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annotate python/utils.py @ 569:0057c04f94d5

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work in progress on intersections (for PET)
author Nicolas Saunier <nicolas.saunier@polymtl.ca>
date Wed, 06 Aug 2014 17:53:38 -0400
parents ee45c6eb6d49
children e24eeb244698
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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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7 from math import sqrt
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9 __metaclass__ = type
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10
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11 datetimeFormat = "%Y-%m-%d %H:%M:%S"
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13 #########################
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14 # Enumerations
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15 #########################
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16
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17 def inverseEnumeration(l):
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18 'Returns the dictionary that provides for each element in the input list its index in the input list'
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19 result = {}
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20 for i,x in enumerate(l):
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21 result[x] = i
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22 return result
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23
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24 #########################
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25 # simple statistics
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26 #########################
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27
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28 def sampleSize(stdev, tolerance, percentConfidence, printLatex = False):
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29 from scipy.stats.distributions import norm
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30 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1)*100)/100. # 1.-(100-percentConfidence)/200.
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31 if printLatex:
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32 print('${0}^2\\frac{{{1}^2}}{{{2}^2}}$'.format(k, stdev, tolerance))
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33 return (k*stdev/tolerance)**2
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34
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35 def confidenceInterval(mean, stdev, nSamples, percentConfidence, trueStd = True, printLatex = False):
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36 '''if trueStd, use normal distribution, otherwise, Student
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37
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38 Use otherwise t.interval or norm.interval
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39 ex: norm.interval(0.95, loc = 0., scale = 2.3/sqrt(11))
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40 t.interval(0.95, 10, loc=1.2, scale = 2.3/sqrt(nSamples))
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41 loc is mean, scale is sigma/sqrt(n) (for Student, 10 is df)'''
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42 from math import sqrt
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43 from scipy.stats.distributions import norm, t
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44 if trueStd:
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45 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1)*100)/100. # 1.-(100-percentConfidence)/200.
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46 else: # use Student
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47 k = round(t.ppf(0.5+percentConfidence/200., nSamples-1)*100)/100.
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48 e = k*stdev/sqrt(nSamples)
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49 if printLatex:
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50 print('${0} \pm {1}\\frac{{{2}}}{{\sqrt{{{3}}}}}$'.format(mean, k, stdev, nSamples))
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51 return mean-e, mean+e
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52
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53 def computeChi2(expected, observed):
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54 '''Returns the Chi2 statistics'''
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55 result = 0.
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56 for e, o in zip(expected, observed):
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57 result += ((e-o)*(e-o))/e
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58 return result
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60 class EmpiricalDistribution:
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61 def nSamples(self):
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62 return sum(self.counts)
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63
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64 def cumulativeDensityFunction(sample):
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65 '''Returns the cumulative density function of the sample of a random variable'''
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66 from numpy.core.multiarray import array
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67 from numpy.lib.function_base import unique
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68 from numpy.core.fromnumeric import sum
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69 a = array(sample)
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70 a.sort()
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71 xaxis = unique(a)
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72 counts = [sum(a <= x) for x in xaxis]
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73 return xaxis, counts
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74
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75 class EmpiricalDiscreteDistribution(EmpiricalDistribution):
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76 '''Class to represent a sample of a distribution for a discrete random variable
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77 '''
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78 from numpy.core.fromnumeric import sum
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79
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80 def __init__(self, categories, counts):
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81 self.categories = categories
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82 self.counts = counts
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83
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84 def mean(self):
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85 result = [float(x*y) for x,y in zip(self.categories, self.counts)]
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86 return sum(result)/self.nSamples()
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87
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88 def var(self, mean = None):
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89 if not mean:
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90 m = self.mean()
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91 else:
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92 m = mean
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93 result = 0.
