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annotate trafficintelligence/utils.py @ 1135:342701cdac30

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bug fix for concatenate
author Nicolas Saunier <nicolas.saunier@polymtl.ca>
date Thu, 05 Mar 2020 16:53:48 -0500
parents 91faf679e898
children f7fbe624fff7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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 random_sample, 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
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90
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91 def findElement(l, num):
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92 i = 0
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93 while l[i].getNum() != num:
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94 i += 1
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95 if i < len(l):
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96 return l[i]
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97 else:
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98 return None
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99
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100 #########################
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101 # Simple statistics
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102 #########################
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103
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104 def logNormalMeanVar(loc, scale):
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105 '''location and scale are respectively the mean and standard deviation of the normal in the log-normal distribution
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106 https://en.wikipedia.org/wiki/Log-normal_distribution
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107
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108 same as lognorm.stats(scale, 0, exp(loc))'''
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109 mean = exp(loc+(scale**2)/2)
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110 var = (exp(scale**2)-1)*exp(2*loc+scale**2)
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111 return mean, var
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112
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113 def fitLogNormal(x):
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114 'returns the fitted location and scale of the lognormal (general definition)'
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115 shape, loc, scale = lognorm.fit(x, floc=0.)
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116 return log(scale), shape
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117
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118 def sampleSize(stdev, tolerance, percentConfidence, nRoundingDigits = None, printLatex = False):
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119 if nRoundingDigits is None:
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120 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1), 2) # 1.-(100-percentConfidence)/200.
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121 else:
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122 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1), nRoundingDigits)
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123 stdev = round(stdev, nRoundingDigits)
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124 tolerance = round(tolerance, nRoundingDigits)
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125 if printLatex:
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126 print('$z_{{{}}}^2\\frac{{s^2}}{{e^2}}={}^2\\frac{{{}^2}}{{{}^2}}$'.format(0.5+percentConfidence/200.,k, stdev, tolerance))
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127 return (k*stdev/tolerance)**2
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128
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129 def confidenceInterval(mean, stdev, nSamples, percentConfidence, trueStd = True, printLatex = False):
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130 '''if trueStd, use normal distribution, otherwise, Student
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131
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132 Use otherwise t.interval or norm.interval for the boundaries
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133 ex: norm.interval(0.95)
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134 t.interval(0.95, nSamples-1)'''
423
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parents: 421
diff changeset
135 if trueStd:
859
a8de3c93f6b7 minor modifications to helper stat functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 856
diff changeset
136 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1), 2)
423
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parents: 421
diff changeset
137 else: # use Student
859
a8de3c93f6b7 minor modifications to helper stat functions
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parents: 856
diff changeset
138 k = round(t.ppf(0.5+percentConfidence/200., nSamples-1), 2)
301
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parents: 297
diff changeset
139 e = k*stdev/sqrt(nSamples)
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 297
diff changeset
140 if printLatex:
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diff changeset
141 print('${0} \pm {1}\\frac{{{2}}}{{\sqrt{{{3}}}}}$'.format(mean, k, stdev, nSamples))
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parents: 297
diff changeset
142 return mean-e, mean+e
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parents: 297
diff changeset
143
31
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diff changeset
144 def computeChi2(expected, observed):
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diff changeset
145 '''Returns the Chi2 statistics'''
876
c7e72d758049 minor update to avoid integer issue
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diff changeset
146 return sum([((e-o)*(e-o))/float(e) for e, o in zip(expected, observed)])
31
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diff changeset
147
1103
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diff changeset
148 class ConstantDistribution(object):
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parents: 1089
diff changeset
149 '''Distribution returning always the same value for the random variable '''
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diff changeset
150 def __init__(self, value):
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diff changeset
151 self.value = value
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diff changeset
152
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parents: 1089
diff changeset
153 def rvs(self, size = 1):
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parents: 1089
diff changeset
154 if size == 1:
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parents: 1089
diff changeset
155 return self.value
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parents: 1089
diff changeset
156 else:
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parents: 1089
diff changeset
157 return array([self.value]*size)
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158
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
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diff changeset
159 class EmpiricalContinuousDistribution(rv_continuous):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
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diff changeset
160 def __init__(self, values, probabilities, **kwargs):
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161 '''The values (and corresponding probabilities) are supposed to be sorted by value
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162 for v, p in zip(values, probabilities): P(X<=v)=p'''
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163 assert probabilities[0]==0
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
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diff changeset
164 super(EmpiricalContinuousDistribution, self).__init__(**kwargs)
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165 self.values = values
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166 self.probabilities = probabilities
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167
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diff changeset
168 def save(self, filename):
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169 import yaml
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170 with open(filename, 'w') as out:
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diff changeset
171 yaml.dump([self.values, self.probabilities], out)
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172
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173 @staticmethod
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174 def load(filename):
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diff changeset
175 import yaml
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diff changeset
176 with open(filename) as f:
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diff changeset
177 values, probabilities = yaml.load(f)
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178 return EmpiricalContinuousDistribution(values, probabilities)
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179
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180 def _cdf(self, x):
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181 if x < self.values[0]:
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diff changeset
182 return self.probabilities[0]
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parents: 1023
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183 else:
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parents: 1023
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184 i=0
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diff changeset
185 while i+1<len(self.values) and self.values[i+1] < x:
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186 i += 1
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diff changeset
187 if i == len(self.values)-1:
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parents: 1023
