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corrected mask bug in feature tracking, updated display-trajectories to display on undistorted image
author Nicolas Saunier <nicolas.saunier@polymtl.ca>
date Fri, 23 May 2014 16:27:26 -0400
parents 343cfd185ca6
children ad518f0c3218
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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, datetime
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8 __metaclass__ = type
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9
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10 datetimeFormat = "%Y-%m-%d %H:%M:%S"
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12 #########################
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13 # Enumerations
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14 #########################
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15
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16 def inverseEnumeration(l):
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17 'Returns the dictionary that provides for each element in the input list its index in the input list'
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18 result = {}
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19 for i,x in enumerate(l):
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20 result[x] = i
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21 return result
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22
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23 #########################
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24 # simple statistics
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25 #########################
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27 def sampleSize(stdev, tolerance, percentConfidence, printLatex = False):
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28 from scipy.stats.distributions import norm
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29 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1)*100)/100. # 1.-(100-percentConfidence)/200.
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30 if printLatex:
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31 print('${0}^2\\frac{{{1}^2}}{{{2}^2}}$'.format(k, stdev, tolerance))
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32 return (k*stdev/tolerance)**2
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33
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34 def confidenceInterval(mean, stdev, nSamples, percentConfidence, trueStd = True, printLatex = False):
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35 'if trueStd, use normal distribution, otherwise, Student'
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36 from math import sqrt
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37 from scipy.stats.distributions import norm, t
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38 if trueStd:
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39 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1)*100)/100. # 1.-(100-percentConfidence)/200.
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40 else: # use Student
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41 k = round(t.ppf(0.5+percentConfidence/200., nSamples-1)*100)/100.
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42 e = k*stdev/sqrt(nSamples)
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43 if printLatex:
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44 print('${0} \pm {1}\\frac{{{2}}}{{\sqrt{{{3}}}}}$'.format(mean, k, stdev, nSamples))
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45 return mean-e, mean+e
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46
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47 def computeChi2(expected, observed):
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48 '''Returns the Chi2 statistics'''
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49 result = 0.
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50 for e, o in zip(expected, observed):
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51 result += ((e-o)*(e-o))/e
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52 return result
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53
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54 class EmpiricalDistribution:
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55 def nSamples(self):
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56 return sum(self.counts)
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57
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58 def cumulativeDensityFunction(sample):
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59 '''Returns the cumulative density function of the sample of a random variable'''
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60 from numpy.core.multiarray import array
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61 from numpy.lib.function_base import unique
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62 from numpy.core.fromnumeric import sum
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63 a = array(sample)
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64 a.sort()
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65 xaxis = unique(a)
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66 counts = [sum(a <= x) for x in xaxis]
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67 return xaxis, counts
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68
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69 class EmpiricalDiscreteDistribution(EmpiricalDistribution):
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70 '''Class to represent a sample of a distribution for a discrete random variable
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71 '''
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72 from numpy.core.fromnumeric import sum
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73
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74 def __init__(self, categories, counts):
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75 self.categories = categories
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76 self.counts = counts
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77
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78 def mean(self):
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79 result = [float(x*y) for x,y in zip(self.categories, self.counts)]
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80 return sum(result)/self.nSamples()
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81
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82 def var(self, mean = None):
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83 if not mean:
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84 m = self.mean()
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85 else:
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86 m = mean
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87 result = 0.
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88 squares = [float((x-m)*(x-m)*y) for x,y in zip(self.categories, self.counts)]
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89 return sum(squares)/(self.nSamples()-1)
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90
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91 def referenceCounts(self, probability):
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92 '''probability is a function that returns the probability of the random variable for the category values'''
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93 refProba = [probability(c) for c in self.categories]
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94 refProba[-1] = 1-sum(refProba[:-1])
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95 refCounts = [r*self.nSamples() for r in refProba]
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96 return refCounts, refProba
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97
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98 class EmpiricalContinuousDistribution(EmpiricalDistribution):
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99 '''Class to represent a sample of a distribution for a continuous random variable
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100 with the number of observations for each interval
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101 intervals (categories variable) are defined by their left limits, the last one being the right limit
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102 categories contain therefore one more element than the counts'''
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103 def __init__(self, categories, counts):
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104 # todo add samples for initialization and everything to None? (or setSamples?)
