window.
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
245 halfWidth is the search radius on either side'''
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
246 from copy import deepcopy
659
784298512b60 minor modifications
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 637
diff changeset
247 smoothed = deepcopy(cat_list)
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parents: 637
diff changeset
248 for point in range(len(cat_list)):
574
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
249 lower_bound_check = max(0,point-halfWidth)
659
784298512b60 minor modifications
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 637
diff changeset
250 upper_bound_check = min(len(cat_list)-1,point+halfWidth+1)
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 637
diff changeset
251 window_values = cat_list[lower_bound_check:upper_bound_check]
574
e24eeb244698 first implementation of projection to curvilinear coordinates
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parents: 569
diff changeset
252 smoothed[point] = max(set(window_values), key=window_values.count)
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parents: 569
diff changeset
253 return smoothed
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parents: 569
diff changeset
254
547
97c5fef5b2d6 corrected bugs
MohamedGomaa
parents: 521
diff changeset
255 def filterMovingWindow(inputSignal, halfWidth):
29
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
256 '''Returns an array obtained after the smoothing of the input by a moving average
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
257 The first and last points are copied from the original.'''
547
97c5fef5b2d6 corrected bugs
MohamedGomaa
parents: 521
diff changeset
258 from numpy import ones,convolve,array
29
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
259 width = float(halfWidth*2+1)
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parents: 27
diff changeset
260 win = ones(width,'d')
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parents: 27
diff changeset
261 result = convolve(win/width,array(inputSignal),'same')
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
262 result[:halfWidth] = inputSignal[:halfWidth]
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
263 result[-halfWidth:] = inputSignal[-halfWidth:]
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
264 return result
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
265
199
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
266 def linearRegression(x, y, deg = 1, plotData = False):
ca9d9104afba added utility to calibrate polynoms and plot
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parents: 197
diff changeset
267 '''returns the least square estimation of the linear regression of y = ax+b
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
268 as well as the plot'''
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
269 from numpy.lib.polynomial import polyfit
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
270 from numpy.core.multiarray import arange
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
271 coef = polyfit(x, y, deg)
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
272 if plotData:
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
273 def poly(x):
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274 result = 0
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275 for i in range(len(coef)):
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276 result += coef[i]*x**(len(coef)-i-1)
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277 return result
668
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278 plt.plot(x, y, 'x')
199
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279 xx = arange(min(x), max(x),(max(x)-min(x))/1000)
668
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280 plt.plot(xx, [poly(z) for z in xx])
199
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281 return coef
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282
668
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283 def correlation(data, correlationMethod = 'pearson', plotFigure = False, displayNames = None, figureFilename = None):
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284 '''Computes (and displays) the correlation matrix for a pandas DataFrame'''
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285 c=data.corr(correlationMethod)
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286 if plotFigure:
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287 fig = plt.figure(figsize=(2+0.4*c.shape[0], 0.4*c.shape[0]))
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288 fig.add_subplot(1,1,1)
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289 #plt.imshow(np.fabs(c), interpolation='none')
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290 plt.imshow(c, vmin=-1., vmax = 1., interpolation='none', cmap = 'RdYlBu_r') # coolwarm
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291 colnames = [displayNames.get(s.strip(), s.strip()) for s in c.columns.tolist()]
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292 #correlation.plot_corr(c, xnames = colnames, normcolor=True, title = filename)
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293 plt.xticks(range(len(colnames)), colnames, rotation=90)
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294 plt.yticks(range(len(colnames)), colnames)
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295 plt.tick_params('both', length=0)
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296 plt.subplots_adjust(bottom = 0.29)
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297 plt.colorbar()
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298 plt.title('Correlation ({})'.format(correlationMethod))
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299 plt.tight_layout()
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300 if figureFilename is not None:
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301 plt.savefig(figureFilename, dpi = 150, transparent = True)
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302 return c
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303
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304 def addDummies(data, variables, allVariables = True):
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305 '''Add binary dummy variables for each value of a nominal variable
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306 in a pandas DataFrame'''
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307 from numpy import NaN, dtype
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308 newVariables = []
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309 for var in variables:
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310 if var in data.columns and data.dtypes[var] == dtype('O') and len(data[var].unique()) > 2:
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311 values = data[var].unique()
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312 if not allVariables:
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313 values = values[:-1]
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314 for val in values:
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315 if val is not NaN:
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316 newVariable = (var+'_{}'.format(val)).replace('.','').replace(' ','').replace('-','')