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188 return self.probabilities[-1]
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parents: 1023
diff changeset
189 else:
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045cb04ad7b8 corrected bug in distribution
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diff changeset
190 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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191
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192 class DistributionSample(object):
85
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193 def nSamples(self):
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diff changeset
194 return sum(self.counts)
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195
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c5406edbcf12 added loading ground truth annotations (ground truth) from polytrack format
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parents: 574
diff changeset
196 def cumulativeDensityFunction(sample, normalized = False):
276
78922b4de3bf minor change
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parents: 266
diff changeset
197 '''Returns the cumulative density function of the sample of a random variable'''
588
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 574
diff changeset
198 xaxis = sorted(sample)
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parents: 574
diff changeset
199 counts = arange(1,len(sample)+1) # dtype = float
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parents: 574
diff changeset
200 if normalized:
1031
045cb04ad7b8 corrected bug in distribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1030
diff changeset
201 counts = counts.astype(float)/float(len(sample))
197
2788b2827670 simple cumulatie function distribution computation
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 185
diff changeset
202 return xaxis, counts
85
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diff changeset
203
749
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diff changeset
204 class DiscreteDistributionSample(DistributionSample):
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parents: 742
diff changeset
205 '''Class to represent a sample of a distribution for a discrete random variable'''
85
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parents: 77
diff changeset
206 def __init__(self, categories, counts):
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diff changeset
207 self.categories = categories
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diff changeset
208 self.counts = counts
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parents: 77
diff changeset
209
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diff changeset
210 def mean(self):
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parents: 77
diff changeset
211 result = [float(x*y) for x,y in zip(self.categories, self.counts)]
672
5473b7460375 moved and rationalized imports in modules
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 671
diff changeset
212 return npsum(result)/self.nSamples()
85
7f1e54234f96 added empirical discrete distribution, modified class organization and names
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parents: 77
diff changeset
213
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
214 def var(self, mean = None):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
215 if not mean:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
216 m = self.mean()
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
217 else:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
218 m = mean
7f1e54234f96 added empirical discrete distribution, modified class organization and names
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
219 result = 0.
7f1e54234f96 added empirical discrete distribution, modified class organization and names
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
220 squares = [float((x-m)*(x-m)*y) for x,y in zip(self.categories, self.counts)]
672
5473b7460375 moved and rationalized imports in modules
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 671
diff changeset
221 return npsum(squares)/(self.nSamples()-1)
85
7f1e54234f96 added empirical discrete distribution, modified class organization and names
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
222
86
f03ec4697a09 corrected discrete distribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 85
diff changeset
223 def referenceCounts(self, probability):
f03ec4697a09 corrected discrete distribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 85
diff changeset
224 '''probability is a function that returns the probability of the random variable for the category values'''
f03ec4697a09 corrected discrete distribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 85
diff changeset
225 refProba = [probability(c) for c in self.categories]
672
5473b7460375 moved and rationalized imports in modules
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 671
diff changeset
226 refProba[-1] = 1-npsum(refProba[:-1])
86
f03ec4697a09 corrected discrete distribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 85
diff changeset
227 refCounts = [r*self.nSamples() for r in refProba]
f03ec4697a09 corrected discrete distribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 85
diff changeset
228 return refCounts, refProba
85
7f1e54234f96 added empirical discrete distribution, modified class organization and names
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parents: 77
diff changeset
229
749
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diff changeset
230 class ContinuousDistributionSample(DistributionSample):
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
231 '''Class to represent a sample of a distribution for a continuous random variable
76
64fde2b1f96d simplified intervales in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 75
diff changeset
232 with the number of observations for each interval
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 75
diff changeset
233 intervals (categories variable) are defined by their left limits, the last one being the right limit
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 75
diff changeset
234 categories contain therefore one more element than the counts'''
35
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
235 def __init__(self, categories, counts):
276
78922b4de3bf minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 266
diff changeset
236 # todo add samples for initialization and everything to None? (or setSamples?)
35
8cafee54466f forgotten update of histogram class
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parents: 32
diff changeset
237 self.categories = categories
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parents: 32
diff changeset
238 self.counts = counts
31
c000f37c316d moved tests to independent file, added chi2 computation
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parents: 29
diff changeset
239
749
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diff changeset
240 @staticmethod
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
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diff changeset
241 def generate(sample, categories):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
242 if min(sample) < min(categories):
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parents: 742
diff changeset
243 print('Sample has lower min than proposed categories ({}, {})'.format(min(sample), min(categories)))
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parents: 742
diff changeset
244 if max(sample) > max(categories):
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parents: 742
diff changeset
245 print('Sample has higher max than proposed categories ({}, {})'.format(max(sample), max(categories)))
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parents: 742
diff changeset
246 dist = ContinuousDistributionSample(sorted(categories), [0]*(len(categories)-1))
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parents: 742
diff changeset
247 for s in sample:
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parents: 742
diff changeset
248 i = 0
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parents: 742
diff changeset
249 while i<len(dist.categories) and dist.categories[i] <= s:
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parents: 742
diff changeset
250 i += 1
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
251 if i <= len(dist.counts):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
252 dist.counts[i-1] += 1
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parents: 742
diff changeset
253 #print('{} in {} {}'.format(s, dist.categories[i-1], dist.categories[i]))
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parents: 742
diff changeset
254 else:
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parents: 742
diff changeset
255 print('Element {} is not in the categories'.format(s))
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parents: 742
diff changeset
256 return dist
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parents: 742
diff changeset
257
35
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
258 def mean(self):
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parents: 32
diff changeset
259 result = 0.
76
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parents: 75
diff changeset
260 for i in range(len(self.counts)-1):
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parents: 75
diff changeset
261 result += self.counts[i]*(self.categories[i]+self.categories[i+1])/2
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parents: 75
diff changeset
262 return result/self.nSamples()
35
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
263
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
264 def var(self, mean = None):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
265 if not mean:
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parents: 32
diff changeset
266 m = self.mean()
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
267 else:
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
268 m = mean
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parents: 32
diff changeset
269 result = 0.
