Mercurial Hosting > traffic-intelligence

annotate python/utils.py @ 969:5d788d2e8ffc

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
work in progress
author Nicolas Saunier <nicolas.saunier@polymtl.ca>
date Thu, 07 Dec 2017 17:03:09 -0500
parents d8ab183a7351
children 9897a13772fb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
2 # -*- coding: utf-8 -*-
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
3 ''' Generic utilities.'''
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
4
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
5 import matplotlib.pyplot as plt
397
b36b00dd27c3 added function to read scene metadata
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 395
diff changeset
6 from datetime import time, datetime
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
7 from math import sqrt, ceil, floor
855
2277ab1a8141 added utility for lognorm estimation
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 854
diff changeset
8 from scipy.stats import kruskal, shapiro, lognorm
689
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
9 from scipy.spatial import distance
840
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
10 from scipy.sparse import dok_matrix
855
2277ab1a8141 added utility for lognorm estimation
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 854
diff changeset
11 from numpy import zeros, array, exp, sum as npsum, int as npint, arange, cumsum, median, isnan, ones, convolve, dtype, isnan, NaN, mean, ma, isinf, savez, load as npload, log
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
12
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
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
969
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
16 sjcamDatetimeFormat = "%Y_%m%d_%H%M%S"#2017_0626_143720
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
17
185
c06379f25ab8 utilities for user types
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 181
diff changeset
18 #########################
742
fe71639f1ee7 merge and added function to up-/lower-case strings
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 741
diff changeset
19 # Strings
fe71639f1ee7 merge and added function to up-/lower-case strings
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 741
diff changeset
20 #########################
fe71639f1ee7 merge and added function to up-/lower-case strings
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 741
diff changeset
21
fe71639f1ee7 merge and added function to up-/lower-case strings
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 741
diff changeset
22 def upperCaseFirstLetter(s):
fe71639f1ee7 merge and added function to up-/lower-case strings
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 741
diff changeset
23 words = s.split(' ')
fe71639f1ee7 merge and added function to up-/lower-case strings
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 741
diff changeset
24 lowerWords = [w[0].upper()+w[1:].lower() for w in words]
fe71639f1ee7 merge and added function to up-/lower-case strings
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 741
diff changeset
25 return ' '.join(lowerWords)
fe71639f1ee7 merge and added function to up-/lower-case strings
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 741
diff changeset
26
fe71639f1ee7 merge and added function to up-/lower-case strings
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 741
diff changeset
27 #########################
185
c06379f25ab8 utilities for user types
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 181
diff changeset
28 # Enumerations
c06379f25ab8 utilities for user types
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 181
diff changeset
29 #########################
c06379f25ab8 utilities for user types
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 181
diff changeset
30
c06379f25ab8 utilities for user types
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 181
diff changeset
31 def inverseEnumeration(l):
c06379f25ab8 utilities for user types
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 181
diff changeset
32 '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
33 result = {}
c06379f25ab8 utilities for user types
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 181
diff changeset
34 for i,x in enumerate(l):
c06379f25ab8 utilities for user types
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 181
diff changeset
35 result[x] = i
c06379f25ab8 utilities for user types
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 181
diff changeset
36 return result
155
f03fe3d6d0c8 added functions to parse options
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 152
diff changeset
37
f03fe3d6d0c8 added functions to parse options
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 152
diff changeset
38 #########################
637
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
39 # Simple statistics
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
40 #########################
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
41
680
da1352b89d02 classification is working
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 677
diff changeset
42 def logNormalMeanVar(loc, scale):
687
de278c5e65f6 minor comments for lognormal parameters (numpy and usual names differ)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 686
diff changeset
43 '''location and scale are respectively the mean and standard deviation of the normal in the log-normal distribution
854
33d296984dd8 rework and more info on speed probabilities for classification
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 847
diff changeset
44 https://en.wikipedia.org/wiki/Log-normal_distribution
33d296984dd8 rework and more info on speed probabilities for classification
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 847
diff changeset
45
33d296984dd8 rework and more info on speed probabilities for classification
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 847
diff changeset
46 same as lognorm.stats(scale, 0, exp(loc))'''
680
da1352b89d02 classification is working
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 677
diff changeset
47 mean = exp(loc+(scale**2)/2)
854
33d296984dd8 rework and more info on speed probabilities for classification
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 847
diff changeset
48 var = (exp(scale**2)-1)*exp(2*loc+scale**2)
680
da1352b89d02 classification is working
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 677
diff changeset
49 return mean, var
da1352b89d02 classification is working
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 677
diff changeset
50
855
2277ab1a8141 added utility for lognorm estimation
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 854
diff changeset
51 def fitLogNormal(x):
2277ab1a8141 added utility for lognorm estimation
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 854
diff changeset
52 'returns the fitted location and scale of the lognormal (general definition)'
2277ab1a8141 added utility for lognorm estimation
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 854
diff changeset
53 shape, loc, scale = lognorm.fit(x, floc=0.)
2277ab1a8141 added utility for lognorm estimation
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 854
diff changeset
54 return log(scale), shape
2277ab1a8141 added utility for lognorm estimation
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 854
diff changeset
55
859
a8de3c93f6b7 minor modifications to helper stat functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 856
diff changeset
56 def sampleSize(stdev, tolerance, percentConfidence, nRoundingDigits = None, printLatex = False):
301
27f06d28036d added simple helper for confidence intervals
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 297
diff changeset
57 from scipy.stats.distributions import norm
859
a8de3c93f6b7 minor modifications to helper stat functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 856
diff changeset
58 if nRoundingDigits is None:
a8de3c93f6b7 minor modifications to helper stat functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 856
diff changeset
59 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1), 2) # 1.-(100-percentConfidence)/200.
