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WIP: Simplify data structure #39

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sebastianw wants to merge 31 commits from 38-simplify-data-structure into develop
pull from: 38-simplify-data-structure
merge into: marcel:develop
Conversation 1 Commits 31 Files Changed 25 +352 -399
7 changed files with 352 additions and 399 deletions
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Showing only changes of commit 76d4ec290c - Show all commits

34
PyLoT.py
View File

@ -1773,7 +1773,7 @@ class MainWindow(QMainWindow):
def getStime(self): def getStime(self):
if self.get_data(): if self.get_data():
return full_range(self.get_data().getWFData())[0] return full_range(self.get_data().get_wf_data())[0]
def addActions(self, target, actions): def addActions(self, target, actions):
for action in actions: for action in actions:
@ -1983,7 +1983,7 @@ class MainWindow(QMainWindow):
tstart = None tstart = None
tstop = None tstop = None
self.data.setWFData(self.fnames, self.data.set_wf_data(self.fnames,
self.fnames_comp, self.fnames_comp,
checkRotated=True, checkRotated=True,
metadata=self.metadata, metadata=self.metadata,
@ -2035,7 +2035,7 @@ class MainWindow(QMainWindow):
def get_npts_to_plot(self): def get_npts_to_plot(self):
if not hasattr(self.data, 'wfdata'): if not hasattr(self.data, 'wfdata'):
return 0 return 0
return sum(trace.stats.npts for trace in self.data.getWFData()) return sum(trace.stats.npts for trace in self.data.get_wf_data())
def connectWFplotEvents(self): def connectWFplotEvents(self):
''' '''
@ -2248,14 +2248,14 @@ class MainWindow(QMainWindow):
zne_text = {'Z': 'vertical', 'N': 'north-south', 'E': 'east-west'} zne_text = {'Z': 'vertical', 'N': 'north-south', 'E': 'east-west'}
comp = self.getComponent() comp = self.getComponent()
title = 'section: {0} components'.format(zne_text[comp]) title = 'section: {0} components'.format(zne_text[comp])
wfst = self.get_data().getWFData() wfst = self.get_data().get_wf_data()
wfsyn = self.get_data().getAltWFdata() wfsyn = self.get_data().getAltWFdata()
if self.filterActionP.isChecked() and filter: if self.filterActionP.isChecked() and filter:
self.filterWaveformData(plot=False, phase='P') self.filterWaveformData(plot=False, phase='P')
elif self.filterActionS.isChecked() and filter: elif self.filterActionS.isChecked() and filter:
self.filterWaveformData(plot=False, phase='S') self.filterWaveformData(plot=False, phase='S')
# wfst = self.get_data().getWFData().select(component=comp) # wfst = self.get_data().get_wf_data().select(component=comp)
# wfst += self.get_data().getWFData().select(component=alter_comp) # wfst += self.get_data().get_wf_data().select(component=alter_comp)
plotWidget = self.getPlotWidget() plotWidget = self.getPlotWidget()
self.adjustPlotHeight() self.adjustPlotHeight()
if get_bool(settings.value('large_dataset')) == True: if get_bool(settings.value('large_dataset')) == True:
@ -2270,7 +2270,7 @@ class MainWindow(QMainWindow):
def adjustPlotHeight(self): def adjustPlotHeight(self):
if self.pg: if self.pg:
return return
height_need = len(self.data.getWFData()) * self.height_factor height_need = len(self.data.get_wf_data()) * self.height_factor
plotWidget = self.getPlotWidget() plotWidget = self.getPlotWidget()
if self.tabs.widget(0).frameSize().height() < height_need: if self.tabs.widget(0).frameSize().height() < height_need:
plotWidget.setMinimumHeight(height_need) plotWidget.setMinimumHeight(height_need)
@ -2290,24 +2290,24 @@ class MainWindow(QMainWindow):
self.plotWaveformDataThread() self.plotWaveformDataThread()
def pushFilterWF(self, param_args): def pushFilterWF(self, param_args):
self.get_data().filterWFData(param_args) self.get_data().filter_wf_data(param_args)
def filterP(self): def filterP(self):
self.filterActionS.setChecked(False) self.filterActionS.setChecked(False)
if self.filterActionP.isChecked(): if self.filterActionP.isChecked():
self.filterWaveformData(phase='P') self.filterWaveformData(phase='P')
else: else:
self.resetWFData() self.reset_wf_data()
def filterS(self): def filterS(self):
self.filterActionP.setChecked(False) self.filterActionP.setChecked(False)
if self.filterActionS.isChecked(): if self.filterActionS.isChecked():
self.filterWaveformData(phase='S') self.filterWaveformData(phase='S')
else: else:
self.resetWFData() self.reset_wf_data()
def resetWFData(self): def reset_wf_data(self):
self.get_data().resetWFData() self.get_data().reset_wf_data()
