[new] first use of Metadata class in autoPyLoT, largely increasing read performance using obspyDMT (single DATALESS-Seed files)
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autoPyLoT.py
18
autoPyLoT.py
@ -22,7 +22,7 @@ from pylot.core.analysis.magnitude import MomentMagnitude, LocalMagnitude
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from pylot.core.io.data import Data
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from pylot.core.io.inputs import PylotParameter
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from pylot.core.pick.autopick import autopickevent, iteratepicker
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from pylot.core.util.dataprocessing import restitute_data, read_metadata
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from pylot.core.util.dataprocessing import restitute_data, read_metadata, Metadata
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from pylot.core.util.defaults import SEPARATOR
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from pylot.core.util.event import Event
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from pylot.core.util.structure import DATASTRUCTURE
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@ -276,7 +276,11 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
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wfdat = check4gaps(wfdat)
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wfdat = check4doubled(wfdat)
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wfdat = trim_station_components(wfdat, trim_start=True, trim_end=False)
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metadata = read_metadata(parameter.get('invdir'))
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if not wfpath_extension:
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metadata = Metadata(parameter.get('invdir'))
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else:
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metadata = Metadata(os.path.join(eventpath, 'resp'))
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# metadata = read_metadata(parameter.get('invdir'))
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# TODO: (idea) read metadata from obspy_dmt database
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# if not wfpath_extension:
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# metadata = read_metadata(parameter.get('invdir'))
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@ -285,10 +289,10 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
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corr_dat = None
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if metadata:
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# rotate stations to ZNE
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wfdat = check4rotated(wfdat, metadata)
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#wfdat = check4rotated(wfdat, metadata) # MP MP TEMPORARILY DISABLED !!!!!!!!!!!
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if locflag:
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print("Restitute data ...")
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corr_dat = restitute_data(wfdat.copy(), *metadata, ncores=ncores)
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corr_dat = restitute_data(wfdat.copy(), metadata, ncores=ncores)
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if not corr_dat and locflag:
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locflag = 2
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print('Working on event %s. Stations: %s' % (eventpath, station))
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@ -363,7 +367,8 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
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WAscaling[2]))
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evt = local_mag.updated_event(magscaling)
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net_ml = local_mag.net_magnitude(magscaling)
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print("Network local magnitude: %4.1f" % net_ml.mag)
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if net_ml:
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print("Network local magnitude: %4.1f" % net_ml.mag)
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if magscaling == None:
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scaling = False
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elif magscaling[0] != 0 and magscaling[1] != 0:
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@ -447,7 +452,8 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
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WAscaling[2]))
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evt = local_mag.updated_event(magscaling)
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net_ml = local_mag.net_magnitude(magscaling)
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print("Network local magnitude: %4.1f" % net_ml.mag)
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if net_ml:
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print("Network local magnitude: %4.1f" % net_ml.mag)
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if magscaling == None:
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scaling = False
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elif magscaling[0] != 0 and magscaling[1] != 0:
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@ -88,9 +88,9 @@ def autopickevent(data, param, iplot=0, fig_dict=None, fig_dict_wadatijack=None,
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print('Autopickstation: Distribute autopicking for {} '
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'stations on {} cores.'.format(len(input_tuples), ncores_str))
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pool = gen_Pool(ncores)
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result = pool.map(call_autopickstation, input_tuples)
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pool.close()
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result = parallel_picking(input_tuples, ncores)
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#result = serial_picking(input_tuples)
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if ncores == 1:
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results = serial_picking(input_tuples)
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@ -120,6 +120,20 @@ def autopickevent(data, param, iplot=0, fig_dict=None, fig_dict_wadatijack=None,
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return wadationsets
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def serial_picking(input_tuples):
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result = []
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for input_tuple in input_tuples:
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result.append(call_autopickstation(input_tuple))
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return result
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def parallel_picking(input_tuples, ncores):
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pool = gen_Pool(ncores)
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result = pool.imap_unordered(call_autopickstation, input_tuples)
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pool.close()
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return result
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def call_autopickstation(input_tuple):
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"""
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helper function used for multiprocessing
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@ -303,13 +317,10 @@ def autopickstation(wfstream, pickparam, verbose=False,
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Lc = np.inf
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print('autopickstation: use_taup flag active.')
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if not metadata:
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metadata = [None, None]
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if not metadata[1]:
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print('Warning: Could not use TauPy to estimate onsets as there are no metadata given.')