a8de3c93f6b7 minor modifications to helper stat functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 856
diff changeset
60 else:
a8de3c93f6b7 minor modifications to helper stat functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 856
diff changeset
61 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1), nRoundingDigits)
a8de3c93f6b7 minor modifications to helper stat functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 856
diff changeset
62 stdev = round(stdev, nRoundingDigits)
a8de3c93f6b7 minor modifications to helper stat functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 856
diff changeset
63 tolerance = round(tolerance, nRoundingDigits)
423
f738fa1b69f0 added sample size and Student distribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 421
diff changeset
64 if printLatex:
859
a8de3c93f6b7 minor modifications to helper stat functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 856
diff changeset
65 print('$z_{{{}}}^2\\frac{{s^2}}{{e^2}}={}^2\\frac{{{}^2}}{{{}^2}}$'.format(0.5+percentConfidence/200.,k, stdev, tolerance))
423
f738fa1b69f0 added sample size and Student distribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 421
diff changeset
66 return (k*stdev/tolerance)**2
f738fa1b69f0 added sample size and Student distribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 421
diff changeset
67
f738fa1b69f0 added sample size and Student distribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 421
diff changeset
68 def confidenceInterval(mean, stdev, nSamples, percentConfidence, trueStd = True, printLatex = False):
499
0a93afea8243 alternative confidence interval
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 491
diff changeset
69 '''if trueStd, use normal distribution, otherwise, Student
0a93afea8243 alternative confidence interval
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 491
diff changeset
70
0a93afea8243 alternative confidence interval
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 491
diff changeset
71 Use otherwise t.interval or norm.interval
0a93afea8243 alternative confidence interval
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 491
diff changeset
72 ex: norm.interval(0.95, loc = 0., scale = 2.3/sqrt(11))
0a93afea8243 alternative confidence interval
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 491
diff changeset
73 t.interval(0.95, 10, loc=1.2, scale = 2.3/sqrt(nSamples))
0a93afea8243 alternative confidence interval
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 491
diff changeset
74 loc is mean, scale is sigma/sqrt(n) (for Student, 10 is df)'''
423
f738fa1b69f0 added sample size and Student distribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 421
diff changeset
75 from scipy.stats.distributions import norm, t
f738fa1b69f0 added sample size and Student distribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 421
diff changeset
76 if trueStd:
859
a8de3c93f6b7 minor modifications to helper stat functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 856
diff changeset
77 k = round(norm.ppf(0.5+percentConfidence/200., 0, 1), 2)
423
f738fa1b69f0 added sample size and Student distribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 421
diff changeset
78 else: # use Student
859
a8de3c93f6b7 minor modifications to helper stat functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 856
diff changeset
79 k = round(t.ppf(0.5+percentConfidence/200., nSamples-1), 2)
301
27f06d28036d added simple helper for confidence intervals
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 297
diff changeset
80 e = k*stdev/sqrt(nSamples)
27f06d28036d added simple helper for confidence intervals
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 297
diff changeset
81 if printLatex:
27f06d28036d added simple helper for confidence intervals
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 297
diff changeset
82 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
83 return mean-e, mean+e
27f06d28036d added simple helper for confidence intervals
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 297
diff changeset
84
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
85 def computeChi2(expected, observed):
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
86 '''Returns the Chi2 statistics'''
876
c7e72d758049 minor update to avoid integer issue
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 859
diff changeset
87 return sum([((e-o)*(e-o))/float(e) for e, o in zip(expected, observed)])
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
88
749
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
89 class DistributionSample(object):
85
7f1e54234f96 added empirical discrete distribution, modified class organization and names
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
90 def nSamples(self):
7f1e54234f96 added empirical discrete distribution, modified class organization and names
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
91 return sum(self.counts)
7f1e54234f96 added empirical discrete distribution, modified class organization and names
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
92
588
c5406edbcf12 added loading ground truth annotations (ground truth) from polytrack format
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 574
diff changeset
93 def cumulativeDensityFunction(sample, normalized = False):
276
78922b4de3bf minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 266
diff changeset
94 '''Returns the cumulative density function of the sample of a random variable'''
588
c5406edbcf12 added loading ground truth annotations (ground truth) from polytrack format
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 574
diff changeset
95 xaxis = sorted(sample)
c5406edbcf12 added loading ground truth annotations (ground truth) from polytrack format
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 574
diff changeset
96 counts = arange(1,len(sample)+1) # dtype = float
c5406edbcf12 added loading ground truth annotations (ground truth) from polytrack format
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 574
diff changeset
97 if normalized:
c5406edbcf12 added loading ground truth annotations (ground truth) from polytrack format
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 574
diff changeset
98 counts /= float(len(sample))
197
2788b2827670 simple cumulatie function distribution computation
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 185
diff changeset
99 return xaxis, counts
85
7f1e54234f96 added empirical discrete distribution, modified class organization and names
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
100
749
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
101 class DiscreteDistributionSample(DistributionSample):
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
102 '''Class to represent a sample of a distribution for a discrete random variable'''
85
7f1e54234f96 added empirical discrete distribution, modified class organization and names
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
103 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
104 self.categories = categories
7f1e54234f96 added empirical discrete distribution, modified class organization and names
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
105 self.counts = counts
7f1e54234f96 added empirical discrete distribution, modified class organization and names
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
106
7f1e54234f96 added empirical discrete distribution, modified class organization and names
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
107 def mean(self):
7f1e54234f96 added empirical discrete distribution, modified class organization and names
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
108 result = [float(x*y) for x,y in zip(self.categories, self.counts)]
672
5473b7460375 moved and rationalized imports in modules
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 671
diff changeset
109 return npsum(result)/self.nSamples()
85
7f1e54234f96 added empirical discrete distribution, modified class organization and names
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
110
7f1e54234f96 added empirical discrete distribution, modified class organization and names
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
111 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
112 if not mean:
7f1e54234f96 added empirical discrete distribution, modified class organization and names
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
113 m = self.mean()
7f1e54234f96 added empirical discrete distribution, modified class organization and names
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
114 else:
7f1e54234f96 added empirical discrete distribution, modified class organization and names
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
115 m = mean
7f1e54234f96 added empirical discrete distribution, modified class organization and names
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
116 result = 0.
7f1e54234f96 added empirical discrete distribution, modified class organization and names
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
117 squares = [float((x-m)*(x-m)*y) for x,y in zip(self.categories, self.counts)]
672
5473b7460375 moved and rationalized imports in modules
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 671
diff changeset
118 return npsum(squares)/(self.nSamples()-1)
85
7f1e54234f96 added empirical discrete distribution, modified class organization and names
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
119
86
f03ec4697a09 corrected discrete distribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 85
diff changeset
120 def referenceCounts(self, probability):
f03ec4697a09 corrected discrete distribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 85
diff changeset
121 '''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
122 refProba = [probability(c) for c in self.categories]
672
5473b7460375 moved and rationalized imports in modules
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 671
diff changeset
123 refProba[-1] = 1-npsum(refProba[:-1])
86
f03ec4697a09 corrected discrete distribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 85
diff changeset
124 refCounts = [r*self.nSamples() for r in refProba]
f03ec4697a09 corrected discrete distribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 85
diff changeset
125 return refCounts, refProba
85
7f1e54234f96 added empirical discrete distribution, modified class organization and names
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 77
diff changeset
126
749
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
127 class ContinuousDistributionSample(DistributionSample):
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
128 '''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
129 with the number of observations for each interval
64fde2b1f96d simplified intervales in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 75
diff changeset
130 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
131 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
132 def __init__(self, categories, counts):
276
78922b4de3bf minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 266
diff changeset
133 # 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
134 self.categories = categories
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
135 self.counts = counts
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
136
749
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
137 @staticmethod
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
138 def generate(sample, categories):
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
139 if min(sample) < min(categories):
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
140 print('Sample has lower min than proposed categories ({}, {})'.format(min(sample), min(categories)))
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
141 if max(sample) > max(categories):
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
142 print('Sample has higher max than proposed categories ({}, {})'.format(max(sample), max(categories)))
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
143 dist = ContinuousDistributionSample(sorted(categories), [0]*(len(categories)-1))
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
144 for s in sample:
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
145 i = 0
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
146 while i<len(dist.categories) and dist.categories[i] <= s:
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
147 i += 1
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
148 if i <= len(dist.counts):
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
149 dist.counts[i-1] += 1
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
150 #print('{} in {} {}'.format(s, dist.categories[i-1], dist.categories[i]))
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
151 else:
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
152 print('Element {} is not in the categories'.format(s))
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
153 return dist
10dbab1e871d modifications in samples and distributions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 742
diff changeset
154
35
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
155 def mean(self):
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
156 result = 0.
76
64fde2b1f96d simplified intervales in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 75
diff changeset
157 for i in range(len(self.counts)-1):
64fde2b1f96d simplified intervales in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 75
diff changeset
158 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
159 return result/self.nSamples()
35
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
160
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
161 def var(self, mean = None):
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
162 if not mean:
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
163 m = self.mean()
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
164 else:
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
165 m = mean
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
166 result = 0.