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317 data[newVariable] = (data[var] == val)
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318 newVariables.append(newVariable)
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319 return newVariables
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320
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321 def kruskalWallis(data, dependentVariable, independentVariable, plotFigure = False, figureFilenamePrefix = None, figureFileType = 'pdf'):
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322 '''Studies the influence of (nominal) independent variable over the dependent variable
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323
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324 Makes tests if the conditional distributions are normal
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325 using the Shapiro-Wilk test (in which case ANOVA could be used)
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326 Implements uses the non-parametric Kruskal Wallis test'''
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327 tmp = data[data[independentVariable].notnull()]
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328 independentVariableValues = sorted(tmp[independentVariable].unique().tolist())
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329 if len(independentVariableValues) >= 2:
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330 for x in independentVariableValues:
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331 print('Shapiro-Wilk normality test for {} when {}={}: {} obs'.format(dependentVariable,independentVariable, x, len(tmp.loc[tmp[independentVariable] == x, dependentVariable])))
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332 if len(tmp.loc[tmp[independentVariable] == x, dependentVariable]) >= 3:
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333 print shapiro(tmp.loc[tmp[independentVariable] == x, dependentVariable])
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diff changeset
334 if plotFigure:
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335 plt.figure()
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336 plt.boxplot([tmp.loc[tmp[independentVariable] == x, dependentVariable] for x in independentVariableValues])
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337 #q25, q75 = tmp[dependentVariable].quantile([.25, .75])
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338 #plt.ylim(ymax = q75+1.5*(q75-q25))
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339 plt.xticks(range(1,len(independentVariableValues)+1), independentVariableValues)
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340 plt.title('{} vs {}'.format(dependentVariable, independentVariable))
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341 if figureFilenamePrefix is not None:
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342 plt.savefig(figureFilenamePrefix+'{}-{}.{}'.format(dependentVariable, independentVariable, figureFileType))
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343 #else:
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344 # TODO formatter le tableau (html?)
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345 print tmp.groupby([independentVariable])[dependentVariable].describe().unstack().sort(['50%'], ascending = False)
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346 return kruskal(*[tmp.loc[tmp[independentVariable] == x, dependentVariable] for x in independentVariableValues])
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347 else:
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348 return None
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349
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350 def prepareRegression(data, dependentVariable, independentVariables, maxCorrelationThreshold, correlations, maxCorrelationP, correlationFunc):
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351 '''Removes variables from candidate independent variables if
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352 - if two independent variables are correlated (> maxCorrelationThreshold), one is removed
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353 - if an independent variable is not correlated with the dependent variable (p>maxCorrelationP)
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354 Returns the remaining non-correlated variables, correlated with the dependent variable
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355
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356 correlationFunc is spearmanr or pearsonr from scipy.stats
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357
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358 TODO: pass the dummies for nominal variables and remove if all dummies are correlated, or none is correlated with the dependentvariable'''
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diff changeset
359 from numpy import dtype
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360 from copy import copy
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361 result = copy(independentVariables)
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362 for v1 in independentVariables:
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363 if v1 in correlations.index:
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364 for v2 in independentVariables:
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365 if v2 != v1 and v2 in correlations.index:
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diff changeset
366 if abs(correlations.loc[v1, v2]) > maxCorrelationThreshold:
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diff changeset
367 if v1 in result and v2 in result:
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368 print('Removing {} (correlation {} with {})'.format(v2, correlations.loc[v1, v2], v1))
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diff changeset
369 result.remove(v2)
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diff changeset
370 #regressionIndependentVariables = result
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371 for var in copy(result):
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diff changeset
372 if data.dtypes[var] != dtype('O'):
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373 cor, p = correlationFunc(data[dependentVariable], data[var])
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374 if p > maxCorrelationP:
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375 print('Removing {} (no correlation p={})'.format(var, p))
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diff changeset
376 result.remove(var)
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377 return result
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378
667
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379
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380 #########################
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381 # regression analysis using statsmodels (and pandas)
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382 #########################
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383
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diff changeset
384 # TODO make class for experiments?
