Mercurial Hosting > traffic-intelligence
annotate python/utils.py @ 689:9990ef119bce dev
added version of LCSS with cdist computations
author | Nicolas Saunier <nicolas.saunier@polymtl.ca> |
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date | Mon, 29 Jun 2015 08:35:27 -0400 |
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children | 8d99a9e16644 |
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1 #! /usr/bin/env python |
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2 # -*- coding: utf-8 -*- |
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3 ''' Generic utilities.''' |
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4 |
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5 import matplotlib.pyplot as plt |
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6 from datetime import time, datetime |
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7 from math import sqrt, ceil, floor |
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8 from scipy.stats import kruskal, shapiro |
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9 from scipy.spatial import distance |
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10 from numpy import zeros, array, exp, sum as npsum, int as npint, arange, cumsum, median, isnan, ones, convolve, dtype, isnan, NaN, mean, ma |
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11 |
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12 |
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13 datetimeFormat = "%Y-%m-%d %H:%M:%S" |
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14 |
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15 ######################### |
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16 # Enumerations |
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17 ######################### |
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18 |
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19 def inverseEnumeration(l): |
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20 'Returns the dictionary that provides for each element in the input list its index in the input list' |
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21 result = {} |
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22 for i,x in enumerate(l): |
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23 result[x] = i |
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24 return result |
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25 |
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26 ######################### |
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27 # Simple statistics |
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28 ######################### |
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29 |
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30 def logNormalMeanVar(loc, scale): |
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31 '''location and scale are respectively the mean and standard deviation of the normal in the log-normal distribution |
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32 https://en.wikipedia.org/wiki/Log-normal_distribution''' |
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33 mean = exp(loc+(scale**2)/2) |
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34 var = (exp(loc**2)-1)*exp(2*loc+scale**2) |
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35 return mean, var |
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36 |
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37 def sampleSize(stdev, tolerance, percentConfidence, printLatex = False): |
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38 from scipy.stats.distributions import norm |
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39 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1)*100)/100. # 1.-(100-percentConfidence)/200. |
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40 if printLatex: |
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41 print('${0}^2\\frac{{{1}^2}}{{{2}^2}}$'.format(k, stdev, tolerance)) |
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42 return (k*stdev/tolerance)**2 |
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43 |
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44 def confidenceInterval(mean, stdev, nSamples, percentConfidence, trueStd = True, printLatex = False): |
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45 '''if trueStd, use normal distribution, otherwise, Student |
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46 |
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47 Use otherwise t.interval or norm.interval |
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48 ex: norm.interval(0.95, loc = 0., scale = 2.3/sqrt(11)) |
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49 t.interval(0.95, 10, loc=1.2, scale = 2.3/sqrt(nSamples)) |
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50 loc is mean, scale is sigma/sqrt(n) (for Student, 10 is df)''' |
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51 from scipy.stats.distributions import norm, t |
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52 if trueStd: |
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53 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1)*100)/100. # 1.-(100-percentConfidence)/200. |
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54 else: # use Student |
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55 k = round(t.ppf(0.5+percentConfidence/200., nSamples-1)*100)/100. |
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56 e = k*stdev/sqrt(nSamples) |
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57 if printLatex: |
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58 print('${0} \pm {1}\\frac{{{2}}}{{\sqrt{{{3}}}}}$'.format(mean, k, stdev, nSamples)) |
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59 return mean-e, mean+e |
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60 |
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61 def computeChi2(expected, observed): |
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62 '''Returns the Chi2 statistics''' |
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63 result = 0. |
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64 for e, o in zip(expected, observed): |
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65 result += ((e-o)*(e-o))/e |
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66 return result |
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67 |
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68 class EmpiricalDistribution(object): |
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69 def nSamples(self): |
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70 return sum(self.counts) |
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71 |
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72 def cumulativeDensityFunction(sample, normalized = False): |
276 | 73 '''Returns the cumulative density function of the sample of a random variable''' |
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74 xaxis = sorted(sample) |
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75 counts = arange(1,len(sample)+1) # dtype = float |
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76 if normalized: |
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77 counts /= float(len(sample)) |
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78 return xaxis, counts |
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79 |
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80 class EmpiricalDiscreteDistribution(EmpiricalDistribution): |
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81 '''Class to represent a sample of a distribution for a discrete random variable |
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82 ''' |
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83 def __init__(self, categories, counts): |
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84 self.categories = categories |
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85 self.counts = counts |
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86 |
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87 def mean(self): |
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88 result = [float(x*y) for x,y in zip(self.categories, self.counts)] |
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89 return npsum(result)/self.nSamples() |
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90 |
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91 def var(self, mean = None): |
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92 if not mean: |
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93 m = self.mean() |
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94 else: |
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95 m = mean |
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96 result = 0. |
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97 squares = [float((x-m)*(x-m)*y) for x,y in zip(self.categories, self.counts)] |
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98 return npsum(squares)/(self.nSamples()-1) |
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99 |
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100 def referenceCounts(self, probability): |
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101 '''probability is a function that returns the probability of the random variable for the category values''' |
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102 refProba = [probability(c) for c in self.categories] |
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103 refProba[-1] = 1-npsum(refProba[:-1]) |
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104 refCounts = [r*self.nSamples() for r in refProba] |
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105 return refCounts, refProba |
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106 |
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107 class EmpiricalContinuousDistribution(EmpiricalDistribution): |
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108 '''Class to represent a sample of a distribution for a continuous random variable |
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109 with the number of observations for each interval |
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110 intervals (categories variable) are defined by their left limits, the last one being the right limit |
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111 categories contain therefore one more element than the counts''' |
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112 def __init__(self, categories, counts): |
276 | 113 # todo add samples for initialization and everything to None? (or setSamples?) |
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114 self.categories = categories |
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115 self.counts = counts |
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116 |
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117 def mean(self): |
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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 result += self.counts[i]*(self.categories[i]+self.categories[i+1])/2 |
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121 return result/self.nSamples() |
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122 |
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123 def var(self, mean = None): |
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124 if not mean: |
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125 m = self.mean() |
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126 else: |
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127 m = mean |
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128 result = 0. |
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129 for i in range(len(self.counts)-1): |
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130 mid = (self.categories[i]+self.categories[i+1])/2 |
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131 result += self.counts[i]*(mid - m)*(mid - m) |
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132 return result/(self.nSamples()-1) |
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133 |
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134 def referenceCounts(self, cdf): |
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135 '''cdf is a cumulative distribution function |
