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

annotate python/utils.py @ 553:3622a5653ee9

added basic info and function to profile code

author	Nicolas Saunier <nicolas.saunier@polymtl.ca>
date	Tue, 08 Jul 2014 17:23:02 -0400
parents	97c5fef5b2d6
children	ee45c6eb6d49

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
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	7
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	8 __metaclass__ = type
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	9
421 4fce27946c60 first example of video metadata using sqlalchemy Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 405 diff changeset	10 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	11
185 c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	12 #########################
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	13 # Enumerations
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	14 #########################
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 def inverseEnumeration(l):
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	17 '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	18 result = {}
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	19 for i,x in enumerate(l):
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	20 result[x] = i
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	21 return result
155 f03fe3d6d0c8 added functions to parse options Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 152 diff changeset	22
f03fe3d6d0c8 added functions to parse options Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 152 diff changeset	23 #########################
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	24 # simple statistics
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	25 #########################
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	26
423 f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	27 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	28 from scipy.stats.distributions import norm
27f06d28036d added simple helper for confidence intervals Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 297 diff changeset	29 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	30 if printLatex:
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	31 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	32 return (kstdev/tolerance)*2
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	33
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	34 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	35 '''if trueStd, use normal distribution, otherwise, Student
0a93afea8243 alternative confidence interval Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 491 diff changeset	36
0a93afea8243 alternative confidence interval Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 491 diff changeset	37 Use otherwise t.interval or norm.interval
0a93afea8243 alternative confidence interval Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 491 diff changeset	38 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	39 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	40 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	41 from math import sqrt
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	42 from scipy.stats.distributions import norm, t
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	43 if trueStd:
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	44 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	45 else: # use Student
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	46 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	47 e = k*stdev/sqrt(nSamples)
27f06d28036d added simple helper for confidence intervals Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 297 diff changeset	48 if printLatex:
27f06d28036d added simple helper for confidence intervals Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 297 diff changeset	49 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	50 return mean-e, mean+e
27f06d28036d added simple helper for confidence intervals Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 297 diff changeset	51
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	52 def computeChi2(expected, observed):
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	53 '''Returns the Chi2 statistics'''
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	54 result = 0.
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	55 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	56 result += ((e-o)*(e-o))/e
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	57 return result
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	58
85 7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	59 class EmpiricalDistribution:
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	60 def nSamples(self):
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	61 return sum(self.counts)
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	62
197 2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	63 def cumulativeDensityFunction(sample):
276 78922b4de3bf minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 266 diff changeset	64 '''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	65 from numpy.core.multiarray import array
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	66 from numpy.lib.function_base import unique
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	67 from numpy.core.fromnumeric import sum
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	68 a = array(sample)
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	69 a.sort()
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	70 xaxis = unique(a)
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	71 counts = [sum(a <= x) for x in xaxis]
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	72 return xaxis, counts
85 7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	73
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	74 class EmpiricalDiscreteDistribution(EmpiricalDistribution):
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	75 '''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	76 '''
86 f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	77 from numpy.core.fromnumeric import sum
f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	78
85 7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	79 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	80 self.categories = categories
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	81 self.counts = counts
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	82
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	83 def mean(self):
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	84 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	85 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	86
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	87 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	88 if not mean:
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	89 m = self.mean()
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	90 else:
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	91 m = mean
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	92 result = 0.
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	93 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	94 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	95
86 f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	96 def referenceCounts(self, probability):
f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	97 '''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	98 refProba = [probability(c) for c in self.categories]
f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	99 refProba[-1] = 1-sum(refProba[:-1])
f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	100 refCounts = [r*self.nSamples() for r in refProba]
f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	101 return refCounts, refProba
85 7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	102
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	103 class EmpiricalContinuousDistribution(EmpiricalDistribution):
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	104 '''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	105 with the number of observations for each interval
64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	106 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	107 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	108 def __init__(self, categories, counts):
276 78922b4de3bf minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 266 diff changeset	109 # 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	110 self.categories = categories
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	111 self.counts = counts
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	112
35 8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	113 def mean(self):
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	114 result = 0.