self.plotWaveformDataThread() self.plotWaveformDataThread()
def filterWaveformData(self, plot=True, phase=None): def filterWaveformData(self, plot=True, phase=None):
@ -2326,11 +2326,11 @@ class MainWindow(QMainWindow):
kwargs = self.getFilterOptions()[phase].parseFilterOptions() kwargs = self.getFilterOptions()[phase].parseFilterOptions()
self.pushFilterWF(kwargs) self.pushFilterWF(kwargs)
else: else:
self.get_data().resetWFData() self.get_data().reset_wf_data()
elif self.filterActionP.isChecked() or self.filterActionS.isChecked(): elif self.filterActionP.isChecked() or self.filterActionS.isChecked():
self.adjustFilterOptions() self.adjustFilterOptions()
else: else:
self.get_data().resetWFData() self.get_data().reset_wf_data()
if plot: if plot:
self.plotWaveformDataThread(filter=False) self.plotWaveformDataThread(filter=False)
@ -2531,10 +2531,10 @@ class MainWindow(QMainWindow):
show_comp_data=self.dataPlot.comp_checkbox.isChecked()) show_comp_data=self.dataPlot.comp_checkbox.isChecked())
if self.filterActionP.isChecked(): if self.filterActionP.isChecked():
pickDlg.currentPhase = "P" pickDlg.currentPhase = "P"
pickDlg.filterWFData() pickDlg.filter_wf_data()
elif self.filterActionS.isChecked(): elif self.filterActionS.isChecked():
pickDlg.currentPhase = "S" pickDlg.currentPhase = "S"
pickDlg.filterWFData() pickDlg.filter_wf_data()
pickDlg.nextStation.setChecked(self.nextStation) pickDlg.nextStation.setChecked(self.nextStation)
pickDlg.nextStation.stateChanged.connect(self.toggle_next_station) pickDlg.nextStation.stateChanged.connect(self.toggle_next_station)
if pickDlg.exec_(): if pickDlg.exec_():
@ -3478,7 +3478,7 @@ class MainWindow(QMainWindow):
if not self.metadata: if not self.metadata:
return None return None
wf_copy = self.get_data().getWFData().copy() wf_copy = self.get_data().get_wf_data().copy()
wf_select = Stream() wf_select = Stream()
# restitute only picked traces # restitute only picked traces

6
autoPyLoT.py
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@ -243,7 +243,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
pylot_event = Event(eventpath) # event should be path to event directory pylot_event = Event(eventpath) # event should be path to event directory
data.setEvtData(pylot_event) data.setEvtData(pylot_event)
if fnames == 'None': if fnames == 'None':
data.setWFData(glob.glob(os.path.join(datapath, event_datapath, '*'))) data.set_wf_data(glob.glob(os.path.join(datapath, event_datapath, '*')))
# the following is necessary because within # the following is necessary because within
# multiple event processing no event ID is provided # multiple event processing no event ID is provided
# in autopylot.in # in autopylot.in
@ -258,7 +258,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
now.minute) now.minute)
parameter.setParam(eventID=eventID) parameter.setParam(eventID=eventID)
else: else:
data.setWFData(fnames) data.set_wf_data(fnames)
eventpath = events[0] eventpath = events[0]
# now = datetime.datetime.now() # now = datetime.datetime.now()
@ -268,7 +268,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
# now.hour, # now.hour,
# now.minute) # now.minute)
parameter.setParam(eventID=eventid) parameter.setParam(eventID=eventid)
wfdat = data.getWFData() # all available streams wfdat = data.get_wf_data() # all available streams
if not station == 'all': if not station == 'all':
wfdat = wfdat.select(station=station) wfdat = wfdat.select(station=station)
if not wfdat: if not wfdat:

13
pylot/core/io/data.py
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@ -9,11 +9,13 @@ from obspy import UTCDateTime
from pylot.core.io.event import EventData from pylot.core.io.event import EventData
from pylot.core.io.waveformdata import WaveformData from pylot.core.io.waveformdata import WaveformData
from pylot.core.util.dataprocessing import Metadata
@dataclass @dataclass
class Data: class Data:
event_data: EventData = field(default_factory=EventData) event_data: EventData = field(default_factory=EventData)
waveform_data: WaveformData = field(default_factory=WaveformData) waveform_data: WaveformData = field(default_factory=WaveformData)
metadata: Metadata = field(default_factory=Metadata)
_parent: Union[None, 'QtWidgets.QWidget'] = None _parent: Union[None, 'QtWidgets.QWidget'] = None
def __init__(self, parent=None, evtdata=None): def __init__(self, parent=None, evtdata=None):
@ -52,10 +54,17 @@ class Data:
self.waveform_data.dirty = True self.waveform_data.dirty = True
