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annotate python/utils.py @ 659:784298512b60

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minor modifications
author Nicolas Saunier <nicolas.saunier@polymtl.ca>
date Thu, 14 May 2015 23:18:44 +0200
parents c9a0b72979fd
children 15e244d2a1b5
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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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8
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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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59
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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, normalized = False):
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65 '''Returns the cumulative density function of the sample of a random variable'''
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66 from numpy import arange, cumsum
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67 xaxis = sorted(sample)
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68 counts = arange(1,len(sample)+1) # dtype = float
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69 if normalized:
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70 counts /= float(len(sample))
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71 return xaxis, counts
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72
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73 class EmpiricalDiscreteDistribution(EmpiricalDistribution):
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74 '''Class to represent a sample of a distribution for a discrete random variable
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75 '''
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76 from numpy.core.fromnumeric import sum
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77
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78 def __init__(self, categories, counts):
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79 self.categories = categories
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80 self.counts = counts
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81
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82 def mean(self):
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83 result = [float(x*y) for x,y in zip(self.categories, self.counts)]
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84 return sum(result)/self.nSamples()
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85
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86 def var(self, mean = None):
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87 if not mean:
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88 m = self.mean()
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89 else:
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90 m = mean
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91 result = 0.
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92 squares = [float((x-m)*(x-m)*y) for x,y in zip(self.categories, self.counts)]
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93 return sum(squares)/(self.nSamples()-1)
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94
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95 def referenceCounts(self, probability):
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96 '''probability is a function that returns the probability of the random variable for the category values'''
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97 refProba = [probability(c) for c in self.categories]
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98 refProba[-1] = 1-sum(refProba[:-1])
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99 refCounts = [r*self.nSamples() for r in refProba]
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100 return refCounts, refProba
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101
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102 class EmpiricalContinuousDistribution(EmpiricalDistribution):
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103 '''Class to represent a sample of a distribution for a continuous random variable
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104 with the number of observations for each interval
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105 intervals (categories variable) are defined by their left limits, the last one being the right limit
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106 categories contain therefore one more element than the counts'''
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107 def __init__(self, categories, counts):
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108 # todo add samples for initialization and everything to None? (or setSamples?)
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109 self.categories = categories
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110 self.counts = counts
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111
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112 def mean(self):
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113 result = 0.
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114 for i in range(len(self.counts)-1):
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115 result += self.counts[i]*(self.categories[i]+self.categories[i+1])/2
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116 return result/self.nSamples()
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117
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118 def var(self, mean = None):
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119 if not mean:
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120 m = self.mean()
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121 else:
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122 m = mean
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123 result = 0.
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124 for i in range(len(self.counts)-1):
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125 mid = (self.categories[i]+self.categories[i+1])/2
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126 result += self.counts[i]*(mid - m)*(mid - m)
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127 return result/(self.nSamples()-1)
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128
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129 def referenceCounts(self, cdf):
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130 '''cdf is a cumulative distribution function
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131 returning the probability of the variable being less that x'''
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132 # refCumulativeCounts = [0]#[cdf(self.categories[0][0])]
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133 # for inter in self.categories:
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134 # refCumulativeCounts.append(cdf(inter[1]))
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diff changeset