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105 self.categories = categories
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106 self.counts = counts
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107
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108 def mean(self):
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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 result += self.counts[i]*(self.categories[i]+self.categories[i+1])/2
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112 return result/self.nSamples()
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113
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114 def var(self, mean = None):
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115 if not mean:
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116 m = self.mean()
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117 else:
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118 m = mean
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119 result = 0.
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120 for i in range(len(self.counts)-1):
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121 mid = (self.categories[i]+self.categories[i+1])/2
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122 result += self.counts[i]*(mid - m)*(mid - m)
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123 return result/(self.nSamples()-1)
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124
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125 def referenceCounts(self, cdf):
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126 '''cdf is a cumulative distribution function
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127 returning the probability of the variable being less that x'''
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128 # refCumulativeCounts = [0]#[cdf(self.categories[0][0])]
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129 # for inter in self.categories:
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130 # refCumulativeCounts.append(cdf(inter[1]))
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131 refCumulativeCounts = [cdf(x) for x in self.categories[1:-1]]
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132
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133 refProba = [refCumulativeCounts[0]]
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134 for i in xrange(1,len(refCumulativeCounts)):
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135 refProba.append(refCumulativeCounts[i]-refCumulativeCounts[i-1])
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136 refProba.append(1-refCumulativeCounts[-1])
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137 refCounts = [p*self.nSamples() for p in refProba]
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diff changeset
138
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diff changeset
139 return refCounts, refProba
31
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140
77
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141 def printReferenceCounts(self, refCounts=None):
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142 if refCounts:
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143 ref = refCounts
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144 else:
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145 ref = self.referenceCounts
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146 for i in xrange(len(ref[0])):
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147 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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148
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149
31
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diff changeset
150 #########################
370
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151 # maths section
27
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diff changeset
152 #########################
24
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153
433
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154 # def kernelSmoothing(sampleX, X, Y, weightFunc, halfwidth):
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155 # '''Returns a smoothed weighted version of Y at the predefined values of sampleX
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156 # Sum_x weight(sample_x,x) * y(x)'''
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157 # from numpy import zeros, array
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158 # smoothed = zeros(len(sampleX))
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159 # for i,x in enumerate(sampleX):
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160 # weights = array([weightFunc(x,xx, halfwidth) for xx in X])
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161 # if sum(weights)>0:
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162 # smoothed[i] = sum(weights*Y)/sum(weights)
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163 # else:
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164 # smoothed[i] = 0
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165 # return smoothed
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166
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167 def kernelSmoothing(x, X, Y, weightFunc, halfwidth):
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168 '''Returns the smoothed estimate of (X,Y) at x
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169 Sum_x weight(sample_x,x) * y(x)'''
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170 from numpy import zeros, array
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171 weights = array([weightFunc(x,observedx, halfwidth) for observedx in X])
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172 if sum(weights)>0:
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173 return sum(weights*Y)/sum(weights)
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174 else:
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175 return 0
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176
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177 def uniform(center, x, halfwidth):
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178 if abs(center-x)<halfwidth:
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179 return 1.
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180 else:
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181 return 0.
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182
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183 def gaussian(center, x, halfwidth):
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184 from numpy import exp
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185 return exp(-((center-x)/halfwidth)**2/2)
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186
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187 def epanechnikov(center, x, halfwidth):
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188 diff = abs(center-x)
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189 if diff<halfwidth:
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190 return 1.-(diff/halfwidth)**2
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191 else:
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192 return 0.
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193
434
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194 def triangular(center, x, halfwidth):
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195 diff = abs(center-x)
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196 if diff<halfwidth:
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197 return 1.-abs(diff/halfwidth)
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198 else:
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199 return 0.
433
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200
370
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diff changeset
201 def argMaxDict(d):
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diff changeset
202 return max(d.iterkeys(), key=(lambda key: d[key]))
279
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203
395
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204 def framesToTime(nFrames, frameRate, initialTime = time()):
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205 '''returns a datetime.time for the time in hour, minutes and seconds
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diff changeset
206 initialTime is a datetime.time'''
248
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207 from math import floor
395
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208 seconds = int(floor(float(nFrames)/float(frameRate))+initialTime.hour*3600+initialTime.minute*60+initialTime.second)
261
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diff changeset
209 h = int(floor(seconds/3600.))
