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annotate python/utils.py @ 395:6fba1ab040f1

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minor modification to framestotime
author Nicolas Saunier <nicolas.saunier@polymtl.ca>
date Fri, 26 Jul 2013 17:52:23 -0400
parents 03dbecd3a887
children b36b00dd27c3
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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 from datetime import time
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8 __metaclass__ = type
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9
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10 commentChar = '#'
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12 delimiterChar = '%';
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13
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14 #########################
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15 # Enumerations
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16 #########################
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17
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18 def inverseEnumeration(l):
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19 'Returns the dictionary that provides for each element in the input list its index in the input list'
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20 result = {}
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21 for i,x in enumerate(l):
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22 result[x] = i
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23 return result
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24
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25 #########################
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26 # simple statistics
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27 #########################
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28
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29 def confidenceInterval(mean, stdev, nSamples, percentConfidence, printLatex = False):
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30 from math import sqrt
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31 from scipy.stats.distributions import norm
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32 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1)*100)/100. # 1.-(100-percentConfidence)/200.
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33 e = k*stdev/sqrt(nSamples)
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34 if printLatex:
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35 print('${0} \pm {1}\\frac{{{2}}}{{\sqrt{{{3}}}}}$'.format(mean, k, stdev, nSamples))
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36 return mean-e, mean+e
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37
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38 def computeChi2(expected, observed):
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39 '''Returns the Chi2 statistics'''
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40 result = 0.
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41 for e, o in zip(expected, observed):
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42 result += ((e-o)*(e-o))/e
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43 return result
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44
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45 class EmpiricalDistribution:
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46 def nSamples(self):
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47 return sum(self.counts)
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48
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49 def cumulativeDensityFunction(sample):
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50 '''Returns the cumulative density function of the sample of a random variable'''
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51 from numpy.core.multiarray import array
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52 from numpy.lib.function_base import unique
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53 from numpy.core.fromnumeric import sum
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54 a = array(sample)
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55 a.sort()
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56 xaxis = unique(a)
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57 counts = [sum(a <= x) for x in xaxis]
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58 return xaxis, counts
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59
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60 class EmpiricalDiscreteDistribution(EmpiricalDistribution):
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61 '''Class to represent a sample of a distribution for a discrete random variable
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62 '''
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63 from numpy.core.fromnumeric import sum
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64
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65 def __init__(self, categories, counts):
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66 self.categories = categories
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67 self.counts = counts
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68
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69 def mean(self):
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70 result = [float(x*y) for x,y in zip(self.categories, self.counts)]
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71 return sum(result)/self.nSamples()
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72
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73 def var(self, mean = None):
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74 if not mean:
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75 m = self.mean()
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76 else:
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77 m = mean
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78 result = 0.
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79 squares = [float((x-m)*(x-m)*y) for x,y in zip(self.categories, self.counts)]
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80 return sum(squares)/(self.nSamples()-1)
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81
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82 def referenceCounts(self, probability):
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83 '''probability is a function that returns the probability of the random variable for the category values'''
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84 refProba = [probability(c) for c in self.categories]
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85 refProba[-1] = 1-sum(refProba[:-1])
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86 refCounts = [r*self.nSamples() for r in refProba]
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87 return refCounts, refProba
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88
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89 class EmpiricalContinuousDistribution(EmpiricalDistribution):
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90 '''Class to represent a sample of a distribution for a continuous random variable
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91 with the number of observations for each interval
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92 intervals (categories variable) are defined by their left limits, the last one being the right limit
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93 categories contain therefore one more element than the counts'''
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94 def __init__(self, categories, counts):
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95 # todo add samples for initialization and everything to None? (or setSamples?)
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96 self.categories = categories
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97 self.counts = counts
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98
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99 def mean(self):
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100 result = 0.
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101 for i in range(len(self.counts)-1):
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102 result += self.counts[i]*(self.categories[i]+self.categories[i+1])/2
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103 return result/self.nSamples()
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104
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105 def var(self, mean = None):
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106 if not mean:
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107 m = self.mean()
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108 else:
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109 m = mean
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110 result = 0.
