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annotate python/utils.py @ 837:e01cabca4c55

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minor modifications to merge-features
author Nicolas Saunier <nicolas.saunier@polymtl.ca>
date Wed, 06 Jul 2016 10:58:18 -0400
parents 10dbab1e871d
children 15a82ebc62c4
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1 #! /usr/bin/env python
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2 # -*- coding: utf-8 -*-
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3 ''' Generic utilities.'''
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4
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5 import matplotlib.pyplot as plt
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6 from datetime import time, datetime
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7 from math import sqrt, ceil, floor
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8 from scipy.stats import kruskal, shapiro
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9 from scipy.spatial import distance
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10 from numpy import zeros, array, exp, sum as npsum, int as npint, arange, cumsum, median, isnan, ones, convolve, dtype, isnan, NaN, mean, ma, isinf
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11
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12
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13 datetimeFormat = "%Y-%m-%d %H:%M:%S"
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15 #########################
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16 # Strings
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17 #########################
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18
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19 def upperCaseFirstLetter(s):
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20 words = s.split(' ')
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21 lowerWords = [w[0].upper()+w[1:].lower() for w in words]
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22 return ' '.join(lowerWords)
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23
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24 #########################
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25 # Enumerations
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26 #########################
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27
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28 def inverseEnumeration(l):
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29 'Returns the dictionary that provides for each element in the input list its index in the input list'
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30 result = {}
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31 for i,x in enumerate(l):
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32 result[x] = i
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33 return result
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34
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35 #########################
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36 # Simple statistics
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37 #########################
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38
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39 def logNormalMeanVar(loc, scale):
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40 '''location and scale are respectively the mean and standard deviation of the normal in the log-normal distribution
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41 https://en.wikipedia.org/wiki/Log-normal_distribution'''
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42 mean = exp(loc+(scale**2)/2)
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43 var = (exp(loc**2)-1)*exp(2*loc+scale**2)
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44 return mean, var
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45
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46 def sampleSize(stdev, tolerance, percentConfidence, printLatex = False):
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47 from scipy.stats.distributions import norm
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48 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1)*100)/100. # 1.-(100-percentConfidence)/200.
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49 if printLatex:
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50 print('${0}^2\\frac{{{1}^2}}{{{2}^2}}$'.format(k, stdev, tolerance))
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51 return (k*stdev/tolerance)**2
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52
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53 def confidenceInterval(mean, stdev, nSamples, percentConfidence, trueStd = True, printLatex = False):
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54 '''if trueStd, use normal distribution, otherwise, Student
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55
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56 Use otherwise t.interval or norm.interval
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57 ex: norm.interval(0.95, loc = 0., scale = 2.3/sqrt(11))
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58 t.interval(0.95, 10, loc=1.2, scale = 2.3/sqrt(nSamples))
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59 loc is mean, scale is sigma/sqrt(n) (for Student, 10 is df)'''
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60 from scipy.stats.distributions import norm, t
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61 if trueStd:
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62 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1)*100)/100. # 1.-(100-percentConfidence)/200.
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63 else: # use Student
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64 k = round(t.ppf(0.5+percentConfidence/200., nSamples-1)*100)/100.
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65 e = k*stdev/sqrt(nSamples)
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66 if printLatex:
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67 print('${0} \pm {1}\\frac{{{2}}}{{\sqrt{{{3}}}}}$'.format(mean, k, stdev, nSamples))
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68 return mean-e, mean+e
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69
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70 def computeChi2(expected, observed):
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71 '''Returns the Chi2 statistics'''
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72 result = 0.
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73 for e, o in zip(expected, observed):
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74 result += ((e-o)*(e-o))/e
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75 return result
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76
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77 class DistributionSample(object):
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78 def nSamples(self):
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79 return sum(self.counts)
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80
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81 def cumulativeDensityFunction(sample, normalized = False):
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82 '''Returns the cumulative density function of the sample of a random variable'''
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83 xaxis = sorted(sample)
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84 counts = arange(1,len(sample)+1) # dtype = float
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85 if normalized:
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86 counts /= float(len(sample))
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87 return xaxis, counts
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88
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89 class DiscreteDistributionSample(DistributionSample):
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90 '''Class to represent a sample of a distribution for a discrete random variable'''
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91 def __init__(self, categories, counts):
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92 self.categories = categories
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93 self.counts = counts
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94
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95 def mean(self):
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96 result = [float(x*y) for x,y in zip(self.categories, self.counts)]
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97 return npsum(result)/self.nSamples()
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98
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99 def var(self, mean = None):
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100 if not mean:
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101 m = self.mean()
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102 else:
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103 m = mean
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104 result = 0.
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105 squares = [float((x-m)*(x-m)*y) for x,y in zip(self.categories, self.counts)]
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106 return npsum(squares)/(self.nSamples()-1)
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107
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108 def referenceCounts(self, probability):
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109 '''probability is a function that returns the probability of the random variable for the category values'''
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110 refProba = [probability(c) for c in self.categories]
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111 refProba[-1] = 1-npsum(refProba[:-1])
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112 refCounts = [r*self.nSamples() for r in refProba]
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113 return refCounts, refProba
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114
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115 class ContinuousDistributionSample(DistributionSample):
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116 '''Class to represent a sample of a distribution for a continuous random variable
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117 with the number of observations for each interval
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118 intervals (categories variable) are defined by their left limits, the last one being the right limit
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119 categories contain therefore one more element than the counts'''
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120 def __init__(self, categories, counts):
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121 # todo add samples for initialization and everything to None? (or setSamples?)