248
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210 seconds = seconds - h*3600
261
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211 m = int(floor(seconds/60))
248
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212 seconds = seconds - m*60
262
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diff changeset
213 return time(h, m, seconds)
248
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diff changeset
214
381
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215 def timeToFrames(t, frameRate):
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216 return frameRate*(t.hour*3600+t.minute*60+t.second)
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diff changeset
217
241
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diff changeset
218 def sortXY(X,Y):
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219 'returns the sorted (x, Y(x)) sorted on X'
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220 D = {}
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221 for x, y in zip(X,Y):
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222 D[x]=y
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223 xsorted = sorted(D.keys())
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224 return xsorted, [D[x] for x in xsorted]
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225
32
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diff changeset
226 def ceilDecimals(v, nDecimals):
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227 '''Rounds the number at the nth decimal
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228 eg 1.23 at 0 decimal is 2, at 1 decimal is 1.3'''
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229 from math import ceil,pow
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diff changeset
230 tens = pow(10,nDecimals)
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diff changeset
231 return ceil(v*tens)/tens
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diff changeset
232
152
74b1fc68d4df re-organized code to avoid cyclic python module dependencies
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diff changeset
233 def inBetween(bound1, bound2, x):
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diff changeset
234 return bound1 <= x <= bound2 or bound2 <= x<= bound1
24
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235
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diff changeset
236 def crossProduct(l1, l2):
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diff changeset
237 return l1[0]*l2[1]-l1[1]*l2[0]
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238
29
ca8e716cc231 added moving average filter
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diff changeset
239 def filterMovingWindow(input, halfWidth):
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diff changeset
240 '''Returns an array obtained after the smoothing of the input by a moving average
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diff changeset
241 The first and last points are copied from the original.'''
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diff changeset
242 width = float(halfWidth*2+1)
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diff changeset
243 win = ones(width,'d')
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diff changeset
244 result = convolve(win/width,array(inputSignal),'same')
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diff changeset
245 result[:halfWidth] = inputSignal[:halfWidth]
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diff changeset
246 result[-halfWidth:] = inputSignal[-halfWidth:]
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diff changeset
247 return result
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diff changeset
248
199
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diff changeset
249 def linearRegression(x, y, deg = 1, plotData = False):
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diff changeset
250 '''returns the least square estimation of the linear regression of y = ax+b
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diff changeset
251 as well as the plot'''
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diff changeset
252 from numpy.lib.polynomial import polyfit
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diff changeset
253 from matplotlib.pyplot import plot
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diff changeset
254 from numpy.core.multiarray import arange
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diff changeset
255 coef = polyfit(x, y, deg)
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diff changeset
256 if plotData:
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diff changeset
257 def poly(x):
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diff changeset
258 result = 0
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diff changeset
259 for i in range(len(coef)):
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diff changeset
260 result += coef[i]*x**(len(coef)-i-1)
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diff changeset
261 return result
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diff changeset
262 plot(x, y, 'x')
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diff changeset
263 xx = arange(min(x), max(x),(max(x)-min(x))/1000)
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diff changeset
264 plot(xx, [poly(z) for z in xx])
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diff changeset
265 return coef
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diff changeset
266
27
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diff changeset
267 #########################
455
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diff changeset
268 # iterable section
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diff changeset
269 #########################
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diff changeset
270
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diff changeset
271 def mostCommon(L):
456
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diff changeset
272 '''Returns the most frequent element in a iterable
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diff changeset
273
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diff changeset
274 taken from http://stackoverflow.com/questions/1518522/python-most-common-element-in-a-list'''
455
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diff changeset
275 from itertools import groupby
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diff changeset
276 from operator import itemgetter
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diff changeset
277 # get an iterable of (item, iterable) pairs
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parents: 434
diff changeset
278 SL = sorted((x, i) for i, x in enumerate(L))
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diff changeset
279 # print 'SL:', SL
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diff changeset
280 groups = groupby(SL, key=itemgetter(0))
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diff changeset
281 # auxiliary function to get "quality" for an item
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diff changeset
282 def _auxfun(g):
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diff changeset
283 item, iterable = g
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diff changeset
284 count = 0
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diff changeset
285 min_index = len(L)
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diff changeset
286 for _, where in iterable:
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parents: 434
diff changeset
287 count += 1
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diff changeset
288 min_index = min(min_index, where)
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parents: 434
diff changeset
289 # print 'item %r, count %r, minind %r' % (item, count, min_index)
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diff changeset
290 return count, -min_index
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parents: 434
diff changeset
291 # pick the highest-count/earliest item
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diff changeset
292 return max(groups, key=_auxfun)[0]