def set_wf_data(self, fnames: List[str], fnames_alt: List[str] = None, check_rotated=False, metadata=None, tstart=0, tstop=0): def set_wf_data(self, fnames: List[str], fnames_alt: List[str] = None, check_rotated=False, metadata=None, tstart=0, tstop=0):
return self.waveform_data.set_wf_data(fnames, fnames_alt, check_rotated, metadata, tstart, tstop) return self.waveform_data.load_waveforms(fnames, fnames_alt, check_rotated, metadata, tstart, tstop)
def reset_wf_data(self): def reset_wf_data(self):
self.waveform_data.reset_wf_data() self.waveform_data.reset()
def get_wf_data(self):
return self.waveform_data.wfdata
def rotate_wf_data(self):
self.waveform_data.rotate_zne(self.metadata)
class GenericDataStructure(object): class GenericDataStructure(object):
""" """

13
pylot/core/io/utils.py Normal file
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@ -0,0 +1,13 @@
import os
from typing import List
def validate_filenames(filenames: List[str]) -> List[str]:
"""
validate a list of filenames for file abundance
:param filenames: list of possible filenames
:type filenames: List[str]
:return: list of valid filenames
:rtype: List[str]
"""
return [fn for fn in filenames if os.path.isfile(fn)]

236
pylot/core/io/waveformdata.py
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@ -1,14 +1,13 @@
import logging import logging
import os
from dataclasses import dataclass, field from dataclasses import dataclass, field
from typing import Union, List from typing import Union, List
import numpy as np
from obspy import Stream, read from obspy import Stream, read
from obspy.io.sac import SacIOError from obspy.io.sac import SacIOError
from obspy.signal.rotate import rotate2zne
from pylot.core.util.utils import full_range, get_stations from pylot.core.io.utils import validate_filenames
from pylot.core.util.dataprocessing import Metadata
from pylot.core.util.utils import get_stations, check_for_nan, check4rotated
@dataclass @dataclass
@ -18,26 +17,39 @@ class WaveformData:
wf_alt: Stream = field(default_factory=Stream) wf_alt: Stream = field(default_factory=Stream)
dirty: bool = False dirty: bool = False
def set_wf_data(self, fnames: List[str], fnames_alt: List[str] = None, check_rotated=False, metadata=None, tstart=0, tstop=0): def load_waveforms(self, fnames: List[str], fnames_alt: List[str] = None, check_rotated=False, metadata=None, tstart=0, tstop=0):
self.clear_data() fn_list = validate_filenames(fnames)
fnames = self.check_fname_exists(fnames) if not fn_list:
fnames_alt = self.check_fname_exists(fnames_alt) logging.warning('No valid filenames given for loading waveforms')
else:
self.clear()
self.add_waveforms(fn_list)
if fnames: if fnames_alt is None:
self.append_wf_data(fnames) pass
if fnames_alt: else:
self.append_wf_data(fnames_alt, alternative=True) alt_fn_list = validate_filenames(fnames_alt)
self.wfdata, _ = self.check_for_gaps_and_merge(self.wfdata) if not alt_fn_list:
self.check_for_nan(self.wfdata) logging.warning('No valid alternative filenames given for loading waveforms')
if check_rotated and metadata: else:
self.wfdata = self.check4rotated(self.wfdata, metadata, verbosity=0) self.add_waveforms(alt_fn_list, alternative=True)
self.trim_station_components(self.wfdata, trim_start=True, trim_end=False)
self.wforiginal = self.wfdata.copy()
self.dirty = False
return True
return False
def append_wf_data(self, fnames: List[str], alternative: bool = False): if not fn_list and not alt_fn_list:
logging.error('No filenames or alternative filenames given for loading waveforms')
return False
self.merge()
self.replace_nan()
if not check_rotated or not metadata:
pass
else:
self.rotate_zne()
self.trim_station_traces()
self.wforiginal = self.wfdata.copy()
self.dirty = False
return True
def add_waveforms(self, fnames: List[str], alternative: bool = False):
data_stream = self.wf_alt if alternative else self.wfdata data_stream = self.wf_alt if alternative else self.wfdata
warnmsg = '' warnmsg = ''
for fname in set(fnames): for fname in set(fnames):
@ -55,189 +67,57 @@ class WaveformData:
warnmsg += f'{fname}\n{se}\n' warnmsg += f'{fname}\n{se}\n'
if warnmsg: if warnmsg:
print(f'WARNING in appendWFData: unable to read waveform data\n{warnmsg}') print(f'WARNING in add_waveforms: unable to read waveform data\n{warnmsg}')
def clear_data(self): def clear(self):
self.wfdata = Stream() self.wfdata = Stream()
self.wforiginal = None self.wforiginal = None
self.wf_alt = Stream() self.wf_alt = Stream()
def reset_wf_data(self): def reset(self):
"""
Resets the waveform data to its original state.