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122 self.categories = categories
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123 self.counts = counts
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124
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125 @staticmethod
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126 def generate(sample, categories):
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127 if min(sample) < min(categories):
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128 print('Sample has lower min than proposed categories ({}, {})'.format(min(sample), min(categories)))
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129 if max(sample) > max(categories):
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130 print('Sample has higher max than proposed categories ({}, {})'.format(max(sample), max(categories)))
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
131 dist = ContinuousDistributionSample(sorted(categories), [0]*(len(categories)-1))
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
132 for s in sample:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
133 i = 0
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
134 while i<len(dist.categories) and dist.categories[i] <= s:
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
135 i += 1
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
136 if i <= len(dist.counts):
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
137 dist.counts[i-1] += 1
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
138 #print('{} in {} {}'.format(s, dist.categories[i-1], dist.categories[i]))
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
139 else:
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
140 print('Element {} is not in the categories'.format(s))
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
141 return dist
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
142
35
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
143 def mean(self):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
144 result = 0.
76
64fde2b1f96d simplified intervales in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 75
diff changeset
145 for i in range(len(self.counts)-1):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 75
diff changeset
146 result += self.counts[i]*(self.categories[i]+self.categories[i+1])/2
64fde2b1f96d simplified intervales in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 75
diff changeset
147 return result/self.nSamples()
35
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
148
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
149 def var(self, mean = None):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
150 if not mean:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
151 m = self.mean()
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
152 else:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
153 m = mean
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
154 result = 0.
76
64fde2b1f96d simplified intervales in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 75
diff changeset
155 for i in range(len(self.counts)-1):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 75
diff changeset
156 mid = (self.categories[i]+self.categories[i+1])/2
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 75
diff changeset
157 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
158 return result/(self.nSamples()-1)
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
159
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
160 def referenceCounts(self, cdf):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
161 '''cdf is a cumulative distribution function
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
162 returning the probability of the variable being less that x'''
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
163 # refCumulativeCounts = [0]#[cdf(self.categories[0][0])]
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
164 # for inter in self.categories:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
165 # refCumulativeCounts.append(cdf(inter[1]))
76
64fde2b1f96d simplified intervales in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 75
diff changeset
166 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
167
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
168 refProba = [refCumulativeCounts[0]]
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
169 for i in xrange(1,len(refCumulativeCounts)):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
170 refProba.append(refCumulativeCounts[i]-refCumulativeCounts[i-1])
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
171 refProba.append(1-refCumulativeCounts[-1])
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
172 refCounts = [p*self.nSamples() for p in refProba]
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
173
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
174 return refCounts, refProba
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
175
77
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
176 def printReferenceCounts(self, refCounts=None):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
177 if refCounts:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
178 ref = refCounts
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
179 else:
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
180 ref = self.referenceCounts
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
181 for i in xrange(len(ref[0])):
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
182 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
183
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
184
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
185 #########################
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
186 # maths section
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
187 #########################
24
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
188
433
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
189 # def kernelSmoothing(sampleX, X, Y, weightFunc, halfwidth):
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
190 # '''Returns a smoothed weighted version of Y at the predefined values of sampleX
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
191 # Sum_x weight(sample_x,x) * y(x)'''
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
192 # from numpy import zeros, array
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
193 # smoothed = zeros(len(sampleX))
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
194 # for i,x in enumerate(sampleX):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
195 # weights = array([weightFunc(x,xx, halfwidth) for xx in X])
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
196 # if sum(weights)>0:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
197 # smoothed[i] = sum(weights*Y)/sum(weights)
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
198 # else:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
199 # smoothed[i] = 0
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
200 # return smoothed
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
201
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
202 def kernelSmoothing(x, X, Y, weightFunc, halfwidth):
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
203 '''Returns the smoothed estimate of (X,Y) at x
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
204 Sum_x weight(sample_x,x) * y(x)'''
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
205 weights = array([weightFunc(x,observedx, halfwidth) for observedx in X])
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
206 if sum(weights)>0:
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
207 return sum(weights*Y)/sum(weights)
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
208 else:
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
209 return 0
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
210
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
211 def uniform(center, x, halfwidth):
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
212 if abs(center-x)<halfwidth:
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
213 return 1.
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
214 else:
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
215 return 0.
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
216
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
217 def gaussian(center, x, halfwidth):
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
218 return exp(-((center-x)/halfwidth)**2/2)
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
219
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
220 def epanechnikov(center, x, halfwidth):
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
221 diff = abs(center-x)
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
222 if diff<halfwidth:
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
223 return 1.-(diff/halfwidth)**2
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
224 else:
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
225 return 0.
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
226
434
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
227 def triangular(center, x, halfwidth):
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
228 diff = abs(center-x)
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
229 if diff<halfwidth:
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
230 return 1.-abs(diff/halfwidth)
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
231 else:
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
232 return 0.
433
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
233
518
0c86c73f3c09 median smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 511
diff changeset
234 def medianSmoothing(x, X, Y, halfwidth):
0c86c73f3c09 median smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 511
diff changeset
235 '''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
236 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
237
521
3707eeb20f25 changed argMaxDict name to argmaxDict
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 518
diff changeset
238 def argmaxDict(d):
561
ee45c6eb6d49 added Mohamed Gomaa Mohamed function to smooth object trajectories
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 553
diff changeset
239 return max(d, key=d.get)
279
3af4c267a7bf generic simple LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 276
diff changeset
240
837
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
241 def deltaFrames(t1, t2, frameRate):
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
242 '''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
243 positive if t1<=t2, negative otherwise'''
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
244 if t1 > t2:
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
245 return -(t1-t2).seconds*frameRate
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
246 else:
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
247 return (t2-t1).seconds*frameRate
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
248
395
6fba1ab040f1 minor modification to framestotime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 391
diff changeset
249 def framesToTime(nFrames, frameRate, initialTime = time()):
6fba1ab040f1 minor modification to framestotime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 391
diff changeset
250 '''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
251 initialTime is a datetime.time'''
6fba1ab040f1 minor modification to framestotime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 391
diff changeset
252 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
253 h = int(floor(seconds/3600.))