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111 for i in range(len(self.counts)-1):
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112 mid = (self.categories[i]+self.categories[i+1])/2
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113 result += self.counts[i]*(mid - m)*(mid - m)
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114 return result/(self.nSamples()-1)
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115
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116 def referenceCounts(self, cdf):
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117 '''cdf is a cumulative distribution function
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118 returning the probability of the variable being less that x'''
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119 # refCumulativeCounts = [0]#[cdf(self.categories[0][0])]
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120 # for inter in self.categories:
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121 # refCumulativeCounts.append(cdf(inter[1]))
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122 refCumulativeCounts = [cdf(x) for x in self.categories[1:-1]]
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123
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124 refProba = [refCumulativeCounts[0]]
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125 for i in xrange(1,len(refCumulativeCounts)):
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126 refProba.append(refCumulativeCounts[i]-refCumulativeCounts[i-1])
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127 refProba.append(1-refCumulativeCounts[-1])
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128 refCounts = [p*self.nSamples() for p in refProba]
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129
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130 return refCounts, refProba
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131
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132 def printReferenceCounts(self, refCounts=None):
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133 if refCounts:
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134 ref = refCounts
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135 else:
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136 ref = self.referenceCounts
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diff changeset
137 for i in xrange(len(ref[0])):
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138 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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139
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140
31
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diff changeset
141 #########################
370
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diff changeset
142 # maths section
27
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diff changeset
143 #########################
24
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144
370
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diff changeset
145 def argMaxDict(d):
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diff changeset
146 return max(d.iterkeys(), key=(lambda key: d[key]))
279
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147
395
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diff changeset
148 def framesToTime(nFrames, frameRate, initialTime = time()):
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149 '''returns a datetime.time for the time in hour, minutes and seconds
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diff changeset
150 initialTime is a datetime.time'''
248
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diff changeset
151 from math import floor
261
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diff changeset
152 from datetime import time
395
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diff changeset
153 seconds = int(floor(float(nFrames)/float(frameRate))+initialTime.hour*3600+initialTime.minute*60+initialTime.second)
261
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diff changeset
154 h = int(floor(seconds/3600.))
248
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diff changeset
155 seconds = seconds - h*3600
261
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diff changeset
156 m = int(floor(seconds/60))
248
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diff changeset
157 seconds = seconds - m*60
262
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diff changeset
158 return time(h, m, seconds)
248
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diff changeset
159
381
387cc0142211 script to replay event annotations
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diff changeset
160 def timeToFrames(t, frameRate):
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161 return frameRate*(t.hour*3600+t.minute*60+t.second)
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diff changeset
162
241
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diff changeset
163 def sortXY(X,Y):
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164 'returns the sorted (x, Y(x)) sorted on X'
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165 D = {}
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166 for x, y in zip(X,Y):
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167 D[x]=y
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168 xsorted = sorted(D.keys())
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diff changeset
169 return xsorted, [D[x] for x in xsorted]
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170
32
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171 def ceilDecimals(v, nDecimals):
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172 '''Rounds the number at the nth decimal
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173 eg 1.23 at 0 decimal is 2, at 1 decimal is 1.3'''
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diff changeset
174 from math import ceil,pow
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175 tens = pow(10,nDecimals)
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diff changeset
176 return ceil(v*tens)/tens
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177
152
74b1fc68d4df re-organized code to avoid cyclic python module dependencies
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diff changeset
178 def inBetween(bound1, bound2, x):
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diff changeset
179 return bound1 <= x <= bound2 or bound2 <= x<= bound1
24
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180
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181 def crossProduct(l1, l2):
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diff changeset
182 return l1[0]*l2[1]-l1[1]*l2[0]
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183
29
ca8e716cc231 added moving average filter
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diff changeset
184 def filterMovingWindow(input, halfWidth):
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diff changeset
185 '''Returns an array obtained after the smoothing of the input by a moving average
