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annotate python/utils.py @ 687:de278c5e65f6 dev

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minor comments for lognormal parameters (numpy and usual names differ)
author Nicolas Saunier <nicolas.saunier@polymtl.ca>
date Mon, 22 Jun 2015 15:27:33 +0200
parents cdee6a3a47b4
children 9990ef119bce
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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 numpy import zeros, array, exp, sum as npsum, int as npint, arange, cumsum, median, isnan, ones, convolve, dtype, isnan, NaN, mean, ma
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11
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12 datetimeFormat = "%Y-%m-%d %H:%M:%S"
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14 #########################
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15 # Enumerations
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16 #########################
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17
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18 def inverseEnumeration(l):
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19 'Returns the dictionary that provides for each element in the input list its index in the input list'
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20 result = {}
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21 for i,x in enumerate(l):
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22 result[x] = i
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23 return result
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24
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25 #########################
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26 # Simple statistics
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27 #########################
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28
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29 def logNormalMeanVar(loc, scale):
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30 '''location and scale are respectively the mean and standard deviation of the normal in the log-normal distribution
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31 https://en.wikipedia.org/wiki/Log-normal_distribution'''
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32 mean = exp(loc+(scale**2)/2)
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33 var = (exp(loc**2)-1)*exp(2*loc+scale**2)
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34 return mean, var
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35
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36 def sampleSize(stdev, tolerance, percentConfidence, printLatex = False):
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37 from scipy.stats.distributions import norm
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38 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1)*100)/100. # 1.-(100-percentConfidence)/200.
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39 if printLatex:
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40 print('${0}^2\\frac{{{1}^2}}{{{2}^2}}$'.format(k, stdev, tolerance))
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41 return (k*stdev/tolerance)**2
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42
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43 def confidenceInterval(mean, stdev, nSamples, percentConfidence, trueStd = True, printLatex = False):
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44 '''if trueStd, use normal distribution, otherwise, Student
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45
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46 Use otherwise t.interval or norm.interval
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47 ex: norm.interval(0.95, loc = 0., scale = 2.3/sqrt(11))
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48 t.interval(0.95, 10, loc=1.2, scale = 2.3/sqrt(nSamples))
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49 loc is mean, scale is sigma/sqrt(n) (for Student, 10 is df)'''
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50 from scipy.stats.distributions import norm, t
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51 if trueStd:
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52 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1)*100)/100. # 1.-(100-percentConfidence)/200.
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53 else: # use Student
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54 k = round(t.ppf(0.5+percentConfidence/200., nSamples-1)*100)/100.
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55 e = k*stdev/sqrt(nSamples)
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56 if printLatex:
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57 print('${0} \pm {1}\\frac{{{2}}}{{\sqrt{{{3}}}}}$'.format(mean, k, stdev, nSamples))
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58 return mean-e, mean+e
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59
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60 def computeChi2(expected, observed):
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61 '''Returns the Chi2 statistics'''
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62 result = 0.
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63 for e, o in zip(expected, observed):
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64 result += ((e-o)*(e-o))/e
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65 return result
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66
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67 class EmpiricalDistribution(object):
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68 def nSamples(self):
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69 return sum(self.counts)
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70
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71 def cumulativeDensityFunction(sample, normalized = False):
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72 '''Returns the cumulative density function of the sample of a random variable'''
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73 xaxis = sorted(sample)
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74 counts = arange(1,len(sample)+1) # dtype = float
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75 if normalized:
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76 counts /= float(len(sample))
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77 return xaxis, counts
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78
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79 class EmpiricalDiscreteDistribution(EmpiricalDistribution):
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80 '''Class to represent a sample of a distribution for a discrete random variable
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81 '''
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82 def __init__(self, categories, counts):
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83 self.categories = categories
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84 self.counts = counts
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85
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86 def mean(self):
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87 result = [float(x*y) for x,y in zip(self.categories, self.counts)]
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88 return npsum(result)/self.nSamples()
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89
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90 def var(self, mean = None):
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91 if not mean:
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92 m = self.mean()
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93 else:
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94 m = mean
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95 result = 0.
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96 squares = [float((x-m)*(x-m)*y) for x,y in zip(self.categories, self.counts)]
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97 return npsum(squares)/(self.nSamples()-1)
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98
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99 def referenceCounts(self, probability):
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100 '''probability is a function that returns the probability of the random variable for the category values'''
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101 refProba = [probability(c) for c in self.categories]
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102 refProba[-1] = 1-npsum(refProba[:-1])
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103 refCounts = [r*self.nSamples() for r in refProba]
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104 return refCounts, refProba
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105
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106 class EmpiricalContinuousDistribution(EmpiricalDistribution):
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107 '''Class to represent a sample of a distribution for a continuous random variable
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108 with the number of observations for each interval
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109 intervals (categories variable) are defined by their left limits, the last one being the right limit
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110 categories contain therefore one more element than the counts'''
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111 def __init__(self, categories, counts):
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112 # todo add samples for initialization and everything to None? (or setSamples?)
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113 self.categories = categories
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114 self.counts = counts
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115
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116 def mean(self):
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117 result = 0.
