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annotate python/utils.py @ 373:d0b86ed50f32

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work in progress on LCSS
author Nicolas Saunier <nicolas.saunier@polymtl.ca>
date Tue, 16 Jul 2013 17:45:07 -0400
parents 349eb1e09f45
children a7af3519687e
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1 #! /usr/bin/env python
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2 ''' Generic utilities.'''
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3
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4 #from numpy import *
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5 #from pylab import *
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6
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7 __metaclass__ = type
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8
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9 commentChar = '#'
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11 delimiterChar = '%';
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12
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13 #########################
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14 # Enumerations
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15 #########################
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16
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17 def inverseEnumeration(l):
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18 'Returns the dictionary that provides for each element in the input list its index in the input list'
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19 result = {}
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20 for i,x in enumerate(l):
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21 result[x] = i
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22 return result
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23
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24 #########################
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25 # simple statistics
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26 #########################
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27
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28 def confidenceInterval(mean, stdev, nSamples, percentConfidence, printLatex = False):
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29 from math import sqrt
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30 from scipy.stats.distributions import norm
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31 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1)*100)/100. # 1.-(100-percentConfidence)/200.
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32 e = k*stdev/sqrt(nSamples)
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33 if printLatex:
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34 print('${0} \pm {1}\\frac{{{2}}}{{\sqrt{{{3}}}}}$'.format(mean, k, stdev, nSamples))
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35 return mean-e, mean+e
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36
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37 def computeChi2(expected, observed):
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38 '''Returns the Chi2 statistics'''
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39 result = 0.
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40 for e, o in zip(expected, observed):
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41 result += ((e-o)*(e-o))/e
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42 return result
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43
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44 class EmpiricalDistribution:
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45 def nSamples(self):
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46 return sum(self.counts)
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47
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48 def cumulativeDensityFunction(sample):
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49 '''Returns the cumulative density function of the sample of a random variable'''
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50 from numpy.core.multiarray import array
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51 from numpy.lib.function_base import unique
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52 from numpy.core.fromnumeric import sum
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53 a = array(sample)
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54 a.sort()
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55 xaxis = unique(a)
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56 counts = [sum(a <= x) for x in xaxis]
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57 return xaxis, counts
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58
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59 class EmpiricalDiscreteDistribution(EmpiricalDistribution):
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60 '''Class to represent a sample of a distribution for a discrete random variable
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61 '''
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62 from numpy.core.fromnumeric import sum
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63
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64 def __init__(self, categories, counts):
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65 self.categories = categories
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66 self.counts = counts
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67
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68 def mean(self):
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69 result = [float(x*y) for x,y in zip(self.categories, self.counts)]
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70 return sum(result)/self.nSamples()
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71
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72 def var(self, mean = None):
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73 if not mean:
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74 m = self.mean()
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75 else:
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76 m = mean
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77 result = 0.
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78 squares = [float((x-m)*(x-m)*y) for x,y in zip(self.categories, self.counts)]
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79 return sum(squares)/(self.nSamples()-1)
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80
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81 def referenceCounts(self, probability):
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82 '''probability is a function that returns the probability of the random variable for the category values'''
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83 refProba = [probability(c) for c in self.categories]
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84 refProba[-1] = 1-sum(refProba[:-1])
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85 refCounts = [r*self.nSamples() for r in refProba]
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86 return refCounts, refProba
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87
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88 class EmpiricalContinuousDistribution(EmpiricalDistribution):
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89 '''Class to represent a sample of a distribution for a continuous random variable
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90 with the number of observations for each interval
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91 intervals (categories variable) are defined by their left limits, the last one being the right limit
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92 categories contain therefore one more element than the counts'''
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93 def __init__(self, categories, counts):
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94 # todo add samples for initialization and everything to None? (or setSamples?)
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95 self.categories = categories
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96 self.counts = counts
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97
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98 def mean(self):
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99 result = 0.
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100 for i in range(len(self.counts)-1):
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101 result += self.counts[i]*(self.categories[i]+self.categories[i+1])/2
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102 return result/self.nSamples()
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103
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104 def var(self, mean = None):
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105 if not mean:
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106 m = self.mean()
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107 else:
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108 m = mean
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109 result = 0.
