repo/traffic-intelligence: python/utils.py annotate

annotate python/utils.py @ 607:84690dfe5560

add some functions for behaviour analysis

author	MohamedGomaa
date	Tue, 25 Nov 2014 22:49:47 -0500
parents	e24eeb244698
children	0954aaf28231

rev	line source
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	1 #! /usr/bin/env python
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	2 ''' Generic utilities.'''
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	3
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	4 #from numpy import *
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	5 #from pylab import *
397 b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	6 from datetime import time, datetime
569 0057c04f94d5 work in progress on intersections (for PET) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 561 diff changeset	7 from math import sqrt
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	8
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	9 __metaclass__ = type
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	10
421 4fce27946c60 first example of video metadata using sqlalchemy Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 405 diff changeset	11 datetimeFormat = "%Y-%m-%d %H:%M:%S"
4fce27946c60 first example of video metadata using sqlalchemy Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 405 diff changeset	12
185 c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	13 #########################
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	14 # Enumerations
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	15 #########################
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	16
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	17 def inverseEnumeration(l):
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	18 'Returns the dictionary that provides for each element in the input list its index in the input list'
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	19 result = {}
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	20 for i,x in enumerate(l):
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	21 result[x] = i
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	22 return result
155 f03fe3d6d0c8 added functions to parse options Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 152 diff changeset	23
f03fe3d6d0c8 added functions to parse options Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 152 diff changeset	24 #########################
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	25 # simple statistics
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	26 #########################
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	27
423 f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	28 def sampleSize(stdev, tolerance, percentConfidence, printLatex = False):
301 27f06d28036d added simple helper for confidence intervals Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 297 diff changeset	29 from scipy.stats.distributions import norm
27f06d28036d added simple helper for confidence intervals Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 297 diff changeset	30 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1)*100)/100. # 1.-(100-percentConfidence)/200.
423 f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	31 if printLatex:
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	32 print('${0}^2\\frac{{{1}^2}}{{{2}^2}}$'.format(k, stdev, tolerance))
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	33 return (kstdev/tolerance)*2
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	34
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	35 def confidenceInterval(mean, stdev, nSamples, percentConfidence, trueStd = True, printLatex = False):
499 0a93afea8243 alternative confidence interval Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 491 diff changeset	36 '''if trueStd, use normal distribution, otherwise, Student
0a93afea8243 alternative confidence interval Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 491 diff changeset	37
0a93afea8243 alternative confidence interval Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 491 diff changeset	38 Use otherwise t.interval or norm.interval
0a93afea8243 alternative confidence interval Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 491 diff changeset	39 ex: norm.interval(0.95, loc = 0., scale = 2.3/sqrt(11))
0a93afea8243 alternative confidence interval Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 491 diff changeset	40 t.interval(0.95, 10, loc=1.2, scale = 2.3/sqrt(nSamples))
0a93afea8243 alternative confidence interval Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 491 diff changeset	41 loc is mean, scale is sigma/sqrt(n) (for Student, 10 is df)'''
423 f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	42 from math import sqrt
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	43 from scipy.stats.distributions import norm, t
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	44 if trueStd:
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	45 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1)*100)/100. # 1.-(100-percentConfidence)/200.
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	46 else: # use Student
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	47 k = round(t.ppf(0.5+percentConfidence/200., nSamples-1)*100)/100.
301 27f06d28036d added simple helper for confidence intervals Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 297 diff changeset	48 e = k*stdev/sqrt(nSamples)
27f06d28036d added simple helper for confidence intervals Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 297 diff changeset	49 if printLatex:
27f06d28036d added simple helper for confidence intervals Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 297 diff changeset	50 print('${0} \pm {1}\\frac{{{2}}}{{\sqrt{{{3}}}}}$'.format(mean, k, stdev, nSamples))
27f06d28036d added simple helper for confidence intervals Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 297 diff changeset	51 return mean-e, mean+e
27f06d28036d added simple helper for confidence intervals Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 297 diff changeset	52
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	53 def computeChi2(expected, observed):
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	54 '''Returns the Chi2 statistics'''
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	55 result = 0.