76
64fde2b1f96d simplified intervales in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 75
diff changeset
167 for i in range(len(self.counts)-1):
64fde2b1f96d simplified intervales in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 75
diff changeset
168 mid = (self.categories[i]+self.categories[i+1])/2
64fde2b1f96d simplified intervales in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 75
diff changeset
169 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
170 return result/(self.nSamples()-1)
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
171
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
172 def referenceCounts(self, cdf):
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
173 '''cdf is a cumulative distribution function
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
174 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
175 # refCumulativeCounts = [0]#[cdf(self.categories[0][0])]
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
176 # for inter in self.categories:
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
177 # refCumulativeCounts.append(cdf(inter[1]))
76
64fde2b1f96d simplified intervales in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 75
diff changeset
178 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
179
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
180 refProba = [refCumulativeCounts[0]]
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
181 for i in xrange(1,len(refCumulativeCounts)):
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
182 refProba.append(refCumulativeCounts[i]-refCumulativeCounts[i-1])
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
183 refProba.append(1-refCumulativeCounts[-1])
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
184 refCounts = [p*self.nSamples() for p in refProba]
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
185
8cafee54466f forgotten update of histogram class
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 32
diff changeset
186 return refCounts, refProba
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
187
77
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
188 def printReferenceCounts(self, refCounts=None):
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
189 if refCounts:
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
190 ref = refCounts
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
191 else:
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
192 ref = self.referenceCounts
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
193 for i in xrange(len(ref[0])):
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
194 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
195
5e6cd36a991c added pretty print in empiricalDistribution
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 76
diff changeset
196
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
197 #########################
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
198 # maths section
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
199 #########################
24
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
200
433
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
201 # def kernelSmoothing(sampleX, X, Y, weightFunc, halfwidth):
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
202 # '''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
203 # Sum_x weight(sample_x,x) * y(x)'''
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
204 # from numpy import zeros, array
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
205 # smoothed = zeros(len(sampleX))
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
206 # for i,x in enumerate(sampleX):
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
207 # weights = array([weightFunc(x,xx, halfwidth) for xx in X])
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
208 # if sum(weights)>0:
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
209 # smoothed[i] = sum(weights*Y)/sum(weights)
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
210 # else:
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
211 # smoothed[i] = 0
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
212 # return smoothed
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
213
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
214 def kernelSmoothing(x, X, Y, weightFunc, halfwidth):
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
215 '''Returns the smoothed estimate of (X,Y) at x
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
216 Sum_x weight(sample_x,x) * y(x)'''
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
217 weights = array([weightFunc(x,observedx, halfwidth) for observedx in X])
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
218 if sum(weights)>0:
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
219 return sum(weights*Y)/sum(weights)
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
220 else:
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
221 return 0
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
222
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
223 def uniform(center, x, halfwidth):
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
224 if abs(center-x)<halfwidth:
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
225 return 1.
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
226 else:
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
227 return 0.
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
228
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
229 def gaussian(center, x, halfwidth):
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
230 return exp(-((center-x)/halfwidth)**2/2)
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
231
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
232 def epanechnikov(center, x, halfwidth):
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
233 diff = abs(center-x)
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
234 if diff<halfwidth:
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
235 return 1.-(diff/halfwidth)**2
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
236 else:
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
237 return 0.
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
238
434
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
239 def triangular(center, x, halfwidth):
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
240 diff = abs(center-x)
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
241 if diff<halfwidth:
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
242 return 1.-abs(diff/halfwidth)
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
243 else:
9a714f32fc9f small updates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 433
diff changeset
244 return 0.
433
d40ad901b272 added kernel smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 423
diff changeset
245
518
0c86c73f3c09 median smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 511
diff changeset
246 def medianSmoothing(x, X, Y, halfwidth):
0c86c73f3c09 median smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 511
diff changeset
247 '''Returns the media of Y's corresponding to X's in the interval [x-halfwidth, x+halfwidth]'''
0c86c73f3c09 median smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 511
diff changeset
248 return median([y for observedx, y in zip(X,Y) if abs(x-observedx)<halfwidth])
0c86c73f3c09 median smoothing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 511
diff changeset
249
521
3707eeb20f25 changed argMaxDict name to argmaxDict
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 518
diff changeset
250 def argmaxDict(d):
561
ee45c6eb6d49 added Mohamed Gomaa Mohamed function to smooth object trajectories
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 553
diff changeset
251 return max(d, key=d.get)
279
3af4c267a7bf generic simple LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 276
diff changeset
252
837
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
253 def deltaFrames(t1, t2, frameRate):
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
254 '''Returns the number of frames between t1 and t2
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
255 positive if t1<=t2, negative otherwise'''
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
256 if t1 > t2:
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
257 return -(t1-t2).seconds*frameRate
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
258 else:
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
259 return (t2-t1).seconds*frameRate
e01cabca4c55 minor modifications to merge-features
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 749
diff changeset
260
395
6fba1ab040f1 minor modification to framestotime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 391
diff changeset
261 def framesToTime(nFrames, frameRate, initialTime = time()):
6fba1ab040f1 minor modification to framestotime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 391
diff changeset
262 '''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
263 initialTime is a datetime.time'''
6fba1ab040f1 minor modification to framestotime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 391
diff changeset
264 seconds = int(floor(float(nFrames)/float(frameRate))+initialTime.hour*3600+initialTime.minute*60+initialTime.second)
261
4aa792cb0fa9 changing framesToTime to return a datetime.time
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 248
diff changeset
265 h = int(floor(seconds/3600.))
248
571ba5ed22e2 added utils for bus processing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 241
diff changeset
266 seconds = seconds - h*3600
261
4aa792cb0fa9 changing framesToTime to return a datetime.time
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 248
diff changeset
267 m = int(floor(seconds/60))
248
571ba5ed22e2 added utils for bus processing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 241
diff changeset
268 seconds = seconds - m*60
262
a048066bd20f correcting bug in framesToTime
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 261
diff changeset
269 return time(h, m, seconds)
248
571ba5ed22e2 added utils for bus processing
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 241
diff changeset
270
381
387cc0142211 script to replay event annotations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 376
diff changeset
271 def timeToFrames(t, frameRate):
387cc0142211 script to replay event annotations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 376
diff changeset
272 return frameRate*(t.hour*3600+t.minute*60+t.second)
387cc0142211 script to replay event annotations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 376
diff changeset
273
241
ee1caff48b03 added function to sort to list of paired data X,Y
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
274 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
275 '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
276 D = {}
ee1caff48b03 added function to sort to list of paired data X,Y
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 235
diff changeset
277 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
278 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
279 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
280 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
281
733
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
282 def compareLengthForSort(i, j):
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
283 if len(i) < len(j):
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
284 return -1
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
285 elif len(i) == len(j):
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
286 return 0
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
287 else:
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
288 return 1
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
289
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
290 def sortByLength(instances, reverse = False):
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
291 '''Returns a new list with the instances sorted by length (method __len__)
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
292 reverse is passed to sorted'''
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
293 return sorted(instances, cmp = compareLengthForSort, reverse = reverse)
c35e4a4b199d sortbylength
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 698
diff changeset
294
32
48e56179c39e added ceil function
Nicolas Saunier <nico@confins.net>
parents: 31
diff changeset
295 def ceilDecimals(v, nDecimals):
48e56179c39e added ceil function
Nicolas Saunier <nico@confins.net>
parents: 31
diff changeset
296 '''Rounds the number at the nth decimal
48e56179c39e added ceil function
Nicolas Saunier <nico@confins.net>
parents: 31
diff changeset
297 eg 1.23 at 0 decimal is 2, at 1 decimal is 1.3'''
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
298 tens = 10**nDecimals
32
48e56179c39e added ceil function
Nicolas Saunier <nico@confins.net>
parents: 31
diff changeset
299 return ceil(v*tens)/tens
48e56179c39e added ceil function
Nicolas Saunier <nico@confins.net>
parents: 31
diff changeset
300
152
74b1fc68d4df re-organized code to avoid cyclic python module dependencies
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 116
diff changeset
301 def inBetween(bound1, bound2, x):
698
8d99a9e16644 added clarification comments
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 689
diff changeset
302 'useful if one does not know the order of bound1/bound2'
569
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
303 return bound1 <= x <= bound2 or bound2 <= x <= bound1
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
304
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
305 def pointDistanceL2(x1,y1,x2,y2):
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
306 ''' Compute point-to-point distance (L2 norm, ie Euclidean distance)'''
0057c04f94d5 work in progress on intersections (for PET)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 561
diff changeset
307 return sqrt((x2-x1)**2+(y2-y1)**2)
24
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
308
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
309 def crossProduct(l1, l2):
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
310 return l1[0]*l2[1]-l1[1]*l2[0]
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
311
574
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
312 def cat_mvgavg(cat_list, halfWidth):
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
313 ''' Return a list of categories/values smoothed according to a window.
