Mercurial Hosting > traffic-intelligence
annotate python/utils.py @ 748:d99866b0528a
merged latest change
author | Nicolas Saunier <nicolas.saunier@polymtl.ca> |
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date | Fri, 02 Oct 2015 11:30:15 -0400 |
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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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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 # Strings |
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17 ######################### |
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18 |
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19 def upperCaseFirstLetter(s): |
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20 words = s.split(' ') |
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21 lowerWords = [w[0].upper()+w[1:].lower() for w in words] |
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22 return ' '.join(lowerWords) |
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23 |
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24 ######################### |
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25 # Enumerations |
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26 ######################### |
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27 |
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28 def inverseEnumeration(l): |
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29 'Returns the dictionary that provides for each element in the input list its index in the input list' |
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30 result = {} |
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31 for i,x in enumerate(l): |
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32 result[x] = i |
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33 return result |
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34 |
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35 ######################### |
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36 # Simple statistics |
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37 ######################### |
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38 |
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39 def logNormalMeanVar(loc, scale): |
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40 '''location and scale are respectively the mean and standard deviation of the normal in the log-normal distribution |
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41 https://en.wikipedia.org/wiki/Log-normal_distribution''' |
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42 mean = exp(loc+(scale**2)/2) |
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43 var = (exp(loc**2)-1)*exp(2*loc+scale**2) |
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44 return mean, var |
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45 |
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46 def sampleSize(stdev, tolerance, percentConfidence, printLatex = False): |
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47 from scipy.stats.distributions import norm |
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48 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1)*100)/100. # 1.-(100-percentConfidence)/200. |
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49 if printLatex: |
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50 print('${0}^2\\frac{{{1}^2}}{{{2}^2}}$'.format(k, stdev, tolerance)) |
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51 return (k*stdev/tolerance)**2 |
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52 |
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53 def confidenceInterval(mean, stdev, nSamples, percentConfidence, trueStd = True, printLatex = False): |
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54 '''if trueStd, use normal distribution, otherwise, Student |
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55 |
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56 Use otherwise t.interval or norm.interval |
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57 ex: norm.interval(0.95, loc = 0., scale = 2.3/sqrt(11)) |
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58 t.interval(0.95, 10, loc=1.2, scale = 2.3/sqrt(nSamples)) |
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59 loc is mean, scale is sigma/sqrt(n) (for Student, 10 is df)''' |
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60 from scipy.stats.distributions import norm, t |
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61 if trueStd: |
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62 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1)*100)/100. # 1.-(100-percentConfidence)/200. |
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63 else: # use Student |
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64 k = round(t.ppf(0.5+percentConfidence/200., nSamples-1)*100)/100. |
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65 e = k*stdev/sqrt(nSamples) |
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66 if printLatex: |
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67 print('${0} \pm {1}\\frac{{{2}}}{{\sqrt{{{3}}}}}$'.format(mean, k, stdev, nSamples)) |
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68 return mean-e, mean+e |
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69 |
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70 def computeChi2(expected, observed): |
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71 '''Returns the Chi2 statistics''' |
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72 result = 0. |
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73 for e, o in zip(expected, observed): |
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74 result += ((e-o)*(e-o))/e |
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75 return result |
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76 |
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77 class EmpiricalDistribution(object): |
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78 def nSamples(self): |
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79 return sum(self.counts) |
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80 |
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81 def cumulativeDensityFunction(sample, normalized = False): |
276 | 82 '''Returns the cumulative density function of the sample of a random variable''' |
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83 xaxis = sorted(sample) |
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84 counts = arange(1,len(sample)+1) # dtype = float |
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85 if normalized: |
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86 counts /= float(len(sample)) |
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87 return xaxis, counts |
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88 |
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89 class EmpiricalDiscreteDistribution(EmpiricalDistribution): |
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90 '''Class to represent a sample of a distribution for a discrete random variable |
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91 ''' |
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92 def __init__(self, categories, counts): |
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93 self.categories = categories |
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94 self.counts = counts |
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95 |
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96 def mean(self): |
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97 result = [float(x*y) for x,y in zip(self.categories, self.counts)] |
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98 return npsum(result)/self.nSamples() |
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99 |
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100 def var(self, mean = None): |
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101 if not mean: |
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102 m = self.mean() |
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103 else: |
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104 m = mean |
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105 result = 0. |
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106 squares = [float((x-m)*(x-m)*y) for x,y in zip(self.categories, self.counts)] |
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107 return npsum(squares)/(self.nSamples()-1) |
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108 |
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109 def referenceCounts(self, probability): |
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110 '''probability is a function that returns the probability of the random variable for the category values''' |
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111 refProba = [probability(c) for c in self.categories] |
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112 refProba[-1] = 1-npsum(refProba[:-1]) |
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113 refCounts = [r*self.nSamples() for r in refProba] |
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114 return refCounts, refProba |
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115 |
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116 class EmpiricalContinuousDistribution(EmpiricalDistribution): |
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117 '''Class to represent a sample of a distribution for a continuous random variable |
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118 with the number of observations for each interval |
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119 intervals (categories variable) are defined by their left limits, the last one being the right limit |
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120 categories contain therefore one more element than the counts''' |
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121 def __init__(self, categories, counts): |
276 | 122 # todo add samples for initialization and everything to None? (or setSamples?) |
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123 self.categories = categories |
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124 self.counts = counts |
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125 |
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126 def mean(self): |
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127 result = 0. |
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128 for i in range(len(self.counts)-1): |
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129 result += self.counts[i]*(self.categories[i]+self.categories[i+1])/2 |
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130 return result/self.nSamples() |
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131 |
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132 def var(self, mean = None): |
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133 if not mean: |
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134 m = self.mean() |
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135 else: |
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136 m = mean |
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137 result = 0. |
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138 for i in range(len(self.counts)-1): |
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139 mid = (self.categories[i]+self.categories[i+1])/2 |
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140 result += self.counts[i]*(mid - m)*(mid - m) |
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141 return result/(self.nSamples()-1) |
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142 |
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143 def referenceCounts(self, cdf): |
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144 '''cdf is a cumulative distribution function |
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145 returning the probability of the variable being less that x''' |
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146 # refCumulativeCounts = [0]#[cdf(self.categories[0][0])] |
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147 # for inter in self.categories: |
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148 # refCumulativeCounts.append(cdf(inter[1])) |