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	56 for e, o in zip(expected, observed):
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	57 result += ((e-o)*(e-o))/e
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	58 return result
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	59
85 7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	60 class EmpiricalDistribution:
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	61 def nSamples(self):
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	62 return sum(self.counts)
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	63
197 2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	64 def cumulativeDensityFunction(sample):
276 78922b4de3bf minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 266 diff changeset	65 '''Returns the cumulative density function of the sample of a random variable'''
197 2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	66 from numpy.core.multiarray import array
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	67 from numpy.lib.function_base import unique
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	68 from numpy.core.fromnumeric import sum
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	69 a = array(sample)
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	70 a.sort()
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	71 xaxis = unique(a)
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	72 counts = [sum(a <= x) for x in xaxis]
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	73 return xaxis, counts
85 7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	74
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	75 class EmpiricalDiscreteDistribution(EmpiricalDistribution):
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	76 '''Class to represent a sample of a distribution for a discrete random variable
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	77 '''
86 f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	78 from numpy.core.fromnumeric import sum
f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	79
85 7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	80 def __init__(self, categories, counts):
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	81 self.categories = categories
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	82 self.counts = counts
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	83
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	84 def mean(self):
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	85 result = [float(x*y) for x,y in zip(self.categories, self.counts)]
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	86 return sum(result)/self.nSamples()
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	87
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	88 def var(self, mean = None):
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	89 if not mean:
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	90 m = self.mean()
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	91 else:
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	92 m = mean
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	93 result = 0.
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	94 squares = [float((x-m)(x-m)y) for x,y in zip(self.categories, self.counts)]
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	95 return sum(squares)/(self.nSamples()-1)
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	96
86 f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	97 def referenceCounts(self, probability):
f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	98 '''probability is a function that returns the probability of the random variable for the category values'''
f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	99 refProba = [probability(c) for c in self.categories]
f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	100 refProba[-1] = 1-sum(refProba[:-1])
f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	101 refCounts = [r*self.nSamples() for r in refProba]
f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	102 return refCounts, refProba
85 7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	103
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	104 class EmpiricalContinuousDistribution(EmpiricalDistribution):
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	105 '''Class to represent a sample of a distribution for a continuous random variable
76 64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	106 with the number of observations for each interval
64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	107 intervals (categories variable) are defined by their left limits, the last one being the right limit
64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	108 categories contain therefore one more element than the counts'''
35 8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	109 def __init__(self, categories, counts):
276 78922b4de3bf minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 266 diff changeset	110 # todo add samples for initialization and everything to None? (or setSamples?)
35 8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	111 self.categories = categories
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	112 self.counts = counts
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	113
35 8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	114 def mean(self):
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	115 result = 0.
76 64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	116 for i in range(len(self.counts)-1):
64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	117 result += self.counts[i]*(self.categories[i]+self.categories[i+1])/2
64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	118 return result/self.nSamples()
35 8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	119
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	120 def var(self, mean = None):
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	121 if not mean:
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	122 m = self.mean()
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	123 else:
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	124 m = mean
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	125 result = 0.
