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annotate trafficintelligence/utils.py @ 1088:0680387a89bb

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added basic saving capability to empirical distribution
author Nicolas Saunier <nicolas.saunier@polymtl.ca>
date Wed, 14 Nov 2018 12:30:50 -0500
parents 8734742c08c0
children 10205bd0e0b7
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aed8eb63cdde initial commit with non-functional python code for NGSIM
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1 #! /usr/bin/env python
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2 ''' Generic utilities.'''
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3
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4 from datetime import time, datetime
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5 from argparse import ArgumentTypeError
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6 from pathlib import Path
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7 from math import sqrt, ceil, floor
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8 from copy import deepcopy, copy
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9 from collections import Counter
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10
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11 from scipy.stats import rv_continuous, kruskal, shapiro, lognorm, norm, t
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12 from scipy.spatial import distance
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13 from scipy.sparse import dok_matrix
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14 from numpy import zeros, array, exp, sum as npsum, int as npint, arange, cumsum, mean, median, percentile, isnan, ones, convolve, dtype, isnan, NaN, ma, isinf, savez, load as npload, log, polyfit, float as npfloat
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15 from numpy.random import permutation as nppermutation
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16 from pandas import DataFrame, concat
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17 import matplotlib.pyplot as plt
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18
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19 datetimeFormat = "%Y-%m-%d %H:%M:%S"
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20
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21 sjcamDatetimeFormat = "%Y_%m%d_%H%M%S"#2017_0626_143720
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22
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23 #########################
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24 # txt files
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25 #########################
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26
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27 commentChar = '#'
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28
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29 delimiterChar = '%';
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30
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31 def openCheck(filename, option = 'r', quitting = False):
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32 '''Open file filename in read mode by default
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33 and checks it is open'''
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34 try:
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35 return open(filename, option)
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36 except IOError:
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37 print('File {} could not be opened.'.format(filename))
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38 if quitting:
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39 from sys import exit
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40 exit()
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41 return None
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42
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43 def readline(f, commentCharacters = commentChar):
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44 '''Modified readline function to skip comments
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45 Can take a list of characters or a string (in will work in both)'''
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46 s = f.readline()
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47 while (len(s) > 0) and s[0] in commentCharacters:
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48 s = f.readline()
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49 return s.strip()
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50
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51 def getLines(f, delimiterChar = delimiterChar, commentCharacters = commentChar):
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52 '''Gets a complete entry (all the lines) in between delimiterChar.'''
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53 dataStrings = []
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54 s = readline(f, commentCharacters)
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55 while len(s) > 0 and s[0] != delimiterChar:
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56 dataStrings += [s.strip()]
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57 s = readline(f, commentCharacters)
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58 return dataStrings
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59
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60 #########################
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61 # Strings
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62 #########################
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63
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64 def upperCaseFirstLetter(s):
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65 words = s.split(' ')
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66 lowerWords = [w[0].upper()+w[1:].lower() for w in words]
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67 return ' '.join(lowerWords)
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68
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69 class TimeConverter:
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70 def __init__(self, datetimeFormat = datetimeFormat):
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71 self.datetimeFormat = datetimeFormat
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72
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73 def convert(self, s):
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74 try:
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75 return datetime.strptime(s, self.datetimeFormat)
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76 except ValueError:
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77 msg = "Not a valid date: '{0}'.".format(s)
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78 raise ArgumentTypeError(msg)
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79
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80 #########################
185
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81 # Enumerations
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82 #########################
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83
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84 def inverseEnumeration(l):
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85 'Returns the dictionary that provides for each element in the input list its index in the input list'
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86 result = {}
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87 for i,x in enumerate(l):
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88 result[x] = i
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89 return result
155
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90
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91 #########################
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92 # Simple statistics
31
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93 #########################
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94
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95 def logNormalMeanVar(loc, scale):
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96 '''location and scale are respectively the mean and standard deviation of the normal in the log-normal distribution
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97 https://en.wikipedia.org/wiki/Log-normal_distribution
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98
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99 same as lognorm.stats(scale, 0, exp(loc))'''
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100 mean = exp(loc+(scale**2)/2)
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101 var = (exp(scale**2)-1)*exp(2*loc+scale**2)
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102 return mean, var
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103
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104 def fitLogNormal(x):
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105 'returns the fitted location and scale of the lognormal (general definition)'
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106 shape, loc, scale = lognorm.fit(x, floc=0.)
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107 return log(scale), shape
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108
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109 def sampleSize(stdev, tolerance, percentConfidence, nRoundingDigits = None, printLatex = False):
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110 if nRoundingDigits is None:
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111 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1), 2) # 1.-(100-percentConfidence)/200.
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112 else:
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113 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1), nRoundingDigits)
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114 stdev = round(stdev, nRoundingDigits)
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115 tolerance = round(tolerance, nRoundingDigits)
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116 if printLatex:
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117 print('$z_{{{}}}^2\\frac{{s^2}}{{e^2}}={}^2\\frac{{{}^2}}{{{}^2}}$'.format(0.5+percentConfidence/200.,k, stdev, tolerance))
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118 return (k*stdev/tolerance)**2
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119
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120 def confidenceInterval(mean, stdev, nSamples, percentConfidence, trueStd = True, printLatex = False):
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121 '''if trueStd, use normal distribution, otherwise, Student
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122
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123 Use otherwise t.interval or norm.interval for the boundaries
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124 ex: norm.interval(0.95)
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125 t.interval(0.95, nSamples-1)'''
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126 if trueStd:
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127 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1), 2)
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128 else: # use Student
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129 k = round(t.ppf(0.5+percentConfidence/200., nSamples-1), 2)
301
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130 e = k*stdev/sqrt(nSamples)
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131 if printLatex:
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132 print('${0} \pm {1}\\frac{{{2}}}{{\sqrt{{{3}}}}}$'.format(mean, k, stdev, nSamples))
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133 return mean-e, mean+e
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134
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135 def computeChi2(expected, observed):
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136 '''Returns the Chi2 statistics'''
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diff changeset
137 return sum([((e-o)*(e-o))/float(e) for e, o in zip(expected, observed)])
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138
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139 class EmpiricalContinuousDistribution(rv_continuous):
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140 def __init__(self, values, probabilities, **kwargs):
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141 '''The values (and corresponding probabilities) are supposed to be sorted by value
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142 for v, p in zip(values, probabilities): P(X<=v)=p'''
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143 assert probabilities[0]==0
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144 super(EmpiricalContinuousDistribution, self).__init__(**kwargs)
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145 self.values = values
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146 self.probabilities = probabilities
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147
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148 def save(self, filename):
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149 import yaml
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150 with open(filename, 'w') as out:
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151 yaml.dump([self.values, self.probabilities], out)
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152
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153 @staticmethod
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154 def load(filename):
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155 import yaml
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156 with open(filename) as f:
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157 values, probabilities = yaml.load(f)
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158 return EmpiricalContinuousDistribution(values, probabilities)
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159
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160 def _cdf(self, x):
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161 if x < self.values[0]:
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162 return self.probabilities[0]
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163 else:
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164 i=0
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165 while i+1<len(self.values) and self.values[i+1] < x:
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166 i += 1
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167 if i == len(self.values)-1:
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168 return self.probabilities[-1]
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169 else:
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170 return self.probabilities[i]+(x-self.values[i])*float(self.probabilities[i+1]-self.probabilities[i])/float(self.values[i+1]-self.values[i])
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171
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172 class DistributionSample(object):
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173 def nSamples(self):
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174 return sum(self.counts)
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175
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176 def cumulativeDensityFunction(sample, normalized = False):
276
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177 '''Returns the cumulative density function of the sample of a random variable'''
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178 xaxis = sorted(sample)
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179 counts = arange(1,len(sample)+1) # dtype = float
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180 if normalized:
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181 counts = counts.astype(float)/float(len(sample))
197
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182 return xaxis, counts
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183
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184 class DiscreteDistributionSample(DistributionSample):
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185 '''Class to represent a sample of a distribution for a discrete random variable'''
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186 def __init__(self, categories, counts):
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187 self.categories = categories
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188 self.counts = counts
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189
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190 def mean(self):
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191 result = [float(x*y) for x,y in zip(self.categories, self.counts)]
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192 return npsum(result)/self.nSamples()
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193
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194 def var(self, mean = None):
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195 if not mean:
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196 m = self.mean()
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197 else:
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198 m = mean
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199 result = 0.