248
571ba5ed22e2 added utils for bus processing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 241
diff changeset
254 seconds = seconds - h*3600
261
4aa792cb0fa9 changing framesToTime to return a datetime.time
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 248
diff changeset
255 m = int(floor(seconds/60))
248
571ba5ed22e2 added utils for bus processing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 241
diff changeset
256 seconds = seconds - m*60
262
a048066bd20f correcting bug in framesToTime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 261
diff changeset
257 return time(h, m, seconds)
248
571ba5ed22e2 added utils for bus processing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 241
diff changeset
258
381
387cc0142211 script to replay event annotations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 376
diff changeset
259 def timeToFrames(t, frameRate):
387cc0142211 script to replay event annotations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 376
diff changeset
260 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
261
241
ee1caff48b03 added function to sort to list of paired data X,Y
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
262 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
263 '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
264 D = {}
ee1caff48b03 added function to sort to list of paired data X,Y
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
265 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
266 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
267 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
268 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
269
733
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
270 def compareLengthForSort(i, j):
c35e4a4b199d sortbylength
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diff changeset
271 if len(i) < len(j):
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diff changeset
272 return -1
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parents: 698
diff changeset
273 elif len(i) == len(j):
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diff changeset
274 return 0
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diff changeset
275 else:
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276 return 1
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diff changeset
277
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diff changeset
278 def sortByLength(instances, reverse = False):
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diff changeset
279 '''Returns a new list with the instances sorted by length (method __len__)
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diff changeset
280 reverse is passed to sorted'''
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diff changeset
281 return sorted(instances, cmp = compareLengthForSort, reverse = reverse)
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282
32
48e56179c39e added ceil function
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diff changeset
283 def ceilDecimals(v, nDecimals):
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diff changeset
284 '''Rounds the number at the nth decimal
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diff changeset
285 eg 1.23 at 0 decimal is 2, at 1 decimal is 1.3'''
670
f72ed51c6b65 corrected other missing imports
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diff changeset
286 tens = 10**nDecimals
32
48e56179c39e added ceil function
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diff changeset
287 return ceil(v*tens)/tens
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diff changeset
288
152
74b1fc68d4df re-organized code to avoid cyclic python module dependencies
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parents: 116
diff changeset
289 def inBetween(bound1, bound2, x):
698
8d99a9e16644 added clarification comments
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parents: 689
diff changeset
290 'useful if one does not know the order of bound1/bound2'
569
0057c04f94d5 work in progress on intersections (for PET)
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parents: 561
diff changeset
291 return bound1 <= x <= bound2 or bound2 <= x <= bound1
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parents: 561
diff changeset
292
0057c04f94d5 work in progress on intersections (for PET)
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parents: 561
diff changeset
293 def pointDistanceL2(x1,y1,x2,y2):
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parents: 561
diff changeset
294 ''' Compute point-to-point distance (L2 norm, ie Euclidean distance)'''
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parents: 561
diff changeset
295 return sqrt((x2-x1)**2+(y2-y1)**2)
24
6fb59cfb201e first version of segmentIntersection
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parents: 19
diff changeset
296
6fb59cfb201e first version of segmentIntersection
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diff changeset
297 def crossProduct(l1, l2):
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diff changeset
298 return l1[0]*l2[1]-l1[1]*l2[0]
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299
574
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parents: 569
diff changeset
300 def cat_mvgavg(cat_list, halfWidth):
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parents: 569
diff changeset
301 ''' Return a list of categories/values smoothed according to a window.
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parents: 569
diff changeset
302 halfWidth is the search radius on either side'''
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parents: 569
diff changeset
303 from copy import deepcopy
659
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diff changeset
304 smoothed = deepcopy(cat_list)
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parents: 637
diff changeset
305 for point in range(len(cat_list)):
574
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parents: 569
diff changeset
306 lower_bound_check = max(0,point-halfWidth)
659
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diff changeset
307 upper_bound_check = min(len(cat_list)-1,point+halfWidth+1)
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parents: 637
diff changeset
308 window_values = cat_list[lower_bound_check:upper_bound_check]
574
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parents: 569
diff changeset
309 smoothed[point] = max(set(window_values), key=window_values.count)
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parents: 569
diff changeset
310 return smoothed
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parents: 569
diff changeset
311
547
97c5fef5b2d6 corrected bugs
MohamedGomaa
parents: 521
diff changeset
312 def filterMovingWindow(inputSignal, halfWidth):
29
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
313 '''Returns an array obtained after the smoothing of the input by a moving average
