[merge] merge branch 'improve-util-utils' of pull request #35 into develop
This commit is contained in:
commit
5b18e9ab71
12
PyLoT.py
12
PyLoT.py
@ -72,11 +72,11 @@ from pylot.core.util.errors import DatastructureError, \
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OverwriteError
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from pylot.core.util.connection import checkurl
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from pylot.core.util.dataprocessing import Metadata, restitute_data
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from pylot.core.util.utils import fnConstructor, getLogin, \
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from pylot.core.util.utils import fnConstructor, get_login, \
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full_range, readFilterInformation, pick_color_plt, \
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pick_linestyle_plt, identifyPhaseID, excludeQualityClasses, \
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transform_colors_mpl, transform_colors_mpl_str, getAutoFilteroptions, check_all_obspy, \
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check_all_pylot, get_bool, get_None, get_pylot_eventfile_with_extension
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check_all_pylot, get_bool, get_none, get_pylot_eventfile_with_extension
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from pylot.core.util.gui import make_pen
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from pylot.core.util.event import Event
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from pylot.core.io.location import create_creation_info, create_event
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@ -196,7 +196,7 @@ class MainWindow(QMainWindow):
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if settings.value("user/FullName", None) is None:
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fulluser = QInputDialog.getText(self, "Enter Name:", "Full name")
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settings.setValue("user/FullName", fulluser)
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settings.setValue("user/Login", getLogin())
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settings.setValue("user/Login", get_login())
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if settings.value("agency_id", None) is None:
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agency = QInputDialog.getText(self,
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"Enter authority/institution name:",
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@ -1990,8 +1990,8 @@ class MainWindow(QMainWindow):
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if len(curr_event.origins) > 0:
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origin_time = curr_event.origins[0].time
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tstart = settings.value('tstart') if get_None(settings.value('tstart')) else 0
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tstop = settings.value('tstop') if get_None(settings.value('tstop')) else 0
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tstart = settings.value('tstart') if get_none(settings.value('tstart')) else 0
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tstop = settings.value('tstop') if get_none(settings.value('tstop')) else 0
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tstart = origin_time + float(tstart)
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tstop = origin_time + float(tstop)
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else:
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@ -2306,7 +2306,7 @@ class MainWindow(QMainWindow):
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# wfst += self.get_data().getWFData().select(component=alter_comp)
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plotWidget = self.getPlotWidget()
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self.adjustPlotHeight()
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if get_bool(settings.value('large_dataset')):
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if get_bool(settings.value('large_dataset')) == True:
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self.plot_method = 'fast'
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else:
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self.plot_method = 'normal'
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10
autoPyLoT.py
10
autoPyLoT.py
@ -28,7 +28,7 @@ from pylot.core.util.dataprocessing import restitute_data, 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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from pylot.core.util.utils import get_None, trim_station_components, check4gapsAndRemove, check4doubled, \
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from pylot.core.util.utils import get_none, trim_station_components, check4gapsAndRemove, check4doubled, \
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check4rotated
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from pylot.core.util.version import get_git_version as _getVersionString
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@ -91,9 +91,9 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
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sp=sp_info)
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print(splash)
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parameter = get_None(parameter)
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inputfile = get_None(inputfile)
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eventid = get_None(eventid)
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parameter = get_none(parameter)
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inputfile = get_none(inputfile)
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eventid = get_none(eventid)
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fig_dict = None
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fig_dict_wadatijack = None
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@ -154,7 +154,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
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datastructure.setExpandFields(exf)
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# check if default location routine NLLoc is available and all stations are used
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if get_None(parameter['nllocbin']) and station == 'all':
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if get_none(parameter['nllocbin']) and station == 'all':
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locflag = 1
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# get NLLoc-root path
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nllocroot = parameter.get('nllocroot')
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@ -1,7 +1,7 @@
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from obspy import UTCDateTime
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from obspy.core import event as ope
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from pylot.core.util.utils import getLogin, getHash
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from pylot.core.util.utils import get_login, get_hash
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def create_amplitude(pickID, amp, unit, category, cinfo):
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@ -61,7 +61,7 @@ def create_creation_info(agency_id=None, creation_time=None, author=None):
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:return:
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'''
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if author is None:
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author = getLogin()
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author = get_login()
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if creation_time is None:
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creation_time = UTCDateTime()
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return ope.CreationInfo(agency_id=agency_id, author=author,
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@ -210,7 +210,7 @@ def create_resourceID(timetohash, restype, authority_id=None, hrstr=None):
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'''
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assert isinstance(timetohash, UTCDateTime), "'timetohash' is not an ObsPy" \
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"UTCDateTime object"
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hid = getHash(timetohash)
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hid = get_hash(timetohash)
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if hrstr is None:
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resID = ope.ResourceIdentifier(restype + '/' + hid[0:6])
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else:
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@ -16,7 +16,7 @@ from pylot.core.io.inputs import PylotParameter
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from pylot.core.io.location import create_event, \
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create_magnitude
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from pylot.core.pick.utils import select_for_phase, get_quality_class
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from pylot.core.util.utils import getOwner, full_range, four_digits, transformFilterString4Export, \
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from pylot.core.util.utils import get_owner, full_range, four_digits, transformFilterString4Export, \
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backtransformFilterString, loopIdentifyPhase, identifyPhase