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110 for i in range(len(self.counts)-1):
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111 mid = (self.categories[i]+self.categories[i+1])/2
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112 result += self.counts[i]*(mid - m)*(mid - m)
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113 return result/(self.nSamples()-1)
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114
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115 def referenceCounts(self, cdf):
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116 '''cdf is a cumulative distribution function
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117 returning the probability of the variable being less that x'''
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118 # refCumulativeCounts = [0]#[cdf(self.categories[0][0])]
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119 # for inter in self.categories:
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120 # refCumulativeCounts.append(cdf(inter[1]))
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121 refCumulativeCounts = [cdf(x) for x in self.categories[1:-1]]
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122
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123 refProba = [refCumulativeCounts[0]]
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124 for i in xrange(1,len(refCumulativeCounts)):
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125 refProba.append(refCumulativeCounts[i]-refCumulativeCounts[i-1])
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126 refProba.append(1-refCumulativeCounts[-1])
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127 refCounts = [p*self.nSamples() for p in refProba]
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128
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129 return refCounts, refProba
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130
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131 def printReferenceCounts(self, refCounts=None):
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132 if refCounts:
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133 ref = refCounts
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134 else:
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135 ref = self.referenceCounts
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136 for i in xrange(len(ref[0])):
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137 print('{0}-{1} & {2:0.3} & {3:0.3} \\\\'.format(self.categories[i],self.categories[i+1],ref[1][i], ref[0][i]))
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138
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139
31
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140 #########################
370
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141 # maths section
27
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142 #########################
24
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143
370
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144 def argMaxDict(d):
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145 return max(d.iterkeys(), key=(lambda key: d[key]))
279
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146
248
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147 def framesToTime(nFrames, frameRate, initialTime = (0.,0.,0.)):
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148 'returns hour, minutes and seconds'
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149 from math import floor
261
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150 from datetime import time
262
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151 seconds = int(floor(float(nFrames)/float(frameRate))+initialTime[0]*3600+initialTime[1]*60+initialTime[2])
261
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152 h = int(floor(seconds/3600.))
248
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153 seconds = seconds - h*3600
261
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154 m = int(floor(seconds/60))
248
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155 seconds = seconds - m*60
262
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156 return time(h, m, seconds)
248
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157
241
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158 def sortXY(X,Y):
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159 'returns the sorted (x, Y(x)) sorted on X'
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160 D = {}
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161 for x, y in zip(X,Y):
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162 D[x]=y
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163 xsorted = sorted(D.keys())
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164 return xsorted, [D[x] for x in xsorted]
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165
32
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166 def ceilDecimals(v, nDecimals):
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167 '''Rounds the number at the nth decimal
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168 eg 1.23 at 0 decimal is 2, at 1 decimal is 1.3'''
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169 from math import ceil,pow
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170 tens = pow(10,nDecimals)
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171 return ceil(v*tens)/tens
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172
152
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173 def inBetween(bound1, bound2, x):
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174 return bound1 <= x <= bound2 or bound2 <= x<= bound1
24
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175
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176 def crossProduct(l1, l2):
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177 return l1[0]*l2[1]-l1[1]*l2[0]
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178
29
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179 def filterMovingWindow(input, halfWidth):
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180 '''Returns an array obtained after the smoothing of the input by a moving average
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181 The first and last points are copied from the original.'''
