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

annotate python/utils.py @ 499:0a93afea8243

alternative confidence interval

author	Nicolas Saunier <nicolas.saunier@polymtl.ca>
date	Fri, 09 May 2014 14:09:02 -0400
parents	343cfd185ca6
children	ad518f0c3218

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
45 74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	10 commentChar = '#'
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	11
48 8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 46 diff changeset	12 delimiterChar = '%';
8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 46 diff changeset	13
421 4fce27946c60 first example of video metadata using sqlalchemy Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 405 diff changeset	14 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	15
185 c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	16 #########################
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	17 # Enumerations
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	18 #########################
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	19
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	20 def inverseEnumeration(l):
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	21 '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	22 result = {}
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	23 for i,x in enumerate(l):
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	24 result[x] = i
c06379f25ab8 utilities for user types Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 181 diff changeset	25 return result
155 f03fe3d6d0c8 added functions to parse options Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 152 diff changeset	26
f03fe3d6d0c8 added functions to parse options Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 152 diff changeset	27 #########################
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	28 # simple statistics
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	29 #########################
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	30
423 f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	31 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	32 from scipy.stats.distributions import norm
27f06d28036d added simple helper for confidence intervals Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 297 diff changeset	33 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	34 if printLatex:
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	35 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	36 return (kstdev/tolerance)*2
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	37
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	38 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	39 '''if trueStd, use normal distribution, otherwise, Student
0a93afea8243 alternative confidence interval Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 491 diff changeset	40
0a93afea8243 alternative confidence interval Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 491 diff changeset	41 Use otherwise t.interval or norm.interval
0a93afea8243 alternative confidence interval Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 491 diff changeset	42 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	43 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	44 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	45 from math import sqrt
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	46 from scipy.stats.distributions import norm, t
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	47 if trueStd:
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	48 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	49 else: # use Student
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	50 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	51 e = k*stdev/sqrt(nSamples)
27f06d28036d added simple helper for confidence intervals Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 297 diff changeset	52 if printLatex:
27f06d28036d added simple helper for confidence intervals Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 297 diff changeset	53 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	54 return mean-e, mean+e
27f06d28036d added simple helper for confidence intervals Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 297 diff changeset	55
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	56 def computeChi2(expected, observed):
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	57 '''Returns the Chi2 statistics'''
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	58 result = 0.
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	59 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	60 result += ((e-o)*(e-o))/e
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	61 return result
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	62
85 7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	63 class EmpiricalDistribution:
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	64 def nSamples(self):
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	65 return sum(self.counts)
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	66
197 2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	67 def cumulativeDensityFunction(sample):
276 78922b4de3bf minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 266 diff changeset	68 '''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	69 from numpy.core.multiarray import array
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	70 from numpy.lib.function_base import unique
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	71 from numpy.core.fromnumeric import sum
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	72 a = array(sample)
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	73 a.sort()
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	74 xaxis = unique(a)
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	75 counts = [sum(a <= x) for x in xaxis]
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	76 return xaxis, counts
85 7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	77
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	78 class EmpiricalDiscreteDistribution(EmpiricalDistribution):
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	79 '''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	80 '''
86 f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	81 from numpy.core.fromnumeric import sum
f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	82
85 7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	83 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	84 self.categories = categories
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	85 self.counts = counts
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 mean(self):
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	88 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	89 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	90
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	91 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	92 if not mean:
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	93 m = self.mean()
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	94 else:
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	95 m = mean
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	96 result = 0.
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	97 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	98 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	99
86 f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	100 def referenceCounts(self, probability):
f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	101 '''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	102 refProba = [probability(c) for c in self.categories]
f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	103 refProba[-1] = 1-sum(refProba[:-1])
f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	104 refCounts = [r*self.nSamples() for r in refProba]
f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	105 return refCounts, refProba
85 7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	106
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	107 class EmpiricalContinuousDistribution(EmpiricalDistribution):
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	108 '''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	109 with the number of observations for each interval
64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	110 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	111 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	112 def __init__(self, categories, counts):
276 78922b4de3bf minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 266 diff changeset	113 # 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	114 self.categories = categories
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	115 self.counts = counts
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	116
35 8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	117 def mean(self):
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	118 result = 0.