76
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parents: 75
diff changeset
270 for i in range(len(self.counts)-1):
64fde2b1f96d simplified intervales in empiricalDistribution
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parents: 75
diff changeset
271 mid = (self.categories[i]+self.categories[i+1])/2
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parents: 75
diff changeset
272 result += self.counts[i]*(mid - m)*(mid - m)
35
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
273 return result/(self.nSamples()-1)
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parents: 32
diff changeset
274
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parents: 32
diff changeset
275 def referenceCounts(self, cdf):
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parents: 32
diff changeset
276 '''cdf is a cumulative distribution function
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parents: 32
diff changeset
277 returning the probability of the variable being less that x'''
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parents: 32
diff changeset
278 # refCumulativeCounts = [0]#[cdf(self.categories[0][0])]
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parents: 32
diff changeset
279 # for inter in self.categories:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
280 # refCumulativeCounts.append(cdf(inter[1]))
76
64fde2b1f96d simplified intervales in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 75
diff changeset
281 refCumulativeCounts = [cdf(x) for x in self.categories[1:-1]]
35
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
282
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
283 refProba = [refCumulativeCounts[0]]
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
284 for i in xrange(1,len(refCumulativeCounts)):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
285 refProba.append(refCumulativeCounts[i]-refCumulativeCounts[i-1])
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
286 refProba.append(1-refCumulativeCounts[-1])
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
287 refCounts = [p*self.nSamples() for p in refProba]
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parents: 32
diff changeset
288
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
289 return refCounts, refProba
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
290
77
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
291 def printReferenceCounts(self, refCounts=None):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
292 if refCounts:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
293 ref = refCounts
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
294 else:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
295 ref = self.referenceCounts
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
296 for i in xrange(len(ref[0])):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
297 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
298
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
299
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
300 #########################
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
301 # maths section
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
302 #########################
24
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
303
433
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
304 # def kernelSmoothing(sampleX, X, Y, weightFunc, halfwidth):
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parents: 423
diff changeset
305 # '''Returns a smoothed weighted version of Y at the predefined values of sampleX
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parents: 423
diff changeset
306 # Sum_x weight(sample_x,x) * y(x)'''
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
307 # from numpy import zeros, array
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
308 # smoothed = zeros(len(sampleX))
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
309 # for i,x in enumerate(sampleX):
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parents: 423
diff changeset
310 # weights = array([weightFunc(x,xx, halfwidth) for xx in X])
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
311 # if sum(weights)>0:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
312 # smoothed[i] = sum(weights*Y)/sum(weights)
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
313 # else:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
314 # smoothed[i] = 0
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
315 # return smoothed
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
316
1124
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1105
diff changeset
317 def generateData(nrows, nvariables, scale):
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1105
diff changeset
318 x = random_sample(nrows*nvariables).reshape(nrows,nvariables)*scale
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1105
diff changeset
319 return DataFrame(x, columns=['x{}'.format(i+1) for i in range(nvariables)])
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1105
diff changeset
320
433
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
321 def kernelSmoothing(x, X, Y, weightFunc, halfwidth):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
322 '''Returns the smoothed estimate of (X,Y) at x
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
323 Sum_x weight(sample_x,x) * y(x)'''
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
324 weights = array([weightFunc(x,observedx, halfwidth) for observedx in X])
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
325 if sum(weights)>0:
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
326 return sum(weights*Y)/sum(weights)
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
327 else:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
328 return 0
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
329
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
330 def uniform(center, x, halfwidth):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
331 if abs(center-x)<halfwidth:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
332 return 1.
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
333 else:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
334 return 0.
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
335
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
336 def gaussian(center, x, halfwidth):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
337 return exp(-((center-x)/halfwidth)**2/2)
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
338
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
339 def epanechnikov(center, x, halfwidth):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
340 diff = abs(center-x)
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
341 if diff<halfwidth:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
342 return 1.-(diff/halfwidth)**2
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
343 else:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
344 return 0.
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
345
434
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
346 def triangular(center, x, halfwidth):
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
347 diff = abs(center-x)
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
348 if diff<halfwidth:
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
349 return 1.-abs(diff/halfwidth)
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
350 else:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
351 return 0.
433
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
352
518
0c86c73f3c09 median smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 511
diff changeset
353 def medianSmoothing(x, X, Y, halfwidth):
0c86c73f3c09 median smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 511
diff changeset
354 '''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
355 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
356
521
3707eeb20f25 changed argMaxDict name to argmaxDict
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 518
diff changeset
357 def argmaxDict(d):
561
ee45c6eb6d49 added Mohamed Gomaa Mohamed function to smooth object trajectories
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 553
diff changeset
358 return max(d, key=d.get)
279
3af4c267a7bf generic simple LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 276
diff changeset
359
837
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
360 def deltaFrames(t1, t2, frameRate):
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
361 '''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
362 positive if t1<=t2, negative otherwise'''
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
363 if t1 > t2:
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
364 return -(t1-t2).seconds*frameRate
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
365 else:
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
366 return (t2-t1).seconds*frameRate
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
367
395
6fba1ab040f1 minor modification to framestotime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 391
diff changeset
368 def framesToTime(nFrames, frameRate, initialTime = time()):
6fba1ab040f1 minor modification to framestotime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 391
diff changeset
369 '''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
370 initialTime is a datetime.time'''
6fba1ab040f1 minor modification to framestotime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 391
diff changeset
371 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
372 h = int(floor(seconds/3600.))
