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

annotate python/utils.py @ 433:d40ad901b272

added kernel smoothing

author	Nicolas Saunier <nicolas.saunier@polymtl.ca>
date	Fri, 29 Nov 2013 02:38:41 -0500
parents	f738fa1b69f0
children	9a714f32fc9f

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):
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	39 'if trueStd, use normal distribution, otherwise, Student'
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	40 from math import sqrt
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	41 from scipy.stats.distributions import norm, t
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	42 if trueStd:
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	43 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	44 else: # use Student
f738fa1b69f0 added sample size and Student distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 421 diff changeset	45 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	46 e = k*stdev/sqrt(nSamples)
27f06d28036d added simple helper for confidence intervals Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 297 diff changeset	47 if printLatex:
27f06d28036d added simple helper for confidence intervals Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 297 diff changeset	48 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	49 return mean-e, mean+e
27f06d28036d added simple helper for confidence intervals Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 297 diff changeset	50
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	51 def computeChi2(expected, observed):
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	52 '''Returns the Chi2 statistics'''
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	53 result = 0.
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	54 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	55 result += ((e-o)*(e-o))/e
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	56 return result
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	57
85 7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	58 class EmpiricalDistribution:
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	59 def nSamples(self):
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	60 return sum(self.counts)
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	61
197 2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	62 def cumulativeDensityFunction(sample):
276 78922b4de3bf minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 266 diff changeset	63 '''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	64 from numpy.core.multiarray import array
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	65 from numpy.lib.function_base import unique
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	66 from numpy.core.fromnumeric import sum
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	67 a = array(sample)
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	68 a.sort()
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	69 xaxis = unique(a)
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	70 counts = [sum(a <= x) for x in xaxis]
2788b2827670 simple cumulatie function distribution computation Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 185 diff changeset	71 return xaxis, counts
85 7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	72
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	73 class EmpiricalDiscreteDistribution(EmpiricalDistribution):
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	74 '''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	75 '''
86 f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	76 from numpy.core.fromnumeric import sum
f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	77
85 7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	78 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	79 self.categories = categories
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	80 self.counts = counts
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	81
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	82 def mean(self):
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	83 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	84 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	85
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	86 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	87 if not mean:
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	88 m = self.mean()
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	89 else:
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	90 m = mean
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	91 result = 0.
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	92 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	93 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	94
86 f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	95 def referenceCounts(self, probability):
f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	96 '''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	97 refProba = [probability(c) for c in self.categories]
f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	98 refProba[-1] = 1-sum(refProba[:-1])
f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	99 refCounts = [r*self.nSamples() for r in refProba]
f03ec4697a09 corrected discrete distribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 85 diff changeset	100 return refCounts, refProba
85 7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	101
7f1e54234f96 added empirical discrete distribution, modified class organization and names Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 77 diff changeset	102 class EmpiricalContinuousDistribution(EmpiricalDistribution):
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	103 '''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	104 with the number of observations for each interval
64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	105 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	106 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	107 def __init__(self, categories, counts):
276 78922b4de3bf minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 266 diff changeset	108 # 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	109 self.categories = categories
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	110 self.counts = counts
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	111
35 8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	112 def mean(self):
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	113 result = 0.
76 64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	114 for i in range(len(self.counts)-1):
64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	115 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	116 return result/self.nSamples()
35 8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	117
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	118 def var(self, mean = None):
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	119 if not mean:
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	120 m = self.mean()
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	121 else:
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	122 m = mean
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	123 result = 0.