76 64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	115 for i in range(len(self.counts)-1):
64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	116 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	117 return result/self.nSamples()
35 8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	118
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	119 def var(self, mean = None):
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	120 if not mean:
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	121 m = self.mean()
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	122 else:
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	123 m = mean
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	124 result = 0.
76 64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	125 for i in range(len(self.counts)-1):
64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	126 mid = (self.categories[i]+self.categories[i+1])/2
64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	127 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	128 return result/(self.nSamples()-1)
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	129
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	130 def referenceCounts(self, cdf):
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	131 '''cdf is a cumulative distribution function
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	132 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	133 # refCumulativeCounts = [0]#[cdf(self.categories[0][0])]
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	134 # for inter in self.categories:
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	135 # refCumulativeCounts.append(cdf(inter[1]))
76 64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	136 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	137
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	138 refProba = [refCumulativeCounts[0]]
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	139 for i in xrange(1,len(refCumulativeCounts)):
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	140 refProba.append(refCumulativeCounts[i]-refCumulativeCounts[i-1])
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	141 refProba.append(1-refCumulativeCounts[-1])
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	142 refCounts = [p*self.nSamples() for p in refProba]
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	143
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	144 return refCounts, refProba
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	145
77 5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	146 def printReferenceCounts(self, refCounts=None):
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	147 if refCounts:
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	148 ref = refCounts
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	149 else:
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	150 ref = self.referenceCounts
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	151 for i in xrange(len(ref[0])):
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	152 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	153
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	154
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	155 #########################
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	156 # maths section
27 44689029a86f updated segmentIntersection and other Nicolas Saunier <nico@confins.net> parents: 24 diff changeset	157 #########################
24 6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	158
433 d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	159 # def kernelSmoothing(sampleX, X, Y, weightFunc, halfwidth):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	160 # '''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	161 # Sum_x weight(sample_x,x) * y(x)'''
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	162 # from numpy import zeros, array
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	163 # smoothed = zeros(len(sampleX))
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	164 # for i,x in enumerate(sampleX):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	165 # weights = array([weightFunc(x,xx, halfwidth) for xx in X])
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	166 # if sum(weights)>0:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	167 # smoothed[i] = sum(weights*Y)/sum(weights)
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	168 # else:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	169 # smoothed[i] = 0
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	170 # return smoothed
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	171
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	172 def kernelSmoothing(x, X, Y, weightFunc, halfwidth):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	173 '''Returns the smoothed estimate of (X,Y) at x
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	174 Sum_x weight(sample_x,x) * y(x)'''
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	175 from numpy import zeros, array
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	176 weights = array([weightFunc(x,observedx, halfwidth) for observedx in X])
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	177 if sum(weights)>0:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	178 return sum(weights*Y)/sum(weights)
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	179 else:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	180 return 0
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	181
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	182 def uniform(center, x, halfwidth):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	183 if abs(center-x)<halfwidth:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	184 return 1.
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	185 else:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	186 return 0.
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	187
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	188 def gaussian(center, x, halfwidth):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	189 from numpy import exp
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	190 return exp(-((center-x)/halfwidth)**2/2)
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	191
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	192 def epanechnikov(center, x, halfwidth):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	193 diff = abs(center-x)
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	194 if diff<halfwidth:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	195 return 1.-(diff/halfwidth)**2
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	196 else:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	197 return 0.
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	198
434 9a714f32fc9f small updates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 433 diff changeset	199 def triangular(center, x, halfwidth):
9a714f32fc9f small updates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 433 diff changeset	200 diff = abs(center-x)
9a714f32fc9f small updates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 433 diff changeset	201 if diff<halfwidth:
9a714f32fc9f small updates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 433 diff changeset	202 return 1.-abs(diff/halfwidth)
9a714f32fc9f small updates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 433 diff changeset	203 else:
9a714f32fc9f small updates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 433 diff changeset	204 return 0.