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200 squares = [float((x-m)*(x-m)*y) for x,y in zip(self.categories, self.counts)]
672
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201 return npsum(squares)/(self.nSamples()-1)
85
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202
86
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diff changeset
203 def referenceCounts(self, probability):
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diff changeset
204 '''probability is a function that returns the probability of the random variable for the category values'''
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205 refProba = [probability(c) for c in self.categories]
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diff changeset
206 refProba[-1] = 1-npsum(refProba[:-1])
86
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diff changeset
207 refCounts = [r*self.nSamples() for r in refProba]
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diff changeset
208 return refCounts, refProba
85
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diff changeset
209
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210 class ContinuousDistributionSample(DistributionSample):
31
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parents: 29
diff changeset
211 '''Class to represent a sample of a distribution for a continuous random variable
76
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diff changeset
212 with the number of observations for each interval
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diff changeset
213 intervals (categories variable) are defined by their left limits, the last one being the right limit
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diff changeset
214 categories contain therefore one more element than the counts'''
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diff changeset
215 def __init__(self, categories, counts):
276
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diff changeset
216 # todo add samples for initialization and everything to None? (or setSamples?)
35
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diff changeset
217 self.categories = categories
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218 self.counts = counts
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219
749
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220 @staticmethod
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221 def generate(sample, categories):
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diff changeset
222 if min(sample) < min(categories):
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223 print('Sample has lower min than proposed categories ({}, {})'.format(min(sample), min(categories)))
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diff changeset
224 if max(sample) > max(categories):
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diff changeset
225 print('Sample has higher max than proposed categories ({}, {})'.format(max(sample), max(categories)))
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226 dist = ContinuousDistributionSample(sorted(categories), [0]*(len(categories)-1))
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227 for s in sample:
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228 i = 0
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diff changeset
229 while i<len(dist.categories) and dist.categories[i] <= s:
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diff changeset
230 i += 1
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231 if i <= len(dist.counts):
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diff changeset
232 dist.counts[i-1] += 1
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diff changeset
233 #print('{} in {} {}'.format(s, dist.categories[i-1], dist.categories[i]))
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diff changeset
234 else:
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235 print('Element {} is not in the categories'.format(s))
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236 return dist
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237
35
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diff changeset
238 def mean(self):
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diff changeset
239 result = 0.
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diff changeset
240 for i in range(len(self.counts)-1):
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diff changeset
241 result += self.counts[i]*(self.categories[i]+self.categories[i+1])/2
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diff changeset
242 return result/self.nSamples()
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243
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diff changeset
244 def var(self, mean = None):
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diff changeset
245 if not mean:
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diff changeset
246 m = self.mean()
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diff changeset
247 else:
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diff changeset
248 m = mean
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diff changeset
249 result = 0.
76
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diff changeset
250 for i in range(len(self.counts)-1):
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diff changeset
251 mid = (self.categories[i]+self.categories[i+1])/2
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diff changeset
252 result += self.counts[i]*(mid - m)*(mid - m)
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diff changeset
253 return result/(self.nSamples()-1)
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diff changeset
254
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diff changeset
255 def referenceCounts(self, cdf):
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diff changeset
256 '''cdf is a cumulative distribution function
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diff changeset
257 returning the probability of the variable being less that x'''
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diff changeset
258 # refCumulativeCounts = [0]#[cdf(self.categories[0][0])]
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diff changeset
259 # for inter in self.categories:
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diff changeset
260 # refCumulativeCounts.append(cdf(inter[1]))
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diff changeset
261 refCumulativeCounts = [cdf(x) for x in self.categories[1:-1]]
35
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diff changeset
262
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diff changeset
263 refProba = [refCumulativeCounts[0]]
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parents: 32
diff changeset
264 for i in xrange(1,len(refCumulativeCounts)):
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parents: 32
diff changeset
265 refProba.append(refCumulativeCounts[i]-refCumulativeCounts[i-1])
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
266 refProba.append(1-refCumulativeCounts[-1])
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
267 refCounts = [p*self.nSamples() for p in refProba]
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
268
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
269 return refCounts, refProba
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
270
77
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
271 def printReferenceCounts(self, refCounts=None):
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
272 if refCounts:
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
273 ref = refCounts
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
274 else:
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
275 ref = self.referenceCounts
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
276 for i in xrange(len(ref[0])):
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
277 print('{0}-{1} & {2:0.3} & {3:0.3} \\\\'.format(self.categories[i],self.categories[i+1],ref[1][i], ref[0][i]))
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
278
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
279
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
280 #########################
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
281 # maths section
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
282 #########################
24
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
283
433
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
284 # def kernelSmoothing(sampleX, X, Y, weightFunc, halfwidth):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
285 # '''Returns a smoothed weighted version of Y at the predefined values of sampleX
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
286 # Sum_x weight(sample_x,x) * y(x)'''
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
287 # from numpy import zeros, array
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
288 # smoothed = zeros(len(sampleX))
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
289 # for i,x in enumerate(sampleX):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
290 # weights = array([weightFunc(x,xx, halfwidth) for xx in X])
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
291 # if sum(weights)>0:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
292 # smoothed[i] = sum(weights*Y)/sum(weights)
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
293 # else:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
294 # smoothed[i] = 0
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
295 # return smoothed
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
296
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
297 def kernelSmoothing(x, X, Y, weightFunc, halfwidth):
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
298 '''Returns the smoothed estimate of (X,Y) at x
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
299 Sum_x weight(sample_x,x) * y(x)'''
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
300 weights = array([weightFunc(x,observedx, halfwidth) for observedx in X])
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
301 if sum(weights)>0:
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
302 return sum(weights*Y)/sum(weights)
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
303 else:
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
304 return 0
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
305
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
306 def uniform(center, x, halfwidth):
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
307 if abs(center-x)<halfwidth:
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
308 return 1.