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@ -58,7 +58,7 @@ def readPILOTEvent(phasfn=None, locfn=None, authority_id='RUB', **kwargs):
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if phasfn is not None and os.path.isfile(phasfn):
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phases = sio.loadmat(phasfn)
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phasctime = UTCDateTime(os.path.getmtime(phasfn))
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phasauthor = getOwner(phasfn)
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phasauthor = get_owner(phasfn)
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else:
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phases = None
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phasctime = None
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@ -66,7 +66,7 @@ def readPILOTEvent(phasfn=None, locfn=None, authority_id='RUB', **kwargs):
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if locfn is not None and os.path.isfile(locfn):
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loc = sio.loadmat(locfn)
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locctime = UTCDateTime(os.path.getmtime(locfn))
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locauthor = getOwner(locfn)
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locauthor = get_owner(locfn)
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else:
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loc = None
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locctime = None
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@ -22,7 +22,7 @@ from pylot.core.pick.picker import AICPicker, PragPicker
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from pylot.core.pick.utils import checksignallength, checkZ4S, earllatepicker, \
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getSNR, fmpicker, checkPonsets, wadaticheck, get_quality_class, PickingFailedException, MissingTraceException
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from pylot.core.util.utils import getPatternLine, gen_Pool, \
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get_bool, identifyPhaseID, get_None, correct_iplot
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get_bool, identifyPhaseID, get_none, correct_iplot
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def autopickevent(data, param, iplot=0, fig_dict=None, fig_dict_wadatijack=None, ncores=0, metadata=None, origin=None):
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@ -258,7 +258,7 @@ class AutopickStation(object):
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self.pickparams = copy.deepcopy(pickparam)
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self.verbose = verbose
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self.iplot = correct_iplot(iplot)
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self.fig_dict = get_None(fig_dict)
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self.fig_dict = get_none(fig_dict)
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self.metadata = metadata
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self.origin = origin
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@ -15,7 +15,7 @@ import numpy as np
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from obspy.core import Stream, UTCDateTime
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from scipy.signal import argrelmax
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from pylot.core.util.utils import get_bool, get_None, SetChannelComponents
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from pylot.core.util.utils import get_bool, get_none, SetChannelComponents
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def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecolor='k'):
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@ -136,7 +136,7 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecol
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PickError = symmetrize_error(diffti_te, diffti_tl)
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if iplot > 1:
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if get_None(fig) is None:
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if get_none(fig) is None:
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fig = plt.figure() # iplot)
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plt_flag = 1
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fig._tight = True
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@ -275,7 +275,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
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try:
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P1 = np.polyfit(xslope1, xraw[islope1], 1)
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datafit1 = np.polyval(P1, xslope1)
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except Exception as e:
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except ValueError as e:
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print("fmpicker: Problems with data fit! {}".format(e))
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print("Skip first motion determination!")
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return FM
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@ -321,7 +321,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
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try:
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P2 = np.polyfit(xslope2, xfilt[islope2], 1)
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datafit2 = np.polyval(P2, xslope2)
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except Exception as e:
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except ValueError as e:
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emsg = 'fmpicker: polyfit failed: {}'.format(e)
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print(emsg)
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return FM
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@ -344,7 +344,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
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print("fmpicker: Found polarity %s" % FM)
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if iplot > 1:
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if get_None(fig) is None:
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if get_none(fig) is None:
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fig = plt.figure() # iplot)
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plt_flag = 1
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fig._tight = True
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@ -868,7 +868,7 @@ def checksignallength(X, pick, minsiglength, pickparams, iplot=0, fig=None, line
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returnflag = 0
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if iplot > 1:
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if get_None(fig) is None:
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if get_none(fig) is None:
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fig = plt.figure() # iplot)
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plt_flag = 1
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fig._tight = True
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@ -1213,14 +1213,14 @@ def checkZ4S(X, pick, pickparams, iplot, fig=None, linecolor='k'):
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t = np.linspace(diff_dict[key], trace.stats.endtime - trace.stats.starttime + diff_dict[key],
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trace.stats.npts)
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if i == 0:
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if get_None(fig) is None:
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if get_none(fig) is None:
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fig = plt.figure() # self.iplot) ### WHY? MP MP
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plt_flag = 1
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ax1 = fig.add_subplot(3, 1, i + 1)
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ax = ax1
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ax.set_title('CheckZ4S, Station %s' % zdat[0].stats.station)
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else:
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if get_None(fig) is None:
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if get_none(fig) is None:
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fig = plt.figure() # self.iplot) ### WHY? MP MP
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plt_flag = 1
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ax = fig.add_subplot(3, 1, i + 1, sharex=ax1)
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@ -1494,7 +1494,7 @@ def getQualityFromUncertainty(uncertainty, Errors):
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# set initial quality to 4 (worst) and change only if one condition is hit
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quality = 4
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if get_None(uncertainty) is None:
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if get_none(uncertainty) is None:
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return quality
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if uncertainty <= Errors[0]:
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@ -8,6 +8,7 @@ import platform
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import re
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import subprocess
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import warnings
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from typing import Literal, Tuple, Type
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from functools import lru_cache