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118 for i in range(len(self.counts)-1):
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119 result += self.counts[i]*(self.categories[i]+self.categories[i+1])/2
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120 return result/self.nSamples()
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121
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122 def var(self, mean = None):
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123 if not mean:
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124 m = self.mean()
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125 else:
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126 m = mean
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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 mid = (self.categories[i]+self.categories[i+1])/2
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130 result += self.counts[i]*(mid - m)*(mid - m)
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131 return result/(self.nSamples()-1)
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diff changeset
132
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parents: 32
diff changeset
133 def referenceCounts(self, cdf):
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parents: 32
diff changeset
134 '''cdf is a cumulative distribution function
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parents: 32
diff changeset
135 returning the probability of the variable being less that x'''
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parents: 32
diff changeset
136 # refCumulativeCounts = [0]#[cdf(self.categories[0][0])]
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parents: 32
diff changeset
137 # for inter in self.categories:
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parents: 32
diff changeset
138 # refCumulativeCounts.append(cdf(inter[1]))
76
64fde2b1f96d simplified intervales in empiricalDistribution
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parents: 75
diff changeset
139 refCumulativeCounts = [cdf(x) for x in self.categories[1:-1]]
35
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parents: 32
diff changeset
140
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parents: 32
diff changeset
141 refProba = [refCumulativeCounts[0]]
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
142 for i in xrange(1,len(refCumulativeCounts)):
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parents: 32
diff changeset
143 refProba.append(refCumulativeCounts[i]-refCumulativeCounts[i-1])
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parents: 32
diff changeset
144 refProba.append(1-refCumulativeCounts[-1])
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parents: 32
diff changeset
145 refCounts = [p*self.nSamples() for p in refProba]
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parents: 32
diff changeset
146
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parents: 32
diff changeset
147 return refCounts, refProba
31
c000f37c316d moved tests to independent file, added chi2 computation
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parents: 29
diff changeset
148
77
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parents: 76
diff changeset
149 def printReferenceCounts(self, refCounts=None):
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parents: 76
diff changeset
150 if refCounts:
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parents: 76
diff changeset
151 ref = refCounts
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parents: 76
diff changeset
152 else:
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parents: 76
diff changeset
153 ref = self.referenceCounts
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parents: 76
diff changeset
154 for i in xrange(len(ref[0])):
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parents: 76
diff changeset
155 print('{0}-{1} & {2:0.3} & {3:0.3} \\\\'.format(self.categories[i],self.categories[i+1],ref[1][i], ref[0][i]))
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parents: 76
diff changeset
156
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parents: 76
diff changeset
157
31
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parents: 29
diff changeset
158 #########################
370
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parents: 369
diff changeset
159 # maths section
27
44689029a86f updated segmentIntersection and other
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parents: 24
diff changeset
160 #########################
24
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161
433
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diff changeset
162 # def kernelSmoothing(sampleX, X, Y, weightFunc, halfwidth):
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163 # '''Returns a smoothed weighted version of Y at the predefined values of sampleX
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164 # Sum_x weight(sample_x,x) * y(x)'''
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diff changeset
165 # from numpy import zeros, array
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diff changeset
166 # smoothed = zeros(len(sampleX))
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parents: 423
diff changeset
167 # for i,x in enumerate(sampleX):
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parents: 423
diff changeset
168 # weights = array([weightFunc(x,xx, halfwidth) for xx in X])
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parents: 423
diff changeset
169 # if sum(weights)>0:
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parents: 423
diff changeset
170 # smoothed[i] = sum(weights*Y)/sum(weights)
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parents: 423
diff changeset
171 # else:
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diff changeset
172 # smoothed[i] = 0
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diff changeset
173 # return smoothed
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174
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parents: 423
diff changeset
175 def kernelSmoothing(x, X, Y, weightFunc, halfwidth):
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parents: 423
diff changeset
176 '''Returns the smoothed estimate of (X,Y) at x
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diff changeset
177 Sum_x weight(sample_x,x) * y(x)'''
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parents: 423
diff changeset
178 weights = array([weightFunc(x,observedx, halfwidth) for observedx in X])
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parents: 423
diff changeset
179 if sum(weights)>0:
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diff changeset
180 return sum(weights*Y)/sum(weights)
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parents: 423
diff changeset
181 else:
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diff changeset
182 return 0
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parents: 423
diff changeset
183
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parents: 423
diff changeset
184 def uniform(center, x, halfwidth):
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parents: 423
diff changeset
185 if abs(center-x)<halfwidth:
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parents: 423
diff changeset
186 return 1.
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parents: 423
diff changeset
187 else:
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diff changeset
188 return 0.
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parents: 423
diff changeset
189
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parents: 423
diff changeset
190 def gaussian(center, x, halfwidth):
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parents: 423
diff changeset
191 return exp(-((center-x)/halfwidth)**2/2)
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parents: 423
diff changeset
192
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parents: 423
diff changeset
193 def epanechnikov(center, x, halfwidth):
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parents: 423
diff changeset
194 diff = abs(center-x)
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parents: 423
diff changeset
195 if diff<halfwidth:
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parents: 423
diff changeset
196 return 1.-(diff/halfwidth)**2
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parents: 423
diff changeset
197 else:
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parents: 423
diff changeset
198 return 0.
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parents: 423
diff changeset
199
434
9a714f32fc9f small updates
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parents: 433
diff changeset
200 def triangular(center, x, halfwidth):
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parents: 433
diff changeset
201 diff = abs(center-x)
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parents: 433
diff changeset
202 if diff<halfwidth:
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parents: 433
diff changeset
203 return 1.-abs(diff/halfwidth)
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parents: 433
diff changeset
204 else:
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parents: 433
diff changeset
205 return 0.
433
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parents: 423
diff changeset
206
518
0c86c73f3c09 median smoothing
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parents: 511
diff changeset
207 def medianSmoothing(x, X, Y, halfwidth):
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parents: 511
diff changeset
208 '''Returns the media of Y's corresponding to X's in the interval [x-halfwidth, x+halfwidth]'''
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parents: 511
diff changeset
209 return median([y for observedx, y in zip(X,Y) if abs(x-observedx)<halfwidth])
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parents: 511
diff changeset
210
521
3707eeb20f25 changed argMaxDict name to argmaxDict
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parents: 518
diff changeset
211 def argmaxDict(d):
561
ee45c6eb6d49 added Mohamed Gomaa Mohamed function to smooth object trajectories
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 553
diff changeset
212 return max(d, key=d.get)
279
3af4c267a7bf generic simple LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 276
diff changeset
213
395
6fba1ab040f1 minor modification to framestotime
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parents: 391
diff changeset
214 def framesToTime(nFrames, frameRate, initialTime = time()):
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parents: 391
diff changeset
215 '''returns a datetime.time for the time in hour, minutes and seconds
6fba1ab040f1 minor modification to framestotime
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parents: 391
diff changeset
216 initialTime is a datetime.time'''
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parents: 391
diff changeset
217 seconds = int(floor(float(nFrames)/float(frameRate))+initialTime.hour*3600+initialTime.minute*60+initialTime.second)
261
4aa792cb0fa9 changing framesToTime to return a datetime.time
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 248
diff changeset
218 h = int(floor(seconds/3600.))
