refactoring picker.py (AICPicker and PragPicker)
This commit is contained in:
Darius Arnold
parent
deaa67bb30
commit
8f721da643
@ -23,44 +23,42 @@ import warnings
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import matplotlib.pyplot as plt
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import numpy as np
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from scipy.signal import argrelmax
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from pylot.core.pick.charfuns import CharacteristicFunction
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from pylot.core.pick.utils import getnoisewin, getsignalwin
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from pylot.core.pick.utils import getnoisewin, getsignalwin, real_Bool, real_None, set_NaNs_to, taper_cf, cf_positive, \
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smooth_cf, check_counts_ms, getSNR, getslopewin, calcSlope
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class AutoPicker(object):
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'''
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"""
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Superclass of different, automated picking algorithms applied on a CF determined
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using AIC, HOS, or AR prediction.
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'''
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"""
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warnings.simplefilter('ignore')
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def __init__(self, cf, TSNR, PickWindow, iplot=0, aus=None, Tsmooth=None, Pick1=None, fig=None, linecolor='k'):
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'''
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:param: cf, characteristic function, on which the picking algorithm is applied
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:type: `~pylot.core.pick.CharFuns.CharacteristicFunction` object
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:param: TSNR, length of time windows around pick used to determine SNR [s]
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:type: tuple (T_noise, T_gap, T_signal)
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:param: PickWindow, length of pick window [s]
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:type: float
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:param: iplot, no. of figure window for plotting interims results
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:type: integer
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:param: aus ("artificial uplift of samples"), find local minimum at i if aic(i-1)*(1+aus) >= aic(i)
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:type: float
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:param: Tsmooth, length of moving smoothing window to calculate smoothed CF [s]
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:type: float
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:param: Pick1, initial (prelimenary) onset time, starting point for PragPicker and
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EarlLatePicker
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:type: float
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'''
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"""
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Create AutoPicker object
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:param cf: characteristic function, on which the picking algorithm is applied
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:type cf: `~pylot.core.pick.CharFuns.CharacteristicFunction`
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:param TSNR: length of time windows around pick used to determine SNR [s], tuple (T_noise, T_gap, T_signal)
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:type TSNR: (float, float, float)
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:param PickWindow: length of pick window [s]
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:type PickWindow: float
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:param iplot: flag used for plotting, if > 1, results will be plotted. Use iplot = 0 to disable plotting
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:type iplot: int
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:param aus: ("artificial uplift of samples"), find local minimum at i if aic(i-1)*(1+aus) >= aic(i)
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:type aus: float
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:param Tsmooth: length of moving smoothing window to calculate smoothed CF [s]
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:type Tsmooth: float
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:param Pick1: initial (preliminary) onset time, starting point for PragPicker and EarlLatePicker
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:type Pick1: float
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:param fig: matplotlib figure used for plotting. If not given and plotting is enabled, a new figure will
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be created
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:type fig: `~matplotlib.figure.Figure`
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:param linecolor: matplotlib line color string
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:type linecolor: str
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"""
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assert isinstance(cf, CharacteristicFunction), "%s is not a CharacteristicFunction object" % str(cf)
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self._linecolor = linecolor
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@ -79,6 +77,11 @@ class AutoPicker(object):
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self.calcPick()
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def __str__(self):
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"""
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String representation of AutoPicker object
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:return:
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:rtype: str
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"""
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return '''\n\t{name} object:\n
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TSNR:\t\t\t{TSNR}\n
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PickWindow:\t{PickWindow}\n
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@ -129,6 +132,13 @@ class AutoPicker(object):
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return self.iplot
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def setiplot(self, iplot):
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try:
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iplot = int(iplot)
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except ValueError:
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if real_Bool(iplot):
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self.iplot = 2
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else:
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self.iplot = 0
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self.iplot = iplot
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def getpick1(self):
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@ -142,134 +152,89 @@ class AutoPicker(object):
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class AICPicker(AutoPicker):
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'''
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"""
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Method to derive the onset time of an arriving phase based on CF
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derived from AIC. In order to get an impression of the quality of this inital pick,
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derived from AIC. In order to get an impression of the quality of this initial pick,
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a quality assessment is applied based on SNR and slope determination derived from the CF,
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from which the AIC has been calculated.