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94 squares = [float((x-m)*(x-m)*y) for x,y in zip(self.categories, self.counts)]
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95 return sum(squares)/(self.nSamples()-1)
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96
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97 def referenceCounts(self, probability):
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98 '''probability is a function that returns the probability of the random variable for the category values'''
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99 refProba = [probability(c) for c in self.categories]
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100 refProba[-1] = 1-sum(refProba[:-1])
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101 refCounts = [r*self.nSamples() for r in refProba]
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102 return refCounts, refProba
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103
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104 class EmpiricalContinuousDistribution(EmpiricalDistribution):
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105 '''Class to represent a sample of a distribution for a continuous random variable
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106 with the number of observations for each interval
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107 intervals (categories variable) are defined by their left limits, the last one being the right limit
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108 categories contain therefore one more element than the counts'''
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109 def __init__(self, categories, counts):
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110 # todo add samples for initialization and everything to None? (or setSamples?)
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111 self.categories = categories
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112 self.counts = counts
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113
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114 def mean(self):
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115 result = 0.
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116 for i in range(len(self.counts)-1):
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117 result += self.counts[i]*(self.categories[i]+self.categories[i+1])/2
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118 return result/self.nSamples()
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119
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120 def var(self, mean = None):
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121 if not mean:
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122 m = self.mean()
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123 else:
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124 m = mean
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125 result = 0.
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126 for i in range(len(self.counts)-1):
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127 mid = (self.categories[i]+self.categories[i+1])/2
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128 result += self.counts[i]*(mid - m)*(mid - m)
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129 return result/(self.nSamples()-1)
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130
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131 def referenceCounts(self, cdf):
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132 '''cdf is a cumulative distribution function
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133 returning the probability of the variable being less that x'''
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134 # refCumulativeCounts = [0]#[cdf(self.categories[0][0])]
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135 # for inter in self.categories:
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diff changeset
136 # refCumulativeCounts.append(cdf(inter[1]))
76
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diff changeset
137 refCumulativeCounts = [cdf(x) for x in self.categories[1:-1]]
35
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parents: 32
diff changeset
138
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parents: 32
diff changeset
139 refProba = [refCumulativeCounts[0]]
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parents: 32
diff changeset
140 for i in xrange(1,len(refCumulativeCounts)):
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parents: 32
diff changeset
141 refProba.append(refCumulativeCounts[i]-refCumulativeCounts[i-1])
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parents: 32
diff changeset
142 refProba.append(1-refCumulativeCounts[-1])
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parents: 32
diff changeset
143 refCounts = [p*self.nSamples() for p in refProba]
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parents: 32
diff changeset
144
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parents: 32
diff changeset
145 return refCounts, refProba
31
c000f37c316d moved tests to independent file, added chi2 computation
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parents: 29
diff changeset
146
77
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parents: 76
diff changeset
147 def printReferenceCounts(self, refCounts=None):
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parents: 76
diff changeset
148 if refCounts:
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parents: 76
diff changeset
149 ref = refCounts
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parents: 76
diff changeset
150 else:
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parents: 76
diff changeset
151 ref = self.referenceCounts
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parents: 76
diff changeset
152 for i in xrange(len(ref[0])):
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parents: 76
diff changeset
153 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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parents: 76
diff changeset
154
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parents: 76
diff changeset
155
31
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parents: 29
diff changeset
156 #########################
370
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diff changeset
157 # maths section
27
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parents: 24
diff changeset
158 #########################
24
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159
433
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diff changeset
160 # def kernelSmoothing(sampleX, X, Y, weightFunc, halfwidth):
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161 # '''Returns a smoothed weighted version of Y at the predefined values of sampleX
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162 # Sum_x weight(sample_x,x) * y(x)'''
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diff changeset
163 # from numpy import zeros, array
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164 # smoothed = zeros(len(sampleX))
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diff changeset
165 # for i,x in enumerate(sampleX):
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diff changeset
166 # weights = array([weightFunc(x,xx, halfwidth) for xx in X])
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diff changeset
167 # if sum(weights)>0:
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diff changeset
168 # smoothed[i] = sum(weights*Y)/sum(weights)
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diff changeset
169 # else:
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diff changeset
170 # smoothed[i] = 0
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diff changeset
171 # return smoothed
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172
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diff changeset
173 def kernelSmoothing(x, X, Y, weightFunc, halfwidth):
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diff changeset
174 '''Returns the smoothed estimate of (X,Y) at x
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diff changeset
175 Sum_x weight(sample_x,x) * y(x)'''
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diff changeset
176 from numpy import zeros, array
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diff changeset
177 weights = array([weightFunc(x,observedx, halfwidth) for observedx in X])
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diff changeset
178 if sum(weights)>0:
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diff changeset
179 return sum(weights*Y)/sum(weights)
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diff changeset
180 else:
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diff changeset
181 return 0
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diff changeset
182
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diff changeset
183 def uniform(center, x, halfwidth):
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diff changeset
184 if abs(center-x)<halfwidth:
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diff changeset
185 return 1.