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136 returning the probability of the variable being less that x''' |
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137 # refCumulativeCounts = [0]#[cdf(self.categories[0][0])] |
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138 # for inter in self.categories: |
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139 # refCumulativeCounts.append(cdf(inter[1])) |
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140 refCumulativeCounts = [cdf(x) for x in self.categories[1:-1]] |
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141 |
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142 refProba = [refCumulativeCounts[0]] |
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143 for i in xrange(1,len(refCumulativeCounts)): |
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144 refProba.append(refCumulativeCounts[i]-refCumulativeCounts[i-1]) |
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145 refProba.append(1-refCumulativeCounts[-1]) |
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146 refCounts = [p*self.nSamples() for p in refProba] |
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147 |
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148 return refCounts, refProba |
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149 |
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150 def printReferenceCounts(self, refCounts=None): |
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151 if refCounts: |
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152 ref = refCounts |
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153 else: |
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154 ref = self.referenceCounts |
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155 for i in xrange(len(ref[0])): |
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156 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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157 |
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158 |
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159 ######################### |
370
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160 # maths section |
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161 ######################### |
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162 |
433
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163 # def kernelSmoothing(sampleX, X, Y, weightFunc, halfwidth): |
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164 # '''Returns a smoothed weighted version of Y at the predefined values of sampleX |
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165 # Sum_x weight(sample_x,x) * y(x)''' |
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166 # from numpy import zeros, array |
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167 # smoothed = zeros(len(sampleX)) |
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168 # for i,x in enumerate(sampleX): |
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169 # weights = array([weightFunc(x,xx, halfwidth) for xx in X]) |
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170 # if sum(weights)>0: |
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171 # smoothed[i] = sum(weights*Y)/sum(weights) |
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172 # else: |
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173 # smoothed[i] = 0 |
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174 # return smoothed |
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175 |
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176 def kernelSmoothing(x, X, Y, weightFunc, halfwidth): |
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177 '''Returns the smoothed estimate of (X,Y) at x |
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178 Sum_x weight(sample_x,x) * y(x)''' |
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179 weights = array([weightFunc(x,observedx, halfwidth) for observedx in X]) |
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180 if sum(weights)>0: |
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181 return sum(weights*Y)/sum(weights) |
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182 else: |
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183 return 0 |
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184 |
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185 def uniform(center, x, halfwidth): |
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186 if abs(center-x)<halfwidth: |
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187 return 1. |
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188 else: |
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189 return 0. |
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190 |
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191 def gaussian(center, x, halfwidth): |
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192 return exp(-((center-x)/halfwidth)**2/2) |
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193 |
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194 def epanechnikov(center, x, halfwidth): |
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195 diff = abs(center-x) |
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196 if diff<halfwidth: |
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197 return 1.-(diff/halfwidth)**2 |
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198 else: |
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199 return 0. |
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200 |
434 | 201 def triangular(center, x, halfwidth): |
202 diff = abs(center-x) | |
203 if diff<halfwidth: | |
204 return 1.-abs(diff/halfwidth) | |
205 else: | |
206 return 0. | |
433
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207 |
518
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208 def medianSmoothing(x, X, Y, halfwidth): |
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209 '''Returns the media of Y's corresponding to X's in the interval [x-halfwidth, x+halfwidth]''' |
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210 return median([y for observedx, y in zip(X,Y) if abs(x-observedx)<halfwidth]) |
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211 |
521
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212 def argmaxDict(d): |
561
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213 return max(d, key=d.get) |
279
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214 |
395
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diff
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215 def framesToTime(nFrames, frameRate, initialTime = time()): |
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216 '''returns a datetime.time for the time in hour, minutes and seconds |
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217 initialTime is a datetime.time''' |
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218 seconds = int(floor(float(nFrames)/float(frameRate))+initialTime.hour*3600+initialTime.minute*60+initialTime.second) |
261
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219 h = int(floor(seconds/3600.)) |
248
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220 seconds = seconds - h*3600 |
261
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221 m = int(floor(seconds/60)) |
248
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222 seconds = seconds - m*60 |
262
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diff
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223 return time(h, m, seconds) |
248
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224 |
381
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diff
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225 def timeToFrames(t, frameRate): |
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226 return frameRate*(t.hour*3600+t.minute*60+t.second) |
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227 |
241
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228 def sortXY(X,Y): |
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229 'returns the sorted (x, Y(x)) sorted on X' |
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230 D = {} |
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231 for x, y in zip(X,Y): |
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232 D[x]=y |
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233 xsorted = sorted(D.keys()) |
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234 return xsorted, [D[x] for x in xsorted] |
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235 |
32 | 236 def ceilDecimals(v, nDecimals): |
237 '''Rounds the number at the nth decimal | |
238 eg 1.23 at 0 decimal is 2, at 1 decimal is 1.3''' | |
670
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corrected other missing imports
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239 tens = 10**nDecimals |
32 | 240 return ceil(v*tens)/tens |
241 | |
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242 def inBetween(bound1, bound2, x): |
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243 return bound1 <= x <= bound2 or bound2 <= x <= bound1 |
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244 |
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245 def pointDistanceL2(x1,y1,x2,y2): |
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246 ''' Compute point-to-point distance (L2 norm, ie Euclidean distance)''' |
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247 return sqrt((x2-x1)**2+(y2-y1)**2) |
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248 |
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249 def crossProduct(l1, l2): |
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250 return l1[0]*l2[1]-l1[1]*l2[0] |
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251 |
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252 def cat_mvgavg(cat_list, halfWidth): |
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253 ''' Return a list of categories/values smoothed according to a window. |
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254 halfWidth is the search radius on either side''' |
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255 from copy import deepcopy |
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256 smoothed = deepcopy(cat_list) |
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257 for point in range(len(cat_list)): |
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258 lower_bound_check = max(0,point-halfWidth) |
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259 upper_bound_check = min(len(cat_list)-1,point+halfWidth+1) |
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260 window_values = cat_list[lower_bound_check:upper_bound_check] |
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261 smoothed[point] = max(set(window_values), key=window_values.count) |
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262 return smoothed |
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263 |
547 | 264 def filterMovingWindow(inputSignal, halfWidth): |
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265 '''Returns an array obtained after the smoothing of the input by a moving average |
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266 The first and last points are copied from the original.''' |
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267 width = float(halfWidth*2+1) |
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268 win = ones(width,'d') |
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269 result = convolve(win/width,array(inputSignal),'same') |
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270 result[:halfWidth] = inputSignal[:halfWidth] |
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271 result[-halfWidth:] = inputSignal[-halfWidth:] |
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272 return result |
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273 |
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274 def linearRegression(x, y, deg = 1, plotData = False): |
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275 '''returns the least square estimation of the linear regression of y = ax+b |
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276 as well as the plot''' |
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277 from numpy.lib.polynomial import polyfit |