668
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385 # TODO add tests with public dataset downloaded from Internet (IRIS et al)
667
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parents: 665
diff changeset
386 def modelString(experiment, dependentVariable, independentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
387 return dependentVariable+' ~ '+' + '.join([independentVariable for independentVariable in independentVariables if experiment[independentVariable]])
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
388
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
389 def runModel(experiment, data, dependentVariable, independentVariables, regressionType = 'ols'):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
390 import statsmodels.formula.api as smf
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
391 modelStr = modelString(experiment, dependentVariable, independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
392 if regressionType == 'ols':
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
393 model = smf.ols(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
394 elif regressionType == 'gls':
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
395 model = smf.gls(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
396 elif regressionType == 'rlm':
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
397 model = smf.rlm(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
398 else:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
399 print('Unknown regression type {}. Exiting'.format(regressionType))
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
400 import sys
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
401 sys.exit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
402 return model.fit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
403
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
404 def runModels(experiments, data, dependentVariable, independentVariables, regressionType = 'ols'):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
405 '''Runs several models and stores 3 statistics
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
406 adjusted R2, condition number (should be small, eg < 1000)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
407 and p-value for Shapiro-Wilk test of residual normality'''
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
408 for i,experiment in experiments.iterrows():
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
409 if experiment[independentVariables].any():
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
410 results = runModel(experiment, data, dependentVariable, independentVariables, regressionType = 'ols')
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
411 experiments.loc[i,'r2adj'] = results.rsquared_adj
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
412 experiments.loc[i,'condNum'] = results.condition_number
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
413 experiments.loc[i, 'shapiroP'] = shapiro(results.resid)[1]
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
414 experiments.loc[i,'nobs'] = int(results.nobs)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
415 return experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
416
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
417 def generateExperiments(independentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
418 '''Generates all possible models for including or not each independent variable'''
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
419 from numpy import nan
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
420 from pandas import DataFrame
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
421 experiments = {}
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
422 nIndependentVariables = len(independentVariables)
669
df6be882f325 bug corrected
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 668
diff changeset
423 if nIndependentVariables != len(set(independentVariables)):
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
424 print("Duplicate variables. Exiting")
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
425 import sys
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
426 sys.exit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
427 nModels = 2**nIndependentVariables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
428 for i,var in enumerate(independentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
429 pattern = [False]*(2**i)+[True]*(2**i)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
430 experiments[var] = pattern*(2**(nIndependentVariables-i-1))
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
431 experiments = DataFrame(experiments)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
432 experiments['r2adj'] = 0.