248
571ba5ed22e2 added utils for bus processing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 241
diff changeset
219 seconds = seconds - h*3600
261
4aa792cb0fa9 changing framesToTime to return a datetime.time
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 248
diff changeset
220 m = int(floor(seconds/60))
248
571ba5ed22e2 added utils for bus processing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 241
diff changeset
221 seconds = seconds - m*60
262
a048066bd20f correcting bug in framesToTime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 261
diff changeset
222 return time(h, m, seconds)
248
571ba5ed22e2 added utils for bus processing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 241
diff changeset
223
381
387cc0142211 script to replay event annotations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 376
diff changeset
224 def timeToFrames(t, frameRate):
387cc0142211 script to replay event annotations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 376
diff changeset
225 return frameRate*(t.hour*3600+t.minute*60+t.second)
387cc0142211 script to replay event annotations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 376
diff changeset
226
241
ee1caff48b03 added function to sort to list of paired data X,Y
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
227 def sortXY(X,Y):
ee1caff48b03 added function to sort to list of paired data X,Y
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parents: 235
diff changeset
228 'returns the sorted (x, Y(x)) sorted on X'
ee1caff48b03 added function to sort to list of paired data X,Y
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
229 D = {}
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
230 for x, y in zip(X,Y):
ee1caff48b03 added function to sort to list of paired data X,Y
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
231 D[x]=y
ee1caff48b03 added function to sort to list of paired data X,Y
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
232 xsorted = sorted(D.keys())
ee1caff48b03 added function to sort to list of paired data X,Y
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
233 return xsorted, [D[x] for x in xsorted]
ee1caff48b03 added function to sort to list of paired data X,Y
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
234
32
48e56179c39e added ceil function
Nicolas Saunier <nico@confins.net>
parents: 31
diff changeset
235 def ceilDecimals(v, nDecimals):
48e56179c39e added ceil function
Nicolas Saunier <nico@confins.net>
parents: 31
diff changeset
236 '''Rounds the number at the nth decimal
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parents: 31
diff changeset
237 eg 1.23 at 0 decimal is 2, at 1 decimal is 1.3'''
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
238 tens = 10**nDecimals
32
48e56179c39e added ceil function
Nicolas Saunier <nico@confins.net>
parents: 31
diff changeset
239 return ceil(v*tens)/tens
48e56179c39e added ceil function
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parents: 31
diff changeset
240
152
74b1fc68d4df re-organized code to avoid cyclic python module dependencies
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 116
diff changeset
241 def inBetween(bound1, bound2, x):
569
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
242 return bound1 <= x <= bound2 or bound2 <= x <= bound1
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
243
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
244 def pointDistanceL2(x1,y1,x2,y2):
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
245 ''' Compute point-to-point distance (L2 norm, ie Euclidean distance)'''
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
246 return sqrt((x2-x1)**2+(y2-y1)**2)
24
6fb59cfb201e first version of segmentIntersection
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parents: 19
diff changeset
247
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
248 def crossProduct(l1, l2):
6fb59cfb201e first version of segmentIntersection
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parents: 19
diff changeset
249 return l1[0]*l2[1]-l1[1]*l2[0]
6fb59cfb201e first version of segmentIntersection
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parents: 19
diff changeset
250
574
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
251 def cat_mvgavg(cat_list, halfWidth):
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
252 ''' Return a list of categories/values smoothed according to a window.
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
253 halfWidth is the search radius on either side'''
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
254 from copy import deepcopy
659
784298512b60 minor modifications
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 637
diff changeset
255 smoothed = deepcopy(cat_list)
784298512b60 minor modifications
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 637
diff changeset
256 for point in range(len(cat_list)):
574
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
257 lower_bound_check = max(0,point-halfWidth)
659
784298512b60 minor modifications
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 637
diff changeset
258 upper_bound_check = min(len(cat_list)-1,point+halfWidth+1)
784298512b60 minor modifications
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 637
diff changeset
259 window_values = cat_list[lower_bound_check:upper_bound_check]
574
e24eeb244698 first implementation of projection to curvilinear coordinates
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parents: 569
diff changeset
260 smoothed[point] = max(set(window_values), key=window_values.count)
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
261 return smoothed
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
262
547
97c5fef5b2d6 corrected bugs
MohamedGomaa
parents: 521
diff changeset
263 def filterMovingWindow(inputSignal, halfWidth):
29
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
264 '''Returns an array obtained after the smoothing of the input by a moving average
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
265 The first and last points are copied from the original.'''
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
266 width = float(halfWidth*2+1)
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
267 win = ones(width,'d')
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
268 result = convolve(win/width,array(inputSignal),'same')
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
269 result[:halfWidth] = inputSignal[:halfWidth]
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
270 result[-halfWidth:] = inputSignal[-halfWidth:]
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
271 return result
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
272
199
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273 def linearRegression(x, y, deg = 1, plotData = False):
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274 '''returns the least square estimation of the linear regression of y = ax+b
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275 as well as the plot'''
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276 from numpy.lib.polynomial import polyfit
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277 from numpy.core.multiarray import arange
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278 coef = polyfit(x, y, deg)
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279 if plotData:
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280 def poly(x):
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281 result = 0
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282 for i in range(len(coef)):
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283 result += coef[i]*x**(len(coef)-i-1)
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284 return result
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285 plt.plot(x, y, 'x')
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286 xx = arange(min(x), max(x),(max(x)-min(x))/1000)
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287 plt.plot(xx, [poly(z) for z in xx])
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288 return coef
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289
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290 def correlation(data, correlationMethod = 'pearson', plotFigure = False, displayNames = None, figureFilename = None):
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291 '''Computes (and displays) the correlation matrix for a pandas DataFrame'''
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292 columns = data.columns.tolist()
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293 for var in data.columns:
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294 uniqueValues = data[var].unique()
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295 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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296 columns.remove(var)
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297 c=data[columns].corr(correlationMethod)
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298 if plotFigure:
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299 fig = plt.figure(figsize=(4+0.4*c.shape[0], 0.4*c.shape[0]))
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300 fig.add_subplot(1,1,1)
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301 #plt.imshow(np.fabs(c), interpolation='none')
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302 plt.imshow(c, vmin=-1., vmax = 1., interpolation='none', cmap = 'RdYlBu_r') # coolwarm
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303 colnames = [displayNames.get(s.strip(), s.strip()) for s in columns]
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304 #correlation.plot_corr(c, xnames = colnames, normcolor=True, title = filename)
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305 plt.xticks(range(len(colnames)), colnames, rotation=90)
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306 plt.yticks(range(len(colnames)), colnames)
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307 plt.tick_params('both', length=0)
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308 plt.subplots_adjust(bottom = 0.29)
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309 plt.colorbar()
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310 plt.title('Correlation ({})'.format(correlationMethod))
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311 plt.tight_layout()
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312 if len(colnames) > 50:
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313 plt.subplots_adjust(left=.06)
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314 if figureFilename is not None:
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315 plt.savefig(figureFilename, dpi = 150, transparent = True)
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316 return c
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317
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318 def addDummies(data, variables, allVariables = True):
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319 '''Add binary dummy variables for each value of a nominal variable
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320 in a pandas DataFrame'''
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321 newVariables = []
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322 for var in variables:
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323 if var in data.columns and data.dtypes[var] == dtype('O') and len(data[var].unique()) > 2:
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324 values = data[var].unique()