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278 from numpy.core.multiarray import arange |
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279 coef = polyfit(x, y, deg) |
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280 if plotData: |
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281 def poly(x): |
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282 result = 0 |
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283 for i in range(len(coef)): |
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284 result += coef[i]*x**(len(coef)-i-1) |
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285 return result |
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286 plt.plot(x, y, 'x') |
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287 xx = arange(min(x), max(x),(max(x)-min(x))/1000) |
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288 plt.plot(xx, [poly(z) for z in xx]) |
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289 return coef |
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290 |
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291 def correlation(data, correlationMethod = 'pearson', plotFigure = False, displayNames = None, figureFilename = None): |
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292 '''Computes (and displays) the correlation matrix for a pandas DataFrame''' |
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293 columns = data.columns.tolist() |
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294 for var in data.columns: |
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295 uniqueValues = data[var].unique() |
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296 if len(uniqueValues) == 1 or data.dtypes[var] == dtype('O') or (len(uniqueValues) == 2 and len(data.loc[~isnan(data[var]), var].unique()) == 1): # last condition: only one other value than nan |
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297 columns.remove(var) |
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298 c=data[columns].corr(correlationMethod) |
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299 if plotFigure: |
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300 fig = plt.figure(figsize=(4+0.4*c.shape[0], 0.4*c.shape[0])) |
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301 fig.add_subplot(1,1,1) |
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302 #plt.imshow(np.fabs(c), interpolation='none') |
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303 plt.imshow(c, vmin=-1., vmax = 1., interpolation='none', cmap = 'RdYlBu_r') # coolwarm |
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304 colnames = [displayNames.get(s.strip(), s.strip()) for s in columns] |
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305 #correlation.plot_corr(c, xnames = colnames, normcolor=True, title = filename) |
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306 plt.xticks(range(len(colnames)), colnames, rotation=90) |
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307 plt.yticks(range(len(colnames)), colnames) |
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308 plt.tick_params('both', length=0) |
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309 plt.subplots_adjust(bottom = 0.29) |
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310 plt.colorbar() |
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311 plt.title('Correlation ({})'.format(correlationMethod)) |
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312 plt.tight_layout() |
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313 if len(colnames) > 50: |
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314 plt.subplots_adjust(left=.06) |
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315 if figureFilename is not None: |
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316 plt.savefig(figureFilename, dpi = 150, transparent = True) |
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317 return c |
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318 |
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319 def addDummies(data, variables, allVariables = True): |
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320 '''Add binary dummy variables for each value of a nominal variable |
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321 in a pandas DataFrame''' |
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322 newVariables = [] |
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323 for var in variables: |
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324 if var in data.columns and data.dtypes[var] == dtype('O') and len(data[var].unique()) > 2: |
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325 values = data[var].unique() |
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326 if not allVariables: |
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327 values = values[:-1] |
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328 for val in values: |
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329 if val is not NaN: |
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330 newVariable = (var+'_{}'.format(val)).replace('.','').replace(' ','').replace('-','') |
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331 data[newVariable] = (data[var] == val) |
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332 newVariables.append(newVariable) |
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333 return newVariables |
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334 |
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335 def kruskalWallis(data, dependentVariable, independentVariable, plotFigure = False, filenamePrefix = None, figureFileType = 'pdf', saveLatex = False, renameVariables = lambda s: s, kwCaption = u''): |
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336 '''Studies the influence of (nominal) independent variable over the dependent variable |
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337 |
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338 Makes tests if the conditional distributions are normal |
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339 using the Shapiro-Wilk test (in which case ANOVA could be used) |
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340 Implements uses the non-parametric Kruskal Wallis test''' |
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341 tmp = data[data[independentVariable].notnull()] |
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342 independentVariableValues = sorted(tmp[independentVariable].unique().tolist()) |
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343 if len(independentVariableValues) >= 2: |
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344 if saveLatex: |
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345 from storage import openCheck |
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346 out = openCheck(filenamePrefix+'-{}-{}.tex'.format(dependentVariable, independentVariable), 'w') |
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347 for x in independentVariableValues: |
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348 print('Shapiro-Wilk normality test for {} when {}={}: {} obs'.format(dependentVariable,independentVariable, x, len(tmp.loc[tmp[independentVariable] == x, dependentVariable]))) |
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349 if len(tmp.loc[tmp[independentVariable] == x, dependentVariable]) >= 3: |
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350 print shapiro(tmp.loc[tmp[independentVariable] == x, dependentVariable]) |
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351 if plotFigure: |
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352 plt.figure() |
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353 plt.boxplot([tmp.loc[tmp[independentVariable] == x, dependentVariable] for x in independentVariableValues]) |
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354 #q25, q75 = tmp[dependentVariable].quantile([.25, .75]) |
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355 #plt.ylim(ymax = q75+1.5*(q75-q25)) |
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356 plt.xticks(range(1,len(independentVariableValues)+1), independentVariableValues) |
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357 plt.title('{} vs {}'.format(dependentVariable, independentVariable)) |
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358 if filenamePrefix is not None: |
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359 plt.savefig(filenamePrefix+'-{}-{}.{}'.format(dependentVariable, independentVariable, figureFileType)) |
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360 table = tmp.groupby([independentVariable])[dependentVariable].describe().unstack().sort(['50%'], ascending = False) |
676 | 361 table['count'] = table['count'].astype(int) |
362 testResult = kruskal(*[tmp.loc[tmp[independentVariable] == x, dependentVariable] for x in independentVariableValues]) | |
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363 if saveLatex: |
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364 out.write('\\begin{minipage}{\\linewidth}\n' |
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365 +'\\centering\n' |
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366 +'\\captionof{table}{'+(kwCaption.format(dependentVariable, independentVariable, *testResult))+'}\n' |
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367 +table.to_latex(float_format = lambda x: '{:.3f}'.format(x)).encode('ascii')+'\n' |
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368 +'\\end{minipage}\n' |
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369 +'\\ \\vspace{0.5cm}\n') |
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370 else: |
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371 print table |
676 | 372 return testResult |
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373 else: |
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374 return None |
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375 |
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376 def prepareRegression(data, dependentVariable, independentVariables, maxCorrelationThreshold, correlations, maxCorrelationP, correlationFunc, stdoutText = ['Removing {} (constant: {})', 'Removing {} (correlation {} with {})', 'Removing {} (no correlation: {}, p={})'], saveFiles = False, filenamePrefix = None, latexHeader = '', latexTable = None, latexFooter=''): |
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377 '''Removes variables from candidate independent variables if |
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378 - if two independent variables are correlated (> maxCorrelationThreshold), one is removed |
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379 - if an independent variable is not correlated with the dependent variable (p>maxCorrelationP) |
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380 Returns the remaining non-correlated variables, correlated with the dependent variable |
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381 |
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382 correlationFunc is spearmanr or pearsonr from scipy.stats |
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383 text is the template to display for the two types of printout (see default): 3 elements if no saving to latex file, 8 otherwise |
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384 |
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385 TODO: pass the dummies for nominal variables and remove if all dummies are correlated, or none is correlated with the dependentvariable''' |
668
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386 from copy import copy |
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387 from pandas import DataFrame |
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388 result = copy(independentVariables) |
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389 table1 = '' |
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390 table2 = {} |
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391 # constant variables |
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392 for var in independentVariables: |
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393 uniqueValues = data[var].unique() |
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394 if (len(uniqueValues) == 1) or (len(uniqueValues) == 2 and uniqueValues.dtype != dtype('O') and len(data.loc[~isnan(data[var]), var].unique()) == 1): |