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
309 else:
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
310 return 0.
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
311
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
312 def gaussian(center, x, halfwidth):
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
313 return exp(-((center-x)/halfwidth)**2/2)
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
314
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
315 def epanechnikov(center, x, halfwidth):
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
316 diff = abs(center-x)
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
317 if diff<halfwidth:
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
318 return 1.-(diff/halfwidth)**2
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
319 else:
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
320 return 0.
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
321
434
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
322 def triangular(center, x, halfwidth):
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
323 diff = abs(center-x)
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
324 if diff<halfwidth:
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
325 return 1.-abs(diff/halfwidth)
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
326 else:
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
327 return 0.
433
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
328
518
0c86c73f3c09 median smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 511
diff changeset
329 def medianSmoothing(x, X, Y, halfwidth):
0c86c73f3c09 median smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 511
diff changeset
330 '''Returns the media of Y's corresponding to X's in the interval [x-halfwidth, x+halfwidth]'''
0c86c73f3c09 median smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 511
diff changeset
331 return median([y for observedx, y in zip(X,Y) if abs(x-observedx)<halfwidth])
0c86c73f3c09 median smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 511
diff changeset
332
521
3707eeb20f25 changed argMaxDict name to argmaxDict
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 518
diff changeset
333 def argmaxDict(d):
561
ee45c6eb6d49 added Mohamed Gomaa Mohamed function to smooth object trajectories
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 553
diff changeset
334 return max(d, key=d.get)
279
3af4c267a7bf generic simple LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 276
diff changeset
335
837
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
336 def deltaFrames(t1, t2, frameRate):
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
337 '''Returns the number of frames between t1 and t2
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
338 positive if t1<=t2, negative otherwise'''
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
339 if t1 > t2:
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
340 return -(t1-t2).seconds*frameRate
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
341 else:
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
342 return (t2-t1).seconds*frameRate
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
343
395
6fba1ab040f1 minor modification to framestotime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 391
diff changeset
344 def framesToTime(nFrames, frameRate, initialTime = time()):
6fba1ab040f1 minor modification to framestotime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 391
diff changeset
345 '''returns a datetime.time for the time in hour, minutes and seconds
6fba1ab040f1 minor modification to framestotime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 391
diff changeset
346 initialTime is a datetime.time'''
6fba1ab040f1 minor modification to framestotime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 391
diff changeset
347 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
348 h = int(floor(seconds/3600.))
248
571ba5ed22e2 added utils for bus processing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 241
diff changeset
349 seconds = seconds - h*3600
261
4aa792cb0fa9 changing framesToTime to return a datetime.time
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 248
diff changeset
350 m = int(floor(seconds/60))
248
571ba5ed22e2 added utils for bus processing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 241
diff changeset
351 seconds = seconds - m*60
262
a048066bd20f correcting bug in framesToTime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 261
diff changeset
352 return time(h, m, seconds)
248
571ba5ed22e2 added utils for bus processing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 241
diff changeset
353
381
387cc0142211 script to replay event annotations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 376
diff changeset
354 def timeToFrames(t, frameRate):
387cc0142211 script to replay event annotations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 376
diff changeset
355 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
356
1059
a87b3072bd26 working version
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1058
diff changeset
357 def timeModulo(t, duration):
a87b3072bd26 working version
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1058
diff changeset
358 'returns the time modulo the duration in min'
a87b3072bd26 working version
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1058
diff changeset
359 return time(t.hour, t.minute//duration, t.second)
a87b3072bd26 working version
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1058
diff changeset
360
241
ee1caff48b03 added function to sort to list of paired data X,Y
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
361 def sortXY(X,Y):
ee1caff48b03 added function to sort to list of paired data X,Y
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
362 '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
363 D = {}
ee1caff48b03 added function to sort to list of paired data X,Y
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
364 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
365 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
366 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
367 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
368
733
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
369 def compareLengthForSort(i, j):
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
370 if len(i) < len(j):
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
371 return -1
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
372 elif len(i) == len(j):
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
373 return 0
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
374 else:
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
375 return 1
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
376
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
377 def sortByLength(instances, reverse = False):
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
378 '''Returns a new list with the instances sorted by length (method __len__)
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
379 reverse is passed to sorted'''
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
380 return sorted(instances, key = len, reverse = reverse)
733
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
381
32
48e56179c39e added ceil function
Nicolas Saunier <nico@confins.net>
parents: 31
diff changeset
382 def ceilDecimals(v, nDecimals):
48e56179c39e added ceil function
Nicolas Saunier <nico@confins.net>
parents: 31
diff changeset
383 '''Rounds the number at the nth decimal
48e56179c39e added ceil function
Nicolas Saunier <nico@confins.net>
parents: 31
diff changeset
384 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
385 tens = 10**nDecimals
32
48e56179c39e added ceil function
Nicolas Saunier <nico@confins.net>
parents: 31
diff changeset
386 return ceil(v*tens)/tens
48e56179c39e added ceil function
Nicolas Saunier <nico@confins.net>
parents: 31
diff changeset
387
152
74b1fc68d4df re-organized code to avoid cyclic python module dependencies
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 116
diff changeset
388 def inBetween(bound1, bound2, x):
698
8d99a9e16644 added clarification comments
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 689
diff changeset
389 'useful if one does not know the order of bound1/bound2'
569
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
390 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
391
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
392 def pointDistanceL2(x1,y1,x2,y2):
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
393 ''' 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
394 return sqrt((x2-x1)**2+(y2-y1)**2)
24
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
395
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
396 def crossProduct(l1, l2):
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
397 return l1[0]*l2[1]-l1[1]*l2[0]
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
398
1086
8734742c08c0 major refactoring of curvilinear trajectory projections
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1060
diff changeset
399 def filterCategoricalMovingWindow(cat_list, halfWidth):
574
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
400 ''' 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
401 halfWidth is the search radius on either side'''
659
784298512b60 minor modifications
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 637
diff changeset
402 smoothed = deepcopy(cat_list)
784298512b60 minor modifications
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 637
diff changeset
403 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
404 lower_bound_check = max(0,point-halfWidth)
659
784298512b60 minor modifications
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 637
diff changeset
405 upper_bound_check = min(len(cat_list)-1,point+halfWidth+1)
784298512b60 minor modifications
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 637
diff changeset
406 window_values = cat_list[lower_bound_check:upper_bound_check]
574
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
407 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
408 return smoothed
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
409
547
97c5fef5b2d6 corrected bugs
MohamedGomaa
parents: 521
diff changeset
410 def filterMovingWindow(inputSignal, halfWidth):