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
314 halfWidth is the search radius on either side'''
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
315 from copy import deepcopy
659
784298512b60 minor modifications
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 637
diff changeset
316 smoothed = deepcopy(cat_list)
784298512b60 minor modifications
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 637
diff changeset
317 for point in range(len(cat_list)):
574
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
318 lower_bound_check = max(0,point-halfWidth)
659
784298512b60 minor modifications
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 637
diff changeset
319 upper_bound_check = min(len(cat_list)-1,point+halfWidth+1)
784298512b60 minor modifications
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 637
diff changeset
320 window_values = cat_list[lower_bound_check:upper_bound_check]
574
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
321 smoothed[point] = max(set(window_values), key=window_values.count)
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
322 return smoothed
e24eeb244698 first implementation of projection to curvilinear coordinates
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 569
diff changeset
323
547
97c5fef5b2d6 corrected bugs
MohamedGomaa
parents: 521
diff changeset
324 def filterMovingWindow(inputSignal, halfWidth):
29
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
325 '''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
326 The first and last points are copied from the original.'''
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
327 width = float(halfWidth*2+1)
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
328 win = ones(width,'d')
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
329 result = convolve(win/width,array(inputSignal),'same')
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
330 result[:halfWidth] = inputSignal[:halfWidth]
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
331 result[-halfWidth:] = inputSignal[-halfWidth:]
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
332 return result
ca8e716cc231 added moving average filter
Nicolas Saunier <nico@confins.net>
parents: 27
diff changeset
333
199
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
334 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
335 '''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
336 as well as the plot'''
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
337 from numpy.lib.polynomial import polyfit
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
338 from numpy.core.multiarray import arange
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
339 coef = polyfit(x, y, deg)
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
340 if plotData:
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
341 def poly(x):
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
342 result = 0
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
343 for i in range(len(coef)):
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
344 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
345 return result
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
346 plt.plot(x, y, 'x')
199
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
347 xx = arange(min(x), max(x),(max(x)-min(x))/1000)
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
348 plt.plot(xx, [poly(z) for z in xx])
199
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
349 return coef
ca9d9104afba added utility to calibrate polynoms and plot
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 197
diff changeset
350
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
351 def correlation(data, correlationMethod = 'pearson', plotFigure = False, displayNames = None, figureFilename = None):
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
352 '''Computes (and displays) the correlation matrix for a pandas DataFrame'''
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
353 columns = data.columns.tolist()
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
354 for var in data.columns:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
355 uniqueValues = data[var].unique()
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
356 if len(uniqueValues) == 1 or data.dtypes[var] == dtype('O') or (len(uniqueValues) == 2 and len(data.loc[~isnan(data[var]), var].unique()) == 1): # last condition: only one other value than nan
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
357 columns.remove(var)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
358 c=data[columns].corr(correlationMethod)
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
359 if plotFigure:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
360 fig = plt.figure(figsize=(4+0.4*c.shape[0], 0.4*c.shape[0]))
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
361 fig.add_subplot(1,1,1)
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
362 #plt.imshow(np.fabs(c), interpolation='none')
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
363 plt.imshow(c, vmin=-1., vmax = 1., interpolation='none', cmap = 'RdYlBu_r') # coolwarm
847
36c5bee9a887 bug correction
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 841
diff changeset
364 if displayNames is not None:
36c5bee9a887 bug correction
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 841
diff changeset
365 colnames = [displayNames.get(s.strip(), s.strip()) for s in columns]
36c5bee9a887 bug correction
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 841
diff changeset
366 else:
36c5bee9a887 bug correction
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 841
diff changeset
367 colnames = columns
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
368 #correlation.plot_corr(c, xnames = colnames, normcolor=True, title = filename)
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
369 plt.xticks(range(len(colnames)), colnames, rotation=90)
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
370 plt.yticks(range(len(colnames)), colnames)
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
371 plt.tick_params('both', length=0)
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
372 plt.subplots_adjust(bottom = 0.29)
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
373 plt.colorbar()
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
374 plt.title('Correlation ({})'.format(correlationMethod))
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
375 plt.tight_layout()
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
376 if len(colnames) > 50:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
377 plt.subplots_adjust(left=.06)
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
378 if figureFilename is not None:
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
379 plt.savefig(figureFilename, dpi = 150, transparent = True)
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
380 return c
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
381
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
382 def addDummies(data, variables, allVariables = True):
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
383 '''Add binary dummy variables for each value of a nominal variable
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
384 in a pandas DataFrame'''
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
385 newVariables = []
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
386 for var in variables:
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
387 if var in data.columns and data.dtypes[var] == dtype('O') and len(data[var].unique()) > 2:
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
388 values = data[var].unique()
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
389 if not allVariables:
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
390 values = values[:-1]
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
391 for val in values:
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
392 if val is not NaN:
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
393 newVariable = (var+'_{}'.format(val)).replace('.','').replace(' ','').replace('-','')
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
394 data[newVariable] = (data[var] == val)
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
395 newVariables.append(newVariable)
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
396 return newVariables
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
397
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
398 def kruskalWallis(data, dependentVariable, independentVariable, plotFigure = False, filenamePrefix = None, figureFileType = 'pdf', saveLatex = False, renameVariables = lambda s: s, kwCaption = u''):
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
399 '''Studies the influence of (nominal) independent variable over the dependent variable
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
400
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
401 Makes tests if the conditional distributions are normal
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
402 using the Shapiro-Wilk test (in which case ANOVA could be used)
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
403 Implements uses the non-parametric Kruskal Wallis test'''
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
404 tmp = data[data[independentVariable].notnull()]
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
405 independentVariableValues = sorted(tmp[independentVariable].unique().tolist())
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
406 if len(independentVariableValues) >= 2:
674
01b89182891a corrected bug for intersection of lines (thanks to Paul for finding)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
407 if saveLatex:
01b89182891a corrected bug for intersection of lines (thanks to Paul for finding)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
408 from storage import openCheck
01b89182891a corrected bug for intersection of lines (thanks to Paul for finding)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
409 out = openCheck(filenamePrefix+'-{}-{}.tex'.format(dependentVariable, independentVariable), 'w')
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
410 for x in independentVariableValues:
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
411 print('Shapiro-Wilk normality test for {} when {}={}: {} obs'.format(dependentVariable,independentVariable, x, len(tmp.loc[tmp[independentVariable] == x, dependentVariable])))
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
412 if len(tmp.loc[tmp[independentVariable] == x, dependentVariable]) >= 3:
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
413 print shapiro(tmp.loc[tmp[independentVariable] == x, dependentVariable])
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
414 if plotFigure:
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
415 plt.figure()
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
416 plt.boxplot([tmp.loc[tmp[independentVariable] == x, dependentVariable] for x in independentVariableValues])
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
417 #q25, q75 = tmp[dependentVariable].quantile([.25, .75])
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
418 #plt.ylim(ymax = q75+1.5*(q75-q25))
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
419 plt.xticks(range(1,len(independentVariableValues)+1), independentVariableValues)
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
420 plt.title('{} vs {}'.format(dependentVariable, independentVariable))
674
01b89182891a corrected bug for intersection of lines (thanks to Paul for finding)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
421 if filenamePrefix is not None:
01b89182891a corrected bug for intersection of lines (thanks to Paul for finding)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
422 plt.savefig(filenamePrefix+'-{}-{}.{}'.format(dependentVariable, independentVariable, figureFileType))
01b89182891a corrected bug for intersection of lines (thanks to Paul for finding)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
423 table = tmp.groupby([independentVariable])[dependentVariable].describe().unstack().sort(['50%'], ascending = False)
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
424 table['count'] = table['count'].astype(int)
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
425 testResult = kruskal(*[tmp.loc[tmp[independentVariable] == x, dependentVariable] for x in independentVariableValues])
674
01b89182891a corrected bug for intersection of lines (thanks to Paul for finding)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
426 if saveLatex:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
427 out.write('\\begin{minipage}{\\linewidth}\n'
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
428 +'\\centering\n'
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
429 +'\\captionof{table}{'+(kwCaption.format(dependentVariable, independentVariable, *testResult))+'}\n'
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
430 +table.to_latex(float_format = lambda x: '{:.3f}'.format(x)).encode('ascii')+'\n'
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
431 +'\\end{minipage}\n'
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
432 +'\\ \\vspace{0.5cm}\n')
674
01b89182891a corrected bug for intersection of lines (thanks to Paul for finding)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
433 else:
01b89182891a corrected bug for intersection of lines (thanks to Paul for finding)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