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395 print(stdoutText[0].format(var, uniqueValues)) |
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396 if saveFiles: |
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397 table1 += latexTable[0].format(var, *uniqueValues) |
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398 result.remove(var) |
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399 # correlated variables |
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400 for v1 in copy(result): |
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401 if v1 in correlations.index: |
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402 for v2 in copy(result): |
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403 if v2 != v1 and v2 in correlations.index: |
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404 if abs(correlations.loc[v1, v2]) > maxCorrelationThreshold: |
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405 if v1 in result and v2 in result: |
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406 if saveFiles: |
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407 table1 += latexTable[1].format(v2, v1, correlations.loc[v1, v2]) |
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408 print(stdoutText[1].format(v2, v1, correlations.loc[v1, v2])) |
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409 result.remove(v2) |
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410 # not correlated with dependent variable |
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411 table2['Correlations'] = [] |
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412 table2['Valeurs p'] = [] |
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413 for var in copy(result): |
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414 if data.dtypes[var] != dtype('O'): |
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415 cor, p = correlationFunc(data[dependentVariable], data[var]) |
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416 if p > maxCorrelationP: |
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417 if saveFiles: |
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418 table1 += latexTable[2].format(var, cor, p) |
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419 print(stdoutText[2].format(var, cor, p)) |
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420 result.remove(var) |
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421 else: |
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422 table2['Correlations'].append(cor) |
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423 table2['Valeurs p'].append(p) |
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424 |
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425 if saveFiles: |
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426 from storage import openCheck |
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427 out = openCheck(filenamePrefix+'-removed-variables.tex', 'w') |
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428 out.write(latexHeader) |
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429 out.write(table1) |
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430 out.write(latexFooter) |
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431 out.close() |
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432 out = openCheck(filenamePrefix+'-correlations.html', 'w') |
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433 table2['Variables'] = [var for var in result if data.dtypes[var] != dtype('O')] |
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434 out.write(DataFrame(table2)[['Variables', 'Correlations', 'Valeurs p']].to_html(formatters = {'Correlations': lambda x: '{:.2f}'.format(x), 'Valeurs p': lambda x: '{:.3f}'.format(x)}, index = False)) |
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435 out.close() |
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436 return result |
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437 |
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438 |
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439 ######################### |
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440 # regression analysis using statsmodels (and pandas) |
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441 ######################### |
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442 |
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443 # TODO make class for experiments? |
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444 # TODO add tests with public dataset downloaded from Internet (IRIS et al) |
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445 def modelString(experiment, dependentVariable, independentVariables): |
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446 return dependentVariable+' ~ '+' + '.join([independentVariable for independentVariable in independentVariables if experiment[independentVariable]]) |
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447 |
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448 def runModel(experiment, data, dependentVariable, independentVariables, regressionType = 'ols'): |
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449 import statsmodels.formula.api as smf |
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450 modelStr = modelString(experiment, dependentVariable, independentVariables) |
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451 if regressionType == 'ols': |
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452 model = smf.ols(modelStr, data = data) |
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453 elif regressionType == 'gls': |
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454 model = smf.gls(modelStr, data = data) |
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455 elif regressionType == 'rlm': |
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|
456 model = smf.rlm(modelStr, data = data) |
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parents:
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|
457 else: |
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parents:
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diff
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|
458 print('Unknown regression type {}. Exiting'.format(regressionType)) |
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459 import sys |
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parents:
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|
460 sys.exit() |
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parents:
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461 return model.fit() |
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|
462 |
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changeset
|
463 def runModels(experiments, data, dependentVariable, independentVariables, regressionType = 'ols'): |
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464 '''Runs several models and stores 3 statistics |
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|
465 adjusted R2, condition number (should be small, eg < 1000) |
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parents:
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changeset
|
466 and p-value for Shapiro-Wilk test of residual normality''' |
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parents:
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467 for i,experiment in experiments.iterrows(): |
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parents:
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468 if experiment[independentVariables].any(): |
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parents:
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469 results = runModel(experiment, data, dependentVariable, independentVariables, regressionType = 'ols') |
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parents:
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|
470 experiments.loc[i,'r2adj'] = results.rsquared_adj |
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parents:
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changeset
|
471 experiments.loc[i,'condNum'] = results.condition_number |
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parents:
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472 experiments.loc[i, 'shapiroP'] = shapiro(results.resid)[1] |
668
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parents:
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diff
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473 experiments.loc[i,'nobs'] = int(results.nobs) |
667
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parents:
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474 return experiments |
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475 |
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476 def generateExperiments(independentVariables): |
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477 '''Generates all possible models for including or not each independent variable''' |
670
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corrected other missing imports
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478 from pandas import DataFrame |
667
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479 experiments = {} |
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480 nIndependentVariables = len(independentVariables) |
669 | 481 if nIndependentVariables != len(set(independentVariables)): |
667
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482 print("Duplicate variables. Exiting") |
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483 import sys |
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484 sys.exit() |
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485 nModels = 2**nIndependentVariables |
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486 for i,var in enumerate(independentVariables): |
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487 pattern = [False]*(2**i)+[True]*(2**i) |
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488 experiments[var] = pattern*(2**(nIndependentVariables-i-1)) |
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489 experiments = DataFrame(experiments) |
667
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490 experiments['r2adj'] = 0. |
677
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491 experiments['condNum'] = NaN |
667
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492 experiments['shapiroP'] = -1 |
668
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493 experiments['nobs'] = -1 |
667
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494 return experiments |
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|
495 |
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496 def findBestModel(data, dependentVariable, independentVariables, regressionType = 'ols', nProcesses = 1): |
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497 '''Generates all possible model with the independentVariables |
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498 and runs them, saving the results in experiments |
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parents:
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499 with multiprocess option''' |
670
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diff
changeset
|
500 from pandas import concat |
671
849f5f8bf4b9
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diff
changeset
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501 from multiprocessing import Pool |
667
179b81faa1f8
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502 experiments = generateExperiments(independentVariables) |
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503 nModels = len(experiments) |
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parents:
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|
504 print("Running {} models with {} processes".format(nModels, nProcesses)) |
674
01b89182891a
corrected bug for intersection of lines (thanks to Paul for finding)
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parents:
672
diff
changeset
|
505 print("IndependentVariables: {}".format(independentVariables)) |
667
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diff
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|
506 if nProcesses == 1: |
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507 return runModels(experiments, data, dependentVariable, independentVariables, regressionType) |