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diff changeset
186 The first and last points are copied from the original.'''
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diff changeset
187 width = float(halfWidth*2+1)
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diff changeset
188 win = ones(width,'d')
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diff changeset
189 result = convolve(win/width,array(inputSignal),'same')
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diff changeset
190 result[:halfWidth] = inputSignal[:halfWidth]
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diff changeset
191 result[-halfWidth:] = inputSignal[-halfWidth:]
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diff changeset
192 return result
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diff changeset
193
199
ca9d9104afba added utility to calibrate polynoms and plot
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parents: 197
diff changeset
194 def linearRegression(x, y, deg = 1, plotData = False):
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diff changeset
195 '''returns the least square estimation of the linear regression of y = ax+b
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parents: 197
diff changeset
196 as well as the plot'''
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parents: 197
diff changeset
197 from numpy.lib.polynomial import polyfit
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diff changeset
198 from matplotlib.pyplot import plot
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diff changeset
199 from numpy.core.multiarray import arange
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diff changeset
200 coef = polyfit(x, y, deg)
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parents: 197
diff changeset
201 if plotData:
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parents: 197
diff changeset
202 def poly(x):
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diff changeset
203 result = 0
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diff changeset
204 for i in range(len(coef)):
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parents: 197
diff changeset
205 result += coef[i]*x**(len(coef)-i-1)
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diff changeset
206 return result
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parents: 197
diff changeset
207 plot(x, y, 'x')
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diff changeset
208 xx = arange(min(x), max(x),(max(x)-min(x))/1000)
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parents: 197
diff changeset
209 plot(xx, [poly(z) for z in xx])
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diff changeset
210 return coef
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parents: 197
diff changeset
211
27
44689029a86f updated segmentIntersection and other
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parents: 24
diff changeset
212 #########################
370
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diff changeset
213 # sequence section
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diff changeset
214 #########################
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diff changeset
215
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diff changeset
216 class LCSS:
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diff changeset
217 '''Class that keeps the LCSS parameters
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diff changeset
218 and puts together the various computations'''
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diff changeset
219 def __init__(self, similarityFunc, delta = float('inf'), aligned = False, lengthFunc = min):
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diff changeset
220 self.similarityFunc = similarityFunc
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diff changeset
221 self.aligned = aligned
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diff changeset
222 self.delta = delta
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diff changeset
223 self.lengthFunc = lengthFunc
389
6d26dcc7bba0 modifications to compute alignment for None indicators
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parents: 381
diff changeset
224 self.subSequenceIndices = [(0,0)]
370
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parents: 369
diff changeset
225
373
d0b86ed50f32 work in progress on LCSS
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diff changeset
226 def similarities(self, l1, l2, jshift=0):
370
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parents: 369
diff changeset
227 from numpy import zeros, int as npint
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diff changeset
228 n1 = len(l1)
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diff changeset
229 n2 = len(l2)
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diff changeset
230 self.similarityTable = zeros((n1+1,n2+1), dtype = npint)
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parents: 369
diff changeset
231 for i in xrange(1,n1+1):
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
232 for j in xrange(max(1,i-jshift-self.delta),min(n2,i-jshift+self.delta)+1):
370
97e8fa0ee9a1 work in progress for complete alignment
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parents: 369
diff changeset
233 if self.similarityFunc(l1[i-1], l2[j-1]):
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diff changeset
234 self.similarityTable[i,j] = self.similarityTable[i-1,j-1]+1
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diff changeset
235 else:
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diff changeset
236 self.similarityTable[i,j] = max(self.similarityTable[i-1,j], self.similarityTable[i,j-1])
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diff changeset
237
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diff changeset
238 def subSequence(self, i, j):
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diff changeset
239 '''Returns the subsequence of two sequences
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parents: 369
diff changeset
240 http://en.wikipedia.org/wiki/Longest_common_subsequence_problem'''
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parents: 369
diff changeset
241 if i == 0 or j == 0:
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parents: 369
diff changeset
242 return []
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diff changeset
243 elif self.similarityTable[i][j] == self.similarityTable[i][j-1]:
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diff changeset
244 return self.subSequence(i, j-1)
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parents: 369
diff changeset
245 elif self.similarityTable[i][j] == self.similarityTable[i-1][j]:
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diff changeset
246 return self.subSequence(i-1, j)
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parents: 369
diff changeset
247 else:
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diff changeset
248 return self.subSequence(i-1, j-1) + [(i-1,j-1)]
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parents: 369
diff changeset
249
373
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parents: 372
diff changeset
250 def _compute(self, _l1, _l2, computeSubSequence = False):
370
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diff changeset
251 '''returns the longest common subsequence similarity
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parents: 369