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import numpy as np
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@ -20,6 +21,10 @@ from pylot.core.io.inputs import PylotParameter, FilterOptions
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from pylot.core.util.obspyDMT_interface import check_obspydmt_eventfolder
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from pylot.styles import style_settings
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Rgba: Type[tuple] = Tuple[int, int, int, int]
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Mplrgba: Type[tuple] = Tuple[float, float, float, float]
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Mplrgbastr: Type[tuple] = Tuple[str, str, str, str]
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def _pickle_method(m):
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if m.im_self is None:
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@ -83,25 +88,6 @@ def fit_curve(x, y):
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return splev, splrep(x, y)
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def getindexbounds(f, eta):
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"""
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Get indices of values closest below and above maximum value in an array
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:param f: array
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:type f: `~numpy.ndarray`
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:param eta: look for value in array that is closes to max_value * eta
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:type eta: float
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:return: tuple containing index of max value, index of value closest below max value,
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index of value closest above max value
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:rtype: (int, int, int)
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"""
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mi = f.argmax() # get indices of max values
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m = max(f) # get maximum value
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b = m * eta #
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l = find_nearest(f[:mi], b) # find closest value below max value
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u = find_nearest(f[mi:], b) + mi # find closest value above max value
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return mi, l, u
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def gen_Pool(ncores=0):
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"""
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Generate mulitprocessing pool object utilizing ncores amount of cores
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@ -167,11 +153,11 @@ def clims(lim1, lim2):
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"""
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takes two pairs of limits and returns one pair of common limts
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:param lim1: limit 1
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:type lim1: int
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:type lim1: List[int]
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:param lim2: limit 2
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:type lim2: int
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:type lim2: List[int]
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:return: new upper and lower limit common to both given limits
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:rtype: [int, int]
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:rtype: List[int]
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>>> clims([0, 4], [1, 3])
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[0, 4]
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@ -303,7 +289,7 @@ def fnConstructor(s):
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if type(s) is str:
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s = s.split(':')[-1]
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else:
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s = getHash(UTCDateTime())
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s = get_hash(UTCDateTime())
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badchars = re.compile(r'[^A-Za-z0-9_. ]+|^\.|\.$|^ | $|^$')
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badsuffix = re.compile(r'(aux|com[1-9]|con|lpt[1-9]|prn)(\.|$)')
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@ -315,15 +301,32 @@ def fnConstructor(s):
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return fn
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def get_None(value):
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def get_none(value):
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"""
|
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Convert "None" to None
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:param value:
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:type value: str, bool
|
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:type value: str, NoneType
|
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:return:
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:rtype: bool
|
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:rtype: type(value) or NoneType
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|
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>>> st = read()
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>>> print(get_none(st))
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3 Trace(s) in Stream:
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BW.RJOB..EHZ | 2009-08-24T00:20:03.000000Z - 2009-08-24T00:20:32.990000Z | 100.0 Hz, 3000 samples
|
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BW.RJOB..EHN | 2009-08-24T00:20:03.000000Z - 2009-08-24T00:20:32.990000Z | 100.0 Hz, 3000 samples
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BW.RJOB..EHE | 2009-08-24T00:20:03.000000Z - 2009-08-24T00:20:32.990000Z | 100.0 Hz, 3000 samples
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>>> get_none('Stream')
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'Stream'
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>>> get_none(0)
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0
|
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>>> get_none(0.)
|
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0.0
|
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>>> print(get_none('None'))
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None
|
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>>> print(get_none(None))
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None
|
||||
"""
|
||||
if value == 'None':
|
||||
if value is None or (type(value) is str and value == 'None'):
|
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return None
|
||||
else:
|
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return value
|
||||
@ -333,9 +336,26 @@ def get_bool(value):
|
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"""
|
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Convert string representations of bools to their true boolean value
|
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:param value:
|
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:type value: str, bool
|
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:type value: str, bool, int, float
|
||||
:return: true boolean value
|
||||
:rtype: bool
|
||||
|
||||
>>> get_bool(True)
|
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True
|
||||
>>> get_bool(False)
|
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False
|
||||
>>> get_bool(0)
|
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False
|
||||
>>> get_bool(0.)
|
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False
|
||||
>>> get_bool(0.1)
|
||||
True
|
||||
>>> get_bool(2)
|
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True
|
||||
>>> get_bool(-1)
|
||||
False
|
||||
>>> get_bool(-0.3)
|
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False
|
||||
"""
|
||||
if type(value) is bool:
|
||||
return value
|
||||
@ -343,8 +363,11 @@ def get_bool(value):
|
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return True
|
||||
elif value in ['False', 'false']:
|
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return False
|
||||
elif value > 0. or value > 0:
|
||||
return True
|
||||
else:
|
||||
return bool(value)
|
||||
return False
|
||||
|
||||
|
||||
def four_digits(year):
|
||||
"""
|
||||
@ -355,8 +378,8 @@ def four_digits(year):
|
||||
:return: four digit year correspondent
|
||||
:rtype: int
|
||||
|
||||
>>> four_digits(20)
|
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1920
|
||||
>>> four_digits(75)
|
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1975
|
||||
>>> four_digits(16)
|
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2016
|
||||
>>> four_digits(00)
|
||||
@ -438,36 +461,53 @@ def backtransformFilterString(st):
|
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return st
|
||||
|
||||
|
||||
def getHash(time):
|
||||
def get_hash(time):
|
||||
"""
|
||||
takes a time object and returns the corresponding SHA1 hash of the formatted date string
|
||||
:param time: time object for which a hash should be calculated
|
||||
:type time: `~obspy.core.utcdatetime.UTCDateTime`
|
||||
:return: SHA1 hash
|
||||
:rtype: str
|
||||
|
||||
>>> time = UTCDateTime(0)
|
||||
>>> get_hash(time)
|
||||
'7627cce3b1b58dd21b005dac008b34d18317dd15'
|
||||
>>> get_hash(0)
|
||||
Traceback (most recent call last):
|
||||
...