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325 if not allVariables:
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326 values = values[:-1]
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327 for val in values:
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328 if val is not NaN:
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329 newVariable = (var+'_{}'.format(val)).replace('.','').replace(' ','').replace('-','')
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330 data[newVariable] = (data[var] == val)
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331 newVariables.append(newVariable)
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332 return newVariables
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333
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334 def kruskalWallis(data, dependentVariable, independentVariable, plotFigure = False, filenamePrefix = None, figureFileType = 'pdf', saveLatex = False, renameVariables = lambda s: s, kwCaption = u''):
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335 '''Studies the influence of (nominal) independent variable over the dependent variable
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336
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337 Makes tests if the conditional distributions are normal
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338 using the Shapiro-Wilk test (in which case ANOVA could be used)
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339 Implements uses the non-parametric Kruskal Wallis test'''
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340 tmp = data[data[independentVariable].notnull()]
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341 independentVariableValues = sorted(tmp[independentVariable].unique().tolist())
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342 if len(independentVariableValues) >= 2:
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343 if saveLatex:
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344 from storage import openCheck
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345 out = openCheck(filenamePrefix+'-{}-{}.tex'.format(dependentVariable, independentVariable), 'w')
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346 for x in independentVariableValues:
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347 print('Shapiro-Wilk normality test for {} when {}={}: {} obs'.format(dependentVariable,independentVariable, x, len(tmp.loc[tmp[independentVariable] == x, dependentVariable])))
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348 if len(tmp.loc[tmp[independentVariable] == x, dependentVariable]) >= 3:
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349 print shapiro(tmp.loc[tmp[independentVariable] == x, dependentVariable])
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350 if plotFigure:
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351 plt.figure()
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352 plt.boxplot([tmp.loc[tmp[independentVariable] == x, dependentVariable] for x in independentVariableValues])
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353 #q25, q75 = tmp[dependentVariable].quantile([.25, .75])
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354 #plt.ylim(ymax = q75+1.5*(q75-q25))
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355 plt.xticks(range(1,len(independentVariableValues)+1), independentVariableValues)
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356 plt.title('{} vs {}'.format(dependentVariable, independentVariable))
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357 if filenamePrefix is not None:
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358 plt.savefig(filenamePrefix+'-{}-{}.{}'.format(dependentVariable, independentVariable, figureFileType))
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359 table = tmp.groupby([independentVariable])[dependentVariable].describe().unstack().sort(['50%'], ascending = False)
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360 table['count'] = table['count'].astype(int)
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361 testResult = kruskal(*[tmp.loc[tmp[independentVariable] == x, dependentVariable] for x in independentVariableValues])
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362 if saveLatex:
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363 out.write('\\begin{minipage}{\\linewidth}\n'
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364 +'\\centering\n'
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365 +'\\captionof{table}{'+(kwCaption.format(dependentVariable, independentVariable, *testResult))+'}\n'
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366 +table.to_latex(float_format = lambda x: '{:.3f}'.format(x)).encode('ascii')+'\n'
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367 +'\\end{minipage}\n'
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368 +'\\ \\vspace{0.5cm}\n')
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369 else:
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370 print table
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371 return testResult
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372 else:
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373 return None
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374
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375 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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376 '''Removes variables from candidate independent variables if
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377 - if two independent variables are correlated (> maxCorrelationThreshold), one is removed
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378 - if an independent variable is not correlated with the dependent variable (p>maxCorrelationP)
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379 Returns the remaining non-correlated variables, correlated with the dependent variable
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380
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381 correlationFunc is spearmanr or pearsonr from scipy.stats
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382 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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383
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384 TODO: pass the dummies for nominal variables and remove if all dummies are correlated, or none is correlated with the dependentvariable'''
668
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
385 from copy import copy
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
386 from pandas import DataFrame
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
387 result = copy(independentVariables)
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
388 table1 = ''
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
389 table2 = {}
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
390 # constant variables
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
391 for var in independentVariables:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
392 uniqueValues = data[var].unique()
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
393 if (len(uniqueValues) == 1) or (len(uniqueValues) == 2 and uniqueValues.dtype != dtype('O') and len(data.loc[~isnan(data[var]), var].unique()) == 1):
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
394 print(stdoutText[0].format(var, uniqueValues))
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
395 if saveFiles:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
396 table1 += latexTable[0].format(var, *uniqueValues)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
397 result.remove(var)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
398 # correlated variables
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
399 for v1 in copy(result):
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
400 if v1 in correlations.index:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
401 for v2 in copy(result):
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
402 if v2 != v1 and v2 in correlations.index:
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
403 if abs(correlations.loc[v1, v2]) > maxCorrelationThreshold:
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
404 if v1 in result and v2 in result:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
405 if saveFiles:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
406 table1 += latexTable[1].format(v2, v1, correlations.loc[v1, v2])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
407 print(stdoutText[1].format(v2, v1, correlations.loc[v1, v2]))
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
408 result.remove(v2)
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
409 # not correlated with dependent variable
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
410 table2['Correlations'] = []
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
411 table2['Valeurs p'] = []
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
412 for var in copy(result):
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
413 if data.dtypes[var] != dtype('O'):
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
414 cor, p = correlationFunc(data[dependentVariable], data[var])
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
415 if p > maxCorrelationP:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
416 if saveFiles:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
417 table1 += latexTable[2].format(var, cor, p)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
418 print(stdoutText[2].format(var, cor, p))
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
419 result.remove(var)
677
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
420 else:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
421 table2['Correlations'].append(cor)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
422 table2['Valeurs p'].append(p)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
423
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
424 if saveFiles:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
425 from storage import openCheck
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
426 out = openCheck(filenamePrefix+'-removed-variables.tex', 'w')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
427 out.write(latexHeader)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
428 out.write(table1)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
429 out.write(latexFooter)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
430 out.close()
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
431 out = openCheck(filenamePrefix+'-correlations.html', 'w')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
432 table2['Variables'] = [var for var in result if data.dtypes[var] != dtype('O')]
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
433 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))
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
434 out.close()
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
435 return result
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
436
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
437
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
438 #########################
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
439 # regression analysis using statsmodels (and pandas)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
440 #########################
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
441
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
442 # TODO make class for experiments?