diff changeset
252 based on the threshold on distance between two elements of lists l1, l2
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parents: 369
diff changeset
253 similarityFunc returns True or False whether the two points are considered similar
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parents: 369
diff changeset
254
373
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parents: 372
diff changeset
255 if aligned, returns the best matching if using a finite delta by shiftinig the series alignments
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parents: 372
diff changeset
256
370
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diff changeset
257 eg distance(p1, p2) < epsilon
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parents: 369
diff changeset
258 '''
372
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parents: 371
diff changeset
259 if len(_l2) < len(_l1): # l1 is the shortest
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parents: 371
diff changeset
260 l1 = _l2
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parents: 371
diff changeset
261 l2 = _l1
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parents: 371
diff changeset
262 revertIndices = True
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parents: 371
diff changeset
263 else:
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parents: 371
diff changeset
264 l1 = _l1
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parents: 371
diff changeset
265 l2 = _l2
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parents: 371
diff changeset
266 revertIndices = False
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parents: 371
diff changeset
267 n1 = len(l1)
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parents: 371
diff changeset
268 n2 = len(l2)
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parents: 371
diff changeset
269
370
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parents: 369
diff changeset
270 if self.aligned:
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diff changeset
271 lcssValues = {}
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diff changeset
272 similarityTables = {}
374
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diff changeset
273 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
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diff changeset
274 self.similarities(l1, l2, i)
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diff changeset
275 lcssValues[i] = self.similarityTable.max()
370
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diff changeset
276 similarityTables[i] = self.similarityTable
374
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diff changeset
277 #print self.similarityTable
389
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diff changeset
278 alignmentShift = argMaxDict(lcssValues) # ideally get the medium alignment shift, the one that minimizes distance
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diff changeset
279 self.similarityTable = similarityTables[alignmentShift]
372
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diff changeset
280 else:
389
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281 alignmentShift = 0
372
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282 self.similarities(l1, l2)
373
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283
374
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284 # threshold values for the useful part of the similarity table are n2-n1-delta and n1-n2-delta
389
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diff changeset
285 self.similarityTable = self.similarityTable[:min(n1, n2+alignmentShift+self.delta)+1, :min(n2, n1-alignmentShift+self.delta)+1]
373
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286
372
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287 if computeSubSequence:
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288 self.subSequenceIndices = self.subSequence(self.similarityTable.shape[0]-1, self.similarityTable.shape[1]-1)
371
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diff changeset
289 if revertIndices:
374
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diff changeset
290 self.subSequenceIndices = [(j,i) for i,j in self.subSequenceIndices]
372
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diff changeset
291 return self.similarityTable[-1,-1]
370
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292
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293 def compute(self, l1, l2, computeSubSequence = False):
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294 '''get methods are to be shadowed in child classes '''
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295 return self._compute(l1, l2, computeSubSequence)
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296
375
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diff changeset
297 def computeAlignment(self):
370
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diff changeset
298 from numpy import mean
374
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299 return mean([j-i for i,j in self.subSequenceIndices])
370
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300
376
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diff changeset
301 def _computeNormalized(self, l1, l2, computeSubSequence = False):
370
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302 ''' compute the normalized LCSS
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303 ie, the LCSS divided by the min or mean of the indicator lengths (using lengthFunc)
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304 lengthFunc = lambda x,y:float(x,y)/2'''
376
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diff changeset
305 return float(self._compute(l1, l2, computeSubSequence))/self.lengthFunc(len(l1), len(l2))
370
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diff changeset
306
376
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diff changeset
307 def computeNormalized(self, l1, l2, computeSubSequence = False):
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diff changeset
308 return self._computeNormalized(l1, l2, computeSubSequence)
370
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diff changeset
309
376
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diff changeset
310 def _computeDistance(self, l1, l2, computeSubSequence = False):
370
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diff changeset
311 ''' compute the LCSS distance'''
376
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diff changeset
312 return 1-self._computeNormalized(l1, l2, computeSubSequence)
370
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diff changeset
313
376
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diff changeset
314 def computeDistance(self, l1, l2, computeSubSequence = False):
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diff changeset
315 return self._computeDistance(l1, l2, computeSubSequence)
370
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316
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diff changeset
317 #########################
45
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diff changeset
318 # plotting section
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diff changeset
319 #########################
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diff changeset
320
332
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diff changeset