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diff changeset
186 else:
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diff changeset
187 return 0.
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188
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diff changeset
189 def gaussian(center, x, halfwidth):
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diff changeset
190 from numpy import exp
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parents: 423
diff changeset
191 return exp(-((center-x)/halfwidth)**2/2)
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192
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parents: 423
diff changeset
193 def epanechnikov(center, x, halfwidth):
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parents: 423
diff changeset
194 diff = abs(center-x)
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diff changeset
195 if diff<halfwidth:
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diff changeset
196 return 1.-(diff/halfwidth)**2
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parents: 423
diff changeset
197 else:
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diff changeset
198 return 0.
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parents: 423
diff changeset
199
434
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diff changeset
200 def triangular(center, x, halfwidth):
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diff changeset
201 diff = abs(center-x)
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parents: 433
diff changeset
202 if diff<halfwidth:
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parents: 433
diff changeset
203 return 1.-abs(diff/halfwidth)
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parents: 433
diff changeset
204 else:
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parents: 433
diff changeset
205 return 0.
433
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parents: 423
diff changeset
206
518
0c86c73f3c09 median smoothing
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parents: 511
diff changeset
207 def medianSmoothing(x, X, Y, halfwidth):
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parents: 511
diff changeset
208 '''Returns the media of Y's corresponding to X's in the interval [x-halfwidth, x+halfwidth]'''
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parents: 511
diff changeset
209 from numpy import median
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parents: 511
diff changeset
210 return median([y for observedx, y in zip(X,Y) if abs(x-observedx)<halfwidth])
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parents: 511
diff changeset
211
521
3707eeb20f25 changed argMaxDict name to argmaxDict
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parents: 518
diff changeset
212 def argmaxDict(d):
561
ee45c6eb6d49 added Mohamed Gomaa Mohamed function to smooth object trajectories
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parents: 553
diff changeset
213 return max(d, key=d.get)
279
3af4c267a7bf generic simple LCSS
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parents: 276
diff changeset
214
395
6fba1ab040f1 minor modification to framestotime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 391
diff changeset
215 def framesToTime(nFrames, frameRate, initialTime = time()):
6fba1ab040f1 minor modification to framestotime
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parents: 391
diff changeset
216 '''returns a datetime.time for the time in hour, minutes and seconds
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parents: 391
diff changeset
217 initialTime is a datetime.time'''
248
571ba5ed22e2 added utils for bus processing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 241
diff changeset
218 from math import floor
395
6fba1ab040f1 minor modification to framestotime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 391
diff changeset
219 seconds = int(floor(float(nFrames)/float(frameRate))+initialTime.hour*3600+initialTime.minute*60+initialTime.second)
261
4aa792cb0fa9 changing framesToTime to return a datetime.time
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 248
diff changeset
220 h = int(floor(seconds/3600.))