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
314 The first and last points are copied from the original.'''
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
315 width = float(halfWidth*2+1)
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
316 win = ones(width,'d')
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
317 result = convolve(win/width,array(inputSignal),'same')
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
318 result[:halfWidth] = inputSignal[:halfWidth]
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
319 result[-halfWidth:] = inputSignal[-halfWidth:]
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
320 return result
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
321
199
ca9d9104afba added utility to calibrate polynoms and plot
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parents: 197
diff changeset
322 def linearRegression(x, y, deg = 1, plotData = False):
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parents: 197
diff changeset
323 '''returns the least square estimation of the linear regression of y = ax+b
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parents: 197
diff changeset
324 as well as the plot'''
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
325 from numpy.lib.polynomial import polyfit
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
326 from numpy.core.multiarray import arange
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
327 coef = polyfit(x, y, deg)
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parents: 197
diff changeset
328 if plotData:
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
329 def poly(x):
ca9d9104afba added utility to calibrate polynoms and plot
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parents: 197
diff changeset
330 result = 0
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
331 for i in range(len(coef)):
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
332 result += coef[i]*x**(len(coef)-i-1)
ca9d9104afba added utility to calibrate polynoms and plot
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parents: 197
diff changeset
333 return result
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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diff changeset
334 plt.plot(x, y, 'x')
199
ca9d9104afba added utility to calibrate polynoms and plot
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parents: 197
diff changeset
335 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
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diff changeset
336 plt.plot(xx, [poly(z) for z in xx])
199
ca9d9104afba added utility to calibrate polynoms and plot
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parents: 197
diff changeset
337 return coef
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parents: 197
diff changeset
338
668
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diff changeset
339 def correlation(data, correlationMethod = 'pearson', plotFigure = False, displayNames = None, figureFilename = None):
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parents: 667
diff changeset
340 '''Computes (and displays) the correlation matrix for a pandas DataFrame'''
677
ae07c7b4cf87 update to utils for pavement results
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diff changeset
341 columns = data.columns.tolist()
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parents: 676
diff changeset
342 for var in data.columns:
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diff changeset
343 uniqueValues = data[var].unique()
ae07c7b4cf87 update to utils for pavement results
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parents: 676
diff changeset
344 if len(uniqueValues) == 1 or data.dtypes[var] == dtype('O') or (len(uniqueValues) == 2 and len(data.loc[~isnan(data[var]), var].unique()) == 1): # last condition: only one other value than nan
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parents: 676
diff changeset
345 columns.remove(var)
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diff changeset
346 c=data[columns].corr(correlationMethod)
668
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diff changeset
347 if plotFigure:
677
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diff changeset
348 fig = plt.figure(figsize=(4+0.4*c.shape[0], 0.4*c.shape[0]))
668
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diff changeset
349 fig.add_subplot(1,1,1)
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diff changeset
350 #plt.imshow(np.fabs(c), interpolation='none')
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diff changeset
351 plt.imshow(c, vmin=-1., vmax = 1., interpolation='none', cmap = 'RdYlBu_r') # coolwarm
677
ae07c7b4cf87 update to utils for pavement results
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parents: 676
diff changeset
352 colnames = [displayNames.get(s.strip(), s.strip()) for s in columns]
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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diff changeset
353 #correlation.plot_corr(c, xnames = colnames, normcolor=True, title = filename)
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diff changeset
354 plt.xticks(range(len(colnames)), colnames, rotation=90)
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diff changeset
355 plt.yticks(range(len(colnames)), colnames)
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parents: 667
diff changeset
356 plt.tick_params('both', length=0)
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parents: 667
diff changeset
357 plt.subplots_adjust(bottom = 0.29)
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parents: 667
diff changeset
358 plt.colorbar()
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diff changeset
359 plt.title('Correlation ({})'.format(correlationMethod))
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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parents: 667
diff changeset
360 plt.tight_layout()
677
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diff changeset
361 if len(colnames) > 50:
ae07c7b4cf87 update to utils for pavement results
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parents: 676
diff changeset
362 plt.subplots_adjust(left=.06)
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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parents: 667
diff changeset
363 if figureFilename is not None:
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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parents: 667
diff changeset
364 plt.savefig(figureFilename, dpi = 150, transparent = True)
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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parents: 667
diff changeset
365 return c
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parents: 667
diff changeset
366
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diff changeset
367 def addDummies(data, variables, allVariables = True):
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parents: 667
diff changeset
368 '''Add binary dummy variables for each value of a nominal variable
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parents: 667
diff changeset
369 in a pandas DataFrame'''
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parents: 667
diff changeset
370 newVariables = []
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parents: 667
diff changeset
371 for var in variables:
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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parents: 667
diff changeset
372 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
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diff changeset
373 values = data[var].unique()
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parents: 667
diff changeset
374 if not allVariables:
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parents: 667
diff changeset
375 values = values[:-1]
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parents: 667
diff changeset
376 for val in values:
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parents: 667
diff changeset
377 if val is not NaN:
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parents: 667
diff changeset
378 newVariable = (var+'_{}'.format(val)).replace('.','').replace(' ','').replace('-','')
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parents: 667
diff changeset
379 data[newVariable] = (data[var] == val)
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
380 newVariables.append(newVariable)
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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parents: 667
diff changeset
381 return newVariables
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parents: 667
diff changeset
382
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
383 def kruskalWallis(data, dependentVariable, independentVariable, plotFigure = False, filenamePrefix = None, figureFileType = 'pdf', saveLatex = False, renameVariables = lambda s: s, kwCaption = u''):
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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parents: 667
diff changeset
384 '''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
385
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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parents: 667
diff changeset
386 Makes tests if the conditional distributions are normal
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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parents: 667
diff changeset
387 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
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parents: 667
diff changeset
388 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
389 tmp = data[data[independentVariable].notnull()]
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parents: 667
diff changeset
390 independentVariableValues = sorted(tmp[independentVariable].unique().tolist())
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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parents: 667
diff changeset
391 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
392 if saveLatex:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
393 from storage import openCheck
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
394 out = openCheck(filenamePrefix+'-{}-{}.tex'.format(dependentVariable, independentVariable), 'w')
668
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diff changeset
395 for x in independentVariableValues:
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parents: 667
diff changeset
396 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
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parents: 667
diff changeset
397 if len(tmp.loc[tmp[independentVariable] == x, dependentVariable]) >= 3:
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parents: 667
diff changeset
398 print shapiro(tmp.loc[tmp[independentVariable] == x, dependentVariable])
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
399 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
400 plt.figure()
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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diff changeset
401 plt.boxplot([tmp.loc[tmp[independentVariable] == x, dependentVariable] for x in independentVariableValues])
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
402 #q25, q75 = tmp[dependentVariable].quantile([.25, .75])
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
403 #plt.ylim(ymax = q75+1.5*(q75-q25))
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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parents: 667
diff changeset
404 plt.xticks(range(1,len(independentVariableValues)+1), independentVariableValues)
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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parents: 667
diff changeset
405 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
406 if filenamePrefix is not None:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
407 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
408 table = tmp.groupby([independentVariable])[dependentVariable].describe().unstack().sort(['50%'], ascending = False)
676
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
409 table['count'] = table['count'].astype(int)
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
410 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
411 if saveLatex:
677