76 64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	126 for i in range(len(self.counts)-1):
64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	127 mid = (self.categories[i]+self.categories[i+1])/2
64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	128 result += self.counts[i](mid - m)(mid - m)
35 8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	129 return result/(self.nSamples()-1)
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	130
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	131 def referenceCounts(self, cdf):
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	132 '''cdf is a cumulative distribution function
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	133 returning the probability of the variable being less that x'''
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	134 # refCumulativeCounts = [0]#[cdf(self.categories[0][0])]
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	135 # for inter in self.categories:
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	136 # refCumulativeCounts.append(cdf(inter[1]))
76 64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	137 refCumulativeCounts = [cdf(x) for x in self.categories[1:-1]]
35 8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	138
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	139 refProba = [refCumulativeCounts[0]]
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	140 for i in xrange(1,len(refCumulativeCounts)):
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	141 refProba.append(refCumulativeCounts[i]-refCumulativeCounts[i-1])
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	142 refProba.append(1-refCumulativeCounts[-1])
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	143 refCounts = [p*self.nSamples() for p in refProba]
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	144
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	145 return refCounts, refProba
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	146
77 5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	147 def printReferenceCounts(self, refCounts=None):
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	148 if refCounts:
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	149 ref = refCounts
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	150 else:
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	151 ref = self.referenceCounts
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	152 for i in xrange(len(ref[0])):
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	153 print('{0}-{1} & {2:0.3} & {3:0.3} \\\\'.format(self.categories[i],self.categories[i+1],ref[1][i], ref[0][i]))
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	154
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	155
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	156 #########################
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	157 # maths section
27 44689029a86f updated segmentIntersection and other Nicolas Saunier <nico@confins.net> parents: 24 diff changeset	158 #########################
24 6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	159
433 d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	160 # def kernelSmoothing(sampleX, X, Y, weightFunc, halfwidth):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	161 # '''Returns a smoothed weighted version of Y at the predefined values of sampleX
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	162 # Sum_x weight(sample_x,x) * y(x)'''
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	163 # from numpy import zeros, array
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	164 # smoothed = zeros(len(sampleX))
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	165 # for i,x in enumerate(sampleX):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	166 # weights = array([weightFunc(x,xx, halfwidth) for xx in X])
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	167 # if sum(weights)>0:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	168 # smoothed[i] = sum(weights*Y)/sum(weights)
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	169 # else:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	170 # smoothed[i] = 0
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	171 # return smoothed
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	172
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	173 def kernelSmoothing(x, X, Y, weightFunc, halfwidth):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	174 '''Returns the smoothed estimate of (X,Y) at x
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	175 Sum_x weight(sample_x,x) * y(x)'''
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	176 from numpy import zeros, array
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	177 weights = array([weightFunc(x,observedx, halfwidth) for observedx in X])
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	178 if sum(weights)>0:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	179 return sum(weights*Y)/sum(weights)
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	180 else:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	181 return 0
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	182
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	183 def uniform(center, x, halfwidth):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	184 if abs(center-x)<halfwidth:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	185 return 1.
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	186 else:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	187 return 0.
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	188
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	189 def gaussian(center, x, halfwidth):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	190 from numpy import exp
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	191 return exp(-((center-x)/halfwidth)**2/2)
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	192
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	193 def epanechnikov(center, x, halfwidth):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	194 diff = abs(center-x)
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	195 if diff<halfwidth:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	196 return 1.-(diff/halfwidth)**2
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	197 else:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	198 return 0.
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	199
434 9a714f32fc9f small updates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 433 diff changeset	200 def triangular(center, x, halfwidth):
9a714f32fc9f small updates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 433 diff changeset	201 diff = abs(center-x)
9a714f32fc9f small updates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 433 diff changeset	202 if diff<halfwidth:
9a714f32fc9f small updates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 433 diff changeset	203 return 1.-abs(diff/halfwidth)
9a714f32fc9f small updates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 433 diff changeset	204 else:
9a714f32fc9f small updates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 433 diff changeset	205 return 0.
433 d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	206
518 0c86c73f3c09 median smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 511 diff changeset	207 def medianSmoothing(x, X, Y, halfwidth):
0c86c73f3c09 median smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 511 diff changeset	208 '''Returns the media of Y's corresponding to X's in the interval [x-halfwidth, x+halfwidth]'''
0c86c73f3c09 median smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 511 diff changeset	209 from numpy import median
0c86c73f3c09 median smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 511 diff changeset	210 return median([y for observedx, y in zip(X,Y) if abs(x-observedx)<halfwidth])
0c86c73f3c09 median smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 511 diff changeset	211
521 3707eeb20f25 changed argMaxDict name to argmaxDict Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 518 diff changeset	212 def argmaxDict(d):
561 ee45c6eb6d49 added Mohamed Gomaa Mohamed function to smooth object trajectories Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 553 diff changeset	213 return max(d, key=d.get)
279 3af4c267a7bf generic simple LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 276 diff changeset	214
395 6fba1ab040f1 minor modification to framestotime Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 391 diff changeset	215 def framesToTime(nFrames, frameRate, initialTime = time()):
6fba1ab040f1 minor modification to framestotime Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 391 diff changeset	216 '''returns a datetime.time for the time in hour, minutes and seconds
6fba1ab040f1 minor modification to framestotime Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 391 diff changeset	217 initialTime is a datetime.time'''
248 571ba5ed22e2 added utils for bus processing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 241 diff changeset	218 from math import floor
395 6fba1ab040f1 minor modification to framestotime Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 391 diff changeset	219 seconds = int(floor(float(nFrames)/float(frameRate))+initialTime.hour3600+initialTime.minute60+initialTime.second)
261 4aa792cb0fa9 changing framesToTime to return a datetime.time Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 248 diff changeset	220 h = int(floor(seconds/3600.))
