marcel/pylot
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Merge branch 'develop'

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This commit is contained in:
Marcel Paffrath 2017-06-22 13:28:34 +02:00
commit 2b6297859b
10 changed files with 81 additions and 59 deletions
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14
QtPyLoT.py
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@ -55,9 +55,9 @@ except ImportError:
from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar
from matplotlib.figure import Figure
from pylot.core.analysis.magnitude import RichterMagnitude, MomentMagnitude
from pylot.core.analysis.magnitude import LocalMagnitude, MomentMagnitude
from pylot.core.io.data import Data
from pylot.core.io.inputs import FilterOptions, AutoPickParameter
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
@ -73,7 +73,7 @@ from pylot.core.util.utils import fnConstructor, getLogin, \
from pylot.core.io.location import create_creation_info, create_event
from pylot.core.util.widgets import FilterOptionsDialog, NewEventDlg, \
WaveformWidget, WaveformWidgetPG, PropertiesDlg, HelpForm, createAction, PickDlg, \
getDataType, ComparisonDialog, TuneAutopicker, AutoPickParaBox
getDataType, ComparisonDialog, TuneAutopicker, PylotParaBox
from pylot.core.util.map_projection import map_projection
from pylot.core.util.structure import DATASTRUCTURE
from pylot.core.util.thread import AutoPickThread, Thread
@ -103,7 +103,7 @@ class MainWindow(QMainWindow):
self.infile = infile[0]
else:
self.infile = infile
self._inputs = AutoPickParameter(infile)
self._inputs = PylotParameter(infile)
self._props = None
self.dirty = False
@ -799,7 +799,7 @@ class MainWindow(QMainWindow):
self.paraBox.setValue(box, dirs[directory])
#show needed parameter in box
self.paraBox.show_parameter(directory)
dirs_box = self.paraBox.get_groupbox_exclusive('Directories')
dirs_box = self.paraBox.get_groupbox_dialog('Directories')
if not dirs_box.exec_():
return
self.project.rootpath = dirs['rootpath']
@ -2150,7 +2150,7 @@ class MainWindow(QMainWindow):
# if not rest_flag:
# raise ProcessingError('Restitution of waveform data failed!')
if type == 'ML':
local_mag = RichterMagnitude(corr_wf, self.get_data().get_evt_data(), self.inputs.get('sstop'), verbosity = True)
local_mag = LocalMagnitude(corr_wf, self.get_data().get_evt_data(), self.inputs.get('sstop'), verbosity = True)
return local_mag.updated_event()
elif type == 'Mw':
moment_mag = MomentMagnitude(corr_wf, self.get_data().get_evt_data(), self.inputs.get('vp'), self.inputs.get('Qp'), self.inputs.get('rho'), verbosity = True)
@ -2331,7 +2331,7 @@ class MainWindow(QMainWindow):
def setParameter(self, show=True):
if not self.paraBox:
self.paraBox = AutoPickParaBox(self._inputs)
self.paraBox = PylotParaBox(self._inputs)
self.paraBox._apply.clicked.connect(self._setDirty)
self.paraBox._okay.clicked.connect(self._setDirty)
if show:

22
autoPyLoT.py
View File

@ -16,9 +16,9 @@ import pylot.core.loc.focmec as focmec
import pylot.core.loc.hash as hash
import pylot.core.loc.nll as nll
#from PySide.QtGui import QWidget, QInputDialog
from pylot.core.analysis.magnitude import MomentMagnitude, RichterMagnitude
from pylot.core.analysis.magnitude import MomentMagnitude, LocalMagnitude
from pylot.core.io.data import Data
from pylot.core.io.inputs import AutoPickParameter
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, \
remove_underscores
@ -35,7 +35,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
:param inputfile: path to the input file containing all parameter
information for automatic picking (for formatting details, see.
`~pylot.core.io.inputs.AutoPickParameter`
`~pylot.core.io.inputs.PylotParameter`
:type inputfile: str
:return:
@ -71,13 +71,13 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
if not parameter:
if inputfile:
parameter = AutoPickParameter(inputfile)
parameter = PylotParameter(inputfile)
iplot = parameter['iplot']
else:
print('No parameters set and no input file given. Choose either of both.')
return
else:
if not type(parameter) == AutoPickParameter:
if not type(parameter) == PylotParameter:
print('Wrong input type for parameter: {}'.format(type(parameter)))
return
if inputfile:
@ -252,9 +252,9 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
for station, props in moment_mag.moment_props.items():
picks[station]['P'].update(props)
evt = moment_mag.updated_event()
local_mag = RichterMagnitude(corr_dat, evt,
parameter.get('sstop'), True,\
iplot)
local_mag = LocalMagnitude(corr_dat, evt,
parameter.get('sstop'), parameter.get('WAscaling'), \
True, iplot)
for station, amplitude in local_mag.amplitudes.items():
picks[station]['S']['Ao'] = amplitude.generic_amplitude
evt = local_mag.updated_event()
@ -310,9 +310,9 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
for station, props in moment_mag.moment_props.items():
picks[station]['P'].update(props)
evt = moment_mag.updated_event()
local_mag = RichterMagnitude(corr_dat, evt,
parameter.get('sstop'), True, \
iplot)
local_mag = LocalMagnitude(corr_dat, evt,
parameter.get('sstop'), parameter.get('WAscaling'), \
True, iplot)
for station, amplitude in local_mag.amplitudes.items():
picks[station]['S']['Ao'] = amplitude.generic_amplitude
evt = local_mag.updated_event()