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parents: 676
diff changeset
412 out.write('\\begin{minipage}{\\linewidth}\n'
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diff changeset
413 +'\\centering\n'
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
414 +'\\captionof{table}{'+(kwCaption.format(dependentVariable, independentVariable, *testResult))+'}\n'
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
415 +table.to_latex(float_format = lambda x: '{:.3f}'.format(x)).encode('ascii')+'\n'
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
416 +'\\end{minipage}\n'
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
417 +'\\ \\vspace{0.5cm}\n')
674
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
418 else:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
419 print table
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
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diff changeset
420 return testResult
668
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diff changeset
421 else:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
422 return None
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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parents: 667
diff changeset
423
677
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diff changeset
424 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
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parents: 667
diff changeset
425 '''Removes variables from candidate independent variables if
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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parents: 667
diff changeset
426 - if two independent variables are correlated (> maxCorrelationThreshold), one is removed
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parents: 667
diff changeset
427 - if an independent variable is not correlated with the dependent variable (p>maxCorrelationP)
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parents: 667
diff changeset
428 Returns the remaining non-correlated variables, correlated with the dependent variable
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
429
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
430 correlationFunc is spearmanr or pearsonr from scipy.stats
677
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
431 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
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parents: 667
diff changeset
432
677
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
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diff changeset
433 TODO: pass the dummies for nominal variables and remove if all dummies are correlated, or none is correlated with the dependentvariable'''
668
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
434 from copy import copy
677
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
435 from pandas import DataFrame
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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diff changeset
436 result = copy(independentVariables)
677
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
437 table1 = ''
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
438 table2 = {}
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
439 # constant variables
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
440 for var in independentVariables:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
441 uniqueValues = data[var].unique()
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
442 if (len(uniqueValues) == 1) or (len(uniqueValues) == 2 and uniqueValues.dtype != dtype('O') and len(data.loc[~isnan(data[var]), var].unique()) == 1):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
443 print(stdoutText[0].format(var, uniqueValues))
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
444 if saveFiles:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
445 table1 += latexTable[0].format(var, *uniqueValues)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
446 result.remove(var)
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
447 # correlated variables
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
448 for v1 in copy(result):
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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diff changeset
449 if v1 in correlations.index:
677
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
450 for v2 in copy(result):
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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parents: 667
diff changeset
451 if v2 != v1 and v2 in correlations.index:
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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parents: 667
diff changeset
452 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
453 if v1 in result and v2 in result:
677
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
454 if saveFiles:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
455 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
456 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
457 result.remove(v2)
677
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
458 # not correlated with dependent variable
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
459 table2['Correlations'] = []
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
460 table2['Valeurs p'] = []
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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parents: 667
diff changeset
461 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
462 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
463 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
464 if p > maxCorrelationP:
677
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
465 if saveFiles:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
466 table1 += latexTable[2].format(var, cor, p)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
467 print(stdoutText[2].format(var, cor, p))
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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parents: 667
diff changeset
468 result.remove(var)
677
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
469 else:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
470 table2['Correlations'].append(cor)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
471 table2['Valeurs p'].append(p)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
472
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
473 if saveFiles:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
474 from storage import openCheck
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
475 out = openCheck(filenamePrefix+'-removed-variables.tex', 'w')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
476 out.write(latexHeader)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
477 out.write(table1)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
478 out.write(latexFooter)
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
479 out.close()
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
480 out = openCheck(filenamePrefix+'-correlations.html', 'w')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
481 table2['Variables'] = [var for var in result if data.dtypes[var] != dtype('O')]
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
482 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
483 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
484 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
485
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
486
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
487 #########################
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
488 # regression analysis using statsmodels (and pandas)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
489 #########################
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
490
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
491 # TODO make class for experiments?
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
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parents: 667
diff changeset
492 # 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
493 def modelString(experiment, dependentVariable, independentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
494 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
495
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
496 def runModel(experiment, data, dependentVariable, independentVariables, regressionType = 'ols'):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
497 import statsmodels.formula.api as smf
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
498 modelStr = modelString(experiment, dependentVariable, independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
499 if regressionType == 'ols':
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
500 model = smf.ols(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
501 elif regressionType == 'gls':
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
502 model = smf.gls(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
503 elif regressionType == 'rlm':
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
504 model = smf.rlm(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
505 else:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
506 print('Unknown regression type {}. Exiting'.format(regressionType))
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
507 import sys
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
508 sys.exit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
509 return model.fit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
510
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
511 def runModels(experiments, data, dependentVariable, independentVariables, regressionType = 'ols'):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
512 '''Runs several models and stores 3 statistics
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
513 adjusted R2, condition number (should be small, eg < 1000)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
514 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
515 for i,experiment in experiments.iterrows():
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
516 if experiment[independentVariables].any():
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
517 results = runModel(experiment, data, dependentVariable, independentVariables, regressionType = 'ols')
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
518 experiments.loc[i,'r2adj'] = results.rsquared_adj
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
519 experiments.loc[i,'condNum'] = results.condition_number
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
520 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
521 experiments.loc[i,'nobs'] = int(results.nobs)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
522 return experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
523
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
524 def generateExperiments(independentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
525 '''Generates all possible models for including or not each independent variable'''
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
526 from pandas import DataFrame
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
527 experiments = {}
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
528 nIndependentVariables = len(independentVariables)
669
df6be882f325 bug corrected
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 668
diff changeset
529 if nIndependentVariables != len(set(independentVariables)):
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
530 print("Duplicate variables. Exiting")
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
531 import sys
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
532 sys.exit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
533 nModels = 2**nIndependentVariables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
534 for i,var in enumerate(independentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
535 pattern = [False]*(2**i)+[True]*(2**i)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
536 experiments[var] = pattern*(2**(nIndependentVariables-i-1))
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
537 experiments = DataFrame(experiments)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
538 experiments['r2adj'] = 0.
