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annotate python/utils.py @ 42:1a2ac2d4f53a

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added loading of the rest of the data for objects
author Nicolas Saunier <nicolas.saunier@polymtl.ca>
date Thu, 01 Jul 2010 10:44:32 -0400
parents 8cafee54466f
children 74d2de078baf
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1 #! /usr/bin/env python
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2 ''' Generic utilities.'''
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3
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4 #from numpy import *
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5 #from pylab import *
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6
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7 import moving
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8
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9 __metaclass__ = type
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10
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11 commentChar = '#';
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12
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13 #########################
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14 # simple statistics
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15 #########################
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16
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17 def computeChi2(expected, observed):
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18 '''Returns the Chi2 statistics'''
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19 result = 0.
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20 for e, o in zip(expected, observed):
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21 result += ((e-o)*(e-o))/e
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22 return result
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23
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24 class histogram:
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25 '''Class to represent a sample of a distribution for a continuous random variable
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26 with the number of observations for each interval'''
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27 def __init__(self, categories, counts):
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28 self.categories = categories
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29 self.counts = counts
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31 def mean(self):
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32 result = 0.
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33 for i,c in zip(self.categories, self.counts):
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34 result += c*(i[1]+i[0])/2
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35 return result/sum(self.counts)
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36
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37 def var(self, mean = None):
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38 if not mean:
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39 m = self.mean()
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40 else:
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41 m = mean
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42 result = 0.
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43 for i,c in zip(self.categories, self.counts):
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44 mid = (i[1]+i[0])/2
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45 result += c*(mid - m)*(mid - m)
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46 return result/(self.nSamples()-1)
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47
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48 def nSamples(self):
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49 return sum(self.counts)
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50
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51 def referenceCounts(self, cdf):
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52 '''cdf is a cumulative distribution function
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53 returning the probability of the variable being less that x'''
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54 # refCumulativeCounts = [0]#[cdf(self.categories[0][0])]
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55 # for inter in self.categories:
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56 # refCumulativeCounts.append(cdf(inter[1]))
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57 refCumulativeCounts = [cdf(inter[1]) for inter in self.categories[:-1]]
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58
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59 refProba = [refCumulativeCounts[0]]
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60 for i in xrange(1,len(refCumulativeCounts)):
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61 refProba.append(refCumulativeCounts[i]-refCumulativeCounts[i-1])
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62 refProba.append(1-refCumulativeCounts[-1])
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63 refCounts = [p*self.nSamples() for p in refProba]
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64
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65 return refCounts, refProba
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66
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67 #########################
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68 # maths section
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69 #########################
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70
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71 def ceilDecimals(v, nDecimals):
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72 '''Rounds the number at the nth decimal
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73 eg 1.23 at 0 decimal is 2, at 1 decimal is 1.3'''
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74 from math import ceil,pow
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75 tens = pow(10,nDecimals)
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76 return ceil(v*tens)/tens
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77
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78 def segmentIntersection(p1, p2, p3, p4):
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79 '''Returns the intersecting point of the segments [p1, p2] and [p3, p4], None otherwise'''
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80 from numpy import matrix
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81 from numpy.linalg import linalg, det
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82
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83 dp1 = p2-p1#[s1[0][1]-s1[0][0], s1[1][1]-s1[1][0]]
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84 dp2 = p4-p3#[s2[0][1]-s2[0][0], s2[1][1]-s2[1][0]]
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85
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86 A = matrix([[dp1.y, -dp1.x],
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87 [dp2.y, -dp2.x]])
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88 B = matrix([[dp1.y*p1.x-dp1.x*p1.y],
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89 [dp2.y*p3.x-dp2.x*p3.y]])
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90
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91 if linalg.det(A) == 0:#crossProduct(ds1, ds2) == 0:
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92 return None
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93 else:
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94 intersection = linalg.solve(A,B)
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95 if (moving.Interval(p1.x, p2.x, True).contains(intersection[0,0])
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96 and moving.Interval(p3.x, p4.x, True).contains(intersection[0,0])
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97 and moving.Interval(p1.y, p2.y, True).contains(intersection[1,0])
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98 and moving.Interval(p3.y, p4.y, True).contains(intersection[1,0])):
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99 return moving.Point(intersection[0,0], intersection[1,0])
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100 else:
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101 return None
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102
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103 def crossProduct(l1, l2):
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104 return l1[0]*l2[1]-l1[1]*l2[0]
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105
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106 def filterMovingWindow(input, halfWidth):
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107 '''Returns an array obtained after the smoothing of the input by a moving average
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108 The first and last points are copied from the original.'''
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109 width = float(halfWidth*2+1)
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110 win = ones(width,'d')
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111 result = convolve(win/width,array(inputSignal),'same')
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112 result[:halfWidth] = inputSignal[:halfWidth]
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113 result[-halfWidth:] = inputSignal[-halfWidth:]
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114 return result
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115
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116 #########################
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117 # file I/O section
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118 #########################
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119
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120 def openCheck(filename, option = 'r', quit = False):
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121 '''Open file filename in read mode by default
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122 and checks it is open'''
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123 try:
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124 return open(filename, option)
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125 except IOError:
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126 print 'File %s could not be opened.' % filename
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127 if quit:
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128 from sys import exit
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129 exit()
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130 return None
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131
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132 def readline(f):
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133 '''Modified readline function to skip comments.'''
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134 s = f.readline()
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135 while (len(s) > 0) and s.startswith(commentChar):
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136 s = f.readline()
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137 return s.strip()
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138
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139 def removeExtension(filename, delimiter = '.'):
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140 '''Returns the filename minus the extension (all characters after last .)'''
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141 i = filename.rfind(delimiter)
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142 if i>0:
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143 return filename[:i]
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144 else:
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145 return filename
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146
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147 def listfiles(dirname, extension, remove = False):
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148 '''Returns the list of files with the extension in the directory dirname
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149 If remove is True, the filenames are stripped from the extension'''
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150 from os import listdir
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151 tmp = [f for f in listdir(dirname) if f.endswith(extension)]
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152 tmp.sort()
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153 if remove:
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154 return [removeExtension(f, extension) for f in tmp]
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155 else:
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156 return tmp
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157
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158 def removeFile(filename):
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159 '''Deletes the file while avoiding raising an error
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160 if the file does not exist'''
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161 if (os.path.exists(filename)):
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162 os.remove(filename)
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163
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164 def invertHomography(homography):
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165 'Returns an inverted homography'
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166 from numpy.linalg.linalg import inv
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167 invH = inv(homography)
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168 invH /= invH[2,2]
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169 return invH
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170
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171 def plotPolygon(poly, options = ''):
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172 from numpy.core.multiarray import array
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173 from matplotlib.pyplot import plot
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174 from shapely.geometry import Polygon
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175
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176 tmp = array(poly.exterior)
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177 plot(tmp[:,0], tmp[:,1], options)
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178
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179 def line2Floats(l, separator=' '):
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180 '''Returns the list of floats corresponding to the string'''
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181 return [float(x) for x in l.split(separator)]
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182
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183 def line2Ints(l, separator=' '):
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184 '''Returns the list of ints corresponding to the string'''
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185 return [int(x) for x in l.split(separator)]
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186
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187 #########################
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188 # running tests
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189 #########################
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190
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191 if __name__ == "__main__":
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192 import doctest
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193 import unittest
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194 suite = doctest.DocFileSuite('tests/utils.txt')
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195 #suite = doctest.DocTestSuite()
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196 unittest.TextTestRunner().run(suite)
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197 #doctest.testmod()
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198 #doctest.testfile("example.txt")