| 1 | #!/usr/bin/python -tt
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| 2 | #
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| 3 | # Dominik Neise, Werner Lustermann
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| 4 | # TU Dortmund, ETH Zurich
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| 5 | #
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| 6 | import numpy as np
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| 7 |
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| 8 | class SignalGenerator(object):
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| 9 | """ Signal Generator
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| 10 | generates signals for testing several helper classes like:
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| 11 | * fir filters
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| 12 | * signal extractors
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| 13 | """
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| 14 |
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| 15 | def __init__(self, option_str = 'len 100 noise 3', name = 'SignalGenerator'):
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| 16 | """ initialize the generator
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| 17 | sets default signal to generate
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| 18 | """
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| 19 | self.__module__ = 'generator'
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| 20 | self.option_str = option_str.lower()
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| 21 | self.options = make_options_from_str(option_str)
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| 22 | self.parse_options()
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| 23 | self.name = name
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| 24 |
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| 25 | def parse_options(self):
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| 26 | o = self.options #shortcut
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| 27 | if 'len' in o:
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| 28 | self.npoints = int(o['len'][0])
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| 29 | else:
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| 30 | self.npoints = 100
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| 31 | if 'noise' in o:
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| 32 | self.sigma = float(o['noise'][0])
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| 33 | else:
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| 34 | self.sigma = 1
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| 35 | if 'bsl' in o:
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| 36 | self.bsl = float(o['bsl'][0])
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| 37 | else:
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| 38 | self.bsl = -0.5
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| 39 |
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| 40 | if 'step' in o:
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| 41 | self.step_height = float(o['step'][0])
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| 42 | self.step_start = int(o['step'][1])
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| 43 | self.step_stop = int(o['step'][2])
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| 44 |
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| 45 | if 'triangle' in o:
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| 46 | self.pulses = []
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| 47 | # append 1st pulse to list of pulses
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| 48 | self.pulses.append( ( float(o['triangle'][0]) , float(o['triangle'][1]), int(o['triangle'][2]), int(o['triangle'][3]) ) )
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| 49 | number_of_pulses_after_1st = (len(o['triangle'])-4)/2
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| 50 | for i in range(number_of_pulses_after_1st):
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| 51 | self.pulses.append( ( float(o['triangle'][2*i+4]) , float(o['triangle'][2*i+5]), int(o['triangle'][2]), int(o['triangle'][3]) ) )
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| 52 |
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| 53 | if 'spike' in o:
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| 54 | self.spikes = []
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| 55 | for i in range(len(o['spike'])/2):
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| 56 | self.spikes.append( ( int(o['spike'][2*i]), float(o['spike'][2*i+1]) ) )
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| 57 |
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| 58 | def __call__(self, option_str = ''):
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| 59 | if option_str:
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| 60 | self.option_str = option_str.lower()
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| 61 | self.options = make_options_from_str(self.option_str)
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| 62 | self.parse_options()
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| 63 |
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| 64 | signal = np.zeros(self.npoints)
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| 65 | signal += self.bsl
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| 66 | signal += np.random.randn(self.npoints) * self.sigma
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| 67 | if 'step' in self.options:
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| 68 | signal[self.step_start:self.step_stop] += self.step_height
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| 69 | if 'triangle' in self.options:
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| 70 | for pulse in self.pulses:
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| 71 | pos = pulse[0]
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| 72 | height = pulse[1]
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| 73 | rise = pulse[2]
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| 74 | fall = pulse[3]
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| 75 | start = pos - rise
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| 76 | stop = pos + fall
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| 77 | signal[start:pos] += np.linspace(0., height, rise)
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| 78 | signal[pos:stop] += np.linspace(height, 0. , fall)
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| 79 | if 'spike' in self.options:
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| 80 | for spike in self.spikes:
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| 81 | signal[spike[0]] += spike[1]
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| 82 | return signal
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| 83 |
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| 84 | def __str__(self):
