marcel/pylot
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Merge branch 'develop' into feature/documentation

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Darius Arnold 2018-11-30 10:27:42 +01:00
commit 0964139799
20 changed files with 303 additions and 144 deletions
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117
PyLoT.py
View File

@ -24,12 +24,11 @@ https://www.iconfinder.com/iconsets/flavour
"""
import argparse
import matplotlib
import os
import platform
import sys
import matplotlib
matplotlib.use('Qt4Agg')
matplotlib.rcParams['backend.qt4'] = 'PySide'
matplotlib.rcParams['savefig.dpi'] = 300
@ -40,8 +39,8 @@ from PySide.QtCore import QCoreApplication, QSettings, Signal, QFile, \
QFileInfo, Qt, QSize
from PySide.QtGui import QMainWindow, QInputDialog, QIcon, QFileDialog, \
QWidget, QHBoxLayout, QVBoxLayout, QStyle, QKeySequence, QLabel, QFrame, QAction, \
QDialog, QErrorMessage, QApplication, QPixmap, QMessageBox, QSplashScreen, \
QActionGroup, QListWidget, QLineEdit, QListView, QAbstractItemView, \
QDialog, QApplication, QPixmap, QMessageBox, QSplashScreen, \
QActionGroup, QListWidget, QListView, QAbstractItemView, \
QTreeView, QComboBox, QTabWidget, QPushButton, QGridLayout
import numpy as np
from obspy import UTCDateTime
@ -56,7 +55,6 @@ try:
from matplotlib.backends.backend_qt4agg import FigureCanvas
except ImportError:
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar
from matplotlib.figure import Figure
from pylot.core.analysis.magnitude import LocalMagnitude, MomentMagnitude
@ -64,24 +62,23 @@ from pylot.core.io.data import Data
from pylot.core.io.inputs import FilterOptions, PylotParameter
from autoPyLoT import autoPyLoT
from pylot.core.pick.compare import Comparison
from pylot.core.pick.utils import symmetrize_error, getQualityFromUncertainty, getPickQuality
from pylot.core.pick.utils import getQualityFromUncertainty
from pylot.core.io.phases import picksdict_from_picks
import pylot.core.loc.nll as nll
from pylot.core.util.defaults import FILTERDEFAULTS
from pylot.core.util.errors import DatastructureError, \
OverwriteError
from pylot.core.util.connection import checkurl
from pylot.core.util.dataprocessing import Metadata, restitute_data
from pylot.core.util.utils import fnConstructor, getLogin, \
full_range, readFilterInformation, trim_station_components, check4gaps, make_pen, pick_color_plt, \
pick_linestyle_plt, remove_underscores, check4doubled, identifyPhaseID, excludeQualityClasses, \
check4rotated, transform_colors_mpl, transform_colors_mpl_str, getAutoFilteroptions, check_all_obspy, \
full_range, readFilterInformation, make_pen, pick_color_plt, \
pick_linestyle_plt, identifyPhaseID, excludeQualityClasses, \
transform_colors_mpl, transform_colors_mpl_str, getAutoFilteroptions, check_all_obspy, \
check_all_pylot, real_Bool, SetChannelComponents
from pylot.core.util.event import Event
from pylot.core.io.location import create_creation_info, create_event
from pylot.core.util.widgets import FilterOptionsDialog, NewEventDlg, \
PylotCanvas, WaveformWidgetPG, PropertiesDlg, HelpForm, createAction, PickDlg, \
getDataType, ComparisonWidget, TuneAutopicker, PylotParaBox, AutoPickDlg, CanvasWidget, AutoPickWidget, \
ComparisonWidget, TuneAutopicker, PylotParaBox, AutoPickDlg, CanvasWidget, AutoPickWidget, \
CompareEventsWidget, ProgressBarWidget, AddMetadataWidget
from pylot.core.util.array_map import Array_map
from pylot.core.util.structure import DATASTRUCTURE
@ -97,6 +94,9 @@ elif sys.version_info.major == 2:
else:
raise ImportError('Could not determine python version.')
# workaround to prevent PyCharm from deleting icons_rc import when optimizing imports
icons_rc = icons_rc
locateTool = dict(nll=nll)
@ -155,6 +155,9 @@ class MainWindow(QMainWindow):
self.data._new = False
self.autodata = Data(self)
self.fnames = None
self._stime = None
while True:
try:
if settings.value("user/FullName", None) is None:
@ -166,6 +169,27 @@ class MainWindow(QMainWindow):
"Enter authority/institution name:",
"Authority")
settings.setValue("agency_id", agency)
structure_setting = settings.value("data/Structure", "PILOT")
if not structure_setting:
structure_setting = 'PILOT'
self.dataStructure = DATASTRUCTURE[structure_setting]()
self.seismicPhase = str(settings.value("phase", "P"))
if settings.value("data/dataRoot", None) is None:
dirname = QFileDialog().getExistingDirectory(
caption='Choose data root ...')
settings.setValue("data/dataRoot", dirname)
if settings.value('compclass', None) is None:
settings.setValue('compclass', SetChannelComponents())
if settings.value('useGuiFilter') is None:
settings.setValue('useGuiFilter', False)
if settings.value('output/Format', None) is None:
outformat = QInputDialog.getText(self,
"Enter output format (*.xml, *.cnv, *.obs):",
"Format")
settings.setValue("output/Format", outformat)
if settings.value('autoFilter', None) is None:
settings.setValue('autoFilter', True)
settings.sync()
break
except Exception as e:
qmb = QMessageBox(self, icon=QMessageBox.Question,
@ -181,30 +205,6 @@ class MainWindow(QMainWindow):
sys.exit()
print('Settings cleared!')
self.fnames = None
self._stime = None
structure_setting = settings.value("data/Structure", "PILOT")
if not structure_setting:
structure_setting = 'PILOT'
self.dataStructure = DATASTRUCTURE[structure_setting]()
self.seismicPhase = str(settings.value("phase", "P"))
if settings.value("data/dataRoot", None) is None:
dirname = QFileDialog().getExistingDirectory(
caption='Choose data root ...')
settings.setValue("data/dataRoot", dirname)
if settings.value('compclass', None) is None:
settings.setValue('compclass', SetChannelComponents())
if settings.value('useGuiFilter') is None:
settings.setValue('useGuiFilter', False)
if settings.value('output/Format', None) is None:
outformat = QInputDialog.getText(self,
"Enter output format (*.xml, *.cnv, *.obs):",
"Format")
settings.setValue("output/Format", outformat)
if settings.value('autoFilter', None) is None:
settings.setValue('autoFilter', True)
settings.sync()
# setup UI
self.setupUi()
@ -542,6 +542,7 @@ class MainWindow(QMainWindow):
self.updateFileMenu()
self.editMenu = self.menuBar().addMenu('&Edit')
editActions = (self.filterActionP, self.filterActionS, filterEditAction, None,
# self.selectPAction, self.selectSAction, None,
self.inventoryAction, self.initMapAction, None,
@ -553,6 +554,7 @@ class MainWindow(QMainWindow):
self.autoPickMenu = self.pickMenu.addMenu(self.autopicksicon_small, 'Automatic picking')
self.autoPickMenu.setEnabled(False)
autoPickActions = (self.auto_pick, self.auto_pick_local, self.auto_pick_sge)
self.helpMenu = self.menuBar().addMenu('&Help')
@ -685,6 +687,7 @@ class MainWindow(QMainWindow):
self.setCentralWidget(_widget)
def init_wfWidget(self):
xlab = self.startTime.strftime('seconds since %Y/%m/%d %H:%M:%S (%Z)')
plottitle = None # "Overview: {0} components ".format(self.getComponent())
@ -830,8 +833,9 @@ class MainWindow(QMainWindow):
s_filter['order'])}
def updateFileMenu(self):
settings = QSettings()
self.fileMenu.clear()
self.recentProjectsMenu = self.fileMenu.addMenu('Recent Projects')
for action in self.fileMenuActions[:-1]:
if action is None:
self.fileMenu.addSeparator()
@ -848,7 +852,6 @@ class MainWindow(QMainWindow):
recentEvents.append(eventID)
recentEvents.reverse()
self.recentfiles = recentEvents[0:5]
settings = QSettings()
settings.setValue()
if recentEvents:
for i, eventID in enumerate(recentEvents):
@ -864,6 +867,18 @@ class MainWindow(QMainWindow):
self.fileMenu.addSeparator()
self.fileMenu.addAction(self.fileMenuActions[-1])
# add recent projects
recentProjects = settings.value('recentProjects', [])
if not type(recentProjects) == list:
recentProjects = [recentProjects]
for project in reversed(recentProjects):
action = self.createAction(self, project,
lambda fnm=project: self.loadProject(fnm),
None, None)
self.recentProjectsMenu.addAction(action)
@property
def inputs(self):
return self._inputs
@ -3273,10 +3288,13 @@ class MainWindow(QMainWindow):
return
if not fnm:
dlg = QFileDialog(parent=self)
fnm = dlg.getOpenFileName(self, 'Open project file...', filter='Pylot project (*.plp)')
fnm = dlg.getOpenFileName(self, 'Open project file...', filter='Pylot project (*.plp)')[0]
if not fnm:
return
fnm = fnm[0]
if not os.path.exists(fnm):
QMessageBox.warning(self, 'Could not open file',
'Could not open project file {}. File does not exist.'.format(fnm))
return
if fnm:
self.project = Project.load(fnm)
if hasattr(self.project, 'parameter'):
@ -3292,8 +3310,24 @@ class MainWindow(QMainWindow):
self.setDirty(False)
self.init_metadata()
message = 'Opened project file {}.'.format(fnm)
print(message)
self.update_status(message)
self.init_array_tab()
self.set_metadata()
self.add2recentProjects(fnm)
def add2recentProjects(self, fnm):
settings = QtCore.QSettings()
recent = settings.value('recentProjects', [])
if not type(recent) == list:
recent = [recent]
if not fnm in recent:
recent.append(fnm)
new_recent = recent[-5:]
settings.setValue('recentProjects', new_recent)
settings.sync()
def saveProjectAs(self, exists=False):
'''
@ -3312,6 +3346,7 @@ class MainWindow(QMainWindow):
self.setDirty(False)
self.saveProjectAsAction.setEnabled(True)
self.update_status('Saved new project to {}'.format(filename), duration=5000)
self.add2recentProjects(filename)
return True
def saveProject(self, new=False):
@ -3445,7 +3480,7 @@ class Project(object):
eventID, date, time, mag, lat, lon, depth = line.split(separator)[:7]
# skip first line
try:
month, day, year = date.split('/')
day, month, year = date.split('/')
except:
continue
year = int(year)
@ -3459,7 +3494,7 @@ class Project(object):
print(e, datetime, filename)
continue
for event in self.eventlist:
if eventID in str(event.resource_id) or event.origins:
if eventID in str(event.resource_id) or eventID in event.origins:
if event.origins:
origin = event.origins[0] # should have only one origin
if origin.time == datetime:

8
autoPyLoT.py
View File

@ -8,6 +8,8 @@ import datetime
import glob
import os
import traceback
from obspy import read_events
from obspy.core.event import ResourceIdentifier
import pylot.core.loc.focmec as focmec
import pylot.core.loc.hash as hash
@ -16,18 +18,16 @@ import pylot.core.loc.hypodd as hypodd
import pylot.core.loc.hyposat as hyposat
import pylot.core.loc.nll as nll
import pylot.core.loc.velest as velest
from obspy import read_events
from obspy.core.event import ResourceIdentifier
# from PySide.QtGui import QWidget, QInputDialog
from pylot.core.analysis.magnitude import MomentMagnitude, LocalMagnitude
from pylot.core.io.data import Data
from pylot.core.io.inputs import PylotParameter
from pylot.core.pick.autopick import autopickevent, iteratepicker
from pylot.core.util.dataprocessing import restitute_data, read_metadata, Metadata
from pylot.core.util.dataprocessing import restitute_data, Metadata
from pylot.core.util.defaults import SEPARATOR
from pylot.core.util.event import Event
from pylot.core.util.structure import DATASTRUCTURE
from pylot.core.util.utils import real_None, remove_underscores, trim_station_components, check4gaps, check4doubled, \
from pylot.core.util.utils import real_None, trim_station_components, check4gaps, check4doubled, \
check4rotated
from pylot.core.util.version import get_git_version as _getVersionString

5
pylot/core/analysis/magnitude.py
View File

@ -11,11 +11,12 @@ import matplotlib.pyplot as plt
import numpy as np
import obspy.core.event as ope
from obspy.geodetics import degrees2kilometers
from scipy import integrate, signal
from scipy.optimize import curve_fit
from pylot.core.pick.utils import getsignalwin, crossings_nonzero_all, \
select_for_phase
from pylot.core.util.utils import common_range, fit_curve
from scipy import integrate, signal
from scipy.optimize import curve_fit
def richter_magnitude_scaling(delta):

9
pylot/core/io/data.py
View File

@ -3,19 +3,18 @@
import copy
import os
from obspy import read_events
from obspy.core import read, Stream, UTCDateTime
from obspy.core.event import Event as ObsPyEvent
from obspy.io.sac import SacIOError
import pylot.core.loc.velest as velest
from pylot.core.io.phases import readPILOTEvent, picks_from_picksdict, \
picksdict_from_pilot, merge_picks
from pylot.core.util.errors import FormatError, OverwriteError
from pylot.core.util.event import Event
from pylot.core.util.utils import fnConstructor, full_range, remove_underscores, check4gaps, check4doubled, \
check4rotated, trim_station_components
import pylot.core.loc.velest as velest
from pylot.core.util.obspyDMT_interface import qml_from_obspyDMT
from pylot.core.util.utils import fnConstructor, full_range, check4rotated, trim_station_components
class Data(object):
@ -405,7 +404,7 @@ class Data(object):
# various pre-processing steps:
# remove possible underscores in station names
#self.wfdata = remove_underscores(self.wfdata)
# self.wfdata = remove_underscores(self.wfdata)
# check for stations with rotated components
if checkRotated and metadata is not None:
self.wfdata = check4rotated(self.wfdata, metadata, verbosity=0)

10
pylot/core/io/phases.py
View File

@ -2,22 +2,22 @@
# -*- coding: utf-8 -*-
import glob
import os
import warnings
import matplotlib.pyplot as plt
import numpy as np
import obspy.core.event as ope
import os
import scipy.io as sio
import warnings
from obspy.core import UTCDateTime
from obspy.core.event import read_events
from obspy.core.util import AttribDict
from pylot.core.io.inputs import PylotParameter
from pylot.core.io.location import create_event, \
create_magnitude
from pylot.core.pick.utils import select_for_phase
from pylot.core.util.utils import getOwner, full_range, four_digits, transformFilteroptions2String, \
transformFilterString4Export, backtransformFilterString
from pylot.core.util.utils import getOwner, full_range, four_digits, transformFilterString4Export, \
backtransformFilterString
def add_amplitudes(event, amplitudes):

2
pylot/core/loc/nll.py
View File

@ -4,8 +4,8 @@
import glob
import os
import subprocess
from obspy import read_events
from pylot.core.io.phases import writephases
from pylot.core.util.utils import getPatternLine, runProgram, which
from pylot.core.util.version import get_git_version as _getVersionString

7
pylot/core/pick/autopick.py
View File

@ -8,10 +8,11 @@ function conglomerate utils.
:author: MAGS2 EP3 working group / Ludger Kueperkoch
"""
import traceback
import matplotlib.pyplot as plt
import numpy as np
import traceback
from obspy.taup import TauPyModel
from pylot.core.pick.charfuns import CharacteristicFunction
from pylot.core.pick.charfuns import HOScf, AICcf, ARZcf, ARHcf, AR3Ccf
from pylot.core.pick.picker import AICPicker, PragPicker
@ -20,8 +21,6 @@ from pylot.core.pick.utils import checksignallength, checkZ4S, earllatepicker, \
from pylot.core.util.utils import getPatternLine, gen_Pool, \
real_Bool, identifyPhaseID
from obspy.taup import TauPyModel
def autopickevent(data, param, iplot=0, fig_dict=None, fig_dict_wadatijack=None, ncores=0, metadata=None, origin=None):
"""