29
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
411 '''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
412 The first and last points are copied from the original.'''
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
413 width = float(halfWidth*2+1)
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
414 win = ones(width,'d')
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
415 result = convolve(win/width,array(inputSignal),'same')
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
416 result[:halfWidth] = inputSignal[:halfWidth]
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
417 result[-halfWidth:] = inputSignal[-halfWidth:]
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
418 return result
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
419
199
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
420 def linearRegression(x, y, deg = 1, plotData = False):
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
421 '''returns the least square estimation of the linear regression of y = ax+b
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
422 as well as the plot'''
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
423 coef = polyfit(x, y, deg)
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
424 if plotData:
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
425 def poly(x):
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
426 result = 0
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
427 for i in range(len(coef)):
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
428 result += coef[i]*x**(len(coef)-i-1)
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
429 return 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
430 plt.plot(x, y, 'x')
199
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
431 xx = arange(min(x), max(x),(max(x)-min(x))/1000)
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
432 plt.plot(xx, [poly(z) for z in xx])
199
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
433 return coef
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
434
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 def correlation(data, correlationMethod = 'pearson', plotFigure = False, displayNames = None, figureFilename = None):
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 '''Computes (and displays) the correlation matrix for a pandas DataFrame'''
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
437 columns = data.columns.tolist()
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
438 for var in data.columns:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
439 uniqueValues = data[var].unique()
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
440 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
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
441 columns.remove(var)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
442 c=data[columns].corr(correlationMethod)
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 if plotFigure:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
444 fig = plt.figure(figsize=(4+0.4*c.shape[0], 0.4*c.shape[0]))
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
445 fig.add_subplot(1,1,1)
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
446 #plt.imshow(np.fabs(c), interpolation='none')
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
447 plt.imshow(c, vmin=-1., vmax = 1., interpolation='none', cmap = 'RdYlBu_r') # coolwarm
847
36c5bee9a887 bug correction
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 841
diff changeset
448 if displayNames is not None:
36c5bee9a887 bug correction
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 841
diff changeset
449 colnames = [displayNames.get(s.strip(), s.strip()) for s in columns]
36c5bee9a887 bug correction
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 841
diff changeset
450 else:
36c5bee9a887 bug correction
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 841
diff changeset
451 colnames = columns
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
452 #correlation.plot_corr(c, xnames = colnames, normcolor=True, title = filename)
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
453 plt.xticks(range(len(colnames)), colnames, rotation=90)
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
454 plt.yticks(range(len(colnames)), colnames)
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
455 plt.tick_params('both', length=0)
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
456 plt.subplots_adjust(bottom = 0.29)
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
457 plt.colorbar()
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
458 plt.title('Correlation ({})'.format(correlationMethod))
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
459 plt.tight_layout()
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
460 if len(colnames) > 50:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
461 plt.subplots_adjust(left=.06)
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
462 if figureFilename is not None:
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
463 plt.savefig(figureFilename, dpi = 150, transparent = True)
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
464 return c
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
465
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
466 def addDummies(data, variables, allVariables = True):
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
467 '''Add binary dummy variables for each value of a nominal variable
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
468 in a pandas DataFrame'''
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
469 newVariables = []
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
470 for var in variables:
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
471 if var in data.columns and data.dtypes[var] == dtype('O') and len(data[var].unique()) > 2:
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 values = data[var].unique()
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
473 if not allVariables:
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
474 values = values[:-1]
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
475 for val in values:
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
476 if val is not NaN:
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
477 newVariable = (var+'_{}'.format(val)).replace('.','').replace(' ','').replace('-','')
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
478 data[newVariable] = (data[var] == val)
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
479 newVariables.append(newVariable)
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
480 return newVariables
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
481
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
482 def kruskalWallis(data, dependentVariable, independentVariable, plotFigure = False, filenamePrefix = None, figureFileType = 'pdf', saveLatex = False, renameVariables = lambda s: s, kwCaption = ''):
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
483 '''Studies the influence of (nominal) independent variable over the dependent variable
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
484
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
485 Makes tests if the conditional distributions are normal
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
486 using the Shapiro-Wilk test (in which case ANOVA could be used)
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
487 Implements uses the non-parametric Kruskal Wallis test'''
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
488 tmp = data[data[independentVariable].notnull()]
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
489 independentVariableValues = sorted(tmp[independentVariable].unique().tolist())
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
490 if len(independentVariableValues) >= 2:
674
01b89182891a corrected bug for intersection of lines (thanks to Paul for finding)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
491 if saveLatex:
01b89182891a corrected bug for intersection of lines (thanks to Paul for finding)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
492 out = openCheck(filenamePrefix+'-{}-{}.tex'.format(dependentVariable, independentVariable), 'w')
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
493 for x in independentVariableValues:
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
494 print('Shapiro-Wilk normality test for {} when {}={}: {} obs'.format(dependentVariable,independentVariable, x, len(tmp.loc[tmp[independentVariable] == x, dependentVariable])))
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
495 if len(tmp.loc[tmp[independentVariable] == x, dependentVariable]) >= 3:
978
184f1dd307f9 corrected print and exception statements for Python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 973
diff changeset
496 print(shapiro(tmp.loc[tmp[independentVariable] == x, dependentVariable]))
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
497 if plotFigure:
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
498 plt.figure()
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
499 plt.boxplot([tmp.loc[tmp[independentVariable] == x, dependentVariable] for x in independentVariableValues])
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
500 plt.xticks(range(1,len(independentVariableValues)+1), independentVariableValues)
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
501 plt.title('{} vs {}'.format(dependentVariable, independentVariable))
674
01b89182891a corrected bug for intersection of lines (thanks to Paul for finding)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
502 if filenamePrefix is not None:
01b89182891a corrected bug for intersection of lines (thanks to Paul for finding)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
503 plt.savefig(filenamePrefix+'-{}-{}.{}'.format(dependentVariable, independentVariable, figureFileType))
01b89182891a corrected bug for intersection of lines (thanks to Paul for finding)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
504 table = tmp.groupby([independentVariable])[dependentVariable].describe().unstack().sort(['50%'], ascending = False)
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
505 table['count'] = table['count'].astype(int)
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
506 testResult = kruskal(*[tmp.loc[tmp[independentVariable] == x, dependentVariable] for x in independentVariableValues])
674
01b89182891a corrected bug for intersection of lines (thanks to Paul for finding)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
507 if saveLatex:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
508 out.write('\\begin{minipage}{\\linewidth}\n'
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
509 +'\\centering\n'
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
510 +'\\captionof{table}{'+(kwCaption.format(dependentVariable, independentVariable, *testResult))+'}\n'
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
511 +table.to_latex(float_format = lambda x: '{:.3f}'.format(x)).encode('ascii')+'\n'
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
512 +'\\end{minipage}\n'
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
513 +'\\ \\vspace{0.5cm}\n')
674
01b89182891a corrected bug for intersection of lines (thanks to Paul for finding)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
514 else:
978
184f1dd307f9 corrected print and exception statements for Python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 973
diff changeset
515 print(table)
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
516 return testResult
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
517 else:
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
518 return None
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
519
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
520 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=''):
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
521 '''Removes variables from candidate independent variables if
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
522 - if two independent variables are correlated (> maxCorrelationThreshold), one is removed
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
523 - if an independent variable is not correlated with the dependent variable (p>maxCorrelationP)
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
524 Returns the remaining non-correlated variables, correlated with the dependent variable
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
525
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
526 correlationFunc is spearmanr or pearsonr from scipy.stats
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