"""
if self.wforiginal: if self.wforiginal:
self.wfdata = self.wforiginal.copy() self.wfdata = self.wforiginal.copy()
else: else:
self.wfdata = Stream() self.wfdata = Stream()
self.dirty = False self.dirty = False
def check_fname_exists(self, filenames: List[str]) -> List[str]: def merge(self):
return [fn for fn in filenames if os.path.isfile(fn)]
def check_for_gaps_and_merge(self, stream):
""" """
check for gaps in Stream and merge if gaps are found check for gaps in Stream and merge if gaps are found
:param stream: stream of seismic data
:type stream: `~obspy.core.stream.Stream`
:return: data stream, gaps returned from obspy get_gaps
:rtype: `~obspy.core.stream.Stream`
""" """
gaps = stream.get_gaps() gaps = self.wfdata.get_gaps()
if gaps: if gaps:
merged = ['{}.{}.{}.{}'.format(*gap[:4]) for gap in gaps] merged = ['{}.{}.{}.{}'.format(*gap[:4]) for gap in gaps]
stream.merge(method=1) self.wfdata.merge(method=1)
print('Merged the following stations because of gaps:') logging.info('Merged the following stations because of gaps:')
for merged_station in merged: for station in merged:
print(merged_station) logging.info(station)
return stream, gaps def replace_nan(self):
def check_for_nan(self, stream):
""" """
Replace all NaNs in data with nan_value (in place) Replace all NaNs in data with 0. (in place)
:param stream: stream of seismic data
:type stream: `~obspy.core.stream.Stream`
:param nan_value: value which all NaNs are set to
:type nan_value: float, int
:return: None
""" """
if not stream: self.wfdata = check_for_nan(self.wfdata)
return
for trace in stream:
np.nan_to_num(trace.data, copy=False, nan=0.)
def rotate_zne(self, metadata: Metadata = None):
def check4rotated(self, stream, metadata=None, verbosity=1):
""" """
Check all traces in data. If a trace is not in ZNE rotation (last symbol of channel code is numeric) and the trace Check all traces in stream for rotation. If a trace is not in ZNE rotation (last symbol of channel code is numeric) and the trace
is in the metadata with azimuth and dip, rotate it to classical ZNE orientation. is in the metadata with azimuth and dip, rotate it to classical ZNE orientation.
Rotating the traces requires them to be of the same length, so, all traces will be trimmed to a common length as a Rotating the traces requires them to be of the same length, so, all traces will be trimmed to a common length as a
side effect. side effect.
:param stream: stream object containing seismic traces
:type stream: `~obspy.core.stream.Stream`
:param metadata: tuple containing metadata type string and metadata parser object
:type metadata: (str, `~obspy.io.xseed.parser.Parser`)
:param verbosity: if 0 print no information at runtime
:type verbosity: int
:return: stream object with traditionally oriented traces (ZNE) for stations that had misaligned traces (123) before
:rtype: `~obspy.core.stream.Stream`
""" """
def rotation_required(trace_ids): self.wfdata = check4rotated(self.wfdata, metadata)
"""
Derive if any rotation is required from the orientation code of the input.