8
pylot/core/pick/compare.py
View File

@ -2,14 +2,12 @@
# -*- coding: utf-8 -*-
import copy
import operator
import os
import matplotlib.pyplot as plt
import numpy as np
from obspy import read_events
import operator
import os
from obspy.core import AttribDict
from pylot.core.io.phases import picksdict_from_picks
from pylot.core.util.pdf import ProbabilityDensityFunction
from pylot.core.util.utils import find_in_list
from pylot.core.util.version import get_git_version as _getVersionString

6
pylot/core/pick/picker.py
View File

@ -19,11 +19,11 @@ calculated after Diehl & Kissling (2009).
:author: MAGS2 EP3 working group / Ludger Kueperkoch
"""
import warnings
import matplotlib.pyplot as plt
import numpy as np
import warnings
from scipy.signal import argrelmax, argrelmin
from pylot.core.pick.charfuns import CharacteristicFunction
from pylot.core.pick.utils import getnoisewin, getsignalwin
@ -265,7 +265,7 @@ class AICPicker(AutoPicker):
else:
islope = np.where((self.Tcf <= min([self.Pick + tslope, self.Tcf[-1]])) \
& (
self.Tcf >= self.Pick + tsafety)) # TODO: put this in a seperate function like getsignalwin
self.Tcf >= self.Pick + tsafety)) # TODO: put this in a seperate function like getsignalwin
# find maximum within slope determination window
# 'cause slope should be calculated up to first local minimum only!
try:

4
pylot/core/pick/utils.py
View File

@ -8,11 +8,11 @@
:author: Ludger Kueperkoch, BESTEC GmbH
"""
import warnings
import matplotlib.pyplot as plt
import numpy as np
import warnings
from obspy.core import Stream, UTCDateTime
from pylot.core.util.utils import real_Bool, real_None, SetChannelComponents