527 text is the template to display for the two types of printout (see default): 3 elements if no saving to latex file, 8 otherwise
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
528
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
529 TODO: pass the dummies for nominal variables and remove if all dummies are correlated, or none is correlated with the dependentvariable'''
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
530 result = copy(independentVariables)
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
531 table1 = ''
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
532 table2 = {}
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
533 # constant variables
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
534 for var in independentVariables:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
535 uniqueValues = data[var].unique()
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
536 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
537 print(stdoutText[0].format(var, uniqueValues))
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
538 if saveFiles:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
539 table1 += latexTable[0].format(var, *uniqueValues)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
540 result.remove(var)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
541 # correlated variables
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
542 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
543 if v1 in correlations.index:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
544 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
545 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
546 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
547 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
548 if saveFiles:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
549 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
550 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
551 result.remove(v2)
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
552 # not correlated with dependent variable
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
553 table2['Correlations'] = []
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
554 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
555 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
556 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
557 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
558 if p > maxCorrelationP:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
559 if saveFiles:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
560 table1 += latexTable[2].format(var, cor, p)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
561 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
562 result.remove(var)
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
563 else:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
564 table2['Correlations'].append(cor)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
565 table2['Valeurs p'].append(p)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
566
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
567 if saveFiles:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
568 out = openCheck(filenamePrefix+'-removed-variables.tex', 'w')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
569 out.write(latexHeader)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
570 out.write(table1)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
571 out.write(latexFooter)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
572 out.close()
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
573 out = openCheck(filenamePrefix+'-correlations.html', 'w')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
574 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
575 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
576 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
577 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
578
841
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 840
diff changeset
579 def saveDokMatrix(filename, m, lowerTriangle = False):
840
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
580 'Saves a dok_matrix using savez'
841
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 840
diff changeset
581 if lowerTriangle:
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
582 keys = [k for k in m if k[0] > k[1]]
841
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 840
diff changeset
583 savez(filename, shape = m.shape, keys = keys, values = [m[k[0],k[1]] for k in keys])
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 840
diff changeset
584 else:
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
585 savez(filename, shape = m.shape, keys = list(m.keys()), values = list(m.values()))
840
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
586
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
587 def loadDokMatrix(filename):
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
588 'Loads a dok_matrix saved using the above saveDokMatrix'
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
589 data = npload(filename)
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
590 m = dok_matrix(tuple(data['shape']))
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
591 for k, v in zip(data['keys'], data['values']):
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
592 m[tuple(k)] = v
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
593 return m
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
594
1023
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
595 def aggregationFunction(funcStr, centile = 50):
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
596 '''return the numpy function corresponding to funcStr
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
597 centile can be a list of centiles to compute at once, eg [25, 50, 75] for the 3 quartiles'''
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
598 if funcStr == 'median':
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
599 return median
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
600 elif funcStr == 'mean':
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
601 return mean
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
602 elif funcStr == 'centile':
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
603 return lambda x: percentile(x, centile)
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
604 elif funcStr == '85centile':
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
605 return lambda x: percentile(x, 85)
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
606 else:
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
607 print('Unknown aggregation method: {}'.format(funcStr))
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
608 return None
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
609
1058
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
610 def aggregationMethods(methods, centiles = None):
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
611 aggFunctions = {}
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
612 headers = []
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
613 for method in methods:
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
614 if method == 'centile':
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
615 aggFunctions[method] = aggregationFunction(method, centiles)
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
616 for c in centiles:
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
617 headers.append('{}{}'.format(method,c))
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
618 else:
1060
c04550f957ab bug corrected
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1059
diff changeset
619 aggFunctions[method] = aggregationFunction(method)
1058
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
620 headers.append(method)
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
621 return aggFunctions, headers
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
622
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
623 #########################
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
624 # regression analysis using statsmodels (and pandas)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
625 #########################
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
626
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
627 # 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
628 # 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
629 def modelString(experiment, dependentVariable, independentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
630 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
631
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
632 def runModel(experiment, data, dependentVariable, independentVariables, regressionType = 'ols'):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
633 import statsmodels.formula.api as smf
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
634 modelStr = modelString(experiment, dependentVariable, independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
635 if regressionType == 'ols':
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
636 model = smf.ols(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
637 elif regressionType == 'gls':
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
638 model = smf.gls(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
639 elif regressionType == 'rlm':
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
640 model = smf.rlm(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
641 else:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
642 print('Unknown regression type {}. Exiting'.format(regressionType))
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
643 import sys
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
644 sys.exit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
645 return model.fit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
646
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
647 def runModels(experiments, data, dependentVariable, independentVariables, regressionType = 'ols'):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
648 '''Runs several models and stores 3 statistics
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
649 adjusted R2, condition number (should be small, eg < 1000)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
650 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
651 for i,experiment in experiments.iterrows():
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
652 if experiment[independentVariables].any():
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
653 results = runModel(experiment, data, dependentVariable, independentVariables, regressionType = 'ols')
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
654 experiments.loc[i,'r2adj'] = results.rsquared_adj
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
655 experiments.loc[i,'condNum'] = results.condition_number
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
656 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
657 experiments.loc[i,'nobs'] = int(results.nobs)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
658 return experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
659
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
660 def generateExperiments(independentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
661 '''Generates all possible models for including or not each independent variable'''
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
662 experiments = {}
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
663 nIndependentVariables = len(independentVariables)
669
df6be882f325 bug corrected
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 668
diff changeset
664 if nIndependentVariables != len(set(independentVariables)):
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
665 print("Duplicate variables. Exiting")
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
666 import sys
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
667 sys.exit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
668 nModels = 2**nIndependentVariables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
669 for i,var in enumerate(independentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
670 pattern = [False]*(2**i)+[True]*(2**i)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
671 experiments[var] = pattern*(2**(nIndependentVariables-i-1))
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
672 experiments = DataFrame(experiments)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
673 experiments['r2adj'] = 0.