135 refCumulativeCounts = [cdf(x) for x in self.categories[1:-1]]
35
8cafee54466f forgotten update of histogram class
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parents: 32
diff changeset
136
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parents: 32
diff changeset
137 refProba = [refCumulativeCounts[0]]
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parents: 32
diff changeset
138 for i in xrange(1,len(refCumulativeCounts)):
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parents: 32
diff changeset
139 refProba.append(refCumulativeCounts[i]-refCumulativeCounts[i-1])
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
140 refProba.append(1-refCumulativeCounts[-1])
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parents: 32
diff changeset
141 refCounts = [p*self.nSamples() for p in refProba]
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parents: 32
diff changeset
142
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parents: 32
diff changeset
143 return refCounts, refProba
31
c000f37c316d moved tests to independent file, added chi2 computation
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parents: 29
diff changeset
144
77
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parents: 76
diff changeset
145 def printReferenceCounts(self, refCounts=None):
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parents: 76
diff changeset
146 if refCounts:
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parents: 76
diff changeset
147 ref = refCounts
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parents: 76
diff changeset
148 else:
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diff changeset
149 ref = self.referenceCounts
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parents: 76
diff changeset
150 for i in xrange(len(ref[0])):
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parents: 76
diff changeset
151 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
152
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parents: 76
diff changeset
153
31
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parents: 29
diff changeset
154 #########################
370
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parents: 369
diff changeset
155 # maths section
27
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parents: 24
diff changeset
156 #########################
24
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157
433
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diff changeset
158 # def kernelSmoothing(sampleX, X, Y, weightFunc, halfwidth):
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159 # '''Returns a smoothed weighted version of Y at the predefined values of sampleX
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diff changeset
160 # Sum_x weight(sample_x,x) * y(x)'''
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diff changeset
161 # from numpy import zeros, array
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diff changeset
162 # smoothed = zeros(len(sampleX))
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diff changeset
163 # for i,x in enumerate(sampleX):
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diff changeset
164 # weights = array([weightFunc(x,xx, halfwidth) for xx in X])
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diff changeset
165 # if sum(weights)>0:
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diff changeset
166 # smoothed[i] = sum(weights*Y)/sum(weights)
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diff changeset
167 # else:
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diff changeset
168 # smoothed[i] = 0
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diff changeset
169 # return smoothed
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170
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diff changeset
171 def kernelSmoothing(x, X, Y, weightFunc, halfwidth):
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diff changeset
172 '''Returns the smoothed estimate of (X,Y) at x
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diff changeset
173 Sum_x weight(sample_x,x) * y(x)'''
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diff changeset
174 from numpy import zeros, array
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diff changeset
175 weights = array([weightFunc(x,observedx, halfwidth) for observedx in X])
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diff changeset
176 if sum(weights)>0:
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parents: 423
diff changeset
177 return sum(weights*Y)/sum(weights)
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diff changeset
178 else:
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diff changeset
179 return 0
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diff changeset
180
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parents: 423
diff changeset
181 def uniform(center, x, halfwidth):
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parents: 423
diff changeset
182 if abs(center-x)<halfwidth:
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parents: 423
diff changeset
183 return 1.
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parents: 423
diff changeset
184 else:
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diff changeset
185 return 0.
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diff changeset
186
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parents: 423
diff changeset
187 def gaussian(center, x, halfwidth):
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diff changeset
188 from numpy import exp
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parents: 423
diff changeset
189 return exp(-((center-x)/halfwidth)**2/2)
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diff changeset
190
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parents: 423
diff changeset
191 def epanechnikov(center, x, halfwidth):
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parents: 423
diff changeset
192 diff = abs(center-x)
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parents: 423
diff changeset
193 if diff<halfwidth:
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parents: 423
diff changeset
194 return 1.-(diff/halfwidth)**2
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parents: 423
diff changeset
195 else:
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parents: 423
diff changeset
196 return 0.
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diff changeset
197
434
9a714f32fc9f small updates
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diff changeset
198 def triangular(center, x, halfwidth):
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diff changeset
199 diff = abs(center-x)
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parents: 433
diff changeset
200 if diff<halfwidth:
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parents: 433
diff changeset
201 return 1.-abs(diff/halfwidth)
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parents: 433
diff changeset
202 else:
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parents: 433
diff changeset
203 return 0.