120
pylot/core/util/array_map.py
View File

@ -1,17 +1,18 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import traceback
import matplotlib.pyplot as plt
import numpy as np
import obspy
import traceback
from PySide import QtGui
from mpl_toolkits.basemap import Basemap
from matplotlib.figure import Figure
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
from pylot.core.util.widgets import PickDlg, PylotCanvas
from mpl_toolkits.basemap import Basemap
from scipy.interpolate import griddata
from pylot.core.util.widgets import PickDlg, PylotCanvas
plt.interactive(False)
@ -30,6 +31,8 @@ class Array_map(QtGui.QWidget):
self.autopicks_dict = None
self.eventLoc = None
self.figure = figure
self.picks_rel = {}
self.marked_stations = []
self.init_graphics()
self.init_stations()
self.init_basemap(resolution='l')
@ -45,7 +48,6 @@ class Array_map(QtGui.QWidget):
hybrids_dict[station] = pick
return hybrids_dict
def init_map(self):
self.init_lat_lon_dimensions()
self.init_lat_lon_grid()
@ -57,8 +59,56 @@ class Array_map(QtGui.QWidget):
def onpick(self, event):
ind = event.ind
button = event.mouseevent.button
if ind == [] or not button == 1:
if ind == []:
return
if button == 1:
self.openPickDlg(ind)
elif button == 2:
self.deletePick(ind)
elif button == 3:
self.pickInfo(ind)
def deletePick(self, ind):
for index in ind:
network, station = self._station_onpick_ids[index].split('.')[:2]
try:
phase = self.comboBox_phase.currentText()
picks = self.current_picks_dict()[station]
pick = picks.get(phase)
if pick:
picker = pick['picker']
message = 'Deleted {} pick for phase {}, station {}.{} at timestamp {}'
message = message.format(picker, phase, network, station,
pick['mpp'])
if picker == 'auto':
del (self.autopicks_dict[station])
elif picker == 'manual':
del (self.picks_dict[station])
else:
raise TypeError('Unknown "picker" {}'.format(picker))
print(message)
pyl_mw = self._parent
pyl_mw.setDirty(True)
pyl_mw.update_status(message)
self._refresh_drawings()
pyl_mw.drawPicks(station)
pyl_mw.draw()
except Exception as e:
print('Could not delete pick for station {}.{}: {}'.format(network, station, e))
def pickInfo(self, ind):
for index in ind:
network, station = self._station_onpick_ids[index].split('.')[:2]
dic = self.current_picks_dict()[station]
for phase, picks in dic.items():
# because of wadati...
if phase == 'SPt':
continue
print('{} - Pick:'.format(phase))
for key, info in picks.items():
print('{}: {}'.format(key, info))
def openPickDlg(self, ind):
data = self._parent.get_data().getWFData()
for index in ind:
network, station = self._station_onpick_ids[index].split('.')[:2]
@ -297,10 +347,50 @@ class Array_map(QtGui.QWidget):
return picks, latitudes, longitudes
def draw_contour_filled(self, nlevel='50'):
# self.test_gradient()
levels = np.linspace(self.get_min_from_picks(), self.get_max_from_picks(), nlevel)
self.contourf = self.basemap.contourf(self.longrid, self.latgrid, self.picksgrid_active,
levels, latlon=True, zorder=9, alpha=0.5)
def test_gradient(self):
st_ids = self.picks_rel.keys()
x, y = np.gradient(self.picksgrid_active)
gradient_modulus = np.sqrt(x ** 2 + y ** 2)
global_mean_gradient = np.nanmean(gradient_modulus)
delta_gradient = []
for st_id in st_ids:
pick_item = self.picks_rel.pop(st_id)
self.init_picksgrid()
x, y = np.gradient(self.picksgrid_active)
gradient_modulus = np.sqrt(x ** 2 + y ** 2)
mean_gradient = np.nanmean(gradient_modulus)
dgradient = global_mean_gradient - mean_gradient
# print('station: {}, mean gradient: {}'.format(st_id, dgradient))
delta_gradient.append(dgradient)
self.picks_rel[st_id] = pick_item
global_std_gradient = np.nanstd(delta_gradient)
marked_stations = []
for st_id, dg in zip(st_ids, delta_gradient):
if abs(dg) > global_std_gradient:
marked_stations.append(st_id)
self.marked_stations = marked_stations
self.init_picksgrid()
# fig = plt.figure()
# x = list(range(len(st_ids)))
# gradients = zip(x, delta_gradient)
# gradients.sort(key=lambda a: a[1])
# plt.plot(gradients[0], gradients[1])
# global_var_gradient = np.nanvar(delta_gradient)
# plt.plot(x, delta_gradient)
# plt.axhline(global_std_gradient, color='green')
# plt.axhline(2 * global_std_gradient, color='blue')
# plt.axhline(global_var_gradient, color='red')
# plt.xticks(x, st_ids)
# plt.show()
def scatter_all_stations(self):
stations, lats, lons = self.get_st_lat_lon_for_plot()
self.sc = self.basemap.scatter(lons, lats, s=50, facecolor='none', latlon=True,
@ -318,21 +408,32 @@ class Array_map(QtGui.QWidget):
return
# workaround because of an issue with latlon transformation of arrays with len <3
if len(lons) <= 2 and len(lats) <= 2:
self.sc_picked = self.basemap.scatter(lons[0], lats[0], s=50, facecolor='white',
self.sc_picked = self.basemap.scatter(lons[0], lats[0], s=50, edgecolors='white',
c=picks[0], latlon=True, zorder=11, label='Picked')
if len(lons) == 2 and len(lats) == 2:
self.sc_picked = self.basemap.scatter(lons[1], lats[1], s=50, facecolor='white',
self.sc_picked = self.basemap.scatter(lons[1], lats[1], s=50, edgecolors='white',
c=picks[1], latlon=True, zorder=11)
else:
self.sc_picked = self.basemap.scatter(lons, lats, s=50, facecolor='white',
self.sc_picked = self.basemap.scatter(lons, lats, s=50, edgecolors='white',
c=picks, latlon=True, zorder=11, label='Picked')
def annotate_ax(self):
self.annotations = []
stations, xs, ys = self.get_st_x_y_for_plot()
# MP MP testing station highlighting if they have high impact on mean gradient of color map
# if self.picks_rel:
# self.test_gradient()
color_marked = {True: 'red',
False: 'white'}
for st, x, y in zip(stations, xs, ys):
if st in self.picks_rel:
color = 'white'
else:
color = 'lightgrey'
if st in self.marked_stations:
color = 'red'
self.annotations.append(self.main_ax.annotate(' %s' % st, xy=(x, y),
fontsize='x-small', color='white', zorder=12))
fontsize='x-small', color=color, zorder=14))
self.legend = self.main_ax.legend(loc=1)
self.legend.get_frame().set_facecolor((1, 1, 1, 0.75))
@ -381,6 +482,7 @@ class Array_map(QtGui.QWidget):
self.canvas.draw()
def remove_drawings(self):
self.remove_annotations()
if hasattr(self, 'cbar'):
self.cbar.remove()
self.cbax_bg.remove()

10
pylot/core/util/dataprocessing.py
View File

@ -2,14 +2,14 @@
# -*- coding: utf-8 -*-
import glob
import numpy as np
import os
import sys
import numpy as np
from obspy import UTCDateTime, read_inventory, read
from obspy.io.xseed import Parser
from pylot.core.util.utils import key_for_set_value, find_in_list, \
remove_underscores, gen_Pool
gen_Pool
class Metadata(object):
@ -274,6 +274,7 @@ class Metadata(object):
"""
# functions used to read metadata for different file endings (or file types)
read_functions = {'dless': self._read_dless,
'dataless': self._read_dless,
'dseed': self._read_dless,
'xml': self._read_inventory_file,
'resp': self._read_inventory_file}
@ -281,6 +282,7 @@ class Metadata(object):
if file_ending in read_functions.keys():
robj, exc = read_functions[file_ending](path_to_inventory_filename)
if exc is not None:
print("Nicht None")
raise exc
return file_ending, robj
# in case file endings did not match the above keys, try and error
@ -616,7 +618,7 @@ def restitute_data(data, metadata, unit='VEL', force=False, ncores=0):
restflag = list()
#data = remove_underscores(data)
# data = remove_underscores(data)
# loop over traces
input_tuples = []

4
pylot/core/util/defaults.py
View File

@ -9,12 +9,12 @@ Created on Wed Feb 26 12:31:25 2014
import os
import platform
from pylot.core.util.utils import readDefaultFilterInformation
from pylot.core.loc import hypo71
from pylot.core.loc import hypodd
from pylot.core.loc import hyposat
from pylot.core.loc import nll
from pylot.core.loc import velest
from pylot.core.util.utils import readDefaultFilterInformation
# determine system dependent path separator
system_name = platform.system()
@ -39,5 +39,3 @@ OUTPUTFORMATS = {'.xml': 'QUAKEML',
'.obs': 'NLLOC_OBS'}
LOCTOOLS = dict(nll=nll, hyposat=hyposat, velest=velest, hypo71=hypo71, hypodd=hypodd)