76 64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	124 for i in range(len(self.counts)-1):
64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	125 mid = (self.categories[i]+self.categories[i+1])/2
64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	126 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	127 return result/(self.nSamples()-1)
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	128
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	129 def referenceCounts(self, cdf):
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	130 '''cdf is a cumulative distribution function
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	131 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	132 # refCumulativeCounts = [0]#[cdf(self.categories[0][0])]
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	133 # for inter in self.categories:
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	134 # refCumulativeCounts.append(cdf(inter[1]))
76 64fde2b1f96d simplified intervales in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 75 diff changeset	135 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	136
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	137 refProba = [refCumulativeCounts[0]]
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	138 for i in xrange(1,len(refCumulativeCounts)):
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	139 refProba.append(refCumulativeCounts[i]-refCumulativeCounts[i-1])
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	140 refProba.append(1-refCumulativeCounts[-1])
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	141 refCounts = [p*self.nSamples() for p in refProba]
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	142
8cafee54466f forgotten update of histogram class Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 32 diff changeset	143 return refCounts, refProba
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	144
77 5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	145 def printReferenceCounts(self, refCounts=None):
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	146 if refCounts:
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	147 ref = refCounts
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	148 else:
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	149 ref = self.referenceCounts
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	150 for i in xrange(len(ref[0])):
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	151 print('{0}-{1} & {2:0.3} & {3:0.3} \\\\'.format(self.categories[i],self.categories[i+1],ref[1][i], ref[0][i]))
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	152
5e6cd36a991c added pretty print in empiricalDistribution Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 76 diff changeset	153
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	154 #########################
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	155 # maths section
27 44689029a86f updated segmentIntersection and other Nicolas Saunier <nico@confins.net> parents: 24 diff changeset	156 #########################
24 6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	157
433 d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	158 # def kernelSmoothing(sampleX, X, Y, weightFunc, halfwidth):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	159 # '''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	160 # Sum_x weight(sample_x,x) * y(x)'''
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	161 # from numpy import zeros, array
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	162 # smoothed = zeros(len(sampleX))
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	163 # for i,x in enumerate(sampleX):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	164 # weights = array([weightFunc(x,xx, halfwidth) for xx in X])
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	165 # if sum(weights)>0:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	166 # smoothed[i] = sum(weights*Y)/sum(weights)
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	167 # else:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	168 # smoothed[i] = 0
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	169 # return smoothed
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	170
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	171 def kernelSmoothing(x, X, Y, weightFunc, halfwidth):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	172 '''Returns the smoothed estimate of (X,Y) at x
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	173 Sum_x weight(sample_x,x) * y(x)'''
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	174 from numpy import zeros, array
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	175 weights = array([weightFunc(x,observedx, halfwidth) for observedx in X])
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	176 if sum(weights)>0:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	177 return sum(weights*Y)/sum(weights)
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	178 else:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	179 return 0
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	180
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	181 def uniform(center, x, halfwidth):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	182 if abs(center-x)<halfwidth:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	183 return 1.
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	184 else:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	185 return 0.
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	186
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	187 def gaussian(center, x, halfwidth):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	188 from numpy import exp
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	189 return exp(-((center-x)/halfwidth)**2/2)
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	190
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	191 def epanechnikov(center, x, halfwidth):
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	192 diff = abs(center-x)
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	193 if diff<halfwidth:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	194 return 1.-(diff/halfwidth)**2
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	195 else:
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	196 return 0.
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	197
d40ad901b272 added kernel smoothing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 423 diff changeset	198
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	199 def argMaxDict(d):
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	200 return max(d.iterkeys(), key=(lambda key: d[key]))
279 3af4c267a7bf generic simple LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 276 diff changeset	201
395 6fba1ab040f1 minor modification to framestotime Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 391 diff changeset	202 def framesToTime(nFrames, frameRate, initialTime = time()):
6fba1ab040f1 minor modification to framestotime Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 391 diff changeset	203 '''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	204 initialTime is a datetime.time'''
248 571ba5ed22e2 added utils for bus processing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 241 diff changeset	205 from math import floor
395 6fba1ab040f1 minor modification to framestotime Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 391 diff changeset	206 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	207 h = int(floor(seconds/3600.))