2
pylot/RELEASE-VERSION
View File

@ -1 +1 @@
6feff-dirty
f91e1-dirty

27
pylot/core/analysis/magnitude.py
View File

@ -38,10 +38,10 @@ class Magnitude(object):
def __init__(self, stream, event, verbosity=False, iplot=0):
self._type = "M"
self._stream = stream
self._plot_flag = iplot
self._verbosity = verbosity
self._event = event
self._stream = stream
self._magnitudes = dict()
def __str__(self):
@ -136,7 +136,7 @@ class Magnitude(object):
return None
class RichterMagnitude(Magnitude):
class LocalMagnitude(Magnitude):
"""
Method to derive peak-to-peak amplitude as seen on a Wood-Anderson-
seismograph. Has to be derived from instrument corrected traces!
@ -153,10 +153,11 @@ class RichterMagnitude(Magnitude):
_amplitudes = dict()
def __init__(self, stream, event, calc_win, verbosity=False, iplot=0):
super(RichterMagnitude, self).__init__(stream, event, verbosity, iplot)
def __init__(self, stream, event, calc_win, wascaling=None, verbosity=False, iplot=0):
super(LocalMagnitude, self).__init__(stream, event, verbosity, iplot)
self._calc_win = calc_win
self._wascaling = wascaling
self._type = 'ML'
self.calc()
@ -168,6 +169,10 @@ class RichterMagnitude(Magnitude):
def calc_win(self, value):
self._calc_win = value
@property
def wascaling(self):
return self._wascaling
@property
def amplitudes(self):
return self._amplitudes
@ -251,10 +256,16 @@ class RichterMagnitude(Magnitude):
self.event.amplitudes.append(amplitude)
self.amplitudes = (station, amplitude)
# using standard Gutenberg-Richter relation
# TODO make the ML calculation more flexible by allowing
# use of custom relation functions
magnitude = ope.StationMagnitude(
mag=np.log10(a0) + richter_magnitude_scaling(delta))
# or scale WA amplitude with given scaling relation
if self.wascaling == None:
print("Calculating original Richter magnitude ...")
magnitude = ope.StationMagnitude(mag=np.log10(a0) \
+ richter_magnitude_scaling(delta))
else:
print("Calculating scaled local magnitude ...")
magnitude = ope.StationMagnitude(mag=np.log10(a0) \
+ self.wascaling[0] * np.log10(delta) + self.wascaling[1]
* delta + self.wascaling[2])
magnitude.origin_id = self.origin_id
magnitude.waveform_id = pick.waveform_id
magnitude.amplitude_id = amplitude.resource_id

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

@ -277,13 +277,13 @@ defaults = {'rootpath': {'type': str,
'tooltip': 'maximum allowed deviation from Wadati-diagram',
'value': 1.0},
'WAscaling': {'type': float,
'tooltip': 'Scaling relation of Wood-Anderson amplitude [nm]',
'value': 1.0},
'WAscaling': {'type': (float, float, float),
'tooltip': 'Scaling relation (log(Ao)+Alog(r)+Br+C) of Wood-Anderson amplitude Ao [nm]',
'value': (1.0, 1.0, 1.0)},
'magscaling': {'type': float,
'magscaling': {'type': (float, float),
'tooltip': 'Scaling relation for derived local magnitude [a*Ml+b]',
'value': 1.0}
'value': (1.0, 1.0)}
}
settings_main={