433 d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	205
518 0c86c73f3c09 median smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 511 diff changeset	206 def medianSmoothing(x, X, Y, halfwidth):
0c86c73f3c09 median smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 511 diff changeset	207 '''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	208 from numpy import median
0c86c73f3c09 median smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 511 diff changeset	209 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	210
521 3707eeb20f25 changed argMaxDict name to argmaxDict Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 518 diff changeset	211 def argmaxDict(d):
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	212 return max(d.iterkeys(), key=(lambda key: d[key]))
279 3af4c267a7bf generic simple LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 276 diff changeset	213
395 6fba1ab040f1 minor modification to framestotime Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 391 diff changeset	214 def framesToTime(nFrames, frameRate, initialTime = time()):
6fba1ab040f1 minor modification to framestotime Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 391 diff changeset	215 '''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	216 initialTime is a datetime.time'''
248 571ba5ed22e2 added utils for bus processing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 241 diff changeset	217 from math import floor
395 6fba1ab040f1 minor modification to framestotime Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 391 diff changeset	218 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	219 h = int(floor(seconds/3600.))
248 571ba5ed22e2 added utils for bus processing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 241 diff changeset	220 seconds = seconds - h*3600
261 4aa792cb0fa9 changing framesToTime to return a datetime.time Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 248 diff changeset	221 m = int(floor(seconds/60))
248 571ba5ed22e2 added utils for bus processing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 241 diff changeset	222 seconds = seconds - m*60
262 a048066bd20f correcting bug in framesToTime Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 261 diff changeset	223 return time(h, m, seconds)
248 571ba5ed22e2 added utils for bus processing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 241 diff changeset	224
381 387cc0142211 script to replay event annotations Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 376 diff changeset	225 def timeToFrames(t, frameRate):
387cc0142211 script to replay event annotations Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 376 diff changeset	226 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	227
241 ee1caff48b03 added function to sort to list of paired data X,Y Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 235 diff changeset	228 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	229 '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	230 D = {}
ee1caff48b03 added function to sort to list of paired data X,Y Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 235 diff changeset	231 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	232 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	233 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	234 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	235
32 48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	236 def ceilDecimals(v, nDecimals):
48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	237 '''Rounds the number at the nth decimal
48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	238 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	239 from math import ceil,pow
48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	240 tens = pow(10,nDecimals)
48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	241 return ceil(v*tens)/tens
48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	242
152 74b1fc68d4df re-organized code to avoid cyclic python module dependencies Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 116 diff changeset	243 def inBetween(bound1, bound2, x):
74b1fc68d4df re-organized code to avoid cyclic python module dependencies Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 116 diff changeset	244 return bound1 <= x <= bound2 or bound2 <= x<= bound1
24 6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	245
6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	246 def crossProduct(l1, l2):
6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	247 return l1[0]l2[1]-l1[1]l2[0]
6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	248
547 97c5fef5b2d6 corrected bugs MohamedGomaa parents: 521 diff changeset	249 def filterMovingWindow(inputSignal, halfWidth):
29 ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	250 '''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	251 The first and last points are copied from the original.'''