433
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parents: 423
diff changeset
204
518
0c86c73f3c09 median smoothing
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parents: 511
diff changeset
205 def medianSmoothing(x, X, Y, halfwidth):
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parents: 511
diff changeset
206 '''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
207 from numpy import median
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parents: 511
diff changeset
208 return median([y for observedx, y in zip(X,Y) if abs(x-observedx)<halfwidth])
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parents: 511
diff changeset
209
521
3707eeb20f25 changed argMaxDict name to argmaxDict
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parents: 518
diff changeset
210 def argmaxDict(d):
561
ee45c6eb6d49 added Mohamed Gomaa Mohamed function to smooth object trajectories
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parents: 553
diff changeset
211 return max(d, key=d.get)
279
3af4c267a7bf generic simple LCSS
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parents: 276
diff changeset
212
395
6fba1ab040f1 minor modification to framestotime
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parents: 391
diff changeset
213 def framesToTime(nFrames, frameRate, initialTime = time()):
6fba1ab040f1 minor modification to framestotime
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parents: 391
diff changeset
214 '''returns a datetime.time for the time in hour, minutes and seconds
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parents: 391
diff changeset
215 initialTime is a datetime.time'''
248
571ba5ed22e2 added utils for bus processing
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parents: 241
diff changeset
216 from math import floor
395
6fba1ab040f1 minor modification to framestotime
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parents: 391
diff changeset
217 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
218 h = int(floor(seconds/3600.))
248
571ba5ed22e2 added utils for bus processing
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parents: 241
diff changeset
219 seconds = seconds - h*3600
261
4aa792cb0fa9 changing framesToTime to return a datetime.time
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 248
diff changeset
220 m = int(floor(seconds/60))
248
571ba5ed22e2 added utils for bus processing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 241
diff changeset
221 seconds = seconds - m*60
262
a048066bd20f correcting bug in framesToTime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 261
diff changeset
222 return time(h, m, seconds)
248
571ba5ed22e2 added utils for bus processing
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parents: 241
diff changeset
223
381
387cc0142211 script to replay event annotations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 376
diff changeset
224 def timeToFrames(t, frameRate):
387cc0142211 script to replay event annotations
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parents: 376
diff changeset
225 return frameRate*(t.hour*3600+t.minute*60+t.second)
387cc0142211 script to replay event annotations
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parents: 376
diff changeset
226
241
ee1caff48b03 added function to sort to list of paired data X,Y
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
227 def sortXY(X,Y):
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parents: 235
diff changeset
228 'returns the sorted (x, Y(x)) sorted on X'
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parents: 235
diff changeset
229 D = {}
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parents: 235
diff changeset
230 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
231 D[x]=y
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
232 xsorted = sorted(D.keys())
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parents: 235
diff changeset
233 return xsorted, [D[x] for x in xsorted]
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parents: 235
diff changeset
234
32
48e56179c39e added ceil function
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parents: 31
diff changeset
235 def ceilDecimals(v, nDecimals):
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parents: 31
diff changeset
236 '''Rounds the number at the nth decimal
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parents: 31
diff changeset
237 eg 1.23 at 0 decimal is 2, at 1 decimal is 1.3'''
48e56179c39e added ceil function
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parents: 31
diff changeset
238 from math import ceil,pow
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parents: 31
diff changeset
239 tens = pow(10,nDecimals)
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parents: 31
diff changeset
240 return ceil(v*tens)/tens
48e56179c39e added ceil function
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parents: 31
diff changeset
241
152
74b1fc68d4df re-organized code to avoid cyclic python module dependencies
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 116
diff changeset
242 def inBetween(bound1, bound2, x):
569
0057c04f94d5 work in progress on intersections (for PET)
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parents: 561
diff changeset
243 return bound1 <= x <= bound2 or bound2 <= x <= bound1
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parents: 561
diff changeset
244
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
245 def pointDistanceL2(x1,y1,x2,y2):
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
246 ''' Compute point-to-point distance (L2 norm, ie Euclidean distance)'''
0057c04f94d5 work in progress on intersections (for PET)
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parents: 561
diff changeset
247 return sqrt((x2-x1)**2+(y2-y1)**2)
24
6fb59cfb201e first version of segmentIntersection
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parents: 19
diff changeset
248
6fb59cfb201e first version of segmentIntersection
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parents: 19
diff changeset
249 def crossProduct(l1, l2):
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parents: 19
diff changeset
250 return l1[0]*l2[1]-l1[1]*l2[0]
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parents: 19
diff changeset
251
574
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
252 def cat_mvgavg(cat_list, halfWidth):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
253 ''' Return a list of categories/values smoothed according to a window.