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149 refCumulativeCounts = [cdf(x) for x in self.categories[1:-1]] |
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150 |
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151 refProba = [refCumulativeCounts[0]] |
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152 for i in xrange(1,len(refCumulativeCounts)): |
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153 refProba.append(refCumulativeCounts[i]-refCumulativeCounts[i-1]) |
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154 refProba.append(1-refCumulativeCounts[-1]) |
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155 refCounts = [p*self.nSamples() for p in refProba] |
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156 |
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157 return refCounts, refProba |
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158 |
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159 def printReferenceCounts(self, refCounts=None): |
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160 if refCounts: |
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161 ref = refCounts |
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162 else: |
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163 ref = self.referenceCounts |
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164 for i in xrange(len(ref[0])): |
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165 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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166 |
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167 |
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168 ######################### |
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169 # maths section |
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170 ######################### |
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171 |
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172 # def kernelSmoothing(sampleX, X, Y, weightFunc, halfwidth): |
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173 # '''Returns a smoothed weighted version of Y at the predefined values of sampleX |
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174 # Sum_x weight(sample_x,x) * y(x)''' |
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175 # from numpy import zeros, array |
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176 # smoothed = zeros(len(sampleX)) |
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177 # for i,x in enumerate(sampleX): |
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178 # weights = array([weightFunc(x,xx, halfwidth) for xx in X]) |
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179 # if sum(weights)>0: |
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180 # smoothed[i] = sum(weights*Y)/sum(weights) |
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181 # else: |
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182 # smoothed[i] = 0 |
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183 # return smoothed |
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184 |
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185 def kernelSmoothing(x, X, Y, weightFunc, halfwidth): |
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186 '''Returns the smoothed estimate of (X,Y) at x |
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187 Sum_x weight(sample_x,x) * y(x)''' |
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188 weights = array([weightFunc(x,observedx, halfwidth) for observedx in X]) |
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189 if sum(weights)>0: |
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190 return sum(weights*Y)/sum(weights) |
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191 else: |
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192 return 0 |
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193 |
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194 def uniform(center, x, halfwidth): |
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195 if abs(center-x)<halfwidth: |
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196 return 1. |
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197 else: |
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198 return 0. |
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199 |
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200 def gaussian(center, x, halfwidth): |
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201 return exp(-((center-x)/halfwidth)**2/2) |
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202 |
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203 def epanechnikov(center, x, halfwidth): |
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204 diff = abs(center-x) |
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205 if diff<halfwidth: |
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206 return 1.-(diff/halfwidth)**2 |
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207 else: |
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208 return 0. |
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209 |
434 | 210 def triangular(center, x, halfwidth): |
211 diff = abs(center-x) | |
212 if diff<halfwidth: | |
213 return 1.-abs(diff/halfwidth) | |
214 else: | |
215 return 0. | |
433
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216 |
518
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217 def medianSmoothing(x, X, Y, halfwidth): |
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218 '''Returns the media of Y's corresponding to X's in the interval [x-halfwidth, x+halfwidth]''' |
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219 return median([y for observedx, y in zip(X,Y) if abs(x-observedx)<halfwidth]) |
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220 |
521
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221 def argmaxDict(d): |
561
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222 return max(d, key=d.get) |
279
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generic simple LCSS
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223 |
395
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diff
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224 def framesToTime(nFrames, frameRate, initialTime = time()): |
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225 '''returns a datetime.time for the time in hour, minutes and seconds |
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226 initialTime is a datetime.time''' |
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227 seconds = int(floor(float(nFrames)/float(frameRate))+initialTime.hour*3600+initialTime.minute*60+initialTime.second) |
261
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228 h = int(floor(seconds/3600.)) |
248
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229 seconds = seconds - h*3600 |
261
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230 m = int(floor(seconds/60)) |
248
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231 seconds = seconds - m*60 |
262
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232 return time(h, m, seconds) |
248
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233 |
381
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234 def timeToFrames(t, frameRate): |
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235 return frameRate*(t.hour*3600+t.minute*60+t.second) |
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236 |
241
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237 def sortXY(X,Y): |
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diff
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238 'returns the sorted (x, Y(x)) sorted on X' |
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239 D = {} |
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240 for x, y in zip(X,Y): |
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241 D[x]=y |
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242 xsorted = sorted(D.keys()) |
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243 return xsorted, [D[x] for x in xsorted] |
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244 |
733 | 245 def compareLengthForSort(i, j): |
246 if len(i) < len(j): | |
247 return -1 | |
248 elif len(i) == len(j): | |
249 return 0 | |
250 else: | |
251 return 1 | |
252 | |
253 def sortByLength(instances, reverse = False): | |
254 '''Returns a new list with the instances sorted by length (method __len__) | |
255 reverse is passed to sorted''' | |
256 return sorted(instances, cmp = compareLengthForSort, reverse = reverse) | |
257 | |
32 | 258 def ceilDecimals(v, nDecimals): |
259 '''Rounds the number at the nth decimal | |
260 eg 1.23 at 0 decimal is 2, at 1 decimal is 1.3''' | |
670
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261 tens = 10**nDecimals |
32 | 262 return ceil(v*tens)/tens |
263 | |
152
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264 def inBetween(bound1, bound2, x): |
698
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265 'useful if one does not know the order of bound1/bound2' |
569
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266 return bound1 <= x <= bound2 or bound2 <= x <= bound1 |
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267 |
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268 def pointDistanceL2(x1,y1,x2,y2): |
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269 ''' Compute point-to-point distance (L2 norm, ie Euclidean distance)''' |
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270 return sqrt((x2-x1)**2+(y2-y1)**2) |
24
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271 |
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272 def crossProduct(l1, l2): |
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273 return l1[0]*l2[1]-l1[1]*l2[0] |
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274 |
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275 def cat_mvgavg(cat_list, halfWidth): |
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276 ''' Return a list of categories/values smoothed according to a window. |
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277 halfWidth is the search radius on either side''' |
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278 from copy import deepcopy |
659
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279 smoothed = deepcopy(cat_list) |
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280 for point in range(len(cat_list)): |
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281 lower_bound_check = max(0,point-halfWidth) |
659
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282 upper_bound_check = min(len(cat_list)-1,point+halfWidth+1) |
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283 window_values = cat_list[lower_bound_check:upper_bound_check] |
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284 smoothed[point] = max(set(window_values), key=window_values.count) |
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285 return smoothed |
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286 |
547 | 287 def filterMovingWindow(inputSignal, halfWidth): |
29
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288 '''Returns an array obtained after the smoothing of the input by a moving average |
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289 The first and last points are copied from the original.''' |
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290 width = float(halfWidth*2+1) |
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291 win = ones(width,'d') |
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292 result = convolve(win/width,array(inputSignal),'same') |
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293 result[:halfWidth] = inputSignal[:halfWidth] |
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294 result[-halfWidth:] = inputSignal[-halfWidth:] |
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295 return result |
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296 |
199
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297 def linearRegression(x, y, deg = 1, plotData = False): |
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298 '''returns the least square estimation of the linear regression of y = ax+b |
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299 as well as the plot''' |
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300 from numpy.lib.polynomial import polyfit |
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301 from numpy.core.multiarray import arange |