76 64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	119 for i in range(len(self.counts)-1):
64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	120 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	121 return result/self.nSamples()
35 8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	122
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	123 def var(self, mean = None):
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	124 if not mean:
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	125 m = self.mean()
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	126 else:
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	127 m = mean
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	128 result = 0.
76 64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	129 for i in range(len(self.counts)-1):
64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	130 mid = (self.categories[i]+self.categories[i+1])/2
64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	131 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	132 return result/(self.nSamples()-1)
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	133
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	134 def referenceCounts(self, cdf):
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	135 '''cdf is a cumulative distribution function
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	136 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	137 # refCumulativeCounts = [0]#[cdf(self.categories[0][0])]
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	138 # for inter in self.categories:
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	139 # refCumulativeCounts.append(cdf(inter[1]))
76 64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	140 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	141
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	142 refProba = [refCumulativeCounts[0]]
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	143 for i in xrange(1,len(refCumulativeCounts)):
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	144 refProba.append(refCumulativeCounts[i]-refCumulativeCounts[i-1])
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	145 refProba.append(1-refCumulativeCounts[-1])
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	146 refCounts = [p*self.nSamples() for p in refProba]
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	147
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	148 return refCounts, refProba
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	149
77 5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	150 def printReferenceCounts(self, refCounts=None):
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	151 if refCounts:
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	152 ref = refCounts
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	153 else:
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	154 ref = self.referenceCounts
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	155 for i in xrange(len(ref[0])):
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	156 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	157
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	158
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	159 #########################
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	160 # maths section
27 44689029a86f updated segmentIntersection and other Nicolas Saunier <nico@confins.net> parents: 24 diff changeset	161 #########################
24 6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	162
433 d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	163 # def kernelSmoothing(sampleX, X, Y, weightFunc, halfwidth):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	164 # '''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	165 # Sum_x weight(sample_x,x) * y(x)'''
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	166 # from numpy import zeros, array
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	167 # smoothed = zeros(len(sampleX))
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	168 # for i,x in enumerate(sampleX):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	169 # weights = array([weightFunc(x,xx, halfwidth) for xx in X])
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	170 # if sum(weights)>0:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	171 # smoothed[i] = sum(weights*Y)/sum(weights)
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	172 # else:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	173 # smoothed[i] = 0
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	174 # return smoothed
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	175
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	176 def kernelSmoothing(x, X, Y, weightFunc, halfwidth):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	177 '''Returns the smoothed estimate of (X,Y) at x
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	178 Sum_x weight(sample_x,x) * y(x)'''
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	179 from numpy import zeros, array
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	180 weights = array([weightFunc(x,observedx, halfwidth) for observedx in X])
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	181 if sum(weights)>0:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	182 return sum(weights*Y)/sum(weights)
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	183 else:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	184 return 0
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	185
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	186 def uniform(center, x, halfwidth):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	187 if abs(center-x)<halfwidth:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	188 return 1.
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	189 else:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	190 return 0.
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 gaussian(center, x, halfwidth):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	193 from numpy import exp
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	194 return exp(-((center-x)/halfwidth)**2/2)
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	195
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	196 def epanechnikov(center, x, halfwidth):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	197 diff = abs(center-x)
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	198 if diff<halfwidth:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	199 return 1.-(diff/halfwidth)**2
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	200 else:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	201 return 0.
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	202
434 9a714f32fc9f small updates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 433 diff changeset	203 def triangular(center, x, halfwidth):
9a714f32fc9f small updates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 433 diff changeset	204 diff = abs(center-x)
9a714f32fc9f small updates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 433 diff changeset	205 if diff<halfwidth:
9a714f32fc9f small updates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 433 diff changeset	206 return 1.-abs(diff/halfwidth)
9a714f32fc9f small updates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 433 diff changeset	207 else:
9a714f32fc9f small updates Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 433 diff changeset	208 return 0.