248 571ba5ed22e2 added utils for bus processing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 241 diff changeset	221 seconds = seconds - h*3600
261 4aa792cb0fa9 changing framesToTime to return a datetime.time Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 248 diff changeset	222 m = int(floor(seconds/60))
248 571ba5ed22e2 added utils for bus processing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 241 diff changeset	223 seconds = seconds - m*60
262 a048066bd20f correcting bug in framesToTime Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 261 diff changeset	224 return time(h, m, seconds)
248 571ba5ed22e2 added utils for bus processing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 241 diff changeset	225
381 387cc0142211 script to replay event annotations Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 376 diff changeset	226 def timeToFrames(t, frameRate):
387cc0142211 script to replay event annotations Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 376 diff changeset	227 return frameRate(t.hour3600+t.minute*60+t.second)
387cc0142211 script to replay event annotations Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 376 diff changeset	228
241 ee1caff48b03 added function to sort to list of paired data X,Y Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 235 diff changeset	229 def sortXY(X,Y):
ee1caff48b03 added function to sort to list of paired data X,Y Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 235 diff changeset	230 'returns the sorted (x, Y(x)) sorted on X'
ee1caff48b03 added function to sort to list of paired data X,Y Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 235 diff changeset	231 D = {}
ee1caff48b03 added function to sort to list of paired data X,Y Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 235 diff changeset	232 for x, y in zip(X,Y):
ee1caff48b03 added function to sort to list of paired data X,Y Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 235 diff changeset	233 D[x]=y
ee1caff48b03 added function to sort to list of paired data X,Y Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 235 diff changeset	234 xsorted = sorted(D.keys())
ee1caff48b03 added function to sort to list of paired data X,Y Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 235 diff changeset	235 return xsorted, [D[x] for x in xsorted]
ee1caff48b03 added function to sort to list of paired data X,Y Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 235 diff changeset	236
32 48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	237 def ceilDecimals(v, nDecimals):
48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	238 '''Rounds the number at the nth decimal
48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	239 eg 1.23 at 0 decimal is 2, at 1 decimal is 1.3'''
48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	240 from math import ceil,pow
48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	241 tens = pow(10,nDecimals)
48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	242 return ceil(v*tens)/tens
48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	243
152 74b1fc68d4df re-organized code to avoid cyclic python module dependencies Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 116 diff changeset	244 def inBetween(bound1, bound2, x):
569 0057c04f94d5 work in progress on intersections (for PET) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 561 diff changeset	245 return bound1 <= x <= bound2 or bound2 <= x <= bound1
0057c04f94d5 work in progress on intersections (for PET) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 561 diff changeset	246
0057c04f94d5 work in progress on intersections (for PET) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 561 diff changeset	247 def pointDistanceL2(x1,y1,x2,y2):
0057c04f94d5 work in progress on intersections (for PET) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 561 diff changeset	248 ''' Compute point-to-point distance (L2 norm, ie Euclidean distance)'''
0057c04f94d5 work in progress on intersections (for PET) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 561 diff changeset	249 return sqrt((x2-x1)2+(y2-y1)2)
24 6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	250
6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	251 def crossProduct(l1, l2):
6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	252 return l1[0]l2[1]-l1[1]l2[0]
6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	253
574 e24eeb244698 first implementation of projection to curvilinear coordinates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 569 diff changeset	254 def cat_mvgavg(cat_list, halfWidth):
e24eeb244698 first implementation of projection to curvilinear coordinates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 569 diff changeset	255 ''' Return a list of categories/values smoothed according to a window.
