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annotate python/utils.py @ 637:c9a0b72979fd

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added function to get canadian public weather data
author Nicolas Saunier <nicolas.saunier@polymtl.ca>
date Thu, 02 Apr 2015 15:53:59 +0200
parents 0954aaf28231
children 784298512b60
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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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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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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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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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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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diff changeset
152
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parents: 76
diff changeset
153
31
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diff changeset
154 #########################
370
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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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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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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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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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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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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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diff changeset
183 return 1.
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diff changeset
184 else:
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diff changeset
185 return 0.
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186
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diff changeset
187 def gaussian(center, x, halfwidth):
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diff changeset
188 from numpy import exp
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diff changeset
189 return exp(-((center-x)/halfwidth)**2/2)
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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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diff changeset
194 return 1.-(diff/halfwidth)**2
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diff changeset
195 else:
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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()):
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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
Nicolas Saunier <nicolas.saunier@polymtl.ca>
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
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parents: 241
diff changeset
221 seconds = seconds - m*60
262
a048066bd20f correcting bug in framesToTime
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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)
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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'''
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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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Nicolas Saunier <nicolas.saunier@polymtl.ca>
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.
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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
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parents: 569
diff changeset
256 catgories = deepcopy(cat_list)
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parents: 569
diff changeset
257 smoothed = catgories
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
258 for point in range(len(catgories)):
e24eeb244698 first implementation of projection to curvilinear coordinates
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parents: 569
diff changeset
259 lower_bound_check = max(0,point-halfWidth)
e24eeb244698 first implementation of projection to curvilinear coordinates
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parents: 569
diff changeset
260 upper_bound_check = min(len(catgories)-1,point+halfWidth+1)
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parents: 569
diff changeset
261 window_values = catgories[lower_bound_check:upper_bound_check]
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parents: 569
diff changeset
262 smoothed[point] = max(set(window_values), key=window_values.count)
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parents: 569
diff changeset
263 return smoothed
e24eeb244698 first implementation of projection to curvilinear coordinates
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parents: 569
diff changeset
264
547
97c5fef5b2d6 corrected bugs
MohamedGomaa
parents: 521
diff changeset
265 def filterMovingWindow(inputSignal, halfWidth):
29
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
266 '''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
267 The first and last points are copied from the original.'''
547
97c5fef5b2d6 corrected bugs
MohamedGomaa
parents: 521
diff changeset
268 from numpy import ones,convolve,array
29
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
269 width = float(halfWidth*2+1)
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parents: 27
diff changeset
270 win = ones(width,'d')
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
271 result = convolve(win/width,array(inputSignal),'same')
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 result[-halfWidth:] = inputSignal[-halfWidth:]
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
274 return result
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
275
199
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
276 def linearRegression(x, y, deg = 1, plotData = False):
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277 '''returns the least square estimation of the linear regression of y = ax+b
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diff changeset
278 as well as the plot'''
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diff changeset
279 from numpy.lib.polynomial import polyfit
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diff changeset
280 from matplotlib.pyplot import plot
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281 from numpy.core.multiarray import arange
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diff changeset
282 coef = polyfit(x, y, deg)
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diff changeset
283 if plotData:
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diff changeset
284 def poly(x):
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diff changeset
285 result = 0
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diff changeset
286 for i in range(len(coef)):
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diff changeset
287 result += coef[i]*x**(len(coef)-i-1)
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diff changeset
288 return result
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289 plot(x, y, 'x')
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diff changeset
290 xx = arange(min(x), max(x),(max(x)-min(x))/1000)
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diff changeset
291 plot(xx, [poly(z) for z in xx])
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diff changeset
292 return coef
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293
27
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parents: 24
diff changeset
294 #########################
455
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diff changeset
295 # iterable section
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parents: 434
diff changeset
296 #########################
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diff changeset
297
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diff changeset
298 def mostCommon(L):
456
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diff changeset
299 '''Returns the most frequent element in a iterable
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diff changeset
300
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parents: 455
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301 taken from http://stackoverflow.com/questions/1518522/python-most-common-element-in-a-list'''
455
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diff changeset
302 from itertools import groupby
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diff changeset
303 from operator import itemgetter
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304 # get an iterable of (item, iterable) pairs
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diff changeset
305 SL = sorted((x, i) for i, x in enumerate(L))
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diff changeset
306 # print 'SL:', SL
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diff changeset
307 groups = groupby(SL, key=itemgetter(0))
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diff changeset
308 # auxiliary function to get "quality" for an item
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diff changeset
309 def _auxfun(g):
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diff changeset
310 item, iterable = g
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311 count = 0
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312 min_index = len(L)
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diff changeset
313 for _, where in iterable:
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diff changeset
314 count += 1
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diff changeset
315 min_index = min(min_index, where)
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diff changeset
316 # print 'item %r, count %r, minind %r' % (item, count, min_index)
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diff changeset
317 return count, -min_index
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diff changeset
318 # pick the highest-count/earliest item
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diff changeset
319 return max(groups, key=_auxfun)[0]
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diff changeset
320
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parents: 434
diff changeset
321 #########################
370
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diff changeset
322 # sequence section
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parents: 369
diff changeset
323 #########################
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diff changeset
324
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diff changeset
325 class LCSS:
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parents: 369
diff changeset
326 '''Class that keeps the LCSS parameters
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parents: 369
diff changeset
327 and puts together the various computations'''
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diff changeset
328 def __init__(self, similarityFunc, delta = float('inf'), aligned = False, lengthFunc = min):
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diff changeset
329 self.similarityFunc = similarityFunc
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diff changeset
330 self.aligned = aligned
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diff changeset
331 self.delta = delta
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diff changeset
332 self.lengthFunc = lengthFunc
389
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diff changeset
333 self.subSequenceIndices = [(0,0)]
370
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diff changeset
334
373
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parents: 372
diff changeset
335 def similarities(self, l1, l2, jshift=0):
370
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parents: 369
diff changeset
336 from numpy import zeros, int as npint
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parents: 369
diff changeset
337 n1 = len(l1)
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diff changeset
338 n2 = len(l2)
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diff changeset
339 self.similarityTable = zeros((n1+1,n2+1), dtype = npint)
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diff changeset
340 for i in xrange(1,n1+1):
374
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parents: 373
diff changeset
341 for j in xrange(max(1,i-jshift-self.delta),min(n2,i-jshift+self.delta)+1):
370
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diff changeset
342 if self.similarityFunc(l1[i-1], l2[j-1]):
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diff changeset
343 self.similarityTable[i,j] = self.similarityTable[i-1,j-1]+1
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diff changeset
344 else:
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diff changeset
345 self.similarityTable[i,j] = max(self.similarityTable[i-1,j], self.similarityTable[i,j-1])
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diff changeset
346
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diff changeset
347 def subSequence(self, i, j):
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diff changeset
348 '''Returns the subsequence of two sequences
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diff changeset
349 http://en.wikipedia.org/wiki/Longest_common_subsequence_problem'''
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parents: 369
diff changeset
350 if i == 0 or j == 0:
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diff changeset
351 return []
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diff changeset
352 elif self.similarityTable[i][j] == self.similarityTable[i][j-1]:
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diff changeset
353 return self.subSequence(i, j-1)
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parents: 369
diff changeset
354 elif self.similarityTable[i][j] == self.similarityTable[i-1][j]:
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parents: 369
diff changeset
355 return self.subSequence(i-1, j)
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parents: 369
diff changeset
356 else:
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diff changeset
357 return self.subSequence(i-1, j-1) + [(i-1,j-1)]
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parents: 369
diff changeset
358
373
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parents: 372
diff changeset
359 def _compute(self, _l1, _l2, computeSubSequence = False):
370
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parents: 369
diff changeset
360 '''returns the longest common subsequence similarity
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parents: 369
diff changeset
361 based on the threshold on distance between two elements of lists l1, l2
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parents: 369
diff changeset
362 similarityFunc returns True or False whether the two points are considered similar
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parents: 369
diff changeset
363
607
84690dfe5560 add some functions for behaviour analysis
MohamedGomaa
parents: 574
diff changeset
364 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
365
370
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parents: 369
diff changeset
366 eg distance(p1, p2) < epsilon
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parents: 369
diff changeset
367 '''
372
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
368 if len(_l2) < len(_l1): # l1 is the shortest
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
369 l1 = _l2
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
370 l2 = _l1
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
371 revertIndices = True
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
372 else:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
373 l1 = _l1
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parents: 371
diff changeset
374 l2 = _l2
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
375 revertIndices = False
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
376 n1 = len(l1)
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parents: 371
diff changeset
377 n2 = len(l2)
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parents: 371
diff changeset
378
370
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parents: 369
diff changeset
379 if self.aligned:
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parents: 369
diff changeset
380 lcssValues = {}
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parents: 369
diff changeset
381 similarityTables = {}
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
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parents: 373
diff changeset
382 for i in xrange(-n2-self.delta+1, n1+self.delta): # interval such that [i-shift-delta, i-shift+delta] is never empty, which happens when i-shift+delta < 1 or when i-shift-delta > n2
373
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
383 self.similarities(l1, l2, i)
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parents: 372
diff changeset
384 lcssValues[i] = self.similarityTable.max()
370
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parents: 369
diff changeset
385 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
386 #print self.similarityTable
521
3707eeb20f25 changed argMaxDict name to argmaxDict
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 518
diff changeset
387 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
388 self.similarityTable = similarityTables[alignmentShift]
372
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
389 else:
389
6d26dcc7bba0 modifications to compute alignment for None indicators
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
390 alignmentShift = 0
372
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
391 self.similarities(l1, l2)
373
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parents: 372
diff changeset
392
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
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parents: 373
diff changeset
393 # 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
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parents: 381
diff changeset
394 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
395
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
396 if computeSubSequence:
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parents: 371
diff changeset
397 self.subSequenceIndices = self.subSequence(self.similarityTable.shape[0]-1, self.similarityTable.shape[1]-1)
371
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 370
diff changeset
398 if revertIndices:
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
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parents: 373
diff changeset
399 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
400 return self.similarityTable[-1,-1]
370
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parents: 369
diff changeset
401
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parents: 369