248
571ba5ed22e2 added utils for bus processing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 241
diff changeset
221 seconds = seconds - h*3600
261
4aa792cb0fa9 changing framesToTime to return a datetime.time
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 248
diff changeset
222 m = int(floor(seconds/60))
248
571ba5ed22e2 added utils for bus processing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 241
diff changeset
223 seconds = seconds - m*60
262
a048066bd20f correcting bug in framesToTime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 261
diff changeset
224 return time(h, m, seconds)
248
571ba5ed22e2 added utils for bus processing
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parents: 241
diff changeset
225
381
387cc0142211 script to replay event annotations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 376
diff changeset
226 def timeToFrames(t, frameRate):
387cc0142211 script to replay event annotations
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parents: 376
diff changeset
227 return frameRate*(t.hour*3600+t.minute*60+t.second)
387cc0142211 script to replay event annotations
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parents: 376
diff changeset
228
241
ee1caff48b03 added function to sort to list of paired data X,Y
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
229 def sortXY(X,Y):
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parents: 235
diff changeset
230 'returns the sorted (x, Y(x)) sorted on X'
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
231 D = {}
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
232 for x, y in zip(X,Y):
ee1caff48b03 added function to sort to list of paired data X,Y
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parents: 235
diff changeset
233 D[x]=y
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
234 xsorted = sorted(D.keys())
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
235 return xsorted, [D[x] for x in xsorted]
ee1caff48b03 added function to sort to list of paired data X,Y
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parents: 235
diff changeset
236
32
48e56179c39e added ceil function
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parents: 31
diff changeset
237 def ceilDecimals(v, nDecimals):
48e56179c39e added ceil function
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parents: 31
diff changeset
238 '''Rounds the number at the nth decimal
48e56179c39e added ceil function
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parents: 31
diff changeset
239 eg 1.23 at 0 decimal is 2, at 1 decimal is 1.3'''
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parents: 31
diff changeset
240 from math import ceil,pow
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parents: 31
diff changeset
241 tens = pow(10,nDecimals)
48e56179c39e added ceil function
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parents: 31
diff changeset
242 return ceil(v*tens)/tens
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parents: 31
diff changeset
243
152
74b1fc68d4df re-organized code to avoid cyclic python module dependencies
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 116
diff changeset
244 def inBetween(bound1, bound2, x):
569
0057c04f94d5 work in progress on intersections (for PET)
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parents: 561
diff changeset
245 return bound1 <= x <= bound2 or bound2 <= x <= bound1
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parents: 561
diff changeset
246
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
247 def pointDistanceL2(x1,y1,x2,y2):
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
248 ''' Compute point-to-point distance (L2 norm, ie Euclidean distance)'''
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
249 return sqrt((x2-x1)**2+(y2-y1)**2)
24
6fb59cfb201e first version of segmentIntersection
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parents: 19
diff changeset
250
6fb59cfb201e first version of segmentIntersection
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parents: 19
diff changeset
251 def crossProduct(l1, l2):
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parents: 19
diff changeset
252 return l1[0]*l2[1]-l1[1]*l2[0]
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parents: 19
diff changeset
253
547
97c5fef5b2d6 corrected bugs
MohamedGomaa
parents: 521
diff changeset
254 def filterMovingWindow(inputSignal, halfWidth):
29
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
255 '''Returns an array obtained after the smoothing of the input by a moving average