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182 width = float(halfWidth*2+1)
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183 win = ones(width,'d')
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184 result = convolve(win/width,array(inputSignal),'same')
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185 result[:halfWidth] = inputSignal[:halfWidth]
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186 result[-halfWidth:] = inputSignal[-halfWidth:]
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187 return result
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188
199
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189 def linearRegression(x, y, deg = 1, plotData = False):
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190 '''returns the least square estimation of the linear regression of y = ax+b
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191 as well as the plot'''
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192 from numpy.lib.polynomial import polyfit
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193 from matplotlib.pyplot import plot
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194 from numpy.core.multiarray import arange
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195 coef = polyfit(x, y, deg)
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196 if plotData:
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197 def poly(x):
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198 result = 0
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199 for i in range(len(coef)):
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200 result += coef[i]*x**(len(coef)-i-1)
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201 return result
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202 plot(x, y, 'x')
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203 xx = arange(min(x), max(x),(max(x)-min(x))/1000)
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204 plot(xx, [poly(z) for z in xx])
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205 return coef
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206
27
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207 #########################
370
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208 # sequence section
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209 #########################
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210
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211 class LCSS:
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212 '''Class that keeps the LCSS parameters
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213 and puts together the various computations'''
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214 def __init__(self, similarityFunc, delta = float('inf'), aligned = False, lengthFunc = min):
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215 self.similarityFunc = similarityFunc
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216 self.aligned = aligned
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217 self.delta = delta
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218 self.lengthFunc = lengthFunc
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219 self.alignmentShift = 0
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220
373
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221 def similarities(self, l1, l2, jshift=0):
370
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222 from numpy import zeros, int as npint
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223 n1 = len(l1)
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224 n2 = len(l2)
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225 self.similarityTable = zeros((n1+1,n2+1), dtype = npint)
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226 for i in xrange(1,n1+1):
373
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diff changeset
227 for j in xrange(max(1,i-jshift-self.delta),min(n2+1,i-jshift+self.delta+1)):
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diff changeset
228 print max(1,i-jshift-self.delta),min(n2+1,i-jshift+self.delta+1)
370
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diff changeset
229 if self.similarityFunc(l1[i-1], l2[j-1]):
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diff changeset
230 self.similarityTable[i,j] = self.similarityTable[i-1,j-1]+1
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diff changeset
231 else:
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232 self.similarityTable[i,j] = max(self.similarityTable[i-1,j], self.similarityTable[i,j-1])
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233
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234 def subSequence(self, i, j):
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235 '''Returns the subsequence of two sequences
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236 http://en.wikipedia.org/wiki/Longest_common_subsequence_problem'''
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diff changeset
237 if i == 0 or j == 0:
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238 return []
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239 elif self.similarityTable[i][j] == self.similarityTable[i][j-1]:
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240 return self.subSequence(i, j-1)
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diff changeset
241 elif self.similarityTable[i][j] == self.similarityTable[i-1][j]:
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242 return self.subSequence(i-1, j)
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243 else:
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244 return self.subSequence(i-1, j-1) + [(i-1,j-1)]
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245
373
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diff changeset
246 # def computeLCSS(self, l1, l2, computeSubSequence = False):
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247 # '''returns the longest common subsequence similarity
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248 # based on the threshold on distance between two elements of lists l1, l2
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249 # similarityFunc returns True or False whether the two points are considered similar
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250
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251 # eg distance(p1, p2) < epsilon
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252 # '''
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diff changeset
253 # #from numpy import argmax
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254 # self.similarities(l1, l2)
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diff changeset
255 # #self.similarityTable = self.similarityTable[:, :min(len(l2), len(l1)+self.delta)+1]
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diff changeset
256 # if computeSubSequence:
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diff changeset
257 # self.subSequenceIndices = self.subSequence(len(l1), len(l2))
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258 # return self.similarityTable.max()
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259
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diff changeset
260 def _compute(self, _l1, _l2, computeSubSequence = False):
370
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diff changeset
261 '''returns the longest common subsequence similarity
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diff changeset
262 based on the threshold on distance between two elements of lists l1, l2
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diff changeset
263 similarityFunc returns True or False whether the two points are considered similar
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diff changeset
264
373
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diff changeset
265 if aligned, returns the best matching if using a finite delta by shiftinig the series alignments
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diff changeset
266
370
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267 eg distance(p1, p2) < epsilon
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diff changeset
268 '''
372
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diff changeset
269 if len(_l2) < len(_l1): # l1 is the shortest
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diff changeset
270 l1 = _l2
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parents: 371
diff changeset
271 l2 = _l1
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parents: 371