:param trace_ids: string identifier of waveform data trace def trim_station_traces(self):
: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 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`
"""
if len(wfs_in) < 3:
print(f"Stream {wfs_in=}, has not enough components to rotate.")
return wfs_in
# 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):
logging.debug(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:
logging.error(
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 = self.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:
msg = 'Warning: could not rotate traces since no metadata was given\nset Inventory file!'
print(msg)
return stream
stations = get_stations(stream)
for station in stations: # loop through all stations and rotate data if neccessary
wf_station = stream.select(station=station)
rotate_components(wf_station, metadata)
return stream
def trim_station_components(stream, 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 trim data stream to common time window
:param stream: stream of seismic data
:type stream: `~obspy.core.stream.Stream`
:param trim_start: trim start of stream
:type trim_start: bool
:param trim_end: trim end of stream
:type trim_end: bool
:return: data stream
:rtype: `~obspy.core.stream.Stream`
""" """
starttime = {False: None}
endtime = {False: None}
stations = get_stations(stream) for station in get_stations(self.wfdata):
station_traces = self.wfdata.select(station=station)
print('trim_station_components: Will trim stream for trim_start: {} and for ' station_traces.trim(starttime=max([trace.stats.starttime for trace in station_traces]),
'trim_end: {}.'.format(trim_start, trim_end)) endtime=min([trace.stats.endtime for trace in station_traces]))
for station in stations:
wf_station = stream.select(station=station)
starttime[True] = max([trace.stats.starttime for trace in wf_station])
endtime[True] = min([trace.stats.endtime for trace in wf_station])
wf_station.trim(starttime=starttime[trim_start], endtime=endtime[trim_end])
return stream

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

@ -474,8 +474,8 @@ class Array_map(QtWidgets.QWidget):
transform=ccrs.PlateCarree(), label='deleted')) transform=ccrs.PlateCarree(), label='deleted'))
def openPickDlg(self, ind): def openPickDlg(self, ind):
wfdata = self._parent.get_data().getWFData() wfdata = self._parent.get_data().get_wf_data()
wfdata_comp = self._parent.get_data().getWFDataComp() wfdata_comp = self._parent.get_data().get_wf_dataComp()
for index in ind: for index in ind:
network, station = self._station_onpick_ids[index].split('.')[:2] network, station = self._station_onpick_ids[index].split('.')[:2]
pyl_mw = self._parent pyl_mw = self._parent

445
pylot/core/util/widgets.py
View File

@ -140,18 +140,6 @@ class LogWidget(QtWidgets.QWidget):
self.stderr.append(60 * '#' + '\n\n') self.stderr.append(60 * '#' + '\n\n')
def getDataType(parent):
type = QInputDialog().getItem(parent, "Select phases type", "Type:",
["manual", "automatic"])
if type[0].startswith('auto'):
type = 'auto'
else:
type = type[0]
return type
def plot_pdf(_axes, x, y, annotation, bbox_props, xlabel=None, ylabel=None, def plot_pdf(_axes, x, y, annotation, bbox_props, xlabel=None, ylabel=None,
title=None): title=None):
# try method or data # try method or data
@ -795,7 +783,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
def connect_signals(self): def connect_signals(self):
self.qcombo_processed.activated.connect(self.parent().newWF) self.qcombo_processed.activated.connect(self.parent().newWF)
self.syn_checkbox.clicked.connect(self.parent().newWF) self.comp_checkbox.clicked.connect(self.parent().newWF)
def init_labels(self): def init_labels(self):
self.label_layout.addWidget(self.status_label) self.label_layout.addWidget(self.status_label)
@ -806,13 +794,13 @@ class WaveformWidgetPG(QtWidgets.QWidget):
# use widgets as placeholder, so that child widgets keep position when others are hidden # use widgets as placeholder, so that child widgets keep position when others are hidden
mid_layout = QHBoxLayout() mid_layout = QHBoxLayout()
