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annotate python/indicators.py @ 322:28661c5887d3

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Corrected a major bug for LCSS Added functions to test all alignments when computing the LCSS with a finite delta
author Nicolas Saunier <nicolas.saunier@polymtl.ca>
date Tue, 07 May 2013 18:43:40 +0200
parents a5e40bd04cf4
children 1046b7346886
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1 #! /usr/bin/env python
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2 '''Class for indicators, temporal indicators, and safety indicators'''
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3
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4 __metaclass__ = type
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5
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6 import moving
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7
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8 # need for a class representing the indicators, their units, how to print them in graphs...
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9 class TemporalIndicator:
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10 '''Class for temporal indicators
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11 i.e. indicators that take a value at specific instants
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12
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13 values should be
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14 * a dict, for the values at specific time instants
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15 * or a list with a time interval object if continuous measurements
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16
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17 it should have more information like name, unit'''
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18
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19 def __init__(self, name, values, timeInterval=None, maxValue = None):
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20 self.name = name
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21 self.isCosine = (name.find('Cosine') >= 0)
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22 if timeInterval:
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23 assert len(values) == timeInterval.length()
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24 self.timeInterval = timeInterval
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25 self.values = {}
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26 for i in xrange(int(round(self.timeInterval.length()))):
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27 self.values[self.timeInterval[i]] = values[i]
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28 else:
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29 self.values = values
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30 instants = sorted(self.values.keys())
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31 if instants:
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32 self.timeInterval = moving.TimeInterval(instants[0], instants[-1])
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33 else:
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34 self.timeInterval = moving.TimeInterval()
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35 self.maxValue = maxValue
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36
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37 def __len__(self):
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38 return len(self.values)
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39
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40 def empty(self):
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41 return len(self.values) == 0
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42
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43 def __getitem__(self, i):
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44 'Returns ith value in time interval'
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45 if i in self.values.keys():
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46 return self.values[i]
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47 else:
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48 return None
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49
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50 def getIthValue(self, i):
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51 sortedKeys = sorted(self.values.keys())
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52 if 0<=i<len(sortedKeys):
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53 return self.values[sortedKeys[i]]
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54 else:
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55 return None
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56
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57 def __iter__(self):
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58 self.iterInstantNum = 0 # index in the interval or keys of the dict
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59 return self
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60
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61 def next(self):
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62 if self.iterInstantNum >= len(self.values):#(self.timeInterval and self.iterInstantNum>=self.timeInterval.length())\
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63 # or (self.iterInstantNum >= self.values)
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64 raise StopIteration
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65 else:
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66 self.iterInstantNum += 1
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67 return self.getIthValue(self.iterInstantNum-1)
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68
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69 def getTimeInterval(self):
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70 return self.timeInterval
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71
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72 def getValues(self):
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73 return [self.__getitem__(t) for t in self.timeInterval]
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74
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75 def getAngleValues(self):
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76 '''if the indicator is a function of an angle,
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77 transform it to an angle (eg cos)
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78 (no transformation otherwise)'''
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79 from numpy import arccos
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80 values = self.getValues()
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81 if self.isCosine:
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82 return [arccos(c) for c in values]
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83 else:
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84 return values
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85
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86 def plot(self, options = '', xfactor = 1., **kwargs):
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87 from matplotlib.pylab import plot,ylim
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88 if self.getTimeInterval().length() == 1:
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89 marker = 'o'
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90 else:
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91 marker = ''
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92 time = sorted(self.values.keys())
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93 plot([x/xfactor for x in time], [self.values[i] for i in time], options+marker, **kwargs)