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
254 halfWidth is the search radius on either side'''
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
255 from copy import deepcopy
659
784298512b60 minor modifications
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 637
diff changeset
256 smoothed = deepcopy(cat_list)
784298512b60 minor modifications
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 637
diff changeset
257 for point in range(len(cat_list)):
574
e24eeb244698 first implementation of projection to curvilinear coordinates
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parents: 569
diff changeset
258 lower_bound_check = max(0,point-halfWidth)
659
784298512b60 minor modifications
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parents: 637
diff changeset
259 upper_bound_check = min(len(cat_list)-1,point+halfWidth+1)
784298512b60 minor modifications
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parents: 637
diff changeset
260 window_values = cat_list[lower_bound_check:upper_bound_check]
574
e24eeb244698 first implementation of projection to curvilinear coordinates
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parents: 569
diff changeset
261 smoothed[point] = max(set(window_values), key=window_values.count)
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parents: 569
diff changeset
262 return smoothed
e24eeb244698 first implementation of projection to curvilinear coordinates
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parents: 569
diff changeset
263
547
97c5fef5b2d6 corrected bugs
MohamedGomaa
parents: 521
diff changeset
264 def filterMovingWindow(inputSignal, halfWidth):
29
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
265 '''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
266 The first and last points are copied from the original.'''
547
97c5fef5b2d6 corrected bugs
MohamedGomaa
parents: 521
diff changeset
267 from numpy import ones,convolve,array
29
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
268 width = float(halfWidth*2+1)
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parents: 27
diff changeset
269 win = ones(width,'d')
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parents: 27
diff changeset
270 result = convolve(win/width,array(inputSignal),'same')
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
271 result[:halfWidth] = inputSignal[:halfWidth]
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
272 result[-halfWidth:] = inputSignal[-halfWidth:]
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
273 return result
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
274
199
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
275 def linearRegression(x, y, deg = 1, plotData = False):
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
276 '''returns the least square estimation of the linear regression of y = ax+b
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277 as well as the plot'''
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278 from numpy.lib.polynomial import polyfit
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279 from matplotlib.pyplot import plot
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280 from numpy.core.multiarray import arange
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281 coef = polyfit(x, y, deg)
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diff changeset
282 if plotData:
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diff changeset
283 def poly(x):
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284 result = 0
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diff changeset
285 for i in range(len(coef)):
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diff changeset
286 result += coef[i]*x**(len(coef)-i-1)
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287 return result
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288 plot(x, y, 'x')
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289 xx = arange(min(x), max(x),(max(x)-min(x))/1000)
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diff changeset
290 plot(xx, [poly(z) for z in xx])
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diff changeset
291 return coef
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292
27
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parents: 24
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293 #########################
455
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294 # iterable section
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parents: 434
diff changeset
295 #########################
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296
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diff changeset
297 def mostCommon(L):
456
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298 '''Returns the most frequent element in a iterable
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299
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300 taken from http://stackoverflow.com/questions/1518522/python-most-common-element-in-a-list'''
455
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301 from itertools import groupby
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302 from operator import itemgetter
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303 # get an iterable of (item, iterable) pairs
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304 SL = sorted((x, i) for i, x in enumerate(L))
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305 # print 'SL:', SL
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306 groups = groupby(SL, key=itemgetter(0))
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307 # auxiliary function to get "quality" for an item
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diff changeset
308 def _auxfun(g):
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309 item, iterable = g
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310 count = 0
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311 min_index = len(L)
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312 for _, where in iterable:
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313 count += 1
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diff changeset
314 min_index = min(min_index, where)
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diff changeset
315 # print 'item %r, count %r, minind %r' % (item, count, min_index)
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diff changeset
316 return count, -min_index
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317 # pick the highest-count/earliest item
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diff changeset
318 return max(groups, key=_auxfun)[0]
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319
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320 #########################
370
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321 # sequence section
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diff changeset
322 #########################
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323
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324 class LCSS:
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325 '''Class that keeps the LCSS parameters
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diff changeset
326 and puts together the various computations'''
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diff changeset
327 def __init__(self, similarityFunc, delta = float('inf'), aligned = False, lengthFunc = min):