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
674 experiments['condNum'] = NaN
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
675 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
676 experiments['nobs'] = -1
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
677 return experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
678
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
679 def findBestModel(data, dependentVariable, independentVariables, regressionType = 'ols', nProcesses = 1):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
680 '''Generates all possible model with the independentVariables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
681 and runs them, saving the results in experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
682 with multiprocess option'''
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
683 experiments = generateExperiments(independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
684 nModels = len(experiments)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
685 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
686 print("IndependentVariables: {}".format(independentVariables))
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
687 if nProcesses == 1:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
688 return runModels(experiments, data, dependentVariable, independentVariables, regressionType)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
689 else:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
690 pool = Pool(processes = nProcesses)
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
691 chunkSize = int(ceil(nModels/nProcesses))
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
692 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
693 return concat([job.get() for job in jobs])
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
694
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
695 def findBestModelFwd(data, dependentVariable, independentVariables, modelFunc, experiments = None):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
696 '''Forward search for best model (based on adjusted R2)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
697 Randomly starting with one variable and adding randomly variables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
698 if they improve the model
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
699
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
700 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
701 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
702 to the binary code derived from the independent variables'''
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
703 if experiments is None:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
704 experiments = generateExperiments(independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
705 nIndependentVariables = len(independentVariables)
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
706 permutation = nppermutation(list(range(nIndependentVariables)))
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
707 variableMapping = {j: independentVariables[i] for i,j in enumerate(permutation)}
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
708 print('Tested variables '+', '.join([variableMapping[i] for i in range(nIndependentVariables)]))
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
709 bestModel = [False]*nIndependentVariables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
710 currentVarNum = 0
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
711 currentR2Adj = 0.
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
712 for currentVarNum in range(nIndependentVariables):
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
713 currentModel = [i for i in bestModel]
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
714 currentModel[currentVarNum] = True
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
715 rowIdx = sum([0]+[2**i for i in range(nIndependentVariables) if currentModel[permutation[i]]])
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
716 #print currentVarNum, sum(currentModel), ', '.join([independentVariables[i] for i in range(nIndependentVariables) if currentModel[permutation[i]]])
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
717 if experiments.loc[rowIdx, 'shapiroP'] < 0:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
718 modelStr = modelString(experiments.loc[rowIdx], dependentVariable, independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
719 model = modelFunc(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
720 results = model.fit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
721 experiments.loc[rowIdx, 'r2adj'] = results.rsquared_adj
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
722 experiments.loc[rowIdx, 'condNum'] = results.condition_number
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
723 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
724 experiments.loc[rowIdx, 'nobs'] = int(results.nobs)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
725 if currentR2Adj < experiments.loc[rowIdx, 'r2adj']:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
726 currentR2Adj = experiments.loc[rowIdx, 'r2adj']
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
727 bestModel[currentVarNum] = True
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
728 return experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
729
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
730 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
731 import statsmodels.api as sm
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
732 '''Displays some model results
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
733
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
734 3 graphics, true-predicted, residuals-predicted, '''
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
735 print(results.summary())
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
736 shapiroResult = shapiro(results.resid)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
737 print(shapiroResult)
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
738 if plotFigures:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
739 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
740 if model is not None:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
741 ax = fig.add_subplot(3,1,1)
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
742 plt.plot(results.predict(), model.endog, 'x')
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
743 x=plt.xlim()
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
744 y=plt.ylim()
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
745 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
746 #plt.axis('equal')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
747 if text is not None:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
748 plt.title(text['title-shapiro'].format(*shapiroResult))
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
749 #plt.title(text['true-predicted.title'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
750 plt.xlabel(text['true-predicted.xlabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
751 plt.ylabel(text['true-predicted.ylabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
752 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
753 plt.plot(results.predict(), results.resid, 'x')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
754 nextSubplotNum = 3
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
755 else:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
756 fig.add_subplot(2,1,1)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
757 plt.plot(results.predict(), results.resid, 'x')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
758 nextSubplotNum = 2
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
759 if text is not None:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
760 if model is None:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
761 plt.title(text['title-shapiro'].format(*shapiroResult))
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
762 plt.xlabel(text['residuals-predicted.xlabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
763 plt.ylabel(text['residuals-predicted.ylabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
764 qqAx = fig.add_subplot(nextSubplotNum,1,nextSubplotNum)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
765 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
766 plt.axis('equal')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
767 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
768 plt.xlabel(text['qqplot.xlabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
769 plt.ylabel(text['qqplot.ylabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
770 plt.tight_layout()
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
771 if filenamePrefix is not None:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
772 out = openCheck(filenamePrefix+'-coefficients.html', 'w')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
773 out.write(results.summary().as_html())
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
774 plt.savefig(filenamePrefix+'-model-results.'+figureFileType)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
775
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
776 #########################
455
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
777 # iterable section
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
778 #########################
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
779
1034
4069d8545922 updated mostCommong function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1031
diff changeset
780 def mostCommon(l):
456
825e5d49325d slight update
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 455
diff changeset
781 '''Returns the most frequent element in a iterable
1034
4069d8545922 updated mostCommong function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1031
diff changeset
782 The element must be hashable
456
825e5d49325d slight update
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 455
diff changeset
783
1034
4069d8545922 updated mostCommong function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1031
diff changeset
784 new version from https://stackoverflow.com/questions/41612368/find-most-common-element
4069d8545922 updated mostCommong function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1031
diff changeset
785 previous version from from http://stackoverflow.com/questions/1518522/python-most-common-element-in-a-list'''
4069d8545922 updated mostCommong function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1031
diff changeset
786 return Counter(l).most_common(1)[0][0]
4069d8545922 updated mostCommong function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1031
diff changeset
787
455
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
788 #########################
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
789 # sequence section
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
790 #########################
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
791
665
15e244d2a1b5 corrected bug with circular import for VideoFilenameAddable, moved to base module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 659
diff changeset
792 class LCSS(object):
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
793 '''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
794 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
795
cdee6a3a47b4 allowing alternate database and filename for classify-objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 680
diff changeset
796 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
797 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
798 ie compute and computeXX methods'''
689
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
799 def __init__(self, similarityFunc = None, metric = None, epsilon = None, delta = float('inf'), aligned = False, lengthFunc = min):
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
800 '''One should provide either a similarity function
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
801 that indicates (return bool) whether elements in the compares lists are similar
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
802
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
803 eg distance(p1, p2) < epsilon
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
804
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
805 or a type of metric usable in scipy.spatial.distance.cdist with an epsilon'''
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
806 if similarityFunc is None and metric is None:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
807 print("No way to compute LCSS, similarityFunc and metric are None. Exiting")
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
808 import sys
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
809 sys.exit()
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
810 elif metric is not None and epsilon is None:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
811 print("Please provide a value for epsilon if using a cdist metric. Exiting")
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
812 import sys
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
813 sys.exit()
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
814 else:
741
5b91b8d97cf3 corrected bug
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 739
diff changeset
815 if similarityFunc is None and metric is not None and not isinf(delta):
737
fb60b54e1041 added warning for finite delta
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 733
diff changeset
816 print('Warning: you are using a cdist metric and a finite delta, which will make probably computation slower than using the equivalent similarityFunc (since all pairwise distances will be computed by cdist).')