248 571ba5ed22e2 added utils for bus processing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 241 diff changeset	208 seconds = seconds - h*3600
261 4aa792cb0fa9 changing framesToTime to return a datetime.time Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 248 diff changeset	209 m = int(floor(seconds/60))
248 571ba5ed22e2 added utils for bus processing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 241 diff changeset	210 seconds = seconds - m*60
262 a048066bd20f correcting bug in framesToTime Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 261 diff changeset	211 return time(h, m, seconds)
248 571ba5ed22e2 added utils for bus processing Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 241 diff changeset	212
381 387cc0142211 script to replay event annotations Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 376 diff changeset	213 def timeToFrames(t, frameRate):
387cc0142211 script to replay event annotations Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 376 diff changeset	214 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	215
241 ee1caff48b03 added function to sort to list of paired data X,Y Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 235 diff changeset	216 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	217 '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	218 D = {}
ee1caff48b03 added function to sort to list of paired data X,Y Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 235 diff changeset	219 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	220 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	221 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	222 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	223
32 48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	224 def ceilDecimals(v, nDecimals):
48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	225 '''Rounds the number at the nth decimal
48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	226 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	227 from math import ceil,pow
48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	228 tens = pow(10,nDecimals)
48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	229 return ceil(v*tens)/tens
48e56179c39e added ceil function Nicolas Saunier <nico@confins.net> parents: 31 diff changeset	230
152 74b1fc68d4df re-organized code to avoid cyclic python module dependencies Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 116 diff changeset	231 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	232 return bound1 <= x <= bound2 or bound2 <= x<= bound1
24 6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	233
6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	234 def crossProduct(l1, l2):
6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	235 return l1[0]l2[1]-l1[1]l2[0]
6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	236
29 ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	237 def filterMovingWindow(input, halfWidth):
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	238 '''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	239 The first and last points are copied from the original.'''
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	240 width = float(halfWidth*2+1)
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	241 win = ones(width,'d')
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	242 result = convolve(win/width,array(inputSignal),'same')
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	243 result[:halfWidth] = inputSignal[:halfWidth]
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	244 result[-halfWidth:] = inputSignal[-halfWidth:]
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	245 return result
ca8e716cc231 added moving average filter Nicolas Saunier <nico@confins.net> parents: 27 diff changeset	246
199 ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	247 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	248 '''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	249 as well as the plot'''
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	250 from numpy.lib.polynomial import polyfit
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	251 from matplotlib.pyplot import plot
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	252 from numpy.core.multiarray import arange
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	253 coef = polyfit(x, y, deg)
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	254 if plotData:
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	255 def poly(x):
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	256 result = 0
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	257 for i in range(len(coef)):
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	258 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	259 return result
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	260 plot(x, y, 'x')
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	261 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	262 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	263 return coef
ca9d9104afba added utility to calibrate polynoms and plot Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 197 diff changeset	264
27 44689029a86f updated segmentIntersection and other Nicolas Saunier <nico@confins.net> parents: 24 diff changeset	265 #########################
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	266 # sequence section
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	267 #########################
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	268
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	269 class LCSS:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	270 '''Class that keeps the LCSS parameters
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	271 and puts together the various computations'''
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	272 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	273 self.similarityFunc = similarityFunc
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	274 self.aligned = aligned
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	275 self.delta = delta
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	276 self.lengthFunc = lengthFunc
389 6d26dcc7bba0 modifications to compute alignment for None indicators Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 381 diff changeset	277 self.subSequenceIndices = [(0,0)]
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	278
373 d0b86ed50f32 work in progress on LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 372 diff changeset	279 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	280 from numpy import zeros, int as npint
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	281 n1 = len(l1)
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	282 n2 = len(l2)
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	283 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	284 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	285 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	286 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	287 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	288 else:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	289 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	290
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	291 def subSequence(self, i, j):
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	292 '''Returns the subsequence of two sequences
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	293 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	294 if i == 0 or j == 0:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	295 return []
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	296 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	297 return self.subSequence(i, j-1)
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	298 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	299 return self.subSequence(i-1, j)
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	300 else:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	301 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	302
373 d0b86ed50f32 work in progress on LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 372 diff changeset	303 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	304 '''returns the longest common subsequence similarity
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	305 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	306 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	307
373 d0b86ed50f32 work in progress on LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 372 diff changeset	308 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	309
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	310 eg distance(p1, p2) < epsilon
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	311 '''
372 349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 371 diff changeset	312 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	313 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	314 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	315 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	316 else:
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 371 diff changeset	317 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	318 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	319 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	320 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	321 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	322
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	323 if self.aligned:
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	324 lcssValues = {}
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	325 similarityTables = {}
374 a7af3519687e finished implementation of aligned LCSS with matching sequence decoded Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 373 diff changeset	326 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	327 self.similarities(l1, l2, i)
d0b86ed50f32 work in progress on LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 372 diff changeset	328 lcssValues[i] = self.similarityTable.max()