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94 if self.maxValue:
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95 ylim(ymax = self.maxValue)
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96
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97 def valueSorted(self):
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98 ''' return the values after sort the keys in the indicator
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99 This should probably not be used: to delete'''
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100 print('Deprecated: values should not be accessed in this way')
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101 values=[]
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102 keys = self.values.keys()
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103 keys.sort()
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104 for key in keys:
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105 values.append(self.values[key])
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106 return values
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107
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108 @staticmethod
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109 def getDLCSS(indic1, indic2, threshold, delta = float('inf') , method ='min' ):
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110 ''' compute the distance between two indicators using LCSS
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111 two common methods are used: min or mean of the indicators length'''
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112 print('Deprecated: this is not appropriate method for indicator comparison')
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113 l1 = indic1.valueSorted
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114 l2 = indic2.valueSorted
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115 DLCSS = None
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116 if method == 'min':
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117 DLCSS = 1- (LCSS(l1,l2, threshold, delta, distance))/min(len(l1),len(l2))
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118 if method == 'mean':
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119 average = len(l1)+len(l2)/2
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120 DLCSS = 1- ((LCSS(l1,l2, threshold, delta, distance))/average)
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121 return DLCSS
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122
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123
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124 def distanceForLCSS(x, y): # lambda x,y:abs(x-y)
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125 if x == None or y == None:
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126 return float('inf')
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127 else:
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128 return abs(x-y)
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diff changeset
129
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diff changeset
130 # non-aligned LCSS computations, ok for delta = inf
321
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diff changeset
131 def computeLCSS(indicator1, indicator2, threshold, delta = float('inf')):
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diff changeset
132 ''' compute the LCSS between two indicators using LCSS'''
286
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diff changeset
133 from utils import LCSS
321
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diff changeset
134 if indicator1 and indicator2:
322
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diff changeset
135 return LCSS(indicator1.getValues(), indicator2.getValues(), threshold, distanceForLCSS, delta)
321
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diff changeset
136 else:
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diff changeset
137 return 0
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diff changeset
138
322
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diff changeset
139 def computeNormalizedLCSS(indicator1, indicator2, threshold, delta = float('inf'), method= min):
321
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diff changeset
140 ''' compute the normalized LCSS between two indicators using LCSS
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diff changeset
141 ie, the LCSS divided by the min or mean of the indicator lengths'''
322
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parents: 321
diff changeset
142 from utils import normalizedLCSS
321
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diff changeset
143 if indicator1 and indicator2:
322
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diff changeset
144 return normalizedLCSS(indicator1.getValues(), indicator2.getValues(), threshold, distanceForLCSS, delta, method)
286
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diff changeset
145 else:
321
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diff changeset
146 return 0.
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diff changeset
147
322
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diff changeset
148 def computeDLCSS(indicator1, indicator2, threshold, delta = float('inf'), method = min):
321
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diff changeset
149 ''' compute the LCSS distance between two indicators using LCSS'''
322
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diff changeset
150 from utils import DLCSS
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diff changeset
151 return DLCSS(indicator1.getValues(), indicator2.getValues(), threshold, distanceForLCSS, delta, method)
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diff changeset
152
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parents: 321
diff changeset
153 # aligned LCSS computations
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diff changeset
154 def computeAlignedLCSS(indicator1, indicator2, threshold, delta = float('inf')):
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diff changeset
155 ''' compute the aligned LCSS between two indicators using LCSS'''
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parents: 321
diff changeset
156 from utils import alignedLCSS
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parents: 321
diff changeset
157 if indicator1 and indicator2:
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parents: 321
diff changeset
158 return alignedLCSS(indicator1.getValues(), indicator2.getValues(), threshold, distanceForLCSS, delta)
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parents: 321
diff changeset
159 else:
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diff changeset
160 return 0
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parents: 321
diff changeset
161
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parents: 321
diff changeset
162 def computeNormalizedAlignedLCSS(indicator1, indicator2, threshold, delta = float('inf'), method= min):
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parents: 321
diff changeset
163 ''' compute the normalized aligned LCSS between two indicators using LCSS
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parents: 321
diff changeset
164 ie, the LCSS divided by the min or mean of the indicator lengths'''
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 321
diff changeset
165 from utils import normalizedAlignedLCSS
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 321
diff changeset
166 if indicator1 and indicator2:
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parents: 321
diff changeset
167 return normalizedAlignedLCSS(indicator1.getValues(), indicator2.getValues(), threshold, distanceForLCSS, delta, method)
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parents: 321
diff changeset
168 else:
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parents: 321
diff changeset
169 return 0.