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diff changeset
328 self.similarityFunc = similarityFunc
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329 self.aligned = aligned
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330 self.delta = delta
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diff changeset
331 self.lengthFunc = lengthFunc
389
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diff changeset
332 self.subSequenceIndices = [(0,0)]
370
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diff changeset
333
373
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diff changeset
334 def similarities(self, l1, l2, jshift=0):
370
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diff changeset
335 from numpy import zeros, int as npint
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336 n1 = len(l1)
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337 n2 = len(l2)
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diff changeset
338 self.similarityTable = zeros((n1+1,n2+1), dtype = npint)
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diff changeset
339 for i in xrange(1,n1+1):
374
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diff changeset
340 for j in xrange(max(1,i-jshift-self.delta),min(n2,i-jshift+self.delta)+1):
370
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diff changeset
341 if self.similarityFunc(l1[i-1], l2[j-1]):
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diff changeset
342 self.similarityTable[i,j] = self.similarityTable[i-1,j-1]+1
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diff changeset
343 else:
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diff changeset
344 self.similarityTable[i,j] = max(self.similarityTable[i-1,j], self.similarityTable[i,j-1])
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345
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346 def subSequence(self, i, j):
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347 '''Returns the subsequence of two sequences
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diff changeset
348 http://en.wikipedia.org/wiki/Longest_common_subsequence_problem'''
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diff changeset
349 if i == 0 or j == 0:
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diff changeset
350 return []
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diff changeset
351 elif self.similarityTable[i][j] == self.similarityTable[i][j-1]:
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diff changeset
352 return self.subSequence(i, j-1)
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diff changeset
353 elif self.similarityTable[i][j] == self.similarityTable[i-1][j]:
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diff changeset
354 return self.subSequence(i-1, j)
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diff changeset
355 else:
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diff changeset
356 return self.subSequence(i-1, j-1) + [(i-1,j-1)]
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diff changeset
357
373
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diff changeset
358 def _compute(self, _l1, _l2, computeSubSequence = False):
370
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diff changeset
359 '''returns the longest common subsequence similarity
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diff changeset
360 based on the threshold on distance between two elements of lists l1, l2
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diff changeset
361 similarityFunc returns True or False whether the two points are considered similar
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diff changeset
362
607
84690dfe5560 add some functions for behaviour analysis
MohamedGomaa
parents: 574
diff changeset
363 if aligned, returns the best matching if using a finite delta by shifting the series alignments
373
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parents: 372
diff changeset
364
370
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diff changeset
365 eg distance(p1, p2) < epsilon
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diff changeset
366 '''
372
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parents: 371
diff changeset
367 if len(_l2) < len(_l1): # l1 is the shortest
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parents: 371
diff changeset
368 l1 = _l2
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parents: 371
diff changeset
369 l2 = _l1
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parents: 371
diff changeset
370 revertIndices = True
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parents: 371
diff changeset
371 else:
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parents: 371
diff changeset
372 l1 = _l1
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parents: 371
diff changeset
373 l2 = _l2
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parents: 371
diff changeset
374 revertIndices = False
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parents: 371
diff changeset
375 n1 = len(l1)
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parents: 371
diff changeset
376 n2 = len(l2)
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parents: 371
diff changeset
377
370
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parents: 369
diff changeset
378 if self.aligned:
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diff changeset
379 lcssValues = {}
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diff changeset
380 similarityTables = {}
374
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diff changeset
381 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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parents: 372
diff changeset
382 self.similarities(l1, l2, i)
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parents: 372
diff changeset
383 lcssValues[i] = self.similarityTable.max()
370
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diff changeset
384 similarityTables[i] = self.similarityTable
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
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diff changeset
385 #print self.similarityTable
521
3707eeb20f25 changed argMaxDict name to argmaxDict
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parents: 518
diff changeset
386 alignmentShift = argmaxDict(lcssValues) # ideally get the medium alignment shift, the one that minimizes distance
389
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parents: 381
diff changeset
387 self.similarityTable = similarityTables[alignmentShift]
372
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parents: 371
diff changeset
388 else:
389
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parents: 381
diff changeset
389 alignmentShift = 0
372
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parents: 371
diff changeset
390 self.similarities(l1, l2)
373
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parents: 372
diff changeset
391
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
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parents: 373
diff changeset
392 # threshold values for the useful part of the similarity table are n2-n1-delta and n1-n2-delta
389
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parents: 381
diff changeset
393 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
394
372
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parents: 371
diff changeset
395 if computeSubSequence:
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parents: 371
diff changeset