|
||||
AssertionError: 'time' is not an ObsPy UTCDateTime object
|
||||
"""
|
||||
assert isinstance(time, UTCDateTime), '\'time\' is not an ObsPy UTCDateTime object'
|
||||
hg = hashlib.sha1()
|
||||
hg.update(time.strftime('%Y-%m-%d %H:%M:%S.%f'))
|
||||
hg.update(time.strftime('%Y-%m-%d %H:%M:%S.%f').encode('utf-8'))
|
||||
return hg.hexdigest()
|
||||
|
||||
|
||||
def getLogin():
|
||||
def get_login():
|
||||
"""
|
||||
returns the actual user's login ID
|
||||
:return: login ID
|
||||
returns the actual user's name
|
||||
:return: login name
|
||||
:rtype: str
|
||||
"""
|
||||
import getpass
|
||||
return getpass.getuser()
|
||||
|
||||
|
||||
def getOwner(fn):
|
||||
def get_owner(fn):
|
||||
"""
|
||||
takes a filename and return the login ID of the actual owner of the file
|
||||
:param fn: filename of the file tested
|
||||
:type fn: str
|
||||
:return: login ID of the file's owner
|
||||
:rtype: str
|
||||
|
||||
>>> import tempfile
|
||||
>>> with tempfile.NamedTemporaryFile() as tmpfile:
|
||||
... tmpfile.write(b'') and True
|
||||
... tmpfile.flush()
|
||||
... get_owner(tmpfile.name) == os.path.expanduser('~').split('/')[-1]
|
||||
0
|
||||
True
|
||||
"""
|
||||
system_name = platform.system()
|
||||
if system_name in ["Linux", "Darwin"]:
|
||||
@ -513,6 +553,11 @@ def is_executable(fn):
|
||||
:param fn: path to the file to be tested
|
||||
:return: True or False
|
||||
:rtype: bool
|
||||
|
||||
>>> is_executable('/bin/ls')
|
||||
True
|
||||
>>> is_executable('/var/log/system.log')
|
||||
False
|
||||
"""
|
||||
return os.path.isfile(fn) and os.access(fn, os.X_OK)
|
||||
|
||||
@ -539,24 +584,36 @@ def isSorted(iterable):
|
||||
>>> isSorted([2,3,1,4])
|
||||
False
|
||||
"""
|
||||
assert isIterable(iterable), 'object is not iterable; object: {' \
|
||||
'}'.format(iterable)
|
||||
assert is_iterable(iterable), "object is not iterable; object: {}".format(iterable)
|
||||
if type(iterable) is str:
|
||||
iterable = [s for s in iterable]
|
||||
return sorted(iterable) == iterable
|
||||
|
||||
|
||||
def isIterable(obj):
|
||||
def is_iterable(obj):
|
||||
"""
|
||||
takes a python object and returns True is the object is iterable and
|
||||
False otherwise
|
||||
:param obj: a python object
|
||||
:type obj: object
|
||||
:type obj: obj
|
||||
:return: True of False
|
||||
:rtype: bool
|
||||
|
||||
>>> is_iterable(1)
|
||||
False
|
||||
>>> is_iterable(True)
|
||||
False
|
||||
>>> is_iterable(0.)
|
||||
False
|
||||
>>> is_iterable((0,1,3,4))
|
||||
True
|
||||
>>> is_iterable([1])
|
||||
True
|
||||
>>> is_iterable('a')
|
||||
True
|
||||
"""
|
||||
try:
|
||||
iterator = iter(obj)
|
||||
iter(obj)
|
||||
except TypeError as te:
|
||||
return False
|
||||
return True
|
||||
@ -565,13 +622,19 @@ def isIterable(obj):
|
||||
def key_for_set_value(d):
|
||||
"""
|
||||
takes a dictionary and returns the first key for which's value the
|
||||
boolean is True
|
||||
boolean representation is True
|
||||
:param d: dictionary containing values
|
||||
:type d: dict
|
||||
:return: key to the first non-False value found; None if no value's
|
||||
boolean equals True
|
||||
:rtype:
|
||||
:rtype: bool or NoneType
|
||||
|
||||
>>> key_for_set_value({'one': 0, 'two': 1})
|
||||
'two'
|
||||
>>> print(key_for_set_value({1: 0, 2: False}))
|
||||
None
|
||||
"""
|
||||
assert type(d) is dict, "Function only defined for inputs of type 'dict'."
|
||||
r = None
|
||||
for k, v in d.items():
|
||||
if v:
|
||||
@ -579,32 +642,53 @@ def key_for_set_value(d):
|
||||
return r
|
||||
|
||||
|
||||
def prepTimeAxis(stime, trace, verbosity=0):
|
||||
def prep_time_axis(offset, trace, verbosity=0):
|
||||
"""
|
||||
takes a starttime and a trace object and returns a valid time axis for
|
||||
takes an offset and a trace object and returns a valid time axis for
|
||||
plotting
|
||||
:param stime: start time of the actual seismogram as UTCDateTime
|
||||
:type stime: `~obspy.core.utcdatetime.UTCDateTime`
|
||||
:param offset: offset of the actual seismogram on plotting axis
|
||||
:type offset: float or int
|
||||
:param trace: seismic trace object
|
||||
:type trace: `~obspy.core.trace.Trace`
|
||||
:param verbosity: if != 0, debug output will be written to console
|
||||
:type verbosity: int
|
||||
:return: valid numpy array with time stamps for plotting
|
||||
:rtype: `~numpy.ndarray`
|
||||
|
||||
>>> tr = read()[0]
|
||||
>>> prep_time_axis(0., tr)
|
||||
array([0.00000000e+00, 1.00033344e-02, 2.00066689e-02, ...,
|
||||
2.99799933e+01, 2.99899967e+01, 3.00000000e+01])
|
||||
>>> prep_time_axis(22.5, tr)
|
||||
array([22.5 , 22.51000333, 22.52000667, ..., 52.47999333,
|
||||
52.48999667, 52.5 ])
|
||||
>>> prep_time_axis(tr.stats.starttime, tr)
|
||||
Traceback (most recent call last):
|
||||
...