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|
508 else: |
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diff
changeset
|
509 pool = Pool(processes = nProcesses) |
670
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changeset
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510 chunkSize = int(ceil(nModels/nProcesses)) |
667
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511 jobs = [pool.apply_async(runModels, args = (experiments[i*chunkSize:(i+1)*chunkSize], data, dependentVariable, independentVariables, regressionType)) for i in range(nProcesses)] |
670
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512 return concat([job.get() for job in jobs]) |
667
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|
513 |
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diff
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514 def findBestModelFwd(data, dependentVariable, independentVariables, modelFunc, experiments = None): |
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diff
changeset
|
515 '''Forward search for best model (based on adjusted R2) |
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changeset
|
516 Randomly starting with one variable and adding randomly variables |
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diff
changeset
|
517 if they improve the model |
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parents:
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diff
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|
518 |
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diff
changeset
|
519 The results are added to experiments if provided as argument |
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diff
changeset
|
520 Storing in experiment relies on the index being the number equal |
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parents:
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diff
changeset
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521 to the binary code derived from the independent variables''' |
670
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diff
changeset
|
522 from numpy.random import permutation as nppermutation |
667
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parents:
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diff
changeset
|
523 if experiments is None: |
179b81faa1f8
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parents:
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diff
changeset
|
524 experiments = generateExperiments(independentVariables) |
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parents:
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diff
changeset
|
525 nIndependentVariables = len(independentVariables) |
670
f72ed51c6b65
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parents:
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diff
changeset
|
526 permutation = nppermutation(range(nIndependentVariables)).tolist() |
667
179b81faa1f8
added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
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diff
changeset
|
527 variableMapping = {j: independentVariables[i] for i,j in enumerate(permutation)} |
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diff
changeset
|
528 print('Tested variables '+', '.join([variableMapping[i] for i in xrange(nIndependentVariables)])) |
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parents:
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diff
changeset
|
529 bestModel = [False]*nIndependentVariables |
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parents:
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diff
changeset
|
530 currentVarNum = 0 |
179b81faa1f8
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parents:
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diff
changeset
|
531 currentR2Adj = 0. |
179b81faa1f8
added regression analysis functions
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parents:
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diff
changeset
|
532 for currentVarNum in xrange(nIndependentVariables): |
179b81faa1f8
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parents:
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diff
changeset
|
533 currentModel = [i for i in bestModel] |
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parents:
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diff
changeset
|
534 currentModel[currentVarNum] = True |
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parents:
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diff
changeset
|
535 rowIdx = sum([0]+[2**i for i in xrange(nIndependentVariables) if currentModel[permutation[i]]]) |
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parents:
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diff
changeset
|
536 #print currentVarNum, sum(currentModel), ', '.join([independentVariables[i] for i in xrange(nIndependentVariables) if currentModel[permutation[i]]]) |
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parents:
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diff
changeset
|
537 if experiments.loc[rowIdx, 'shapiroP'] < 0: |
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parents:
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diff
changeset
|
538 modelStr = modelString(experiments.loc[rowIdx], dependentVariable, independentVariables) |
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parents:
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diff
changeset
|
539 model = modelFunc(modelStr, data = data) |
179b81faa1f8
added regression analysis functions
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parents:
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diff
changeset
|
540 results = model.fit() |
179b81faa1f8
added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
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diff
changeset
|
541 experiments.loc[rowIdx, 'r2adj'] = results.rsquared_adj |
179b81faa1f8
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parents:
665
diff
changeset
|
542 experiments.loc[rowIdx, 'condNum'] = results.condition_number |
179b81faa1f8
added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
665
diff
changeset
|
543 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
|
544 experiments.loc[rowIdx, 'nobs'] = int(results.nobs) |
667
179b81faa1f8
added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
665
diff
changeset
|
545 if currentR2Adj < experiments.loc[rowIdx, 'r2adj']: |
179b81faa1f8
added regression analysis functions
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parents:
665
diff
changeset
|
546 currentR2Adj = experiments.loc[rowIdx, 'r2adj'] |
179b81faa1f8
added regression analysis functions
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parents:
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diff
changeset
|
547 bestModel[currentVarNum] = True |
179b81faa1f8
added regression analysis functions
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parents:
665
diff
changeset
|
548 return experiments |
179b81faa1f8
added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
665
diff
changeset
|
549 |
677
ae07c7b4cf87
update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
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diff
changeset
|
550 def displayModelResults(results, model = None, plotFigures = True, filenamePrefix = None, figureFileType = 'pdf', text = {'title-shapiro': 'Shapiro-Wilk normality test for residuals: {:.2f} (p={:.3f})', 'true-predicted.xlabel': 'Predicted values', 'true-predicted.ylabel': 'True values', 'residuals-predicted.xlabel': 'Predicted values', 'residuals-predicted.ylabel': 'Residuals'}): |
667
179b81faa1f8
added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
665
diff
changeset
|
551 import statsmodels.api as sm |
677
ae07c7b4cf87
update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
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diff
changeset
|
552 '''Displays some model results |
ae07c7b4cf87
update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
676
diff
changeset
|
553 |
ae07c7b4cf87
update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
676
diff
changeset
|
554 3 graphics, true-predicted, residuals-predicted, ''' |
676 | 555 print(results.summary()) |
677
ae07c7b4cf87
update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
676
diff
changeset
|
556 shapiroResult = shapiro(results.resid) |
ae07c7b4cf87
update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
676
diff
changeset
|
557 print(shapiroResult) |
676 | 558 if plotFigures: |
677
ae07c7b4cf87
update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
676
diff
changeset
|
559 fig = plt.figure(figsize=(7,6.3*(2+int(model is not None)))) |
676 | 560 if model is not None: |
677
ae07c7b4cf87
update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
676
diff
changeset
|
561 ax = fig.add_subplot(3,1,1) |
676 | 562 plt.plot(results.predict(), model.endog, 'x') |
563 x=plt.xlim() | |
564 y=plt.ylim() | |
565 plt.plot([max(x[0], y[0]), min(x[1], y[1])], [max(x[0], y[0]), min(x[1], y[1])], 'r') | |
677
ae07c7b4cf87
update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
676
diff
changeset
|
566 #plt.axis('equal') |
ae07c7b4cf87
update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
676
diff
changeset
|
567 if text is not None: |
ae07c7b4cf87
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
676
diff
changeset
|
568 plt.title(text['title-shapiro'].format(*shapiroResult)) |
ae07c7b4cf87
update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
676
diff
changeset
|
569 #plt.title(text['true-predicted.title']) |
ae07c7b4cf87
update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
676
diff
changeset
|
570 plt.xlabel(text['true-predicted.xlabel']) |
ae07c7b4cf87
update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
676
diff
changeset
|
571 plt.ylabel(text['true-predicted.ylabel']) |
ae07c7b4cf87
update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
676
diff
changeset
|
572 fig.add_subplot(3,1,2, sharex = ax) |
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573 plt.plot(results.predict(), results.resid, 'x') |
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574 nextSubplotNum = 3 |
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575 else: |
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576 fig.add_subplot(2,1,1) |
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577 plt.plot(results.predict(), results.resid, 'x') |
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578 nextSubplotNum = 2 |
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579 if text is not None: |
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580 if model is None: |
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581 plt.title(text['title-shapiro'].format(*shapiroResult)) |
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582 plt.xlabel(text['residuals-predicted.xlabel']) |
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583 plt.ylabel(text['residuals-predicted.ylabel']) |
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584 qqAx = fig.add_subplot(nextSubplotNum,1,nextSubplotNum) |
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585 sm.qqplot(results.resid, fit = True, line = '45', ax = qqAx) |
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586 plt.axis('equal') |
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587 if text is not None and 'qqplot.xlabel' in text: |
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588 plt.xlabel(text['qqplot.xlabel']) |
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589 plt.ylabel(text['qqplot.ylabel']) |
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590 plt.tight_layout() |
676 | 591 if filenamePrefix is not None: |
677
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592 from storage import openCheck |
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593 out = openCheck(filenamePrefix+'-coefficients.html', 'w') |
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594 out.write(results.summary().as_html()) |
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595 plt.savefig(filenamePrefix+'-model-results.'+figureFileType) |
667
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596 |
27
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597 ######################### |
455
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598 # iterable section |
