| 1 | #!/usr/bin/python -tt
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| 2 | #
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| 3 | # Werner Lustermann
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| 4 | # 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 | import fir_filter as fir
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| 9 |
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| 10 | class DRSSpikes(object):
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| 11 | """ remove spikes (single or double false readings) from DRS4 data
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| 12 | Strategy:
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| 13 | * filter the data, removing the signal, thus spike(s) are clearly visible
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| 14 | * search single and double spikes
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| 15 | * replace the spike by a value derived from the neighbors
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| 16 |
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| 17 | """
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| 18 |
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| 19 | def __init__(self, threshold=7.,
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| 20 | single_pattern=np.array( [-0.5, 1.0, -0.5]) ,
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| 21 | double_pattern=np.array([-1., 1., 1., -1.]),
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| 22 | user_action=lambda candidates, singles, doubles, data, ind: None,
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| 23 | debug = False):
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| 24 | """ initialize spike filter
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| 25 | template_single: template of a single slice spike
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| 26 | template_double: template of a two slice spike
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| 27 |
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| 28 | """
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| 29 |
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| 30 | self.threshold = threshold
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| 31 | self.single_pattern = single_pattern * threshold
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| 32 | self.double_pattern = double_pattern * threshold
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| 33 |
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| 34 | self.remove_signal = fir.RemoveSignal()
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| 35 |
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| 36 | self.user_action = user_action
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| 37 | self.debug = debug
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| 38 |
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| 39 | def __call__(self, data):
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| 40 |
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| 41 | self.row, self.col = data.shape
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| 42 | indicator = self.remove_signal(data)
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| 43 | a = indicator.flatten()
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| 44 | singles = []
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| 45 | doubles = []
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| 46 |
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| 47 | # a spike in the first or last channel is considered as a filter artefact
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| 48 | candidates = np.where(a[1:-2] > self.threshold)
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| 49 | # candidates = np.where(a[1:1022] > self.threshold)
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| 50 | cc = candidates[0]
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| 51 | #print 'cc: ', cc
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| 52 | #: find single spikes
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| 53 | p = self.single_pattern * np.sign( self.single_pattern )
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| 54 | for i, can in enumerate( zip(a[cc], a[cc+1], a[cc+2]) ):
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| 55 | #print 'can : p', can, p
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| 56 | can = can * np.sign(self.single_pattern)
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| 57 | if np.all(can > p):
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| 58 | singles.append(cc[i])
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| 59 |
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| 60 | #: find double spikes
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| 61 | p = self.double_pattern * np.sign( self.double_pattern )
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| 62 | for i, can in enumerate( zip(a[cc], a[cc+1], a[cc+2], a[cc+3]) ):
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| 63 | #print 'data: ', [data[0,cc[i]+k] for k in range(3)]
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| 64 | #print 'can : p', can, p
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| 65 | can = can * np.sign(self.double_pattern)
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| 66 | if np.all(can > p):
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| 67 | doubles.append(cc[i])
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| 68 |
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| 69 | if self.debug:
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| 70 | print 'singles: ', singles
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| 71 | print 'doubles: ', doubles
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| 72 |
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| 73 | self.user_action(cc, singles, doubles, data, a)
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| 74 |
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| 75 | data = self.remove_single_spikes(singles, data)
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| 76 | data = self.remove_double_spikes(doubles, data)
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| 77 | return data
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| 78 |
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| 79 | def remove_single_spikes(self, singles, data):
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| 80 | data = data.flatten()
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| 81 | for spike in singles:
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| 82 | data[spike] = (data[spike-1] + data[spike+1]) / 2.
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| 83 | return data.reshape(self.row, self.col)
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| 84 |
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| 85 | def remove_double_spikes(self, doubles, data):
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| 86 | data = data.flatten()
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| 87 | for spike in doubles:
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| 88 | data[spike:spike+2] = (data[spike-1] + data[spike+2]) / 2.
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| 89 | return data.reshape(self.row, self.col)
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| 90 |
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| 91 | def _test():
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| 92 |
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| 93 | a = np.ones((3,12)) * 3.
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| 94 | a[0,3] = 7.
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| 95 | a[1,7] = 14.
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| 96 | a[1,8] = 14.
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| 97 | a[2,4] = 50.
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| 98 | a[2,5] = 45.
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| 99 | a[2,8] = 20.
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| 100 |
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| 101 | print a
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| 102 |
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| 103 | SpikeRemover = DRSSpikes(3., debug=True)
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| 104 | print 'single spike pattern ', SpikeRemover.single_pattern
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| 105 | print 'double spike pattern ', SpikeRemover.double_pattern
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| 106 | afilt = SpikeRemover(a)
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| 107 | print afilt
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| 108 |
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| 109 | if __name__ == '__main__':
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| 110 | """ test the class """
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| 111 | _test()
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| 112 |
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| 113 |
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