e24eeb244698 first implementation of projection to curvilinear coordinates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 569 diff changeset	256 halfWidth is the search radius on either side'''
e24eeb244698 first implementation of projection to curvilinear coordinates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 569 diff changeset	257 from copy import deepcopy
e24eeb244698 first implementation of projection to curvilinear coordinates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 569 diff changeset	258 catgories = deepcopy(cat_list)
e24eeb244698 first implementation of projection to curvilinear coordinates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 569 diff changeset	259 smoothed = catgories
e24eeb244698 first implementation of projection to curvilinear coordinates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 569 diff changeset	260 for point in range(len(catgories)):
e24eeb244698 first implementation of projection to curvilinear coordinates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 569 diff changeset	261 lower_bound_check = max(0,point-halfWidth)
e24eeb244698 first implementation of projection to curvilinear coordinates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 569 diff changeset	262 upper_bound_check = min(len(catgories)-1,point+halfWidth+1)
e24eeb244698 first implementation of projection to curvilinear coordinates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 569 diff changeset	263 window_values = catgories[lower_bound_check:upper_bound_check]
e24eeb244698 first implementation of projection to curvilinear coordinates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 569 diff changeset	264 smoothed[point] = max(set(window_values), key=window_values.count)
e24eeb244698 first implementation of projection to curvilinear coordinates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 569 diff changeset	265 return smoothed
e24eeb244698 first implementation of projection to curvilinear coordinates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 569 diff changeset	266
547 97c5fef5b2d6 corrected bugs MohamedGomaa parents: 521 diff changeset	267 def filterMovingWindow(inputSignal, halfWidth):
29 ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	268 '''Returns an array obtained after the smoothing of the input by a moving average
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	269 The first and last points are copied from the original.'''
547 97c5fef5b2d6 corrected bugs MohamedGomaa parents: 521 diff changeset	270 from numpy import ones,convolve,array
29 ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	271 width = float(halfWidth*2+1)
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	272 win = ones(width,'d')
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	273 result = convolve(win/width,array(inputSignal),'same')
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	274 result[:halfWidth] = inputSignal[:halfWidth]
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	275 result[-halfWidth:] = inputSignal[-halfWidth:]
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	276 return result
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	277
199 ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	278 def linearRegression(x, y, deg = 1, plotData = False):
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	279 '''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	280 as well as the plot'''
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	281 from numpy.lib.polynomial import polyfit
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	282 from matplotlib.pyplot import plot
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	283 from numpy.core.multiarray import arange
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	284 coef = polyfit(x, y, deg)
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	285 if plotData:
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	286 def poly(x):
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	287 result = 0
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	288 for i in range(len(coef)):
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	289 result += coef[i]x*(len(coef)-i-1)
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	290 return result
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	291 plot(x, y, 'x')
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	292 xx = arange(min(x), max(x),(max(x)-min(x))/1000)
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	293 plot(xx, [poly(z) for z in xx])
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	294 return coef
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	295
27 44689029a86f updated segmentIntersection and other Nicolas Saunier <nico@confins.net> parents: 24 diff changeset	296 #########################
455 abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	297 # iterable section
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	298 #########################
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	299
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	300 def mostCommon(L):
456 825e5d49325d slight update Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 455 diff changeset	301 '''Returns the most frequent element in a iterable
825e5d49325d slight update Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 455 diff changeset	302
825e5d49325d slight update Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 455 diff changeset	303 taken from http://stackoverflow.com/questions/1518522/python-most-common-element-in-a-list'''
455 abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	304 from itertools import groupby
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	305 from operator import itemgetter
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	306 # get an iterable of (item, iterable) pairs
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	307 SL = sorted((x, i) for i, x in enumerate(L))
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	308 # print 'SL:', SL
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	309 groups = groupby(SL, key=itemgetter(0))
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	310 # auxiliary function to get "quality" for an item
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	311 def _auxfun(g):
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	312 item, iterable = g
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	313 count = 0
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	314 min_index = len(L)
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	315 for _, where in iterable:
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	316 count += 1
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	317 min_index = min(min_index, where)
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	318 # print 'item %r, count %r, minind %r' % (item, count, min_index)
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	319 return count, -min_index
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	320 # pick the highest-count/earliest item
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	321 return max(groups, key=_auxfun)[0]
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	322
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	323 #########################
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	324 # sequence section
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	325 #########################
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	326
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	327 class LCSS:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	328 '''Class that keeps the LCSS parameters
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	329 and puts together the various computations'''
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	330 def __init__(self, similarityFunc, delta = float('inf'), aligned = False, lengthFunc = min):
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	331 self.similarityFunc = similarityFunc
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	332 self.aligned = aligned