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'''
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"""
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def calcPick(self):
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def prepareCF(self):
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"""
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data pre processing: remove invalid entries, taper cf, remove offset
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"""
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print('AICPicker: Get initial onset time (pick) from AIC-CF ...')
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self.Pick = None
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self.slope = None
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self.SNR = None
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plt_flag = 0
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try:
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iplot = int(self.iplot)
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except:
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if self.iplot == True or self.iplot == 'True':
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iplot = 2
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else:
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iplot = 0
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# find NaN's
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nn = np.isnan(self.cf)
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if len(nn) > 1:
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self.cf[nn] = 0
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# taper AIC-CF to get rid off side maxima
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tap = np.hanning(len(self.cf))
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aic = tap * self.cf + max(abs(self.cf))
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self.cf = set_NaNs_to(self.cf, 0)
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self.cf = taper_cf(self.cf)
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self.cf = cf_positive(self.cf)
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# smooth AIC-CF
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ismooth = int(round(self.Tsmooth / self.dt))
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aicsmooth = np.zeros(len(aic))
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if len(aic) < ismooth:
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try:
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self.aicsmooth = smooth_cf(self.cf, self.Tsmooth, self.dt)
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except ValueError as e:
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print('AICPicker: Tsmooth larger than CF!')
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return
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else:
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for i in range(1, len(aic)):
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if i > ismooth:
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ii1 = i - ismooth
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aicsmooth[i] = aicsmooth[i - 1] + (aic[i] - aic[ii1]) / ismooth
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else:
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aicsmooth[i] = np.mean(aic[1: i])
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# remove offset in AIC function
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offset = abs(min(aic) - min(aicsmooth))
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aicsmooth = aicsmooth - offset
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# get maximum of HOS/AR-CF as startimg point for searching
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raise e
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def findMinimum(self):
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"""
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Find minimum representing the preliminary onset, sets Pick to minimum
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"""
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# get maximum of HOS/AR-CF as starting point for searching
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# minimum in AIC function
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icfmax = np.argmax(self.Data[0].data)
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# find minimum in AIC-CF front of maximum of HOS/AR-CF
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lpickwindow = int(round(self.PickWindow / self.dt))
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for i in range(icfmax - 1, max([icfmax - lpickwindow, 2]), -1):
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if aicsmooth[i - 1] >= aicsmooth[i]:
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if self.aicsmooth[i - 1] >= self.aicsmooth[i]:
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self.Pick = self.Tcf[i]
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break
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# if no minimum could be found:
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# search in 1st derivative of AIC-CF
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if self.Pick is None:
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diffcf = np.diff(aicsmooth)
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# find NaN's
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nn = np.isnan(diffcf)
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if len(nn) > 1:
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diffcf[nn] = 0
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diffcf = np.diff(self.aicsmooth)
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diffcf = set_NaNs_to(diffcf, 0)
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# taper CF to get rid off side maxima
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tap = np.hanning(len(diffcf))
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diffcf = tap * diffcf * max(abs(aicsmooth))
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diffcf = taper_cf(diffcf)
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diffcf = cf_positive(diffcf)
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for i in range(icfmax - 1, max([icfmax - lpickwindow, 2]), -1):
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if diffcf[i - 1] >= diffcf[i]:
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self.Pick = self.Tcf[i]
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break
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def calcPick(self):
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"""
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Calculate pick using cf derived from AIC
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:return:
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:rtype: None
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"""
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print('AICPicker: Get initial onset time (pick) from AIC-CF ...')
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self.Pick = None
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self.slope = -1
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self.SNR = -1
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plt_flag = 0
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iplot = self.iplot
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try:
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self.prepareCF()
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except ValueError:
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return
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self.findMinimum()
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# quality assessment using SNR and slope from CF
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if self.Pick is not None:
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# get noise window
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inoise = getnoisewin(self.Tcf, self.Pick, self.TSNR[0], self.TSNR[1])
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# check, if these are counts or m/s, important for slope estimation!
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# this is quick and dirty, better solution?
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if max(self.Data[0].data < 1e-3) and max(self.Data[0].data >= 1e-6):
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self.Data[0].data = self.Data[0].data * 1000000.