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
256 The first and last points are copied from the original.'''
547
97c5fef5b2d6 corrected bugs
MohamedGomaa
parents: 521
diff changeset
257 from numpy import ones,convolve,array
29
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
258 width = float(halfWidth*2+1)
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parents: 27
diff changeset
259 win = ones(width,'d')
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parents: 27
diff changeset
260 result = convolve(win/width,array(inputSignal),'same')
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
261 result[:halfWidth] = inputSignal[:halfWidth]
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
262 result[-halfWidth:] = inputSignal[-halfWidth:]
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parents: 27
diff changeset
263 return result
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
264
199
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
265 def linearRegression(x, y, deg = 1, plotData = False):
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parents: 197
diff changeset
266 '''returns the least square estimation of the linear regression of y = ax+b
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parents: 197
diff changeset
267 as well as the plot'''
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parents: 197
diff changeset
268 from numpy.lib.polynomial import polyfit
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parents: 197
diff changeset
269 from matplotlib.pyplot import plot
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parents: 197
diff changeset
270 from numpy.core.multiarray import arange
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parents: 197
diff changeset
271 coef = polyfit(x, y, deg)
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parents: 197
diff changeset
272 if plotData:
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parents: 197
diff changeset
273 def poly(x):
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parents: 197
diff changeset
274 result = 0
ca9d9104afba added utility to calibrate polynoms and plot
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parents: 197
diff changeset
275 for i in range(len(coef)):
ca9d9104afba added utility to calibrate polynoms and plot
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parents: 197
diff changeset
276 result += coef[i]*x**(len(coef)-i-1)
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parents: 197
diff changeset
277 return result
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diff changeset
278 plot(x, y, 'x')
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diff changeset
279 xx = arange(min(x), max(x),(max(x)-min(x))/1000)
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diff changeset
280 plot(xx, [poly(z) for z in xx])
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parents: 197
diff changeset
281 return coef
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parents: 197
diff changeset
282
27
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parents: 24
diff changeset
283 #########################
455
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parents: 434
diff changeset
284 # iterable section
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parents: 434
diff changeset
285 #########################
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parents: 434
diff changeset
286
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diff changeset
287 def mostCommon(L):
456
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parents: 455
diff changeset
288 '''Returns the most frequent element in a iterable
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289
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parents: 455
diff changeset
290 taken from http://stackoverflow.com/questions/1518522/python-most-common-element-in-a-list'''
455
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parents: 434
diff changeset
291 from itertools import groupby
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parents: 434
diff changeset
292 from operator import itemgetter
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parents: 434
diff changeset
293 # get an iterable of (item, iterable) pairs
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diff changeset
294 SL = sorted((x, i) for i, x in enumerate(L))
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diff changeset
295 # print 'SL:', SL
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diff changeset
296 groups = groupby(SL, key=itemgetter(0))
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diff changeset
297 # auxiliary function to get "quality" for an item
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diff changeset
298 def _auxfun(g):
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diff changeset
299 item, iterable = g
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diff changeset
300 count = 0
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diff changeset
301 min_index = len(L)
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diff changeset
302 for _, where in iterable:
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diff changeset
303 count += 1
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diff changeset
304 min_index = min(min_index, where)
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diff changeset
305 # print 'item %r, count %r, minind %r' % (item, count, min_index)
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diff changeset
306 return count, -min_index
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diff changeset
307 # pick the highest-count/earliest item
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diff changeset
308 return max(groups, key=_auxfun)[0]
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diff changeset
309
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parents: 434
diff changeset
310 #########################
370
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diff changeset
311 # sequence section
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parents: 369
diff changeset
312 #########################
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313
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diff changeset
314 class LCSS:
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diff changeset
315 '''Class that keeps the LCSS parameters
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parents: 369
diff changeset
316 and puts together the various computations'''
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diff changeset
317 def __init__(self, similarityFunc, delta = float('inf'), aligned = False, lengthFunc = min):
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diff changeset
318 self.similarityFunc = similarityFunc
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diff changeset
319 self.aligned = aligned
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diff changeset
320 self.delta = delta
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diff changeset
321 self.lengthFunc = lengthFunc
389
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diff changeset
322 self.subSequenceIndices = [(0,0)]
370
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diff changeset
323
373
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parents: 372
diff changeset
324 def similarities(self, l1, l2, jshift=0):
370
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parents: 369
diff changeset
325 from numpy import zeros, int as npint
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parents: 369
diff changeset
326 n1 = len(l1)
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parents: 369
diff changeset
327 n2 = len(l2)
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parents: 369
diff changeset
328 self.similarityTable = zeros((n1+1,n2+1), dtype = npint)
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parents: 369