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else:
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station_id = wfstream[0].get_id()
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parser = metadata[1]
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station_coords = get_source_coords(parser, station_id)
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station_coords = metadata.get_coordinates(station_id)
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if station_coords and origin:
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source_origin = origin[0]
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model = TauPyModel(taup_model)
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@ -191,9 +191,24 @@ class AICPicker(AutoPicker):
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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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cf = self.Data[0].data
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# get maximum of HOS/AR-CF as startimg 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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icfmax = np.argmax(cf)
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# MP MP testing threshold
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thresh_hit = False
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thresh_factor = 0.6
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thresh = thresh_factor * cf[icfmax]
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for index, sample in enumerate(cf):
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if sample >= thresh:
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thresh_hit = True
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# go on searching for the following maximum
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if index > 0 and thresh_hit:
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if sample <= cf[index - 1]:
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icfmax = index - 1
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break
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# MP MP ---
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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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@ -233,14 +248,14 @@ class AICPicker(AutoPicker):
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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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cf[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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# calculate SNR from CF
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self.SNR = max(abs(self.Data[0].data[isignal])) / \
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abs(np.mean(self.Data[0].data[inoise]))
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self.SNR = max(abs(cf[isignal])) / \
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abs(np.mean(cf[inoise]))
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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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@ -253,7 +268,7 @@ class AICPicker(AutoPicker):
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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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dataslope = cf[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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@ -282,8 +297,8 @@ class AICPicker(AutoPicker):
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else:
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fig = self.fig
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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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cf = cf
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ax.plot(self.Tcf, cf / max(cf), 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.legend(loc=1)
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ax.set_xlabel('Time [s] since %s' % self.Data[0].stats.starttime)
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@ -296,7 +311,16 @@ class AICPicker(AutoPicker):
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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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# MP MP change slope calculation
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# get all maxima of aicsmooth
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iaicmaxima = argrelmax(aicsmooth)[0]
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# get first index of maximum after pickindex (indices saved in iaicmaxima)
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aicmax = iaicmaxima[np.where(iaicmaxima > pickindex)[0]]
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if len(aicmax) > 0:
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iaicmax = aicmax[0]
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else:
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iaicmax = -1
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dataslope = aicsmooth[pickindex : iaicmax]
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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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@ -306,7 +330,7 @@ class AICPicker(AutoPicker):
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else:
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self.slope = 1 / (len(dataslope) * self.Data[0].stats.delta) * (datafit[-1] - datafit[0])
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# normalize slope to maximum of cf to make it unit independent
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self.slope /= self.Data[0].data[icfmax]
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self.slope /= aicsmooth[iaicmax]
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else:
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self.SNR = None
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@ -320,10 +344,9 @@ class AICPicker(AutoPicker):
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fig = self.fig
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fig._tight = True
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ax1 = fig.add_subplot(211)
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x = self.Data[0].data
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if len(self.Tcf) > len(self.Data[0].data): # why? LK
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if len(self.Tcf) > len(cf): # 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, cf / max(cf), 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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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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@ -333,7 +356,7 @@ class AICPicker(AutoPicker):
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if self.Pick 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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ax2.plot(self.Tcf, aicsmooth, color='r', 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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ax1.axvspan(self.Tcf[isignal[0]], self.Tcf[isignal[-1]], color='b', alpha=0.2, lw=0,
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label='Signal Window')
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@ -345,7 +368,7 @@ class AICPicker(AutoPicker):
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label='Signal Window')
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ax2.axvspan(self.Tcf[iislope[0]], self.Tcf[iislope[-1]], color='g', alpha=0.2, lw=0,
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label='Slope Window')
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ax2.plot(self.Tcf[iislope], datafit, 'g', linewidth=2, label='Slope')
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ax2.plot(self.Tcf[pickindex : iaicmax], datafit, 'g', linewidth=2, label='Slope') # MP MP changed temporarily!
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if self.slope is not None:
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ax1.set_title('Station %s, SNR=%7.2f, Slope= %12.2f counts/s' % (self.Data[0].stats.station,
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@ -100,12 +100,13 @@ class Metadata(object):
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if not seed_id in self.seed_ids.keys():
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print('No data found for seed id {}. Trying to find it in all known inventories...'.format(seed_id))
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self.read_all()
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for inv_fname, metadata in self.inventory_files.items():
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for inv_fname, metadata_dict in self.inventory_files.items():
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# use get_coordinates to check for seed_id
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try:
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metadata['data'].get_coordinates(seed_id)
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metadata_dict['data'].get_coordinates(seed_id)
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self.seed_ids[seed_id] = inv_fname
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return metadata
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print('Found metadata for station {}!'.format(seed_id))
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return metadata_dict
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except Exception as e:
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continue
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print('Could not find metadata for station {}'.format(seed_id))
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@ -127,6 +128,7 @@ class Metadata(object):
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def read_single_file(self, inv_fname):
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# try to read a single file as Parser/Inventory if it was not already read before
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if not inv_fname in self.inventory_files.keys():
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pass
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else:
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@ -460,6 +462,11 @@ def read_metadata(path_to_inventory):
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def restitute_trace(input_tuple):
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def no_metadata(tr, seed_id):
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print('no metadata file found '
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'for trace {0}'.format(seed_id))
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return tr, True
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tr, metadata, unit, force = input_tuple
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remove_trace = False
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@ -467,6 +474,9 @@ def restitute_trace(input_tuple):
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seed_id = tr.get_id()
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mdata = metadata.get_metadata(seed_id)
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if not mdata:
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return no_metadata(tr, seed_id)
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invtype = mdata['invtype']
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inobj = mdata['data']
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@ -481,8 +491,7 @@ def restitute_trace(input_tuple):
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if invtype == 'resp':
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fresp = find_in_list(inobj, seed_id)
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if not fresp:
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raise IOError('no response file found '
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'for trace {0}'.format(seed_id))
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return no_metadata(tr, seed_id)
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fname = fresp
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seedresp = dict(filename=fname,
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date=stime,
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@ -505,8 +514,7 @@ def restitute_trace(input_tuple):
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finv = invlist[0]
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inventory = read_inventory(finv, format='STATIONXML')
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elif invtype == None:
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print("No restitution possible, as there are no station-meta data available!")
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return tr, True
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return no_metadata(tr, seed_id)
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else:
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remove_trace = True
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# apply restitution to data
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@ -562,7 +570,7 @@ def restitute_data(data, metadata, unit='VEL', force=False, ncores=0):
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data.remove(tr)
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pool = gen_Pool(ncores)
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result = pool.map(restitute_trace, input_tuples)
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result = pool.imap_unordered(restitute_trace, input_tuples)
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pool.close()
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for tr, remove_trace in result:
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