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
433 experiments['condNum'] = nan
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
434 experiments['shapiroP'] = -1
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
435 experiments['nobs'] = -1
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
436 return experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
437
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
438 def findBestModel(data, dependentVariable, independentVariables, regressionType = 'ols', nProcesses = 1):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
439 '''Generates all possible model with the independentVariables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
440 and runs them, saving the results in experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
441 with multiprocess option'''
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
442 from pandas import concat
671
849f5f8bf4b9 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 670
diff changeset
443 from multiprocessing import Pool
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
444 experiments = generateExperiments(independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
445 nModels = len(experiments)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
446 print("Running {} models with {} processes".format(nModels, nProcesses))
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
447 if nProcesses == 1:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
448 return runModels(experiments, data, dependentVariable, independentVariables, regressionType)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
449 else:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
450 pool = Pool(processes = nProcesses)
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
451 chunkSize = int(ceil(nModels/nProcesses))
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
452 jobs = [pool.apply_async(runModels, args = (experiments[i*chunkSize:(i+1)*chunkSize], data, dependentVariable, independentVariables, regressionType)) for i in range(nProcesses)]
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
453 return concat([job.get() for job in jobs])
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
454
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
455 def findBestModelFwd(data, dependentVariable, independentVariables, modelFunc, experiments = None):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
456 '''Forward search for best model (based on adjusted R2)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
457 Randomly starting with one variable and adding randomly variables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
458 if they improve the model
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
459
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
460 The results are added to experiments if provided as argument
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
461 Storing in experiment relies on the index being the number equal
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
462 to the binary code derived from the independent variables'''
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
463 from numpy.random import permutation as nppermutation
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
464 if experiments is None:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
465 experiments = generateExperiments(independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
466 nIndependentVariables = len(independentVariables)
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
467 permutation = nppermutation(range(nIndependentVariables)).tolist()
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
468 variableMapping = {j: independentVariables[i] for i,j in enumerate(permutation)}
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
469 print('Tested variables '+', '.join([variableMapping[i] for i in xrange(nIndependentVariables)]))
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
470 bestModel = [False]*nIndependentVariables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
471 currentVarNum = 0
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
472 currentR2Adj = 0.
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
473 for currentVarNum in xrange(nIndependentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
474 currentModel = [i for i in bestModel]
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
475 currentModel[currentVarNum] = True
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
476 rowIdx = sum([0]+[2**i for i in xrange(nIndependentVariables) if currentModel[permutation[i]]])
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
477 #print currentVarNum, sum(currentModel), ', '.join([independentVariables[i] for i in xrange(nIndependentVariables) if currentModel[permutation[i]]])
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
478 if experiments.loc[rowIdx, 'shapiroP'] < 0:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
479 modelStr = modelString(experiments.loc[rowIdx], dependentVariable, independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
480 model = modelFunc(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
481 results = model.fit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
482 experiments.loc[rowIdx, 'r2adj'] = results.rsquared_adj
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
483 experiments.loc[rowIdx, 'condNum'] = results.condition_number
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
484 experiments.loc[rowIdx, 'shapiroP'] = shapiro(results.resid)[1]
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
485 experiments.loc[rowIdx, 'nobs'] = int(results.nobs)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
486 if currentR2Adj < experiments.loc[rowIdx, 'r2adj']:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
487 currentR2Adj = experiments.loc[rowIdx, 'r2adj']
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
488 bestModel[currentVarNum] = True
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
489 return experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
490
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
491 def displayModelResults(results, model = None):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
492 import statsmodels.api as sm
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
493 '''Displays some model results'''
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
494 print results.summary()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
495 print('Shapiro-Wilk normality test for residuals: {}'.format(shapiro(results.resid)))
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
496 if model is not None:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
497 plt.figure()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
498 plt.plot(results.predict(), model.endog, 'x')
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
499 x=plt.xlim()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
500 y=plt.ylim()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
501 plt.plot([max(x[0], y[0]), min(x[1], y[1])], [max(x[0], y[0]), min(x[1], y[1])], 'r')
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
502 plt.title('true vs predicted')
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
503 plt.figure()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
504 plt.plot(results.predict(), results.resid, 'x')
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
505 plt.title('residuals vs predicted')