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diff changeset
293
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parents: 434
diff changeset
294 #########################
370
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diff changeset
295 # sequence section
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parents: 369
diff changeset
296 #########################
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diff changeset
297
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diff changeset
298 class LCSS:
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diff changeset
299 '''Class that keeps the LCSS parameters
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parents: 369
diff changeset
300 and puts together the various computations'''
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diff changeset
301 def __init__(self, similarityFunc, delta = float('inf'), aligned = False, lengthFunc = min):
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diff changeset
302 self.similarityFunc = similarityFunc
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diff changeset
303 self.aligned = aligned
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diff changeset
304 self.delta = delta
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diff changeset
305 self.lengthFunc = lengthFunc
389
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diff changeset
306 self.subSequenceIndices = [(0,0)]
370
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diff changeset
307
373
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diff changeset
308 def similarities(self, l1, l2, jshift=0):
370
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diff changeset
309 from numpy import zeros, int as npint
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diff changeset
310 n1 = len(l1)
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diff changeset
311 n2 = len(l2)
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diff changeset
312 self.similarityTable = zeros((n1+1,n2+1), dtype = npint)
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diff changeset
313 for i in xrange(1,n1+1):
374
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diff changeset
314 for j in xrange(max(1,i-jshift-self.delta),min(n2,i-jshift+self.delta)+1):
370
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parents: 369
diff changeset
315 if self.similarityFunc(l1[i-1], l2[j-1]):
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diff changeset
316 self.similarityTable[i,j] = self.similarityTable[i-1,j-1]+1
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diff changeset
317 else:
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diff changeset
318 self.similarityTable[i,j] = max(self.similarityTable[i-1,j], self.similarityTable[i,j-1])
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diff changeset
319
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diff changeset
320 def subSequence(self, i, j):
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diff changeset
321 '''Returns the subsequence of two sequences
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diff changeset
322 http://en.wikipedia.org/wiki/Longest_common_subsequence_problem'''
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parents: 369
diff changeset
323 if i == 0 or j == 0:
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parents: 369
diff changeset
324 return []
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diff changeset
325 elif self.similarityTable[i][j] == self.similarityTable[i][j-1]:
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parents: 369
diff changeset
326 return self.subSequence(i, j-1)
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parents: 369
diff changeset
327 elif self.similarityTable[i][j] == self.similarityTable[i-1][j]:
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diff changeset
328 return self.subSequence(i-1, j)
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parents: 369
diff changeset
329 else:
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parents: 369
diff changeset
330 return self.subSequence(i-1, j-1) + [(i-1,j-1)]
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parents: 369
diff changeset
331
373
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parents: 372
diff changeset
332 def _compute(self, _l1, _l2, computeSubSequence = False):
370
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parents: 369
diff changeset
333 '''returns the longest common subsequence similarity
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parents: 369
diff changeset
334 based on the threshold on distance between two elements of lists l1, l2
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parents: 369
diff changeset
335 similarityFunc returns True or False whether the two points are considered similar
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parents: 369
diff changeset
336
373
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parents: 372
diff changeset
337 if aligned, returns the best matching if using a finite delta by shiftinig the series alignments
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parents: 372
diff changeset
338
370
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parents: 369
diff changeset
339 eg distance(p1, p2) < epsilon
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parents: 369
diff changeset
340 '''
372
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
341 if len(_l2) < len(_l1): # l1 is the shortest
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
342 l1 = _l2
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
343 l2 = _l1
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
344 revertIndices = True
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
345 else:
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parents: 371
diff changeset
346 l1 = _l1
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parents: 371
diff changeset
347 l2 = _l2
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parents: 371
diff changeset
348 revertIndices = False
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parents: 371
diff changeset
349 n1 = len(l1)
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parents: 371
diff changeset
350 n2 = len(l2)
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parents: 371
diff changeset
351
370
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parents: 369
diff changeset
352 if self.aligned:
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parents: 369
diff changeset
353 lcssValues = {}
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parents: 369
diff changeset
354 similarityTables = {}
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
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diff changeset
355 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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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
356 self.similarities(l1, l2, i)
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parents: 372
diff changeset
357 lcssValues[i] = self.similarityTable.max()
370
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parents: 369
diff changeset
358 similarityTables[i] = self.similarityTable
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
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parents: 373
diff changeset
359 #print self.similarityTable
389
6d26dcc7bba0 modifications to compute alignment for None indicators
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
360 alignmentShift = argMaxDict(lcssValues) # ideally get the medium alignment shift, the one that minimizes distance
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
361 self.similarityTable = similarityTables[alignmentShift]
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
362 else:
389
6d26dcc7bba0 modifications to compute alignment for None indicators
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
363 alignmentShift = 0
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
364 self.similarities(l1, l2)
373
d0b86ed50f32 work in progress on LCSS
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parents: 372
diff changeset
365
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