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
443 # TODO add tests with public dataset downloaded from Internet (IRIS et al)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
444 def modelString(experiment, dependentVariable, independentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
445 return dependentVariable+' ~ '+' + '.join([independentVariable for independentVariable in independentVariables if experiment[independentVariable]])
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
446
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
447 def runModel(experiment, data, dependentVariable, independentVariables, regressionType = 'ols'):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
448 import statsmodels.formula.api as smf
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
449 modelStr = modelString(experiment, dependentVariable, independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
450 if regressionType == 'ols':
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
451 model = smf.ols(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
452 elif regressionType == 'gls':
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
453 model = smf.gls(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
454 elif regressionType == 'rlm':
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
455 model = smf.rlm(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
456 else:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
457 print('Unknown regression type {}. Exiting'.format(regressionType))
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
458 import sys
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
459 sys.exit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
460 return model.fit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
461
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
462 def runModels(experiments, data, dependentVariable, independentVariables, regressionType = 'ols'):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
463 '''Runs several models and stores 3 statistics
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
464 adjusted R2, condition number (should be small, eg < 1000)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
465 and p-value for Shapiro-Wilk test of residual normality'''
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
466 for i,experiment in experiments.iterrows():
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
467 if experiment[independentVariables].any():
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
468 results = runModel(experiment, data, dependentVariable, independentVariables, regressionType = 'ols')
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
469 experiments.loc[i,'r2adj'] = results.rsquared_adj
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
470 experiments.loc[i,'condNum'] = results.condition_number
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
471 experiments.loc[i, 'shapiroP'] = shapiro(results.resid)[1]
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
472 experiments.loc[i,'nobs'] = int(results.nobs)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
473 return experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
474
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
475 def generateExperiments(independentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
476 '''Generates all possible models for including or not each independent variable'''
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
477 from pandas import DataFrame
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
478 experiments = {}
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
479 nIndependentVariables = len(independentVariables)
669
df6be882f325 bug corrected
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 668
diff changeset
480 if nIndependentVariables != len(set(independentVariables)):
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
481 print("Duplicate variables. Exiting")
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
482 import sys
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
483 sys.exit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
484 nModels = 2**nIndependentVariables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
485 for i,var in enumerate(independentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
486 pattern = [False]*(2**i)+[True]*(2**i)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
487 experiments[var] = pattern*(2**(nIndependentVariables-i-1))
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
488 experiments = DataFrame(experiments)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
489 experiments['r2adj'] = 0.
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
490 experiments['condNum'] = NaN
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
491 experiments['shapiroP'] = -1
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
492 experiments['nobs'] = -1
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
493 return experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
494
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
495 def findBestModel(data, dependentVariable, independentVariables, regressionType = 'ols', nProcesses = 1):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
496 '''Generates all possible model with the independentVariables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
497 and runs them, saving the results in experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
498 with multiprocess option'''
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
499 from pandas import concat
671
849f5f8bf4b9 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 670
diff changeset
500 from multiprocessing import Pool
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
501 experiments = generateExperiments(independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
502 nModels = len(experiments)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
503 print("Running {} models with {} processes".format(nModels, nProcesses))
674
01b89182891a corrected bug for intersection of lines (thanks to Paul for finding)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
504 print("IndependentVariables: {}".format(independentVariables))
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
505 if nProcesses == 1:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
506 return runModels(experiments, data, dependentVariable, independentVariables, regressionType)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
507 else:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
508 pool = Pool(processes = nProcesses)
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
509 chunkSize = int(ceil(nModels/nProcesses))
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
510 jobs = [pool.apply_async(runModels, args = (experiments[i*chunkSize:(i+1)*chunkSize], data, dependentVariable, independentVariables, regressionType)) for i in range(nProcesses)]
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
511 return concat([job.get() for job in jobs])
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
512
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
513 def findBestModelFwd(data, dependentVariable, independentVariables, modelFunc, experiments = None):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
514 '''Forward search for best model (based on adjusted R2)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
515 Randomly starting with one variable and adding randomly variables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
516 if they improve the model
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
517
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
518 The results are added to experiments if provided as argument
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
519 Storing in experiment relies on the index being the number equal
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
520 to the binary code derived from the independent variables'''
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
521 from numpy.random import permutation as nppermutation
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
522 if experiments is None:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
523 experiments = generateExperiments(independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
524 nIndependentVariables = len(independentVariables)
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
525 permutation = nppermutation(range(nIndependentVariables)).tolist()
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
526 variableMapping = {j: independentVariables[i] for i,j in enumerate(permutation)}
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
527 print('Tested variables '+', '.join([variableMapping[i] for i in xrange(nIndependentVariables)]))
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
528 bestModel = [False]*nIndependentVariables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
529 currentVarNum = 0
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
530 currentR2Adj = 0.
