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annotate python/utils.py @ 65:75cf537b8d88

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moved and generalized map making functions to the library
author Nicolas Saunier <nicolas.saunier@polymtl.ca>
date Sun, 07 Nov 2010 01:09:50 -0500
parents 8aed225f71d8
children 46ec876ce90e
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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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7 import moving
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8
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9 __metaclass__ = type
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11 commentChar = '#'
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13 delimiterChar = '%';
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15 #########################
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16 # simple statistics
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17 #########################
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18
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19 def computeChi2(expected, observed):
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20 '''Returns the Chi2 statistics'''
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21 result = 0.
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22 for e, o in zip(expected, observed):
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23 result += ((e-o)*(e-o))/e
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24 return result
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25
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26 class histogram:
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27 '''Class to represent a sample of a distribution for a continuous random variable
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28 with the number of observations for each interval'''
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29 def __init__(self, categories, counts):
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30 self.categories = categories
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31 self.counts = counts
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33 def mean(self):
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34 result = 0.
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35 for i,c in zip(self.categories, self.counts):
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36 result += c*(i[1]+i[0])/2
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37 return result/sum(self.counts)
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38
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39 def var(self, mean = None):
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40 if not mean:
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41 m = self.mean()
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42 else:
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43 m = mean
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44 result = 0.
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45 for i,c in zip(self.categories, self.counts):
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46 mid = (i[1]+i[0])/2
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47 result += c*(mid - m)*(mid - m)
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48 return result/(self.nSamples()-1)
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49
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50 def nSamples(self):
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51 return sum(self.counts)
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52
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53 def referenceCounts(self, cdf):
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54 '''cdf is a cumulative distribution function
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55 returning the probability of the variable being less that x'''
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56 # refCumulativeCounts = [0]#[cdf(self.categories[0][0])]
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57 # for inter in self.categories:
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58 # refCumulativeCounts.append(cdf(inter[1]))
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59 refCumulativeCounts = [cdf(inter[1]) for inter in self.categories[:-1]]
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60
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61 refProba = [refCumulativeCounts[0]]
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62 for i in xrange(1,len(refCumulativeCounts)):
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63 refProba.append(refCumulativeCounts[i]-refCumulativeCounts[i-1])
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64 refProba.append(1-refCumulativeCounts[-1])
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65 refCounts = [p*self.nSamples() for p in refProba]
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66
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67 return refCounts, refProba
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68
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69 #########################
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70 # maths section
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71 #########################
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72
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73 def ceilDecimals(v, nDecimals):
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74 '''Rounds the number at the nth decimal
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75 eg 1.23 at 0 decimal is 2, at 1 decimal is 1.3'''
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76 from math import ceil,pow
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77 tens = pow(10,nDecimals)
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78 return ceil(v*tens)/tens
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79
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80 def segmentIntersection(p1, p2, p3, p4):
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81 '''Returns the intersecting point of the segments [p1, p2] and [p3, p4], None otherwise'''
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82 from numpy import matrix
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83 from numpy.linalg import linalg, det
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84
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85 dp1 = p2-p1#[s1[0][1]-s1[0][0], s1[1][1]-s1[1][0]]
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86 dp2 = p4-p3#[s2[0][1]-s2[0][0], s2[1][1]-s2[1][0]]
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87
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88 A = matrix([[dp1.y, -dp1.x],
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89 [dp2.y, -dp2.x]])
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90 B = matrix([[dp1.y*p1.x-dp1.x*p1.y],
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91 [dp2.y*p3.x-dp2.x*p3.y]])
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92
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93 if linalg.det(A) == 0:#crossProduct(ds1, ds2) == 0:
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94 return None
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95 else:
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96 intersection = linalg.solve(A,B)
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97 if (moving.Interval(p1.x, p2.x, True).contains(intersection[0,0])
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98 and moving.Interval(p3.x, p4.x, True).contains(intersection[0,0])
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99 and moving.Interval(p1.y, p2.y, True).contains(intersection[1,0])
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100 and moving.Interval(p3.y, p4.y, True).contains(intersection[1,0])):
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101 return moving.Point(intersection[0,0], intersection[1,0])
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102 else:
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103 return None
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104
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105 def crossProduct(l1, l2):
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106 return l1[0]*l2[1]-l1[1]*l2[0]
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107
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108 def filterMovingWindow(input, halfWidth):
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109 '''Returns an array obtained after the smoothing of the input by a moving average
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110 The first and last points are copied from the original.'''