right_layout = QHBoxLayout() right_layout = QHBoxLayout()
mid_layout.addWidget(self.syn_checkbox) mid_layout.addWidget(self.comp_checkbox)
right_layout.addWidget(self.qcombo_processed) right_layout.addWidget(self.qcombo_processed)
mid_widget.setLayout(mid_layout) mid_widget.setLayout(mid_layout)
right_widget.setLayout(right_layout) right_widget.setLayout(right_layout)
self.label_layout.addWidget(mid_widget) self.label_layout.addWidget(mid_widget)
self.label_layout.addWidget(right_widget) self.label_layout.addWidget(right_widget)
self.syn_checkbox.setLayoutDirection(Qt.RightToLeft) self.comp_checkbox.setLayoutDirection(Qt.RightToLeft)
self.label_layout.setStretch(0, 4) self.label_layout.setStretch(0, 4)
self.label_layout.setStretch(1, 0) self.label_layout.setStretch(1, 0)
self.label_layout.setStretch(2, 0) self.label_layout.setStretch(2, 0)
@ -827,7 +815,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
label = QtWidgets.QLabel() label = QtWidgets.QLabel()
self.perm_labels.append(label) self.perm_labels.append(label)
self.qcombo_processed = QtWidgets.QComboBox() self.qcombo_processed = QtWidgets.QComboBox()
self.syn_checkbox = QtWidgets.QCheckBox('synthetics') self.comp_checkbox = QtWidgets.QCheckBox('Load comparison data')
self.addQCboxItem('processed', 'green') self.addQCboxItem('processed', 'green')
self.addQCboxItem('raw', 'black') self.addQCboxItem('raw', 'black')
# self.perm_qcbox_right.setAlignment(2) # self.perm_qcbox_right.setAlignment(2)
@ -836,9 +824,11 @@ class WaveformWidgetPG(QtWidgets.QWidget):
def getPlotDict(self): def getPlotDict(self):
return self.plotdict return self.plotdict
def activateObspyDMToptions(self, activate): def activateObspyDMToptions(self, activate: bool) -> None:
self.syn_checkbox.setVisible(activate) self.qcombo_processed.setEnabled(activate)
self.qcombo_processed.setVisible(activate)
def activateCompareOptions(self, activate: bool) -> None:
self.comp_checkbox.setEnabled(activate)
def setPermText(self, number, text=None, color='black'): def setPermText(self, number, text=None, color='black'):
if not 0 <= number < len(self.perm_labels): if not 0 <= number < len(self.perm_labels):
@ -961,7 +951,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
[time for index, time in enumerate(time_ax_syn) if not index % nth_sample] if st_syn else []) [time for index, time in enumerate(time_ax_syn) if not index % nth_sample] if st_syn else [])
trace.data = np.array( trace.data = np.array(
[datum * gain + n for index, datum in enumerate(trace.data) if not index % nth_sample]) [datum * gain + n for index, datum in enumerate(trace.data) if not index % nth_sample])
trace_syn.data = np.array([datum + n for index, datum in enumerate(trace_syn.data) trace_syn.data = np.array([datum + n + shift_syn for index, datum in enumerate(trace_syn.data)
if not index % nth_sample] if st_syn else []) if not index % nth_sample] if st_syn else [])
plots.append((times, trace.data, plots.append((times, trace.data,
times_syn, trace_syn.data)) times_syn, trace_syn.data))
@ -1007,15 +997,6 @@ class WaveformWidgetPG(QtWidgets.QWidget):
time_ax = np.linspace(time_ax[0], time_ax[-1], num=len(data)) time_ax = np.linspace(time_ax[0], time_ax[-1], num=len(data))
return data, time_ax return data, time_ax
# def getAxes(self):
# return self.axes
# def getXLims(self):
# return self.getAxes().get_xlim()
# def getYLims(self):
# return self.getAxes().get_ylim()
def setXLims(self, lims): def setXLims(self, lims):
vb = self.plotWidget.getPlotItem().getViewBox() vb = self.plotWidget.getPlotItem().getViewBox()
vb.setXRange(float(lims[0]), float(lims[1]), padding=0) vb.setXRange(float(lims[0]), float(lims[1]), padding=0)
@ -1169,8 +1150,6 @@ class PylotCanvas(FigureCanvas):
break break
if not ax_check: return if not ax_check: return
# self.updateCurrentLimits() #maybe put this down to else:
# calculate delta (relative values in axis) # calculate delta (relative values in axis)
old_x, old_y = self.press_rel old_x, old_y = self.press_rel