366 # threshold values for the useful part of the similarity table are n2-n1-delta and n1-n2-delta
389
6d26dcc7bba0 modifications to compute alignment for None indicators
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
367 self.similarityTable = self.similarityTable[:min(n1, n2+alignmentShift+self.delta)+1, :min(n2, n1-alignmentShift+self.delta)+1]
373
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parents: 372
diff changeset
368
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
369 if computeSubSequence:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
370 self.subSequenceIndices = self.subSequence(self.similarityTable.shape[0]-1, self.similarityTable.shape[1]-1)
371
924e38c9f70e work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 370
diff changeset
371 if revertIndices:
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
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parents: 373
diff changeset
372 self.subSequenceIndices = [(j,i) for i,j in self.subSequenceIndices]
372
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
373 return self.similarityTable[-1,-1]
370
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parents: 369
diff changeset
374
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parents: 369
diff changeset
375 def compute(self, l1, l2, computeSubSequence = False):
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parents: 369
diff changeset
376 '''get methods are to be shadowed in child classes '''
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parents: 369
diff changeset
377 return self._compute(l1, l2, computeSubSequence)
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parents: 369
diff changeset
378
375
2ea8584aa80a making indicator LCSS work
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parents: 374
diff changeset
379 def computeAlignment(self):
370
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parents: 369
diff changeset
380 from numpy import mean
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
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parents: 373
diff changeset
381 return mean([j-i for i,j in self.subSequenceIndices])
370
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parents: 369
diff changeset
382
376
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
383 def _computeNormalized(self, l1, l2, computeSubSequence = False):
370
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parents: 369
diff changeset
384 ''' compute the normalized LCSS
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parents: 369
diff changeset
385 ie, the LCSS divided by the min or mean of the indicator lengths (using lengthFunc)
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parents: 369
diff changeset
386 lengthFunc = lambda x,y:float(x,y)/2'''
376
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parents: 375
diff changeset
387 return float(self._compute(l1, l2, computeSubSequence))/self.lengthFunc(len(l1), len(l2))
370
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parents: 369
diff changeset
388
376
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
389 def computeNormalized(self, l1, l2, computeSubSequence = False):
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parents: 375
diff changeset
390 return self._computeNormalized(l1, l2, computeSubSequence)
370
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parents: 369
diff changeset
391
376
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
392 def _computeDistance(self, l1, l2, computeSubSequence = False):
370
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parents: 369
diff changeset
393 ''' compute the LCSS distance'''
376
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parents: 375
diff changeset
394 return 1-self._computeNormalized(l1, l2, computeSubSequence)
370
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parents: 369
diff changeset
395
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
396 def computeDistance(self, l1, l2, computeSubSequence = False):
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parents: 375
diff changeset
397 return self._computeDistance(l1, l2, computeSubSequence)
370
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
398
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
399 #########################
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
400 # plotting section
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
401 #########################
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
402
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
403 def plotPolygon(poly, options = ''):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
404 'Plots shapely polygon poly'
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
405 from numpy.core.multiarray import array
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
406 from matplotlib.pyplot import plot
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
407 from shapely.geometry import Polygon
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
408
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
409 tmp = array(poly.exterior)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
410 plot(tmp[:,0], tmp[:,1], options)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
411
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
412 def stepPlot(X, firstX, lastX, initialCount = 0, increment = 1):
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
413 '''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
414 returns the lists that can be plotted
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
415 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
416 firstX and lastX should be respectively smaller and larger than all elements in X'''
297
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
417
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
418 sortedX = []
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
419 counts = [initialCount]
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
420 for x in sorted(X):
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
421 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
422 counts.append(counts[-1])
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
423 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
424 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
425 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
426
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
427 class PlottingPropertyValues:
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
428 def __init__(self, values):
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
429 self.values = values
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
430
116
2bf5b76320c0 moved intersection plotting and added markers for scatter plots
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 115
diff changeset
431 def __getitem__(self, i):
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
432 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
433
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
434 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
435 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
436
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
437 linestyles = PlottingPropertyValues(['-', '--', '-.', ':'])
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
438
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
439 colors = PlottingPropertyValues('brgmyck') # 'w'
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
440
115
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
441 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
442 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
443 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
444 coords = array(indicatorMap.keys())
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
445 minX = min(coords[:,0])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
446 minY = min(coords[:,1])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
447 X = arange(minX, max(coords[:,0])+1.1)*squareSize
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
448 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
449 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
450 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
451 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