|
||||
AssertionError: 'offset' is not of type 'float' or 'int'; type: <class 'obspy.core.utcdatetime.UTCDateTime'>
|
||||
>>> tr.stats.npts -= 1
|
||||
>>> prep_time_axis(0, tr)
|
||||
array([0.00000000e+00, 1.00033356e-02, 2.00066711e-02, ...,
|
||||
2.99699933e+01, 2.99799967e+01, 2.99900000e+01])
|
||||
>>> tr.stats.npts += 2
|
||||
>>> prep_time_axis(0, tr)
|
||||
array([0.00000000e+00, 1.00033333e-02, 2.00066667e-02, ...,
|
||||
2.99899933e+01, 2.99999967e+01, 3.00100000e+01])
|
||||
"""
|
||||
assert isinstance(offset, (float, int)), "'offset' is not of type 'float' or 'int'; type: {}".format(type(offset))
|
||||
nsamp = trace.stats.npts
|
||||
srate = trace.stats.sampling_rate
|
||||
tincr = trace.stats.delta
|
||||
etime = stime + nsamp / srate
|
||||
time_ax = np.linspace(stime, etime, nsamp)
|
||||
etime = offset + nsamp / srate
|
||||
time_ax = np.linspace(offset, etime, nsamp)
|
||||
if len(time_ax) < nsamp:
|
||||
if verbosity:
|
||||
print('elongate time axes by one datum')
|
||||
time_ax = np.arange(stime, etime + tincr, tincr)
|
||||
time_ax = np.arange(offset, etime + tincr, tincr)
|
||||
elif len(time_ax) > nsamp:
|
||||
if verbosity:
|
||||
print('shorten time axes by one datum')
|
||||
time_ax = np.arange(stime, etime - tincr, tincr)
|
||||
time_ax = np.arange(offset, etime - tincr, tincr)
|
||||
if len(time_ax) != nsamp:
|
||||
print('Station {0}, {1} samples of data \n '
|
||||
'{2} length of time vector \n'
|
||||
@ -620,13 +704,13 @@ def find_horizontals(data):
|
||||
:param data: waveform data
|
||||
:type data: `obspy.core.stream.Stream`
|
||||
:return: components list
|
||||
:rtype: list
|
||||
:rtype: List(str)
|
||||
|
||||
..example::
|
||||
|
||||
>>> st = read()
|
||||
>>> find_horizontals(st)
|
||||
[u'N', u'E']
|
||||
['N', 'E']
|
||||
"""
|
||||
rval = []
|
||||
for tr in data:
|
||||
@ -637,7 +721,7 @@ def find_horizontals(data):
|
||||
return rval
|
||||
|
||||
|
||||
def pick_color(picktype, phase, quality=0):
|
||||
def pick_color(picktype: Literal['manual', 'automatic'], phase: Literal['P', 'S'], quality: int = 0) -> Rgba:
|
||||
"""
|
||||
Create pick color by modifying the base color by the quality.
|
||||
|
||||
@ -650,7 +734,7 @@ def pick_color(picktype, phase, quality=0):
|
||||
:param quality: quality of pick. Decides the new intensity of the modifier color
|
||||
:type quality: int
|
||||
:return: tuple containing modified rgba color values
|
||||
:rtype: (int, int, int, int)
|
||||
:rtype: Rgba
|
||||
"""
|
||||
min_quality = 3
|
||||
bpc = base_phase_colors(picktype, phase) # returns dict like {'modifier': 'g', 'rgba': (0, 0, 255, 255)}
|
||||
@ -706,17 +790,17 @@ def pick_linestyle_plt(picktype, key):
|
||||
return linestyles[picktype][key]
|
||||
|
||||
|
||||
def modify_rgba(rgba, modifier, intensity):
|
||||
def modify_rgba(rgba: Rgba, modifier: Literal['r', 'g', 'b'], intensity: float) -> Rgba:
|
||||
"""
|
||||
Modify rgba color by adding the given intensity to the modifier color
|
||||
:param rgba: tuple containing rgba values
|
||||
:type rgba: (int, int, int, int)
|
||||
:param modifier: which color should be modified, eg. 'r', 'g', 'b'
|
||||
:type modifier: str
|
||||
:type rgba: Rgba
|
||||
:param modifier: which color should be modified; options: 'r', 'g', 'b'
|
||||
:type modifier: Literal['r', 'g', 'b']
|
||||
:param intensity: intensity to be added to selected color
|
||||
:type intensity: float
|
||||
:return: tuple containing rgba values
|
||||
:rtype: (int, int, int, int)
|
||||
:rtype: Rgba
|
||||
"""
|
||||
rgba = list(rgba)
|
||||
index = {'r': 0,
|
||||
@ -750,18 +834,20 @@ def transform_colors_mpl_str(colors, no_alpha=False):
|
||||
Transforms rgba color values to a matplotlib string of color values with a range of [0, 1]
|
||||
:param colors: tuple of rgba color values ranging from [0, 255]
|
||||
:type colors: (float, float, float, float)
|
||||
:param no_alpha: Wether to return a alpha value in the matplotlib color string
|
||||
:param no_alpha: Whether to return an alpha value in the matplotlib color string
|
||||
:type no_alpha: bool
|
||||
:return: String containing r, g, b values and alpha value if no_alpha is False (default)
|
||||
:rtype: str
|
||||
|
||||
>>> transform_colors_mpl_str((255., 255., 255., 255.), True)
|
||||
'(1.0, 1.0, 1.0)'
|
||||
>>> transform_colors_mpl_str((255., 255., 255., 255.))
|
||||
'(1.0, 1.0, 1.0, 1.0)'
|
||||
"""
|
||||
colors = list(colors)
|
||||
colors_mpl = tuple([color / 255. for color in colors])
|
||||
if no_alpha:
|
||||
colors_mpl = '({}, {}, {})'.format(*colors_mpl)
|
||||
return '({}, {}, {})'.format(*transform_colors_mpl(colors))
|
||||
else:
|
||||
colors_mpl = '({}, {}, {}, {})'.format(*colors_mpl)
|
||||
return colors_mpl
|
||||
return '({}, {}, {}, {})'.format(*transform_colors_mpl(colors))
|
||||
|
||||
|
||||
def transform_colors_mpl(colors):
|
||||
@ -771,27 +857,16 @@ def transform_colors_mpl(colors):
|
||||
:type colors: (float, float, float, float)
|
||||
:return: tuple of rgba color values ranging from [0, 1]
|
||||
:rtype: (float, float, float, float)
|
||||
|
||||
>>> transform_colors_mpl((127.5, 0., 63.75, 255.))