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elif max(self.Data[0].data < 1e-6):
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self.Data[0].data = self.Data[0].data * 1e13
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# get signal window
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isignal = getsignalwin(self.Tcf, self.Pick, self.TSNR[2])
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if len(isignal) == 0:
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return
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ii = min([isignal[len(isignal) - 1], len(self.Tcf)])
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isignal = isignal[0:ii]
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try:
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self.Data[0].data[isignal]
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except IndexError as e:
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msg = "Time series out of bounds! {}".format(e)
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print(msg)
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return
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self.Data[0].data = check_counts_ms(self.Data[0].data)
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# calculate SNR from CF
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self.SNR = max(abs(self.Data[0].data[isignal] - np.mean(self.Data[0].data[isignal]))) / \
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max(abs(self.Data[0].data[inoise] - np.mean(self.Data[0].data[inoise])))
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self.SNR = getSNR(self.Data, self.TSNR, self.Pick)[0] # TODO Check wether this yields similar results
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# calculate slope from CF after initial pick
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# get slope window
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tslope = self.TSNR[3] # slope determination window
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islope = np.where((self.Tcf <= min([self.Pick + tslope, self.Tcf[-1]])) \
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& (self.Tcf >= self.Pick)) # TODO: put this in a seperate function like getsignalwin
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# find maximum within slope determination window
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# 'cause slope should be calculated up to first local minimum only!
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try:
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dataslope = self.Data[0].data[islope[0][0:-1]]
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except IndexError:
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print("Slope Calculation: empty array islope, check signal window")
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return
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if len(dataslope) <= 1:
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print('No or not enough data in slope window found!')
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return
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imaxs, = argrelmax(dataslope)
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if imaxs.size:
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imax = imaxs[0]
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else:
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imax = np.argmax(dataslope)
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iislope = islope[0][0:imax + 1]
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if len(iislope) < 2:
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# calculate slope from initial onset to maximum of AIC function
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print("AICPicker: Not enough data samples left for slope calculation!")
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print("Calculating slope from initial onset to maximum of AIC function ...")
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imax = np.argmax(aicsmooth[islope[0][0:-1]])
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if imax == 0:
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print("AICPicker: Maximum for slope determination right at the beginning of the window!")
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print("Choose longer slope determination window!")
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self.slope, iislope, datafit = calcSlope(self.Data, self.aicsmooth, self.Tcf, self.Pick, self.TSNR)
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except Exception:
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if self.iplot > 1:
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if self.fig == None or self.fig == 'None':
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if real_None(self.fig) is None:
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fig = plt.figure()
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plt_flag = 1
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else:
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@ -277,34 +242,27 @@ class AICPicker(AutoPicker):
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ax = fig.add_subplot(111)
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x = self.Data[0].data
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ax.plot(self.Tcf, x / max(x), color=self._linecolor, linewidth=0.7, label='(HOS-/AR-) Data')
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ax.plot(self.Tcf, aicsmooth / max(aicsmooth), 'r', label='Smoothed AIC-CF')
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ax.plot(self.Tcf, self.aicsmooth / max(self.aicsmooth), 'r', label='Smoothed AIC-CF')
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ax.legend(loc=1)
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ax.set_xlabel('Time [s] since %s' % self.Data[0].stats.starttime)
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ax.set_yticks([])
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ax.set_title(self.Data[0].stats.station)
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if plt_flag == 1:
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fig.show()
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try: input()
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except SyntaxError: pass
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try:
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input()
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except SyntaxError:
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pass
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plt.close(fig)
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return
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iislope = islope[0][0:imax+1]
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dataslope = self.Data[0].data[iislope]
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# calculate slope as polynomal fit of order 1
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xslope = np.arange(0, len(dataslope), 1)
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P = np.polyfit(xslope, dataslope, 1)
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datafit = np.polyval(P, xslope)
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if datafit[0] >= datafit[-1]:
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print('AICPicker: Negative slope, bad onset skipped!')