xdiff = gui_event.x - old_x xdiff = gui_event.x - old_x
@ -1373,110 +1352,145 @@ class PylotCanvas(FigureCanvas):
plot_positions[channel] = plot_pos plot_positions[channel] = plot_pos
return plot_positions return plot_positions
def plotWFData(self, wfdata, title=None, zoomx=None, zoomy=None, def plotWFData(self, wfdata, wfdata_compare=None, title=None, zoomx=None, zoomy=None,
noiselevel=None, scaleddata=False, mapping=True, noiselevel=None, scaleddata=False, mapping=True,
component='*', nth_sample=1, iniPick=None, verbosity=0, 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): snr=None):
ax = self.prepare_plot()
self.clearPlotDict()
wfstart, wfend = self.get_wf_range(wfdata)
compclass = self.get_comp_class()
plot_streams = self.get_plot_streams(wfdata, wfdata_compare, component, compclass)
st_main = plot_streams['wfdata']['data']
if mapping:
plot_positions = self.calcPlotPositions(st_main, compclass)
nslc = self.get_sorted_nslc(st_main)
nmax = self.plot_traces(ax, plot_streams, nslc, wfstart, mapping, plot_positions,
scaleToChannel, noiselevel, scaleddata, nth_sample, verbosity)
if plot_additional and additional_channel:
self.plot_additional_trace(ax, wfdata, additional_channel, scaleToChannel,
scaleddata, nth_sample, wfstart)
self.finalize_plot(ax, wfstart, wfend, nmax, zoomx, zoomy, iniPick, title, snr)
def prepare_plot(self):
ax = self.axes[0] ax = self.axes[0]
ax.cla() ax.cla()
return ax
self.clearPlotDict() def get_wf_range(self, wfdata):
wfstart, wfend = full_range(wfdata) return full_range(wfdata)
nmax = 0
def get_comp_class(self):
settings = QSettings() settings = QSettings()
compclass = SetChannelComponents.from_qsettings(settings) return SetChannelComponents.from_qsettings(settings)
if not component == '*': def get_plot_streams(self, wfdata, wfdata_compare, component, compclass):
alter_comp = compclass.getCompPosition(component) def get_wf_dict(data=Stream(), linecolor='k', offset=0., **plot_kwargs):
# alter_comp = str(alter_comp[0]) return dict(data=data, linecolor=linecolor, offset=offset, plot_kwargs=plot_kwargs)
st_select = wfdata.select(component=component)
st_select += wfdata.select(component=alter_comp)
else:
st_select = wfdata
if mapping:
plot_positions = self.calcPlotPositions(st_select, compclass)
# list containing tuples of network, station, channel and plot position (for sorting)
nslc = []
for plot_pos, trace in enumerate(st_select):
if not trace.stats.channel[-1] in ['Z', 'N', 'E', '1', '2', '3']:
print('Warning: Unrecognized channel {}'.format(trace.stats.channel))
continue
nslc.append(trace.get_id())
nslc.sort()
nslc.reverse()
linecolor = (0., 0., 0., 1.) if not self.style else self.style['linecolor']['rgba_mpl'] linecolor = (0., 0., 0., 1.) if not self.style else self.style['linecolor']['rgba_mpl']
plot_streams = {
'wfdata': get_wf_dict(linecolor=linecolor, linewidth=0.7),
'wfdata_comp': get_wf_dict(offset=0.1, linecolor='b', alpha=0.7, linewidth=0.5)
}
if component != '*':
alter_comp = compclass.getCompPosition(component)
plot_streams['wfdata']['data'] = wfdata.select(component=component) + wfdata.select(component=alter_comp)
if wfdata_compare:
plot_streams['wfdata_comp']['data'] = wfdata_compare.select(
component=component) + wfdata_compare.select(component=alter_comp)
else:
plot_streams['wfdata']['data'] = wfdata
if wfdata_compare:
plot_streams['wfdata_comp']['data'] = wfdata_compare
return plot_streams
def get_sorted_nslc(self, st_main):
nslc = [trace.get_id() for trace in st_main if trace.stats.channel[-1] in ['Z', 'N', 'E', '1', '2', '3']]
nslc.sort(reverse=True)
return nslc
def plot_traces(self, ax, plot_streams, nslc, wfstart, mapping, plot_positions, scaleToChannel, noiselevel,
scaleddata, nth_sample, verbosity):
nmax = 0
for n, seed_id in enumerate(nslc): for n, seed_id in enumerate(nslc):
network, station, location, channel = seed_id.split('.') network, station, location, channel = seed_id.split('.')