diff changeset
329 for i in xrange(1,n1+1):
374
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parents: 373
diff changeset
330 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
331 if self.similarityFunc(l1[i-1], l2[j-1]):
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parents: 369
diff changeset
332 self.similarityTable[i,j] = self.similarityTable[i-1,j-1]+1
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parents: 369
diff changeset
333 else:
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diff changeset
334 self.similarityTable[i,j] = max(self.similarityTable[i-1,j], self.similarityTable[i,j-1])
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parents: 369
diff changeset
335
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diff changeset
336 def subSequence(self, i, j):
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parents: 369
diff changeset
337 '''Returns the subsequence of two sequences
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parents: 369
diff changeset
338 http://en.wikipedia.org/wiki/Longest_common_subsequence_problem'''
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parents: 369
diff changeset
339 if i == 0 or j == 0:
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parents: 369
diff changeset
340 return []
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parents: 369
diff changeset
341 elif self.similarityTable[i][j] == self.similarityTable[i][j-1]:
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parents: 369
diff changeset
342 return self.subSequence(i, j-1)
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parents: 369
diff changeset
343 elif self.similarityTable[i][j] == self.similarityTable[i-1][j]:
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parents: 369
diff changeset
344 return self.subSequence(i-1, j)
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parents: 369
diff changeset
345 else:
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parents: 369
diff changeset
346 return self.subSequence(i-1, j-1) + [(i-1,j-1)]
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parents: 369
diff changeset
347
373
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parents: 372
diff changeset
348 def _compute(self, _l1, _l2, computeSubSequence = False):
370
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parents: 369
diff changeset
349 '''returns the longest common subsequence similarity
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parents: 369
diff changeset
350 based on the threshold on distance between two elements of lists l1, l2
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parents: 369
diff changeset
351 similarityFunc returns True or False whether the two points are considered similar
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parents: 369
diff changeset
352
373
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parents: 372
diff changeset
353 if aligned, returns the best matching if using a finite delta by shiftinig the series alignments
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parents: 372
diff changeset
354
370
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parents: 369
diff changeset
355 eg distance(p1, p2) < epsilon
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parents: 369
diff changeset
356 '''
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
357 if len(_l2) < len(_l1): # l1 is the shortest
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
358 l1 = _l2
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
359 l2 = _l1
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
360 revertIndices = True
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
361 else:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
362 l1 = _l1
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
363 l2 = _l2
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
364 revertIndices = False
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
365 n1 = len(l1)
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
366 n2 = len(l2)
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
367
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
368 if self.aligned:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
369 lcssValues = {}
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
370 similarityTables = {}
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
371 for i in xrange(-n2-self.delta+1, n1+self.delta): # interval such that [i-shift-delta, i-shift+delta] is never empty, which happens when i-shift+delta < 1 or when i-shift-delta > n2
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
372 self.similarities(l1, l2, i)
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
373 lcssValues[i] = self.similarityTable.max()
370
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parents: 369
diff changeset
374 similarityTables[i] = self.similarityTable
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
375 #print self.similarityTable
521
3707eeb20f25 changed argMaxDict name to argmaxDict
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 518
diff changeset
376 alignmentShift = argmaxDict(lcssValues) # ideally get the medium alignment shift, the one that minimizes distance
389
6d26dcc7bba0 modifications to compute alignment for None indicators
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
377 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
378 else:
389
6d26dcc7bba0 modifications to compute alignment for None indicators
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
379 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
380 self.similarities(l1, l2)
373
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
381
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
382 # 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
383 self.similarityTable = self.similarityTable[:min(n1, n2+alignmentShift+self.delta)+1, :min(n2, n1-alignmentShift+self.delta)+1]
373
d0b86ed50f32 work in progress on LCSS
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parents: 372
diff changeset
384
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
385 if computeSubSequence:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
386 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
387 if revertIndices:
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
388 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
389 return self.similarityTable[-1,-1]
370
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
390
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parents: 369
diff changeset
391 def compute(self, l1, l2, computeSubSequence = False):
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parents: 369
diff changeset
392 '''get methods are to be shadowed in child classes '''
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parents: 369
diff changeset
393 return self._compute(l1, l2, computeSubSequence)
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parents: 369
diff changeset
394
375
2ea8584aa80a making indicator LCSS work
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 374
diff changeset
395 def computeAlignment(self):
370
97e8fa0ee9a1 work in progress for complete alignment
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parents: 369
diff changeset
396 from numpy import mean
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
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parents: 373
diff changeset
397 return mean([j-i for i,j in self.subSequenceIndices])
370
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
398
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
399 def _computeNormalized(self, l1, l2, computeSubSequence = False):
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
400 ''' compute the normalized LCSS
97e8fa0ee9a1 work in progress for complete alignment
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parents: 369
diff changeset
401 ie, the LCSS divided by the min or mean of the indicator lengths (using lengthFunc)