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	333 self.delta = delta
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	334 self.lengthFunc = lengthFunc
389 6d26dcc7bba0 modifications to compute alignment for None indicators Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 381 diff changeset	335 self.subSequenceIndices = [(0,0)]
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	336
373 d0b86ed50f32 work in progress on LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 372 diff changeset	337 def similarities(self, l1, l2, jshift=0):
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	338 from numpy import zeros, int as npint
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	339 n1 = len(l1)
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	340 n2 = len(l2)
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	341 self.similarityTable = zeros((n1+1,n2+1), dtype = npint)
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	342 for i in xrange(1,n1+1):
374 a7af3519687e finished implementation of aligned LCSS with matching sequence decoded Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 373 diff changeset	343 for j in xrange(max(1,i-jshift-self.delta),min(n2,i-jshift+self.delta)+1):
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	344 if self.similarityFunc(l1[i-1], l2[j-1]):
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	345 self.similarityTable[i,j] = self.similarityTable[i-1,j-1]+1
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	346 else:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	347 self.similarityTable[i,j] = max(self.similarityTable[i-1,j], self.similarityTable[i,j-1])
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	348
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	349 def subSequence(self, i, j):
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	350 '''Returns the subsequence of two sequences
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	351 http://en.wikipedia.org/wiki/Longest_common_subsequence_problem'''
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	352 if i == 0 or j == 0:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	353 return []
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	354 elif self.similarityTable[i][j] == self.similarityTable[i][j-1]:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	355 return self.subSequence(i, j-1)
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	356 elif self.similarityTable[i][j] == self.similarityTable[i-1][j]:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	357 return self.subSequence(i-1, j)
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	358 else:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	359 return self.subSequence(i-1, j-1) + [(i-1,j-1)]
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	360
373 d0b86ed50f32 work in progress on LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 372 diff changeset	361 def _compute(self, _l1, _l2, computeSubSequence = False):
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	362 '''returns the longest common subsequence similarity
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	363 based on the threshold on distance between two elements of lists l1, l2
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	364 similarityFunc returns True or False whether the two points are considered similar
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	365
607 84690dfe5560 add some functions for behaviour analysis MohamedGomaa parents: 574 diff changeset	366 if aligned, returns the best matching if using a finite delta by shifting the series alignments
373 d0b86ed50f32 work in progress on LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 372 diff changeset	367
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	368 eg distance(p1, p2) < epsilon
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	369 '''
372 349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 371 diff changeset	370 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	371 l1 = _l2
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 371 diff changeset	372 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	373 revertIndices = True
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 371 diff changeset	374 else:
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 371 diff changeset	375 l1 = _l1
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 371 diff changeset	376 l2 = _l2
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 371 diff changeset	377 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	378 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	379 n2 = len(l2)
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 371 diff changeset	380
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	381 if self.aligned:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	382 lcssValues = {}
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	383 similarityTables = {}
374 a7af3519687e finished implementation of aligned LCSS with matching sequence decoded Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 373 diff changeset	384 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	385 self.similarities(l1, l2, i)
d0b86ed50f32 work in progress on LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 372 diff changeset	386 lcssValues[i] = self.similarityTable.max()
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	387 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	388 #print self.similarityTable
521 3707eeb20f25 changed argMaxDict name to argmaxDict Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 518 diff changeset	389 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	390 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	391 else:
389 6d26dcc7bba0 modifications to compute alignment for None indicators Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 381 diff changeset	392 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	393 self.similarities(l1, l2)
373 d0b86ed50f32 work in progress on LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 372 diff changeset	394
374 a7af3519687e finished implementation of aligned LCSS with matching sequence decoded Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 373 diff changeset	395 # 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	396 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	397
372 349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 371 diff changeset	398 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	399 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	400 if revertIndices:
374 a7af3519687e finished implementation of aligned LCSS with matching sequence decoded Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 373 diff changeset	401 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	402 return self.similarityTable[-1,-1]
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	403
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	404 def compute(self, l1, l2, computeSubSequence = False):
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	405 '''get methods are to be shadowed in child classes '''
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	406 return self._compute(l1, l2, computeSubSequence)
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	407
375 2ea8584aa80a making indicator LCSS work Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 374 diff changeset	408 def computeAlignment(self):
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	409 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	410 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	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):
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	413 ''' compute the normalized LCSS
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	414 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	415 lengthFunc = lambda x,y:float(x,y)/2'''
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	416 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	417