434 print table
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
435 return testResult
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
436 else:
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
437 return None
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
438
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
439 def prepareRegression(data, dependentVariable, independentVariables, maxCorrelationThreshold, correlations, maxCorrelationP, correlationFunc, stdoutText = ['Removing {} (constant: {})', 'Removing {} (correlation {} with {})', 'Removing {} (no correlation: {}, p={})'], saveFiles = False, filenamePrefix = None, latexHeader = '', latexTable = None, latexFooter=''):
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
440 '''Removes variables from candidate independent variables if
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
441 - if two independent variables are correlated (> maxCorrelationThreshold), one is removed
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
442 - if an independent variable is not correlated with the dependent variable (p>maxCorrelationP)
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
443 Returns the remaining non-correlated variables, correlated with the dependent variable
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
444
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
445 correlationFunc is spearmanr or pearsonr from scipy.stats
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
446 text is the template to display for the two types of printout (see default): 3 elements if no saving to latex file, 8 otherwise
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
447
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
448 TODO: pass the dummies for nominal variables and remove if all dummies are correlated, or none is correlated with the dependentvariable'''
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
449 from copy import copy
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
450 from pandas import DataFrame
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
451 result = copy(independentVariables)
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
452 table1 = ''
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
453 table2 = {}
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
454 # constant variables
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
455 for var in independentVariables:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
456 uniqueValues = data[var].unique()
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
457 if (len(uniqueValues) == 1) or (len(uniqueValues) == 2 and uniqueValues.dtype != dtype('O') and len(data.loc[~isnan(data[var]), var].unique()) == 1):
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
458 print(stdoutText[0].format(var, uniqueValues))
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
459 if saveFiles:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
460 table1 += latexTable[0].format(var, *uniqueValues)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
461 result.remove(var)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
462 # correlated variables
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
463 for v1 in copy(result):
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
464 if v1 in correlations.index:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
465 for v2 in copy(result):
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
466 if v2 != v1 and v2 in correlations.index:
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
467 if abs(correlations.loc[v1, v2]) > maxCorrelationThreshold:
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
468 if v1 in result and v2 in result:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
469 if saveFiles:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
470 table1 += latexTable[1].format(v2, v1, correlations.loc[v1, v2])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
471 print(stdoutText[1].format(v2, v1, correlations.loc[v1, v2]))
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
472 result.remove(v2)
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
473 # not correlated with dependent variable
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
474 table2['Correlations'] = []
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
475 table2['Valeurs p'] = []
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
476 for var in copy(result):
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
477 if data.dtypes[var] != dtype('O'):
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
478 cor, p = correlationFunc(data[dependentVariable], data[var])
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
479 if p > maxCorrelationP:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
480 if saveFiles:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
481 table1 += latexTable[2].format(var, cor, p)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
482 print(stdoutText[2].format(var, cor, p))
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
483 result.remove(var)
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
484 else:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
485 table2['Correlations'].append(cor)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
486 table2['Valeurs p'].append(p)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
487
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
488 if saveFiles:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
489 from storage import openCheck
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
490 out = openCheck(filenamePrefix+'-removed-variables.tex', 'w')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
491 out.write(latexHeader)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
492 out.write(table1)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
493 out.write(latexFooter)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
494 out.close()
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
495 out = openCheck(filenamePrefix+'-correlations.html', 'w')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
496 table2['Variables'] = [var for var in result if data.dtypes[var] != dtype('O')]
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
497 out.write(DataFrame(table2)[['Variables', 'Correlations', 'Valeurs p']].to_html(formatters = {'Correlations': lambda x: '{:.2f}'.format(x), 'Valeurs p': lambda x: '{:.3f}'.format(x)}, index = False))
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
498 out.close()
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
499 return result
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
500
841
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 840
diff changeset
501 def saveDokMatrix(filename, m, lowerTriangle = False):
840
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
502 'Saves a dok_matrix using savez'
841
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 840
diff changeset
503 if lowerTriangle:
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 840
diff changeset
504 keys = [k for k in m.keys() if k[0] > k[1]]
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 840
diff changeset
505 savez(filename, shape = m.shape, keys = keys, values = [m[k[0],k[1]] for k in keys])
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 840
diff changeset
506 else:
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 840
diff changeset
507 savez(filename, shape = m.shape, keys = m.keys(), values = m.values())
840
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
508
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
509 def loadDokMatrix(filename):
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
510 'Loads a dok_matrix saved using the above saveDokMatrix'
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
511 data = npload(filename)
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
512 m = dok_matrix(tuple(data['shape']))
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
513 for k, v in zip(data['keys'], data['values']):
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
514 m[tuple(k)] = v
15a82ebc62c4 utils for sparse matrix
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 837
diff changeset
515 return m
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
516
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
517 #########################
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
518 # regression analysis using statsmodels (and pandas)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
519 #########################
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
520
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
521 # TODO make class for experiments?
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
522 # TODO add tests with public dataset downloaded from Internet (IRIS et al)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
523 def modelString(experiment, dependentVariable, independentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
524 return dependentVariable+' ~ '+' + '.join([independentVariable for independentVariable in independentVariables if experiment[independentVariable]])
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
525
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
526 def runModel(experiment, data, dependentVariable, independentVariables, regressionType = 'ols'):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
527 import statsmodels.formula.api as smf
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
528 modelStr = modelString(experiment, dependentVariable, independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
529 if regressionType == 'ols':
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
530 model = smf.ols(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
531 elif regressionType == 'gls':
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
532 model = smf.gls(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
533 elif regressionType == 'rlm':
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
534 model = smf.rlm(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
535 else:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
536 print('Unknown regression type {}. Exiting'.format(regressionType))
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
537 import sys
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
538 sys.exit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
539 return model.fit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
540
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
541 def runModels(experiments, data, dependentVariable, independentVariables, regressionType = 'ols'):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
542 '''Runs several models and stores 3 statistics
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
543 adjusted R2, condition number (should be small, eg < 1000)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
544 and p-value for Shapiro-Wilk test of residual normality'''
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
545 for i,experiment in experiments.iterrows():
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
546 if experiment[independentVariables].any():
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
547 results = runModel(experiment, data, dependentVariable, independentVariables, regressionType = 'ols')
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
548 experiments.loc[i,'r2adj'] = results.rsquared_adj
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
549 experiments.loc[i,'condNum'] = results.condition_number
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
550 experiments.loc[i, 'shapiroP'] = shapiro(results.resid)[1]
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
551 experiments.loc[i,'nobs'] = int(results.nobs)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
552 return experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
553
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
554 def generateExperiments(independentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
555 '''Generates all possible models for including or not each independent variable'''
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
556 from pandas import DataFrame
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
557 experiments = {}
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
558 nIndependentVariables = len(independentVariables)
669
df6be882f325 bug corrected
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 668
diff changeset
559 if nIndependentVariables != len(set(independentVariables)):
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
560 print("Duplicate variables. Exiting")
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
561 import sys
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
562 sys.exit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
563 nModels = 2**nIndependentVariables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
564 for i,var in enumerate(independentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
565 pattern = [False]*(2**i)+[True]*(2**i)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
566 experiments[var] = pattern*(2**(nIndependentVariables-i-1))
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
567 experiments = DataFrame(experiments)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
568 experiments['r2adj'] = 0.