diff changeset
402 def compute(self, l1, l2, computeSubSequence = False):
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parents: 369
diff changeset
403 '''get methods are to be shadowed in child classes '''
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parents: 369
diff changeset
404 return self._compute(l1, l2, computeSubSequence)
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parents: 369
diff changeset
405
375
2ea8584aa80a making indicator LCSS work
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 374
diff changeset
406 def computeAlignment(self):
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
407 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
408 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
409
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
410 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
411 ''' compute the normalized LCSS
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
412 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
413 lengthFunc = lambda x,y:float(x,y)/2'''
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
414 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
415
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
416 def computeNormalized(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
417 return self._computeNormalized(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
418
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
419 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
420 ''' compute the LCSS distance'''
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
421 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
422
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
423 def computeDistance(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
424 return self._computeDistance(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
425
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
426 #########################
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
427 # plotting section
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
428 #########################
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
429
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
430 def plotPolygon(poly, options = ''):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
431 'Plots shapely polygon poly'
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
432 from numpy.core.multiarray import array
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
433 from matplotlib.pyplot import plot
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
434 from shapely.geometry import Polygon
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
435
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
436 tmp = array(poly.exterior)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
437 plot(tmp[:,0], tmp[:,1], options)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
438
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
439 def stepPlot(X, firstX, lastX, initialCount = 0, increment = 1):
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
440 '''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
441 returns the lists that can be plotted
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
442 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
443 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
444
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
445 sortedX = []
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
446 counts = [initialCount]
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
447 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
448 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
449 counts.append(counts[-1])
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
450 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
451 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
452 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
453
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
454 class PlottingPropertyValues:
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
455 def __init__(self, values):
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
456 self.values = values
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
457
116
2bf5b76320c0 moved intersection plotting and added markers for scatter plots
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 115
diff changeset
458 def __getitem__(self, i):
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
459 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
460
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
461 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
462 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
463
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
464 linestyles = PlottingPropertyValues(['-', '--', '-.', ':'])
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
465
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
466 colors = PlottingPropertyValues('brgmyck') # 'w'
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
467
115
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
468 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
469 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
470 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
471 coords = array(indicatorMap.keys())
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
472 minX = min(coords[:,0])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
473 minY = min(coords[:,1])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
474 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
475 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
476 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
477 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
478 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
479 if masked:
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
480 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
481 else:
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
482 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
483
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
484 #########################
637
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
485 # Data download
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
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
488 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
489 '''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
490 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
491 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
492
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
493 Example: MONTREAL MCTAVISH 10761
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
494 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
495
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
496 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
497 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
498 import urllib2
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
499 if english:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
500 language = 'e'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
501 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
502 language = 'f'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
503 if len(months) == 0:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
504 timeFrame = 2
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
505 months = [1]
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
506 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
507 timeFrame = 1
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
508
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
509 for year in years:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
510 for month in months:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
511 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
512 data = url.read()
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
513 outFilename = '{}/{}-{}'.format(outputDirectoryname, stationID, year)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
514 if timeFrame == 1:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
515 outFilename += '-{}-hourly'.format(month)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
516 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
517 outFilename += '-daily'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
518 outFilename += '.csv'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
519 out = open(outFilename, 'w')
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
520 out.write(data)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
521 out.close()
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 #########################
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
524 # File I/O
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
525 #########################
24
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
526
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
527 def removeExtension(filename, delimiter = '.'):
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
528 '''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
529 i = filename.rfind(delimiter)
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
530 if i>0:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
531 return filename[:i]
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
532 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
533 return filename
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
534
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
535 def cleanFilename(s):
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
536 'cleans filenames obtained when contatenating figure characteristics'
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
537 return s.replace(' ','-').replace('.','').replace('/','-')
46
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parents: 45
diff changeset
538
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
539 def listfiles(dirname, extension, remove = False):
14
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parents: 7
diff changeset
540 '''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
541 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
542 from os import listdir
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
543 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
544 tmp.sort()
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
545 if remove:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
546 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
547 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
548 return tmp
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
549
266
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diff changeset
550 def mkdir(dirname):
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parents: 262
diff changeset
551 'Creates a directory if it does not exist'
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
552 import os
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parents: 262
diff changeset
553 if not os.path.exists(dirname):
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
554 os.mkdir(dirname)
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parents: 262
diff changeset
555 else:
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parents: 262
diff changeset
556 print(dirname+' already exists')
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parents: 262
diff changeset
557
14
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
558 def removeFile(filename):
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
559 '''Deletes the file while avoiding raising an error
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
560 if the file does not exist'''
266
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
561 import os
14
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
562 if (os.path.exists(filename)):
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
563 os.remove(filename)
266
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
564 else:
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parents: 262
diff changeset
565 print(filename+' does not exist')
14
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
566
42
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
567 def line2Floats(l, separator=' '):
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parents: 35
diff changeset
568 '''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
569 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
570
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
571 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
572 '''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
573 return [int(x) for x in l.split(separator)]
31
c000f37c316d moved tests to independent file, added chi2 computation
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parents: 29
diff changeset
574
c000f37c316d moved tests to independent file, added chi2 computation
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parents: 29
diff changeset
575 #########################
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
576 # CLI utils
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
577 #########################
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
578
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
579 def parseCLIOptions(helpMessage, options, cliArgs, optionalOptions=[]):
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
580 ''' Simple function to handle similar argument parsing
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
581 Returns the dictionary of options and their values
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
582
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parents: 324
diff changeset
583 * cliArgs are most likely directly sys.argv
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
584 (only the elements after the first one are considered)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
585
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
586 * options should be a list of strings for getopt options,
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
587 eg ['frame=','correspondences=','video=']
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
588 A value must be provided for each option, or the program quits'''
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
589 import sys, getopt
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
590 from numpy.core.fromnumeric import all
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
591 optionValues, args = getopt.getopt(cliArgs[1:], 'h', ['help']+options+optionalOptions)
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
592 optionValues = dict(optionValues)
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
593
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
594 if '--help' in optionValues.keys() or '-h' in optionValues.keys():
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
595 print(helpMessage+
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
596 '\n - Compulsory options: '+' '.join([opt.replace('=','') for opt in options])+
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
597 '\n - Non-compulsory options: '+' '.join([opt.replace('=','') for opt in optionalOptions]))
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
598 sys.exit()
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
599
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
600 missingArgument = [('--'+opt.replace('=','') in optionValues.keys()) for opt in options]
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
601 if not all(missingArgument):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
602 print('Missing argument')
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
603 print(optionValues)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
604 sys.exit()
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
605
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
606 return optionValues
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
607
397
b36b00dd27c3 added function to read scene metadata
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 395
diff changeset
608
b36b00dd27c3 added function to read scene metadata
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 395
diff changeset
609 #########################
553
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
610 # Profiling
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
611 #########################
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
612
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
613 def analyzeProfile(profileFilename, stripDirs = True):
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
614 '''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
615
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
616 obtained by for example:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
617 - call in script (for main() function in script)
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
618 import cProfile, os
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
619 cProfile.run('main()', os.path.join(os.getcwd(),'main.profile'))
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
620
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
621 - or on the command line:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
622 python -m cProfile [-o profile.bin] [-s sort] scriptfile [arg]'''
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
623 import pstats, os
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
624 p = pstats.Stats(os.path.join(os.pardir, profileFilename))
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
625 if stripDirs:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
626 p.strip_dirs()
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
627 p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
628 p.print_stats(.2)
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
629 #p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
630 # p.print_callees(.1, 'int_prediction.py:')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
631 return p
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
632
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
633 #########################
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
634 # running tests
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
635 #########################
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
636
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
637 if __name__ == "__main__":
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
638 import doctest
2
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
639 import unittest
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
640 suite = doctest.DocFileSuite('tests/utils.txt')
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
641 #suite = doctest.DocTestSuite()
2
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
642 unittest.TextTestRunner().run(suite)
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
643 #doctest.testmod()
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
644 #doctest.testfile("example.txt")