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	329 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	330 #print self.similarityTable
389 6d26dcc7bba0 modifications to compute alignment for None indicators Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 381 diff changeset	331 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	332 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	333 else:
389 6d26dcc7bba0 modifications to compute alignment for None indicators Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 381 diff changeset	334 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	335 self.similarities(l1, l2)
373 d0b86ed50f32 work in progress on LCSS Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 372 diff changeset	336
374 a7af3519687e finished implementation of aligned LCSS with matching sequence decoded Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 373 diff changeset	337 # 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	338 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	339
372 349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 371 diff changeset	340 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	341 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	342 if revertIndices:
374 a7af3519687e finished implementation of aligned LCSS with matching sequence decoded Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 373 diff changeset	343 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	344 return self.similarityTable[-1,-1]
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	345
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	346 def compute(self, l1, l2, computeSubSequence = False):
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	347 '''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	348 return self._compute(l1, l2, computeSubSequence)
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	349
375 2ea8584aa80a making indicator LCSS work Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 374 diff changeset	350 def computeAlignment(self):
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	351 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	352 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	353
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	354 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	355 ''' compute the normalized LCSS
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	356 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	357 lengthFunc = lambda x,y:float(x,y)/2'''
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	358 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	359
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	360 def computeNormalized(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	361 return self._computeNormalized(l1, l2, computeSubSequence)
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	362
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	363 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	364 ''' compute the LCSS distance'''
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	365 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	366
376 2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	367 def computeDistance(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 375 diff changeset	368 return self._computeDistance(l1, l2, computeSubSequence)
370 97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	369
97e8fa0ee9a1 work in progress for complete alignment Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 369 diff changeset	370 #########################
45 74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	371 # plotting section
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	372 #########################
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	373
332 a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	374 def plotPolygon(poly, options = ''):
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	375 'Plots shapely polygon poly'
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	376 from numpy.core.multiarray import array
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	377 from matplotlib.pyplot import plot
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	378 from shapely.geometry import Polygon
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	379
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	380 tmp = array(poly.exterior)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	381 plot(tmp[:,0], tmp[:,1], options)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	382
324 99ca91a46007 minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 323 diff changeset	383 def stepPlot(X, firstX, lastX, initialCount = 0, increment = 1):
99ca91a46007 minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 323 diff changeset	384 '''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	385 returns the lists that can be plotted
324 99ca91a46007 minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 323 diff changeset	386 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	387 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	388
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 286 diff changeset	389 sortedX = []
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 286 diff changeset	390 counts = [initialCount]
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 286 diff changeset	391 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	392 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	393 counts.append(counts[-1])
324 99ca91a46007 minor change Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 323 diff changeset	394 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	395 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	396 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	397
45 74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	398 class PlottingPropertyValues:
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	399 def __init__(self, values):
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	400 self.values = values
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	401
116 2bf5b76320c0 moved intersection plotting and added markers for scatter plots Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 115 diff changeset	402 def __getitem__(self, i):
45 74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	403 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	404
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	405 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	406 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	407
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	408 linestyles = PlottingPropertyValues(['-', '--', '-.', ':'])
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	409
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	410 colors = PlottingPropertyValues('brgmyck') # 'w'
74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	411
115 550556378466 added functionalities to indicator maps Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 86 diff changeset	412 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	413 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	414 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	415 coords = array(indicatorMap.keys())
75cf537b8d88 moved and generalized map making functions to the library Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 48 diff changeset	416 minX = min(coords[:,0])
75cf537b8d88 moved and generalized map making functions to the library Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 48 diff changeset	417 minY = min(coords[:,1])
75cf537b8d88 moved and generalized map making functions to the library Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 48 diff changeset	418 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	419 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	420 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	421 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	422 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	423 if masked:
550556378466 added functionalities to indicator maps Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 86 diff changeset	424 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	425 else:
550556378466 added functionalities to indicator maps Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 86 diff changeset	426 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	427
45 74d2de078baf added colors, linestyles and markers to pick from Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 42 diff changeset	428 #########################
27 44689029a86f updated segmentIntersection and other Nicolas Saunier <nico@confins.net> parents: 24 diff changeset	429 # file I/O section
44689029a86f updated segmentIntersection and other Nicolas Saunier <nico@confins.net> parents: 24 diff changeset	430 #########################
24 6fb59cfb201e first version of segmentIntersection Nicolas Saunier <nico@confins.net> parents: 19 diff changeset	431
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	432 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	433 '''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	434 and checks it is open'''
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	435 try:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	436 return open(filename, option)
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	437 except IOError:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	438 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	439 if quit:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	440 from sys import exit
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	441 exit()
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	442 return None
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	443
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	444 def readline(f, commentCharacter = commentChar):
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	445 '''Modified readline function to skip comments.'''