321 def plotPolygon(poly, options = ''):
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diff changeset
322 'Plots shapely polygon poly'
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diff changeset
323 from numpy.core.multiarray import array
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diff changeset
324 from matplotlib.pyplot import plot
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diff changeset
325 from shapely.geometry import Polygon
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diff changeset
326
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diff changeset
327 tmp = array(poly.exterior)
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diff changeset
328 plot(tmp[:,0], tmp[:,1], options)
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329
324
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diff changeset
330 def stepPlot(X, firstX, lastX, initialCount = 0, increment = 1):
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diff changeset
331 '''for each value in X, increment by increment the initial count
297
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diff changeset
332 returns the lists that can be plotted
324
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diff changeset
333 to obtain a step plot increasing by one for each value in x, from first to last value
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diff changeset
334 firstX and lastX should be respectively smaller and larger than all elements in X'''
297
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diff changeset
335
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diff changeset
336 sortedX = []
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diff changeset
337 counts = [initialCount]
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diff changeset
338 for x in sorted(X):
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diff changeset
339 sortedX += [x,x]
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diff changeset
340 counts.append(counts[-1])
324
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diff changeset
341 counts.append(counts[-1]+increment)
297
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diff changeset
342 counts.append(counts[-1])
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diff changeset
343 return [firstX]+sortedX+[lastX], counts
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diff changeset
344
45
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diff changeset
345 class PlottingPropertyValues:
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diff changeset
346 def __init__(self, values):
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diff changeset
347 self.values = values
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diff changeset
348
116
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diff changeset
349 def __getitem__(self, i):
45
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diff changeset
350 return self.values[i%len(self.values)]
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diff changeset
351
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diff changeset
352 markers = PlottingPropertyValues(['+', '*', ',', '.', 'x', 'D', 's', 'o'])
116
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diff changeset
353 scatterMarkers = PlottingPropertyValues(['s','o','^','>','v','<','d','p','h','8','+','x'])
45
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diff changeset
354
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diff changeset
355 linestyles = PlottingPropertyValues(['-', '--', '-.', ':'])
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diff changeset
356
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diff changeset
357 colors = PlottingPropertyValues('brgmyck') # 'w'
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diff changeset
358
115
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diff changeset
359 def plotIndicatorMap(indicatorMap, squareSize, masked = True, defaultValue=-1):
65
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diff changeset
360 from numpy import array, arange, ones, ma
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diff changeset
361 from matplotlib.pyplot import pcolor
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diff changeset
362 coords = array(indicatorMap.keys())
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diff changeset
363 minX = min(coords[:,0])
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diff changeset
364 minY = min(coords[:,1])
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diff changeset
365 X = arange(minX, max(coords[:,0])+1.1)*squareSize
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diff changeset
366 Y = arange(minY, max(coords[:,1])+1.1)*squareSize
115
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diff changeset
367 C = defaultValue*ones((len(Y), len(X)))
65
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diff changeset
368 for k,v in indicatorMap.iteritems():
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diff changeset
369 C[k[1]-minY,k[0]-minX] = v
115
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diff changeset
370 if masked:
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diff changeset
371 pcolor(X, Y, ma.masked_where(C==defaultValue,C))
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diff changeset
372 else:
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diff changeset
373 pcolor(X, Y, C)
65
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diff changeset
374
45
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parents: 42
diff changeset
375 #########################
27
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parents: 24
diff changeset
376 # file I/O section
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parents: 24
diff changeset
377 #########################
24
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parents: 19
diff changeset
378
0
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parents:
diff changeset
379 def openCheck(filename, option = 'r', quit = False):
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parents:
diff changeset
380 '''Open file filename in read mode by default
31
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diff changeset
381 and checks it is open'''
0
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parents:
diff changeset
382 try:
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parents:
diff changeset
383 return open(filename, option)
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parents:
diff changeset
384 except IOError:
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parents:
diff changeset
385 print 'File %s could not be opened.' % filename
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parents:
diff changeset
386 if quit:
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diff changeset
387 from sys import exit
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388 exit()
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parents:
diff changeset
389 return None
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parents:
diff changeset
390
48
8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils
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parents: 46
diff changeset
391 def readline(f, commentCharacter = commentChar):
0
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parents:
diff changeset
392 '''Modified readline function to skip comments.'''