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parents: 369
diff changeset
402 lengthFunc = lambda x,y:float(x,y)/2'''
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
403 return float(self._compute(l1, l2, computeSubSequence))/self.lengthFunc(len(l1), len(l2))
370
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
404
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
405 def computeNormalized(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
406 return self._computeNormalized(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
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parents: 369
diff changeset
407
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
408 def _computeDistance(self, l1, l2, computeSubSequence = False):
370
97e8fa0ee9a1 work in progress for complete alignment
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parents: 369
diff changeset
409 ''' compute the LCSS distance'''
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
410 return 1-self._computeNormalized(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
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parents: 369
diff changeset
411
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
412 def computeDistance(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity
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parents: 375
diff changeset
413 return self._computeDistance(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
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parents: 369
diff changeset
414
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
415 #########################
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
416 # plotting section
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
417 #########################
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
418
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
419 def plotPolygon(poly, options = ''):
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
420 'Plots shapely polygon poly'
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
421 from numpy.core.multiarray import array
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
422 from matplotlib.pyplot import plot
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
423 from shapely.geometry import Polygon
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
424
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
425 tmp = array(poly.exterior)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
426 plot(tmp[:,0], tmp[:,1], options)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
427
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
428 def stepPlot(X, firstX, lastX, initialCount = 0, increment = 1):
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
429 '''for each value in X, increment by increment the initial count
297
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
430 returns the lists that can be plotted
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
431 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
432 firstX and lastX should be respectively smaller and larger than all elements in X'''
297
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parents: 286
diff changeset
433
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
434 sortedX = []
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
435 counts = [initialCount]
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
436 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
437 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
438 counts.append(counts[-1])
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
439 counts.append(counts[-1]+increment)
297
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
440 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
441 return [firstX]+sortedX+[lastX], counts
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
442
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
443 class PlottingPropertyValues:
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
444 def __init__(self, values):
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
445 self.values = values
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
446
116
2bf5b76320c0 moved intersection plotting and added markers for scatter plots
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 115
diff changeset
447 def __getitem__(self, i):
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
448 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
449
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
450 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
451 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
452
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
453 linestyles = PlottingPropertyValues(['-', '--', '-.', ':'])
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
454
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
455 colors = PlottingPropertyValues('brgmyck') # 'w'
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
456
115
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
457 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
458 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
459 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
460 coords = array(indicatorMap.keys())
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
461 minX = min(coords[:,0])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
462 minY = min(coords[:,1])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
463 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
464 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
465 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
466 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
467 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
468 if masked:
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
469 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
470 else:
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
471 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
472
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
473 #########################
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
474 # file I/O section
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
475 #########################
24
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
476
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
477 def removeExtension(filename, delimiter = '.'):
31
c000f37c316d moved tests to independent file, added chi2 computation
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parents: 29
diff changeset
478 '''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
479 i = filename.rfind(delimiter)
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
480 if i>0:
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
481 return filename[:i]
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
482 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
483 return filename
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
484
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
485 def cleanFilename(s):
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
486 'cleans filenames obtained when contatenating figure characteristics'
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
487 return s.replace(' ','-').replace('.','').replace('/','-')
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
488
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
489 def listfiles(dirname, extension, remove = False):
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
490 '''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
491 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
492 from os import listdir
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
493 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
494 tmp.sort()
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
495 if remove:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