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	446 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	447 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	448 s = f.readline()
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	449 return s.strip()
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	450
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	451 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	452 '''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	453 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	454 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	455 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	456 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	457 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	458 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	459
304 20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	460 class FakeSecHead(object):
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	461 '''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	462
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	463 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	464 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	465 '''
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	466 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	467 self.fp = fp
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	468 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	469
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	470 def readline(self):
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	471 if self.sechead:
20f9cd972dde added capability to parse cfg file for display-trajectories.py Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 301 diff changeset	472 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	473 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	474 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	475
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	476 def removeExtension(filename, delimiter = '.'):
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	477 '''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	478 i = filename.rfind(delimiter)
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	479 if i>0:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	480 return filename[:i]
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	481 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	482 return filename
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	483
46 b5d007612e16 added filename util Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 45 diff changeset	484 def cleanFilename(s):
b5d007612e16 added filename util Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 45 diff changeset	485 'cleans filenames obtained when contatenating figure characteristics'
266 aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	486 return s.replace(' ','-').replace('.','').replace('/','-')
46 b5d007612e16 added filename util Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 45 diff changeset	487
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	488 def listfiles(dirname, extension, remove = False):
14 e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	489 '''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	490 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	491 from os import listdir
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	492 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	493 tmp.sort()
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	494 if remove:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	495 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	496 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	497 return tmp
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	498
266 aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	499 def mkdir(dirname):
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	500 'Creates a directory if it does not exist'
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	501 import os
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	502 if not os.path.exists(dirname):
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	503 os.mkdir(dirname)
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	504 else:
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	505 print(dirname+' already exists')
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	506
14 e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	507 def removeFile(filename):
e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	508 '''Deletes the file while avoiding raising an error
e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	509 if the file does not exist'''
266 aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	510 import os
14 e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	511 if (os.path.exists(filename)):
e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	512 os.remove(filename)
266 aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	513 else:
aba9711b3149 small modificatons and reorganization Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 262 diff changeset	514 print(filename+' does not exist')
14 e7bbe8465591 homography and other utils Nicolas Saunier <nico@confins.net> parents: 7 diff changeset	515
42 1a2ac2d4f53a added loading of the rest of the data for objects Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 35 diff changeset	516 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	517 '''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	518 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	519
1a2ac2d4f53a added loading of the rest of the data for objects Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 35 diff changeset	520 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	521 '''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	522 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	523
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	524 #########################
332 a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	525 # CLI utils
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	526 #########################
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	527
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	528 def parseCLIOptions(helpMessage, options, cliArgs, optionalOptions=[]):
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	529 ''' Simple function to handle similar argument parsing
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	530 Returns the dictionary of options and their values
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	531
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	532 * cliArgs are most likely directly sys.argv
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	533 (only the elements after the first one are considered)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	534