diff changeset
272 revertIndices = True
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parents: 371
diff changeset
273 else:
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parents: 371
diff changeset
274 l1 = _l1
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parents: 371
diff changeset
275 l2 = _l2
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parents: 371
diff changeset
276 revertIndices = False
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parents: 371
diff changeset
277 n1 = len(l1)
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parents: 371
diff changeset
278 n2 = len(l2)
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parents: 371
diff changeset
279
370
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parents: 369
diff changeset
280 if self.aligned:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
281 lcssValues = {}
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parents: 369
diff changeset
282 similarityTables = {}
373
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
283 for i in xrange(-n1-self.delta-1, +max(n1,n2)+self.delta): # larger interval
371
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parents: 370
diff changeset
284 #print l1[min(-i-1,n1):] # min(n1+n2-i,n1)
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parents: 370
diff changeset
285 #print l2[max(0,i-n1):]
372
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parents: 371
diff changeset
286 #lcssValues[i] = self.computeLCSS(l1[min(-i-1,n1):], l2[max(0,i-n1):])
371
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parents: 370
diff changeset
287 #print i, lcssValues[i]
373
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
288 self.similarities(l1, l2, i)
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parents: 372
diff changeset
289 lcssValues[i] = self.similarityTable.max()
370
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parents: 369
diff changeset
290 similarityTables[i] = self.similarityTable
372
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parents: 371
diff changeset
291 print self.similarityTable
373
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
292 self.alignmentShift = argMaxDict(lcssValues) # ideally get the medium alignment shift, the one that minimizes distance
372
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diff changeset
293 self.similarityTable = similarityTables[self.alignmentShift]
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parents: 371
diff changeset
294 else:
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diff changeset
295 self.alignmentShift = 0
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parents: 371
diff changeset
296 self.similarities(l1, l2)
373
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parents: 372
diff changeset
297
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parents: 372
diff changeset
298 self.similarityTable = self.similarityTable[:, :min(len(l2), len(l1)+self.delta-self.alignmentShift)+1]
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parents: 372
diff changeset
299
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
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parents: 371
diff changeset
300 if computeSubSequence:
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diff changeset
301 self.subSequenceIndices = self.subSequence(self.similarityTable.shape[0]-1, self.similarityTable.shape[1]-1)
371
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diff changeset
302 if revertIndices:
372
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parents: 371
diff changeset
303 self.subSequenceIndices = [(j+self.alignmentShift,i) for i,j in self.subSequenceIndices]
371
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parents: 370
diff changeset
304 else:
372
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parents: 371
diff changeset
305 self.subSequenceIndices = [(i+self.alignmentShift,j) for i,j in self.subSequenceIndices]
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parents: 371
diff changeset
306 return self.similarityTable[-1,-1]
370
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parents: 369
diff changeset
307
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diff changeset
308 def compute(self, l1, l2, computeSubSequence = False):
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parents: 369
diff changeset
309 '''get methods are to be shadowed in child classes '''
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diff changeset
310 return self._compute(l1, l2, computeSubSequence)
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parents: 369
diff changeset
311
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diff changeset
312 def computeAlignement(self):
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parents: 369
diff changeset
313 from numpy import mean
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parents: 369
diff changeset
314 return mean([j-i for i,j in self.subSequenceIndices])+self.alignmentShift
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parents: 369
diff changeset
315
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parents: 369
diff changeset
316 def _computeNormalized(self, l1, l2):
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parents: 369
diff changeset
317 ''' compute the normalized LCSS
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parents: 369
diff changeset
318 ie, the LCSS divided by the min or mean of the indicator lengths (using lengthFunc)
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parents: 369
diff changeset
319 lengthFunc = lambda x,y:float(x,y)/2'''
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parents: 369
diff changeset
320 return float(self.compute(l1, l2))/self.lengthFunc(len(l1), len(l2))
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parents: 369
diff changeset
321
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diff changeset
322 def computeNormalized(self, l1, l2):
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parents: 369
diff changeset
323 return self._computeNormalized(l1, l2)
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parents: 369
diff changeset
324
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diff changeset
325 def _computeDistance(self, l1, l2):
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parents: 369
diff changeset
326 ''' compute the LCSS distance'''
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parents: 369
diff changeset
327 return 1-self.computeNormalized(l1, l2)
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diff changeset
328
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diff changeset
329 def computeDistance(self, l1, l2):
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parents: 369
diff changeset
330 return self._computeDistance(l1, l2)
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parents: 369
diff changeset
331
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parents: 369
diff changeset
332 #########################
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
333 # plotting section
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parents: 42
diff changeset
334 #########################
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parents: 42
diff changeset
335
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
336 def plotPolygon(poly, options = ''):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
337 'Plots shapely polygon poly'
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
338 from numpy.core.multiarray import array
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parents: 324
diff changeset
339 from matplotlib.pyplot import plot
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
340 from shapely.geometry import Polygon
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
341
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
342 tmp = array(poly.exterior)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
343 plot(tmp[:,0], tmp[:,1], options)
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
344
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
345 def stepPlot(X, firstX, lastX, initialCount = 0, increment = 1):
99ca91a46007 minor change
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parents: 323
diff changeset
346 '''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
347 returns the lists that can be plotted
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
348 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
349 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)
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parents: 286
diff changeset
350
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