689
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
817 self.similarityFunc = similarityFunc
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
818 self.metric = metric
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
819 self.epsilon = epsilon
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
820 self.aligned = aligned
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
821 self.delta = delta
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
822 self.lengthFunc = lengthFunc
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
823 self.subSequenceIndices = [(0,0)]
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
824
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
825 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
826 n1 = len(l1)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
827 n2 = len(l2)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
828 self.similarityTable = zeros((n1+1,n2+1), dtype = npint)
689
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
829 if self.similarityFunc is not None:
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
830 for i in range(1,n1+1):
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
831 for j in range(max(1,i-jshift-self.delta),min(n2,i-jshift+self.delta)+1):
689
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
832 if self.similarityFunc(l1[i-1], l2[j-1]):
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
833 self.similarityTable[i,j] = self.similarityTable[i-1,j-1]+1
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
834 else:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
835 self.similarityTable[i,j] = max(self.similarityTable[i-1,j], self.similarityTable[i,j-1])
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
836 elif self.metric is not None:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
837 similarElements = distance.cdist(l1, l2, self.metric) <= self.epsilon
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
838 for i in range(1,n1+1):
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
839 for j in range(max(1,i-jshift-self.delta),min(n2,i-jshift+self.delta)+1):
689
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
840 if similarElements[i-1, j-1]:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
841 self.similarityTable[i,j] = self.similarityTable[i-1,j-1]+1
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
842 else:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
843 self.similarityTable[i,j] = max(self.similarityTable[i-1,j], self.similarityTable[i,j-1])
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
844
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
845
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
846 def subSequence(self, i, j):
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
847 '''Returns the subsequence of two sequences
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
848 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
849 if i == 0 or j == 0:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
850 return []
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
851 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
852 return self.subSequence(i, j-1)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
853 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
854 return self.subSequence(i-1, j)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
855 else:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
856 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
857
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
858 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
859 '''returns the longest common subsequence similarity
689
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
860 l1 and l2 should be the right format
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
861 eg list of tuple points for cdist
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
862 or elements that can be compare using similarityFunc
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
863
607
84690dfe5560 add some functions for behaviour analysis
MohamedGomaa
parents: 574
diff changeset
864 if aligned, returns the best matching if using a finite delta by shifting the series alignments
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
865 '''
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
866 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
867 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
868 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
869 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
870 else:
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
871 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
872 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
873 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
874 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
875 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
876
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
877 if self.aligned:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
878 lcssValues = {}
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
879 similarityTables = {}
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
880 for i in range(-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
881 self.similarities(l1, l2, i)
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
882 lcssValues[i] = self.similarityTable.max()
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
883 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
884 #print self.similarityTable
521
3707eeb20f25 changed argMaxDict name to argmaxDict
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 518
diff changeset
885 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
886 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
887 else:
389
6d26dcc7bba0 modifications to compute alignment for None indicators
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
888 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
889 self.similarities(l1, l2)
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
890
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
891 # 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
892 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
893
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
894 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
895 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
896 if revertIndices:
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
897 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
898 return self.similarityTable[-1,-1]
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
899
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
900 def compute(self, l1, l2, computeSubSequence = False):
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
901 '''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
902 return self._compute(l1, l2, computeSubSequence)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
903
375
2ea8584aa80a making indicator LCSS work
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 374
diff changeset
904 def computeAlignment(self):
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
905 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
906
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
907 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
908 ''' compute the normalized LCSS
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
909 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
910 lengthFunc = lambda x,y:float(x,y)/2'''
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
911 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
912
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
913 def computeNormalized(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
914 return self._computeNormalized(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
915
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
916 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
917 ''' compute the LCSS distance'''
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
918 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
919
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
920 def computeDistance(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
921 return self._computeDistance(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
922
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
923 #########################
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
924 # plotting section
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
925 #########################
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
926
940
d8ab183a7351 verified motion prediction with prototypes at constant speed (test needed)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 876
diff changeset
927 def plotPolygon(poly, options = '', **kwargs):
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
928 'Plots shapely polygon poly'
940
d8ab183a7351 verified motion prediction with prototypes at constant speed (test needed)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 876
diff changeset
929 x,y = poly.exterior.xy
1029
c6cf75a2ed08 reorganization of imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1028
diff changeset
930 plt.plot(x, y, options, **kwargs)
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
931
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
932 def stepPlot(X, firstX, lastX, initialCount = 0, increment = 1):
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
933 '''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
934 returns the lists that can be plotted
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
935 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
936 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
937
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
938 sortedX = []
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
939 counts = [initialCount]
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
940 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
941 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
942 counts.append(counts[-1])
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
943 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
944 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
945 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
946
665
15e244d2a1b5 corrected bug with circular import for VideoFilenameAddable, moved to base module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 659
diff changeset
947 class PlottingPropertyValues(object):
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
948 def __init__(self, values):
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
949 self.values = values
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
950
116
2bf5b76320c0 moved intersection plotting and added markers for scatter plots
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 115
diff changeset
951 def __getitem__(self, i):
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
952 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
953
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
954 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
955 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
956
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
957 linestyles = PlottingPropertyValues(['-', '--', '-.', ':'])
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
958
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
959 colors = PlottingPropertyValues('brgmyck') # 'w'
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
960
990
94bee7b604eb addition
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 978
diff changeset
961 def monochromeCycler(withMarker = False):
94bee7b604eb addition
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 978
diff changeset
962 from cycler import cycler
94bee7b604eb addition
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 978
diff changeset
963 if withMarker:
94bee7b604eb addition
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 978
diff changeset
964 monochrome = (cycler('color', ['k']) * cycler('linestyle', ['-', '--', ':', '-.']) * cycler('marker', ['^',',', '.']))
94bee7b604eb addition
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 978
diff changeset
965 else:
94bee7b604eb addition
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 978
diff changeset
966 monochrome = (cycler('color', ['k']) * cycler('linestyle', ['-', '--', ':', '-.']))