433 d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	209
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	210 def argMaxDict(d):
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	211 return max(d.iterkeys(), key=(lambda key: d[key]))
279 3af4c267a7bf generic simple LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 276 diff changeset	212
395 6fba1ab040f1 minor modification to framestotime Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 391 diff changeset	213 def framesToTime(nFrames, frameRate, initialTime = time()):
6fba1ab040f1 minor modification to framestotime Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 391 diff changeset	214 '''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	215 initialTime is a datetime.time'''
248 571ba5ed22e2 added utils for bus processing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 241 diff changeset	216 from math import floor
395 6fba1ab040f1 minor modification to framestotime Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 391 diff changeset	217 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	218 h = int(floor(seconds/3600.))
248 571ba5ed22e2 added utils for bus processing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 241 diff changeset	219 seconds = seconds - h*3600
261 4aa792cb0fa9 changing framesToTime to return a datetime.time Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 248 diff changeset	220 m = int(floor(seconds/60))
248 571ba5ed22e2 added utils for bus processing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 241 diff changeset	221 seconds = seconds - m*60
262 a048066bd20f correcting bug in framesToTime Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 261 diff changeset	222 return time(h, m, seconds)
248 571ba5ed22e2 added utils for bus processing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 241 diff changeset	223
381 387cc0142211 script to replay event annotations Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 376 diff changeset	224 def timeToFrames(t, frameRate):
387cc0142211 script to replay event annotations Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 376 diff changeset	225 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	226
241 ee1caff48b03 added function to sort to list of paired data X,Y Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 235 diff changeset	227 def sortXY(X,Y):
ee1caff48b03 added function to sort to list of paired data X,Y Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 235 diff changeset	228 '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	229 D = {}
ee1caff48b03 added function to sort to list of paired data X,Y Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 235 diff changeset	230 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	231 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	232 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	233 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	234
32 48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	235 def ceilDecimals(v, nDecimals):
48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	236 '''Rounds the number at the nth decimal
48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	237 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	238 from math import ceil,pow
48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	239 tens = pow(10,nDecimals)
48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	240 return ceil(v*tens)/tens
48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	241
152 74b1fc68d4df re-organized code to avoid cyclic python module dependencies Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 116 diff changeset	242 def inBetween(bound1, bound2, x):
74b1fc68d4df re-organized code to avoid cyclic python module dependencies Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 116 diff changeset	243 return bound1 <= x <= bound2 or bound2 <= x<= bound1
24 6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	244
6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	245 def crossProduct(l1, l2):
6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	246 return l1[0]l2[1]-l1[1]l2[0]
6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	247
29 ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	248 def filterMovingWindow(input, halfWidth):
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	249 '''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	250 The first and last points are copied from the original.'''
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	251 width = float(halfWidth*2+1)
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	252 win = ones(width,'d')
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	253 result = convolve(win/width,array(inputSignal),'same')
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	254 result[:halfWidth] = inputSignal[:halfWidth]
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	255 result[-halfWidth:] = inputSignal[-halfWidth:]
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	256 return result
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	257
199 ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	258 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	259 '''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	260 as well as the plot'''
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	261 from numpy.lib.polynomial import polyfit
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	262 from matplotlib.pyplot import plot
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	263 from numpy.core.multiarray import arange
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	264 coef = polyfit(x, y, deg)
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	265 if plotData:
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	266 def poly(x):
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	267 result = 0
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	268 for i in range(len(coef)):
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	269 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	270 return result
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	271 plot(x, y, 'x')
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	272 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	273 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	274 return coef
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	275
27 44689029a86f updated segmentIntersection and other Nicolas Saunier <nico@confins.net> parents: 24 diff changeset	276 #########################
455 abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	277 # iterable section
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	278 #########################
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	279
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	280 def mostCommon(L):
456 825e5d49325d slight update Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 455 diff changeset	281 '''Returns the most frequent element in a iterable
825e5d49325d slight update Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 455 diff changeset	282
825e5d49325d slight update Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 455 diff changeset	283 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	284 from itertools import groupby
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	285 from operator import itemgetter
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	286 # get an iterable of (item, iterable) pairs
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	287 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	288 # print 'SL:', SL
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	289 groups = groupby(SL, key=itemgetter(0))
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	290 # auxiliary function to get "quality" for an item
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	291 def _auxfun(g):
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	292 item, iterable = g
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	293 count = 0
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	294 min_index = len(L)
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	295 for _, where in iterable:
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	296 count += 1
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	297 min_index = min(min_index, where)
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	298 # 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	299 return count, -min_index
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	300 # pick the highest-count/earliest item
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	301 return max(groups, key=_auxfun)[0]
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	302
abe0b2347d4c added most common utility function Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 434 diff changeset	303 #########################
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	304 # sequence section
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	305 #########################
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	306
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	307 class LCSS:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	308 '''Class that keeps the LCSS parameters
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	309 and puts together the various computations'''
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	310 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	311 self.similarityFunc = similarityFunc
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	312 self.aligned = aligned
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	313 self.delta = delta
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	314 self.lengthFunc = lengthFunc
389 6d26dcc7bba0 modifications to compute alignment for None indicators Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 381 diff changeset	315 self.subSequenceIndices = [(0,0)]
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	316
373 d0b86ed50f32 work in progress on LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 372 diff changeset	317 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	318 from numpy import zeros, int as npint
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	319 n1 = len(l1)
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	320 n2 = len(l2)
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	321 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	322 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	323 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	324 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	325 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	326 else:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	327 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	328
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	329 def subSequence(self, i, j):
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	330 '''Returns the subsequence of two sequences
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	331 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	332 if i == 0 or j == 0:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	333 return []
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	334 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	335 return self.subSequence(i, j-1)
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-1][j]:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	337 return self.subSequence(i-1, j)
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	338 else:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	339 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	340
373 d0b86ed50f32 work in progress on LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 372 diff changeset	341 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	342 '''returns the longest common subsequence similarity
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	343 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	344 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	345
373 d0b86ed50f32 work in progress on LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 372 diff changeset	346 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	347
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	348 eg distance(p1, p2) < epsilon
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	349 '''
372 349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 371 diff changeset	350 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	351 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	352 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	353 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	354 else:
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 371 diff changeset	355 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	356 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	357 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	358 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	359 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	360
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	361 if self.aligned:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	362 lcssValues = {}
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	363 similarityTables = {}
374 a7af3519687e finished implementation of aligned LCSS with matching sequence decoded Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 373 diff changeset	364 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	365 self.similarities(l1, l2, i)
d0b86ed50f32 work in progress on LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 372 diff changeset	366 lcssValues[i] = self.similarityTable.max()
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	367 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	368 #print self.similarityTable
389 6d26dcc7bba0 modifications to compute alignment for None indicators Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 381 diff changeset	369 alignmentShift = argMaxDict(lcssValues) # ideally get the medium alignment shift, the one that minimizes distance
6d26dcc7bba0 modifications to compute alignment for None indicators Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 381 diff changeset	370 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	371 else:
389 6d26dcc7bba0 modifications to compute alignment for None indicators Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 381 diff changeset	372 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	373 self.similarities(l1, l2)
373 d0b86ed50f32 work in progress on LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 372 diff changeset	374
374 a7af3519687e finished implementation of aligned LCSS with matching sequence decoded Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 373 diff changeset	375 # 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	376 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	377
372 349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 371 diff changeset	378 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	379 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	380 if revertIndices:
374 a7af3519687e finished implementation of aligned LCSS with matching sequence decoded Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 373 diff changeset	381 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	382 return self.similarityTable[-1,-1]
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	383
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	384 def compute(self, l1, l2, computeSubSequence = False):
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	385 '''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	386 return self._compute(l1, l2, computeSubSequence)
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	387
375 2ea8584aa80a making indicator LCSS work Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 374 diff changeset	388 def computeAlignment(self):
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	389 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	390 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	391
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	392 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	393 ''' compute the normalized LCSS