396 self.subSequenceIndices = self.subSequence(self.similarityTable.shape[0]-1, self.similarityTable.shape[1]-1)
371
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parents: 370
diff changeset
397 if revertIndices:
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
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parents: 373
diff changeset
398 self.subSequenceIndices = [(j,i) for i,j in self.subSequenceIndices]
372
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parents: 371
diff changeset
399 return self.similarityTable[-1,-1]
370
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parents: 369
diff changeset
400
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diff changeset
401 def compute(self, l1, l2, computeSubSequence = False):
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diff changeset
402 '''get methods are to be shadowed in child classes '''
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parents: 369
diff changeset
403 return self._compute(l1, l2, computeSubSequence)
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parents: 369
diff changeset
404
375
2ea8584aa80a making indicator LCSS work
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parents: 374
diff changeset
405 def computeAlignment(self):
370
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parents: 369
diff changeset
406 from numpy import mean
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
407 return mean([j-i for i,j in self.subSequenceIndices])
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
408
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
409 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
410 ''' compute the normalized LCSS
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
411 ie, the LCSS divided by the min or mean of the indicator lengths (using lengthFunc)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
412 lengthFunc = lambda x,y:float(x,y)/2'''
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
413 return float(self._compute(l1, l2, computeSubSequence))/self.lengthFunc(len(l1), len(l2))
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
414
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
415 def computeNormalized(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
416 return self._computeNormalized(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
417
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
418 def _computeDistance(self, l1, l2, computeSubSequence = False):
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
419 ''' compute the LCSS distance'''
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
420 return 1-self._computeNormalized(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
421
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
422 def computeDistance(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
423 return self._computeDistance(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
424
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
425 #########################
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
426 # plotting section
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
427 #########################
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
428
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
429 def plotPolygon(poly, options = ''):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
430 'Plots shapely polygon poly'
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
431 from numpy.core.multiarray import array
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
432 from matplotlib.pyplot import plot
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
433 from shapely.geometry import Polygon
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
434
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
435 tmp = array(poly.exterior)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
436 plot(tmp[:,0], tmp[:,1], options)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
437
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
438 def stepPlot(X, firstX, lastX, initialCount = 0, increment = 1):
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
439 '''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
440 returns the lists that can be plotted
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
441 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
442 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
443
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
444 sortedX = []
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
445 counts = [initialCount]
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
446 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
447 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
448 counts.append(counts[-1])
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
449 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
450 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
451 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
452
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
453 class PlottingPropertyValues:
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
454 def __init__(self, values):
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
455 self.values = values
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
456
116
2bf5b76320c0 moved intersection plotting and added markers for scatter plots
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 115
diff changeset
457 def __getitem__(self, i):
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
458 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
459
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
460 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
461 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
462
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
463 linestyles = PlottingPropertyValues(['-', '--', '-.', ':'])
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
464
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
465 colors = PlottingPropertyValues('brgmyck') # 'w'
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
466
115
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
467 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
468 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
469 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
470 coords = array(indicatorMap.keys())
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
471 minX = min(coords[:,0])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
472 minY = min(coords[:,1])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
473 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
474 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
475 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
476 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
477 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
478 if masked:
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
479 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
480 else:
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
481 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
482
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
483 #########################
637
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
484 # Data download
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
485 #########################
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
486
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