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	535 * options should be a list of strings for getopt options,
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	536 eg ['frame=','correspondences=','video=']
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	537 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	538 import sys, getopt
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	539 from numpy.core.fromnumeric import all
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	540 optionValues, args = getopt.getopt(cliArgs[1:], 'h', ['help']+options+optionalOptions)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	541 optionValues = dict(optionValues)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	542
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	543 if '--help' in optionValues.keys() or '-h' in optionValues.keys():
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	544 print(helpMessage+
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	545 '\n - Compulsory options: '+' '.join([opt.replace('=','') for opt in options])+
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	546 '\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	547 sys.exit()
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	548
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	549 missingArgument = [('--'+opt.replace('=','') in optionValues.keys()) for opt in options]
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	550 if not all(missingArgument):
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	551 print('Missing argument')
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	552 print(optionValues)
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	553 sys.exit()
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	554
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	555 return optionValues
a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	556
397 b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	557
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	558 #########################
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	559 # 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	560 #########################
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	561
333 c9201f6b143a moved the config parser to utils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 332 diff changeset	562 class TrackingParameters:
c9201f6b143a moved the config parser to utils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 332 diff changeset	563 def loadConfigFile(self, filename):
c9201f6b143a moved the config parser to utils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 332 diff changeset	564 from ConfigParser import ConfigParser
c9201f6b143a moved the config parser to utils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 332 diff changeset	565 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	566 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	567
333 c9201f6b143a moved the config parser to utils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 332 diff changeset	568 config = ConfigParser()
c9201f6b143a moved the config parser to utils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 332 diff changeset	569 config.readfp(FakeSecHead(openCheck(filename)))
c9201f6b143a moved the config parser to utils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 332 diff changeset	570 self.sectionHeader = config.sections()[0]
c9201f6b143a moved the config parser to utils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 332 diff changeset	571 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	572 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	573 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	574 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	575 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	576 else:
a50a69e04c2a script modification so that command line arguments take precedence over config file Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 352 diff changeset	577 self.homography = None
333 c9201f6b143a moved the config parser to utils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 332 diff changeset	578 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	579 self.videoFrameRate = config.getfloat(self.sectionHeader, 'video-fps')
332 a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	580
350 7e9ad2d9d79c added new parameters in safety analysis script Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 348 diff changeset	581 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	582 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	583 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	584 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	585 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	586 self.nPredictedTrajectories = config.getint(self.sectionHeader, 'npredicted-trajectories')
7e9ad2d9d79c added new parameters in safety analysis script Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 348 diff changeset	587 self.minAcceleration = config.getfloat(self.sectionHeader, 'min-acceleration')/self.videoFrameRate**2
7e9ad2d9d79c added new parameters in safety analysis script Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 348 diff changeset	588 self.maxAcceleration = config.getfloat(self.sectionHeader, 'max-acceleration')/self.videoFrameRate**2
7e9ad2d9d79c added new parameters in safety analysis script Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 348 diff changeset	589 self.maxSteering = config.getfloat(self.sectionHeader, 'max-steering')/self.videoFrameRate
351 891858351bcb added new parameter (use features) for safety analysis Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 350 diff changeset	590 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	591
397 b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	592 class SceneParameters:
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	593 def __init__(self, config, sectionName):
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	594 from ConfigParser import NoOptionError
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	595 from ast import literal_eval
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	596 try:
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	597 self.sitename = config.get(sectionName, 'sitename')
405 a9e275b4ecb7 modification of the scene.cfg format Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 398 diff changeset	598 self.databaseFilename = config.get(sectionName, 'data-filename')
a9e275b4ecb7 modification of the scene.cfg format Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 398 diff changeset	599 self.homographyFilename = config.get(sectionName, 'homography-filename')