547 97c5fef5b2d6 corrected bugs MohamedGomaa parents: 521 diff changeset	252 from numpy import ones,convolve,array
29 ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	253 width = float(halfWidth*2+1)
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	254 win = ones(width,'d')
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	255 result = convolve(win/width,array(inputSignal),'same')
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	256 result[:halfWidth] = inputSignal[:halfWidth]
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	257 result[-halfWidth:] = inputSignal[-halfWidth:]
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	258 return result
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	259
199 ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	260 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	261 '''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	262 as well as the plot'''
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	263 from numpy.lib.polynomial import polyfit
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	264 from matplotlib.pyplot import plot
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	265 from numpy.core.multiarray import arange
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	266 coef = polyfit(x, y, deg)
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	267 if plotData:
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	268 def poly(x):
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	269 result = 0
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	270 for i in range(len(coef)):
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	271 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	272 return result
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	273 plot(x, y, 'x')
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	274 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	275 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	276 return coef
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	277
27 44689029a86f updated segmentIntersection and other Nicolas Saunier <nico@confins.net> parents: 24 diff changeset	278 #########################
455 abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	279 # iterable section
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	280 #########################
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	281
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	282 def mostCommon(L):
456 825e5d49325d slight update Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 455 diff changeset	283 '''Returns the most frequent element in a iterable
825e5d49325d slight update Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 455 diff changeset	284
825e5d49325d slight update Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 455 diff changeset	285 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	286 from itertools import groupby
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	287 from operator import itemgetter
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	288 # get an iterable of (item, iterable) pairs
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	289 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	290 # print 'SL:', SL
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	291 groups = groupby(SL, key=itemgetter(0))
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	292 # auxiliary function to get "quality" for an item
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	293 def _auxfun(g):
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	294 item, iterable = g
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	295 count = 0
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	296 min_index = len(L)
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	297 for _, where in iterable:
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	298 count += 1
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	299 min_index = min(min_index, where)
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	300 # 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	301 return count, -min_index
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	302 # pick the highest-count/earliest item
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	303 return max(groups, key=_auxfun)[0]
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	304
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	305 #########################
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	306 # sequence section
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	307 #########################
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	308
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	309 class LCSS:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	310 '''Class that keeps the LCSS parameters
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	311 and puts together the various computations'''
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	312 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	313 self.similarityFunc = similarityFunc
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	314 self.aligned = aligned
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	315 self.delta = delta
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	316 self.lengthFunc = lengthFunc
389 6d26dcc7bba0 modifications to compute alignment for None indicators Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 381 diff changeset	317 self.subSequenceIndices = [(0,0)]
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	318
373 d0b86ed50f32 work in progress on LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 372 diff changeset	319 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	320 from numpy import zeros, int as npint
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	321 n1 = len(l1)
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	322 n2 = len(l2)
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	323 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	324 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	325 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	326 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	327 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	328 else:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	329 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	330
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	331 def subSequence(self, i, j):
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	332 '''Returns the subsequence of two sequences
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	333 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	334 if i == 0 or j == 0:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	335 return []
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	336 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	337 return self.subSequence(i, j-1)
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	338 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	339 return self.subSequence(i-1, j)
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	340 else:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	341 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	342
373 d0b86ed50f32 work in progress on LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 372 diff changeset	343 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	344 '''returns the longest common subsequence similarity
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	345 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	346 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	347
373 d0b86ed50f32 work in progress on LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 372 diff changeset	348 if aligned, returns the best matching if using a finite delta by shiftinig the series alignments
d0b86ed50f32 work in progress on LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 372 diff changeset	349
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	350 eg distance(p1, p2) < epsilon
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	351 '''
372 349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 371 diff changeset	352 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	353 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	354 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	355 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	356 else:
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 371 diff changeset	357 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	358 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	359 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	360 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	361 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	362
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	363 if self.aligned:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	364 lcssValues = {}
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	365 similarityTables = {}
374 a7af3519687e finished implementation of aligned LCSS with matching sequence decoded Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 373 diff changeset	366 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	367 self.similarities(l1, l2, i)