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parents:
diff changeset
393 s = f.readline()
48
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diff changeset
394 while (len(s) > 0) and s.startswith(commentCharacter):
0
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parents:
diff changeset
395 s = f.readline()
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parents:
diff changeset
396 return s.strip()
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parents:
diff changeset
397
48
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parents: 46
diff changeset
398 def getLines(f, delimiterCharacter = delimiterChar):
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parents: 46
diff changeset
399 '''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
400 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
401 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
402 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
403 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
404 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
405 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
406
304
20f9cd972dde added capability to parse cfg file for display-trajectories.py
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 301
diff changeset
407 class FakeSecHead(object):
20f9cd972dde added capability to parse cfg file for display-trajectories.py
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 301
diff changeset
408 '''Add fake section header [asection]
20f9cd972dde added capability to parse cfg file for display-trajectories.py
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 301
diff changeset
409
20f9cd972dde added capability to parse cfg file for display-trajectories.py
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 301
diff changeset
410 from http://stackoverflow.com/questions/2819696/parsing-properties-file-in-python/2819788#2819788
20f9cd972dde added capability to parse cfg file for display-trajectories.py
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 301
diff changeset
411 use read_file in Python 3.2+
20f9cd972dde added capability to parse cfg file for display-trajectories.py
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 301
diff changeset
412 '''
20f9cd972dde added capability to parse cfg file for display-trajectories.py
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 301
diff changeset
413 def __init__(self, fp):
20f9cd972dde added capability to parse cfg file for display-trajectories.py
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 301
diff changeset
414 self.fp = fp
20f9cd972dde added capability to parse cfg file for display-trajectories.py
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 301
diff changeset
415 self.sechead = '[main]\n'
20f9cd972dde added capability to parse cfg file for display-trajectories.py
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 301
diff changeset
416
20f9cd972dde added capability to parse cfg file for display-trajectories.py
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 301
diff changeset
417 def readline(self):
20f9cd972dde added capability to parse cfg file for display-trajectories.py
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 301
diff changeset
418 if self.sechead:
20f9cd972dde added capability to parse cfg file for display-trajectories.py
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 301
diff changeset
419 try: return self.sechead
20f9cd972dde added capability to parse cfg file for display-trajectories.py
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 301
diff changeset
420 finally: self.sechead = None
20f9cd972dde added capability to parse cfg file for display-trajectories.py
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 301
diff changeset
421 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
422
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
423 def removeExtension(filename, delimiter = '.'):
31
c000f37c316d moved tests to independent file, added chi2 computation
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parents: 29
diff changeset
424 '''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
425 i = filename.rfind(delimiter)
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
426 if i>0:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
427 return filename[:i]
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
428 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
429 return filename
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
430
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
431 def cleanFilename(s):
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
432 'cleans filenames obtained when contatenating figure characteristics'
266
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
433 return s.replace(' ','-').replace('.','').replace('/','-')
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
434
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
435 def listfiles(dirname, extension, remove = False):
14
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
436 '''Returns the list of files with the extension in the directory dirname
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
437 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
438 from os import listdir
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
439 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
440 tmp.sort()
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
441 if remove:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
442 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
443 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
444 return tmp
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
445
266
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
446 def mkdir(dirname):
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
447 'Creates a directory if it does not exist'
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
448 import os
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
449 if not os.path.exists(dirname):
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
450 os.mkdir(dirname)
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
451 else:
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
452 print(dirname+' already exists')
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
453
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
454 def removeFile(filename):
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
455 '''Deletes the file while avoiding raising an error
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
456 if the file does not exist'''
266
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
457 import os
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
458 if (os.path.exists(filename)):
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
459 os.remove(filename)
266
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
460 else:
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
461 print(filename+' does not exist')
14
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
462
42
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
463 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
464 '''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
465 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
466
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
467 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
468 '''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
469 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
470
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
471 #########################
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
472 # CLI utils
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
473 #########################
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
474
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
475 def parseCLIOptions(helpMessage, options, cliArgs, optionalOptions=[]):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
476 ''' Simple function to handle similar argument parsing
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
477 Returns the dictionary of options and their values
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
478
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
479 * cliArgs are most likely directly sys.argv
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
480 (only the elements after the first one are considered)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
481
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
482 * options should be a list of strings for getopt options,
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