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302 coef = polyfit(x, y, deg) |
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303 if plotData: |
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304 def poly(x): |
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305 result = 0 |
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306 for i in range(len(coef)): |
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307 result += coef[i]*x**(len(coef)-i-1) |
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308 return result |
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309 plt.plot(x, y, 'x') |
199
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310 xx = arange(min(x), max(x),(max(x)-min(x))/1000) |
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311 plt.plot(xx, [poly(z) for z in xx]) |
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312 return coef |
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313 |
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314 def correlation(data, correlationMethod = 'pearson', plotFigure = False, displayNames = None, figureFilename = None): |
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315 '''Computes (and displays) the correlation matrix for a pandas DataFrame''' |
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316 columns = data.columns.tolist() |
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317 for var in data.columns: |
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318 uniqueValues = data[var].unique() |
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319 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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320 columns.remove(var) |
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321 c=data[columns].corr(correlationMethod) |
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322 if plotFigure: |
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323 fig = plt.figure(figsize=(4+0.4*c.shape[0], 0.4*c.shape[0])) |
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324 fig.add_subplot(1,1,1) |
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325 #plt.imshow(np.fabs(c), interpolation='none') |
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326 plt.imshow(c, vmin=-1., vmax = 1., interpolation='none', cmap = 'RdYlBu_r') # coolwarm |
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327 colnames = [displayNames.get(s.strip(), s.strip()) for s in columns] |
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328 #correlation.plot_corr(c, xnames = colnames, normcolor=True, title = filename) |
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329 plt.xticks(range(len(colnames)), colnames, rotation=90) |
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330 plt.yticks(range(len(colnames)), colnames) |
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331 plt.tick_params('both', length=0) |
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332 plt.subplots_adjust(bottom = 0.29) |
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333 plt.colorbar() |
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334 plt.title('Correlation ({})'.format(correlationMethod)) |
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335 plt.tight_layout() |
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336 if len(colnames) > 50: |
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337 plt.subplots_adjust(left=.06) |
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338 if figureFilename is not None: |
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339 plt.savefig(figureFilename, dpi = 150, transparent = True) |
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340 return c |
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341 |
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342 def addDummies(data, variables, allVariables = True): |
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343 '''Add binary dummy variables for each value of a nominal variable |
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344 in a pandas DataFrame''' |
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345 newVariables = [] |
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346 for var in variables: |
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347 if var in data.columns and data.dtypes[var] == dtype('O') and len(data[var].unique()) > 2: |
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348 values = data[var].unique() |
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349 if not allVariables: |
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350 values = values[:-1] |
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351 for val in values: |
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352 if val is not NaN: |
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353 newVariable = (var+'_{}'.format(val)).replace('.','').replace(' ','').replace('-','') |
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354 data[newVariable] = (data[var] == val) |
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355 newVariables.append(newVariable) |
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356 return newVariables |
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357 |
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358 def kruskalWallis(data, dependentVariable, independentVariable, plotFigure = False, filenamePrefix = None, figureFileType = 'pdf', saveLatex = False, renameVariables = lambda s: s, kwCaption = u''): |
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359 '''Studies the influence of (nominal) independent variable over the dependent variable |
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360 |
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361 Makes tests if the conditional distributions are normal |
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362 using the Shapiro-Wilk test (in which case ANOVA could be used) |
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363 Implements uses the non-parametric Kruskal Wallis test''' |
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364 tmp = data[data[independentVariable].notnull()] |
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365 independentVariableValues = sorted(tmp[independentVariable].unique().tolist()) |
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366 if len(independentVariableValues) >= 2: |
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367 if saveLatex: |
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368 from storage import openCheck |
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369 out = openCheck(filenamePrefix+'-{}-{}.tex'.format(dependentVariable, independentVariable), 'w') |
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370 for x in independentVariableValues: |
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371 print('Shapiro-Wilk normality test for {} when {}={}: {} obs'.format(dependentVariable,independentVariable, x, len(tmp.loc[tmp[independentVariable] == x, dependentVariable]))) |
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372 if len(tmp.loc[tmp[independentVariable] == x, dependentVariable]) >= 3: |
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373 print shapiro(tmp.loc[tmp[independentVariable] == x, dependentVariable]) |
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374 if plotFigure: |
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375 plt.figure() |
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376 plt.boxplot([tmp.loc[tmp[independentVariable] == x, dependentVariable] for x in independentVariableValues]) |
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377 #q25, q75 = tmp[dependentVariable].quantile([.25, .75]) |
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378 #plt.ylim(ymax = q75+1.5*(q75-q25)) |
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379 plt.xticks(range(1,len(independentVariableValues)+1), independentVariableValues) |
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380 plt.title('{} vs {}'.format(dependentVariable, independentVariable)) |
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381 if filenamePrefix is not None: |
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382 plt.savefig(filenamePrefix+'-{}-{}.{}'.format(dependentVariable, independentVariable, figureFileType)) |
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383 table = tmp.groupby([independentVariable])[dependentVariable].describe().unstack().sort(['50%'], ascending = False) |
676 | 384 table['count'] = table['count'].astype(int) |
385 testResult = kruskal(*[tmp.loc[tmp[independentVariable] == x, dependentVariable] for x in independentVariableValues]) | |
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386 if saveLatex: |
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387 out.write('\\begin{minipage}{\\linewidth}\n' |
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388 +'\\centering\n' |
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389 +'\\captionof{table}{'+(kwCaption.format(dependentVariable, independentVariable, *testResult))+'}\n' |
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390 +table.to_latex(float_format = lambda x: '{:.3f}'.format(x)).encode('ascii')+'\n' |
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391 +'\\end{minipage}\n' |
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392 +'\\ \\vspace{0.5cm}\n') |
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393 else: |
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394 print table |
676 | 395 return testResult |
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396 else: |
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397 return None |
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398 |
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399 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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400 '''Removes variables from candidate independent variables if |
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401 - if two independent variables are correlated (> maxCorrelationThreshold), one is removed |
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402 - if an independent variable is not correlated with the dependent variable (p>maxCorrelationP) |
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403 Returns the remaining non-correlated variables, correlated with the dependent variable |
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404 |
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405 correlationFunc is spearmanr or pearsonr from scipy.stats |
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406 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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407 |
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408 TODO: pass the dummies for nominal variables and remove if all dummies are correlated, or none is correlated with the dependentvariable''' |
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409 from copy import copy |
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410 from pandas import DataFrame |
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411 result = copy(independentVariables) |
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412 table1 = '' |
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413 table2 = {} |
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414 # constant variables |
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415 for var in independentVariables: |
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416 uniqueValues = data[var].unique() |
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417 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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418 print(stdoutText[0].format(var, uniqueValues)) |
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419 if saveFiles: |
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420 table1 += latexTable[0].format(var, *uniqueValues) |
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421 result.remove(var) |
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422 # correlated variables |
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423 for v1 in copy(result): |
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424 if v1 in correlations.index: |
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425 for v2 in copy(result): |