351 sortedX = []
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
352 counts = [initialCount]
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
353 for x in sorted(X):
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
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parents: 286
diff changeset
354 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
355 counts.append(counts[-1])
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
356 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
357 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
358 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
359
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
360 class PlottingPropertyValues:
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
361 def __init__(self, values):
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
362 self.values = values
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
363
116
2bf5b76320c0 moved intersection plotting and added markers for scatter plots
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 115
diff changeset
364 def __getitem__(self, i):
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
365 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
366
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
367 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
368 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
369
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
370 linestyles = PlottingPropertyValues(['-', '--', '-.', ':'])
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
371
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
372 colors = PlottingPropertyValues('brgmyck') # 'w'
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
373
115
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
374 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
375 from numpy import array, arange, ones, ma
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
376 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
377 coords = array(indicatorMap.keys())
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
378 minX = min(coords[:,0])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
379 minY = min(coords[:,1])
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
380 X = arange(minX, max(coords[:,0])+1.1)*squareSize
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
381 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
382 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
383 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
384 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
385 if masked:
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
386 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
387 else:
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
388 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
389
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
390 #########################
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
391 # file I/O section
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
392 #########################
24
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
393
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
394 def openCheck(filename, option = 'r', quit = False):
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
395 '''Open file filename in read mode by default
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
396 and checks it is open'''
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
397 try:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
398 return open(filename, option)
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
399 except IOError:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
400 print 'File %s could not be opened.' % filename
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
401 if quit:
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
402 from sys import exit
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
403 exit()
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
404 return None
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
405
48
8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 46
diff changeset
406 def readline(f, commentCharacter = commentChar):
0
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parents:
diff changeset
407 '''Modified readline function to skip comments.'''
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
408 s = f.readline()
48
8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 46
diff changeset
409 while (len(s) > 0) and s.startswith(commentCharacter):
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
410 s = f.readline()
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
411 return s.strip()
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
412
48
8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 46
diff changeset
413 def getLines(f, delimiterCharacter = delimiterChar):
8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 46
diff changeset
414 '''Gets a complete entry (all the lines) in between delimiterChar.'''
8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 46
diff changeset
415 dataStrings = []
8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils
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parents: 46
diff changeset
416 s = readline(f)
8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 46
diff changeset
417 while (len(s) > 0) and (not s.startswith(delimiterCharacter)):
8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 46
diff changeset
418 dataStrings += [s.strip()]
8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 46
diff changeset
419 s = readline(f)
8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils
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parents: 46
diff changeset
420 return dataStrings
8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 46
diff changeset
421
304
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parents: 301
diff changeset
422 class FakeSecHead(object):
20f9cd972dde added capability to parse cfg file for display-trajectories.py
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parents: 301
diff changeset
423 '''Add fake section header [asection]
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parents: 301
diff changeset
424
20f9cd972dde added capability to parse cfg file for display-trajectories.py
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 301
diff changeset
425 from http://stackoverflow.com/questions/2819696/parsing-properties-file-in-python/2819788#2819788
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parents: 301
diff changeset
426 use read_file in Python 3.2+
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parents: 301
diff changeset
427 '''
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parents: 301
diff changeset
428 def __init__(self, fp):
20f9cd972dde added capability to parse cfg file for display-trajectories.py
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parents: 301
diff changeset
429 self.fp = fp
20f9cd972dde added capability to parse cfg file for display-trajectories.py
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parents: 301
diff changeset
430 self.sechead = '[main]\n'
20f9cd972dde added capability to parse cfg file for display-trajectories.py
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parents: 301
diff changeset
431
20f9cd972dde added capability to parse cfg file for display-trajectories.py
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parents: 301
diff changeset
432 def readline(self):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 301
diff changeset
433 if self.sechead:
20f9cd972dde added capability to parse cfg file for display-trajectories.py
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 301
diff changeset
434 try: return self.sechead
20f9cd972dde added capability to parse cfg file for display-trajectories.py
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parents: 301
diff changeset
435 finally: self.sechead = None
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 301
diff changeset
436 else: return self.fp.readline()
20f9cd972dde added capability to parse cfg file for display-trajectories.py
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 301
diff changeset
437
0
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parents:
diff changeset
438 def removeExtension(filename, delimiter = '.'):
31
c000f37c316d moved tests to independent file, added chi2 computation
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parents: 29
diff changeset
439 '''Returns the filename minus the extension (all characters after last .)'''