|
||||
(0.5, 0.0, 0.25, 1.0)
|
||||
>>> transform_colors_mpl(())
|
||||
"""
|
||||
colors = list(colors)
|
||||
colors_mpl = tuple([color / 255. for color in colors])
|
||||
return colors_mpl
|
||||
|
||||
|
||||
def remove_underscores(data):
|
||||
"""
|
||||
takes a `obspy.core.stream.Stream` object and removes all underscores
|
||||
from station names
|
||||
:param data: stream of seismic data
|
||||
:type data: `~obspy.core.stream.Stream`
|
||||
:return: data stream
|
||||
:rtype: `~obspy.core.stream.Stream`
|
||||
"""
|
||||
# for tr in data:
|
||||
# # remove underscores
|
||||
# tr.stats.station = tr.stats.station.strip('_')
|
||||
return data
|
||||
|
||||
|
||||
def trim_station_components(data, trim_start=True, trim_end=True):
|
||||
"""
|
||||
cut a stream so only the part common to all three traces is kept to avoid dealing with offsets
|
||||
@ -928,11 +1003,11 @@ def get_possible_pylot_eventfile_extensions(event, fext):
|
||||
|
||||
def get_stations(data):
|
||||
"""
|
||||
Get list of all station names in data stream
|
||||
Get list of all station names in data-stream
|
||||
:param data: stream containing seismic traces
|
||||
:type data: `~obspy.core.stream.Stream`
|
||||
:return: list of all station names in data, no duplicates
|
||||
:rtype: list of str
|
||||
:rtype: List(str)
|
||||
"""
|
||||
stations = []
|
||||
for tr in data:
|
||||
@ -959,66 +1034,87 @@ def check4rotated(data, metadata=None, verbosity=1):
|
||||
:rtype: `~obspy.core.stream.Stream`
|
||||
"""
|
||||
|
||||
def rotate_components(wfstream, metadata=None):
|
||||
def rotation_required(trace_ids):
|
||||
"""
|
||||
Derive if any rotation is required from the orientation code of the input.
|
||||
|
||||
:param trace_ids: string identifier of waveform data trace
|
||||
:type trace_ids: List(str)
|
||||
:return: boolean representing if rotation is necessary for any of the traces
|
||||
:rtype: bool
|
||||
"""
|
||||
orientations = [trace_id[-1] for trace_id in trace_ids]
|
||||
return any([orientation.isnumeric() for orientation in orientations])
|
||||
|
||||
def rotate_components(wfs_in, metadata=None):
|
||||
"""
|
||||
Rotate components if orientation code is numeric (= non traditional orientation).
|
||||
|
||||
Azimut and dip are fetched from metadata. To be rotated, traces of a station have to be cut to the same length.
|
||||
Returns unrotated traces of no metadata is provided
|
||||
:param wfstream: stream containing seismic traces of a station
|
||||
:type wfstream: `~obspy.core.stream.Stream`
|
||||
:param wfs_in: stream containing seismic traces of a station
|
||||
:type wfs_in: `~obspy.core.stream.Stream`
|
||||
:param metadata: tuple containing metadata type string and metadata parser object
|
||||
:type metadata: (str, `~obspy.io.xseed.parser.Parser`)
|
||||
:return: stream object with traditionally oriented traces (ZNE)
|
||||
:rtype: `~obspy.core.stream.Stream`
|
||||
"""
|
||||
|
||||
# check if any traces in this station need to be rotated
|
||||
trace_ids = [trace.id for trace in wfstream]
|
||||
orientations = [trace_id[-1] for trace_id in trace_ids]
|
||||
rotation_required = [orientation.isnumeric() for orientation in orientations]
|
||||
if any(rotation_required):
|
||||
t_start = full_range(wfstream)
|
||||
try:
|
||||
azimuts = []
|
||||
dips = []
|
||||
for tr_id in trace_ids:
|
||||
azimuts.append(metadata.get_coordinates(tr_id, t_start)['azimuth'])
|
||||
dips.append(metadata.get_coordinates(tr_id, t_start)['dip'])
|
||||
except (KeyError, TypeError) as e:
|
||||
print('Failed to rotate trace {}, no azimuth or dip available in metadata'.format(tr_id))
|
||||
return wfstream
|
||||
if len(wfstream) < 3:
|
||||
print('Failed to rotate Stream {}, not enough components available.'.format(wfstream))
|
||||
return wfstream
|
||||
# to rotate all traces must have same length, so trim them
|
||||
wfstream = trim_station_components(wfstream, trim_start=True, trim_end=True)
|
||||
try:
|
||||
z, n, e = rotate2zne(wfstream[0], azimuts[0], dips[0],
|
||||
wfstream[1], azimuts[1], dips[1],
|
||||
wfstream[2], azimuts[2], dips[2])
|
||||
print('check4rotated: rotated trace {} to ZNE'.format(trace_ids))
|
||||
# replace old data with rotated data, change the channel code to ZNE
|
||||
z_index = dips.index(min(
|
||||
dips)) # get z-trace index, z has minimum dip of -90 (dip is measured from 0 to -90, with -90 being vertical)
|
||||
wfstream[z_index].data = z
|
||||
wfstream[z_index].stats.channel = wfstream[z_index].stats.channel[0:-1] + 'Z'
|
||||
del trace_ids[z_index]
|
||||
for trace_id in trace_ids:
|
||||
coordinates = metadata.get_coordinates(trace_id, t_start)
|
||||
dip, az = coordinates['dip'], coordinates['azimuth']
|
||||
trace = wfstream.select(id=trace_id)[0]
|
||||
if az > 315 or az <= 45 or az > 135 and az <= 225:
|
||||
trace.data = n
|
||||
trace.stats.channel = trace.stats.channel[0:-1] + 'N'
|
||||
elif az > 45 and az <= 135 or az > 225 and az <= 315:
|
||||
trace.data = e
|
||||
trace.stats.channel = trace.stats.channel[0:-1] + 'E'
|
||||
except (ValueError) as e:
|
||||
print(e)
|
||||
return wfstream
|
||||
if len(wfs_in) < 3:
|
||||
print(f"Stream {wfs_in=}, has not enough components to rotate.")