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return
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self.slope = 1 / (len(dataslope) * self.Data[0].stats.delta) * (datafit[-1] - datafit[0])
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else:
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self.SNR = None
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self.slope = None
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self.SNR = -1
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self.slope = -1
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if iplot > 1:
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if self.fig == None or self.fig == 'None':
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inoise = getnoisewin(self.Tcf, self.Pick, self.TSNR[0], self.TSNR[1])
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isignal = getsignalwin(self.Tcf, self.Pick, self.TSNR[2])
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if real_None(self.fig) is None:
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fig = plt.figure() # self.iplot)
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plt_flag = 1
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else:
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@ -315,14 +273,14 @@ class AICPicker(AutoPicker):
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if len(self.Tcf) > len(self.Data[0].data): # why? LK
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self.Tcf = self.Tcf[0:len(self.Tcf)-1]
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ax1.plot(self.Tcf, x / max(x), color=self._linecolor, linewidth=0.7, label='(HOS-/AR-) Data')
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ax1.plot(self.Tcf, aicsmooth / max(aicsmooth), 'r', label='Smoothed AIC-CF')
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ax1.plot(self.Tcf, self.aicsmooth / max(self.aicsmooth), 'r', label='Smoothed AIC-CF')
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if self.Pick is not None:
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ax1.plot([self.Pick, self.Pick], [-0.1, 0.5], 'b', linewidth=2, label='AIC-Pick')
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ax1.set_xlabel('Time [s] since %s' % self.Data[0].stats.starttime)
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ax1.set_yticks([])
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ax1.legend(loc=1)
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if self.Pick is not None:
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if self.Pick is not None and self.SNR is not None:
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ax2 = fig.add_subplot(2, 1, 2, sharex=ax1)
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ax2.plot(self.Tcf, x, color=self._linecolor, linewidth=0.7, label='Data')
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ax1.axvspan(self.Tcf[inoise[0]], self.Tcf[inoise[-1]], color='y', alpha=0.2, lw=0, label='Noise Window')
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@ -364,19 +322,13 @@ class AICPicker(AutoPicker):
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class PragPicker(AutoPicker):
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'''
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"""
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Method of pragmatic picking exploiting information given by CF.
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'''
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"""
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def calcPick(self):
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try:
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iplot = int(self.getiplot())
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except:
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if self.getiplot() == True or self.getiplot() == 'True':
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iplot = 2
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else:
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iplot = 0
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iplot = self.getiplot()
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if self.getpick1() is not None:
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print('PragPicker: Get most likely pick from HOS- or AR-CF using pragmatic picking algorithm ...')
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@ -387,19 +339,7 @@ class PragPicker(AutoPicker):
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pickflag = 0
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plt_flag = 0
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# smooth CF
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ismooth = int(round(self.Tsmooth / self.dt))
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cfsmooth = np.zeros(len(self.cf))
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if len(self.cf) < ismooth:
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print('PragPicker: Tsmooth larger than CF!')
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return
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else:
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for i in range(1, len(self.cf)):
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if i > ismooth:
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ii1 = i - ismooth
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cfsmooth[i] = cfsmooth[i - 1] + (self.cf[i] - self.cf[ii1]) / ismooth
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else:
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cfsmooth[i] = np.mean(self.cf[1: i])
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cfsmooth = smooth_cf(self.cf, self.Tsmooth, self.dt)
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# select picking window
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# which is centered around tpick1
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ipick = np.where((self.Tcf >= self.getpick1() - self.PickWindow / 2) \
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@ -474,7 +414,7 @@ class PragPicker(AutoPicker):
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pickflag = 0
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if iplot > 1:
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if self.fig == None or self.fig == 'None':
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if real_None(self.fig) is None:
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fig = plt.figure() # self.getiplot())
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plt_flag = 1
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else:
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@ -12,6 +12,7 @@ import warnings
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import matplotlib.pyplot as plt
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import numpy as np
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from scipy.signal import argrelmax
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from obspy.core import Stream, UTCDateTime
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from pylot.core.util.utils import real_Bool, real_None
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@ -413,9 +414,9 @@ def getSNR(X, TSNR, t1, tracenum=0):
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assert isinstance(X, Stream), "%s is not a stream object" % str(X)
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SNR = None
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SNRdB = None
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noiselevel = None
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SNR = -1
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SNRdB = -1
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noiselevel = -1
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x = X[tracenum].data
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npts = X[tracenum].stats.npts
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@ -485,13 +486,13 @@ def getsignalwin(t, t1, tsignal):
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Function to extract data out of time series for signal level calculation.