0
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parents:
diff changeset
440 i = filename.rfind(delimiter)
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
441 if i>0:
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
442 return filename[:i]
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
443 else:
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parents:
diff changeset
444 return filename
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
445
46
b5d007612e16 added filename util
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parents: 45
diff changeset
446 def cleanFilename(s):
b5d007612e16 added filename util
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parents: 45
diff changeset
447 'cleans filenames obtained when contatenating figure characteristics'
266
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
448 return s.replace(' ','-').replace('.','').replace('/','-')
46
b5d007612e16 added filename util
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parents: 45
diff changeset
449
0
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parents:
diff changeset
450 def listfiles(dirname, extension, remove = False):
14
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
451 '''Returns the list of files with the extension in the directory dirname
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parents: 7
diff changeset
452 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
453 from os import listdir
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
454 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
455 tmp.sort()
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
456 if remove:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
457 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
458 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
459 return tmp
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
460
266
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
461 def mkdir(dirname):
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
462 'Creates a directory if it does not exist'
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
463 import os
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
464 if not os.path.exists(dirname):
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parents: 262
diff changeset
465 os.mkdir(dirname)
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
466 else:
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
467 print(dirname+' already exists')
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parents: 262
diff changeset
468
14
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
469 def removeFile(filename):
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
470 '''Deletes the file while avoiding raising an error
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
471 if the file does not exist'''
266
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
472 import os
14
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
473 if (os.path.exists(filename)):
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
474 os.remove(filename)
266
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
475 else:
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
476 print(filename+' does not exist')
14
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
477
42
1a2ac2d4f53a added loading of the rest of the data for objects
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parents: 35
diff changeset
478 def line2Floats(l, separator=' '):
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parents: 35
diff changeset
479 '''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
480 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
481
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
482 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
483 '''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
484 return [int(x) for x in l.split(separator)]
31
c000f37c316d moved tests to independent file, added chi2 computation
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parents: 29
diff changeset
485
c000f37c316d moved tests to independent file, added chi2 computation
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parents: 29
diff changeset
486 #########################
332
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
487 # CLI utils
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
488 #########################
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
489
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
490 def parseCLIOptions(helpMessage, options, cliArgs, optionalOptions=[]):
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parents: 324
diff changeset
491 ''' Simple function to handle similar argument parsing
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
492 Returns the dictionary of options and their values
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
493
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
494 * cliArgs are most likely directly sys.argv
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
495 (only the elements after the first one are considered)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
496
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
497 * options should be a list of strings for getopt options,
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
498 eg ['frame=','correspondences=','video=']
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
499 A value must be provided for each option, or the program quits'''
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
500 import sys, getopt
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
501 from numpy.core.fromnumeric import all
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
502 optionValues, args = getopt.getopt(cliArgs[1:], 'h', ['help']+options+optionalOptions)
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
503 optionValues = dict(optionValues)
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
504
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
505 if '--help' in optionValues.keys() or '-h' in optionValues.keys():
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
506 print(helpMessage+
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
507 '\n - Compulsory options: '+' '.join([opt.replace('=','') for opt in options])+
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
508 '\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
509 sys.exit()
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
510
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
511 missingArgument = [('--'+opt.replace('=','') in optionValues.keys()) for opt in options]
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
512 if not all(missingArgument):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
513 print('Missing argument')
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
514 print(optionValues)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
515 sys.exit()
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
516
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
517 return optionValues