248
571ba5ed22e2 added utils for bus processing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 241
diff changeset
373 seconds = seconds - h*3600
261
4aa792cb0fa9 changing framesToTime to return a datetime.time
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 248
diff changeset
374 m = int(floor(seconds/60))
248
571ba5ed22e2 added utils for bus processing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 241
diff changeset
375 seconds = seconds - m*60
262
a048066bd20f correcting bug in framesToTime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 261
diff changeset
376 return time(h, m, seconds)
248
571ba5ed22e2 added utils for bus processing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 241
diff changeset
377
381
387cc0142211 script to replay event annotations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 376
diff changeset
378 def timeToFrames(t, frameRate):
387cc0142211 script to replay event annotations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 376
diff changeset
379 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
380
1059
a87b3072bd26 working version
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1058
diff changeset
381 def timeModulo(t, duration):
a87b3072bd26 working version
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1058
diff changeset
382 'returns the time modulo the duration in min'
a87b3072bd26 working version
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1058
diff changeset
383 return time(t.hour, t.minute//duration, t.second)
a87b3072bd26 working version
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1058
diff changeset
384
241
ee1caff48b03 added function to sort to list of paired data X,Y
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
385 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
386 '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
387 D = {}
ee1caff48b03 added function to sort to list of paired data X,Y
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
388 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
389 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
390 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
391 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
392
733
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
393 def compareLengthForSort(i, j):
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
394 if len(i) < len(j):
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
395 return -1
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
396 elif len(i) == len(j):
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
397 return 0
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
398 else:
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
399 return 1
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
400
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
401 def sortByLength(instances, reverse = False):
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
402 '''Returns a new list with the instances sorted by length (method __len__)
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
403 reverse is passed to sorted'''
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
404 return sorted(instances, key = len, reverse = reverse)
733
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
405
32
48e56179c39e added ceil function
Nicolas Saunier <nico@confins.net>
parents: 31
diff changeset
406 def ceilDecimals(v, nDecimals):
48e56179c39e added ceil function
Nicolas Saunier <nico@confins.net>
parents: 31
diff changeset
407 '''Rounds the number at the nth decimal
48e56179c39e added ceil function
Nicolas Saunier <nico@confins.net>
parents: 31
diff changeset
408 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
409 tens = 10**nDecimals
32
48e56179c39e added ceil function
Nicolas Saunier <nico@confins.net>
parents: 31
diff changeset
410 return ceil(v*tens)/tens
48e56179c39e added ceil function
Nicolas Saunier <nico@confins.net>
parents: 31
diff changeset
411
152
74b1fc68d4df re-organized code to avoid cyclic python module dependencies
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 116
diff changeset
412 def inBetween(bound1, bound2, x):
698
8d99a9e16644 added clarification comments
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 689
diff changeset
413 '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
414 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
415
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
416 def pointDistanceL2(x1,y1,x2,y2):
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
417 ''' 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
418 return sqrt((x2-x1)**2+(y2-y1)**2)
24
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
419
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
420 def crossProduct(l1, l2):
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
421 return l1[0]*l2[1]-l1[1]*l2[0]
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
422
1086
8734742c08c0 major refactoring of curvilinear trajectory projections
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1060
diff changeset
423 def filterCategoricalMovingWindow(cat_list, halfWidth):
574
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
424 ''' 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
425 halfWidth is the search radius on either side'''
659
784298512b60 minor modifications
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 637
diff changeset
426 smoothed = deepcopy(cat_list)
784298512b60 minor modifications
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 637
diff changeset
427 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
428 lower_bound_check = max(0,point-halfWidth)
659
784298512b60 minor modifications
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 637
diff changeset
429 upper_bound_check = min(len(cat_list)-1,point+halfWidth+1)
784298512b60 minor modifications
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 637
diff changeset
430 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
431 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
432 return smoothed
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
433
547
97c5fef5b2d6 corrected bugs
MohamedGomaa
parents: 521
diff changeset
434 def filterMovingWindow(inputSignal, halfWidth):
29
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
435 '''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
436 The first and last points are copied from the original.'''
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
437 width = float(halfWidth*2+1)
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
438 win = ones(width,'d')
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
439 result = convolve(win/width,array(inputSignal),'same')
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
440 result[:halfWidth] = inputSignal[:halfWidth]
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
441 result[-halfWidth:] = inputSignal[-halfWidth:]
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
442 return result
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
443
199
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
444 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
445 '''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
446 as well as the plot'''
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
447 coef = polyfit(x, y, deg)
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
448 if plotData:
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
449 def poly(x):
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
450 result = 0
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
451 for i in range(len(coef)):
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
452 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
453 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
454 plt.plot(x, y, 'x')
199
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
455 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
456 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
457 return coef
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
458
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
459 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
460 '''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
461 columns = data.columns.tolist()
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
462 for var in data.columns:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
463 uniqueValues = data[var].unique()
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
464 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
465 columns.remove(var)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
466 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
467 if plotFigure:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
468 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
469 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
470 #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
471 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
472 if displayNames is not None:
36c5bee9a887 bug correction
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 841
diff changeset
473 colnames = [displayNames.get(s.strip(), s.strip()) for s in columns]
36c5bee9a887 bug correction
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 841
diff changeset
474 else:
36c5bee9a887 bug correction
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 841
diff changeset
475 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
476 #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
477 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
478 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
479 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
480 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
481 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
482 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
483 plt.tight_layout()
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
484 if len(colnames) > 50:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
485 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
486 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
487 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
488 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
489
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 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
491 '''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
492 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
493 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
494 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
495 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
496 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
497 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
498 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
499 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
500 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
501 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
502 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
503 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
504 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
505
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
506 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
507 '''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
508
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
509 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
510 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
511 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
512 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
513 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
514 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
515 if saveLatex:
01b89182891a corrected bug for intersection of lines (thanks to Paul for finding)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
516 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
517 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
518 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
519 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
520 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
521 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
522 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
523 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
524 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
525 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
526 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
527 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
528 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
529 table['count'] = table['count'].astype(int)
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
530 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
531 if saveLatex:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
532 out.write('\\begin{minipage}{\\linewidth}\n'
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
533 +'\\centering\n'
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
534 +'\\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
535 +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
536 +'\\end{minipage}\n'
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
537 +'\\ \\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
538 else:
978
184f1dd307f9 corrected print and exception statements for Python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 973
diff changeset
539 print(table)
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
540 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
541 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
542 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
543
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
544 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