6
pylot/core/io/inputs.py
View File

@ -4,9 +4,9 @@
from pylot.core.util.errors import ParameterError
import default_parameters
class AutoPickParameter(object):
class PylotParameter(object):
'''
AutoPickParameters is a parameter type object capable to read and/or write
PylotParameter is a parameter type object capable to read and/or write
parameter ASCII.
:param fn str: Filename of the input file
@ -78,7 +78,7 @@ class AutoPickParameter(object):
# String representation of the object
def __repr__(self):
return "AutoPickParameter('%s')" % self.__filename
return "PylotParameter('%s')" % self.__filename
# Boolean test
def __nonzero__(self):

8
pylot/core/io/phases.py
View File

@ -8,7 +8,7 @@ import scipy.io as sio
import warnings
from obspy.core import UTCDateTime
from pylot.core.io.inputs import AutoPickParameter
from pylot.core.io.inputs import PylotParameter
from pylot.core.io.location import create_arrival, create_event, \
create_magnitude, create_origin, create_pick
from pylot.core.pick.utils import select_for_phase
@ -116,7 +116,7 @@ def picksdict_from_pilot(fn):
picks = dict()
phases_pilot = sio.loadmat(fn)
stations = stations_from_pilot(phases_pilot['stat'])
params = AutoPickParameter(TIMEERROR_DEFAULTS)
params = PylotParameter(TIMEERROR_DEFAULTS)
timeerrors = dict(P=params.get('timeerrorsP'),
S=params.get('timeerrorsS'))
for n, station in enumerate(stations):
@ -295,14 +295,14 @@ def reassess_pilot_db(root_dir, db_dir, out_dir=None, fn_param=None, verbosity=0
def reassess_pilot_event(root_dir, db_dir, event_id, out_dir=None, fn_param=None, verbosity=0):
from obspy import read
from pylot.core.io.inputs import AutoPickParameter
from pylot.core.io.inputs import PylotParameter
from pylot.core.pick.utils import earllatepicker
if fn_param is None:
import pylot.core.util.defaults as defaults
fn_param = defaults.AUTOMATIC_DEFAULTS
default = AutoPickParameter(fn_param, verbosity)
default = PylotParameter(fn_param, verbosity)
search_base = os.path.join(root_dir, db_dir, event_id)
phases_file = glob.glob(os.path.join(search_base, 'PHASES.mat'))

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

@ -11,7 +11,7 @@ function conglomerate utils.
import matplotlib.pyplot as plt
import numpy as np
from pylot.core.io.inputs import AutoPickParameter
from pylot.core.io.inputs import PylotParameter
from pylot.core.pick.picker import AICPicker, PragPicker
from pylot.core.pick.charfuns import CharacteristicFunction
from pylot.core.pick.charfuns import HOScf, AICcf, ARZcf, ARHcf, AR3Ccf
@ -81,7 +81,7 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
:param pickparam: container of picking parameters from input file,
usually autoPyLoT.in
:type pickparam: AutoPickParameter
:type pickparam: PylotParameter
:param verbose:
:type verbose: bool

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

@ -10,7 +10,7 @@ import re
import warnings
import subprocess
from obspy import UTCDateTime, read
from pylot.core.io.inputs import AutoPickParameter
from pylot.core.io.inputs import PylotParameter
def _pickle_method(m):
@ -497,7 +497,7 @@ def which(program, infile=None):
bpath = os.path.join(os.path.expanduser('~'), '.pylot', infile)
if os.path.exists(bpath):
nllocpath = ":" + AutoPickParameter(bpath).get('nllocbin')
nllocpath = ":" + PylotParameter(bpath).get('nllocbin')
os.environ['PATH'] += nllocpath
except ImportError as e:
print(e.message)