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
506 sm.qqplot(results.resid, fit = True, line = '45')
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
507
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
508
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
509 #########################
455
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
510 # iterable section
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
511 #########################
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
512
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
513 def mostCommon(L):
456
825e5d49325d slight update
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 455
diff changeset
514 '''Returns the most frequent element in a iterable
825e5d49325d slight update
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 455
diff changeset
515
825e5d49325d slight update
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 455
diff changeset
516 taken from http://stackoverflow.com/questions/1518522/python-most-common-element-in-a-list'''
455
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
517 from itertools import groupby
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
518 from operator import itemgetter
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
519 # get an iterable of (item, iterable) pairs
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
520 SL = sorted((x, i) for i, x in enumerate(L))
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
521 # print 'SL:', SL
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
522 groups = groupby(SL, key=itemgetter(0))
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
523 # auxiliary function to get "quality" for an item
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
524 def _auxfun(g):
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
525 item, iterable = g
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
526 count = 0
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
527 min_index = len(L)
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
528 for _, where in iterable:
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
529 count += 1
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
530 min_index = min(min_index, where)
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
531 # print 'item %r, count %r, minind %r' % (item, count, min_index)
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
532 return count, -min_index
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
533 # pick the highest-count/earliest item
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
534 return max(groups, key=_auxfun)[0]
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
535
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
536 #########################
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
537 # sequence section
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
538 #########################
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
539
665
15e244d2a1b5 corrected bug with circular import for VideoFilenameAddable, moved to base module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 659
diff changeset
540 class LCSS(object):
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
541 '''Class that keeps the LCSS parameters
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
542 and puts together the various computations'''
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
543 def __init__(self, similarityFunc, delta = float('inf'), aligned = False, lengthFunc = min):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
544 self.similarityFunc = similarityFunc
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
545 self.aligned = aligned
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
546 self.delta = delta
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
547 self.lengthFunc = lengthFunc
389
6d26dcc7bba0 modifications to compute alignment for None indicators
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
548 self.subSequenceIndices = [(0,0)]
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
549
373
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
550 def similarities(self, l1, l2, jshift=0):
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
551 from numpy import zeros, int as npint
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
552 n1 = len(l1)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
553 n2 = len(l2)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
554 self.similarityTable = zeros((n1+1,n2+1), dtype = npint)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
555 for i in xrange(1,n1+1):
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
556 for j in xrange(max(1,i-jshift-self.delta),min(n2,i-jshift+self.delta)+1):
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
557 if self.similarityFunc(l1[i-1], l2[j-1]):
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
558 self.similarityTable[i,j] = self.similarityTable[i-1,j-1]+1
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
559 else:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
560 self.similarityTable[i,j] = max(self.similarityTable[i-1,j], self.similarityTable[i,j-1])
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
561
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
562 def subSequence(self, i, j):
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
563 '''Returns the subsequence of two sequences
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
564 http://en.wikipedia.org/wiki/Longest_common_subsequence_problem'''
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
565 if i == 0 or j == 0:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
566 return []
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
567 elif self.similarityTable[i][j] == self.similarityTable[i][j-1]:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
568 return self.subSequence(i, j-1)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
569 elif self.similarityTable[i][j] == self.similarityTable[i-1][j]:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
570 return self.subSequence(i-1, j)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
571 else:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
572 return self.subSequence(i-1, j-1) + [(i-1,j-1)]
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
573
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
574 def _compute(self, _l1, _l2, computeSubSequence = False):
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
575 '''returns the longest common subsequence similarity
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
576 based on the threshold on distance between two elements of lists l1, l2
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
577 similarityFunc returns True or False whether the two points are considered similar
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
578
607
84690dfe5560 add some functions for behaviour analysis
MohamedGomaa
parents: 574
diff changeset
579 if aligned, returns the best matching if using a finite delta by shifting the series alignments
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
580
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
581 eg distance(p1, p2) < epsilon
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
582 '''
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
583 if len(_l2) < len(_l1): # l1 is the shortest
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
584 l1 = _l2
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
585 l2 = _l1