545 '''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
546 - 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
547 - 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
548 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
549
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
550 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
551 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
552
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
553 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
554 result = copy(independentVariables)
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
555 table1 = ''
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
556 table2 = {}
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
557 # constant variables
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
558 for var in independentVariables:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
559 uniqueValues = data[var].unique()
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
560 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
561 print(stdoutText[0].format(var, uniqueValues))
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
562 if saveFiles:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
563 table1 += latexTable[0].format(var, *uniqueValues)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
564 result.remove(var)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
565 # correlated variables
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
566 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
567 if v1 in correlations.index:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
568 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
569 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
570 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
571 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
572 if saveFiles:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
573 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
574 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
575 result.remove(v2)
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
576 # not correlated with dependent variable
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
577 table2['Correlations'] = []
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
578 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
579 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
580 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
581 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
582 if p > maxCorrelationP:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
583 if saveFiles:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
584 table1 += latexTable[2].format(var, cor, p)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
585 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
586 result.remove(var)
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
587 else:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
588 table2['Correlations'].append(cor)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
589 table2['Valeurs p'].append(p)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
590
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
591 if saveFiles:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
592 out = openCheck(filenamePrefix+'-removed-variables.tex', 'w')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
593 out.write(latexHeader)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
594 out.write(table1)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
595 out.write(latexFooter)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
596 out.close()
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
597 out = openCheck(filenamePrefix+'-correlations.html', 'w')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
598 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
599 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
600 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
601 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
602
841
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 840
diff changeset
603 def saveDokMatrix(filename, m, lowerTriangle = False):
840
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
604 'Saves a dok_matrix using savez'
841
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 840
diff changeset
605 if lowerTriangle:
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
606 keys = [k for k in m if k[0] > k[1]]
841
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 840
diff changeset
607 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
608 else:
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
609 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
610
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
611 def loadDokMatrix(filename):
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
612 'Loads a dok_matrix saved using the above saveDokMatrix'
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
613 data = npload(filename)
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
614 m = dok_matrix(tuple(data['shape']))
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
615 for k, v in zip(data['keys'], data['values']):
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
616 m[tuple(k)] = v
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
617 return m
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
618
1023
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
619 def aggregationFunction(funcStr, centile = 50):
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
620 '''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
621 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
622 if funcStr == 'median':
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
623 return median
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
624 elif funcStr == 'mean':
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
625 return mean
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
626 elif funcStr == 'centile':
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
627 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
628 elif funcStr == '85centile':
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
629 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
630 else:
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
631 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
632 return None
a13f47c8931d work on processing large datasets (generate speed data)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1022
diff changeset
633
1058
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
634 def aggregationMethods(methods, centiles = None):
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
635 aggFunctions = {}
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
636 headers = []
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
637 for method in methods:
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
638 if method == 'centile':
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
639 aggFunctions[method] = aggregationFunction(method, centiles)
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
640 for c in centiles:
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
641 headers.append('{}{}'.format(method,c))
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
642 else:
1060
c04550f957ab bug corrected
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1059
diff changeset
643 aggFunctions[method] = aggregationFunction(method)
1058
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
644 headers.append(method)
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
645 return aggFunctions, headers
1105
e62c2f5e25e6 added sampling function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1103
diff changeset
646
e62c2f5e25e6 added sampling function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1103
diff changeset
647 def maxSumSample(d, maxSum):
e62c2f5e25e6 added sampling function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1103
diff changeset
648 '''Generates a sample from distribution d (type scipy.stats, using rvs method)
e62c2f5e25e6 added sampling function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1103
diff changeset
649 until the sum of all elements is larger than maxSum'''
e62c2f5e25e6 added sampling function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1103
diff changeset
650 s = 0 # sum
e62c2f5e25e6 added sampling function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1103
diff changeset
651 sample = []
e62c2f5e25e6 added sampling function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1103
diff changeset
652 while s < maxSum:
e62c2f5e25e6 added sampling function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1103
diff changeset
653 x = d.rvs()
e62c2f5e25e6 added sampling function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1103
diff changeset
654 sample.append(x)
e62c2f5e25e6 added sampling function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1103
diff changeset
655 s += x
e62c2f5e25e6 added sampling function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1103
diff changeset
656 return sample
1058
16575ca4537d work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1034
diff changeset
657
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
658 #########################
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
659 # regression analysis using statsmodels (and pandas)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
660 #########################
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
661
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
662 # 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
663 # 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
664 def modelString(experiment, dependentVariable, independentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
665 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
666
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
667 def runModel(experiment, data, dependentVariable, independentVariables, regressionType = 'ols'):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
668 import statsmodels.formula.api as smf
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
669 modelStr = modelString(experiment, dependentVariable, independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
670 if regressionType == 'ols':
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
671 model = smf.ols(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
672 elif regressionType == 'gls':
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
673 model = smf.gls(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
674 elif regressionType == 'rlm':
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
675 model = smf.rlm(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
676 else:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
677 print('Unknown regression type {}. Exiting'.format(regressionType))
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
678 import sys
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
679 sys.exit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
680 return model.fit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
681
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
682 def runModels(experiments, data, dependentVariable, independentVariables, regressionType = 'ols'):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
683 '''Runs several models and stores 3 statistics
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
684 adjusted R2, condition number (should be small, eg < 1000)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
685 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
686 for i,experiment in experiments.iterrows():
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
687 if experiment[independentVariables].any():
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
688 results = runModel(experiment, data, dependentVariable, independentVariables, regressionType = 'ols')
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
689 experiments.loc[i,'r2adj'] = results.rsquared_adj
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
690 experiments.loc[i,'condNum'] = results.condition_number
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
691 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
692 experiments.loc[i,'nobs'] = int(results.nobs)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
693 return experiments
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 generateExperiments(independentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
696 '''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
697 experiments = {}
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
698 nIndependentVariables = len(independentVariables)
669
df6be882f325 bug corrected
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 668
diff changeset
699 if nIndependentVariables != len(set(independentVariables)):
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
700 print("Duplicate variables. Exiting")
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
701 import sys
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
702 sys.exit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
703 nModels = 2**nIndependentVariables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
704 for i,var in enumerate(independentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
705 pattern = [False]*(2**i)+[True]*(2**i)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
706 experiments[var] = pattern*(2**(nIndependentVariables-i-1))
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
707 experiments = DataFrame(experiments)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
708 experiments['r2adj'] = 0.