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
531 for currentVarNum in xrange(nIndependentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
532 currentModel = [i for i in bestModel]
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
533 currentModel[currentVarNum] = True
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
534 rowIdx = sum([0]+[2**i for i in xrange(nIndependentVariables) if currentModel[permutation[i]]])
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
535 #print currentVarNum, sum(currentModel), ', '.join([independentVariables[i] for i in xrange(nIndependentVariables) if currentModel[permutation[i]]])
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
536 if experiments.loc[rowIdx, 'shapiroP'] < 0:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
537 modelStr = modelString(experiments.loc[rowIdx], dependentVariable, independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
538 model = modelFunc(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
539 results = model.fit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
540 experiments.loc[rowIdx, 'r2adj'] = results.rsquared_adj
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
541 experiments.loc[rowIdx, 'condNum'] = results.condition_number
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
542 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
543 experiments.loc[rowIdx, 'nobs'] = int(results.nobs)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
544 if currentR2Adj < experiments.loc[rowIdx, 'r2adj']:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
545 currentR2Adj = experiments.loc[rowIdx, 'r2adj']
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
546 bestModel[currentVarNum] = True
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
547 return experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
548
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
549 def displayModelResults(results, model = None, plotFigures = True, filenamePrefix = None, figureFileType = 'pdf', text = {'title-shapiro': 'Shapiro-Wilk normality test for residuals: {:.2f} (p={:.3f})', 'true-predicted.xlabel': 'Predicted values', 'true-predicted.ylabel': 'True values', 'residuals-predicted.xlabel': 'Predicted values', 'residuals-predicted.ylabel': 'Residuals'}):
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
550 import statsmodels.api as sm
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
551 '''Displays some model results
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
552
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
553 3 graphics, true-predicted, residuals-predicted, '''
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
554 print(results.summary())
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
555 shapiroResult = shapiro(results.resid)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
556 print(shapiroResult)
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
557 if plotFigures:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
558 fig = plt.figure(figsize=(7,6.3*(2+int(model is not None))))
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
559 if model is not None:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
560 ax = fig.add_subplot(3,1,1)
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
561 plt.plot(results.predict(), model.endog, 'x')
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
562 x=plt.xlim()
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
563 y=plt.ylim()
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
564 plt.plot([max(x[0], y[0]), min(x[1], y[1])], [max(x[0], y[0]), min(x[1], y[1])], 'r')
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
565 #plt.axis('equal')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
566 if text is not None:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
567 plt.title(text['title-shapiro'].format(*shapiroResult))
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
568 #plt.title(text['true-predicted.title'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
569 plt.xlabel(text['true-predicted.xlabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
570 plt.ylabel(text['true-predicted.ylabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
571 fig.add_subplot(3,1,2, sharex = ax)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
572 plt.plot(results.predict(), results.resid, 'x')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
573 nextSubplotNum = 3
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
574 else:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
575 fig.add_subplot(2,1,1)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
576 plt.plot(results.predict(), results.resid, 'x')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
577 nextSubplotNum = 2
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
578 if text is not None:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
579 if model is None:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
580 plt.title(text['title-shapiro'].format(*shapiroResult))
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
581 plt.xlabel(text['residuals-predicted.xlabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
582 plt.ylabel(text['residuals-predicted.ylabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
583 qqAx = fig.add_subplot(nextSubplotNum,1,nextSubplotNum)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
584 sm.qqplot(results.resid, fit = True, line = '45', ax = qqAx)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
585 plt.axis('equal')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
586 if text is not None and 'qqplot.xlabel' in text:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
587 plt.xlabel(text['qqplot.xlabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
588 plt.ylabel(text['qqplot.ylabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
589 plt.tight_layout()
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
590 if filenamePrefix is not None:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
591 from storage import openCheck
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
592 out = openCheck(filenamePrefix+'-coefficients.html', 'w')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
593 out.write(results.summary().as_html())
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
594 plt.savefig(filenamePrefix+'-model-results.'+figureFileType)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
595
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
596 #########################
455
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
597 # iterable section
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
598 #########################
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
599
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
600 def mostCommon(L):
456
825e5d49325d slight update
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 455
diff changeset
601 '''Returns the most frequent element in a iterable
825e5d49325d slight update
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 455
diff changeset
602
825e5d49325d slight update
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 455
diff changeset
603 taken from http://stackoverflow.com/questions/1518522/python-most-common-element-in-a-list'''
455
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
604 from itertools import groupby
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
605 from operator import itemgetter
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
606 # get an iterable of (item, iterable) pairs
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
607 SL = sorted((x, i) for i, x in enumerate(L))
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
608 # print 'SL:', SL
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
609 groups = groupby(SL, key=itemgetter(0))
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
610 # auxiliary function to get "quality" for an item
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
611 def _auxfun(g):
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
612 item, iterable = g
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
613 count = 0
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
614 min_index = len(L)
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
615 for _, where in iterable:
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
616 count += 1
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
617 min_index = min(min_index, where)
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
618 # print 'item %r, count %r, minind %r' % (item, count, min_index)
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
619 return count, -min_index
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
620 # pick the highest-count/earliest item
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
621 return max(groups, key=_auxfun)[0]
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
622
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
623 #########################
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
624 # sequence section
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
625 #########################
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
626
665
15e244d2a1b5 corrected bug with circular import for VideoFilenameAddable, moved to base module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 659
diff changeset
627 class LCSS(object):
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
628 '''Class that keeps the LCSS parameters
686
cdee6a3a47b4 allowing alternate database and filename for classify-objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 680
diff changeset
629 and puts together the various computations
cdee6a3a47b4 allowing alternate database and filename for classify-objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 680
diff changeset
630
cdee6a3a47b4 allowing alternate database and filename for classify-objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 680
diff changeset
631 the methods with names starting with _ are not to be shadowed
cdee6a3a47b4 allowing alternate database and filename for classify-objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 680
diff changeset
632 in child classes, who will shadow the other methods,
cdee6a3a47b4 allowing alternate database and filename for classify-objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 680
diff changeset
633 ie compute and computeXX methods'''
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
634 def __init__(self, similarityFunc, delta = float('inf'), aligned = False, lengthFunc = min):
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
635 self.similarityFunc = similarityFunc
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
636 self.aligned = aligned
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
637 self.delta = delta
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
638 self.lengthFunc = lengthFunc
389
6d26dcc7bba0 modifications to compute alignment for None indicators
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
639 self.subSequenceIndices = [(0,0)]
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
640
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
641 def similarities(self, l1, l2, jshift=0):
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
642 n1 = len(l1)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
643 n2 = len(l2)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
644 self.similarityTable = zeros((n1+1,n2+1), dtype = npint)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
645 for i in xrange(1,n1+1):
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
646 for j in xrange(max(1,i-jshift-self.delta),min(n2,i-jshift+self.delta)+1):
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
647 if self.similarityFunc(l1[i-1], l2[j-1]):
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
648 self.similarityTable[i,j] = self.similarityTable[i-1,j-1]+1
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
649 else:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
650 self.similarityTable[i,j] = max(self.similarityTable[i-1,j], self.similarityTable[i,j-1])
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
651
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
652 def subSequence(self, i, j):
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
653 '''Returns the subsequence of two sequences
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
654 http://en.wikipedia.org/wiki/Longest_common_subsequence_problem'''
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
655 if i == 0 or j == 0:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
656 return []
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
657 elif self.similarityTable[i][j] == self.similarityTable[i][j-1]:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