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	418 def computeNormalized(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	419 return self._computeNormalized(l1, l2, computeSubSequence)
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	420
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	421 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	422 ''' compute the LCSS distance'''
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	423 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	424
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	425 def computeDistance(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	426 return self._computeDistance(l1, l2, computeSubSequence)
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	427
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	428 #########################
45 74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	429 # plotting section
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	430 #########################
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	431
332 a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	432 def plotPolygon(poly, options = ''):
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	433 'Plots shapely polygon poly'
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	434 from numpy.core.multiarray import array
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	435 from matplotlib.pyplot import plot
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	436 from shapely.geometry import Polygon
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	437
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	438 tmp = array(poly.exterior)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	439 plot(tmp[:,0], tmp[:,1], options)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	440
324 99ca91a46007 minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 323 diff changeset	441 def stepPlot(X, firstX, lastX, initialCount = 0, increment = 1):
99ca91a46007 minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 323 diff changeset	442 '''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	443 returns the lists that can be plotted
324 99ca91a46007 minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 323 diff changeset	444 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	445 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	446
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 286 diff changeset	447 sortedX = []
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 286 diff changeset	448 counts = [initialCount]
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 286 diff changeset	449 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	450 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	451 counts.append(counts[-1])
324 99ca91a46007 minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 323 diff changeset	452 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	453 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	454 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	455
45 74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	456 class PlottingPropertyValues:
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	457 def __init__(self, values):
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	458 self.values = values
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	459
116 2bf5b76320c0 moved intersection plotting and added markers for scatter plots Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 115 diff changeset	460 def __getitem__(self, i):
45 74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	461 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	462
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	463 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	464 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	465
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	466 linestyles = PlottingPropertyValues(['-', '--', '-.', ':'])
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	467
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	468 colors = PlottingPropertyValues('brgmyck') # 'w'
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	469
115 550556378466 added functionalities to indicator maps Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 86 diff changeset	470 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	471 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	472 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	473 coords = array(indicatorMap.keys())
75cf537b8d88 moved and generalized map making functions to the library Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 48 diff changeset	474 minX = min(coords[:,0])
75cf537b8d88 moved and generalized map making functions to the library Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 48 diff changeset	475 minY = min(coords[:,1])
75cf537b8d88 moved and generalized map making functions to the library Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 48 diff changeset	476 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	477 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	478 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	479 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	480 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	481 if masked:
550556378466 added functionalities to indicator maps Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 86 diff changeset	482 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	483 else:
550556378466 added functionalities to indicator maps Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 86 diff changeset	484 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	485
45 74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	486 #########################
27 44689029a86f updated segmentIntersection and other Nicolas Saunier <nico@confins.net> parents: 24 diff changeset	487 # file I/O section
44689029a86f updated segmentIntersection and other Nicolas Saunier <nico@confins.net> parents: 24 diff changeset	488 #########################
24 6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	489
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	490 def removeExtension(filename, delimiter = '.'):
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	491 '''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	492 i = filename.rfind(delimiter)
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	493 if i>0:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	494 return filename[:i]
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	495 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	496 return filename
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	497
46 b5d007612e16 added filename util Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 45 diff changeset	498 def cleanFilename(s):
b5d007612e16 added filename util Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 45 diff changeset	499 'cleans filenames obtained when contatenating figure characteristics'
266 aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	500 return s.replace(' ','-').replace('.','').replace('/','-')
46 b5d007612e16 added filename util Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 45 diff changeset	501
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	502 def listfiles(dirname, extension, remove = False):
14 e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	503 '''Returns the list of files with the extension in the directory dirname
e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	504 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	505 from os import listdir
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	506 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	507 tmp.sort()
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	508 if remove:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	509 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	510 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	511 return tmp
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	512
266 aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	513 def mkdir(dirname):