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111 width = float(halfWidth*2+1)
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112 win = ones(width,'d')
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113 result = convolve(win/width,array(inputSignal),'same')
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114 result[:halfWidth] = inputSignal[:halfWidth]
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115 result[-halfWidth:] = inputSignal[-halfWidth:]
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116 return result
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117
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118 #########################
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119 # plotting section
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120 #########################
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121
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122 class PlottingPropertyValues:
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123 def __init__(self, values):
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124 self.values = values
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125
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126 def get(self,i):
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127 return self.values[i%len(self.values)]
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128
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129 markers = PlottingPropertyValues(['+', '*', ',', '.', 'x', 'D', 's', 'o'])
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130
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131 linestyles = PlottingPropertyValues(['-', '--', '-.', ':'])
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132
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133 colors = PlottingPropertyValues('brgmyck') # 'w'
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134
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135 def plotIndicatorMap(indicatorMap, squareSize):
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136 from numpy import array, arange, ones, ma
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137 from matplotlib.pyplot import pcolor
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138 coords = array(indicatorMap.keys())
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139 minX = min(coords[:,0])
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140 minY = min(coords[:,1])
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141 X = arange(minX, max(coords[:,0])+1.1)*squareSize
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142 Y = arange(minY, max(coords[:,1])+1.1)*squareSize
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143 C = -ones((len(Y), len(X)))
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144 for k,v in indicatorMap.iteritems():
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145 C[k[1]-minY,k[0]-minX] = v
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146 masked = ma.masked_where(C<0,C)
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147 pcolor(X, Y, masked)
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148
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149 #########################
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150 # file I/O section
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151 #########################
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152
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153 def openCheck(filename, option = 'r', quit = False):
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154 '''Open file filename in read mode by default
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155 and checks it is open'''
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156 try:
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157 return open(filename, option)
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158 except IOError:
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159 print 'File %s could not be opened.' % filename
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160 if quit:
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161 from sys import exit
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162 exit()
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163 return None
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164
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165 def readline(f, commentCharacter = commentChar):
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166 '''Modified readline function to skip comments.'''
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167 s = f.readline()
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168 while (len(s) > 0) and s.startswith(commentCharacter):
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169 s = f.readline()
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170 return s.strip()
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171
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172 def getLines(f, delimiterCharacter = delimiterChar):
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173 '''Gets a complete entry (all the lines) in between delimiterChar.'''
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174 dataStrings = []
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175 s = readline(f)
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176 while (len(s) > 0) and (not s.startswith(delimiterCharacter)):
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177 dataStrings += [s.strip()]
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178 s = readline(f)
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179 return dataStrings
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180
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181 def removeExtension(filename, delimiter = '.'):
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182 '''Returns the filename minus the extension (all characters after last .)'''
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183 i = filename.rfind(delimiter)
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184 if i>0:
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185 return filename[:i]
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186 else:
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187 return filename
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188
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189 def cleanFilename(s):
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190 'cleans filenames obtained when contatenating figure characteristics'
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191 return s.replace(' ','-').replace('.','')
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192
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193 def listfiles(dirname, extension, remove = False):
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194 '''Returns the list of files with the extension in the directory dirname
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195 If remove is True, the filenames are stripped from the extension'''
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196 from os import listdir
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197 tmp = [f for f in listdir(dirname) if f.endswith(extension)]
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198 tmp.sort()
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199 if remove:
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200 return [removeExtension(f, extension) for f in tmp]
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201 else:
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202 return tmp
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203
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204 def removeFile(filename):
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205 '''Deletes the file while avoiding raising an error
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206 if the file does not exist'''
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207 if (os.path.exists(filename)):
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208 os.remove(filename)
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209
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210 def plotPolygon(poly, options = ''):
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211 from numpy.core.multiarray import array
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212 from matplotlib.pyplot import plot
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213 from shapely.geometry import Polygon
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214
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215 tmp = array(poly.exterior)
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216 plot(tmp[:,0], tmp[:,1], options)
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217
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218 def line2Floats(l, separator=' '):
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219 '''Returns the list of floats corresponding to the string'''
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220 return [float(x) for x in l.split(separator)]
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221
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222 def line2Ints(l, separator=' '):
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223 '''Returns the list of ints corresponding to the string'''
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224 return [int(x) for x in l.split(separator)]
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225
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226 #########################
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227 # running tests
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228 #########################
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229
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230 if __name__ == "__main__":
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231 import doctest
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232 import unittest
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233 suite = doctest.DocFileSuite('tests/utils.txt')
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234 #suite = doctest.DocTestSuite()
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235 unittest.TextTestRunner().run(suite)
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236 #doctest.testmod()
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237 #doctest.testfile("example.txt")