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	394 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	395 lengthFunc = lambda x,y:float(x,y)/2'''
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	396 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	397
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	398 def computeNormalized(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	399 return self._computeNormalized(l1, l2, computeSubSequence)
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	400
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	401 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	402 ''' compute the LCSS distance'''
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	403 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	404
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	405 def computeDistance(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	406 return self._computeDistance(l1, l2, computeSubSequence)
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	407
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	408 #########################
45 74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	409 # plotting section
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	410 #########################
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	411
332 a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	412 def plotPolygon(poly, options = ''):
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	413 'Plots shapely polygon poly'
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	414 from numpy.core.multiarray import array
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	415 from matplotlib.pyplot import plot
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	416 from shapely.geometry import Polygon
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	417
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	418 tmp = array(poly.exterior)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	419 plot(tmp[:,0], tmp[:,1], options)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	420
324 99ca91a46007 minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 323 diff changeset	421 def stepPlot(X, firstX, lastX, initialCount = 0, increment = 1):
99ca91a46007 minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 323 diff changeset	422 '''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	423 returns the lists that can be plotted
324 99ca91a46007 minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 323 diff changeset	424 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	425 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	426
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 286 diff changeset	427 sortedX = []
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 286 diff changeset	428 counts = [initialCount]
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 286 diff changeset	429 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	430 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	431 counts.append(counts[-1])
324 99ca91a46007 minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 323 diff changeset	432 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	433 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	434 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	435
45 74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	436 class PlottingPropertyValues:
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	437 def __init__(self, values):
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	438 self.values = values
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	439
116 2bf5b76320c0 moved intersection plotting and added markers for scatter plots Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 115 diff changeset	440 def __getitem__(self, i):
45 74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	441 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	442
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	443 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	444 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	445
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	446 linestyles = PlottingPropertyValues(['-', '--', '-.', ':'])
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 colors = PlottingPropertyValues('brgmyck') # 'w'
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	449
115 550556378466 added functionalities to indicator maps Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 86 diff changeset	450 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	451 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	452 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	453 coords = array(indicatorMap.keys())
75cf537b8d88 moved and generalized map making functions to the library Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 48 diff changeset	454 minX = min(coords[:,0])
75cf537b8d88 moved and generalized map making functions to the library Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 48 diff changeset	455 minY = min(coords[:,1])
75cf537b8d88 moved and generalized map making functions to the library Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 48 diff changeset	456 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	457 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	458 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	459 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	460 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	461 if masked:
550556378466 added functionalities to indicator maps Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 86 diff changeset	462 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	463 else:
550556378466 added functionalities to indicator maps Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 86 diff changeset	464 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	465
45 74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	466 #########################
27 44689029a86f updated segmentIntersection and other Nicolas Saunier <nico@confins.net> parents: 24 diff changeset	467 # file I/O section
44689029a86f updated segmentIntersection and other Nicolas Saunier <nico@confins.net> parents: 24 diff changeset	468 #########################
24 6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	469
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	470 def openCheck(filename, option = 'r', quit = False):
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	471 '''Open file filename in read mode by default
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	472 and checks it is open'''
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	473 try:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	474 return open(filename, option)
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	475 except IOError:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	476 print 'File %s could not be opened.' % filename
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	477 if quit:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	478 from sys import exit
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	479 exit()
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	480 return None
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	481
48 8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 46 diff changeset	482 def readline(f, commentCharacter = commentChar):
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	483 '''Modified readline function to skip comments.'''
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	484 s = f.readline()
48 8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 46 diff changeset	485 while (len(s) > 0) and s.startswith(commentCharacter):
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	486 s = f.readline()
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	487 return s.strip()
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	488
48 8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 46 diff changeset	489 def getLines(f, delimiterCharacter = delimiterChar):
8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 46 diff changeset	490 '''Gets a complete entry (all the lines) in between delimiterChar.'''