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	514 'Creates a directory if it does not exist'
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	515 import os
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	516 if not os.path.exists(dirname):
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	517 os.mkdir(dirname)
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	518 else:
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	519 print(dirname+' already exists')
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	520
14 e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	521 def removeFile(filename):
e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	522 '''Deletes the file while avoiding raising an error
e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	523 if the file does not exist'''
266 aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	524 import os
14 e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	525 if (os.path.exists(filename)):
e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	526 os.remove(filename)
266 aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	527 else:
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	528 print(filename+' does not exist')
14 e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	529
42 1a2ac2d4f53a added loading of the rest of the data for objects Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 35 diff changeset	530 def line2Floats(l, separator=' '):
1a2ac2d4f53a added loading of the rest of the data for objects Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 35 diff changeset	531 '''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	532 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	533
1a2ac2d4f53a added loading of the rest of the data for objects Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 35 diff changeset	534 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	535 '''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	536 return [int(x) for x in l.split(separator)]
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	537
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	538 #########################
332 a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	539 # CLI utils
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	540 #########################
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	541
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	542 def parseCLIOptions(helpMessage, options, cliArgs, optionalOptions=[]):
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	543 ''' Simple function to handle similar argument parsing
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	544 Returns the dictionary of options and their values
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	545
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	546 * cliArgs are most likely directly sys.argv
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	547 (only the elements after the first one are considered)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	548
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	549 * options should be a list of strings for getopt options,
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	550 eg ['frame=','correspondences=','video=']
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	551 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	552 import sys, getopt
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	553 from numpy.core.fromnumeric import all
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	554 optionValues, args = getopt.getopt(cliArgs[1:], 'h', ['help']+options+optionalOptions)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	555 optionValues = dict(optionValues)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	556
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	557 if '--help' in optionValues.keys() or '-h' in optionValues.keys():
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	558 print(helpMessage+
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	559 '\n - Compulsory options: '+' '.join([opt.replace('=','') for opt in options])+
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	560 '\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	561 sys.exit()
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	562
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	563 missingArgument = [('--'+opt.replace('=','') in optionValues.keys()) for opt in options]
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	564 if not all(missingArgument):
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	565 print('Missing argument')
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	566 print(optionValues)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	567 sys.exit()
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	568
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	569 return optionValues
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	570
397 b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	571
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	572 #########################
553 3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	573 # Profiling
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	574 #########################
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	575
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	576 def analyzeProfile(profileFilename, stripDirs = True):
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	577 '''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	578
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	579 obtained by for example:
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	580 - 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	581 import cProfile, os
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	582 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	583
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	584 - or on the command line:
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	585 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	586 import pstats, os
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	587 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	588 if stripDirs:
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	589 p.strip_dirs()
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	590 p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	591 p.print_stats(.2)
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	592 #p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	593 # 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	594 return p
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	595
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	596 #########################
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	597 # running tests
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	598 #########################
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	599
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	600 if __name__ == "__main__":
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	601 import doctest
2 de5642925615 started implementation of TimeInterval and Spatio-temporal object Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 0 diff changeset	602 import unittest
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	603 suite = doctest.DocFileSuite('tests/utils.txt')
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	604 #suite = doctest.DocTestSuite()
2 de5642925615 started implementation of TimeInterval and Spatio-temporal object Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 0 diff changeset	605 unittest.TextTestRunner().run(suite)
de5642925615 started implementation of TimeInterval and Spatio-temporal object Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 0 diff changeset	606 #doctest.testmod()
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	607 #doctest.testfile("example.txt")

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annotate python/utils.py @ 607:84690dfe5560