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
569 experiments['condNum'] = NaN
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
570 experiments['shapiroP'] = -1
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
571 experiments['nobs'] = -1
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
572 return experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
573
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
574 def findBestModel(data, dependentVariable, independentVariables, regressionType = 'ols', nProcesses = 1):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
575 '''Generates all possible model with the independentVariables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
576 and runs them, saving the results in experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
577 with multiprocess option'''
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
578 from pandas import concat
671
849f5f8bf4b9 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 670
diff changeset
579 from multiprocessing import Pool
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
580 experiments = generateExperiments(independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
581 nModels = len(experiments)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
582 print("Running {} models with {} processes".format(nModels, nProcesses))
674
01b89182891a corrected bug for intersection of lines (thanks to Paul for finding)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 672
diff changeset
583 print("IndependentVariables: {}".format(independentVariables))
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
584 if nProcesses == 1:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
585 return runModels(experiments, data, dependentVariable, independentVariables, regressionType)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
586 else:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
587 pool = Pool(processes = nProcesses)
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
588 chunkSize = int(ceil(nModels/nProcesses))
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
589 jobs = [pool.apply_async(runModels, args = (experiments[i*chunkSize:(i+1)*chunkSize], data, dependentVariable, independentVariables, regressionType)) for i in range(nProcesses)]
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
590 return concat([job.get() for job in jobs])
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
591
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
592 def findBestModelFwd(data, dependentVariable, independentVariables, modelFunc, experiments = None):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
593 '''Forward search for best model (based on adjusted R2)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
594 Randomly starting with one variable and adding randomly variables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
595 if they improve the model
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
596
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
597 The results are added to experiments if provided as argument
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
598 Storing in experiment relies on the index being the number equal
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
599 to the binary code derived from the independent variables'''
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
600 from numpy.random import permutation as nppermutation
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
601 if experiments is None:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
602 experiments = generateExperiments(independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
603 nIndependentVariables = len(independentVariables)
670
f72ed51c6b65 corrected other missing imports
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 669
diff changeset
604 permutation = nppermutation(range(nIndependentVariables)).tolist()
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
605 variableMapping = {j: independentVariables[i] for i,j in enumerate(permutation)}
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
606 print('Tested variables '+', '.join([variableMapping[i] for i in xrange(nIndependentVariables)]))
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
607 bestModel = [False]*nIndependentVariables
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
608 currentVarNum = 0
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
609 currentR2Adj = 0.
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
610 for currentVarNum in xrange(nIndependentVariables):
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
611 currentModel = [i for i in bestModel]
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
612 currentModel[currentVarNum] = True
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
613 rowIdx = sum([0]+[2**i for i in xrange(nIndependentVariables) if currentModel[permutation[i]]])
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
614 #print currentVarNum, sum(currentModel), ', '.join([independentVariables[i] for i in xrange(nIndependentVariables) if currentModel[permutation[i]]])
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
615 if experiments.loc[rowIdx, 'shapiroP'] < 0:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
616 modelStr = modelString(experiments.loc[rowIdx], dependentVariable, independentVariables)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
617 model = modelFunc(modelStr, data = data)
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
618 results = model.fit()
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
619 experiments.loc[rowIdx, 'r2adj'] = results.rsquared_adj
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
620 experiments.loc[rowIdx, 'condNum'] = results.condition_number
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
621 experiments.loc[rowIdx, 'shapiroP'] = shapiro(results.resid)[1]
668
f8dcf483b296 code to prepare regression variables (remove correlated variables) and record dataset size in experimnets
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 667
diff changeset
622 experiments.loc[rowIdx, 'nobs'] = int(results.nobs)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
623 if currentR2Adj < experiments.loc[rowIdx, 'r2adj']:
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
624 currentR2Adj = experiments.loc[rowIdx, 'r2adj']
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
625 bestModel[currentVarNum] = True
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
626 return experiments
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
627
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
628 def displayModelResults(results, model = None, plotFigures = True, filenamePrefix = None, figureFileType = 'pdf', text = {'title-shapiro': 'Shapiro-Wilk normality test for residuals: {:.2f} (p={:.3f})', 'true-predicted.xlabel': 'Predicted values', 'true-predicted.ylabel': 'True values', 'residuals-predicted.xlabel': 'Predicted values', 'residuals-predicted.ylabel': 'Residuals'}):
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
629 import statsmodels.api as sm
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
630 '''Displays some model results
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
631
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
632 3 graphics, true-predicted, residuals-predicted, '''
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
633 print(results.summary())
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
634 shapiroResult = shapiro(results.resid)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
635 print(shapiroResult)
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
636 if plotFigures:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
637 fig = plt.figure(figsize=(7,6.3*(2+int(model is not None))))
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
638 if model is not None:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
639 ax = fig.add_subplot(3,1,1)
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
640 plt.plot(results.predict(), model.endog, 'x')
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
641 x=plt.xlim()
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
642 y=plt.ylim()
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
643 plt.plot([max(x[0], y[0]), min(x[1], y[1])], [max(x[0], y[0]), min(x[1], y[1])], 'r')
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
644 #plt.axis('equal')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
645 if text is not None:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
646 plt.title(text['title-shapiro'].format(*shapiroResult))
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
647 #plt.title(text['true-predicted.title'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
648 plt.xlabel(text['true-predicted.xlabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
649 plt.ylabel(text['true-predicted.ylabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
650 fig.add_subplot(3,1,2, sharex = ax)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
651 plt.plot(results.predict(), results.resid, 'x')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
652 nextSubplotNum = 3
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
653 else:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
654 fig.add_subplot(2,1,1)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
655 plt.plot(results.predict(), results.resid, 'x')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
656 nextSubplotNum = 2
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
657 if text is not None:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
658 if model is None:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
659 plt.title(text['title-shapiro'].format(*shapiroResult))
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
660 plt.xlabel(text['residuals-predicted.xlabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
661 plt.ylabel(text['residuals-predicted.ylabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
662 qqAx = fig.add_subplot(nextSubplotNum,1,nextSubplotNum)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
663 sm.qqplot(results.resid, fit = True, line = '45', ax = qqAx)
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
664 plt.axis('equal')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
665 if text is not None and 'qqplot.xlabel' in text:
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
666 plt.xlabel(text['qqplot.xlabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
667 plt.ylabel(text['qqplot.ylabel'])
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
668 plt.tight_layout()
676
58b9ac2f262f fine tuning
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 675
diff changeset
669 if filenamePrefix is not None:
677
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
670 from storage import openCheck
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
671 out = openCheck(filenamePrefix+'-coefficients.html', 'w')
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
672 out.write(results.summary().as_html())
ae07c7b4cf87 update to utils for pavement results
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 676
diff changeset
673 plt.savefig(filenamePrefix+'-model-results.'+figureFileType)
667
179b81faa1f8 added regression analysis functions
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 665
diff changeset
674
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
675 #########################
455
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
676 # iterable section
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
677 #########################
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
678
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
679 def mostCommon(L):
456
825e5d49325d slight update
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 455
diff changeset
680 '''Returns the most frequent element in a iterable
825e5d49325d slight update
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 455
diff changeset
681
825e5d49325d slight update
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 455
diff changeset
682 taken from http://stackoverflow.com/questions/1518522/python-most-common-element-in-a-list'''
455
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
683 from itertools import groupby
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
684 from operator import itemgetter
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
685 # get an iterable of (item, iterable) pairs
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
686 SL = sorted((x, i) for i, x in enumerate(L))
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
687 # print 'SL:', SL
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
688 groups = groupby(SL, key=itemgetter(0))
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
689 # auxiliary function to get "quality" for an item
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
690 def _auxfun(g):
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
691 item, iterable = g
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
692 count = 0
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
693 min_index = len(L)
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
694 for _, where in iterable:
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
695 count += 1
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
696 min_index = min(min_index, where)
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
697 # print 'item %r, count %r, minind %r' % (item, count, min_index)
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
698 return count, -min_index
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
699 # pick the highest-count/earliest item
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
700 return max(groups, key=_auxfun)[0]
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
701
abe0b2347d4c added most common utility function
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 434
diff changeset
702 #########################
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
703 # sequence section
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
704 #########################
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
705
665
15e244d2a1b5 corrected bug with circular import for VideoFilenameAddable, moved to base module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 659
diff changeset
706 class LCSS(object):
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
707 '''Class that keeps the LCSS parameters
686
cdee6a3a47b4 allowing alternate database and filename for classify-objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 680
diff changeset
708 and puts together the various computations
cdee6a3a47b4 allowing alternate database and filename for classify-objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 680
diff changeset
709
cdee6a3a47b4 allowing alternate database and filename for classify-objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 680
diff changeset
710 the methods with names starting with _ are not to be shadowed
cdee6a3a47b4 allowing alternate database and filename for classify-objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 680
diff changeset
711 in child classes, who will shadow the other methods,
cdee6a3a47b4 allowing alternate database and filename for classify-objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 680
diff changeset
712 ie compute and computeXX methods'''
689
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
713 def __init__(self, similarityFunc = None, metric = None, epsilon = None, delta = float('inf'), aligned = False, lengthFunc = min):
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
714 '''One should provide either a similarity function
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
715 that indicates (return bool) whether elements in the compares lists are similar
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
716
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
717 eg distance(p1, p2) < epsilon
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
718
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
719 or a type of metric usable in scipy.spatial.distance.cdist with an epsilon'''
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
720 if similarityFunc is None and metric is None:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
721 print("No way to compute LCSS, similarityFunc and metric are None. Exiting")
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
722 import sys
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
723 sys.exit()
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
724 elif metric is not None and epsilon is None:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
725 print("Please provide a value for epsilon if using a cdist metric. Exiting")
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
726 import sys
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
727 sys.exit()
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
728 else:
741
5b91b8d97cf3 corrected bug
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 739
diff changeset
729 if similarityFunc is None and metric is not None and not isinf(delta):
737
fb60b54e1041 added warning for finite delta
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 733
diff changeset
730 print('Warning: you are using a cdist metric and a finite delta, which will make probably computation slower than using the equivalent similarityFunc (since all pairwise distances will be computed by cdist).')