d0b86ed50f32 work in progress on LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 372 diff changeset	368 lcssValues[i] = self.similarityTable.max()
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	369 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	370 #print self.similarityTable
521 3707eeb20f25 changed argMaxDict name to argmaxDict Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 518 diff changeset	371 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	372 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	373 else:
389 6d26dcc7bba0 modifications to compute alignment for None indicators Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 381 diff changeset	374 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	375 self.similarities(l1, l2)
373 d0b86ed50f32 work in progress on LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 372 diff changeset	376
374 a7af3519687e finished implementation of aligned LCSS with matching sequence decoded Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 373 diff changeset	377 # 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	378 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	379
372 349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 371 diff changeset	380 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	381 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	382 if revertIndices:
374 a7af3519687e finished implementation of aligned LCSS with matching sequence decoded Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 373 diff changeset	383 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	384 return self.similarityTable[-1,-1]
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	385
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	386 def compute(self, l1, l2, computeSubSequence = False):
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	387 '''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	388 return self._compute(l1, l2, computeSubSequence)
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	389
375 2ea8584aa80a making indicator LCSS work Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 374 diff changeset	390 def computeAlignment(self):
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	391 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	392 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	393
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	394 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	395 ''' compute the normalized LCSS
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	396 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	397 lengthFunc = lambda x,y:float(x,y)/2'''
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	398 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	399
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	400 def computeNormalized(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	401 return self._computeNormalized(l1, l2, computeSubSequence)
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	402
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	403 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	404 ''' compute the LCSS distance'''
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	405 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	406
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	407 def computeDistance(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	408 return self._computeDistance(l1, l2, computeSubSequence)
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	409
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	410 #########################
45 74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	411 # plotting section
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	412 #########################
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	413
332 a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	414 def plotPolygon(poly, options = ''):
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	415 'Plots shapely polygon poly'
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	416 from numpy.core.multiarray import array
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	417 from matplotlib.pyplot import plot
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	418 from shapely.geometry import Polygon
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	419
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	420 tmp = array(poly.exterior)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	421 plot(tmp[:,0], tmp[:,1], options)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	422
324 99ca91a46007 minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 323 diff changeset	423 def stepPlot(X, firstX, lastX, initialCount = 0, increment = 1):
99ca91a46007 minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 323 diff changeset	424 '''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	425 returns the lists that can be plotted
324 99ca91a46007 minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 323 diff changeset	426 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	427 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	428
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 286 diff changeset	429 sortedX = []
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 286 diff changeset	430 counts = [initialCount]
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 286 diff changeset	431 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	432 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	433 counts.append(counts[-1])
324 99ca91a46007 minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 323 diff changeset	434 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	435 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	436 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	437
45 74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	438 class PlottingPropertyValues:
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	439 def __init__(self, values):
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	440 self.values = values
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	441
116 2bf5b76320c0 moved intersection plotting and added markers for scatter plots Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 115 diff changeset	442 def __getitem__(self, i):
45 74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	443 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	444
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	445 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	446 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	447
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	448 linestyles = PlottingPropertyValues(['-', '--', '-.', ':'])
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	449
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	450 colors = PlottingPropertyValues('brgmyck') # 'w'
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	451
115 550556378466 added functionalities to indicator maps Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 86 diff changeset	452 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	453 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	454 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	455 coords = array(indicatorMap.keys())
75cf537b8d88 moved and generalized map making functions to the library Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 48 diff changeset	456 minX = min(coords[:,0])
75cf537b8d88 moved and generalized map making functions to the library Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 48 diff changeset	457 minY = min(coords[:,1])
75cf537b8d88 moved and generalized map making functions to the library Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 48 diff changeset	458 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	459 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	460 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	461 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	462 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	463 if masked:
550556378466 added functionalities to indicator maps Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 86 diff changeset	464 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	465 else:
550556378466 added functionalities to indicator maps Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 86 diff changeset	466 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	467
45 74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	468 #########################
27 44689029a86f updated segmentIntersection and other Nicolas Saunier <nico@confins.net> parents: 24 diff changeset	469 # file I/O section
44689029a86f updated segmentIntersection and other Nicolas Saunier <nico@confins.net> parents: 24 diff changeset	470 #########################
24 6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	471
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	472 def removeExtension(filename, delimiter = '.'):
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	473 '''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	474 i = filename.rfind(delimiter)
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	475 if i>0:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	476 return filename[:i]
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	477 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	478 return filename