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
539 experiments['condNum'] = NaN
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
540 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
541 experiments['nobs'] = -1
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
542 return experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
543
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
544 def findBestModel(data, dependentVariable, independentVariables, regressionType = 'ols', nProcesses = 1):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
545 '''Generates all possible model with the independentVariables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
546 and runs them, saving the results in experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
547 with multiprocess option'''
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
548 from pandas import concat
671
849f5f8bf4b9 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 670
diff changeset
549 from multiprocessing import Pool
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
550 experiments = generateExperiments(independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
551 nModels = len(experiments)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
552 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
553 print("IndependentVariables: {}".format(independentVariables))
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
554 if nProcesses == 1:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
555 return runModels(experiments, data, dependentVariable, independentVariables, regressionType)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
556 else:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
557 pool = Pool(processes = nProcesses)
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
558 chunkSize = int(ceil(nModels/nProcesses))
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
559 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
560 return concat([job.get() for job in jobs])
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
561
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
562 def findBestModelFwd(data, dependentVariable, independentVariables, modelFunc, experiments = None):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
563 '''Forward search for best model (based on adjusted R2)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
564 Randomly starting with one variable and adding randomly variables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
565 if they improve the model
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
566
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
567 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
568 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
569 to the binary code derived from the independent variables'''
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
570 from numpy.random import permutation as nppermutation
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
571 if experiments is None:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
572 experiments = generateExperiments(independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
573 nIndependentVariables = len(independentVariables)
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
574 permutation = nppermutation(range(nIndependentVariables)).tolist()
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
575 variableMapping = {j: independentVariables[i] for i,j in enumerate(permutation)}
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
576 print('Tested variables '+', '.join([variableMapping[i] for i in xrange(nIndependentVariables)]))
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
577 bestModel = [False]*nIndependentVariables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
578 currentVarNum = 0
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
579 currentR2Adj = 0.
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
580 for currentVarNum in xrange(nIndependentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
581 currentModel = [i for i in bestModel]
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
582 currentModel[currentVarNum] = True
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
583 rowIdx = sum([0]+[2**i for i in xrange(nIndependentVariables) if currentModel[permutation[i]]])
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
584 #print currentVarNum, sum(currentModel), ', '.join([independentVariables[i] for i in xrange(nIndependentVariables) if currentModel[permutation[i]]])
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
585 if experiments.loc[rowIdx, 'shapiroP'] < 0:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
586 modelStr = modelString(experiments.loc[rowIdx], dependentVariable, independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
587 model = modelFunc(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
588 results = model.fit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
589 experiments.loc[rowIdx, 'r2adj'] = results.rsquared_adj
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
590 experiments.loc[rowIdx, 'condNum'] = results.condition_number
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
591 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
592 experiments.loc[rowIdx, 'nobs'] = int(results.nobs)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
593 if currentR2Adj < experiments.loc[rowIdx, 'r2adj']:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
594 currentR2Adj = experiments.loc[rowIdx, 'r2adj']
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
595 bestModel[currentVarNum] = True
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
596 return experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
597
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
598 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
599 import statsmodels.api as sm
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
600 '''Displays some model results
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
601
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
602 3 graphics, true-predicted, residuals-predicted, '''
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
603 print(results.summary())
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
604 shapiroResult = shapiro(results.resid)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
605 print(shapiroResult)
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
606 if plotFigures:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
607 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
608 if model is not None:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
609 ax = fig.add_subplot(3,1,1)
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
610 plt.plot(results.predict(), model.endog, 'x')
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
611 x=plt.xlim()
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
612 y=plt.ylim()
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
613 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
614 #plt.axis('equal')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
615 if text is not None:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
616 plt.title(text['title-shapiro'].format(*shapiroResult))
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
617 #plt.title(text['true-predicted.title'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
618 plt.xlabel(text['true-predicted.xlabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
619 plt.ylabel(text['true-predicted.ylabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
620 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
621 plt.plot(results.predict(), results.resid, 'x')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
622 nextSubplotNum = 3
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
623 else:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
624 fig.add_subplot(2,1,1)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
625 plt.plot(results.predict(), results.resid, 'x')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
626 nextSubplotNum = 2
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
627 if text is not None:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
628 if model is None:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
629 plt.title(text['title-shapiro'].format(*shapiroResult))
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
630 plt.xlabel(text['residuals-predicted.xlabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
631 plt.ylabel(text['residuals-predicted.ylabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
632 qqAx = fig.add_subplot(nextSubplotNum,1,nextSubplotNum)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
633 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
634 plt.axis('equal')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
635 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
636 plt.xlabel(text['qqplot.xlabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
637 plt.ylabel(text['qqplot.ylabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
638 plt.tight_layout()
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
639 if filenamePrefix is not None:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
640 from storage import openCheck
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
641 out = openCheck(filenamePrefix+'-coefficients.html', 'w')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
642 out.write(results.summary().as_html())
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
643 plt.savefig(filenamePrefix+'-model-results.'+figureFileType)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
644
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
645 #########################
455
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
646 # iterable section
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
647 #########################
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
648
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
649 def mostCommon(L):
456
825e5d49325d slight update
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 455
diff changeset
650 '''Returns the most frequent element in a iterable
825e5d49325d slight update
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 455
diff changeset
651
825e5d49325d slight update
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 455
diff changeset
652 taken from http://stackoverflow.com/questions/1518522/python-most-common-element-in-a-list'''
455
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
653 from itertools import groupby
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
654 from operator import itemgetter
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
655 # get an iterable of (item, iterable) pairs
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
656 SL = sorted((x, i) for i, x in enumerate(L))
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
657 # print 'SL:', SL
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
658 groups = groupby(SL, key=itemgetter(0))
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
659 # auxiliary function to get "quality" for an item
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
660 def _auxfun(g):
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
661 item, iterable = g
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
662 count = 0
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
663 min_index = len(L)
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
664 for _, where in iterable:
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
665 count += 1
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
666 min_index = min(min_index, where)
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
667 # print 'item %r, count %r, minind %r' % (item, count, min_index)
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
668 return count, -min_index
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
669 # pick the highest-count/earliest item
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
670 return max(groups, key=_auxfun)[0]
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
671
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
672 #########################
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
673 # sequence section
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
674 #########################
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
675
665
15e244d2a1b5 corrected bug with circular import for VideoFilenameAddable, moved to base module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 659
diff changeset
676 class LCSS(object):
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
677 '''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
678 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
679
cdee6a3a47b4 allowing alternate database and filename for classify-objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 680
diff changeset
680 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
681 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
682 ie compute and computeXX methods'''
689
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
683 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
684 '''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