658 return self.subSequence(i, j-1)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
659 elif self.similarityTable[i][j] == self.similarityTable[i-1][j]:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
660 return self.subSequence(i-1, j)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
661 else:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
662 return self.subSequence(i-1, j-1) + [(i-1,j-1)]
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
663
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
664 def _compute(self, _l1, _l2, computeSubSequence = False):
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
665 '''returns the longest common subsequence similarity
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
666 based on the threshold on distance between two elements of lists l1, l2
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
667 similarityFunc returns True or False whether the two points are considered similar
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
668
607
84690dfe5560 add some functions for behaviour analysis
MohamedGomaa
parents: 574
diff changeset
669 if aligned, returns the best matching if using a finite delta by shifting the series alignments
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
670
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
671 eg distance(p1, p2) < epsilon
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
672 '''
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
673 if len(_l2) < len(_l1): # l1 is the shortest
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
674 l1 = _l2
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
675 l2 = _l1
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
676 revertIndices = True
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
677 else:
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
678 l1 = _l1
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
679 l2 = _l2
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
680 revertIndices = False
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
681 n1 = len(l1)
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
682 n2 = len(l2)
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
683
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
684 if self.aligned:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
685 lcssValues = {}
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
686 similarityTables = {}
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
687 for i in xrange(-n2-self.delta+1, n1+self.delta): # interval such that [i-shift-delta, i-shift+delta] is never empty, which happens when i-shift+delta < 1 or when i-shift-delta > n2
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
688 self.similarities(l1, l2, i)
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
689 lcssValues[i] = self.similarityTable.max()
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
690 similarityTables[i] = self.similarityTable
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
691 #print self.similarityTable
521
3707eeb20f25 changed argMaxDict name to argmaxDict
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 518
diff changeset
692 alignmentShift = argmaxDict(lcssValues) # ideally get the medium alignment shift, the one that minimizes distance
389
6d26dcc7bba0 modifications to compute alignment for None indicators
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
693 self.similarityTable = similarityTables[alignmentShift]
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
694 else:
389
6d26dcc7bba0 modifications to compute alignment for None indicators
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
695 alignmentShift = 0
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
696 self.similarities(l1, l2)
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
697
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
698 # threshold values for the useful part of the similarity table are n2-n1-delta and n1-n2-delta
389
6d26dcc7bba0 modifications to compute alignment for None indicators
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
699 self.similarityTable = self.similarityTable[:min(n1, n2+alignmentShift+self.delta)+1, :min(n2, n1-alignmentShift+self.delta)+1]
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
700
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
701 if computeSubSequence:
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
702 self.subSequenceIndices = self.subSequence(self.similarityTable.shape[0]-1, self.similarityTable.shape[1]-1)
371
924e38c9f70e work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 370
diff changeset
703 if revertIndices:
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
704 self.subSequenceIndices = [(j,i) for i,j in self.subSequenceIndices]
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
705 return self.similarityTable[-1,-1]
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
706
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
707 def compute(self, l1, l2, computeSubSequence = False):
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
708 '''get methods are to be shadowed in child classes '''
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
709 return self._compute(l1, l2, computeSubSequence)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
710
375
2ea8584aa80a making indicator LCSS work
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 374
diff changeset
711 def computeAlignment(self):
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
712 return mean([j-i for i,j in self.subSequenceIndices])
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
713
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
714 def _computeNormalized(self, l1, l2, computeSubSequence = False):
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
715 ''' compute the normalized LCSS
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
716 ie, the LCSS divided by the min or mean of the indicator lengths (using lengthFunc)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
717 lengthFunc = lambda x,y:float(x,y)/2'''
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
718 return float(self._compute(l1, l2, computeSubSequence))/self.lengthFunc(len(l1), len(l2))
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
719
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
720 def computeNormalized(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
721 return self._computeNormalized(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
722
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
723 def _computeDistance(self, l1, l2, computeSubSequence = False):
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
724 ''' compute the LCSS distance'''
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
725 return 1-self._computeNormalized(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
726
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
727 def computeDistance(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
728 return self._computeDistance(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
729
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
730 #########################
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
731 # plotting section
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
732 #########################
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
733
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
734 def plotPolygon(poly, options = ''):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
735 'Plots shapely polygon poly'
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
736 from numpy.core.multiarray import array
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
737 from matplotlib.pyplot import plot
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
738 from shapely.geometry import Polygon
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
739
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
740 tmp = array(poly.exterior)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
741 plot(tmp[:,0], tmp[:,1], options)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
742
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
743 def stepPlot(X, firstX, lastX, initialCount = 0, increment = 1):
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
744 '''for each value in X, increment by increment the initial count
297
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
745 returns the lists that can be plotted
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
746 to obtain a step plot increasing by one for each value in x, from first to last value
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
747 firstX and lastX should be respectively smaller and larger than all elements in X'''
297
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
748
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
749 sortedX = []
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
750 counts = [initialCount]
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
751 for x in sorted(X):
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
752 sortedX += [x,x]
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
753 counts.append(counts[-1])
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
754 counts.append(counts[-1]+increment)
297
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
755 counts.append(counts[-1])
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
756 return [firstX]+sortedX+[lastX], counts
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
757
665
15e244d2a1b5 corrected bug with circular import for VideoFilenameAddable, moved to base module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 659
diff changeset
758 class PlottingPropertyValues(object):
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
759 def __init__(self, values):
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
760 self.values = values
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
761
116
2bf5b76320c0 moved intersection plotting and added markers for scatter plots
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 115
diff changeset
762 def __getitem__(self, i):
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
763 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
764
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
765 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
766 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
767
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
768 linestyles = PlottingPropertyValues(['-', '--', '-.', ':'])
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
769
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
770 colors = PlottingPropertyValues('brgmyck') # 'w'
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
771
115
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
772 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
773 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
774 coords = array(indicatorMap.keys())
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
775 minX = min(coords[:,0])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
776 minY = min(coords[:,1])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
777 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
778 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
779 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
780 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
781 C[k[1]-minY,k[0]-minX] = v
115
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
782 if masked:
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
783 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
784 else:
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
785 pcolor(X, Y, C)
65
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
786
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
787 #########################
637
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
788 # Data download
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
789 #########################
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
790
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
791 def downloadECWeather(stationID, years, months = [], outputDirectoryname = '.', english = True):
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
792 '''Downloads monthly weather data from Environment Canada
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
793 If month is provided (number 1 to 12), it means hourly data for the whole month
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
794 Otherwise, means the data for each day, for the whole year
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
795
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
796 Example: MONTREAL MCTAVISH 10761
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
797 MONTREALPIERRE ELLIOTT TRUDEAU INTL A 5415