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
518
333
c9201f6b143a moved the config parser to utils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 332
diff changeset
519 class TrackingParameters:
c9201f6b143a moved the config parser to utils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 332
diff changeset
520 def loadConfigFile(self, filename):
c9201f6b143a moved the config parser to utils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 332
diff changeset
521 from ConfigParser import ConfigParser
c9201f6b143a moved the config parser to utils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 332
diff changeset
522 from numpy import loadtxt
364
a50a69e04c2a script modification so that command line arguments take precedence over config file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 352
diff changeset
523 from os import path
a50a69e04c2a script modification so that command line arguments take precedence over config file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 352
diff changeset
524
333
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 332
diff changeset
525 config = ConfigParser()
c9201f6b143a moved the config parser to utils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 332
diff changeset
526 config.readfp(FakeSecHead(openCheck(filename)))
c9201f6b143a moved the config parser to utils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 332
diff changeset
527 self.sectionHeader = config.sections()[0]
c9201f6b143a moved the config parser to utils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 332
diff changeset
528 self.videoFilename = config.get(self.sectionHeader, 'video-filename')
c9201f6b143a moved the config parser to utils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 332
diff changeset
529 self.databaseFilename = config.get(self.sectionHeader, 'database-filename')
c9201f6b143a moved the config parser to utils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 332
diff changeset
530 self.homographyFilename = config.get(self.sectionHeader, 'homography-filename')
364
a50a69e04c2a script modification so that command line arguments take precedence over config file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 352
diff changeset
531 if (path.exists(self.homographyFilename)):
a50a69e04c2a script modification so that command line arguments take precedence over config file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 352
diff changeset
532 self.homography = loadtxt(self.homographyFilename)
a50a69e04c2a script modification so that command line arguments take precedence over config file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 352
diff changeset
533 else:
a50a69e04c2a script modification so that command line arguments take precedence over config file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 352
diff changeset
534 self.homography = None
333
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parents: 332
diff changeset
535 self.firstFrameNum = config.getint(self.sectionHeader, 'frame1')
348
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536 self.videoFrameRate = config.getfloat(self.sectionHeader, 'video-fps')
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537
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538 self.maxPredictedSpeed = config.getfloat(self.sectionHeader, 'max-predicted-speed')/3.6/self.videoFrameRate
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539 self.predictionTimeHorizon = config.getfloat(self.sectionHeader, 'prediction-time-horizon')*self.videoFrameRate
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540 self.collisionDistance = config.getfloat(self.sectionHeader, 'collision-distance')
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541 self.crossingZones = config.getboolean(self.sectionHeader, 'crossing-zones')
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542 self.predictionMethod = config.get(self.sectionHeader, 'prediction-method')
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543 self.nPredictedTrajectories = config.getint(self.sectionHeader, 'npredicted-trajectories')
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544 self.minAcceleration = config.getfloat(self.sectionHeader, 'min-acceleration')/self.videoFrameRate**2
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545 self.maxAcceleration = config.getfloat(self.sectionHeader, 'max-acceleration')/self.videoFrameRate**2
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546 self.maxSteering = config.getfloat(self.sectionHeader, 'max-steering')/self.videoFrameRate
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547 self.useFeaturesForPrediction = config.getboolean(self.sectionHeader, 'use-features-prediction')
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548
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549 #########################
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550 # sqlite
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551 #########################
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552
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553 def printDBError(error):
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554 print('DB Error: {}'.format(error))
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555
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556 def dropTables(connection, tableNames):
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557 'deletes the table with names in tableNames'
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558 import sqlite3
344
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559 try:
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560 cursor = connection.cursor()
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561 for tableName in tableNames:
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562 cursor.execute('DROP TABLE '+tableName)
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563 except sqlite3.OperationalError as error:
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564 printDBError(error)
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565
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566 #########################
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567 # running tests
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568 #########################
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569
0
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570 if __name__ == "__main__":
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571 import doctest
2
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572 import unittest
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573 suite = doctest.DocFileSuite('tests/utils.txt')
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574 #suite = doctest.DocTestSuite()
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575 unittest.TextTestRunner().run(suite)
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576 #doctest.testmod()
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577 #doctest.testfile("example.txt")