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599 ######################### |
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600 |
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601 def mostCommon(L): |
456 | 602 '''Returns the most frequent element in a iterable |
603 | |
604 taken from http://stackoverflow.com/questions/1518522/python-most-common-element-in-a-list''' | |
455
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605 from itertools import groupby |
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606 from operator import itemgetter |
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607 # get an iterable of (item, iterable) pairs |
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608 SL = sorted((x, i) for i, x in enumerate(L)) |
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609 # print 'SL:', SL |
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610 groups = groupby(SL, key=itemgetter(0)) |
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611 # auxiliary function to get "quality" for an item |
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612 def _auxfun(g): |
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613 item, iterable = g |
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614 count = 0 |
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615 min_index = len(L) |
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616 for _, where in iterable: |
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617 count += 1 |
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618 min_index = min(min_index, where) |
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619 # print 'item %r, count %r, minind %r' % (item, count, min_index) |
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620 return count, -min_index |
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621 # pick the highest-count/earliest item |
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622 return max(groups, key=_auxfun)[0] |
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623 |
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624 ######################### |
370
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625 # sequence section |
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626 ######################### |
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627 |
665
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628 class LCSS(object): |
370
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629 '''Class that keeps the LCSS parameters |
686
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630 and puts together the various computations |
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631 |
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632 the methods with names starting with _ are not to be shadowed |
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633 in child classes, who will shadow the other methods, |
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634 ie compute and computeXX methods''' |
689
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635 def __init__(self, similarityFunc = None, metric = None, epsilon = None, delta = float('inf'), aligned = False, lengthFunc = min): |
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636 '''One should provide either a similarity function |
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637 that indicates (return bool) whether elements in the compares lists are similar |
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638 |
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639 eg distance(p1, p2) < epsilon |
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640 |
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641 or a type of metric usable in scipy.spatial.distance.cdist with an epsilon''' |
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642 if similarityFunc is None and metric is None: |
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643 print("No way to compute LCSS, similarityFunc and metric are None. Exiting") |
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644 import sys |
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645 sys.exit() |
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|
646 elif metric is not None and epsilon is None: |
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647 print("Please provide a value for epsilon if using a cdist metric. Exiting") |
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648 import sys |
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649 sys.exit() |
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650 else: |
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651 self.similarityFunc = similarityFunc |
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652 self.metric = metric |
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653 self.epsilon = epsilon |
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654 self.aligned = aligned |
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655 self.delta = delta |
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656 self.lengthFunc = lengthFunc |
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657 self.subSequenceIndices = [(0,0)] |
370
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658 |
373
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659 def similarities(self, l1, l2, jshift=0): |
370
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660 n1 = len(l1) |
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661 n2 = len(l2) |
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662 self.similarityTable = zeros((n1+1,n2+1), dtype = npint) |
689
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663 if self.similarityFunc is not None: |
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664 for i in xrange(1,n1+1): |
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665 for j in xrange(max(1,i-jshift-self.delta),min(n2,i-jshift+self.delta)+1): |
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666 if self.similarityFunc(l1[i-1], l2[j-1]): |
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667 self.similarityTable[i,j] = self.similarityTable[i-1,j-1]+1 |
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668 else: |
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669 self.similarityTable[i,j] = max(self.similarityTable[i-1,j], self.similarityTable[i,j-1]) |
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670 elif self.metric is not None: |
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671 similarElements = distance.cdist(l1, l2, self.metric) <= self.epsilon |
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672 for i in xrange(1,n1+1): |
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673 for j in xrange(max(1,i-jshift-self.delta),min(n2,i-jshift+self.delta)+1): |
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674 if similarElements[i-1, j-1]: |
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675 self.similarityTable[i,j] = self.similarityTable[i-1,j-1]+1 |
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676 else: |
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677 self.similarityTable[i,j] = max(self.similarityTable[i-1,j], self.similarityTable[i,j-1]) |
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678 |
370
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679 |
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680 def subSequence(self, i, j): |
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681 '''Returns the subsequence of two sequences |
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682 http://en.wikipedia.org/wiki/Longest_common_subsequence_problem''' |
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683 if i == 0 or j == 0: |
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684 return [] |
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685 elif self.similarityTable[i][j] == self.similarityTable[i][j-1]: |
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686 return self.subSequence(i, j-1) |
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687 elif self.similarityTable[i][j] == self.similarityTable[i-1][j]: |
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688 return self.subSequence(i-1, j) |
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689 else: |
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690 return self.subSequence(i-1, j-1) + [(i-1,j-1)] |
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691 |
373
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|
692 def _compute(self, _l1, _l2, computeSubSequence = False): |
370
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693 '''returns the longest common subsequence similarity |
689
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687
diff
changeset
|
694 l1 and l2 should be the right format |
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parents:
687
diff
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|
695 eg list of tuple points for cdist |
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687
diff
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|
696 or elements that can be compare using similarityFunc |
370
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697 |
607 | 698 if aligned, returns the best matching if using a finite delta by shifting the series alignments |
370
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699 ''' |
372
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700 if len(_l2) < len(_l1): # l1 is the shortest |
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701 l1 = _l2 |
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diff
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702 l2 = _l1 |
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diff
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703 revertIndices = True |
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704 else: |
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diff
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|
705 l1 = _l1 |
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706 l2 = _l2 |
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707 revertIndices = False |
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708 n1 = len(l1) |
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709 n2 = len(l2) |
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|
710 |
370
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|
711 if self.aligned: |
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712 lcssValues = {} |
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713 similarityTables = {} |
374
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714 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
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715 self.similarities(l1, l2, i) |
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716 lcssValues[i] = self.similarityTable.max() |
370
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717 similarityTables[i] = self.similarityTable |
374
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718 #print self.similarityTable |
521
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changed argMaxDict name to argmaxDict
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518
diff
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|
719 alignmentShift = argmaxDict(lcssValues) # ideally get the medium alignment shift, the one that minimizes distance |
389
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|
720 self.similarityTable = similarityTables[alignmentShift] |
372
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|
721 else: |
389
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|
722 alignmentShift = 0 |
372
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723 self.similarities(l1, l2) |
373
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724 |
374
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|
725 # threshold values for the useful part of the similarity table are n2-n1-delta and n1-n2-delta |
389
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|
726 self.similarityTable = self.similarityTable[:min(n1, n2+alignmentShift+self.delta)+1, :min(n2, n1-alignmentShift+self.delta)+1] |
373
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|
727 |
372
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diff
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|
728 if computeSubSequence: |