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426 if v2 != v1 and v2 in correlations.index: |
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427 if abs(correlations.loc[v1, v2]) > maxCorrelationThreshold: |
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428 if v1 in result and v2 in result: |
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429 if saveFiles: |
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430 table1 += latexTable[1].format(v2, v1, correlations.loc[v1, v2]) |
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431 print(stdoutText[1].format(v2, v1, correlations.loc[v1, v2])) |
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432 result.remove(v2) |
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433 # not correlated with dependent variable |
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434 table2['Correlations'] = [] |
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435 table2['Valeurs p'] = [] |
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436 for var in copy(result): |
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437 if data.dtypes[var] != dtype('O'): |
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438 cor, p = correlationFunc(data[dependentVariable], data[var]) |
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439 if p > maxCorrelationP: |
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440 if saveFiles: |
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441 table1 += latexTable[2].format(var, cor, p) |
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442 print(stdoutText[2].format(var, cor, p)) |
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443 result.remove(var) |
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444 else: |
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445 table2['Correlations'].append(cor) |
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446 table2['Valeurs p'].append(p) |
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447 |
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448 if saveFiles: |
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449 from storage import openCheck |
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450 out = openCheck(filenamePrefix+'-removed-variables.tex', 'w') |
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451 out.write(latexHeader) |
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452 out.write(table1) |
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453 out.write(latexFooter) |
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454 out.close() |
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455 out = openCheck(filenamePrefix+'-correlations.html', 'w') |
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456 table2['Variables'] = [var for var in result if data.dtypes[var] != dtype('O')] |
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457 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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458 out.close() |
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459 return result |
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460 |
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461 |
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462 ######################### |
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463 # regression analysis using statsmodels (and pandas) |
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464 ######################### |
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465 |
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466 # TODO make class for experiments? |
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467 # TODO add tests with public dataset downloaded from Internet (IRIS et al) |
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468 def modelString(experiment, dependentVariable, independentVariables): |
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469 return dependentVariable+' ~ '+' + '.join([independentVariable for independentVariable in independentVariables if experiment[independentVariable]]) |
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470 |
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471 def runModel(experiment, data, dependentVariable, independentVariables, regressionType = 'ols'): |
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472 import statsmodels.formula.api as smf |
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473 modelStr = modelString(experiment, dependentVariable, independentVariables) |
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474 if regressionType == 'ols': |
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475 model = smf.ols(modelStr, data = data) |
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476 elif regressionType == 'gls': |
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477 model = smf.gls(modelStr, data = data) |
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478 elif regressionType == 'rlm': |
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479 model = smf.rlm(modelStr, data = data) |
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480 else: |
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481 print('Unknown regression type {}. Exiting'.format(regressionType)) |
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482 import sys |
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483 sys.exit() |
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484 return model.fit() |
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485 |
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486 def runModels(experiments, data, dependentVariable, independentVariables, regressionType = 'ols'): |
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487 '''Runs several models and stores 3 statistics |
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488 adjusted R2, condition number (should be small, eg < 1000) |
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489 and p-value for Shapiro-Wilk test of residual normality''' |
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490 for i,experiment in experiments.iterrows(): |
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491 if experiment[independentVariables].any(): |
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492 results = runModel(experiment, data, dependentVariable, independentVariables, regressionType = 'ols') |
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493 experiments.loc[i,'r2adj'] = results.rsquared_adj |
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494 experiments.loc[i,'condNum'] = results.condition_number |
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495 experiments.loc[i, 'shapiroP'] = shapiro(results.resid)[1] |
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496 experiments.loc[i,'nobs'] = int(results.nobs) |
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497 return experiments |
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498 |
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499 def generateExperiments(independentVariables): |
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500 '''Generates all possible models for including or not each independent variable''' |
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501 from pandas import DataFrame |
667
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502 experiments = {} |
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503 nIndependentVariables = len(independentVariables) |
669 | 504 if nIndependentVariables != len(set(independentVariables)): |
667
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505 print("Duplicate variables. Exiting") |
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506 import sys |
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507 sys.exit() |
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508 nModels = 2**nIndependentVariables |
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509 for i,var in enumerate(independentVariables): |
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510 pattern = [False]*(2**i)+[True]*(2**i) |
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511 experiments[var] = pattern*(2**(nIndependentVariables-i-1)) |
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512 experiments = DataFrame(experiments) |
667
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513 experiments['r2adj'] = 0. |
677
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514 experiments['condNum'] = NaN |
667
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515 experiments['shapiroP'] = -1 |
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516 experiments['nobs'] = -1 |
667
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517 return experiments |
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|
518 |
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519 def findBestModel(data, dependentVariable, independentVariables, regressionType = 'ols', nProcesses = 1): |
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520 '''Generates all possible model with the independentVariables |
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521 and runs them, saving the results in experiments |
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522 with multiprocess option''' |
670
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523 from pandas import concat |
671
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524 from multiprocessing import Pool |
667
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525 experiments = generateExperiments(independentVariables) |
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526 nModels = len(experiments) |
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527 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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diff
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528 print("IndependentVariables: {}".format(independentVariables)) |
667
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529 if nProcesses == 1: |
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530 return runModels(experiments, data, dependentVariable, independentVariables, regressionType) |
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diff
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|
531 else: |
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|
532 pool = Pool(processes = nProcesses) |
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533 chunkSize = int(ceil(nModels/nProcesses)) |
667
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|
534 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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|
535 return concat([job.get() for job in jobs]) |
667
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diff
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|
536 |
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|
537 def findBestModelFwd(data, dependentVariable, independentVariables, modelFunc, experiments = None): |
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diff
changeset
|
538 '''Forward search for best model (based on adjusted R2) |
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diff
changeset
|
539 Randomly starting with one variable and adding randomly variables |
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diff
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|
540 if they improve the model |
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parents:
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diff
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|
541 |
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diff
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|
542 The results are added to experiments if provided as argument |
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parents:
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diff
changeset
|
543 Storing in experiment relies on the index being the number equal |
179b81faa1f8
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diff
changeset
|
544 to the binary code derived from the independent variables''' |
670
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parents:
669
diff
changeset
|
545 from numpy.random import permutation as nppermutation |
667
179b81faa1f8
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parents:
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diff
changeset
|
546 if experiments is None: |
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parents:
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diff
changeset
|
547 experiments = generateExperiments(independentVariables) |
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parents:
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diff
changeset
|
548 nIndependentVariables = len(independentVariables) |
670
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diff
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|
549 permutation = nppermutation(range(nIndependentVariables)).tolist() |
667
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parents:
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diff
changeset
|
550 variableMapping = {j: independentVariables[i] for i,j in enumerate(permutation)} |
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diff
changeset
|
551 print('Tested variables '+', '.join([variableMapping[i] for i in xrange(nIndependentVariables)])) |
179b81faa1f8
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diff
changeset
|
552 bestModel = [False]*nIndependentVariables |
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diff
changeset
|
553 currentVarNum = 0 |
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parents:
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diff
changeset
|
554 currentR2Adj = 0. |
179b81faa1f8
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parents:
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diff
changeset
|
555 for currentVarNum in xrange(nIndependentVariables): |
179b81faa1f8
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changeset
|
556 currentModel = [i for i in bestModel] |
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diff
changeset
|
557 currentModel[currentVarNum] = True |
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diff
changeset
|
558 rowIdx = sum([0]+[2**i for i in xrange(nIndependentVariables) if currentModel[permutation[i]]]) |
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diff
changeset
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559 #print currentVarNum, sum(currentModel), ', '.join([independentVariables[i] for i in xrange(nIndependentVariables) if currentModel[permutation[i]]]) |
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diff
changeset
|
560 if experiments.loc[rowIdx, 'shapiroP'] < 0: |
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parents:
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diff
changeset
|
561 modelStr = modelString(experiments.loc[rowIdx], dependentVariable, independentVariables) |
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diff
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|
562 model = modelFunc(modelStr, data = data) |
179b81faa1f8
added regression analysis functions
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parents:
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diff
changeset
|
563 results = model.fit() |
179b81faa1f8
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parents:
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diff
changeset
|
564 experiments.loc[rowIdx, 'r2adj'] = results.rsquared_adj |
179b81faa1f8
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parents:
665
diff
changeset
|
565 experiments.loc[rowIdx, 'condNum'] = results.condition_number |
179b81faa1f8
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parents:
665
diff
changeset
|
566 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
|
567 experiments.loc[rowIdx, 'nobs'] = int(results.nobs) |
667
179b81faa1f8
added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
665
diff
changeset
|
568 if currentR2Adj < experiments.loc[rowIdx, 'r2adj']: |
179b81faa1f8
added regression analysis functions
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parents:
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diff
changeset
|
569 currentR2Adj = experiments.loc[rowIdx, 'r2adj'] |
179b81faa1f8
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parents:
665
diff
changeset
|
570 bestModel[currentVarNum] = True |
179b81faa1f8
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parents:
665
diff
changeset
|
571 return experiments |
179b81faa1f8
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parents:
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diff
changeset
|
572 |
677
ae07c7b4cf87
update to utils for pavement results
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parents:
676
diff
changeset
|
573 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
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parents:
665
diff
changeset
|
574 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
|
575 '''Displays some model results |
ae07c7b4cf87
update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
676
diff
changeset
|
576 |
ae07c7b4cf87
update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
676
diff
changeset
|
577 3 graphics, true-predicted, residuals-predicted, ''' |
676 | 578 print(results.summary()) |
677
ae07c7b4cf87
update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
676
diff
changeset
|
579 shapiroResult = shapiro(results.resid) |
ae07c7b4cf87
update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
676
diff
changeset
|
580 print(shapiroResult) |
676 | 581 if plotFigures: |
677
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582 fig = plt.figure(figsize=(7,6.3*(2+int(model is not None)))) |
676 | 583 if model is not None: |
677
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584 ax = fig.add_subplot(3,1,1) |
676 | 585 plt.plot(results.predict(), model.endog, 'x') |
586 x=plt.xlim() | |
587 y=plt.ylim() | |
588 plt.plot([max(x[0], y[0]), min(x[1], y[1])], [max(x[0], y[0]), min(x[1], y[1])], 'r') | |
677
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589 #plt.axis('equal') |
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590 if text is not None: |
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591 plt.title(text['title-shapiro'].format(*shapiroResult)) |
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592 #plt.title(text['true-predicted.title']) |
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593 plt.xlabel(text['true-predicted.xlabel']) |
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594 plt.ylabel(text['true-predicted.ylabel']) |
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595 fig.add_subplot(3,1,2, sharex = ax) |
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596 plt.plot(results.predict(), results.resid, 'x') |
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597 nextSubplotNum = 3 |
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598 else: |
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599 fig.add_subplot(2,1,1) |
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600 plt.plot(results.predict(), results.resid, 'x') |
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601 nextSubplotNum = 2 |
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602 if text is not None: |
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603 if model is None: |
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604 plt.title(text['title-shapiro'].format(*shapiroResult)) |
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605 plt.xlabel(text['residuals-predicted.xlabel']) |
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606 plt.ylabel(text['residuals-predicted.ylabel']) |
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607 qqAx = fig.add_subplot(nextSubplotNum,1,nextSubplotNum) |
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608 sm.qqplot(results.resid, fit = True, line = '45', ax = qqAx) |
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|
609 plt.axis('equal') |
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610 if text is not None and 'qqplot.xlabel' in text: |
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611 plt.xlabel(text['qqplot.xlabel']) |
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612 plt.ylabel(text['qqplot.ylabel']) |
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613 plt.tight_layout() |
676 | 614 if filenamePrefix is not None: |
677
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615 from storage import openCheck |
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616 out = openCheck(filenamePrefix+'-coefficients.html', 'w') |
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617 out.write(results.summary().as_html()) |
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618 plt.savefig(filenamePrefix+'-model-results.'+figureFileType) |
667
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619 |
27
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620 ######################### |
455
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621 # iterable section |
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622 ######################### |
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623 |
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624 def mostCommon(L): |
456 | 625 '''Returns the most frequent element in a iterable |
626 | |
627 taken from http://stackoverflow.com/questions/1518522/python-most-common-element-in-a-list''' | |
455
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628 from itertools import groupby |
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629 from operator import itemgetter |
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630 # get an iterable of (item, iterable) pairs |
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631 SL = sorted((x, i) for i, x in enumerate(L)) |
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632 # print 'SL:', SL |
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633 groups = groupby(SL, key=itemgetter(0)) |
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634 # auxiliary function to get "quality" for an item |
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635 def _auxfun(g): |
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636 item, iterable = g |
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637 count = 0 |
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638 min_index = len(L) |
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639 for _, where in iterable: |
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640 count += 1 |
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641 min_index = min(min_index, where) |
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642 # print 'item %r, count %r, minind %r' % (item, count, min_index) |
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643 return count, -min_index |
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644 # pick the highest-count/earliest item |
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645 return max(groups, key=_auxfun)[0] |
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646 |
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647 ######################### |
370
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648 # sequence section |
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649 ######################### |
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|
650 |
665
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651 class LCSS(object): |
370
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652 '''Class that keeps the LCSS parameters |
686
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653 and puts together the various computations |
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654 |
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655 the methods with names starting with _ are not to be shadowed |
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656 in child classes, who will shadow the other methods, |
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657 ie compute and computeXX methods''' |
689
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658 def __init__(self, similarityFunc = None, metric = None, epsilon = None, delta = float('inf'), aligned = False, lengthFunc = min): |
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659 '''One should provide either a similarity function |
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660 that indicates (return bool) whether elements in the compares lists are similar |
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661 |
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662 eg distance(p1, p2) < epsilon |
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663 |
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664 or a type of metric usable in scipy.spatial.distance.cdist with an epsilon''' |