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| 85 | s = self.name + '\n'
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| 86 | s += 'possible options and parameters\n'
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| 87 | s += ' * len: number of samples (100)\n'
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| 88 | s += ' * noise: sigma (1)\n'
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| 89 | s += ' * bsl: level (-0.5)\n'
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| 90 | s += ' * step: height, start, end\n'
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| 91 | s += ' * triangle: pos height risingedge, fallingedge [pos height ...]\n'
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| 92 | s += ' * spike: pos height [pos height ...]\n'
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| 93 |
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| 94 | s += 'current options are:\n'
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| 95 | for key in self.options.keys():
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| 96 | s += key + ':' + str(self.options[key]) + '\n'
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| 97 | return s
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| 98 |
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| 99 |
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| 100 | class SignalGeneratorCSV(object):
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| 101 |
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| 102 | def __init__(self, file_name, option_str = 'len 100 noise 3', name = 'SignalGenerator'):
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| 103 | time, maxprob, mean, median = np.loadtxt( file_name, delimiter=',', unpack=True)
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| 104 | csv_data = maxprob
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| 105 |
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| 106 | # csv data was downshifted, I shift it up here
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| 107 | self.csv_data = csv_data - csv_data.min()
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| 108 |
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| 109 |
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| 110 | self.__module__ = 'CSV generator'
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| 111 | self.option_str = option_str.lower()
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| 112 | self.options = make_options_from_str(option_str)
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| 113 | self.parse_options()
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| 114 | self.name = name
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| 115 |
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| 116 | def parse_options(self):
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| 117 | o = self.options #shortcut
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| 118 | if 'len' in o:
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| 119 | self.npoints = int(o['len'][0])
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| 120 | else:
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| 121 | self.npoints = 100
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| 122 | if 'noise' in o:
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| 123 | self.sigma = float(o['noise'][0])
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| 124 | else:
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| 125 | self.sigma = 1
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| 126 | if 'bsl' in o:
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| 127 | self.bsl = float(o['bsl'][0])
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| 128 | else:
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| 129 | self.bsl = -0.5
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| 130 |
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| 131 | if 'step' in o:
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| 132 | self.step_height = float(o['step'][0])
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| 133 | self.step_start = int(o['step'][1])
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| 134 | self.step_stop = int(o['step'][2])
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| 135 |
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| 136 | if 'triangle' in o:
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| 137 | self.pulses = []
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| 138 | # append 1st pulse to list of pulses
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| 139 | self.pulses.append( ( float(o['triangle'][0]) , float(o['triangle'][1]), int(o['triangle'][2]), int(o['triangle'][3]) ) )
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| 140 | number_of_pulses_after_1st = (len(o['triangle'])-4)/2
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| 141 | for i in range(number_of_pulses_after_1st):
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| 142 | self.pulses.append( ( float(o['triangle'][2*i+4]) , float(o['triangle'][2*i+5]), int(o['triangle'][2]), int(o['triangle'][3]) ) )
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| 143 |
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| 144 | if 'spike' in o:
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| 145 | self.spikes = []
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| 146 | for i in range(len(o['spike'])/2):
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| 147 | self.spikes.append( ( int(o['spike'][2*i]), float(o['spike'][2*i+1]) ) )
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| 148 |
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| 149 | if 'csv' in o:
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| 150 | self.csvs = []
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| 151 | for i in range(len(o['csv'])/2):
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| 152 | time = int( o['csv'][2*i] )
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| 153 | amplitude = float( o['csv'][2*i+1] )
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| 154 | self.csvs.append( (time, amplitude) )
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| 155 |
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| 156 | def __call__(self, option_str = ''):
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| 157 | if option_str:
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| 158 | self.option_str = option_str.lower()
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| 159 | self.options = make_options_from_str(self.option_str)
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| 160 | self.parse_options()
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| 161 |
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| 162 | signal = np.zeros(self.npoints)
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| 163 | signal += self.bsl
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| 164 |
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| 165 | if 'step' in self.options:
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| 166 | signal[self.step_start:self.step_stop] += self.step_height
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| 167 | if 'triangle' in self.options:
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| 168 | for pulse in self.pulses:
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| 169 | pos = pulse[0]
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| 170 | height = pulse[1]
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| 171 | rise = pulse[2]
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| 172 | fall = pulse[3]
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| 173 | start = pos - rise
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| 174 | stop = pos + fall
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| 175 | signal[start:pos] += np.linspace(0., height, rise)
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| 176 | signal[pos:stop] += np.linspace(height, 0. , fall)
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| 177 | if 'spike' in self.options:
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| 178 | for spike in self.spikes:
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| 179 | signal[spike[0]] += spike[1]
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| 180 | if 'csv' in self.options:
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| 181 | for csv in self.csvs:
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| 182 | amplitude = csv[1]
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| 183 | time = csv[0]
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| 184 | csv_data = self.csv_data.copy()
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| 185 | #scale
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| 186 | csv_data *= amplitude
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| 187 | # add shifted
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| 188 | print 'bumm', len(csv_data)
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| 189 | print csv_data.shape
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| 190 | print signal[time:time+len(csv_data)].shape
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| 191 | signal[time:time+len(csv_data)] += csv_data
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| 192 |
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| 193 | # add noise
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| 194 | signal += + np.random.normal(0.0,self.sigma, signal.shape)
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| 195 | return signal
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| 196 |
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| 197 | def __str__(self):
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| 198 | s = self.name + '\n'
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| 199 | s += 'possible options and parameters\n'
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| 200 | s += ' * len: number of samples (100)\n'
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| 201 | s += ' * noise: sigma (1)\n'
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| 202 | s += ' * bsl: level (-0.5)\n'
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| 203 | s += ' * step: height, start, end\n'
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| 204 | s += ' * triangle: pos height risingedge, fallingedge [pos height ...]\n'
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| 205 | s += ' * spike: pos height [pos height ...]\n'
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| 206 | s += ' * csv: pos height [pos height ...]\n'
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| 207 |
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| 208 | s += 'current options are:\n'
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| 209 | for key in self.options.keys():
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| 210 | s += key + ':' + str(self.options[key]) + '\n'
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| 211 | return s
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| 212 |
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| 213 |
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| 214 | # Helper function to parse signalname and create a dictionary
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| 215 | # dictionary layout :
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| 216 | # key : string
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| 217 | # value : [list of parameters]
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| 218 | def make_options_from_str(signalname):
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| 219 | options = {}
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| 220 | for word in (signalname.lower()).split():
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| 221 | if word.isalpha():
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| 222 | current_key = word
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| 223 | options[current_key] = []
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| 224 | # if word.isdigit():
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| 225 | else:
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| 226 | options[current_key].append(word)
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| 227 | # else:
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| 228 | # print '-nothing'
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| 229 | return options
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| 230 |
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| 231 | if __name__ == '__main__':
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| 232 | from plotters import Plotter
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| 233 | myGenerator = SignalGenerator('len 400 noise 0.3 bsl -2.5 triangle 50 10.2 10 100 65 10 150 20 spike 100 50. 20 50 21 49')
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| 234 | sig = myGenerator()
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| 235 | print myGenerator
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| 236 |
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| 237 | p = Plotter('generator test')
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| 238 | p(sig)
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| 239 |
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| 240 | anothergen = SignalGeneratorCSV('PulseTemplate_PointSet_0.csv',
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| 241 | 'len 1000 noise 0.4 bsl -2.0 csv 300 1 60 2 650 1 spike 110 50')
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| 242 | sig2 = anothergen()
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| 243 | print anothergen
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| 244 |
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| 245 | pp = Plotter('CSV Gen Test')
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| 246 | pp(sig2)
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| 247 |
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| 248 | raw_input('any key to quit')
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