689
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
731 self.similarityFunc = similarityFunc
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
732 self.metric = metric
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
733 self.epsilon = epsilon
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
734 self.aligned = aligned
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
735 self.delta = delta
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
736 self.lengthFunc = lengthFunc
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
737 self.subSequenceIndices = [(0,0)]
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
738
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
739 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
740 n1 = len(l1)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
741 n2 = len(l2)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
742 self.similarityTable = zeros((n1+1,n2+1), dtype = npint)
689
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
743 if self.similarityFunc is not None:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
744 for i in xrange(1,n1+1):
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
745 for j in xrange(max(1,i-jshift-self.delta),min(n2,i-jshift+self.delta)+1):
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
746 if self.similarityFunc(l1[i-1], l2[j-1]):
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
747 self.similarityTable[i,j] = self.similarityTable[i-1,j-1]+1
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
748 else:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
749 self.similarityTable[i,j] = max(self.similarityTable[i-1,j], self.similarityTable[i,j-1])
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
750 elif self.metric is not None:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
751 similarElements = distance.cdist(l1, l2, self.metric) <= self.epsilon
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
752 for i in xrange(1,n1+1):
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
753 for j in xrange(max(1,i-jshift-self.delta),min(n2,i-jshift+self.delta)+1):
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
754 if similarElements[i-1, j-1]:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
755 self.similarityTable[i,j] = self.similarityTable[i-1,j-1]+1
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
756 else:
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
757 self.similarityTable[i,j] = max(self.similarityTable[i-1,j], self.similarityTable[i,j-1])
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
758
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
759
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
760 def subSequence(self, i, j):
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
761 '''Returns the subsequence of two sequences
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
762 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
763 if i == 0 or j == 0:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
764 return []
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
765 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
766 return self.subSequence(i, j-1)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
767 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
768 return self.subSequence(i-1, j)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
769 else:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
770 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
771
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
772 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
773 '''returns the longest common subsequence similarity
689
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
774 l1 and l2 should be the right format
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
775 eg list of tuple points for cdist
9990ef119bce added version of LCSS with cdist computations
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 687
diff changeset
776 or elements that can be compare using similarityFunc
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
777
607
84690dfe5560 add some functions for behaviour analysis
MohamedGomaa
parents: 574
diff changeset
778 if aligned, returns the best matching if using a finite delta by shifting the series alignments
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
779 '''
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
780 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
781 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
782 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
783 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
784 else:
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
785 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
786 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
787 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
788 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
789 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
790
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
791 if self.aligned:
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
792 lcssValues = {}
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
793 similarityTables = {}
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
794 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
795 self.similarities(l1, l2, i)
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
796 lcssValues[i] = self.similarityTable.max()
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
797 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
798 #print self.similarityTable
521
3707eeb20f25 changed argMaxDict name to argmaxDict
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 518
diff changeset
799 alignmentShift = argmaxDict(lcssValues) # ideally get the medium alignment shift, the one that minimizes distance
389
6d26dcc7bba0 modifications to compute alignment for None indicators
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
800 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
801 else:
389
6d26dcc7bba0 modifications to compute alignment for None indicators
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 381
diff changeset
802 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
803 self.similarities(l1, l2)
373
d0b86ed50f32 work in progress on LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 372
diff changeset
804
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
805 # 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
806 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
807
372
349eb1e09f45 Cleaned the methods/functions indicating if a point is in a polygon
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 371
diff changeset
808 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
809 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
810 if revertIndices:
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
811 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
812 return self.similarityTable[-1,-1]
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
813
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
814 def compute(self, l1, l2, computeSubSequence = False):
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
815 '''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
816 return self._compute(l1, l2, computeSubSequence)
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
817
375
2ea8584aa80a making indicator LCSS work
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 374
diff changeset
818 def computeAlignment(self):
374
a7af3519687e finished implementation of aligned LCSS with matching sequence decoded
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 373
diff changeset
819 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
820
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
821 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
822 ''' compute the normalized LCSS
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
823 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
824 lengthFunc = lambda x,y:float(x,y)/2'''
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
825 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
826
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
827 def computeNormalized(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
828 return self._computeNormalized(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
829
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
830 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
831 ''' compute the LCSS distance'''
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
832 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
833
376
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
834 def computeDistance(self, l1, l2, computeSubSequence = False):
2e6b8610bcaa work on indicator similarity
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 375
diff changeset
835 return self._computeDistance(l1, l2, computeSubSequence)
370
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
836
97e8fa0ee9a1 work in progress for complete alignment
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 369
diff changeset
837 #########################
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
838 # plotting section
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
839 #########################
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
840
940
d8ab183a7351 verified motion prediction with prototypes at constant speed (test needed)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 876
diff changeset
841 def plotPolygon(poly, options = '', **kwargs):
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
842 'Plots shapely polygon poly'
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
843 from matplotlib.pyplot import plot
940
d8ab183a7351 verified motion prediction with prototypes at constant speed (test needed)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 876
diff changeset
844 x,y = poly.exterior.xy
d8ab183a7351 verified motion prediction with prototypes at constant speed (test needed)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 876
diff changeset
845 plot(x, y, options, **kwargs)
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
846
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
847 def stepPlot(X, firstX, lastX, initialCount = 0, increment = 1):
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
848 '''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
849 returns the lists that can be plotted
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
850 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
851 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
852
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
853 sortedX = []
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
854 counts = [initialCount]
f6f423e25c7f adding function to generate step plots (for cumulative number of vehicles)
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 286
diff changeset
855 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
856 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
857 counts.append(counts[-1])
324
99ca91a46007 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 323
diff changeset
858 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
859 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
860 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
861
665
15e244d2a1b5 corrected bug with circular import for VideoFilenameAddable, moved to base module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 659
diff changeset
862 class PlottingPropertyValues(object):
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
863 def __init__(self, values):
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
864 self.values = values
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
865
116
2bf5b76320c0 moved intersection plotting and added markers for scatter plots
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 115
diff changeset
866 def __getitem__(self, i):
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
867 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
868
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
869 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
870 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
871
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
872 linestyles = PlottingPropertyValues(['-', '--', '-.', ':'])
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
873
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
874 colors = PlottingPropertyValues('brgmyck') # 'w'
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
875
115
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
876 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
877 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
878 coords = array(indicatorMap.keys())
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
879 minX = min(coords[:,0])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
880 minY = min(coords[:,1])
75cf537b8d88 moved and generalized map making functions to the library
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 48
diff changeset
881 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
882 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
883 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
884 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
885 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
886 if masked:
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
887 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
888 else:
550556378466 added functionalities to indicator maps
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 86
diff changeset
889 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
890
45
74d2de078baf added colors, linestyles and markers to pick from
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 42
diff changeset
891 #########################
637
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
892 # Data download
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
893 #########################
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
894
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
895 def downloadECWeather(stationID, years, months = [], outputDirectoryname = '.', english = True):
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
896 '''Downloads monthly weather data from Environment Canada
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
897 If month is provided (number 1 to 12), it means hourly data for the whole month
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
898 Otherwise, means the data for each day, for the whole year
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