|
||||
return wfs_in
|
||||
|
||||
return wfstream
|
||||
# check if any traces in this station need to be rotated
|
||||
trace_ids = [trace.id for trace in wfs_in]
|
||||
if not rotation_required(trace_ids):
|
||||
print(f"Stream does not need any rotation: Traces are {trace_ids=}")
|
||||
return wfs_in
|
||||
|
||||
# check metadata quality
|
||||
t_start = full_range(wfs_in)
|
||||
try:
|
||||
azimuths = []
|
||||
dips = []
|
||||
for tr_id in trace_ids:
|
||||
azimuths.append(metadata.get_coordinates(tr_id, t_start)['azimuth'])
|
||||
dips.append(metadata.get_coordinates(tr_id, t_start)['dip'])
|
||||
except (KeyError, TypeError) as err:
|
||||
print(f"{type(err)=} occurred: {err=} Rotating not possible, not all azimuth and dip information "
|
||||
f"available in metadata. Stream remains unchanged.")
|
||||
return wfs_in
|
||||
except Exception as err:
|
||||
print(f"Unexpected {err=}, {type(err)=}")
|
||||
raise
|
||||
|
||||
# to rotate all traces must have same length, so trim them
|
||||
wfs_out = trim_station_components(wfs_in, trim_start=True, trim_end=True)
|
||||
try:
|
||||
z, n, e = rotate2zne(wfs_out[0], azimuths[0], dips[0],
|
||||
wfs_out[1], azimuths[1], dips[1],
|
||||
wfs_out[2], azimuths[2], dips[2])
|
||||
print('check4rotated: rotated trace {} to ZNE'.format(trace_ids))
|
||||
# replace old data with rotated data, change the channel code to ZNE
|
||||
z_index = dips.index(min(
|
||||
dips)) # get z-trace index, z has minimum dip of -90 (dip is measured from 0 to -90, with -90
|
||||
# being vertical)
|
||||
wfs_out[z_index].data = z
|
||||
wfs_out[z_index].stats.channel = wfs_out[z_index].stats.channel[0:-1] + 'Z'
|
||||
del trace_ids[z_index]
|
||||
for trace_id in trace_ids:
|
||||
coordinates = metadata.get_coordinates(trace_id, t_start)
|
||||
dip, az = coordinates['dip'], coordinates['azimuth']
|
||||
trace = wfs_out.select(id=trace_id)[0]
|
||||
if az > 315 or az <= 45 or 135 < az <= 225:
|
||||
trace.data = n
|
||||
trace.stats.channel = trace.stats.channel[0:-1] + 'N'
|
||||
elif 45 < az <= 135 or 225 < az <= 315:
|
||||
trace.data = e
|
||||
trace.stats.channel = trace.stats.channel[0:-1] + 'E'
|
||||
except ValueError as err:
|
||||
print(f"{err=} Rotation failed. Stream remains unchanged.")
|
||||
return wfs_in
|
||||
|
||||
return wfs_out
|
||||
|
||||
if metadata is None:
|
||||
if verbosity:
|
||||
@ -1032,38 +1128,6 @@ def check4rotated(data, metadata=None, verbosity=1):
|
||||
return data
|
||||
|
||||
|
||||
def scaleWFData(data, factor=None, components='all'):
|
||||
"""
|
||||
produce scaled waveforms from given waveform data and a scaling factor,
|
||||
waveform may be selected by their components name
|
||||
:param data: waveform data to be scaled
|
||||
:type data: `~obspy.core.stream.Stream` object
|
||||
:param factor: scaling factor
|
||||
:type factor: float
|
||||
:param components: components labels for the traces in data to be scaled by
|
||||
the scaling factor (optional, default: 'all')
|
||||
:type components: tuple
|
||||
:return: scaled waveform data
|
||||
:rtype: `~obspy.core.stream.Stream` object
|
||||
"""
|
||||
if components != 'all':
|
||||
for comp in components:
|
||||
if factor is None:
|
||||
max_val = np.max(np.abs(data.select(component=comp)[0].data))
|
||||
data.select(component=comp)[0].data /= 2 * max_val
|
||||
else:
|
||||
data.select(component=comp)[0].data /= 2 * factor
|
||||
else:
|
||||
for tr in data:
|
||||
if factor is None:
|
||||
max_val = float(np.max(np.abs(tr.data)))
|
||||
tr.data /= 2 * max_val
|
||||
else:
|
||||
tr.data /= 2 * factor
|
||||
|
||||
return data
|
||||
|
||||
|
||||
def runProgram(cmd, parameter=None):
|
||||
"""
|
||||
run an external program specified by cmd with parameters input returning the
|
||||
|
||||
@ -7,6 +7,7 @@ Created on Wed Mar 19 11:27:35 2014
|
||||
import copy
|
||||
import datetime
|
||||
import getpass
|
||||
import glob
|
||||
import multiprocessing
|
||||
import os
|
||||
import subprocess
|
||||
@ -16,6 +17,7 @@ import traceback
|
||||
|
||||
import matplotlib
|
||||
import numpy as np
|
||||
from pylot.core.io.phases import getQualitiesfromxml
|
||||
|
||||
matplotlib.use('QT5Agg')
|
||||
|
||||
@ -49,11 +51,11 @@ from pylot.core.pick.utils import getSNR, earllatepicker, getnoisewin, \
|
||||
from pylot.core.pick.compare import Comparison
|
||||
from pylot.core.pick.autopick import fmpicker
|
||||