8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 46 diff changeset	491 dataStrings = []
8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 46 diff changeset	492 s = readline(f)
8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 46 diff changeset	493 while (len(s) > 0) and (not s.startswith(delimiterCharacter)):
8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 46 diff changeset	494 dataStrings += [s.strip()]
8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 46 diff changeset	495 s = readline(f)
8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 46 diff changeset	496 return dataStrings
8aed225f71d8 rearranged code for function readline and getlines (and characters), moved invertHomography to cvutils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 46 diff changeset	497
304 20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	498 class FakeSecHead(object):
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	499 '''Add fake section header [asection]
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	500
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	501 from http://stackoverflow.com/questions/2819696/parsing-properties-file-in-python/2819788#2819788
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	502 use read_file in Python 3.2+
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	503 '''
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	504 def __init__(self, fp):
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	505 self.fp = fp
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	506 self.sechead = '[main]\n'
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	507
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	508 def readline(self):
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	509 if self.sechead:
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	510 try: return self.sechead
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	511 finally: self.sechead = None
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	512 else: return self.fp.readline()
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	513
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	514 def removeExtension(filename, delimiter = '.'):
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	515 '''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	516 i = filename.rfind(delimiter)
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	517 if i>0:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	518 return filename[:i]
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	519 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	520 return filename
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	521
46 b5d007612e16 added filename util Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 45 diff changeset	522 def cleanFilename(s):
b5d007612e16 added filename util Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 45 diff changeset	523 'cleans filenames obtained when contatenating figure characteristics'
266 aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	524 return s.replace(' ','-').replace('.','').replace('/','-')
46 b5d007612e16 added filename util Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 45 diff changeset	525
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	526 def listfiles(dirname, extension, remove = False):
14 e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	527 '''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	528 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	529 from os import listdir
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	530 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	531 tmp.sort()
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	532 if remove:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	533 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	534 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	535 return tmp
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	536
266 aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	537 def mkdir(dirname):
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	538 'Creates a directory if it does not exist'
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	539 import os
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	540 if not os.path.exists(dirname):
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	541 os.mkdir(dirname)
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	542 else:
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	543 print(dirname+' already exists')
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	544
14 e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	545 def removeFile(filename):
e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	546 '''Deletes the file while avoiding raising an error
e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	547 if the file does not exist'''
266 aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	548 import os
14 e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	549 if (os.path.exists(filename)):
e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	550 os.remove(filename)
266 aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	551 else:
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	552 print(filename+' does not exist')
14 e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	553
42 1a2ac2d4f53a added loading of the rest of the data for objects Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 35 diff changeset	554 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	555 '''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	556 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	557
1a2ac2d4f53a added loading of the rest of the data for objects Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 35 diff changeset	558 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	559 '''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	560 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	561
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	562 #########################
332 a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	563 # CLI utils
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	564 #########################
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	565
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	566 def parseCLIOptions(helpMessage, options, cliArgs, optionalOptions=[]):
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	567 ''' Simple function to handle similar argument parsing
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	568 Returns the dictionary of options and their values
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	569
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	570 * cliArgs are most likely directly sys.argv
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	571 (only the elements after the first one are considered)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	572
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	573 * options should be a list of strings for getopt options,
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	574 eg ['frame=','correspondences=','video=']
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	575 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	576 import sys, getopt
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	577 from numpy.core.fromnumeric import all
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	578 optionValues, args = getopt.getopt(cliArgs[1:], 'h', ['help']+options+optionalOptions)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	579 optionValues = dict(optionValues)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	580
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	581 if '--help' in optionValues.keys() or '-h' in optionValues.keys():
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	582 print(helpMessage+
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	583 '\n - Compulsory options: '+' '.join([opt.replace('=','') for opt in options])+
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	584 '\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	585 sys.exit()
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	586
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	587 missingArgument = [('--'+opt.replace('=','') in optionValues.keys()) for opt in options]
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	588 if not all(missingArgument):
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	589 print('Missing argument')
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	590 print(optionValues)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	591 sys.exit()
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	592
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	593 return optionValues
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	594
397 b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	595
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	596 #########################
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	597 # Utils to read .ini type text files for configuration, meta data...