2
pylot/core/util/event.py
View File

@ -2,10 +2,10 @@
# -*- coding: utf-8 -*-
import os
from obspy import UTCDateTime
from obspy.core.event import Event as ObsPyEvent
from obspy.core.event import Origin, ResourceIdentifier
from pylot.core.io.phases import picks_from_picksdict
from pylot.core.util.obspyDMT_interface import qml_from_obspyDMT

4
pylot/core/util/pdf.py
View File

@ -1,10 +1,10 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import warnings
import numpy as np
import warnings
from obspy import UTCDateTime
from pylot.core.util.utils import fit_curve, clims
from pylot.core.util.version import get_git_version as _getVersionString

8
pylot/core/util/thread.py
View File

@ -1,8 +1,11 @@
# -*- coding: utf-8 -*-
import sys, os, traceback
import multiprocessing
import os
import sys
import traceback
from PySide.QtCore import QThread, Signal, Qt, Slot, QRunnable, QObject
from PySide.QtGui import QDialog, QProgressBar, QLabel, QHBoxLayout, QPushButton
from PySide.QtGui import QDialog, QProgressBar, QLabel, QHBoxLayout
class Thread(QThread):
@ -40,7 +43,6 @@ class Thread(QThread):
def showProgressbar(self):
if self.progressText:
# # generate widget if not given in init
# if not self.pb_widget:
# self.pb_widget = ProgressBarWidget(self.parent())

20
pylot/core/util/utils.py
View File

@ -2,27 +2,23 @@
# -*- coding: utf-8 -*-
import hashlib
import numpy as np
import os
import platform
import pyqtgraph as pg
import re
import subprocess
import warnings
import numpy as np
from PySide import QtCore
from obspy import UTCDateTime, read
from obspy.core import AttribDict
from obspy.signal.rotate import rotate2zne
from obspy.io.xseed.utils import SEEDParserException
from pylot.core.util.obspyDMT_interface import check_obspydmt_eventfolder
from scipy.interpolate import splrep, splev
from pylot.core.io.inputs import PylotParameter, FilterOptions
from pylot.core.util.obspyDMT_interface import check_obspydmt_eventfolder
from pylot.styles import style_settings
from scipy.interpolate import splrep, splev
from PySide import QtCore, QtGui
import pyqtgraph as pg
def _pickle_method(m):
if m.im_self is None:
@ -835,7 +831,7 @@ def remove_underscores(data):
:return: data stream
:rtype: `~obspy.core.stream.Stream`
"""
#for tr in data:
# for tr in data:
# # remove underscores
# tr.stats.station = tr.stats.station.strip('_')
return data
@ -874,7 +870,7 @@ def merge_stream(stream):
if gaps:
# list of merged stations (seed_ids)
merged = ['{}.{}.{}.{}'.format(*gap[:4]) for gap in gaps]
stream.merge()
stream.merge(method=1)
print('Merged the following stations because of gaps:')
for merged_station in merged:
print(merged_station)
@ -1279,4 +1275,4 @@ class SetChannelComponents(object):
return self.compPosition_Map[self.compName_Map[component]]
else:
errMsg = 'getCompPosition: Unrecognized component {}. Expecting one of {} or {}.'
raise ValueError(errMsg.format(component, self.compPosition_Map.keys(), self.compName_Map.keys()))
raise ValueError(errMsg.format(component, self.compPosition_Map.keys(), self.compName_Map.keys()))