from pylot.core.util.defaults import OUTPUTFORMATS, FILTERDEFAULTS
|
||||
from pylot.core.util.utils import prepTimeAxis, full_range, demeanTrace, isSorted, findComboBoxIndex, clims, \
|
||||
from pylot.core.util.utils import prep_time_axis, full_range, demeanTrace, isSorted, findComboBoxIndex, clims, \
|
||||
pick_linestyle_plt, pick_color_plt, \
|
||||
check4rotated, check4doubled, check_for_gaps_and_merge, check_for_nan, identifyPhase, \
|
||||
loopIdentifyPhase, trim_station_components, transformFilteroptions2String, \
|
||||
identifyPhaseID, get_bool, get_None, pick_color, getAutoFilteroptions, SetChannelComponents, \
|
||||
identifyPhaseID, get_bool, get_none, pick_color, getAutoFilteroptions, SetChannelComponents, \
|
||||
station_id_remove_channel, get_pylot_eventfile_with_extension, get_possible_pylot_eventfile_extensions
|
||||
from autoPyLoT import autoPyLoT
|
||||
from pylot.core.util.thread import Thread
|
||||
@ -936,10 +938,10 @@ class WaveformWidgetPG(QtWidgets.QWidget):
|
||||
msg = 'plotting %s channel of station %s' % (channel, station)
|
||||
print(msg)
|
||||
stime = trace.stats.starttime - self.wfstart
|
||||
time_ax = prepTimeAxis(stime, trace)
|
||||
time_ax = prep_time_axis(stime, trace)
|
||||
if st_syn:
|
||||
stime_syn = trace_syn.stats.starttime - self.wfstart
|
||||
time_ax_syn = prepTimeAxis(stime_syn, trace_syn)
|
||||
time_ax_syn = prep_time_axis(stime_syn, trace_syn)
|
||||
|
||||
if method == 'fast':
|
||||
trace.data, time_ax = self.minMax(trace, time_ax)
|
||||
@ -1422,7 +1424,7 @@ class PylotCanvas(FigureCanvas):
|
||||
msg = 'plotting %s channel of station %s' % (channel, station)
|
||||
print(msg)
|
||||
stime = trace.stats.starttime - wfstart
|
||||
time_ax = prepTimeAxis(stime, trace)
|
||||
time_ax = prep_time_axis(stime, trace)
|
||||
if time_ax is not None:
|
||||
if scaleToChannel:
|
||||
st_scale = wfdata.select(channel=scaleToChannel)
|
||||
@ -1460,7 +1462,7 @@ class PylotCanvas(FigureCanvas):
|
||||
if not scaleddata:
|
||||
trace.detrend('constant')
|
||||
trace.normalize(np.max(np.abs(trace.data)) * 2)
|
||||
time_ax = prepTimeAxis(stime, trace)
|
||||
time_ax = prep_time_axis(stime, trace)
|
||||
times = [time for index, time in enumerate(time_ax) if not index % nth_sample]
|
||||
p_data = compare_stream[0].data
|
||||
# #normalize
|
||||
@ -2267,7 +2269,7 @@ class PickDlg(QDialog):
|
||||
|
||||
# create action and add to menu
|
||||
# phase name transferred using lambda function
|
||||
slot = lambda phase=phase, phaseID=phaseID: phaseSelect[phaseID](phase)
|
||||
slot = lambda ph=phase, phID=phaseID: phaseSelect[phID](ph)
|
||||
picksAction = createAction(parent=self, text=phase,
|
||||
slot=slot,
|
||||
shortcut=shortcut)
|
||||
@ -2671,7 +2673,7 @@ class PickDlg(QDialog):
|
||||
|
||||
# prepare plotting of data
|
||||
for trace in data:
|
||||
t = prepTimeAxis(trace.stats.starttime - stime, trace)
|
||||
t = prep_time_axis(trace.stats.starttime - stime, trace)
|
||||
inoise = getnoisewin(t, ini_pick, noise_win, gap_win)
|
||||
trace = demeanTrace(trace, inoise)
|
||||
# upscale trace data in a way that each trace is vertically zoomed to noiselevel*factor
|
||||
@ -4794,8 +4796,8 @@ class InputsTab(PropTab):
|
||||
self.tstopBox = QSpinBox()
|
||||
for spinbox in [self.tstartBox, self.tstopBox]:
|
||||
spinbox.setRange(-99999, 99999)
|
||||
self.tstartBox.setValue(float(settings.value('tstart')) if get_None(settings.value('tstart')) else 0)
|
||||
self.tstopBox.setValue(float(settings.value('tstop')) if get_None(settings.value('tstop')) else 1e6)
|
||||
self.tstartBox.setValue(float(settings.value('tstart')) if get_none(settings.value('tstart')) else 0)
|
||||
self.tstopBox.setValue(float(settings.value('tstop')) if get_none(settings.value('tstop')) else 1e6)
|
||||
self.cuttimesLayout.addWidget(self.tstartBox, 10)
|
||||
self.cuttimesLayout.addWidget(QLabel('[s] and'), 0)
|
||||
self.cuttimesLayout.addWidget(self.tstopBox, 10)
|
||||
@ -5791,7 +5793,7 @@ class ChooseWaveFormWindow(QWidget):
|
||||
#self.currentSpectro = self.traces[
|
||||
# self.chooseBoxTraces.currentText()[3:]][self.chooseBoxComponent.currentText()].spectrogram(show=False, title=t)
|
||||
#self.currentSpectro.show()
|
||||
applyFFT()
|
||||
self.applyFFT()
|
||||
|
||||
def applyFFT(self, trace):
|
||||
tra = self.traces[self.chooseBoxTraces.currentText()[3:]]['Z']
|
||||
|
||||
Loading…
Reference in New Issue
Block a user