685 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
686
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
687 eg distance(p1, p2) < epsilon
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
688
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
689 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
690 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
691 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
692 import sys
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
693 sys.exit()
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
694 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
695 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
696 import sys
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
697 sys.exit()
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
698 else:
741
5b91b8d97cf3 corrected bug
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 739
diff changeset
699 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
700 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
701 self.similarityFunc = similarityFunc
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
702 self.metric = metric
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
703 self.epsilon = epsilon
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
704 self.aligned = aligned
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
705 self.delta = delta
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
706 self.lengthFunc = lengthFunc
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
707 self.subSequenceIndices = [(0,0)]
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
708
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
709 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
710 n1 = len(l1)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
711 n2 = len(l2)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
712 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
713 if self.similarityFunc is not None:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
714 for i in xrange(1,n1+1):
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
715 for j in xrange(max(1,i-jshift-self.delta),min(n2,i-jshift+self.delta)+1):
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
716 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
717 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
718 else:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
719 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
720 elif self.metric is not None:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
721 similarElements = distance.cdist(l1, l2, self.metric) <= self.epsilon
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
722 for i in xrange(1,n1+1):
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
723 for j in xrange(max(1,i-jshift-self.delta),min(n2,i-jshift+self.delta)+1):
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
724 if similarElements[i-1, j-1]:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
725 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
726 else:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
727 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
728
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
729
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
730 def subSequence(self, i, j):
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
731 '''Returns the subsequence of two sequences
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
732 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
733 if i == 0 or j == 0:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
734 return []
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
735 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
736 return self.subSequence(i, j-1)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
737 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
738 return self.subSequence(i-1, j)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
739 else:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
740 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
741
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
742 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
743 '''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
744 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
745 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
746 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
747
607
84690dfe5560 add some functions for behaviour analysis
MohamedGomaa
parents: 574
diff changeset
748 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
749 '''
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
750 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
751 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
752 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
753 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
754 else:
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
755 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
756 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
757 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
758 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
759 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
760
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
761 if self.aligned:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
762 lcssValues = {}
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
763 similarityTables = {}
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
764 for i in xrange(-n2-self.delta+1, n1+self.delta): # interval such that [i-shift-delta, i-shift+delta] is never empty, which happens when i-shift+delta < 1 or when i-shift-delta > n2
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
765 self.similarities(l1, l2, i)
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
766 lcssValues[i] = self.similarityTable.max()
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
767 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
768 #print self.similarityTable
521
3707eeb20f25 changed argMaxDict name to argmaxDict
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 518
diff changeset
769 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
770 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
771 else:
389
6d26dcc7bba0 modifications to compute alignment for None indicators
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
772 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
773 self.similarities(l1, l2)
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
774
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
775 # 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
776 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
777
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
778 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
779 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
780 if revertIndices:
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
781 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
782 return self.similarityTable[-1,-1]
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
783
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
784 def compute(self, l1, l2, computeSubSequence = False):
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
785 '''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
786 return self._compute(l1, l2, computeSubSequence)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
787
375
2ea8584aa80a making indicator LCSS work
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 374
diff changeset
788 def computeAlignment(self):
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
789 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
790
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
791 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
792 ''' compute the normalized LCSS
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
793 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
794 lengthFunc = lambda x,y:float(x,y)/2'''
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
795 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
796
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
797 def computeNormalized(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
798 return self._computeNormalized(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
799
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
800 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
801 ''' compute the LCSS distance'''
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
802 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
803
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
804 def computeDistance(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
805 return self._computeDistance(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
806
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
807 #########################
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
808 # plotting section
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
809 #########################
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
810
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
811 def plotPolygon(poly, options = ''):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
812 'Plots shapely polygon poly'
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
813 from numpy.core.multiarray import array
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
814 from matplotlib.pyplot import plot
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
815 from shapely.geometry import Polygon
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
816
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
817 tmp = array(poly.exterior)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
818 plot(tmp[:,0], tmp[:,1], options)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
819
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
820 def stepPlot(X, firstX, lastX, initialCount = 0, increment = 1):
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
821 '''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
822 returns the lists that can be plotted
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
823 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
824 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
825
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
826 sortedX = []
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
827 counts = [initialCount]
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
828 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
829 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
830 counts.append(counts[-1])
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
831 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
832 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
833 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
834
665
15e244d2a1b5 corrected bug with circular import for VideoFilenameAddable, moved to base module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 659
diff changeset
835 class PlottingPropertyValues(object):
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
836 def __init__(self, values):
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
837 self.values = values
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
838
116
2bf5b76320c0 moved intersection plotting and added markers for scatter plots
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 115
diff changeset
839 def __getitem__(self, i):
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
840 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
841
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
842 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
843 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
844
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
845 linestyles = PlottingPropertyValues(['-', '--', '-.', ':'])
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
846
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
847 colors = PlottingPropertyValues('brgmyck') # 'w'
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
848
115
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
849 def plotIndicatorMap(indicatorMap, squareSize, masked = True, defaultValue=-1):
65
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
850 from matplotlib.pyplot import pcolor
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
851 coords = array(indicatorMap.keys())
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
852 minX = min(coords[:,0])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
853 minY = min(coords[:,1])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
854 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
855 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
856 C = defaultValue*ones((len(Y), len(X)))
65
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
857 for k,v in indicatorMap.iteritems():
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
858 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
859 if masked:
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
860 pcolor(X, Y, ma.masked_where(C==defaultValue,C))
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