899
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
900 Example: MONTREAL MCTAVISH 10761
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
901 MONTREALPIERRE ELLIOTT TRUDEAU INTL A 5415
856
e310577cc0b8 updated function (url) for weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 855
diff changeset
902 see ftp://client_climate@ftp.tor.ec.gc.ca/Pub/Get_More_Data_Plus_de_donnees/Station%20Inventory%20EN.csv
637
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
903
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
904 To get daily data for 2010 and 2011, downloadECWeather(10761, [2010,2011], [], '/tmp')
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
905 To get hourly data for 2009 and 2012, January, March and October, downloadECWeather(10761, [2009,2012], [1,3,10], '/tmp')'''
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
906 import urllib2
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
907 if english:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
908 language = 'e'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
909 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
910 language = 'f'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
911 if len(months) == 0:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
912 timeFrame = 2
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
913 months = [1]
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
914 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
915 timeFrame = 1
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
916
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
917 for year in years:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
918 for month in months:
856
e310577cc0b8 updated function (url) for weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 855
diff changeset
919 url = urllib2.urlopen('http://climate.weather.gc.ca/climate_data/bulk_data_{}.html?format=csv&stationID={}&Year={}&Month={}&Day=1&timeframe={}&submit= Download+Data'.format(language, stationID, year, month, timeFrame))
e310577cc0b8 updated function (url) for weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 855
diff changeset
920 #http://climat.meteo.gc.ca/climateData/bulkdata_{}.html?format=csv&stationID={}&Year={}&Month={}&Day=1&timeframe={}&submit=++T%C3%A9l%C3%A9charger+%0D%0Ades+donn%C3%A9es
637
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
921 data = url.read()
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
922 outFilename = '{}/{}-{}'.format(outputDirectoryname, stationID, year)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
923 if timeFrame == 1:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
924 outFilename += '-{}-hourly'.format(month)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
925 else:
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
926 outFilename += '-daily'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
927 outFilename += '.csv'
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
928 out = open(outFilename, 'w')
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
929 out.write(data)
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
930 out.close()
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
931
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
932 #########################
c9a0b72979fd added function to get canadian public weather data
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 615
diff changeset
933 # File I/O
27
44689029a86f updated segmentIntersection and other
Nicolas Saunier <nico@confins.net>
parents: 24
diff changeset
934 #########################
24
6fb59cfb201e first version of segmentIntersection
Nicolas Saunier <nico@confins.net>
parents: 19
diff changeset
935
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
936 def removeExtension(filename, delimiter = '.'):
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
937 '''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
938 i = filename.rfind(delimiter)
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
939 if i>0:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
940 return filename[:i]
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
941 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
942 return filename
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
943
969
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
944 def getExtension(filename, delimiter = '.'):
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
945 '''Returns the filename minus the extension (all characters after last .)'''
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
946 i = filename.rfind(delimiter)
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
947 if i>0:
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
948 return filename[i+1:]
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
949 else:
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
950 return ''
5d788d2e8ffc work in progress
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 940
diff changeset
951
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
952 def cleanFilename(s):
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
953 'cleans filenames obtained when contatenating figure characteristics'
739
25e78d756823 minor change
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 737
diff changeset
954 return s.replace(' ','-').replace('.','').replace('/','-').replace(',','')
46
b5d007612e16 added filename util
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 45
diff changeset
955
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
956 def listfiles(dirname, extension, remove = False):
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
957 '''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
958 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
959 from os import listdir
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
960 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
961 tmp.sort()
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
962 if remove:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
963 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
964 else:
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
965 return tmp
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
966
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
967 def mkdir(dirname):
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
968 'Creates a directory if it does not exist'
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
969 import os
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
970 if not os.path.exists(dirname):
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
971 os.mkdir(dirname)
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
972 else:
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
973 print(dirname+' already exists')
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
974
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
975 def removeFile(filename):
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
976 '''Deletes the file while avoiding raising an error
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
977 if the file does not exist'''
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
978 import os
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
979 if (os.path.exists(filename)):
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
980 os.remove(filename)
266
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
981 else:
aba9711b3149 small modificatons and reorganization
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 262
diff changeset
982 print(filename+' does not exist')
14
e7bbe8465591 homography and other utils
Nicolas Saunier <nico@confins.net>
parents: 7
diff changeset
983
42
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
984 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
985 '''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
986 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
987
1a2ac2d4f53a added loading of the rest of the data for objects
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 35
diff changeset
988 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
989 '''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
990 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
991
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
992 #########################
332
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
993 # CLI utils
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
994 #########################
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
995
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
996 def parseCLIOptions(helpMessage, options, cliArgs, optionalOptions=[]):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
997 ''' Simple function to handle similar argument parsing
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
998 Returns the dictionary of options and their values
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
999
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1000 * cliArgs are most likely directly sys.argv
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1001 (only the elements after the first one are considered)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1002
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1003 * options should be a list of strings for getopt options,
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1004 eg ['frame=','correspondences=','video=']
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1005 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
1006 import sys, getopt
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1007 from numpy.core.fromnumeric import all
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1008 optionValues, args = getopt.getopt(cliArgs[1:], 'h', ['help']+options+optionalOptions)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1009 optionValues = dict(optionValues)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1010
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1011 if '--help' in optionValues.keys() or '-h' in optionValues.keys():
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1012 print(helpMessage+
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1013 '\n - Compulsory options: '+' '.join([opt.replace('=','') for opt in options])+
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1014 '\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
1015 sys.exit()
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1016
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1017 missingArgument = [('--'+opt.replace('=','') in optionValues.keys()) for opt in options]
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1018 if not all(missingArgument):
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1019 print('Missing argument')
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1020 print(optionValues)
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1021 sys.exit()
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1022
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1023 return optionValues
a6ca86107f27 reorganized utils module
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 324
diff changeset
1024
397
b36b00dd27c3 added function to read scene metadata
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 395
diff changeset
1025
b36b00dd27c3 added function to read scene metadata
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 395
diff changeset
1026 #########################
553
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1027 # Profiling
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1028 #########################
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1029
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1030 def analyzeProfile(profileFilename, stripDirs = True):
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1031 '''Analyze the file produced by cProfile
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1032
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1033 obtained by for example:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1034 - call in script (for main() function in script)
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1035 import cProfile, os
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1036 cProfile.run('main()', os.path.join(os.getcwd(),'main.profile'))
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1037
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1038 - or on the command line:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1039 python -m cProfile [-o profile.bin] [-s sort] scriptfile [arg]'''
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1040 import pstats, os
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1041 p = pstats.Stats(os.path.join(os.pardir, profileFilename))
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1042 if stripDirs:
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1043 p.strip_dirs()
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1044 p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1045 p.print_stats(.2)
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1046 #p.sort_stats('time')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1047 # p.print_callees(.1, 'int_prediction.py:')
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1048 return p
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1049
3622a5653ee9 added basic info and function to profile code
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 547
diff changeset
1050 #########################
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1051 # running tests
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1052 #########################
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1053
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1054 if __name__ == "__main__":
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1055 import doctest
2
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
1056 import unittest
31
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1057 suite = doctest.DocFileSuite('tests/utils.txt')
c000f37c316d moved tests to independent file, added chi2 computation
Nicolas Saunier <nico@confins.net>
parents: 29
diff changeset
1058 #suite = doctest.DocTestSuite()
2
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
1059 unittest.TextTestRunner().run(suite)
de5642925615 started implementation of TimeInterval and Spatio-temporal object
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 0
diff changeset
1060 #doctest.testmod()
0
aed8eb63cdde initial commit with non-functional python code for NGSIM
Nicolas Saunier <nico@confins.net>
parents:
diff changeset
1061 #doctest.testfile("example.txt")