a9e275b4ecb7 modification of the scene.cfg format Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 398 diff changeset	600 self.calibrationFilename = config.get(sectionName, 'calibration-filename')
a9e275b4ecb7 modification of the scene.cfg format Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 398 diff changeset	601 self.videoFilename = config.get(sectionName, 'video-filename')
a9e275b4ecb7 modification of the scene.cfg format Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 398 diff changeset	602 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	603 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	604 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	605 self.rotation = config.getfloat(sectionName, 'rotation')
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	606 self.duration = config.getint(sectionName, 'duration')
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	607 except NoOptionError as e:
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	608 print(e)
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	609 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	610
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	611 @staticmethod
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	612 def loadConfigFile(filename):
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	613 from ConfigParser import ConfigParser
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	614 config = ConfigParser()
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	615 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	616 configDict = dict()
3399bd48cb40 Ajout d'une méthode pour obtenir le nombre de FPS Jean-Philippe Jodoin <jpjodoin@gmail.com> parents: 397 diff changeset	617 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	618 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	619 return configDict
397 b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	620
b36b00dd27c3 added function to read scene metadata Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 395 diff changeset	621
332 a6ca86107f27 reorganized utils module Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 324 diff changeset	622 #########################
233 ab1a11176d7b initial sqlite code and bug corrected in cvutils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 199 diff changeset	623 # sqlite
ab1a11176d7b initial sqlite code and bug corrected in cvutils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 199 diff changeset	624 #########################
ab1a11176d7b initial sqlite code and bug corrected in cvutils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 199 diff changeset	625
344 14a2405f54f8 slight modification to safety analysis and generalized script to delete computed data (objects and interactions) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 333 diff changeset	626 def printDBError(error):
14a2405f54f8 slight modification to safety analysis and generalized script to delete computed data (objects and interactions) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 333 diff changeset	627 print('DB Error: {}'.format(error))
14a2405f54f8 slight modification to safety analysis and generalized script to delete computed data (objects and interactions) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 333 diff changeset	628
235 584613399513 added script and functions to remove object tables Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 233 diff changeset	629 def dropTables(connection, tableNames):
584613399513 added script and functions to remove object tables Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 233 diff changeset	630 'deletes the table with names in tableNames'
352 72aa44072093 safety analysis script with option for prediction method Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 351 diff changeset	631 import sqlite3
344 14a2405f54f8 slight modification to safety analysis and generalized script to delete computed data (objects and interactions) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 333 diff changeset	632 try:
14a2405f54f8 slight modification to safety analysis and generalized script to delete computed data (objects and interactions) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 333 diff changeset	633 cursor = connection.cursor()
14a2405f54f8 slight modification to safety analysis and generalized script to delete computed data (objects and interactions) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 333 diff changeset	634 for tableName in tableNames:
391 03dbecd3a887 modified feature grouping to return vectors of pointers to feature trajectories Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 389 diff changeset	635 cursor.execute('DROP TABLE IF EXISTS '+tableName)
344 14a2405f54f8 slight modification to safety analysis and generalized script to delete computed data (objects and interactions) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 333 diff changeset	636 except sqlite3.OperationalError as error:
14a2405f54f8 slight modification to safety analysis and generalized script to delete computed data (objects and interactions) Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 333 diff changeset	637 printDBError(error)
233 ab1a11176d7b initial sqlite code and bug corrected in cvutils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 199 diff changeset	638
ab1a11176d7b initial sqlite code and bug corrected in cvutils Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 199 diff changeset	639 #########################
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	640 # running tests
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	641 #########################
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	642
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	643 if __name__ == "__main__":
aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	644 import doctest
2 de5642925615 started implementation of TimeInterval and Spatio-temporal object Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 0 diff changeset	645 import unittest
31 c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	646 suite = doctest.DocFileSuite('tests/utils.txt')
c000f37c316d moved tests to independent file, added chi2 computation Nicolas Saunier <nico@confins.net> parents: 29 diff changeset	647 #suite = doctest.DocTestSuite()
2 de5642925615 started implementation of TimeInterval and Spatio-temporal object Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 0 diff changeset	648 unittest.TextTestRunner().run(suite)
de5642925615 started implementation of TimeInterval and Spatio-temporal object Nicolas Saunier <nicolas.saunier@polymtl.ca> parents: 0 diff changeset	649 #doctest.testmod()
0 aed8eb63cdde initial commit with non-functional python code for NGSIM Nicolas Saunier <nico@confins.net> parents: diff changeset	650 #doctest.testfile("example.txt")

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