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	479
46 b5d007612e16 added filename util Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 45 diff changeset	480 def cleanFilename(s):
b5d007612e16 added filename util Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 45 diff changeset	481 'cleans filenames obtained when contatenating figure characteristics'
266 aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	482 return s.replace(' ','-').replace('.','').replace('/','-')
46 b5d007612e16 added filename util Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 45 diff changeset	483
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	484 def listfiles(dirname, extension, remove = False):
14 e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	485 '''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	486 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	487 from os import listdir
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	488 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	489 tmp.sort()
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	490 if remove:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	491 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	492 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	493 return tmp
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	494
266 aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	495 def mkdir(dirname):
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	496 'Creates a directory if it does not exist'
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	497 import os
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	498 if not os.path.exists(dirname):
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	499 os.mkdir(dirname)
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	500 else:
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	501 print(dirname+' already exists')
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	502
14 e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	503 def removeFile(filename):
e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	504 '''Deletes the file while avoiding raising an error
e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	505 if the file does not exist'''
266 aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	506 import os
14 e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	507 if (os.path.exists(filename)):
e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	508 os.remove(filename)
266 aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	509 else:
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	510 print(filename+' does not exist')
14 e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	511
42 1a2ac2d4f53a added loading of the rest of the data for objects Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 35 diff changeset	512 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	513 '''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	514 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	515
1a2ac2d4f53a added loading of the rest of the data for objects Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 35 diff changeset	516 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	517 '''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	518 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	519
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	520 #########################
332 a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	521 # CLI utils
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	522 #########################
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	523
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	524 def parseCLIOptions(helpMessage, options, cliArgs, optionalOptions=[]):
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	525 ''' Simple function to handle similar argument parsing
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	526 Returns the dictionary of options and their values
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	527
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	528 * cliArgs are most likely directly sys.argv
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	529 (only the elements after the first one are considered)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	530
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	531 * options should be a list of strings for getopt options,
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	532 eg ['frame=','correspondences=','video=']
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	533 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	534 import sys, getopt
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	535 from numpy.core.fromnumeric import all
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	536 optionValues, args = getopt.getopt(cliArgs[1:], 'h', ['help']+options+optionalOptions)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	537 optionValues = dict(optionValues)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	538
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	539 if '--help' in optionValues.keys() or '-h' in optionValues.keys():
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	540 print(helpMessage+
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	541 '\n - Compulsory options: '+' '.join([opt.replace('=','') for opt in options])+
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	542 '\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	543 sys.exit()
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	544
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	545 missingArgument = [('--'+opt.replace('=','') in optionValues.keys()) for opt in options]
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	546 if not all(missingArgument):
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	547 print('Missing argument')
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	548 print(optionValues)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	549 sys.exit()
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	550
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	551 return optionValues
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	552
397 b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	553
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	554 #########################
553 3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	555 # Profiling
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	556 #########################
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	557
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	558 def analyzeProfile(profileFilename, stripDirs = True):
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	559 '''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	560
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	561 obtained by for example:
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	562 - 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	563 import cProfile, os
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	564 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	565
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	566 - or on the command line:
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	567 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	568 import pstats, os
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	569 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	570 if stripDirs:
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	571 p.strip_dirs()
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	572 p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	573 p.print_stats(.2)
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	574 #p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	575 # 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	576 return p
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	577
3622a5653ee9 added basic info and function to profile code Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 547 diff changeset	578 #########################
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	579 # running tests
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	580 #########################
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	581
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	582 if __name__ == "__main__":
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	583 import doctest
2 de5642925615 started implementation of TimeInterval and Spatio-temporal object Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 0 diff changeset	584 import unittest
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	585 suite = doctest.DocFileSuite('tests/utils.txt')
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	586 #suite = doctest.DocTestSuite()
2 de5642925615 started implementation of TimeInterval and Spatio-temporal object Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 0 diff changeset	587 unittest.TextTestRunner().run(suite)
de5642925615 started implementation of TimeInterval and Spatio-temporal object Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 0 diff changeset	588 #doctest.testmod()
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	589 #doctest.testfile("example.txt")

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annotate python/utils.py @ 553:3622a5653ee9