95
pylot/core/util/widgets.py
View File

@ -8,16 +8,14 @@ Created on Wed Mar 19 11:27:35 2014
import copy
import datetime
import getpass
import matplotlib
import multiprocessing
import numpy as np
import os
import subprocess
import sys
import time
import numpy as np
import matplotlib
matplotlib.use('QT4Agg')
from matplotlib.figure import Figure
@ -28,8 +26,6 @@ except ImportError:
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT
from matplotlib.widgets import MultiCursor
from matplotlib.tight_layout import get_renderer, get_subplotspec_list, get_tight_layout_figure
from scipy.signal import argrelmin, argrelmax
from obspy import read
from PySide import QtCore, QtGui
@ -38,7 +34,7 @@ from PySide.QtGui import QAction, QApplication, QCheckBox, QComboBox, \
QGridLayout, QIcon, QLabel, QLineEdit, QMessageBox, \
QPixmap, QSpinBox, QTabWidget, QToolBar, QVBoxLayout, QHBoxLayout, QWidget, \
QPushButton, QFileDialog, QInputDialog, QKeySequence
from PySide.QtCore import QSettings, Qt, QUrl, Signal, Slot
from PySide.QtCore import QSettings, Qt, QUrl, Signal
from PySide.QtWebKit import QWebView
from obspy import Stream, Trace, UTCDateTime
from obspy.core.util import AttribDict
@ -50,9 +46,9 @@ from pylot.core.pick.utils import getSNR, earllatepicker, getnoisewin, \
getResolutionWindow, getQualityFromUncertainty
from pylot.core.pick.compare import Comparison
from pylot.core.util.defaults import OUTPUTFORMATS, FILTERDEFAULTS
from pylot.core.util.utils import prepTimeAxis, full_range, scaleWFData, \
demeanTrace, isSorted, findComboBoxIndex, clims, pick_linestyle_plt, pick_color_plt, \
check4rotated, check4doubled, check4gaps, merge_stream, remove_underscores, find_horizontals, identifyPhase, \
from pylot.core.util.utils import prepTimeAxis, full_range, demeanTrace, isSorted, findComboBoxIndex, clims, \
pick_linestyle_plt, pick_color_plt, \
check4rotated, check4doubled, merge_stream, identifyPhase, \
loopIdentifyPhase, trim_station_components, transformFilteroptions2String, \
identifyPhaseID, real_Bool, pick_color, getAutoFilteroptions, SetChannelComponents
from autoPyLoT import autoPyLoT
@ -66,6 +62,9 @@ elif sys.version_info.major == 2:
else:
raise ImportError('Could not determine python version.')
# workaround to prevent PyCharm from deleting icons_rc import when optimizing imports
icons_rc = icons_rc
def getDataType(parent):
type = QInputDialog().getItem(parent, "Select phases type", "Type:",
@ -148,7 +147,7 @@ class AddMetadataWidget(QWidget):
self.center()
self.show()
#self.__test__()
# self.__test__()
def __test__(self):
self.add_item(r'/rscratch/minos14/marcel/git/pylot/tests')
@ -529,7 +528,7 @@ class ComparisonWidget(QWidget):
legend.draggable()
for ax in axes_dict['P'].values():
ax.set_ylabel('Frequency [-]')
ax.set_ylabel('number of picks [-]')
self.canvas.draw()
else:
@ -739,7 +738,8 @@ class WaveformWidgetPG(QtGui.QWidget):
# list containing tuples of network, station, channel (for sorting)
nslc = []
for trace in st_select:
nslc.append(trace.get_id())#(trace.stats.network, trace.stats.station, trace.stats.location trace.stats.channel))
nslc.append(
trace.get_id()) # (trace.stats.network, trace.stats.station, trace.stats.location trace.stats.channel))
nslc.sort()
nslc.reverse()
plots = []
@ -1203,7 +1203,8 @@ class PylotCanvas(FigureCanvas):
def plotWFData(self, wfdata, title=None, zoomx=None, zoomy=None,
noiselevel=None, scaleddata=False, mapping=True,
component='*', nth_sample=1, iniPick=None, verbosity=0,
plot_additional=False, additional_channel=None, scaleToChannel=None):
plot_additional=False, additional_channel=None, scaleToChannel=None,
snr=None):
ax = self.axes[0]
ax.cla()
@ -1232,7 +1233,7 @@ class PylotCanvas(FigureCanvas):
gaps = st_select.get_gaps()
if gaps:
merged = ['{}.{}.{}.{}'.format(*gap[:4]) for gap in gaps]
st_select.merge()
st_select.merge(method=1)
print('Merged the following stations because of gaps:')
for merged_station in merged:
print(merged_station)
@ -1323,6 +1324,14 @@ class PylotCanvas(FigureCanvas):
self.setXLims(ax, zoomx)
if zoomy is not None:
self.setYLims(ax, zoomy)
if snr is not None:
if snr < 2:
warning = 'LOW SNR'
if snr < 1.5:
warning = 'VERY LOW SNR'
ax.text(0.1, 0.9, 'WARNING - {}'.format(warning), ha='center', va='center', transform=ax.transAxes,
color='red')
self.draw()
@staticmethod
@ -2280,6 +2289,12 @@ class PickDlg(QDialog):
filterphase = 'S'
return filterphase
def getNoiseWin(self, phase):
twins_phase = {'P': 'tsnrz',
'S': 'tsnrh'}
return self.parameter.get(twins_phase[phase])[:3]
def setIniPickP(self, gui_event):
self.setIniPickPS(gui_event, phase='P')
@ -2291,17 +2306,12 @@ class PickDlg(QDialog):
nfac_phase = {'P': 'nfacP',
'S': 'nfacS'}
twins_phase = {'P': 'tsnrz',
'S': 'tsnrh'}
parameter = self.parameter
ini_pick = gui_event.xdata
nfac = parameter.get(nfac_phase[phase])
twins = parameter.get(twins_phase[phase])
noise_win = twins[0]
gap_win = twins[1]
signal_win = twins[2]
noise_win, gap_win, signal_win = self.getNoiseWin(phase)
stime = self.getStartTime()
@ -2355,12 +2365,14 @@ class PickDlg(QDialog):
trace.data *= noiseScaleFactor
noiselevels[channel] *= noiseScaleFactor