43
pylot/core/util/widgets.py
View File

@ -36,7 +36,7 @@ from PySide.QtCore import QSettings, Qt, QUrl, Signal, Slot
from PySide.QtWebKit import QWebView
from obspy import Stream, UTCDateTime
from pylot.core.io.data import Data
from pylot.core.io.inputs import FilterOptions, AutoPickParameter
from pylot.core.io.inputs import FilterOptions, PylotParameter
from pylot.core.pick.utils import getSNR, earllatepicker, getnoisewin, \
getResolutionWindow
from pylot.core.pick.compare import Comparison
@ -1662,7 +1662,7 @@ class TuneAutopicker(QWidget):
self.stb_names = ['aicARHfig', 'refSpick', 'el_S1pick', 'el_S2pick']
def add_parameters(self):
self.paraBox = AutoPickParaBox(self.parameter)
self.paraBox = PylotParaBox(self.parameter)
self.paraBox.set_tune_mode(True)
self.update_eventID()
self.parameter_layout.addWidget(self.paraBox)
@ -1968,13 +1968,13 @@ class TuneAutopicker(QWidget):
self.qmb.show()
class AutoPickParaBox(QtGui.QWidget):
class PylotParaBox(QtGui.QWidget):
def __init__(self, parameter, parent=None):
'''
Generate Widget containing parameters for automatic picking algorithm.
:param: parameter
:type: AutoPickParameter (object)
:type: PylotParameter (object)
'''
QtGui.QWidget.__init__(self, parent)
@ -1987,6 +1987,7 @@ class AutoPickParaBox(QtGui.QWidget):
self.labels = {}
self.boxes = {}
self.groupboxes = {}
self._exclusive_widgets = []
self._init_sublayouts()
self.setLayout(self.layout)
self.add_main_parameters_tab()
@ -2034,7 +2035,7 @@ class AutoPickParaBox(QtGui.QWidget):
def _create_advanced_cb(self):
self._advanced_cb = QtGui.QCheckBox('Enable Advanced Settings')
self._advanced_layout.addWidget(self._advanced_cb)
self._advanced_layout.insertWidget(0, self._advanced_cb)
self._advanced_cb.toggled.connect(self._toggle_advanced_settings)
def _toggle_advanced_settings(self):
@ -2140,13 +2141,13 @@ class AutoPickParaBox(QtGui.QWidget):
def add_special_pick_parameters_tab(self):
self.add_to_layout(self._advanced_layout, 'Z-component',
self.parameter.get_special_para_names()['z'], 0)
self.parameter.get_special_para_names()['z'], 1)
self.add_to_layout(self._advanced_layout, 'H-components',
self.parameter.get_special_para_names()['h'], 1)
self.parameter.get_special_para_names()['h'], 2)
self.add_to_layout(self._advanced_layout, 'First-motion picker',
self.parameter.get_special_para_names()['fm'], 2)
self.parameter.get_special_para_names()['fm'], 3)
self.add_to_layout(self._advanced_layout, 'Quality assessment',
self.parameter.get_special_para_names()['quality'], 3)
self.parameter.get_special_para_names()['quality'], 4)
self.add_tab(self._advanced_layout, 'Advanced Settings')
# def gen_h_seperator(self):
@ -2168,20 +2169,29 @@ class AutoPickParaBox(QtGui.QWidget):
layout.insertWidget(position, groupbox)
def get_groupbox_exclusive(self, name):
widget = QtGui.QWidget(self, 1)
layout = QtGui.QVBoxLayout()
widget.setLayout(layout)
layout.addWidget(self.groupboxes[name])
self._exclusive_widgets.append(widget)
return widget
def get_groupbox_dialog(self, name):
widget = self.get_groupbox_exclusive(name)
dialog = QtGui.QDialog(self.parent())
buttonbox = QtGui.QDialogButtonBox(QDialogButtonBox.Ok |
QDialogButtonBox.Cancel)
self._exclusive_dialog = dialog
layout = QtGui.QVBoxLayout()
dialog.setLayout(layout)
layout.addWidget(self.groupboxes[name])
layout.addWidget(buttonbox)
buttonbox = QtGui.QDialogButtonBox(QDialogButtonBox.Ok |
QDialogButtonBox.Cancel)
buttonbox.accepted.connect(dialog.accept)
buttonbox.accepted.connect(self.refresh)
buttonbox.accepted.connect(self.params_from_gui)
buttonbox.rejected.connect(dialog.reject)
buttonbox.rejected.connect(self.refresh)
buttonbox.rejected.connect(self.params_to_gui)
layout.addWidget(widget)
layout.addWidget(buttonbox)
self._exclusive_dialog = dialog
return dialog
def add_to_layout(self, layout, name, items, position):
@ -2342,6 +2352,7 @@ class AutoPickParaBox(QtGui.QWidget):
self.show_parameter()
if hasattr(self, '_exclusive_dialog'):
self._exclusive_dialog.close()
self._exclusive_widgets = []
QtGui.QWidget.show(self)
def _warn(self, message):
@ -2510,7 +2521,7 @@ class InputsTab(PropTab):
return values
def resetValues(self, infile):
para = AutoPickParameter(infile)
para = PylotParameter(infile)
datstruct = para.get('datastructure')
if datstruct == 'SeisComp':
index = 0
@ -2766,7 +2777,7 @@ class LocalisationTab(PropTab):
return values
def resetValues(self, infile):
para = AutoPickParameter(infile)
para = PylotParameter(infile)
nllocroot = para.get('nllocroot')
nllocbin = para.get('nllocbin')
loctool = self.locToolComboBox.setCurrentIndex(3)