861 else:
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
862 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
863
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
864 #########################
637
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
865 # Data download
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
866 #########################
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
867
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
868 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
869 '''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
870 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
871 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
872
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
873 Example: MONTREAL MCTAVISH 10761
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
874 MONTREALPIERRE ELLIOTT TRUDEAU INTL A 5415
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
875
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
876 To get daily data for 2010 and 2011, downloadECWeather(10761, [2010,2011], [], '/tmp')
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
877 To get hourly data for 2009 and 2012, January, March and October, downloadECWeather(10761, [2009,2012], [1,3,10], '/tmp')'''
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
878 import urllib2
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
879 if english:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
880 language = 'e'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
881 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
882 language = 'f'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
883 if len(months) == 0:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
884 timeFrame = 2
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
885 months = [1]
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
886 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
887 timeFrame = 1
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
888
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
889 for year in years:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
890 for month in months:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
891 url = urllib2.urlopen('http://climat.meteo.gc.ca/climateData/bulkdata_{}.html?format=csv&stationID={}&Year={}&Month={}&Day=1&timeframe={}&submit=++T%C3%A9l%C3%A9charger+%0D%0Ades+donn%C3%A9es'.format(language, stationID, year, month, timeFrame))
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
892 data = url.read()
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
893 outFilename = '{}/{}-{}'.format(outputDirectoryname, stationID, year)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
894 if timeFrame == 1:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
895 outFilename += '-{}-hourly'.format(month)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
896 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
897 outFilename += '-daily'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
898 outFilename += '.csv'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
899 out = open(outFilename, 'w')
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
900 out.write(data)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
901 out.close()
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
902
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
903 #########################
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
904 # File I/O
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
905 #########################
24
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
906
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
907 def removeExtension(filename, delimiter = '.'):
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
908 '''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
909 i = filename.rfind(delimiter)
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
910 if i>0:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
911 return filename[:i]
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
912 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
913 return filename
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
914
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
915 def cleanFilename(s):
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
916 'cleans filenames obtained when contatenating figure characteristics'
739
25e78d756823 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 737
diff changeset
917 return s.replace(' ','-').replace('.','').replace('/','-').replace(',','')
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
918
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
919 def listfiles(dirname, extension, remove = False):
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
920 '''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
921 If remove is True, the filenames are stripped from the extension'''
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
922 from os import listdir
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
923 tmp = [f for f in listdir(dirname) if f.endswith(extension)]
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
924 tmp.sort()
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
925 if remove:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
926 return [removeExtension(f, extension) for f in tmp]
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
927 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
928 return tmp
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
929
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
930 def mkdir(dirname):
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
931 'Creates a directory if it does not exist'
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
932 import os
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
933 if not os.path.exists(dirname):
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
934 os.mkdir(dirname)
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
935 else:
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
936 print(dirname+' already exists')
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
937
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
938 def removeFile(filename):
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
939 '''Deletes the file while avoiding raising an error
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
940 if the file does not exist'''
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
941 import os
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
942 if (os.path.exists(filename)):
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
943 os.remove(filename)
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
944 else:
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
945 print(filename+' does not exist')
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
946
42
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
947 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
948 '''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
949 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
950
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
951 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
952 '''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
953 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
954
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
955 #########################
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
956 # CLI utils
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
957 #########################
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
958
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
959 def parseCLIOptions(helpMessage, options, cliArgs, optionalOptions=[]):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
960 ''' Simple function to handle similar argument parsing
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
961 Returns the dictionary of options and their values
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
962
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
963 * cliArgs are most likely directly sys.argv
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
964 (only the elements after the first one are considered)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
965
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
966 * options should be a list of strings for getopt options,
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
967 eg ['frame=','correspondences=','video=']
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
968 A value must be provided for each option, or the program quits'''
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
969 import sys, getopt
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
970 from numpy.core.fromnumeric import all
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
971 optionValues, args = getopt.getopt(cliArgs[1:], 'h', ['help']+options+optionalOptions)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
972 optionValues = dict(optionValues)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
973
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
974 if '--help' in optionValues.keys() or '-h' in optionValues.keys():
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
975 print(helpMessage+
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
976 '\n - Compulsory options: '+' '.join([opt.replace('=','') for opt in options])+
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
977 '\n - Non-compulsory options: '+' '.join([opt.replace('=','') for opt in optionalOptions]))
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
978 sys.exit()
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
979
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
980 missingArgument = [('--'+opt.replace('=','') in optionValues.keys()) for opt in options]
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
981 if not all(missingArgument):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
982 print('Missing argument')
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
983 print(optionValues)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
984 sys.exit()
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
985
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
986 return optionValues
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
987
397
b36b00dd27c3 added function to read scene metadata
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 395
diff changeset
988
b36b00dd27c3 added function to read scene metadata
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 395
diff changeset
989 #########################
553
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
990 # Profiling
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
991 #########################
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
992
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
993 def analyzeProfile(profileFilename, stripDirs = True):
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
994 '''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
995
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
996 obtained by for example:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
997 - 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
998 import cProfile, os
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
999 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
1000
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1001 - or on the command line:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1002 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
1003 import pstats, os
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1004 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
1005 if stripDirs:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1006 p.strip_dirs()
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1007 p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1008 p.print_stats(.2)
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1009 #p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1010 # 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
1011 return p
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1012
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1013 #########################
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1014 # running tests
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1015 #########################
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1016
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1017 if __name__ == "__main__":
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1018 import doctest
2
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
1019 import unittest
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1020 suite = doctest.DocFileSuite('tests/utils.txt')
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1021 #suite = doctest.DocTestSuite()
2
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
1022 unittest.TextTestRunner().run(suite)
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
1023 #doctest.testmod()
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1024 #doctest.testfile("example.txt")