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
709 experiments['condNum'] = NaN
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
710 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
711 experiments['nobs'] = -1
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
712 return experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
713
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
714 def findBestModel(data, dependentVariable, independentVariables, regressionType = 'ols', nProcesses = 1):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
715 '''Generates all possible model with the independentVariables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
716 and runs them, saving the results in experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
717 with multiprocess option'''
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
718 experiments = generateExperiments(independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
719 nModels = len(experiments)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
720 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
721 print("IndependentVariables: {}".format(independentVariables))
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
722 if nProcesses == 1:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
723 return runModels(experiments, data, dependentVariable, independentVariables, regressionType)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
724 else:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
725 pool = Pool(processes = nProcesses)
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
726 chunkSize = int(ceil(nModels/nProcesses))
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
727 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
728 return concat([job.get() for job in jobs])
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
729
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
730 def findBestModelFwd(data, dependentVariable, independentVariables, modelFunc, experiments = None):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
731 '''Forward search for best model (based on adjusted R2)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
732 Randomly starting with one variable and adding randomly variables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
733 if they improve the model
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
734
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
735 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
736 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
737 to the binary code derived from the independent variables'''
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
738 if experiments is None:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
739 experiments = generateExperiments(independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
740 nIndependentVariables = len(independentVariables)
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
741 permutation = nppermutation(list(range(nIndependentVariables)))
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
742 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
743 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
744 bestModel = [False]*nIndependentVariables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
745 currentVarNum = 0
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
746 currentR2Adj = 0.
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
747 for currentVarNum in range(nIndependentVariables):
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
748 currentModel = [i for i in bestModel]
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
749 currentModel[currentVarNum] = True
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
750 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
751 #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
752 if experiments.loc[rowIdx, 'shapiroP'] < 0:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
753 modelStr = modelString(experiments.loc[rowIdx], dependentVariable, independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
754 model = modelFunc(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
755 results = model.fit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
756 experiments.loc[rowIdx, 'r2adj'] = results.rsquared_adj
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
757 experiments.loc[rowIdx, 'condNum'] = results.condition_number
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
758 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
759 experiments.loc[rowIdx, 'nobs'] = int(results.nobs)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
760 if currentR2Adj < experiments.loc[rowIdx, 'r2adj']:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
761 currentR2Adj = experiments.loc[rowIdx, 'r2adj']
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
762 bestModel[currentVarNum] = True
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
763 return experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
764
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
765 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
766 import statsmodels.api as sm
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
767 '''Displays some model results
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
768
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
769 3 graphics, true-predicted, residuals-predicted, '''
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
770 print(results.summary())
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
771 shapiroResult = shapiro(results.resid)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
772 print(shapiroResult)
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
773 if plotFigures:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
774 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
775 if model is not None:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
776 ax = fig.add_subplot(3,1,1)
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
777 plt.plot(results.predict(), model.endog, 'x')
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
778 x=plt.xlim()
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
779 y=plt.ylim()
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
780 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
781 #plt.axis('equal')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
782 if text is not None:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
783 plt.title(text['title-shapiro'].format(*shapiroResult))
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
784 #plt.title(text['true-predicted.title'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
785 plt.xlabel(text['true-predicted.xlabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
786 plt.ylabel(text['true-predicted.ylabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
787 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
788 plt.plot(results.predict(), results.resid, 'x')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
789 nextSubplotNum = 3
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
790 else:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
791 fig.add_subplot(2,1,1)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
792 plt.plot(results.predict(), results.resid, 'x')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
793 nextSubplotNum = 2
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
794 if text is not None:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
795 if model is None:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
796 plt.title(text['title-shapiro'].format(*shapiroResult))
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
797 plt.xlabel(text['residuals-predicted.xlabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
798 plt.ylabel(text['residuals-predicted.ylabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
799 qqAx = fig.add_subplot(nextSubplotNum,1,nextSubplotNum)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
800 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
801 plt.axis('equal')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
802 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
803 plt.xlabel(text['qqplot.xlabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
804 plt.ylabel(text['qqplot.ylabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
805 plt.tight_layout()
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
806 if filenamePrefix is not None:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
807 out = openCheck(filenamePrefix+'-coefficients.html', 'w')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
808 out.write(results.summary().as_html())
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
809 plt.savefig(filenamePrefix+'-model-results.'+figureFileType)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
810
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
811 #########################
455
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
812 # iterable section
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
813 #########################
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
814
1034
4069d8545922 updated mostCommong function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1031
diff changeset
815 def mostCommon(l):
456
825e5d49325d slight update
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 455
diff changeset
816 '''Returns the most frequent element in a iterable
1034
4069d8545922 updated mostCommong function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1031
diff changeset
817 The element must be hashable
456
825e5d49325d slight update
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 455
diff changeset
818
1034
4069d8545922 updated mostCommong function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1031
diff changeset
819 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
820 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
821 return Counter(l).most_common(1)[0][0]
4069d8545922 updated mostCommong function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1031
diff changeset
822
455
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
823 #########################
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
824 # sequence section
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
825 #########################
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
826
665
15e244d2a1b5 corrected bug with circular import for VideoFilenameAddable, moved to base module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 659
diff changeset
827 class LCSS(object):
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
828 '''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
829 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
830
cdee6a3a47b4 allowing alternate database and filename for classify-objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 680
diff changeset
831 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
832 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
833 ie compute and computeXX methods'''
689
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
834 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
835 '''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
836 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
837
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
838 eg distance(p1, p2) < epsilon
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
839
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
840 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
841 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
842 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
843 import sys
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
844 sys.exit()
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
845 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
846 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
847 import sys
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
848 sys.exit()
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
849 else:
741
5b91b8d97cf3 corrected bug
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 739
diff changeset
850 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
851 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
852 self.similarityFunc = similarityFunc
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
853 self.metric = metric
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
854 self.epsilon = epsilon
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
855 self.aligned = aligned
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
856 self.delta = delta
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
857 self.lengthFunc = lengthFunc
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
858 self.subSequenceIndices = [(0,0)]
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
859
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
860 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
861 n1 = len(l1)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
862 n2 = len(l2)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
863 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
864 if self.similarityFunc is not None:
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
865 for i in range(1,n1+1):
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
866 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
867 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
868 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
869 else:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
870 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
871 elif self.metric is not None:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
872 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
873 for i in range(1,n1+1):
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
874 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
875 if similarElements[i-1, j-1]:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
876 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
877 else:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
878 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
879
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
880
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
881 def subSequence(self, i, j):
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
882 '''Returns the subsequence of two sequences
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
883 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
884 if i == 0 or j == 0:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
885 return []
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
886 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
887 return self.subSequence(i, j-1)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
888 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
889 return self.subSequence(i-1, j)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
890 else:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
891 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
892
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
893 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
894 '''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
895 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
896 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
897 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
898
607
84690dfe5560 add some functions for behaviour analysis
MohamedGomaa
parents: 574
diff changeset
899 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
900 '''
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
901 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
902 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
903 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
904 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
905 else:
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
906 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
907 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
908 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
909 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
910 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
911
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
912 if self.aligned:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
913 lcssValues = {}
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
914 similarityTables = {}
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
915 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
916 self.similarities(l1, l2, i)
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
917 lcssValues[i] = self.similarityTable.max()
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
918 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
919 #print self.similarityTable
521
3707eeb20f25 changed argMaxDict name to argmaxDict
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 518
diff changeset
920 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
921 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
922 else:
389
6d26dcc7bba0 modifications to compute alignment for None indicators
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
923 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
924 self.similarities(l1, l2)
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
925
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
926 # 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
927 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
928
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
929 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
930 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
931 if revertIndices:
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
932 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
933 return self.similarityTable[-1,-1]
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
934
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
935 def compute(self, l1, l2, computeSubSequence = False):
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
936 '''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
937 return self._compute(l1, l2, computeSubSequence)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
938
375
2ea8584aa80a making indicator LCSS work
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 374
diff changeset
939 def computeAlignment(self):
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
940 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
941
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
942 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
943 ''' compute the normalized LCSS
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
944 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
945 lengthFunc = lambda x,y:float(x,y)/2'''
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
946 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
947
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
948 def computeNormalized(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
949 return self._computeNormalized(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
950
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
951 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
952 ''' compute the LCSS distance'''
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
953 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
954
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
955 def computeDistance(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
956 return self._computeDistance(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
957
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
958 #########################
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
959 # plotting section
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
960 #########################
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
961
940
d8ab183a7351 verified motion prediction with prototypes at constant speed (test needed)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 876
diff changeset
962 def plotPolygon(poly, options = '', **kwargs):
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
963 '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
964 x,y = poly.exterior.xy
1029
c6cf75a2ed08 reorganization of imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1028
diff changeset
965 plt.plot(x, y, options, **kwargs)
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
966
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
967 def stepPlot(X, firstX, lastX, initialCount = 0, increment = 1):
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
968 '''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
969 returns the lists that can be plotted
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
970 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
971 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
972
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
973 sortedX = []
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
974 counts = [initialCount]
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
975 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
976 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
977 counts.append(counts[-1])
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
978 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
979 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
980 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
981
665
15e244d2a1b5 corrected bug with circular import for VideoFilenameAddable, moved to base module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 659
diff changeset
982 class PlottingPropertyValues(object):
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
983 def __init__(self, values):
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
984 self.values = values
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
985
116
2bf5b76320c0 moved intersection plotting and added markers for scatter plots
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 115
diff changeset
986 def __getitem__(self, i):
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
987 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
988
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
989 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
990 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
991
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
992 linestyles = PlottingPropertyValues(['-', '--', '-.', ':'])
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
993
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
994 colors = PlottingPropertyValues('brgmyck') # 'w'
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
995
990
94bee7b604eb addition
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 978
diff changeset
996 def monochromeCycler(withMarker = False):
94bee7b604eb addition
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 978
diff changeset
997 from cycler import cycler
94bee7b604eb addition
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 978
diff changeset
998 if withMarker:
94bee7b604eb addition
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 978
diff changeset
999 monochrome = (cycler('color', ['k']) * cycler('linestyle', ['-', '--', ':', '-.']) * cycler('marker', ['^',',', '.']))