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Returns an array of indices.
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:param t: array of time stamps
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:type t: `numpy.ndarray`
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:type t: `~numpy.ndarray`
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:param t1: time from which relative to it signal window is extracted
|
||||
:type t1: float
|
||||
:param tsignal: length of time window [s] for signal level calculation
|
||||
:type tsignal: float
|
||||
:return: indices of signal window i t
|
||||
:rtype: `numpy.ndarray`
|
||||
:return: indices of signal window in t
|
||||
:rtype: `~numpy.ndarray`
|
||||
"""
|
||||
|
||||
# get signal window
|
||||
@ -503,6 +504,26 @@ def getsignalwin(t, t1, tsignal):
|
||||
return isignal
|
||||
|
||||
|
||||
def getslopewin(Tcf, Pick, tslope):
|
||||
"""
|
||||
Function to extract slope window out of time series
|
||||
|
||||
>>> (np.arange(15., 85.), 30.0, 10.0)
|
||||
array([15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25])
|
||||
|
||||
:param Tcf:
|
||||
:type Tcf:
|
||||
:param Pick:
|
||||
:type Pick:
|
||||
:param tslope:a
|
||||
:type tslope:
|
||||
:return:
|
||||
:rtype: `numpy.ndarray`
|
||||
"""
|
||||
# TODO: fill out docstring
|
||||
slope = np.where( (Tcf <= min(Pick + tslope, Tcf[-1])) & (Tcf >= Pick) )
|
||||
return slope[0]
|
||||
|
||||
def getResolutionWindow(snr, extent):
|
||||
"""
|
||||
Produce the half of the time resolution window width from given SNR value
|
||||
@ -1206,6 +1227,145 @@ def getQualityFromUncertainty(uncertainty, Errors):
|
||||
|
||||
return quality
|
||||
|
||||
def set_NaNs_to(data, nan_value):
|
||||
"""
|
||||
Replace all NaNs in data with nan_value
|
||||
:param data: array holding data
|
||||
:type data: `~numpy.ndarray`
|
||||
:param nan_value: value which all NaNs are set to
|
||||
:type nan_value: float, int
|
||||
:return: data array with all NaNs replaced with nan_value
|
||||
:rtype: `~numpy.ndarray`
|
||||
"""
|
||||
nn = np.isnan(data)
|
||||
if np.any(nn):
|
||||
data[nn] = nan_value
|
||||
return data
|
||||
|
||||
def taper_cf(cf):
|
||||
"""
|
||||
Taper cf data to get rid off of side maximas
|
||||
:param cf: characteristic function data
|
||||
:type cf: `~numpy.ndarray`
|
||||
:return: tapered cf
|
||||
:rtype: `~numpy.ndarray`
|
||||
"""
|
||||
tap = np.hanning(len(cf))
|
||||
return tap * cf
|
||||
|
||||
def cf_positive(cf):
|
||||
"""
|
||||
Shifts cf so that all values are positive
|
||||
:param cf:
|
||||
:type cf: `~numpy.ndarray`
|
||||
:return:
|
||||
:rtype: `~numpy.ndarray`
|
||||
"""
|
||||
return cf + max(abs(cf))
|
||||
|
||||
def smooth_cf(cf, t_smooth, delta):
|
||||
"""
|
||||
Smooth cf by taking samples over t_smooth length
|
||||
:param cf: characteristic function data
|
||||
:type cf: `~numpy.ndarray`
|
||||
:param t_smooth: Time from which samples for smoothing will be taken (s)
|
||||
:type t_smooth: float
|
||||
:param delta: Sample rate of cf
|
||||
:type delta: float
|
||||
:return: smoothed cf data
|
||||
:rtype: `~numpy.ndarray`
|
||||
"""
|
||||
|
||||
ismooth = int(round(t_smooth / delta)) # smooth values this many indexes apart
|
||||
cf_smooth = np.zeros(len(cf))
|
||||
|
||||
if len(cf) < ismooth:
|
||||
raise ValueError
|
||||
|
||||
for i, val in enumerate(cf):
|
||||
if i <= ismooth:
|
||||
cf_smooth[i] = np.mean(cf[0:i+1])
|
||||
elif i > ismooth:
|
||||
ii1 = i - ismooth
|
||||
cf_smooth[i] = cf_smooth[i - 1] + (cf[i] - cf[ii1]) / ismooth
|
||||
offset = abs(min(cf) - min(cf_smooth))
|
||||
cf_smooth -= offset # remove offset from smoothed function
|
||||
return cf_smooth
|
||||
|
||||
def check_counts_ms(data):
|
||||
"""
|
||||
check if data is in counts or m/s
|
||||
:param data: data array
|
||||
:type data: `~numpy.ndarray`
|
||||
:return:
|
||||
:rtype: `~numpy.ndarray`
|
||||
"""