x_res = getResolutionWindow(np.mean(snr), parameter.get('extent'))
mean_snr = np.mean(snr)
x_res = getResolutionWindow(mean_snr, parameter.get('extent'))
xlims = [ini_pick - x_res, ini_pick + x_res]
ylims = list(np.array([-.5, .5]) + [0, len(data) - 1])
title = self.getStation() + ' picking mode'
title += ' | SNR: {}'.format(mean_snr)
if filterphase:
filtops_str = transformFilteroptions2String(filteroptions)
title += ' | Filteroptions: {}'.format(filtops_str)
@ -2375,7 +2387,8 @@ class PickDlg(QDialog):
scaleddata=True,
iniPick=ini_pick,
plot_additional=plot_additional,
additional_channel=additional_channel)
additional_channel=additional_channel,
snr=mean_snr)
def setPick(self, gui_event):
@ -2447,6 +2460,11 @@ class PickDlg(QDialog):
self.zoomAction.setEnabled(True)
# self.pick_block = self.togglPickBlocker()
# self.resetZoom()
noise_win, gap_win, signal_win = self.getNoiseWin(phase)
snr, snrDB, noiselevel = getSNR(wfdata, (noise_win, gap_win, signal_win), pick - stime_diff)
print('SNR of final pick: {}'.format(snr))
if snr < 1.5:
QMessageBox.warning(self, 'SNR too low', 'WARNING! SNR of final pick below 1.5! SNR = {}'.format(snr))
self.leave_picking_mode()
def savePick(self, phase, phasepicks):
@ -2520,25 +2538,25 @@ class PickDlg(QDialog):
linestyle_mpp, width_mpp = pick_linestyle_plt(picktype, 'mpp')
vl = ax.axvline(mpp, ylims[0], ylims[1], color=color, linestyle=linestyle_mpp, linewidth=width_mpp,
label='{}-{}-Pick (quality: {})'.format(phase, picktype, quality), picker=5,
zorder=baseorder+9)
zorder=baseorder + 9)
phaseLineKey = '{}-{}'.format(phase, picktype)
self.phaseLines[phaseLineKey] = vl
if spe:
ax.fill_between([mpp - spe, mpp + spe], ylims[0], ylims[1],
alpha=.25, color=color, label='{}-{}-SPE'.format(phase, picktype), zorder=baseorder+1)
alpha=.25, color=color, label='{}-{}-SPE'.format(phase, picktype), zorder=baseorder + 1)
if picks['epp']:
linestyle_epp, width_epp = pick_linestyle_plt(picktype, 'epp')
ax.axvline(epp, ylims[0], ylims[1], color=color, linestyle=linestyle_epp,
linewidth=width_epp, label='{}-{}-EPP'.format(phase, picktype), zorder=baseorder+2)
linewidth=width_epp, label='{}-{}-EPP'.format(phase, picktype), zorder=baseorder + 2)
if picks['lpp']:
linestyle_lpp, width_lpp = pick_linestyle_plt(picktype, 'lpp')
ax.axvline(lpp, ylims[0], ylims[1], color=color, linestyle=linestyle_lpp,
linewidth=width_lpp, label='{}-{}-LPP'.format(phase, picktype), zorder=baseorder+2)
linewidth=width_lpp, label='{}-{}-LPP'.format(phase, picktype), zorder=baseorder + 2)
if picktype == 'auto':
ax.plot(mpp, ylims[1], color=color, marker='v', zorder=baseorder+3)
ax.plot(mpp, ylims[0], color=color, marker='^', zorder=baseorder+3)
ax.plot(mpp, ylims[1], color=color, marker='v', zorder=baseorder + 3)
ax.plot(mpp, ylims[0], color=color, marker='^', zorder=baseorder + 3)
# append phase text (if textOnly: draw with current ylims)
self.phaseText.append(ax.text(mpp, ylims[1], phase, color=color, zorder=baseorder+10))
self.phaseText.append(ax.text(mpp, ylims[1], phase, color=color, zorder=baseorder + 10))
ax.legend(loc=1)
def connect_mouse_motion(self):
@ -3326,11 +3344,11 @@ class TuneAutopicker(QWidget):
self.data.setWFData(fnames)
wfdat = self.data.getWFData() # all available streams
# remove possible underscores in station names
#wfdat = remove_underscores(wfdat)
# wfdat = remove_underscores(wfdat)
# rotate misaligned stations to ZNE
# check for gaps and doubled channels
wfdat, gaps = merge_stream(wfdat)
#check4gaps(wfdat)
# check4gaps(wfdat)
check4doubled(wfdat)
wfdat = check4rotated(wfdat, self.parent().metadata, verbosity=0)
# trim station components to same start value
@ -3398,6 +3416,7 @@ class TuneAutopicker(QWidget):
return str(self.stationBox.currentText()).split('.')[1]
def get_current_station_id(self):
print(self.stationBox, self.stationBox.currentText())
return str(self.stationBox.currentText())
@staticmethod
@ -3415,7 +3434,15 @@ class TuneAutopicker(QWidget):
self.pdlg_widget = None
return
self.load_wf_data()
network, station, location, channel = self.get_current_station_id()
try:
network, station, location, channel = self.get_current_station_id()
except ValueError as e:
vmsg = '{0}'.format(e)
print(vmsg)
station = self.get_current_station()
location = None
network = None
wfdata = self.data.getWFData()
metadata = self.parent().metadata
event = self.get_current_event()
@ -4587,7 +4614,7 @@ class GraphicsTab(PropTab):
super(GraphicsTab, self).__init__(parent)
self.pylot_mainwindow = parent._pylot_mainwindow
self.init_layout()
#self.add_pg_cb()
# self.add_pg_cb()
self.add_nth_sample()
self.add_style_settings()
self.setLayout(self.main_layout)

6
tests/test_Metadata/test_Metadata.py
View File

@ -1,9 +1,9 @@
import unittest
import os
import unittest
from obspy import UTCDateTime
from obspy.io.xseed.utils import SEEDParserException
from obspy.io.xseed import Parser
from obspy.io.xseed.utils import SEEDParserException
from pylot.core.util.dataprocessing import Metadata
from tests.utils import HidePrints

2
tests/utils.py
View File

@ -3,8 +3,8 @@
"""Utilities/helpers for testing"""
import sys
import os
import sys
class HidePrints: