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annotate python/utils.py @ 665:15e244d2a1b5

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corrected bug with circular import for VideoFilenameAddable, moved to base module
author Nicolas Saunier <nicolas.saunier@polymtl.ca>
date Wed, 20 May 2015 13:57:47 +0200
parents 784298512b60
children 179b81faa1f8
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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 datetime import time, datetime
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5 from math import sqrt
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7
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8 datetimeFormat = "%Y-%m-%d %H:%M:%S"
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9
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10 #########################
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11 # Enumerations
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12 #########################
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13
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14 def inverseEnumeration(l):
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15 'Returns the dictionary that provides for each element in the input list its index in the input list'
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16 result = {}
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17 for i,x in enumerate(l):
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18 result[x] = i
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19 return result
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20
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21 #########################
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22 # Simple statistics
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23 #########################
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24
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25 def sampleSize(stdev, tolerance, percentConfidence, printLatex = False):
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26 from scipy.stats.distributions import norm
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27 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1)*100)/100. # 1.-(100-percentConfidence)/200.
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28 if printLatex:
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29 print('${0}^2\\frac{{{1}^2}}{{{2}^2}}$'.format(k, stdev, tolerance))
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30 return (k*stdev/tolerance)**2
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31
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32 def confidenceInterval(mean, stdev, nSamples, percentConfidence, trueStd = True, printLatex = False):
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33 '''if trueStd, use normal distribution, otherwise, Student
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34
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35 Use otherwise t.interval or norm.interval
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36 ex: norm.interval(0.95, loc = 0., scale = 2.3/sqrt(11))
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37 t.interval(0.95, 10, loc=1.2, scale = 2.3/sqrt(nSamples))
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38 loc is mean, scale is sigma/sqrt(n) (for Student, 10 is df)'''
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39 from math import sqrt
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40 from scipy.stats.distributions import norm, t
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41 if trueStd:
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42 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1)*100)/100. # 1.-(100-percentConfidence)/200.
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43 else: # use Student
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44 k = round(t.ppf(0.5+percentConfidence/200., nSamples-1)*100)/100.
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45 e = k*stdev/sqrt(nSamples)
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46 if printLatex:
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47 print('${0} \pm {1}\\frac{{{2}}}{{\sqrt{{{3}}}}}$'.format(mean, k, stdev, nSamples))
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48 return mean-e, mean+e
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49
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50 def computeChi2(expected, observed):
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51 '''Returns the Chi2 statistics'''
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52 result = 0.
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53 for e, o in zip(expected, observed):
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54 result += ((e-o)*(e-o))/e
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55 return result
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56
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57 class EmpiricalDistribution(object):
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58 def nSamples(self):
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59 return sum(self.counts)
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60
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61 def cumulativeDensityFunction(sample, normalized = False):
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62 '''Returns the cumulative density function of the sample of a random variable'''
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63 from numpy import arange, cumsum
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64 xaxis = sorted(sample)
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65 counts = arange(1,len(sample)+1) # dtype = float
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66 if normalized:
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67 counts /= float(len(sample))
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68 return xaxis, counts
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70 class EmpiricalDiscreteDistribution(EmpiricalDistribution):
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71 '''Class to represent a sample of a distribution for a discrete random variable
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72 '''
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73 from numpy.core.fromnumeric import sum
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74
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75 def __init__(self, categories, counts):
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76 self.categories = categories
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77 self.counts = counts
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78
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79 def mean(self):
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80 result = [float(x*y) for x,y in zip(self.categories, self.counts)]
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81 return sum(result)/self.nSamples()
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82
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83 def var(self, mean = None):
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84 if not mean:
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85 m = self.mean()
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86 else:
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87 m = mean
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88 result = 0.
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89 squares = [float((x-m)*(x-m)*y) for x,y in zip(self.categories, self.counts)]
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90 return sum(squares)/(self.nSamples()-1)
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91
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92 def referenceCounts(self, probability):
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93 '''probability is a function that returns the probability of the random variable for the category values'''
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94 refProba = [probability(c) for c in self.categories]
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95 refProba[-1] = 1-sum(refProba[:-1])
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96 refCounts = [r*self.nSamples() for r in refProba]
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97 return refCounts, refProba
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98
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99 class EmpiricalContinuousDistribution(EmpiricalDistribution):
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100 '''Class to represent a sample of a distribution for a continuous random variable
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101 with the number of observations for each interval
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102 intervals (categories variable) are defined by their left limits, the last one being the right limit
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103 categories contain therefore one more element than the counts'''
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104 def __init__(self, categories, counts):
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105 # todo add samples for initialization and everything to None? (or setSamples?)
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106 self.categories = categories
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107 self.counts = counts
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108
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109 def mean(self):
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110 result = 0.
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111 for i in range(len(self.counts)-1):
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112 result += self.counts[i]*(self.categories[i]+self.categories[i+1])/2
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113 return result/self.nSamples()
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114
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115 def var(self, mean = None):
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116 if not mean:
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117 m = self.mean()
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118 else:
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119 m = mean
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120 result = 0.
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121 for i in range(len(self.counts)-1):
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122 mid = (self.categories[i]+self.categories[i+1])/2
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123 result += self.counts[i]*(mid - m)*(mid - m)
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124 return result/(self.nSamples()-1)
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125
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126 def referenceCounts(self, cdf):
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127 '''cdf is a cumulative distribution function
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128 returning the probability of the variable being less that x'''
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129 # refCumulativeCounts = [0]#[cdf(self.categories[0][0])]
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130 # for inter in self.categories:
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131 # refCumulativeCounts.append(cdf(inter[1]))
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132 refCumulativeCounts = [cdf(x) for x in self.categories[1:-1]]
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133
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parents: 32
diff changeset
134 refProba = [refCumulativeCounts[0]]
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parents: 32
diff changeset
135 for i in xrange(1,len(refCumulativeCounts)):
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parents: 32
diff changeset
136 refProba.append(refCumulativeCounts[i]-refCumulativeCounts[i-1])
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parents: 32
diff changeset
137 refProba.append(1-refCumulativeCounts[-1])
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parents: 32
diff changeset
138 refCounts = [p*self.nSamples() for p in refProba]
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parents: 32
diff changeset
139
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parents: 32
diff changeset
140 return refCounts, refProba
31
c000f37c316d moved tests to independent file, added chi2 computation
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parents: 29
diff changeset
141
77
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parents: 76
diff changeset
142 def printReferenceCounts(self, refCounts=None):
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parents: 76
diff changeset
143 if refCounts:
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parents: 76
diff changeset
144 ref = refCounts
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parents: 76
diff changeset
145 else:
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parents: 76
diff changeset
146 ref = self.referenceCounts
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parents: 76
diff changeset
147 for i in xrange(len(ref[0])):
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diff changeset
148 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
149
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parents: 76
diff changeset
150
31
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parents: 29
diff changeset
151 #########################
370
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diff changeset
152 # maths section
27
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diff changeset
153 #########################
24
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154
433
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diff changeset
155 # def kernelSmoothing(sampleX, X, Y, weightFunc, halfwidth):
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156 # '''Returns a smoothed weighted version of Y at the predefined values of sampleX
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diff changeset
157 # Sum_x weight(sample_x,x) * y(x)'''
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diff changeset
158 # from numpy import zeros, array
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159 # smoothed = zeros(len(sampleX))
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diff changeset
160 # for i,x in enumerate(sampleX):
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diff changeset
161 # weights = array([weightFunc(x,xx, halfwidth) for xx in X])
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diff changeset
162 # if sum(weights)>0:
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diff changeset
163 # smoothed[i] = sum(weights*Y)/sum(weights)
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diff changeset
164 # else:
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diff changeset
165 # smoothed[i] = 0
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diff changeset
166 # return smoothed
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167
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diff changeset
168 def kernelSmoothing(x, X, Y, weightFunc, halfwidth):
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diff changeset
169 '''Returns the smoothed estimate of (X,Y) at x
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diff changeset
170 Sum_x weight(sample_x,x) * y(x)'''
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diff changeset
171 from numpy import zeros, array
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diff changeset
172 weights = array([weightFunc(x,observedx, halfwidth) for observedx in X])
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diff changeset
173 if sum(weights)>0:
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parents: 423
diff changeset
174 return sum(weights*Y)/sum(weights)
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diff changeset
175 else:
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diff changeset
176 return 0
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diff changeset
177
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diff changeset
178 def uniform(center, x, halfwidth):
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parents: 423
diff changeset
179 if abs(center-x)<halfwidth:
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diff changeset
180 return 1.
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diff changeset
181 else:
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diff changeset
182 return 0.
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183
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diff changeset
184 def gaussian(center, x, halfwidth):
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diff changeset
185 from numpy import exp
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diff changeset
186 return exp(-((center-x)/halfwidth)**2/2)
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187
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diff changeset
188 def epanechnikov(center, x, halfwidth):
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189 diff = abs(center-x)
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diff changeset
190 if diff<halfwidth:
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diff changeset
191 return 1.-(diff/halfwidth)**2
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diff changeset
192 else:
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diff changeset
193 return 0.
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194
434
9a714f32fc9f small updates
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diff changeset
195 def triangular(center, x, halfwidth):
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diff changeset
196 diff = abs(center-x)
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diff changeset
197 if diff<halfwidth:
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diff changeset
198 return 1.-abs(diff/halfwidth)
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diff changeset
199 else:
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diff changeset
200 return 0.
433
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parents: 423
diff changeset
201
518
0c86c73f3c09 median smoothing
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parents: 511
diff changeset
202 def medianSmoothing(x, X, Y, halfwidth):
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parents: 511
diff changeset
203 '''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
204 from numpy import median
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parents: 511
diff changeset
205 return median([y for observedx, y in zip(X,Y) if abs(x-observedx)<halfwidth])
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parents: 511
diff changeset
206
521
3707eeb20f25 changed argMaxDict name to argmaxDict
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parents: 518
diff changeset
207 def argmaxDict(d):
561
ee45c6eb6d49 added Mohamed Gomaa Mohamed function to smooth object trajectories
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parents: 553
diff changeset
208 return max(d, key=d.get)
279
3af4c267a7bf generic simple LCSS
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parents: 276
diff changeset
209
395
6fba1ab040f1 minor modification to framestotime
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parents: 391
diff changeset
210 def framesToTime(nFrames, frameRate, initialTime = time()):
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parents: 391
diff changeset
211 '''returns a datetime.time for the time in hour, minutes and seconds
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parents: 391
diff changeset
212 initialTime is a datetime.time'''
248
571ba5ed22e2 added utils for bus processing
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parents: 241
diff changeset
213 from math import floor
395
6fba1ab040f1 minor modification to framestotime
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parents: 391
diff changeset
214 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
215 h = int(floor(seconds/3600.))
248
571ba5ed22e2 added utils for bus processing
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parents: 241
diff changeset
216 seconds = seconds - h*3600
261
4aa792cb0fa9 changing framesToTime to return a datetime.time
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 248
diff changeset
217 m = int(floor(seconds/60))
248
571ba5ed22e2 added utils for bus processing
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parents: 241
diff changeset
218 seconds = seconds - m*60
262
a048066bd20f correcting bug in framesToTime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 261
diff changeset
219 return time(h, m, seconds)
248
571ba5ed22e2 added utils for bus processing
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parents: 241
diff changeset
220
381
387cc0142211 script to replay event annotations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 376
diff changeset
221 def timeToFrames(t, frameRate):
387cc0142211 script to replay event annotations
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parents: 376
diff changeset
222 return frameRate*(t.hour*3600+t.minute*60+t.second)
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parents: 376
diff changeset
223
241
ee1caff48b03 added function to sort to list of paired data X,Y
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
224 def sortXY(X,Y):
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parents: 235
diff changeset
225 'returns the sorted (x, Y(x)) sorted on X'
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parents: 235
diff changeset
226 D = {}
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parents: 235
diff changeset
227 for x, y in zip(X,Y):
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parents: 235
diff changeset
228 D[x]=y
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parents: 235
diff changeset
229 xsorted = sorted(D.keys())
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parents: 235
diff changeset
230 return xsorted, [D[x] for x in xsorted]
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parents: 235
diff changeset
231
32
48e56179c39e added ceil function
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parents: 31
diff changeset
232 def ceilDecimals(v, nDecimals):
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parents: 31
diff changeset
233 '''Rounds the number at the nth decimal
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parents: 31
diff changeset
234 eg 1.23 at 0 decimal is 2, at 1 decimal is 1.3'''
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parents: 31
diff changeset
235 from math import ceil,pow
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parents: 31
diff changeset
236 tens = pow(10,nDecimals)
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parents: 31
diff changeset
237 return ceil(v*tens)/tens
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parents: 31
diff changeset
238
152
74b1fc68d4df re-organized code to avoid cyclic python module dependencies
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 116
diff changeset
239 def inBetween(bound1, bound2, x):
569
0057c04f94d5 work in progress on intersections (for PET)
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parents: 561
diff changeset
240 return bound1 <= x <= bound2 or bound2 <= x <= bound1
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parents: 561
diff changeset
241
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
242 def pointDistanceL2(x1,y1,x2,y2):
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
243 ''' 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
244 return sqrt((x2-x1)**2+(y2-y1)**2)
24
6fb59cfb201e first version of segmentIntersection
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parents: 19
diff changeset
245
6fb59cfb201e first version of segmentIntersection
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parents: 19
diff changeset
246 def crossProduct(l1, l2):
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parents: 19
diff changeset
247 return l1[0]*l2[1]-l1[1]*l2[0]
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parents: 19
diff changeset
248
574
e24eeb244698 first implementation of projection to curvilinear coordinates
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parents: 569
diff changeset
249 def cat_mvgavg(cat_list, halfWidth):
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parents: 569
diff changeset
250 ''' Return a list of categories/values smoothed according to a window.
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
251 halfWidth is the search radius on either side'''
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parents: 569
diff changeset
252 from copy import deepcopy
659
784298512b60 minor modifications
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parents: 637
diff changeset
253 smoothed = deepcopy(cat_list)
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parents: 637
diff changeset
254 for point in range(len(cat_list)):
574
e24eeb244698 first implementation of projection to curvilinear coordinates
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parents: 569
diff changeset
255 lower_bound_check = max(0,point-halfWidth)
659
784298512b60 minor modifications
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parents: 637
diff changeset
256 upper_bound_check = min(len(cat_list)-1,point+halfWidth+1)
784298512b60 minor modifications
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parents: 637
diff changeset
257 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
258 smoothed[point] = max(set(window_values), key=window_values.count)
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parents: 569
diff changeset
259 return smoothed
e24eeb244698 first implementation of projection to curvilinear coordinates
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parents: 569
diff changeset
260
547
97c5fef5b2d6 corrected bugs
MohamedGomaa
parents: 521
diff changeset
261 def filterMovingWindow(inputSignal, halfWidth):
29
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
262 '''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
263 The first and last points are copied from the original.'''
547
97c5fef5b2d6 corrected bugs
MohamedGomaa
parents: 521
diff changeset
264 from numpy import ones,convolve,array
29
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
265 width = float(halfWidth*2+1)
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parents: 27
diff changeset
266 win = ones(width,'d')
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parents: 27
diff changeset
267 result = convolve(win/width,array(inputSignal),'same')
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
268 result[:halfWidth] = inputSignal[:halfWidth]
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
269 result[-halfWidth:] = inputSignal[-halfWidth:]
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
270 return result
ca8e716cc231 added moving average filter
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parents: 27
diff changeset
271
199
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
272 def linearRegression(x, y, deg = 1, plotData = False):
ca9d9104afba added utility to calibrate polynoms and plot
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parents: 197
diff changeset
273 '''returns the least square estimation of the linear regression of y = ax+b
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
274 as well as the plot'''
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
275 from numpy.lib.polynomial import polyfit
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parents: 197
diff changeset
276 from matplotlib.pyplot import plot
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diff changeset
277 from numpy.core.multiarray import arange
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parents: 197
diff changeset
278 coef = polyfit(x, y, deg)
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parents: 197
diff changeset
279 if plotData:
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parents: 197
diff changeset
280 def poly(x):
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diff changeset
281 result = 0
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parents: 197
diff changeset
282 for i in range(len(coef)):
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parents: 197
diff changeset
283 result += coef[i]*x**(len(coef)-i-1)
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parents: 197
diff changeset
284 return result
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parents: 197
diff changeset
285 plot(x, y, 'x')
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parents: 197
diff changeset
286 xx = arange(min(x), max(x),(max(x)-min(x))/1000)
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parents: 197
diff changeset
287 plot(xx, [poly(z) for z in xx])
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parents: 197
diff changeset
288 return coef
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parents: 197
diff changeset
289
27
44689029a86f updated segmentIntersection and other
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parents: 24
diff changeset
290 #########################
455
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parents: 434
diff changeset
291 # iterable section
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parents: 434
diff changeset
292 #########################
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parents: 434
diff changeset
293
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parents: 434
diff changeset
294 def mostCommon(L):
456
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parents: 455
diff changeset
295 '''Returns the most frequent element in a iterable
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parents: 455
diff changeset
296
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parents: 455
diff changeset
297 taken from http://stackoverflow.com/questions/1518522/python-most-common-element-in-a-list'''
455
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parents: 434
diff changeset
298 from itertools import groupby
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parents: 434
diff changeset
299 from operator import itemgetter
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parents: 434
diff changeset
300 # get an iterable of (item, iterable) pairs
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parents: 434
diff changeset
301 SL = sorted((x, i) for i, x in enumerate(L))
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parents: 434
diff changeset
302 # print 'SL:', SL
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parents: 434
diff changeset
303 groups = groupby(SL, key=itemgetter(0))
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parents: 434
diff changeset
304 # auxiliary function to get "quality" for an item
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parents: 434
diff changeset
305 def _auxfun(g):
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parents: 434
diff changeset
306 item, iterable = g
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diff changeset
307 count = 0
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diff changeset
308 min_index = len(L)
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parents: 434
diff changeset
309 for _, where in iterable:
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diff changeset
310 count += 1
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diff changeset
311 min_index = min(min_index, where)
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parents: 434
diff changeset
312 # print 'item %r, count %r, minind %r' % (item, count, min_index)
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diff changeset
313 return count, -min_index
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parents: 434
diff changeset
314 # pick the highest-count/earliest item
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parents: 434
diff changeset
315 return max(groups, key=_auxfun)[0]
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parents: 434
diff changeset
316
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parents: 434
diff changeset
317 #########################
370
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parents: 369
diff changeset
318 # sequence section
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parents: 369
diff changeset
319 #########################
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parents: 369
diff changeset
320
665
15e244d2a1b5 corrected bug with circular import for VideoFilenameAddable, moved to base module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 659
diff changeset
321 class LCSS(object):
370
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parents: 369
diff changeset
322 '''Class that keeps the LCSS parameters
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parents: 369
diff changeset
323 and puts together the various computations'''
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parents: 369
diff changeset
324 def __init__(self, similarityFunc, delta = float('inf'), aligned = False, lengthFunc = min):
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parents: 369
diff changeset
325 self.similarityFunc = similarityFunc
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parents: 369
diff changeset
326 self.aligned = aligned
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parents: 369
diff changeset
327 self.delta = delta
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parents: 369
diff changeset
328 self.lengthFunc = lengthFunc
389
6d26dcc7bba0 modifications to compute alignment for None indicators
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parents: 381
diff changeset
329 self.subSequenceIndices = [(0,0)]
370
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parents: 369
diff changeset
330
373
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parents: 372
diff changeset
331 def similarities(self, l1, l2, jshift=0):
370
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parents: 369
diff changeset
332 from numpy import zeros, int as npint
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parents: 369
diff changeset
333 n1 = len(l1)
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parents: 369
diff changeset
334 n2 = len(l2)
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parents: 369
diff changeset
335 self.similarityTable = zeros((n1+1,n2+1), dtype = npint)
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parents: 369
diff changeset
336 for i in xrange(1,n1+1):
374
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parents: 373
diff changeset
337 for j in xrange(max(1,i-jshift-self.delta),min(n2,i-jshift+self.delta)+1):
370
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parents: 369
diff changeset
338 if self.similarityFunc(l1[i-1], l2[j-1]):
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parents: 369
diff changeset
339 self.similarityTable[i,j] = self.similarityTable[i-1,j-1]+1
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parents: 369
diff changeset
340 else:
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diff changeset
341 self.similarityTable[i,j] = max(self.similarityTable[i-1,j], self.similarityTable[i,j-1])
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parents: 369
diff changeset
342
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parents: 369
diff changeset
343 def subSequence(self, i, j):
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parents: 369
diff changeset
344 '''Returns the subsequence of two sequences
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parents: 369
diff changeset
345 http://en.wikipedia.org/wiki/Longest_common_subsequence_problem'''
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parents: 369
diff changeset
346 if i == 0 or j == 0:
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parents: 369
diff changeset
347 return []
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parents: 369
diff changeset
348 elif self.similarityTable[i][j] == self.similarityTable[i][j-1]:
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parents: 369
diff changeset
349 return self.subSequence(i, j-1)
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parents: 369
diff changeset
350 elif self.similarityTable[i][j] == self.similarityTable[i-1][j]:
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parents: 369
diff changeset
351 return self.subSequence(i-1, j)
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parents: 369
diff changeset
352 else:
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parents: 369
diff changeset
353 return self.subSequence(i-1, j-1) + [(i-1,j-1)]
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parents: 369
diff changeset
354
373
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parents: 372
diff changeset
355 def _compute(self, _l1, _l2, computeSubSequence = False):
370
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parents: 369
diff changeset
356 '''returns the longest common subsequence similarity
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parents: 369
diff changeset
357 based on the threshold on distance between two elements of lists l1, l2
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parents: 369
diff changeset
358 similarityFunc returns True or False whether the two points are considered similar
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parents: 369
diff changeset
359
607
84690dfe5560 add some functions for behaviour analysis
MohamedGomaa
parents: 574
diff changeset
360 if aligned, returns the best matching if using a finite delta by shifting the series alignments
373
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
361
370
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
362 eg distance(p1, p2) < epsilon
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parents: 369
diff changeset
363 '''
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
364 if len(_l2) < len(_l1): # l1 is the shortest
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
365 l1 = _l2
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
366 l2 = _l1
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
367 revertIndices = True
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
368 else:
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
369 l1 = _l1
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
370 l2 = _l2
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
371 revertIndices = False
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
372 n1 = len(l1)
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
373 n2 = len(l2)
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
374
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
375 if self.aligned:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
376 lcssValues = {}
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
377 similarityTables = {}
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
378 for i in xrange(-n2-self.delta+1, n1+self.delta): # interval such that [i-shift-delta, i-shift+delta] is never empty, which happens when i-shift+delta < 1 or when i-shift-delta > n2
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
379 self.similarities(l1, l2, i)
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
380 lcssValues[i] = self.similarityTable.max()
370
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parents: 369
diff changeset
381 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
382 #print self.similarityTable
521
3707eeb20f25 changed argMaxDict name to argmaxDict
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 518
diff changeset
383 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
384 self.similarityTable = similarityTables[alignmentShift]
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
385 else:
389
6d26dcc7bba0 modifications to compute alignment for None indicators
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
386 alignmentShift = 0
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
387 self.similarities(l1, l2)
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
388
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
389 # threshold values for the useful part of the similarity table are n2-n1-delta and n1-n2-delta
389
6d26dcc7bba0 modifications to compute alignment for None indicators
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
390 self.similarityTable = self.similarityTable[:min(n1, n2+alignmentShift+self.delta)+1, :min(n2, n1-alignmentShift+self.delta)+1]
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
391
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
392 if computeSubSequence:
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
393 self.subSequenceIndices = self.subSequence(self.similarityTable.shape[0]-1, self.similarityTable.shape[1]-1)
371
924e38c9f70e work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 370
diff changeset
394 if revertIndices:
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
395 self.subSequenceIndices = [(j,i) for i,j in self.subSequenceIndices]
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 return self.similarityTable[-1,-1]
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
397
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
398 def compute(self, l1, l2, computeSubSequence = False):
97e8fa0ee9a1 work in progress for complete alignment
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parents: 369
diff changeset
399 '''get methods are to be shadowed in child classes '''
97e8fa0ee9a1 work in progress for complete alignment
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parents: 369
diff changeset
400 return self._compute(l1, l2, computeSubSequence)
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parents: 369
diff changeset
401
375
2ea8584aa80a making indicator LCSS work
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 374
diff changeset
402 def computeAlignment(self):
370
97e8fa0ee9a1 work in progress for complete alignment
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parents: 369
diff changeset
403 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
404 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
405
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
406 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
407 ''' compute the normalized LCSS
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
408 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
409 lengthFunc = lambda x,y:float(x,y)/2'''
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
410 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
411
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
412 def computeNormalized(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
413 return self._computeNormalized(l1, l2, computeSubSequence)
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 _computeDistance(self, l1, l2, computeSubSequence = False):
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
416 ''' compute the LCSS distance'''
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
417 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
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):
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
420 return self._computeDistance(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
421
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
422 #########################
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
423 # plotting section
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
424 #########################
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
425
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
426 def plotPolygon(poly, options = ''):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
427 'Plots shapely polygon poly'
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
428 from numpy.core.multiarray import array
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
429 from matplotlib.pyplot import plot
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
430 from shapely.geometry import Polygon
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
431
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
432 tmp = array(poly.exterior)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
433 plot(tmp[:,0], tmp[:,1], options)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
434
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
435 def stepPlot(X, firstX, lastX, initialCount = 0, increment = 1):
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
436 '''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
437 returns the lists that can be plotted
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
438 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
439 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
440
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
441 sortedX = []
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
442 counts = [initialCount]
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
443 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
444 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
445 counts.append(counts[-1])
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
446 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
447 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
448 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
449
665
15e244d2a1b5 corrected bug with circular import for VideoFilenameAddable, moved to base module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 659
diff changeset
450 class PlottingPropertyValues(object):
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
451 def __init__(self, values):
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
452 self.values = values
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
453
116
2bf5b76320c0 moved intersection plotting and added markers for scatter plots
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 115
diff changeset
454 def __getitem__(self, i):
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
455 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
456
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
457 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
458 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