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
798
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
799 To get daily data for 2010 and 2011, downloadECWeather(10761, [2010,2011], [], '/tmp')
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
800 To get hourly data for 2009 and 2012, January, March and October, downloadECWeather(10761, [2009,2012], [1,3,10], '/tmp')'''
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
801 import urllib2
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
802 if english:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
803 language = 'e'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
804 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
805 language = 'f'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
806 if len(months) == 0:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
807 timeFrame = 2
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
808 months = [1]
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
809 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
810 timeFrame = 1
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
811
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
812 for year in years:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
813 for month in months:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
814 url = urllib2.urlopen('http://climat.meteo.gc.ca/climateData/bulkdata_{}.html?format=csv&stationID={}&Year={}&Month={}&Day=1&timeframe={}&submit=++T%C3%A9l%C3%A9charger+%0D%0Ades+donn%C3%A9es'.format(language, stationID, year, month, timeFrame))
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
815 data = url.read()
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
816 outFilename = '{}/{}-{}'.format(outputDirectoryname, stationID, year)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
817 if timeFrame == 1:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
818 outFilename += '-{}-hourly'.format(month)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
819 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
820 outFilename += '-daily'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
821 outFilename += '.csv'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
822 out = open(outFilename, 'w')
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
823 out.write(data)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
824 out.close()
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
825
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
826 #########################
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
827 # File I/O
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
828 #########################
24
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
829
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
830 def removeExtension(filename, delimiter = '.'):
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
831 '''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
832 i = filename.rfind(delimiter)
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
833 if i>0:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
834 return filename[:i]
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
835 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
836 return filename
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
837
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
838 def cleanFilename(s):
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
839 'cleans filenames obtained when contatenating figure characteristics'
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
840 return s.replace(' ','-').replace('.','').replace('/','-')
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
841
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
842 def listfiles(dirname, extension, remove = False):
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
843 '''Returns the list of files with the extension in the directory dirname
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
844 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
845 from os import listdir
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
846 tmp = [f for f in listdir(dirname) if f.endswith(extension)]
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
847 tmp.sort()
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
848 if remove:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
849 return [removeExtension(f, extension) for f in tmp]
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
850 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
851 return tmp
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
852
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
853 def mkdir(dirname):
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
854 'Creates a directory if it does not exist'
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
855 import os
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
856 if not os.path.exists(dirname):
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
857 os.mkdir(dirname)
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
858 else:
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
859 print(dirname+' already exists')
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
860
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
861 def removeFile(filename):
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
862 '''Deletes the file while avoiding raising an error
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
863 if the file does not exist'''
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
864 import os
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
865 if (os.path.exists(filename)):
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
866 os.remove(filename)
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
867 else:
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
868 print(filename+' does not exist')
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
869
42
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
870 def line2Floats(l, separator=' '):
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
871 '''Returns the list of floats corresponding to the string'''
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
872 return [float(x) for x in l.split(separator)]
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
873
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
874 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
875 '''Returns the list of ints corresponding to the string'''
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
876 return [int(x) for x in l.split(separator)]
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
877
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
878 #########################
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
879 # CLI utils
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
880 #########################
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
881
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
882 def parseCLIOptions(helpMessage, options, cliArgs, optionalOptions=[]):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
883 ''' Simple function to handle similar argument parsing
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
884 Returns the dictionary of options and their values
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
885
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
886 * cliArgs are most likely directly sys.argv
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
887 (only the elements after the first one are considered)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
888
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
889 * options should be a list of strings for getopt options,
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
890 eg ['frame=','correspondences=','video=']
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
891 A value must be provided for each option, or the program quits'''
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
892 import sys, getopt
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
893 from numpy.core.fromnumeric import all
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
894 optionValues, args = getopt.getopt(cliArgs[1:], 'h', ['help']+options+optionalOptions)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
895 optionValues = dict(optionValues)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
896
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
897 if '--help' in optionValues.keys() or '-h' in optionValues.keys():
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
898 print(helpMessage+
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
899 '\n - Compulsory options: '+' '.join([opt.replace('=','') for opt in options])+
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
900 '\n - Non-compulsory options: '+' '.join([opt.replace('=','') for opt in optionalOptions]))
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
901 sys.exit()
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
902
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
903 missingArgument = [('--'+opt.replace('=','') in optionValues.keys()) for opt in options]
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
904 if not all(missingArgument):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
905 print('Missing argument')
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
906 print(optionValues)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
907 sys.exit()
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
908
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
909 return optionValues
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
910
397
b36b00dd27c3 added function to read scene metadata
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 395
diff changeset
911
b36b00dd27c3 added function to read scene metadata
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 395
diff changeset
912 #########################
553
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
913 # Profiling
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
914 #########################
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
915
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
916 def analyzeProfile(profileFilename, stripDirs = True):
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
917 '''Analyze the file produced by cProfile
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
918
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
919 obtained by for example:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
920 - call in script (for main() function in script)
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
921 import cProfile, os
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
922 cProfile.run('main()', os.path.join(os.getcwd(),'main.profile'))
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
923
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
924 - or on the command line:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
925 python -m cProfile [-o profile.bin] [-s sort] scriptfile [arg]'''
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
926 import pstats, os
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
927 p = pstats.Stats(os.path.join(os.pardir, profileFilename))
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
928 if stripDirs:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
929 p.strip_dirs()
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
930 p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
931 p.print_stats(.2)
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
932 #p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
933 # p.print_callees(.1, 'int_prediction.py:')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
934 return p
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
935
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
936 #########################
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
937 # running tests
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
938 #########################
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
939
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
940 if __name__ == "__main__":
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
941 import doctest
2
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
942 import unittest
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
943 suite = doctest.DocFileSuite('tests/utils.txt')
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
944 #suite = doctest.DocTestSuite()
2
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
945 unittest.TextTestRunner().run(suite)
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
946 #doctest.testmod()
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
947 #doctest.testfile("example.txt")