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665 if similarityFunc is None and metric is None: |
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|
666 print("No way to compute LCSS, similarityFunc and metric are None. Exiting") |
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667 import sys |
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668 sys.exit() |
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669 elif metric is not None and epsilon is None: |
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670 print("Please provide a value for epsilon if using a cdist metric. Exiting") |
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671 import sys |
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672 sys.exit() |
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|
673 else: |
741 | 674 if similarityFunc is None and metric is not None and not isinf(delta): |
737
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added warning for finite delta
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diff
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|
675 print('Warning: you are using a cdist metric and a finite delta, which will make probably computation slower than using the equivalent similarityFunc (since all pairwise distances will be computed by cdist).') |
689
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676 self.similarityFunc = similarityFunc |
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677 self.metric = metric |
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678 self.epsilon = epsilon |
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679 self.aligned = aligned |
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680 self.delta = delta |
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681 self.lengthFunc = lengthFunc |
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682 self.subSequenceIndices = [(0,0)] |
370
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683 |
373
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684 def similarities(self, l1, l2, jshift=0): |
370
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685 n1 = len(l1) |
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686 n2 = len(l2) |
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687 self.similarityTable = zeros((n1+1,n2+1), dtype = npint) |
689
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688 if self.similarityFunc is not None: |
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|
689 for i in xrange(1,n1+1): |
9990ef119bce
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|
690 for j in xrange(max(1,i-jshift-self.delta),min(n2,i-jshift+self.delta)+1): |
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691 if self.similarityFunc(l1[i-1], l2[j-1]): |
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|
692 self.similarityTable[i,j] = self.similarityTable[i-1,j-1]+1 |
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693 else: |
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|
694 self.similarityTable[i,j] = max(self.similarityTable[i-1,j], self.similarityTable[i,j-1]) |
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695 elif self.metric is not None: |
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696 similarElements = distance.cdist(l1, l2, self.metric) <= self.epsilon |
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|
697 for i in xrange(1,n1+1): |
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changeset
|
698 for j in xrange(max(1,i-jshift-self.delta),min(n2,i-jshift+self.delta)+1): |
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|
699 if similarElements[i-1, j-1]: |
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700 self.similarityTable[i,j] = self.similarityTable[i-1,j-1]+1 |
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|
701 else: |
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|
702 self.similarityTable[i,j] = max(self.similarityTable[i-1,j], self.similarityTable[i,j-1]) |
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diff
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|
703 |
370
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|
704 |
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|
705 def subSequence(self, i, j): |
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diff
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|
706 '''Returns the subsequence of two sequences |
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|
707 http://en.wikipedia.org/wiki/Longest_common_subsequence_problem''' |
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diff
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|
708 if i == 0 or j == 0: |
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|
709 return [] |
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|
710 elif self.similarityTable[i][j] == self.similarityTable[i][j-1]: |
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711 return self.subSequence(i, j-1) |
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|
712 elif self.similarityTable[i][j] == self.similarityTable[i-1][j]: |
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|
713 return self.subSequence(i-1, j) |
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|
714 else: |
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|
715 return self.subSequence(i-1, j-1) + [(i-1,j-1)] |
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|
716 |
373
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|
717 def _compute(self, _l1, _l2, computeSubSequence = False): |
370
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|
718 '''returns the longest common subsequence similarity |
689
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diff
changeset
|
719 l1 and l2 should be the right format |
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diff
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|
720 eg list of tuple points for cdist |
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diff
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|
721 or elements that can be compare using similarityFunc |
370
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722 |
607 | 723 if aligned, returns the best matching if using a finite delta by shifting the series alignments |
370
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724 ''' |
372
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|
725 if len(_l2) < len(_l1): # l1 is the shortest |
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726 l1 = _l2 |
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727 l2 = _l1 |
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diff
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728 revertIndices = True |
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729 else: |
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|
730 l1 = _l1 |
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|
731 l2 = _l2 |
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732 revertIndices = False |
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733 n1 = len(l1) |
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734 n2 = len(l2) |
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|
735 |
370
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|
736 if self.aligned: |
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737 lcssValues = {} |
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738 similarityTables = {} |
374
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|
739 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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740 self.similarities(l1, l2, i) |
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741 lcssValues[i] = self.similarityTable.max() |
370
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|
742 similarityTables[i] = self.similarityTable |
374
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diff
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|
743 #print self.similarityTable |
521
3707eeb20f25
changed argMaxDict name to argmaxDict
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parents:
518
diff
changeset
|
744 alignmentShift = argmaxDict(lcssValues) # ideally get the medium alignment shift, the one that minimizes distance |
389
6d26dcc7bba0
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diff
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|
745 self.similarityTable = similarityTables[alignmentShift] |
372
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diff
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|
746 else: |
389
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diff
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|
747 alignmentShift = 0 |
372
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diff
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|
748 self.similarities(l1, l2) |
373
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diff
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|
749 |
374
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373
diff
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|
750 # threshold values for the useful part of the similarity table are n2-n1-delta and n1-n2-delta |
389
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diff
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|
751 self.similarityTable = self.similarityTable[:min(n1, n2+alignmentShift+self.delta)+1, :min(n2, n1-alignmentShift+self.delta)+1] |
373
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diff
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|
752 |
372
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diff
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|
753 if computeSubSequence: |
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371
diff
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|
754 self.subSequenceIndices = self.subSequence(self.similarityTable.shape[0]-1, self.similarityTable.shape[1]-1) |
371
924e38c9f70e
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370
diff
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|
755 if revertIndices: |
374
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diff
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|
756 self.subSequenceIndices = [(j,i) for i,j in self.subSequenceIndices] |
372
349eb1e09f45
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diff
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|
757 return self.similarityTable[-1,-1] |
370
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diff
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|
758 |
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|
759 def compute(self, l1, l2, computeSubSequence = False): |
97e8fa0ee9a1
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diff
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|
760 '''get methods are to be shadowed in child classes ''' |
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|
761 return self._compute(l1, l2, computeSubSequence) |
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diff
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|
762 |
375
2ea8584aa80a
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374
diff
changeset
|
763 def computeAlignment(self): |
374
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|
764 return mean([j-i for i,j in self.subSequenceIndices]) |
370
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|
765 |
376
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|
766 def _computeNormalized(self, l1, l2, computeSubSequence = False): |
370
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diff
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|
767 ''' compute the normalized LCSS |
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|
768 ie, the LCSS divided by the min or mean of the indicator lengths (using lengthFunc) |
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|
769 lengthFunc = lambda x,y:float(x,y)/2''' |
376
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changeset
|
770 return float(self._compute(l1, l2, computeSubSequence))/self.lengthFunc(len(l1), len(l2)) |
370
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|
771 |
376
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diff
changeset
|
772 def computeNormalized(self, l1, l2, computeSubSequence = False): |
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|
773 return self._computeNormalized(l1, l2, computeSubSequence) |
370
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diff
changeset
|
774 |
376