459
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
460 linestyles = PlottingPropertyValues(['-', '--', '-.', ':'])
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
461
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
462 colors = PlottingPropertyValues('brgmyck') # 'w'
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
463
115
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
464 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
465 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
466 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
467 coords = array(indicatorMap.keys())
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
468 minX = min(coords[:,0])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
469 minY = min(coords[:,1])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
470 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
471 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
472 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
473 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
474 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
475 if masked:
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
476 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
477 else:
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
478 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
479
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
480 #########################
637
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
481 # Data download
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
482 #########################
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
483
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
484 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
485 '''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
486 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
487 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
488
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
489 Example: MONTREAL MCTAVISH 10761
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
490 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
491
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
492 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
493 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
494 import urllib2
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
495 if english:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
496 language = 'e'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
497 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
498 language = 'f'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
499 if len(months) == 0:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
500 timeFrame = 2
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
501 months = [1]
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
502 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
503 timeFrame = 1
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
504
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
505 for year in years:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
506 for month in months:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
507 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
508 data = url.read()
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
509 outFilename = '{}/{}-{}'.format(outputDirectoryname, stationID, year)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
510 if timeFrame == 1:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
511 outFilename += '-{}-hourly'.format(month)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
512 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
513 outFilename += '-daily'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
514 outFilename += '.csv'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
515 out = open(outFilename, 'w')
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
516 out.write(data)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
517 out.close()
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
518
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
519 #########################
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
520 # File I/O
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
521 #########################
24
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
522
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
523 def removeExtension(filename, delimiter = '.'):
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
524 '''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
525 i = filename.rfind(delimiter)
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
526 if i>0:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
527 return filename[:i]
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
528 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
529 return filename
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
530
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
531 def cleanFilename(s):
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
532 'cleans filenames obtained when contatenating figure characteristics'
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
533 return s.replace(' ','-').replace('.','').replace('/','-')
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
534
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
535 def listfiles(dirname, extension, remove = False):
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
536 '''Returns the list of files with the extension in the directory dirname
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parents: 7
diff changeset
537 If remove is True, the filenames are stripped from the extension'''
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
538 from os import listdir
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
539 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
540 tmp.sort()
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
541 if remove:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
542 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
543 else:
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Nicolas Saunier <nico@confins.net>
parents:
diff changeset
544 return tmp
aed8eb63cdde initial commit with non-functional python code for NGSIM
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parents:
diff changeset
545
266
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
546 def mkdir(dirname):
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
547 'Creates a directory if it does not exist'
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
548 import os
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parents: 262
diff changeset
549 if not os.path.exists(dirname):
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diff changeset
550 os.mkdir(dirname)
aba9711b3149 small modificatons and reorganization
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diff changeset
551 else:
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parents: 262
diff changeset
552 print(dirname+' already exists')
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
553
14
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
554 def removeFile(filename):
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
555 '''Deletes the file while avoiding raising an error
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parents: 7
diff changeset
556 if the file does not exist'''