496 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
497 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
498 return tmp
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
499
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
500 def mkdir(dirname):
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
501 'Creates a directory if it does not exist'
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
502 import os
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
503 if not os.path.exists(dirname):
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
504 os.mkdir(dirname)
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
505 else:
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
506 print(dirname+' already exists')
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
507
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
508 def removeFile(filename):
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
509 '''Deletes the file while avoiding raising an error
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
510 if the file does not exist'''
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
511 import os
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
512 if (os.path.exists(filename)):
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
513 os.remove(filename)
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
514 else:
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
515 print(filename+' does not exist')
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
516
42
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
517 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
518 '''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
519 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
520
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
521 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
522 '''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
523 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
524
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
525 #########################
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
526 # CLI utils
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
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
529 def parseCLIOptions(helpMessage, options, cliArgs, optionalOptions=[]):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
530 ''' Simple function to handle similar argument parsing
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
531 Returns the dictionary of options and their values
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
532
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
533 * cliArgs are most likely directly sys.argv
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
534 (only the elements after the first one are considered)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
535
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
536 * options should be a list of strings for getopt options,
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
537 eg ['frame=','correspondences=','video=']
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
538 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
539 import sys, getopt
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
540 from numpy.core.fromnumeric import all
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
541 optionValues, args = getopt.getopt(cliArgs[1:], 'h', ['help']+options+optionalOptions)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
542 optionValues = dict(optionValues)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
543
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544 if '--help' in optionValues.keys() or '-h' in optionValues.keys():
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545 print(helpMessage+
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546 '\n - Compulsory options: '+' '.join([opt.replace('=','') for opt in options])+
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547 '\n - Non-compulsory options: '+' '.join([opt.replace('=','') for opt in optionalOptions]))
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548 sys.exit()
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549
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550 missingArgument = [('--'+opt.replace('=','') in optionValues.keys()) for opt in options]
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551 if not all(missingArgument):
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552 print('Missing argument')
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553 print(optionValues)
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554 sys.exit()
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555
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556 return optionValues
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557
397
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558
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559 #########################
553
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560 # Profiling
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561 #########################
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562
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563 def analyzeProfile(profileFilename, stripDirs = True):
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564 '''Analyze the file produced by cProfile
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565
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566 obtained by for example:
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567 - call in script (for main() function in script)
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568 import cProfile, os
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569 cProfile.run('main()', os.path.join(os.getcwd(),'main.profile'))
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570
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571 - or on the command line:
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572 python -m cProfile [-o profile.bin] [-s sort] scriptfile [arg]'''
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573 import pstats, os
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574 p = pstats.Stats(os.path.join(os.pardir, profileFilename))
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575 if stripDirs:
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576 p.strip_dirs()
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577 p.sort_stats('time')
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578 p.print_stats(.2)
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579 #p.sort_stats('time')
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580 # p.print_callees(.1, 'int_prediction.py:')
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581 return p
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582
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583 #########################
31
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584 # running tests
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585 #########################
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586
0
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587 if __name__ == "__main__":
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588 import doctest
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589 import unittest
31
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590 suite = doctest.DocFileSuite('tests/utils.txt')
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591 #suite = doctest.DocTestSuite()
2
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592 unittest.TextTestRunner().run(suite)
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593 #doctest.testmod()
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594 #doctest.testfile("example.txt")