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diff
changeset
|
775 def _computeDistance(self, l1, l2, computeSubSequence = False): |
370
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diff
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|
776 ''' compute the LCSS distance''' |
376
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diff
changeset
|
777 return 1-self._computeNormalized(l1, l2, computeSubSequence) |
370
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|
778 |
376
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diff
changeset
|
779 def computeDistance(self, l1, l2, computeSubSequence = False): |
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375
diff
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|
780 return self._computeDistance(l1, l2, computeSubSequence) |
370
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diff
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|
781 |
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diff
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|
782 ######################### |
45
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42
diff
changeset
|
783 # plotting section |
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diff
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|
784 ######################### |
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42
diff
changeset
|
785 |
332
a6ca86107f27
reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
324
diff
changeset
|
786 def plotPolygon(poly, options = ''): |
a6ca86107f27
reorganized utils module
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parents:
324
diff
changeset
|
787 'Plots shapely polygon poly' |
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diff
changeset
|
788 from numpy.core.multiarray import array |
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diff
changeset
|
789 from matplotlib.pyplot import plot |
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diff
changeset
|
790 from shapely.geometry import Polygon |
a6ca86107f27
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diff
changeset
|
791 |
a6ca86107f27
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324
diff
changeset
|
792 tmp = array(poly.exterior) |
a6ca86107f27
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324
diff
changeset
|
793 plot(tmp[:,0], tmp[:,1], options) |
a6ca86107f27
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324
diff
changeset
|
794 |
324 | 795 def stepPlot(X, firstX, lastX, initialCount = 0, increment = 1): |
796 '''for each value in X, increment by increment the initial count | |
297
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diff
changeset
|
797 returns the lists that can be plotted |
324 | 798 to obtain a step plot increasing by one for each value in x, from first to last value |
799 firstX and lastX should be respectively smaller and larger than all elements in X''' | |
297
f6f423e25c7f
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diff
changeset
|
800 |
f6f423e25c7f
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286
diff
changeset
|
801 sortedX = [] |
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diff
changeset
|
802 counts = [initialCount] |
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diff
changeset
|
803 for x in sorted(X): |
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diff
changeset
|
804 sortedX += [x,x] |
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diff
changeset
|
805 counts.append(counts[-1]) |
324 | 806 counts.append(counts[-1]+increment) |
297
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diff
changeset
|
807 counts.append(counts[-1]) |
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diff
changeset
|
808 return [firstX]+sortedX+[lastX], counts |
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diff
changeset
|
809 |
665
15e244d2a1b5
corrected bug with circular import for VideoFilenameAddable, moved to base module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
659
diff
changeset
|
810 class PlottingPropertyValues(object): |
45
74d2de078baf
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42
diff
changeset
|
811 def __init__(self, values): |
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diff
changeset
|
812 self.values = values |
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diff
changeset
|
813 |
116
2bf5b76320c0
moved intersection plotting and added markers for scatter plots
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parents:
115
diff
changeset
|
814 def __getitem__(self, i): |
45
74d2de078baf
added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
42
diff
changeset
|
815 return self.values[i%len(self.values)] |
74d2de078baf
added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
42
diff
changeset
|
816 |
74d2de078baf
added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
42
diff
changeset
|
817 markers = PlottingPropertyValues(['+', '*', ',', '.', 'x', 'D', 's', 'o']) |
116
2bf5b76320c0
moved intersection plotting and added markers for scatter plots
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
115
diff
changeset
|
818 scatterMarkers = PlottingPropertyValues(['s','o','^','>','v','<','d','p','h','8','+','x']) |
45
74d2de078baf
added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
42
diff
changeset
|
819 |
74d2de078baf
added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
42
diff
changeset
|
820 linestyles = PlottingPropertyValues(['-', '--', '-.', ':']) |
74d2de078baf
added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
42
diff
changeset
|
821 |
74d2de078baf
added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
42
diff
changeset
|
822 colors = PlottingPropertyValues('brgmyck') # 'w' |
74d2de078baf
added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
42
diff
changeset
|
823 |
115
550556378466
added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
86
diff
changeset
|
824 def plotIndicatorMap(indicatorMap, squareSize, masked = True, defaultValue=-1): |
65
75cf537b8d88
moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
48
diff
changeset
|
825 from matplotlib.pyplot import pcolor |
75cf537b8d88
moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
48
diff
changeset
|
826 coords = array(indicatorMap.keys()) |
75cf537b8d88
moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
48
diff
changeset
|
827 minX = min(coords[:,0]) |
75cf537b8d88
moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
48
diff
changeset
|
828 minY = min(coords[:,1]) |
75cf537b8d88
moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
48
diff
changeset
|
829 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
|
830 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
|
831 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
|
832 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
|
833 C[k[1]-minY,k[0]-minX] = v |
115
550556378466
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
86
diff
changeset
|
834 if masked: |
550556378466
added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
86
diff
changeset
|
835 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
|
836 else: |
550556378466
added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
86
diff
changeset
|
837 pcolor(X, Y, C) |
65
75cf537b8d88
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
48
diff
changeset
|
838 |
45
74d2de078baf
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
42
diff
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|
839 ######################### |
637
c9a0b72979fd
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diff
changeset
|
840 # Data download |
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diff
changeset
|
841 ######################### |
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diff
changeset
|
842 |
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diff
changeset
|
843 def downloadECWeather(stationID, years, months = [], outputDirectoryname = '.', english = True): |
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parents:
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diff
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|
844 '''Downloads monthly weather data from Environment Canada |
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parents:
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diff
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|
845 If month is provided (number 1 to 12), it means hourly data for the whole month |
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parents:
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diff
changeset
|
846 Otherwise, means the data for each day, for the whole year |
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diff
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|
847 |
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diff
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|
848 Example: MONTREAL MCTAVISH 10761 |
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
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diff
changeset
|
849 MONTREALPIERRE ELLIOTT TRUDEAU INTL A 5415 |
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parents:
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diff
changeset
|
850 |
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diff
changeset
|
851 To get daily data for 2010 and 2011, downloadECWeather(10761, [2010,2011], [], '/tmp') |
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parents:
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diff
changeset
|
852 To get hourly data for 2009 and 2012, January, March and October, downloadECWeather(10761, [2009,2012], [1,3,10], '/tmp')''' |
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diff
changeset
|
853 import urllib2 |
c9a0b72979fd
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
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diff
changeset
|
854 if english: |
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parents:
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diff
changeset
|
855 language = 'e' |
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diff
changeset
|
856 else: |
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parents:
615
diff
changeset
|
857 language = 'f' |
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parents:
615
diff
changeset
|
858 if len(months) == 0: |
c9a0b72979fd
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
859 timeFrame = 2 |
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
860 months = [1] |
c9a0b72979fd
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
861 else: |
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
862 timeFrame = 1 |
c9a0b72979fd
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parents:
615
diff
changeset
|
863 |
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
864 for year in years: |
c9a0b72979fd
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
865 for month in months: |
c9a0b72979fd
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parents:
615
diff
changeset
|
866 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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parents:
615
diff
changeset
|
867 data = url.read() |
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parents:
615
diff
changeset
|
868 outFilename = '{}/{}-{}'.format(outputDirectoryname, stationID, year) |
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parents:
615
diff
changeset
|
869 if timeFrame == 1: |
c9a0b72979fd
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parents:
615
diff
changeset
|
870 outFilename += '-{}-hourly'.format(month) |
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parents:
615
diff
changeset
|
871 else: |
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
872 outFilename += '-daily' |
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
873 outFilename += '.csv' |
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added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
874 out = open(outFilename, 'w') |
c9a0b72979fd
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
875 out.write(data) |
c9a0b72979fd
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
876 out.close() |
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
877 |
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parents:
615
diff
changeset
|
878 ######################### |
c9a0b72979fd
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
615
diff
changeset
|
879 # File I/O |
27
44689029a86f
updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents:
24
diff
changeset
|