|
||||
# this is quick and dirty, better solution?
|
||||
if max(data < 1e-3) and max(data >= 1e-6):
|
||||
data = data * 1000000.
|
||||
elif max(data < 1e-6):
|
||||
data = data * 1e13
|
||||
return data
|
||||
|
||||
|
||||
def calcSlope(Data, datasmooth, Tcf, Pick, TSNR):
|
||||
"""
|
||||
Calculate Slope for Data around a given time Pick.
|
||||
|
||||
:param Data: trace containing data for which a slope will be calculated
|
||||
:type Data: `~obspy.core.trace.Trace`
|
||||
:param datasmooth: smoothed data array
|
||||
:type datasmooth: ~numpy.ndarray`
|
||||
:param Tcf: array of time indices for Data array
|
||||
:type Tcf: ~numpy.ndarray`
|
||||
:param Pick: onset time around which the slope should be calculated
|
||||
:type Pick: float
|
||||
:param TSNR: tuple containing (tnoise, tsafety, tsignal, tslope). Slope will be calculated in time
|
||||
window tslope around the onset
|
||||
:type TSNR: (float, float, float, float)
|
||||
:return: tuple containing (slope of onset, slope index array, data fit information)
|
||||
:rtype: (float, `~numpy.ndarray`, `~numpy.ndarray`
|
||||
"""
|
||||
islope = getslopewin(Tcf, Pick, TSNR[3])
|
||||
try:
|
||||
dataslope = Data[0].data[islope]
|
||||
except IndexError as e:
|
||||
print("Slope Calculation: empty array islope, check signal window")
|
||||
raise e
|
||||
if len(dataslope) <= 1:
|
||||
print('Slope window outside data. No or not enough data in slope window found!')
|
||||
raise ValueError
|
||||
# find maximum within slope determination window
|
||||
# 'cause slope should be calculated up to first local minimum only!
|
||||
imaxs, = argrelmax(dataslope)
|
||||
if imaxs.size:
|
||||
imax = imaxs[0]
|
||||
else:
|
||||
imax = np.argmax(dataslope)
|
||||
iislope = islope[0:imax + 1] # cut index so it contains only the first maximum
|
||||
if len(iislope) < 2:
|
||||
# calculate slope from initial onset to maximum of AIC function
|
||||
print("AICPicker: Not enough data samples left for slope calculation!")
|
||||
print("Calculating slope from initial onset to maximum of AIC function ...")
|
||||
imax = np.argmax(datasmooth[islope])
|
||||
if imax == 0:
|
||||
print("AICPicker: Maximum for slope determination right at the beginning of the window!")
|
||||
print("Choose longer slope determination window!")
|
||||
raise IndexError
|
||||
iislope = islope[0][0:imax + 1] # cut index so it contains only the first maximum
|
||||
dataslope = Data[0].data[iislope] # slope will only be calculated to the first maximum
|
||||
# calculate slope as polynomal fit of order 1
|
||||
xslope = np.arange(0, len(dataslope))
|
||||
P = np.polyfit(xslope, dataslope, 1)
|
||||
datafit = np.polyval(P, xslope)
|
||||
if datafit[0] >= datafit[-1]:
|
||||
print('AICPicker: Negative slope, bad onset skipped!')
|
||||
raise ValueError
|
||||
|
||||
slope = 1 / (len(dataslope) * Data[0].stats.delta) * (datafit[-1] - datafit[0])
|
||||
return slope, iislope, datafit
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
import doctest
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user