452 if masked:
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
453 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
454 else:
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
455 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
456
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
457 #########################
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
458 # file I/O section
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
459 #########################
24
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
460
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
461 def removeExtension(filename, delimiter = '.'):
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
462 '''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
463 i = filename.rfind(delimiter)
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
464 if i>0:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
465 return filename[:i]
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
466 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
467 return filename
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
468
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
469 def cleanFilename(s):
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
470 'cleans filenames obtained when contatenating figure characteristics'
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
471 return s.replace(' ','-').replace('.','').replace('/','-')
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
472
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
473 def listfiles(dirname, extension, remove = False):
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
474 '''Returns the list of files with the extension in the directory dirname
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
475 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
476 from os import listdir
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
477 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
478 tmp.sort()
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
479 if remove:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
480 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
481 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
482 return tmp
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
483
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
484 def mkdir(dirname):
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
485 'Creates a directory if it does not exist'
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
486 import os
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
487 if not os.path.exists(dirname):
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
488 os.mkdir(dirname)
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
489 else:
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
490 print(dirname+' already exists')
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
491
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
492 def removeFile(filename):
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
493 '''Deletes the file while avoiding raising an error
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
494 if the file does not exist'''
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
495 import os
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
496 if (os.path.exists(filename)):
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
497 os.remove(filename)
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
498 else:
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
499 print(filename+' does not exist')
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
500
42
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
501 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
502 '''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
503 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
504
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
505 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
506 '''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
507 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
508
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
509 #########################
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
510 # CLI utils
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
511 #########################
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
512
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
513 def parseCLIOptions(helpMessage, options, cliArgs, optionalOptions=[]):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
514 ''' Simple function to handle similar argument parsing
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
515 Returns the dictionary of options and their values
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
516
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
517 * cliArgs are most likely directly sys.argv
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
518 (only the elements after the first one are considered)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
519
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
520 * options should be a list of strings for getopt options,
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
521 eg ['frame=','correspondences=','video=']
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
522 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
523 import sys, getopt
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
524 from numpy.core.fromnumeric import all
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
525 optionValues, args = getopt.getopt(cliArgs[1:], 'h', ['help']+options+optionalOptions)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
526 optionValues = dict(optionValues)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
527
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
528 if '--help' in optionValues.keys() or '-h' in optionValues.keys():
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
529 print(helpMessage+
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
530 '\n - Compulsory options: '+' '.join([opt.replace('=','') for opt in options])+
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
531 '\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
532 sys.exit()
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
533
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
534 missingArgument = [('--'+opt.replace('=','') in optionValues.keys()) for opt in options]
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
535 if not all(missingArgument):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
536 print('Missing argument')
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
537 print(optionValues)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
538 sys.exit()
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
539
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
540 return optionValues
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
541
397
b36b00dd27c3 added function to read scene metadata
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 395
diff changeset
542
b36b00dd27c3 added function to read scene metadata
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 395
diff changeset
543 #########################
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
544 # running tests
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
545 #########################
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546
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547 if __name__ == "__main__":
aed8eb63cdde initial commit with non-functional python code for NGSIM
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548 import doctest
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549 import unittest
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550 suite = doctest.DocFileSuite('tests/utils.txt')
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551 #suite = doctest.DocTestSuite()
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552 unittest.TextTestRunner().run(suite)
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553 #doctest.testmod()
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554 #doctest.testfile("example.txt")