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 321
diff changeset
170
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 321
diff changeset
171 def computeAlignedDLCSS(indicator1, indicator2, threshold, delta = float('inf'), method = min):
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parents: 321
diff changeset
172 ''' compute the aligned LCSS distance between two indicators using LCSS'''
28661c5887d3 Corrected a major bug for LCSS
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 321
diff changeset
173 from utils import alignedDLCSS
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 321
diff changeset
174 return alignedDLCSS(indicator1.getValues(), indicator2.getValues(), threshold, distanceForLCSS, delta, method)
285
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parents: 282
diff changeset
175
244
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parents:
diff changeset
176 class SeverityIndicator(TemporalIndicator):
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
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177 '''Class for severity indicators
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parents:
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178 field mostSevereIsMax is True
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
179 if the most severe value taken by the indicator is the maximum'''
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parents:
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180
286
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parents: 285
diff changeset
181 def __init__(self, name, values, timeInterval=None, mostSevereIsMax=True, maxValue = None):
269
a9988971aac8 removed legacy code + tweaks
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 265
diff changeset
182 TemporalIndicator.__init__(self, name, values, timeInterval, maxValue)
244
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
183 self.mostSevereIsMax = mostSevereIsMax
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parents:
diff changeset
184
285
5957aa1d69e1 Integrating Mohamed's changes
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents: 282
diff changeset
185 def getMostSevereValue(self, minNInstants=1): # TODO use scoreatpercentile
244
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
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parents:
diff changeset
186 from matplotlib.mlab import find
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parents:
diff changeset
187 from numpy.core.multiarray import array
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parents:
diff changeset
188 from numpy.core.fromnumeric import mean
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
189 values = array(self.values.values())
286
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parents: 285
diff changeset
190 indices = range(len(values))
244
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
191 if len(indices) >= minNInstants:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
192 values = sorted(values[indices], reverse = self.mostSevereIsMax) # inverted if most severe is max -> take the first values
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parents:
diff changeset
193 return mean(values[:minNInstants])
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
194 else:
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
195 return None
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parents:
diff changeset
196
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
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parents:
diff changeset
197 # functions to aggregate discretized maps of indicators
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parents:
diff changeset
198 # TODO add values in the cells between the positions (similar to discretizing vector graphics to bitmap)
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parents:
diff changeset
199
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
200 def indicatorMap(indicatorValues, trajectory, squareSize):
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parents:
diff changeset
201 '''Returns a dictionary
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
202 with keys for the indices of the cells (squares)
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
203 in which the trajectory positions are located
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parents:
diff changeset
204 at which the indicator values are attached
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
205
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
206 ex: speeds and trajectory'''
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
207
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
208 from numpy import floor, mean
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
209 assert len(indicatorValues) == trajectory.length()
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
210 indicatorMap = {}
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
211 for k in xrange(trajectory.length()):
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
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parents:
diff changeset
212 p = trajectory[k]
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
213 i = floor(p.x/squareSize)
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
214 j = floor(p.y/squareSize)
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
215 if indicatorMap.has_key((i,j)):
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
216 indicatorMap[(i,j)].append(indicatorValues[k])
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
217 else:
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
218 indicatorMap[(i,j)] = [indicatorValues[k]]
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
219 for k in indicatorMap.keys():
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
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parents:
diff changeset
220 indicatorMap[k] = mean(indicatorMap[k])
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
221 return indicatorMap
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
222
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
223 def indicatorMapFromPolygon(value, polygon, squareSize):
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
224 '''Fills an indicator map with the value within the polygon
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
225 (array of Nx2 coordinates of the polygon vertices)'''
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
226 import matplotlib.nxutils as nx
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
227 from numpy.core.multiarray import array, arange
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
228 from numpy import floor
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
229
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
230 points = []
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
231 for x in arange(min(polygon[:,0])+squareSize/2, max(polygon[:,0]), squareSize):
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
232 for y in arange(min(polygon[:,1])+squareSize/2, max(polygon[:,1]), squareSize):
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
233 points.append([x,y])
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
234 inside = nx.points_inside_poly(array(points), polygon)
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
235 indicatorMap = {}
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
236 for i in xrange(len(inside)):
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
237 if inside[i]:
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
238 indicatorMap[(floor(points[i][0]/squareSize), floor(points[i][1]/squareSize))] = 0
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
239 return indicatorMap
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
240
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
241 def indicatorMapFromAxis(value, limits, squareSize):
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
242 '''axis = [xmin, xmax, ymin, ymax] '''
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
243 from numpy.core.multiarray import arange
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
244 from numpy import floor
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Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
245 indicatorMap = {}
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
246 for x in arange(limits[0], limits[1], squareSize):
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
247 for y in arange(limits[2], limits[3], squareSize):
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
248 indicatorMap[(floor(x/squareSize), floor(y/squareSize))] = value
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
249 return indicatorMap
5027c174ab90 moved indicators to new file, added ExtrapolatedTrajectory class to extrapolation file
Nicolas Saunier <nicolas.saunier@polymtl.ca>
parents:
diff changeset
250
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251 def combineIndicatorMaps(maps, squareSize, combinationFunction):
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252 '''Puts many indicator maps together
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253 (averaging the values in each cell
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254 if more than one maps has a value)'''
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255 #from numpy import mean
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256 indicatorMap = {}
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257 for m in maps:
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258 for k,v in m.iteritems():
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259 if indicatorMap.has_key(k):
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260 indicatorMap[k].append(v)
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261 else:
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262 indicatorMap[k] = [v]
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263 for k in indicatorMap.keys():
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264 indicatorMap[k] = combinationFunction(indicatorMap[k])
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265 return indicatorMap
247
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266
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267 if __name__ == "__main__":
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268 import doctest
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269 import unittest
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270 suite = doctest.DocFileSuite('tests/indicators.txt')
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271 unittest.TextTestRunner().run(suite)
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272 # #doctest.testmod()
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273 # #doctest.testfile("example.txt")