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	598 #########################
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	599
333 c9201f6b143a moved the config parser to utils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 332 diff changeset	600 class TrackingParameters:
483 30b3455978d9 Corrected issues with safety-analysis script, variable names are changed and tracking.cfg accordingly Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 456 diff changeset	601 '''Class for tracking and safety parameters
30b3455978d9 Corrected issues with safety-analysis script, variable names are changed and tracking.cfg accordingly Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 456 diff changeset	602
30b3455978d9 Corrected issues with safety-analysis script, variable names are changed and tracking.cfg accordingly Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 456 diff changeset	603 Note: framerate is already taken into account'''
333 c9201f6b143a moved the config parser to utils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 332 diff changeset	604 def loadConfigFile(self, filename):
c9201f6b143a moved the config parser to utils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 332 diff changeset	605 from ConfigParser import ConfigParser
c9201f6b143a moved the config parser to utils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 332 diff changeset	606 from numpy import loadtxt
364 a50a69e04c2a script modification so that command line arguments take precedence over config file Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 352 diff changeset	607 from os import path
a50a69e04c2a script modification so that command line arguments take precedence over config file Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 352 diff changeset	608
333 c9201f6b143a moved the config parser to utils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 332 diff changeset	609 config = ConfigParser()
c9201f6b143a moved the config parser to utils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 332 diff changeset	610 config.readfp(FakeSecHead(openCheck(filename)))
c9201f6b143a moved the config parser to utils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 332 diff changeset	611 self.sectionHeader = config.sections()[0]
c9201f6b143a moved the config parser to utils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 332 diff changeset	612 self.videoFilename = config.get(self.sectionHeader, 'video-filename')
c9201f6b143a moved the config parser to utils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 332 diff changeset	613 self.databaseFilename = config.get(self.sectionHeader, 'database-filename')
c9201f6b143a moved the config parser to utils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 332 diff changeset	614 self.homographyFilename = config.get(self.sectionHeader, 'homography-filename')
364 a50a69e04c2a script modification so that command line arguments take precedence over config file Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 352 diff changeset	615 if (path.exists(self.homographyFilename)):
a50a69e04c2a script modification so that command line arguments take precedence over config file Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 352 diff changeset	616 self.homography = loadtxt(self.homographyFilename)
a50a69e04c2a script modification so that command line arguments take precedence over config file Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 352 diff changeset	617 else:
a50a69e04c2a script modification so that command line arguments take precedence over config file Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 352 diff changeset	618 self.homography = None
333 c9201f6b143a moved the config parser to utils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 332 diff changeset	619 self.firstFrameNum = config.getint(self.sectionHeader, 'frame1')
348 c64a4f889b97 added safety analysis options to feature tracking (with default values for backward compatibility) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 344 diff changeset	620 self.videoFrameRate = config.getfloat(self.sectionHeader, 'video-fps')
332 a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	621
350 7e9ad2d9d79c added new parameters in safety analysis script Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 348 diff changeset	622 self.maxPredictedSpeed = config.getfloat(self.sectionHeader, 'max-predicted-speed')/3.6/self.videoFrameRate
7e9ad2d9d79c added new parameters in safety analysis script Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 348 diff changeset	623 self.predictionTimeHorizon = config.getfloat(self.sectionHeader, 'prediction-time-horizon')*self.videoFrameRate
7e9ad2d9d79c added new parameters in safety analysis script Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 348 diff changeset	624 self.collisionDistance = config.getfloat(self.sectionHeader, 'collision-distance')
7e9ad2d9d79c added new parameters in safety analysis script Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 348 diff changeset	625 self.crossingZones = config.getboolean(self.sectionHeader, 'crossing-zones')
352 72aa44072093 safety analysis script with option for prediction method Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 351 diff changeset	626 self.predictionMethod = config.get(self.sectionHeader, 'prediction-method')
350 7e9ad2d9d79c added new parameters in safety analysis script Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 348 diff changeset	627 self.nPredictedTrajectories = config.getint(self.sectionHeader, 'npredicted-trajectories')
483 30b3455978d9 Corrected issues with safety-analysis script, variable names are changed and tracking.cfg accordingly Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 456 diff changeset	628 self.maxNormalAcceleration = config.getfloat(self.sectionHeader, 'max-normal-acceleration')/self.videoFrameRate**2
30b3455978d9 Corrected issues with safety-analysis script, variable names are changed and tracking.cfg accordingly Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 456 diff changeset	629 self.maxNormalSteering = config.getfloat(self.sectionHeader, 'max-normal-steering')/self.videoFrameRate