94bee7b604eb addition
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 978
diff changeset
967 plt.rc('axes', prop_cycle=monochrome)
94bee7b604eb addition
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 978
diff changeset
968
115
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
969 def plotIndicatorMap(indicatorMap, squareSize, masked = True, defaultValue=-1):
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
970 coords = array(list(indicatorMap.keys()))
65
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
971 minX = min(coords[:,0])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
972 minY = min(coords[:,1])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
973 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
974 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
975 C = defaultValue*ones((len(Y), len(X)))
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
976 for k,v in indicatorMap.items():
65
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
977 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
978 if masked:
1029
c6cf75a2ed08 reorganization of imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1028
diff changeset
979 plt.pcolor(X, Y, ma.masked_where(C==defaultValue,C))
115
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
980 else:
1029
c6cf75a2ed08 reorganization of imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1028
diff changeset
981 plt.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
982
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
983 #########################
637
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
984 # Data download
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
985 #########################
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
986
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
987 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
988 '''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
989 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
990 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
991
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
992 Example: MONTREAL MCTAVISH 10761
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
993 MONTREALPIERRE ELLIOTT TRUDEAU INTL A 5415
856
e310577cc0b8 updated function (url) for weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 855
diff changeset
994 see ftp://client_climate@ftp.tor.ec.gc.ca/Pub/Get_More_Data_Plus_de_donnees/Station%20Inventory%20EN.csv
637
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
995
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
996 To get daily data for 2010 and 2011, downloadECWeather(10761, [2010,2011], [], '/tmp')
973
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 971
diff changeset
997 To get hourly data for 2009 and 2012, January, March and October, downloadECWeather(10761, [2009,2012], [1,3,10], '/tmp')
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 971
diff changeset
998
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 971
diff changeset
999 for annee in `seq 2016 2017`;do wget --content-disposition "http://climat.meteo.gc.ca/climate_data/bulk_data_f.html?format=csv&stationID=10761&Year=${annee}&timeframe=2&submit=++T%C3%A9l%C3%A9charger+%0D%0Ades+donn%C3%A9es" ;done
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 971
diff changeset
1000 for annee in `seq 2016 2017`;do for mois in `seq 1 12`;do wget --content-disposition "http://climat.meteo.gc.ca/climate_data/bulk_data_f.html?format=csv&stationID=10761&Year=${annee}&Month=${mois}&timeframe=1&submit=++T%C3%A9l%C3%A9charger+%0D%0Ades+donn%C3%A9es" ;done;done
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 971
diff changeset
1001 '''
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
1002 import urllib.request
637
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1003 if english:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1004 language = 'e'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1005 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1006 language = 'f'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1007 if len(months) == 0:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1008 timeFrame = 2
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1009 months = [1]
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1010 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1011 timeFrame = 1
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1012
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1013 for year in years:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1014 for month in months:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1015 outFilename = '{}/{}-{}'.format(outputDirectoryname, stationID, year)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1016 if timeFrame == 1:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1017 outFilename += '-{}-hourly'.format(month)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1018 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1019 outFilename += '-daily'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1020 outFilename += '.csv'
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
1021 url = urllib.request.urlretrieve('http://climate.weather.gc.ca/climate_data/bulk_data_{}.html?format=csv&stationID={}&Year={}&Month={}&Day=1&timeframe={}&submit=Download+Data'.format(language, stationID, year, month, timeFrame), outFilename)
637
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1022
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1023 #########################
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1024 # File I/O
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
1025 #########################
24
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
1026
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1027 def removeExtension(filename, delimiter = '.'):
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1028 '''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
1029 i = filename.rfind(delimiter)
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1030 if i>0:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1031 return filename[:i]
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1032 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1033 return filename
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1034
969
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
1035 def getExtension(filename, delimiter = '.'):
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
1036 '''Returns the filename minus the extension (all characters after last .)'''
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
1037 i = filename.rfind(delimiter)
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
1038 if i>0:
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
1039 return filename[i+1:]
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
1040 else:
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
1041 return ''
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
1042
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
1043 def cleanFilename(s):
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
1044 'cleans filenames obtained when contatenating figure characteristics'
739
25e78d756823 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 737
diff changeset
1045 return s.replace(' ','-').replace('.','').replace('/','-').replace(',','')
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
1046
1021
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1047 def getRelativeFilename(parentPath, filename):
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1048 'Returns filename if absolute, otherwise parentPath/filename as string'
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1049 filePath = Path(filename)
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1050 if filePath.is_absolute():
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1051 return filename
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1052 else:
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1053 return str(parentPath/filePath)
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1054
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1055 def listfiles(dirname, extension, remove = False):
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
1056 '''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
1057 If remove is True, the filenames are stripped from the extension'''
1021
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1058 d = Path(dirname)
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1059 if d.is_dir():
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1060 tmp = [str(f) for f in d.glob('*.extension')]
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1061 if remove:
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1062 return [removeExtension(f, extension) for f in tmp]
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1063 else:
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1064 return tmp
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1065 else:
1021
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1066 print(dirname+' is not a directory')
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1067 return []
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1068
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
1069 def mkdir(dirname):
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
1070 'Creates a directory if it does not exist'
1021
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1071 p = Path(dirname)
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1072 if not p.exists():
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1073 p.mkdir()
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
1074 else:
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
1075 print(dirname+' already exists')
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
1076
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
1077 def removeFile(filename):
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
1078 '''Deletes the file while avoiding raising an error
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
1079 if the file does not exist'''
1021
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1080 f = Path(filename)
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1081 if (f.exists()):
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1082 f.unlink()
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
1083 else:
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
1084 print(filename+' does not exist')
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
1085
42
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
1086 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
1087 '''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
1088 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
1089
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
1090 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
1091 '''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
1092 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
1093
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1094 #########################
553
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1095 # Profiling
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1096 #########################
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1097
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1098 def analyzeProfile(profileFilename, stripDirs = True):
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1099 '''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
1100
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1101 obtained by for example:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1102 - 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
1103 import cProfile, os
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1104 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
1105
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1106 - or on the command line:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1107 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
1108 import pstats, os
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1109 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
1110 if stripDirs:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1111 p.strip_dirs()
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1112 p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1113 p.print_stats(.2)
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1114 #p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1115 # 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
1116 return p
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1117
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1118 #########################
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1119 # running tests
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1120 #########################
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1121
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1122 if __name__ == "__main__":
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1123 import doctest
2
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
1124 import unittest
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1125 suite = doctest.DocFileSuite('tests/utils.txt')
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1126 #suite = doctest.DocTestSuite()
2
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
1127 unittest.TextTestRunner().run(suite)
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
1128 #doctest.testmod()
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1129 #doctest.testfile("example.txt")