880 ######################### |
24
6fb59cfb201e
first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents:
19
diff
changeset
|
881 |
0
aed8eb63cdde
initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
882 def removeExtension(filename, delimiter = '.'): |
31
c000f37c316d
moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents:
29
diff
changeset
|
883 '''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
|
884 i = filename.rfind(delimiter) |
aed8eb63cdde
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parents:
diff
changeset
|
885 if i>0: |
aed8eb63cdde
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Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
886 return filename[:i] |
aed8eb63cdde
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Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
887 else: |
aed8eb63cdde
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Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
888 return filename |
aed8eb63cdde
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Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
889 |
46
b5d007612e16
added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
45
diff
changeset
|
890 def cleanFilename(s): |
b5d007612e16
added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
45
diff
changeset
|
891 'cleans filenames obtained when contatenating figure characteristics' |
739 | 892 return s.replace(' ','-').replace('.','').replace('/','-').replace(',','') |
46
b5d007612e16
added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
45
diff
changeset
|
893 |
0
aed8eb63cdde
initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
894 def listfiles(dirname, extension, remove = False): |
14
e7bbe8465591
homography and other utils
Nicolas Saunier <nico@confins.net>
parents:
7
diff
changeset
|
895 '''Returns the list of files with the extension in the directory dirname |
e7bbe8465591
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parents:
7
diff
changeset
|
896 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
|
897 from os import listdir |
aed8eb63cdde
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parents:
diff
changeset
|
898 tmp = [f for f in listdir(dirname) if f.endswith(extension)] |
aed8eb63cdde
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Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
899 tmp.sort() |
aed8eb63cdde
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Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
900 if remove: |
aed8eb63cdde
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Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
901 return [removeExtension(f, extension) for f in tmp] |
aed8eb63cdde
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Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
902 else: |
aed8eb63cdde
initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff
changeset
|
903 return tmp |
aed8eb63cdde
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parents:
diff
changeset
|
904 |
266
aba9711b3149
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262
diff
changeset
|
905 def mkdir(dirname): |
aba9711b3149
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262
diff
changeset
|
906 'Creates a directory if it does not exist' |
aba9711b3149
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diff
changeset
|
907 import os |
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diff
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|
908 if not os.path.exists(dirname): |
aba9711b3149
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262
diff
changeset
|
909 os.mkdir(dirname) |
aba9711b3149
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262
diff
changeset
|
910 else: |
aba9711b3149
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262
diff
changeset
|
911 print(dirname+' already exists') |
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262
diff
changeset
|
912 |
14
e7bbe8465591
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parents:
7
diff
changeset
|
913 def removeFile(filename): |
e7bbe8465591
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parents:
7
diff
changeset
|
914 '''Deletes the file while avoiding raising an error |
e7bbe8465591
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parents:
7
diff
changeset
|
915 if the file does not exist''' |
266
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diff
changeset
|
916 import os |
14
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parents:
7
diff
changeset
|
917 if (os.path.exists(filename)): |
e7bbe8465591
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parents:
7
diff
changeset
|
918 os.remove(filename) |
266
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diff
changeset
|
919 else: |
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diff
changeset
|
920 print(filename+' does not exist') |
14
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homography and other utils
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parents:
7
diff
changeset
|
921 |
42
1a2ac2d4f53a
added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
35
diff
changeset
|
922 def line2Floats(l, separator=' '): |
1a2ac2d4f53a
added loading of the rest of the data for objects
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parents:
35
diff
changeset
|
923 '''Returns the list of floats corresponding to the string''' |
1a2ac2d4f53a
added loading of the rest of the data for objects
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parents:
35
diff
changeset
|
924 return [float(x) for x in l.split(separator)] |
1a2ac2d4f53a
added loading of the rest of the data for objects
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parents:
35
diff
changeset
|
925 |
1a2ac2d4f53a
added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
35
diff
changeset
|
926 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
|
927 '''Returns the list of ints corresponding to the string''' |
1a2ac2d4f53a
added loading of the rest of the data for objects
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parents:
35
diff
changeset
|
928 return [int(x) for x in l.split(separator)] |
31
c000f37c316d
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parents:
29
diff
changeset
|
929 |
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moved tests to independent file, added chi2 computation
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parents:
29
diff
changeset
|
930 ######################### |
332
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931 # CLI utils |
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932 ######################### |
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933 |
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934 def parseCLIOptions(helpMessage, options, cliArgs, optionalOptions=[]): |
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935 ''' Simple function to handle similar argument parsing |
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936 Returns the dictionary of options and their values |
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937 |
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938 * cliArgs are most likely directly sys.argv |
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939 (only the elements after the first one are considered) |
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940 |
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941 * options should be a list of strings for getopt options, |
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942 eg ['frame=','correspondences=','video='] |
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943 A value must be provided for each option, or the program quits''' |
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944 import sys, getopt |
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945 from numpy.core.fromnumeric import all |
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946 optionValues, args = getopt.getopt(cliArgs[1:], 'h', ['help']+options+optionalOptions) |
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947 optionValues = dict(optionValues) |
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948 |
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949 if '--help' in optionValues.keys() or '-h' in optionValues.keys(): |
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950 print(helpMessage+ |
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951 '\n - Compulsory options: '+' '.join([opt.replace('=','') for opt in options])+ |
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952 '\n - Non-compulsory options: '+' '.join([opt.replace('=','') for opt in optionalOptions])) |
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953 sys.exit() |
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954 |
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955 missingArgument = [('--'+opt.replace('=','') in optionValues.keys()) for opt in options] |
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956 if not all(missingArgument): |
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957 print('Missing argument') |
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958 print(optionValues) |
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959 sys.exit() |
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960 |
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961 return optionValues |
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962 |
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963 |
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964 ######################### |
553
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965 # Profiling |
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966 ######################### |
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967 |
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968 def analyzeProfile(profileFilename, stripDirs = True): |
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969 '''Analyze the file produced by cProfile |
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970 |
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971 obtained by for example: |
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972 - call in script (for main() function in script) |
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973 import cProfile, os |
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974 cProfile.run('main()', os.path.join(os.getcwd(),'main.profile')) |
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975 |
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976 - or on the command line: |
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977 python -m cProfile [-o profile.bin] [-s sort] scriptfile [arg]''' |
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978 import pstats, os |
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979 p = pstats.Stats(os.path.join(os.pardir, profileFilename)) |
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980 if stripDirs: |
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981 p.strip_dirs() |
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982 p.sort_stats('time') |
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983 p.print_stats(.2) |
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984 #p.sort_stats('time') |
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985 # p.print_callees(.1, 'int_prediction.py:') |
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986 return p |
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987 |
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988 ######################### |
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989 # running tests |
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990 ######################### |
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991 |
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992 if __name__ == "__main__": |
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993 import doctest |
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994 import unittest |
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995 suite = doctest.DocFileSuite('tests/utils.txt') |
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996 #suite = doctest.DocTestSuite() |
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997 unittest.TextTestRunner().run(suite) |
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998 #doctest.testmod() |
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999 #doctest.testfile("example.txt") |