30b3455978d9 Corrected issues with safety-analysis script, variable names are changed and tracking.cfg accordingly Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 456 diff changeset	630 self.minExtremeAcceleration = config.getfloat(self.sectionHeader, 'min-extreme-acceleration')/self.videoFrameRate**2
30b3455978d9 Corrected issues with safety-analysis script, variable names are changed and tracking.cfg accordingly Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 456 diff changeset	631 self.maxExtremeAcceleration = config.getfloat(self.sectionHeader, 'max-extreme-acceleration')/self.videoFrameRate**2
30b3455978d9 Corrected issues with safety-analysis script, variable names are changed and tracking.cfg accordingly Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 456 diff changeset	632 self.maxExtremeSteering = config.getfloat(self.sectionHeader, 'max-extreme-steering')/self.videoFrameRate
351 891858351bcb added new parameter (use features) for safety analysis Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 350 diff changeset	633 self.useFeaturesForPrediction = config.getboolean(self.sectionHeader, 'use-features-prediction')
350 7e9ad2d9d79c added new parameters in safety analysis script Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 348 diff changeset	634
397 b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	635 class SceneParameters:
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	636 def __init__(self, config, sectionName):
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	637 from ConfigParser import NoOptionError
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	638 from ast import literal_eval
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	639 try:
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	640 self.sitename = config.get(sectionName, 'sitename')
405 a9e275b4ecb7 modification of the scene.cfg format Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 398 diff changeset	641 self.databaseFilename = config.get(sectionName, 'data-filename')
a9e275b4ecb7 modification of the scene.cfg format Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 398 diff changeset	642 self.homographyFilename = config.get(sectionName, 'homography-filename')
a9e275b4ecb7 modification of the scene.cfg format Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 398 diff changeset	643 self.calibrationFilename = config.get(sectionName, 'calibration-filename')
a9e275b4ecb7 modification of the scene.cfg format Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 398 diff changeset	644 self.videoFilename = config.get(sectionName, 'video-filename')
a9e275b4ecb7 modification of the scene.cfg format Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 398 diff changeset	645 self.frameRate = config.getfloat(sectionName, 'framerate')
421 4fce27946c60 first example of video metadata using sqlalchemy Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 405 diff changeset	646 self.date = datetime.strptime(config.get(sectionName, 'date'), datetimeFormat) # 2011-06-22 11:00:39
397 b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	647 self.translation = literal_eval(config.get(sectionName, 'translation')) # = [0.0, 0.0]
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	648 self.rotation = config.getfloat(sectionName, 'rotation')
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	649 self.duration = config.getint(sectionName, 'duration')
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	650 except NoOptionError as e:
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	651 print(e)
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	652 print('Not a section for scene meta-data')
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	653
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	654 @staticmethod
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	655 def loadConfigFile(filename):
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	656 from ConfigParser import ConfigParser
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	657 config = ConfigParser()
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	658 config.readfp(openCheck(filename))
398 3399bd48cb40 Ajout d'une méthode pour obtenir le nombre de FPS Jean-Philippe Jodoin <jpjodoin@gmail.com> parents: 397 diff changeset	659 configDict = dict()
3399bd48cb40 Ajout d'une méthode pour obtenir le nombre de FPS Jean-Philippe Jodoin <jpjodoin@gmail.com> parents: 397 diff changeset	660 for sectionName in config.sections():
3399bd48cb40 Ajout d'une méthode pour obtenir le nombre de FPS Jean-Philippe Jodoin <jpjodoin@gmail.com> parents: 397 diff changeset	661 configDict[sectionName] = SceneParameters(config, sectionName)
3399bd48cb40 Ajout d'une méthode pour obtenir le nombre de FPS Jean-Philippe Jodoin <jpjodoin@gmail.com> parents: 397 diff changeset	662 return configDict
397 b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	663
233 ab1a11176d7b initial sqlite code and bug corrected in cvutils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 199 diff changeset	664 #########################
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	665 # running tests
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	666 #########################
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	667
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	668 if __name__ == "__main__":
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	669 import doctest
2 de5642925615 started implementation of TimeInterval and Spatio-temporal object Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 0 diff changeset	670 import unittest
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	671 suite = doctest.DocFileSuite('tests/utils.txt')
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	672 #suite = doctest.DocTestSuite()
2 de5642925615 started implementation of TimeInterval and Spatio-temporal object Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 0 diff changeset	673 unittest.TextTestRunner().run(suite)
de5642925615 started implementation of TimeInterval and Spatio-temporal object Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 0 diff changeset	674 #doctest.testmod()
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	675 #doctest.testfile("example.txt")

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annotate python/utils.py @ 499:0a93afea8243