266
aba9711b3149 small modificatons and reorganization
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parents: 262
diff changeset
557 import os
14
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
558 if (os.path.exists(filename)):
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
559 os.remove(filename)
266
aba9711b3149 small modificatons and reorganization
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diff changeset
560 else:
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parents: 262
diff changeset
561 print(filename+' does not exist')
14
e7bbe8465591 homography and other utils
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parents: 7
diff changeset
562
42
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
563 def line2Floats(l, separator=' '):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
564 '''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
565 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
566
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
567 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
568 '''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
569 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
570
c000f37c316d moved tests to independent file, added chi2 computation
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parents: 29
diff changeset
571 #########################
332
a6ca86107f27 reorganized utils module
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parents: 324
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572 # CLI utils
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
573 #########################
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
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574
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
575 def parseCLIOptions(helpMessage, options, cliArgs, optionalOptions=[]):
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parents: 324
diff changeset
576 ''' Simple function to handle similar argument parsing
a6ca86107f27 reorganized utils module
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parents: 324
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577 Returns the dictionary of options and their values
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
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578
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
579 * cliArgs are most likely directly sys.argv
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
580 (only the elements after the first one are considered)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
581
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
582 * options should be a list of strings for getopt options,
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
583 eg ['frame=','correspondences=','video=']
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
584 A value must be provided for each option, or the program quits'''
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
585 import sys, getopt
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
586 from numpy.core.fromnumeric import all
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
587 optionValues, args = getopt.getopt(cliArgs[1:], 'h', ['help']+options+optionalOptions)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
588 optionValues = dict(optionValues)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
589
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
590 if '--help' in optionValues.keys() or '-h' in optionValues.keys():
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
591 print(helpMessage+
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
592 '\n - Compulsory options: '+' '.join([opt.replace('=','') for opt in options])+
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
593 '\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
594 sys.exit()
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
595
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
596 missingArgument = [('--'+opt.replace('=','') in optionValues.keys()) for opt in options]
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
597 if not all(missingArgument):
a6ca86107f27 reorganized utils module
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parents: 324
diff changeset
598 print('Missing argument')
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
599 print(optionValues)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
600 sys.exit()
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
601
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
602 return optionValues
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
603
397
b36b00dd27c3 added function to read scene metadata
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 395
diff changeset
604
b36b00dd27c3 added function to read scene metadata
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 395
diff changeset
605 #########################
553
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
606 # Profiling
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
607 #########################
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
608
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
609 def analyzeProfile(profileFilename, stripDirs = True):
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
610 '''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
611
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
612 obtained by for example:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
613 - 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
614 import cProfile, os
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
615 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
616
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
617 - or on the command line:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
618 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
619 import pstats, os
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
620 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
621 if stripDirs:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
622 p.strip_dirs()
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
623 p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
624 p.print_stats(.2)
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
625 #p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
626 # 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
627 return p
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
628
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
629 #########################
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
630 # running tests
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
631 #########################
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
632
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
633 if __name__ == "__main__":
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
634 import doctest
2
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
635 import unittest
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
636 suite = doctest.DocFileSuite('tests/utils.txt')
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
637 #suite = doctest.DocTestSuite()
2
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
638 unittest.TextTestRunner().run(suite)
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
639 #doctest.testmod()
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
640 #doctest.testfile("example.txt")