487 def downloadECWeather(stationID, years, months = [], outputDirectoryname = '.', english = True):
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
488 '''Downloads monthly weather data from Environment Canada
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
489 If month is provided (number 1 to 12), it means hourly data for the whole month
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
490 Otherwise, means the data for each day, for the whole year
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
491
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
492 Example: MONTREAL MCTAVISH 10761
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
493 MONTREALPIERRE ELLIOTT TRUDEAU INTL A 5415
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
494
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
495 To get daily data for 2010 and 2011, downloadECWeather(10761, [2010,2011], [], '/tmp')
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
496 To get hourly data for 2009 and 2012, January, March and October, downloadECWeather(10761, [2009,2012], [1,3,10], '/tmp')'''
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
497 import urllib2
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
498 if english:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
499 language = 'e'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
500 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
501 language = 'f'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
502 if len(months) == 0:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
503 timeFrame = 2
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
504 months = [1]
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
505 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
506 timeFrame = 1
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
507
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
508 for year in years:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
509 for month in months:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
510 url = urllib2.urlopen('http://climat.meteo.gc.ca/climateData/bulkdata_{}.html?format=csv&stationID={}&Year={}&Month={}&Day=1&timeframe={}&submit=++T%C3%A9l%C3%A9charger+%0D%0Ades+donn%C3%A9es'.format(language, stationID, year, month, timeFrame))
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
511 data = url.read()
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
512 outFilename = '{}/{}-{}'.format(outputDirectoryname, stationID, year)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
513 if timeFrame == 1:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
514 outFilename += '-{}-hourly'.format(month)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
515 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
516 outFilename += '-daily'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
517 outFilename += '.csv'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
518 out = open(outFilename, 'w')
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
519 out.write(data)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
520 out.close()
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
521
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
522 #########################
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
523 # File I/O
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
524 #########################
24
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
525
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
526 def removeExtension(filename, delimiter = '.'):
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
527 '''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
528 i = filename.rfind(delimiter)
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
529 if i>0:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
530 return filename[:i]
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
531 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
532 return filename
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
533
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
534 def cleanFilename(s):
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
535 'cleans filenames obtained when contatenating figure characteristics'
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
536 return s.replace(' ','-').replace('.','').replace('/','-')
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
537
0
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diff changeset
538 def listfiles(dirname, extension, remove = False):
14
e7bbe8465591 homography and other utils
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539 '''Returns the list of files with the extension in the directory dirname
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diff changeset
540 If remove is True, the filenames are stripped from the extension'''
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
541 from os import listdir
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
542 tmp = [f for f in listdir(dirname) if f.endswith(extension)]
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parents:
diff changeset
543 tmp.sort()
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
544 if remove:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
545 return [removeExtension(f, extension) for f in tmp]
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
546 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
547 return tmp
aed8eb63cdde initial commit with non-functional python code for NGSIM
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548
266
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549 def mkdir(dirname):
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550 'Creates a directory if it does not exist'
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551 import os
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552 if not os.path.exists(dirname):
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553 os.mkdir(dirname)
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554 else:
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555 print(dirname+' already exists')
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556
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557 def removeFile(filename):
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558 '''Deletes the file while avoiding raising an error
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559 if the file does not exist'''
266
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560 import os
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561 if (os.path.exists(filename)):
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562 os.remove(filename)
266
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563 else:
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564 print(filename+' does not exist')
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565
42
1a2ac2d4f53a added loading of the rest of the data for objects
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parents: 35
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566 def line2Floats(l, separator=' '):
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567 '''Returns the list of floats corresponding to the string'''
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568 return [float(x) for x in l.split(separator)]
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569
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570 def line2Ints(l, separator=' '):
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571 '''Returns the list of ints corresponding to the string'''
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572 return [int(x) for x in l.split(separator)]
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573
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574 #########################
332
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575 # CLI utils
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576 #########################
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577
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578 def parseCLIOptions(helpMessage, options, cliArgs, optionalOptions=[]):
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579 ''' Simple function to handle similar argument parsing
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580 Returns the dictionary of options and their values
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581
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582 * cliArgs are most likely directly sys.argv
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583 (only the elements after the first one are considered)
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584
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585 * options should be a list of strings for getopt options,
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586 eg ['frame=','correspondences=','video=']
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587 A value must be provided for each option, or the program quits'''
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588 import sys, getopt
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589 from numpy.core.fromnumeric import all
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590 optionValues, args = getopt.getopt(cliArgs[1:], 'h', ['help']+options+optionalOptions)
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591 optionValues = dict(optionValues)
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592
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593 if '--help' in optionValues.keys() or '-h' in optionValues.keys():
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594 print(helpMessage+
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595 '\n - Compulsory options: '+' '.join([opt.replace('=','') for opt in options])+
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596 '\n - Non-compulsory options: '+' '.join([opt.replace('=','') for opt in optionalOptions]))
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597 sys.exit()
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598
a6ca86107f27 reorganized utils module
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599 missingArgument = [('--'+opt.replace('=','') in optionValues.keys()) for opt in options]
a6ca86107f27 reorganized utils module
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diff changeset
600 if not all(missingArgument):
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diff changeset
601 print('Missing argument')
a6ca86107f27 reorganized utils module
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602 print(optionValues)
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603 sys.exit()
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diff changeset
604
a6ca86107f27 reorganized utils module
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diff changeset
605 return optionValues
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
606
397
b36b00dd27c3 added function to read scene metadata
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parents: 395
diff changeset
607
b36b00dd27c3 added function to read scene metadata
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parents: 395
diff changeset
608 #########################
553
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diff changeset
609 # Profiling
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parents: 547
diff changeset
610 #########################
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
611
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
612 def analyzeProfile(profileFilename, stripDirs = True):
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parents: 547
diff changeset
613 '''Analyze the file produced by cProfile
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
614
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
615 obtained by for example:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
616 - call in script (for main() function in script)
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
617 import cProfile, os
3622a5653ee9 added basic info and function to profile code
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parents: 547
diff changeset
618 cProfile.run('main()', os.path.join(os.getcwd(),'main.profile'))
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
619
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
620 - or on the command line:
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parents: 547
diff changeset
621 python -m cProfile [-o profile.bin] [-s sort] scriptfile [arg]'''
3622a5653ee9 added basic info and function to profile code
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parents: 547
diff changeset
622 import pstats, os
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
623 p = pstats.Stats(os.path.join(os.pardir, profileFilename))
3622a5653ee9 added basic info and function to profile code
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parents: 547
diff changeset
624 if stripDirs:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
625 p.strip_dirs()
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
626 p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
627 p.print_stats(.2)
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
628 #p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
629 # p.print_callees(.1, 'int_prediction.py:')
3622a5653ee9 added basic info and function to profile code
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parents: 547
diff changeset
630 return p
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
631
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
632 #########################
31
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diff changeset
633 # running tests
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parents: 29
diff changeset
634 #########################
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parents: 29
diff changeset
635
0
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parents:
diff changeset
636 if __name__ == "__main__":
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
637 import doctest
2
de5642925615 started implementation of TimeInterval and Spatio-temporal object
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parents: 0
diff changeset
638 import unittest
31
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parents: 29
diff changeset
639 suite = doctest.DocFileSuite('tests/utils.txt')
c000f37c316d moved tests to independent file, added chi2 computation
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parents: 29
diff changeset
640 #suite = doctest.DocTestSuite()
2
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parents: 0
diff changeset
641 unittest.TextTestRunner().run(suite)
de5642925615 started implementation of TimeInterval and Spatio-temporal object
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parents: 0
diff changeset
642 #doctest.testmod()
0
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parents:
diff changeset
643 #doctest.testfile("example.txt")