483 eg ['frame=','correspondences=','video=']
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
484 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
485 import sys, getopt
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
486 from numpy.core.fromnumeric import all
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
487 optionValues, args = getopt.getopt(cliArgs[1:], 'h', ['help']+options+optionalOptions)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
488 optionValues = dict(optionValues)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
489
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
490 if '--help' in optionValues.keys() or '-h' in optionValues.keys():
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
491 print(helpMessage+
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
492 '\n - Compulsory options: '+' '.join([opt.replace('=','') for opt in options])+
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
493 '\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
494 sys.exit()
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
495
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
496 missingArgument = [('--'+opt.replace('=','') in optionValues.keys()) for opt in options]
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
497 if not all(missingArgument):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
498 print('Missing argument')
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
499 print(optionValues)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
500 sys.exit()
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
501
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
502 return optionValues
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
503
333
c9201f6b143a moved the config parser to utils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 332
diff changeset
504 class TrackingParameters:
c9201f6b143a moved the config parser to utils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 332
diff changeset
505 def loadConfigFile(self, filename):
c9201f6b143a moved the config parser to utils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 332
diff changeset
506 from ConfigParser import ConfigParser
c9201f6b143a moved the config parser to utils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 332
diff changeset
507 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
508 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
509
333
c9201f6b143a moved the config parser to utils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 332
diff changeset
510 config = ConfigParser()
c9201f6b143a moved the config parser to utils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 332
diff changeset
511 config.readfp(FakeSecHead(openCheck(filename)))
c9201f6b143a moved the config parser to utils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 332
diff changeset
512 self.sectionHeader = config.sections()[0]
c9201f6b143a moved the config parser to utils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 332
diff changeset
513 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
514 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
515 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
516 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
517 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
518 else:
a50a69e04c2a script modification so that command line arguments take precedence over config file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 352
diff changeset
519 self.homography = None
333
c9201f6b143a moved the config parser to utils
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 332
diff changeset
520 self.firstFrameNum = config.getint(self.sectionHeader, 'frame1')
348
c64a4f889b97 added safety analysis options to feature tracking (with default values for backward compatibility)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 344
diff changeset
521 self.videoFrameRate = config.getfloat(self.sectionHeader, 'video-fps')
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
522
350
7e9ad2d9d79c added new parameters in safety analysis script
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 348
diff changeset
523 self.maxPredictedSpeed = config.getfloat(self.sectionHeader, 'max-predicted-speed')/3.6/self.videoFrameRate
7e9ad2d9d79c added new parameters in safety analysis script
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 348
diff changeset
524 self.predictionTimeHorizon = config.getfloat(self.sectionHeader, 'prediction-time-horizon')*self.videoFrameRate
7e9ad2d9d79c added new parameters in safety analysis script
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 348
diff changeset
525 self.collisionDistance = config.getfloat(self.sectionHeader, 'collision-distance')
7e9ad2d9d79c added new parameters in safety analysis script
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 348
diff changeset
526 self.crossingZones = config.getboolean(self.sectionHeader, 'crossing-zones')
352
72aa44072093 safety analysis script with option for prediction method
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 351
diff changeset
527 self.predictionMethod = config.get(self.sectionHeader, 'prediction-method')
350
7e9ad2d9d79c added new parameters in safety analysis script
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 348
diff changeset
528 self.nPredictedTrajectories = config.getint(self.sectionHeader, 'npredicted-trajectories')
7e9ad2d9d79c added new parameters in safety analysis script
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 348
diff changeset
529 self.minAcceleration = config.getfloat(self.sectionHeader, 'min-acceleration')/self.videoFrameRate**2
7e9ad2d9d79c added new parameters in safety analysis script
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 348
diff changeset
530 self.maxAcceleration = config.getfloat(self.sectionHeader, 'max-acceleration')/self.videoFrameRate**2
7e9ad2d9d79c added new parameters in safety analysis script
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 348
diff changeset
531 self.maxSteering = config.getfloat(self.sectionHeader, 'max-steering')/self.videoFrameRate
351
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532 self.useFeaturesForPrediction = config.getboolean(self.sectionHeader, 'use-features-prediction')
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533
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534 #########################
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535 # sqlite
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536 #########################
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537
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538 def printDBError(error):
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539 print('DB Error: {}'.format(error))
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540
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541 def dropTables(connection, tableNames):
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542 'deletes the table with names in tableNames'
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543 import sqlite3
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544 try:
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545 cursor = connection.cursor()
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546 for tableName in tableNames:
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547 cursor.execute('DROP TABLE IF EXISTS '+tableName)
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548 except sqlite3.OperationalError as error:
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549 printDBError(error)
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550
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551 #########################
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552 # running tests
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553 #########################
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554
0
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555 if __name__ == "__main__":
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556 import doctest
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557 import unittest
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558 suite = doctest.DocFileSuite('tests/utils.txt')
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559 #suite = doctest.DocTestSuite()
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560 unittest.TextTestRunner().run(suite)
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561 #doctest.testmod()
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562 #doctest.testfile("example.txt")