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
586 revertIndices = True
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
587 else:
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
588 l1 = _l1
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
589 l2 = _l2
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
590 revertIndices = False
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
591 n1 = len(l1)
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
592 n2 = len(l2)
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
593
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
594 if self.aligned:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
595 lcssValues = {}
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
596 similarityTables = {}
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
597 for i in xrange(-n2-self.delta+1, n1+self.delta): # interval such that [i-shift-delta, i-shift+delta] is never empty, which happens when i-shift+delta < 1 or when i-shift-delta > n2
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
598 self.similarities(l1, l2, i)
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
599 lcssValues[i] = self.similarityTable.max()
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
600 similarityTables[i] = self.similarityTable
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
601 #print self.similarityTable
521
3707eeb20f25 changed argMaxDict name to argmaxDict
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 518
diff changeset
602 alignmentShift = argmaxDict(lcssValues) # ideally get the medium alignment shift, the one that minimizes distance
389
6d26dcc7bba0 modifications to compute alignment for None indicators
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
603 self.similarityTable = similarityTables[alignmentShift]
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
604 else:
389
6d26dcc7bba0 modifications to compute alignment for None indicators
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
605 alignmentShift = 0
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
606 self.similarities(l1, l2)
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
607
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
608 # threshold values for the useful part of the similarity table are n2-n1-delta and n1-n2-delta
389
6d26dcc7bba0 modifications to compute alignment for None indicators
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
609 self.similarityTable = self.similarityTable[:min(n1, n2+alignmentShift+self.delta)+1, :min(n2, n1-alignmentShift+self.delta)+1]
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
610
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
611 if computeSubSequence:
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
612 self.subSequenceIndices = self.subSequence(self.similarityTable.shape[0]-1, self.similarityTable.shape[1]-1)
371
924e38c9f70e work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 370
diff changeset
613 if revertIndices:
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
614 self.subSequenceIndices = [(j,i) for i,j in self.subSequenceIndices]
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
615 return self.similarityTable[-1,-1]
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
616
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
617 def compute(self, l1, l2, computeSubSequence = False):
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
618 '''get methods are to be shadowed in child classes '''
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
619 return self._compute(l1, l2, computeSubSequence)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
620
375
2ea8584aa80a making indicator LCSS work
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 374
diff changeset
621 def computeAlignment(self):
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
622 from numpy import mean
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
623 return mean([j-i for i,j in self.subSequenceIndices])
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
624
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
625 def _computeNormalized(self, l1, l2, computeSubSequence = False):
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
626 ''' compute the normalized LCSS
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
627 ie, the LCSS divided by the min or mean of the indicator lengths (using lengthFunc)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
628 lengthFunc = lambda x,y:float(x,y)/2'''
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
629 return float(self._compute(l1, l2, computeSubSequence))/self.lengthFunc(len(l1), len(l2))
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
630
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
631 def computeNormalized(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
632 return self._computeNormalized(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
633
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
634 def _computeDistance(self, l1, l2, computeSubSequence = False):
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
635 ''' compute the LCSS distance'''
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
636 return 1-self._computeNormalized(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
637
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
638 def computeDistance(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
639 return self._computeDistance(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
640
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
641 #########################
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
642 # plotting section
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
643 #########################
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
644
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
645 def plotPolygon(poly, options = ''):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
646 'Plots shapely polygon poly'
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
647 from numpy.core.multiarray import array
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
648 from matplotlib.pyplot import plot
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
649 from shapely.geometry import Polygon
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
650
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
651 tmp = array(poly.exterior)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
652 plot(tmp[:,0], tmp[:,1], options)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
653
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
654 def stepPlot(X, firstX, lastX, initialCount = 0, increment = 1):
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
655 '''for each value in X, increment by increment the initial count
297
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
656 returns the lists that can be plotted
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
657 to obtain a step plot increasing by one for each value in x, from first to last value
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
658 firstX and lastX should be respectively smaller and larger than all elements in X'''
297
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
659
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
660 sortedX = []
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
661 counts = [initialCount]
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
662 for x in sorted(X):
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
663 sortedX += [x,x]
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
664 counts.append(counts[-1])
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
665 counts.append(counts[-1]+increment)
297
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
666 counts.append(counts[-1])
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
667 return [firstX]+sortedX+[lastX], counts
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
668
665
15e244d2a1b5 corrected bug with circular import for VideoFilenameAddable, moved to base module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 659
diff changeset
669 class PlottingPropertyValues(object):
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
670 def __init__(self, values):
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
671 self.values = values
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
672
116
2bf5b76320c0 moved intersection plotting and added markers for scatter plots
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 115
diff changeset
673 def __getitem__(self, i):
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
674 return self.values[i%len(self.values)]
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
675
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
676 markers = PlottingPropertyValues(['+', '*', ',', '.', 'x', 'D', 's', 'o'])
116
2bf5b76320c0 moved intersection plotting and added markers for scatter plots
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 115
diff changeset
677 scatterMarkers = PlottingPropertyValues(['s','o','^','>','v','<','d','p','h','8','+','x'])
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
678
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
679 linestyles = PlottingPropertyValues(['-', '--', '-.', ':'])
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
680
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
681 colors = PlottingPropertyValues('brgmyck') # 'w'
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
682
115
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
683 def plotIndicatorMap(indicatorMap, squareSize, masked = True, defaultValue=-1):
65
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
684 from numpy import array, arange, ones, ma
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
685 from matplotlib.pyplot import pcolor
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
686 coords = array(indicatorMap.keys())
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
687 minX = min(coords[:,0])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
688 minY = min(coords[:,1])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
689 X = arange(minX, max(coords[:,0])+1.1)*squareSize
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
690 Y = arange(minY, max(coords[:,1])+1.1)*squareSize
115
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
691 C = defaultValue*ones((len(Y), len(X)))
65
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
692 for k,v in indicatorMap.iteritems():
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
693 C[k[1]-minY,k[0]-minX] = v
115
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
694 if masked:
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
695 pcolor(X, Y, ma.masked_where(C==defaultValue,C))
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
696 else:
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
697 pcolor(X, Y, C)
65
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
698
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
699 #########################
637
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
700 # Data download
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
701 #########################
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
702
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
703 def downloadECWeather(stationID, years, months = [], outputDirectoryname = '.', english = True):
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
704 '''Downloads monthly weather data from Environment Canada
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
705 If month is provided (number 1 to 12), it means hourly data for the whole month
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
706 Otherwise, means the data for each day, for the whole year
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
707
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
708 Example: MONTREAL MCTAVISH 10761
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
709 MONTREALPIERRE ELLIOTT TRUDEAU INTL A 5415
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
710
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
711 To get daily data for 2010 and 2011, downloadECWeather(10761, [2010,2011], [], '/tmp')
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
712 To get hourly data for 2009 and 2012, January, March and October, downloadECWeather(10761, [2009,2012], [1,3,10], '/tmp')'''
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
713 import urllib2
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
714 if english:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
715 language = 'e'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
716 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
717 language = 'f'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
718 if len(months) == 0:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
719 timeFrame = 2
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
720 months = [1]
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
721 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
722 timeFrame = 1
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
723
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
724 for year in years:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
725 for month in months:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
726 url = urllib2.urlopen('http://climat.meteo.gc.ca/climateData/bulkdata_{}.html?format=csv&stationID={}&Year={}&Month={}&Day=1&timeframe={}&submit=++T%C3%A9l%C3%A9charger+%0D%0Ades+donn%C3%A9es'.format(language, stationID, year, month, timeFrame))
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
727 data = url.read()
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
728 outFilename = '{}/{}-{}'.format(outputDirectoryname, stationID, year)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
729 if timeFrame == 1:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
730 outFilename += '-{}-hourly'.format(month)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
731 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
732 outFilename += '-daily'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
733 outFilename += '.csv'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
734 out = open(outFilename, 'w')
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
735 out.write(data)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
736 out.close()
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
737
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
738 #########################
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
739 # File I/O
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
740 #########################
24
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
741
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
742 def removeExtension(filename, delimiter = '.'):
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
743 '''Returns the filename minus the extension (all characters after last .)'''