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diff
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|
729 self.subSequenceIndices = self.subSequence(self.similarityTable.shape[0]-1, self.similarityTable.shape[1]-1) |
371
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diff
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|
730 if revertIndices: |
374
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diff
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|
731 self.subSequenceIndices = [(j,i) for i,j in self.subSequenceIndices] |
372
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|
732 return self.similarityTable[-1,-1] |
370
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|
733 |
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|
734 def compute(self, l1, l2, computeSubSequence = False): |
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|
735 '''get methods are to be shadowed in child classes ''' |
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736 return self._compute(l1, l2, computeSubSequence) |
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|
737 |
375
2ea8584aa80a
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diff
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|
738 def computeAlignment(self): |
374
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|
739 return mean([j-i for i,j in self.subSequenceIndices]) |
370
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|
740 |
376
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diff
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|
741 def _computeNormalized(self, l1, l2, computeSubSequence = False): |
370
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|
742 ''' compute the normalized LCSS |
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|
743 ie, the LCSS divided by the min or mean of the indicator lengths (using lengthFunc) |
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|
744 lengthFunc = lambda x,y:float(x,y)/2''' |
376
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|
745 return float(self._compute(l1, l2, computeSubSequence))/self.lengthFunc(len(l1), len(l2)) |
370
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|
746 |
376
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|
747 def computeNormalized(self, l1, l2, computeSubSequence = False): |
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748 return self._computeNormalized(l1, l2, computeSubSequence) |
370
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|
749 |
376
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diff
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|
750 def _computeDistance(self, l1, l2, computeSubSequence = False): |
370
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|
751 ''' compute the LCSS distance''' |
376
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diff
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|
752 return 1-self._computeNormalized(l1, l2, computeSubSequence) |
370
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diff
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|
753 |
376
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375
diff
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|
754 def computeDistance(self, l1, l2, computeSubSequence = False): |
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375
diff
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|
755 return self._computeDistance(l1, l2, computeSubSequence) |
370
97e8fa0ee9a1
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diff
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|
756 |
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diff
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|
757 ######################### |
45
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42
diff
changeset
|
758 # plotting section |
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diff
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|
759 ######################### |
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diff
changeset
|
760 |
332
a6ca86107f27
reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
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324
diff
changeset
|
761 def plotPolygon(poly, options = ''): |
a6ca86107f27
reorganized utils module
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324
diff
changeset
|
762 'Plots shapely polygon poly' |
a6ca86107f27
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324
diff
changeset
|
763 from numpy.core.multiarray import array |
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diff
changeset
|
764 from matplotlib.pyplot import plot |
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diff
changeset
|
765 from shapely.geometry import Polygon |
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diff
changeset
|
766 |
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diff
changeset
|
767 tmp = array(poly.exterior) |
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diff
changeset
|
768 plot(tmp[:,0], tmp[:,1], options) |
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diff
changeset
|
769 |
324 | 770 def stepPlot(X, firstX, lastX, initialCount = 0, increment = 1): |
771 '''for each value in X, increment by increment the initial count | |
297
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diff
changeset
|
772 returns the lists that can be plotted |
324 | 773 to obtain a step plot increasing by one for each value in x, from first to last value |
774 firstX and lastX should be respectively smaller and larger than all elements in X''' | |
297
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diff
changeset
|
775 |
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diff
changeset
|
776 sortedX = [] |
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diff
changeset
|
777 counts = [initialCount] |
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diff
changeset
|
778 for x in sorted(X): |
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diff
changeset
|
779 sortedX += [x,x] |
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diff
changeset
|
780 counts.append(counts[-1]) |
324 | 781 counts.append(counts[-1]+increment) |
297
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diff
changeset
|
782 counts.append(counts[-1]) |
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|
783 return [firstX]+sortedX+[lastX], counts |
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diff
changeset
|
784 |
665
15e244d2a1b5
corrected bug with circular import for VideoFilenameAddable, moved to base module
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parents:
659
diff
changeset
|
785 class PlottingPropertyValues(object): |
45
74d2de078baf
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diff
changeset
|
786 def __init__(self, values): |
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diff
changeset
|
787 self.values = values |
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diff
changeset
|
788 |
116
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115
diff
changeset
|
789 def __getitem__(self, i): |
45
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changeset
|
790 return self.values[i%len(self.values)] |
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diff
changeset
|
791 |
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diff
changeset
|
792 markers = PlottingPropertyValues(['+', '*', ',', '.', 'x', 'D', 's', 'o']) |
116
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diff
changeset
|
793 scatterMarkers = PlottingPropertyValues(['s','o','^','>','v','<','d','p','h','8','+','x']) |
45
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diff
changeset
|
794 |
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diff
changeset
|
795 linestyles = PlottingPropertyValues(['-', '--', '-.', ':']) |
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diff
changeset
|
796 |
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diff
changeset
|
797 colors = PlottingPropertyValues('brgmyck') # 'w' |
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diff
changeset
|
798 |
115
550556378466
added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
86
diff
changeset
|
799 def plotIndicatorMap(indicatorMap, squareSize, masked = True, defaultValue=-1): |
65
75cf537b8d88
moved and generalized map making functions to the library
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48
diff
changeset
|
800 from matplotlib.pyplot import pcolor |
75cf537b8d88
moved and generalized map making functions to the library
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diff
changeset
|
801 coords = array(indicatorMap.keys()) |
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diff
changeset
|
802 minX = min(coords[:,0]) |
75cf537b8d88
moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
48
diff
changeset
|
803 minY = min(coords[:,1]) |
75cf537b8d88
moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
48
diff
changeset
|
804 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
|
805 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
|
806 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
|
807 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
|
808 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
|
809 if masked: |
550556378466
added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
86
diff
changeset
|
810 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
|
811 else: |
550556378466
added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
86
diff
changeset
|
812 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
|
813 |
45
74d2de078baf
added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
42
diff
changeset
|
814 ######################### |
637
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
815 # Data download |
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
816 ######################### |
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
817 |
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
818 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
|
819 '''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
|
820 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
|
821 Otherwise, means the data for each day, for the whole year |
c9a0b72979fd
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
822 |
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added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
823 Example: MONTREAL MCTAVISH 10761 |
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
824 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
|
825 |
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
826 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
|
827 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
|
828 import urllib2 |
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
829 if english: |
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
830 language = 'e' |
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
831 else: |
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
832 language = 'f' |
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
833 if len(months) == 0: |
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
834 timeFrame = 2 |
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
835 months = [1] |
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
836 else: |
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
837 timeFrame = 1 |
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
838 |
c9a0b72979fd
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
839 for year in years: |
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
840 for month in months: |
c9a0b72979fd
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
841 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)) |
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
842 data = url.read() |
c9a0b72979fd
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
843 outFilename = '{}/{}-{}'.format(outputDirectoryname, stationID, year) |
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
844 if timeFrame == 1: |
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added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
845 outFilename += '-{}-hourly'.format(month) |
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
846 else: |
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added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
847 outFilename += '-daily' |
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