94bee7b604eb addition
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 978
diff changeset
1000 else:
94bee7b604eb addition
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 978
diff changeset
1001 monochrome = (cycler('color', ['k']) * cycler('linestyle', ['-', '--', ':', '-.']))
94bee7b604eb addition
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 978
diff changeset
1002 plt.rc('axes', prop_cycle=monochrome)
94bee7b604eb addition
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 978
diff changeset
1003
115
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
1004 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
1005 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
1006 minX = min(coords[:,0])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
1007 minY = min(coords[:,1])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
1008 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
1009 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
1010 C = defaultValue*ones((len(Y), len(X)))
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
1011 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
1012 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
1013 if masked:
1029
c6cf75a2ed08 reorganization of imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1028
diff changeset
1014 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
1015 else:
1029
c6cf75a2ed08 reorganization of imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1028
diff changeset
1016 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
1017
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
1018 #########################
637
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1019 # Data download
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1020 #########################
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1021
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1022 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
1023 '''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
1024 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
1025 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
1026
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1027 Example: MONTREAL MCTAVISH 10761
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1028 MONTREALPIERRE ELLIOTT TRUDEAU INTL A 5415
856
e310577cc0b8 updated function (url) for weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 855
diff changeset
1029 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
1030
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1031 To get daily data for 2010 and 2011, downloadECWeather(10761, [2010,2011], [], '/tmp')
973
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 971
diff changeset
1032 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
1033
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 971
diff changeset
1034 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=${annee}&timeframe=2&submit=++T%C3%A9l%C3%A9charger+%0D%0Ades+donn%C3%A9es" ;done
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 971
diff changeset
1035 for annee in `seq 2016 2017`;do for mois in `seq 1 12`;do wget --content-disposition "http://climat.meteo.gc.ca/climate_data/bulk_data_f.html?format=csv&stationID=10761&Year=${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
1036 '''
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
1037 import urllib.request
637
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1038 if english:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1039 language = 'e'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1040 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1041 language = 'f'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1042 if len(months) == 0:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1043 timeFrame = 2
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1044 months = [1]
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1045 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1046 timeFrame = 1
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1047
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1048 for year in years:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1049 for month in months:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1050 outFilename = '{}/{}-{}'.format(outputDirectoryname, stationID, year)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1051 if timeFrame == 1:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1052 outFilename += '-{}-hourly'.format(month)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1053 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1054 outFilename += '-daily'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1055 outFilename += '.csv'
997
4f3387a242a1 updated utils to python 3
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 990
diff changeset
1056 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
1057
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1058 #########################
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
1059 # File I/O
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
1060 #########################
24
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
1061
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1062 def removeExtension(filename, delimiter = '.'):
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1063 '''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
1064 i = filename.rfind(delimiter)
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1065 if i>0:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1066 return filename[:i]
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1067 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1068 return filename
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1069
969
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
1070 def getExtension(filename, delimiter = '.'):
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
1071 '''Returns the filename minus the extension (all characters after last .)'''
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
1072 i = filename.rfind(delimiter)
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
1073 if i>0:
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
1074 return filename[i+1:]
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
1075 else:
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
1076 return ''
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
1077
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
1078 def cleanFilename(s):
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
1079 'cleans filenames obtained when contatenating figure characteristics'
739
25e78d756823 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 737
diff changeset
1080 return s.replace(' ','-').replace('.','').replace('/','-').replace(',','')
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
1081
1021
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1082 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
1083 '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
1084 filePath = Path(filename)
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1085 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
1086 return filename
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1087 else:
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1088 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
1089
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1090 def listfiles(dirname, extension, remove = False):
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
1091 '''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
1092 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
1093 d = Path(dirname)
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1094 if d.is_dir():
1089
10205bd0e0b7 corrected bug
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 1088
diff changeset
1095 tmp = [str(f) for f in d.glob('*.'+extension)]
1021
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1096 if remove:
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1097 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
1098 else:
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1099 return tmp
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1100 else:
1021
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1101 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
1102 return []
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1103
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
1104 def mkdir(dirname):
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
1105 '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
1106 p = Path(dirname)
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1107 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
1108 p.mkdir()
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
1109 else:
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
1110 print(dirname+' already exists')
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
1111
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
1112 def removeFile(filename):
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
1113 '''Deletes the file while avoiding raising an error
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
1114 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
1115 f = Path(filename)
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1116 if (f.exists()):
16932cefabc1 work on paths in line with new configurations from tracker
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 997
diff changeset
1117 f.unlink()
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
1118 else:
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
1119 print(filename+' does not exist')
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
1120
42
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
1121 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
1122 '''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
1123 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
1124
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
1125 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
1126 '''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
1127 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
1128
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1129 #########################
553
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1130 # Profiling
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1131 #########################
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1132
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1133 def analyzeProfile(profileFilename, stripDirs = True):
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1134 '''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
1135
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1136 obtained by for example:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1137 - 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
1138 import cProfile, os
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1139 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
1140
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1141 - or on the command line:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1142 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
1143 import pstats, os
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1144 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
1145 if stripDirs:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1146 p.strip_dirs()
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1147 p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1148 p.print_stats(.2)
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1149 #p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1150 # 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
1151 return p
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1152
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1153 #########################
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1154 # running tests
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1155 #########################
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1156
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1157 if __name__ == "__main__":
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1158 import doctest
2
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
1159 import unittest
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1160 suite = doctest.DocFileSuite('tests/utils.txt')
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1161 #suite = doctest.DocTestSuite()
2
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
1162 unittest.TextTestRunner().run(suite)
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
1163 #doctest.testmod()
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1164 #doctest.testfile("example.txt")