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
744 i = filename.rfind(delimiter)
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
745 if i>0:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
746 return filename[:i]
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
747 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
748 return filename
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
749
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
750 def cleanFilename(s):
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
751 'cleans filenames obtained when contatenating figure characteristics'
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
752 return s.replace(' ','-').replace('.','').replace('/','-')
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
753
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
754 def listfiles(dirname, extension, remove = False):
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
755 '''Returns the list of files with the extension in the directory dirname
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
756 If remove is True, the filenames are stripped from the extension'''
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
757 from os import listdir
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
758 tmp = [f for f in listdir(dirname) if f.endswith(extension)]
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
759 tmp.sort()
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
760 if remove:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
761 return [removeExtension(f, extension) for f in tmp]
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
762 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
763 return tmp
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
764
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
765 def mkdir(dirname):
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
766 'Creates a directory if it does not exist'
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
767 import os
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
768 if not os.path.exists(dirname):
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
769 os.mkdir(dirname)
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
770 else:
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
771 print(dirname+' already exists')
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
772
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
773 def removeFile(filename):
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
774 '''Deletes the file while avoiding raising an error
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
775 if the file does not exist'''
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
776 import os
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
777 if (os.path.exists(filename)):
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
778 os.remove(filename)
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
779 else:
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
780 print(filename+' does not exist')
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
781
42
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
782 def line2Floats(l, separator=' '):
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
783 '''Returns the list of floats corresponding to the string'''
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
784 return [float(x) for x in l.split(separator)]
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
785
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
786 def line2Ints(l, separator=' '):
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
787 '''Returns the list of ints corresponding to the string'''
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
788 return [int(x) for x in l.split(separator)]
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
789
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
790 #########################
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
791 # CLI utils
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
792 #########################
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
793
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
794 def parseCLIOptions(helpMessage, options, cliArgs, optionalOptions=[]):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
795 ''' Simple function to handle similar argument parsing
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
796 Returns the dictionary of options and their values
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
797
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
798 * cliArgs are most likely directly sys.argv
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
799 (only the elements after the first one are considered)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
800
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
801 * options should be a list of strings for getopt options,
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
802 eg ['frame=','correspondences=','video=']
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
803 A value must be provided for each option, or the program quits'''
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
804 import sys, getopt
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
805 from numpy.core.fromnumeric import all
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
806 optionValues, args = getopt.getopt(cliArgs[1:], 'h', ['help']+options+optionalOptions)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
807 optionValues = dict(optionValues)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
808
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
809 if '--help' in optionValues.keys() or '-h' in optionValues.keys():
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
810 print(helpMessage+
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
811 '\n - Compulsory options: '+' '.join([opt.replace('=','') for opt in options])+
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
812 '\n - Non-compulsory options: '+' '.join([opt.replace('=','') for opt in optionalOptions]))
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
813 sys.exit()
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
814
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
815 missingArgument = [('--'+opt.replace('=','') in optionValues.keys()) for opt in options]
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
816 if not all(missingArgument):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
817 print('Missing argument')
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
818 print(optionValues)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
819 sys.exit()
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
820
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
821 return optionValues
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
822
397
b36b00dd27c3 added function to read scene metadata
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 395
diff changeset
823
b36b00dd27c3 added function to read scene metadata
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 395
diff changeset
824 #########################
553
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
825 # Profiling
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
826 #########################
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
827
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
828 def analyzeProfile(profileFilename, stripDirs = True):
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
829 '''Analyze the file produced by cProfile
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
830
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
831 obtained by for example:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
832 - call in script (for main() function in script)
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
833 import cProfile, os
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
834 cProfile.run('main()', os.path.join(os.getcwd(),'main.profile'))
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
835
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
836 - or on the command line:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
837 python -m cProfile [-o profile.bin] [-s sort] scriptfile [arg]'''
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
838 import pstats, os
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
839 p = pstats.Stats(os.path.join(os.pardir, profileFilename))
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
840 if stripDirs:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
841 p.strip_dirs()
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
842 p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
843 p.print_stats(.2)
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
844 #p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
845 # p.print_callees(.1, 'int_prediction.py:')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
846 return p
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
847
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
848 #########################
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
849 # running tests
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
850 #########################
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
851
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
852 if __name__ == "__main__":
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
853 import doctest
2
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
854 import unittest
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
855 suite = doctest.DocFileSuite('tests/utils.txt')
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
856 #suite = doctest.DocTestSuite()
2
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
857 unittest.TextTestRunner().run(suite)
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
858 #doctest.testmod()
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
859 #doctest.testfile("example.txt")