848 outFilename += '.csv' |
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
849 out = open(outFilename, 'w') |
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added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
850 out.write(data) |
c9a0b72979fd
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
851 out.close() |
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
852 |
c9a0b72979fd
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
853 ######################### |
c9a0b72979fd
added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
854 # File I/O |
27
44689029a86f
updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents:
24
diff
changeset
|
855 ######################### |
24
6fb59cfb201e
first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents:
19
diff
changeset
|
856 |
0
aed8eb63cdde
initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
857 def removeExtension(filename, delimiter = '.'): |
31
c000f37c316d
moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents:
29
diff
changeset
|
858 '''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
|
859 i = filename.rfind(delimiter) |
aed8eb63cdde
initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
860 if i>0: |
aed8eb63cdde
initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
861 return filename[:i] |
aed8eb63cdde
initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
862 else: |
aed8eb63cdde
initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
863 return filename |
aed8eb63cdde
initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
864 |
46
b5d007612e16
added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
45
diff
changeset
|
865 def cleanFilename(s): |
b5d007612e16
added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
45
diff
changeset
|
866 'cleans filenames obtained when contatenating figure characteristics' |
266
aba9711b3149
small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
262
diff
changeset
|
867 return s.replace(' ','-').replace('.','').replace('/','-') |
46
b5d007612e16
added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
45
diff
changeset
|
868 |
0
aed8eb63cdde
initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
869 def listfiles(dirname, extension, remove = False): |
14
e7bbe8465591
homography and other utils
Nicolas Saunier <nico@confins.net>
parents:
7
diff
changeset
|
870 '''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
|
871 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
|
872 from os import listdir |
aed8eb63cdde
initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
873 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
|
874 tmp.sort() |
aed8eb63cdde
initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
875 if remove: |
aed8eb63cdde
initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
876 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
|
877 else: |
aed8eb63cdde
initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
878 return tmp |
aed8eb63cdde
initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
879 |
266
aba9711b3149
small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
262
diff
changeset
|
880 def mkdir(dirname): |
aba9711b3149
small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
262
diff
changeset
|
881 'Creates a directory if it does not exist' |
aba9711b3149
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
262
diff
changeset
|
882 import os |
aba9711b3149
small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
262
diff
changeset
|
883 if not os.path.exists(dirname): |
aba9711b3149
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
262
diff
changeset
|
884 os.mkdir(dirname) |
aba9711b3149
small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
262
diff
changeset
|
885 else: |
aba9711b3149
small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
262
diff
changeset
|
886 print(dirname+' already exists') |
aba9711b3149
small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
262
diff
changeset
|
887 |
14
e7bbe8465591
homography and other utils
Nicolas Saunier <nico@confins.net>
parents:
7
diff
changeset
|
888 def removeFile(filename): |
e7bbe8465591
homography and other utils
Nicolas Saunier <nico@confins.net>
parents:
7
diff
changeset
|
889 '''Deletes the file while avoiding raising an error |
e7bbe8465591
homography and other utils
Nicolas Saunier <nico@confins.net>
parents:
7
diff
changeset
|
890 if the file does not exist''' |
266
aba9711b3149
small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
262
diff
changeset
|
891 import os |
14
e7bbe8465591
homography and other utils
Nicolas Saunier <nico@confins.net>
parents:
7
diff
changeset
|
892 if (os.path.exists(filename)): |
e7bbe8465591
homography and other utils
Nicolas Saunier <nico@confins.net>
parents:
7
diff
changeset
|
893 os.remove(filename) |
266
aba9711b3149
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
262
diff
changeset
|
894 else: |
aba9711b3149
small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
262
diff
changeset
|
895 print(filename+' does not exist') |
14
e7bbe8465591
homography and other utils
Nicolas Saunier <nico@confins.net>
parents:
7
diff
changeset
|
896 |
42
1a2ac2d4f53a
added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
35
diff
changeset
|
897 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
|
898 '''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
|
899 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
|
900 |
1a2ac2d4f53a
added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
35
diff
changeset
|
901 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
|
902 '''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
|
903 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
|
904 |
c000f37c316d
moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents:
29
diff
changeset
|
905 ######################### |
332
a6ca86107f27
reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
324
diff
changeset
|
906 # CLI utils |
a6ca86107f27
reorganized utils module
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parents:
324
diff
changeset
|
907 ######################### |
a6ca86107f27
reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
324
diff
changeset
|
908 |
a6ca86107f27
reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
324
diff
changeset
|
909 def parseCLIOptions(helpMessage, options, cliArgs, optionalOptions=[]): |
a6ca86107f27
reorganized utils module
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parents:
324
diff
changeset
|
910 ''' Simple function to handle similar argument parsing |
a6ca86107f27
reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
324
diff
changeset
|
911 Returns the dictionary of options and their values |
a6ca86107f27
reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
324
diff
changeset
|
912 |
a6ca86107f27
reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
324
diff
changeset
|
913 * cliArgs are most likely directly sys.argv |
a6ca86107f27
reorganized utils module
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parents:
324
diff
changeset
|
914 (only the elements after the first one are considered) |
a6ca86107f27
reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
324
diff
changeset
|
915 |
a6ca86107f27
reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
324
diff
changeset
|
916 * options should be a list of strings for getopt options, |
a6ca86107f27
reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
324
diff
changeset
|
917 eg ['frame=','correspondences=','video='] |
a6ca86107f27
reorganized utils module
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parents:
324
diff
changeset
|
918 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
|
919 import sys, getopt |
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920 from numpy.core.fromnumeric import all |
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921 optionValues, args = getopt.getopt(cliArgs[1:], 'h', ['help']+options+optionalOptions) |
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922 optionValues = dict(optionValues) |
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923 |
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924 if '--help' in optionValues.keys() or '-h' in optionValues.keys(): |
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925 print(helpMessage+ |
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926 '\n - Compulsory options: '+' '.join([opt.replace('=','') for opt in options])+ |
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927 '\n - Non-compulsory options: '+' '.join([opt.replace('=','') for opt in optionalOptions])) |
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928 sys.exit() |
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929 |
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930 missingArgument = [('--'+opt.replace('=','') in optionValues.keys()) for opt in options] |
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931 if not all(missingArgument): |
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932 print('Missing argument') |
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933 print(optionValues) |
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934 sys.exit() |
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935 |
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936 return optionValues |
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937 |
397
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938 |
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939 ######################### |
553
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940 # Profiling |
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941 ######################### |
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942 |
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943 def analyzeProfile(profileFilename, stripDirs = True): |
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944 '''Analyze the file produced by cProfile |
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945 |
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946 obtained by for example: |
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947 - call in script (for main() function in script) |
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948 import cProfile, os |
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949 cProfile.run('main()', os.path.join(os.getcwd(),'main.profile')) |
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950 |
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951 - or on the command line: |
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952 python -m cProfile [-o profile.bin] [-s sort] scriptfile [arg]''' |
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953 import pstats, os |
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954 p = pstats.Stats(os.path.join(os.pardir, profileFilename)) |
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955 if stripDirs: |
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956 p.strip_dirs() |
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957 p.sort_stats('time') |
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958 p.print_stats(.2) |
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959 #p.sort_stats('time') |
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960 # p.print_callees(.1, 'int_prediction.py:') |
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961 return p |
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962 |
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963 ######################### |
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964 # running tests |
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965 ######################### |
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966 |
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967 if __name__ == "__main__": |
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968 import doctest |
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969 import unittest |
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970 suite = doctest.DocFileSuite('tests/utils.txt') |
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971 #suite = doctest.DocTestSuite() |
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972 unittest.TextTestRunner().run(suite) |
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973 #doctest.testmod() |
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974 #doctest.testfile("example.txt") |