st = st_select.select(id=seed_id) for wf_name, wf_dict in plot_streams.items():
trace = st[0].copy() st_select = wf_dict.get('data')
if mapping: if not st_select:
n = plot_positions[trace.stats.channel] continue
if n > nmax: trace = st_select.select(id=seed_id)[0].copy()
nmax = n if mapping:
if verbosity: n = plot_positions[trace.stats.channel]
msg = 'plotting %s channel of station %s' % (channel, station) if n > nmax:
print(msg) nmax = n
stime = trace.stats.starttime - wfstart if verbosity:
time_ax = prep_time_axis(stime, trace) print(f'plotting {channel} channel of station {station}')
if time_ax is not None: time_ax = prep_time_axis(trace.stats.starttime - wfstart, trace)
if scaleToChannel: self.plot_trace(ax, trace, time_ax, wf_dict, n, scaleToChannel, noiselevel, scaleddata, nth_sample)
st_scale = wfdata.select(channel=scaleToChannel)
if st_scale:
tr = st_scale[0]
trace.detrend('constant')
trace.normalize(np.max(np.abs(tr.data)) * 2)
scaleddata = True
if not scaleddata:
trace.detrend('constant')
trace.normalize(np.max(np.abs(trace.data)) * 2)
times = [time for index, time in enumerate(time_ax) if not index % nth_sample]
data = [datum + n for index, datum in enumerate(trace.data) if not index % nth_sample]
ax.axhline(n, color="0.5", lw=0.5)
ax.plot(times, data, color=linecolor, linewidth=0.7)
if noiselevel is not None:
for level in [-noiselevel[channel], noiselevel[channel]]:
ax.plot([time_ax[0], time_ax[-1]],
[n + level, n + level],
color=linecolor,
linestyle='dashed')
self.setPlotDict(n, seed_id) self.setPlotDict(n, seed_id)
if plot_additional and additional_channel: return nmax
compare_stream = wfdata.select(channel=additional_channel)
if compare_stream:
trace = compare_stream[0]
if scaleToChannel:
st_scale = wfdata.select(channel=scaleToChannel)
if st_scale:
tr = st_scale[0]
trace.detrend('constant')
trace.normalize(np.max(np.abs(tr.data)) * 2)
scaleddata = True
if not scaleddata:
trace.detrend('constant')
trace.normalize(np.max(np.abs(trace.data)) * 2)
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
# p_max = max(abs(p_data))
# p_data /= p_max
for index in range(3):
ax.plot(times, p_data, color='red', alpha=0.5, linewidth=0.7)
p_data += 1
def plot_trace(self, ax, trace, time_ax, wf_dict, n, scaleToChannel, noiselevel, scaleddata, nth_sample):
if time_ax is not None:
if scaleToChannel:
self.scale_trace(trace, scaleToChannel)
scaleddata = True
if not scaleddata:
trace.detrend('constant')
trace.normalize(np.max(np.abs(trace.data)) * 2)
offset = wf_dict.get('offset')
times = [time for index, time in enumerate(time_ax) if not index % nth_sample]
data = [datum + n + offset for index, datum in enumerate(trace.data) if not index % nth_sample]
ax.axhline(n, color="0.5", lw=0.5)
ax.plot(times, data, color=wf_dict.get('linecolor'), **wf_dict.get('plot_kwargs'))
if noiselevel is not None:
self.plot_noise_level(ax, time_ax, noiselevel, channel, n, wf_dict.get('linecolor'))
def scale_trace(self, trace, scaleToChannel):
st_scale = wfdata.select(channel=scaleToChannel)
if st_scale:
tr = st_scale[0]
trace.detrend('constant')
trace.normalize(np.max(np.abs(tr.data)) * 2)
def plot_noise_level(self, ax, time_ax, noiselevel, channel, n, linecolor):
for level in [-noiselevel[channel], noiselevel[channel]]:
ax.plot([time_ax[0], time_ax[-1]], [n + level, n + level], color=linecolor, linestyle='dashed')
def plot_additional_trace(self, ax, wfdata, additional_channel, scaleToChannel, scaleddata, nth_sample, wfstart):
compare_stream = wfdata.select(channel=additional_channel)
if compare_stream:
trace = compare_stream[0]
if scaleToChannel:
self.scale_trace(trace, scaleToChannel)
scaleddata = True
if not scaleddata:
trace.detrend('constant')
trace.normalize(np.max(np.abs(trace.data)) * 2)
time_ax = prep_time_axis(trace.stats.starttime - wfstart, trace)
self.plot_additional_data(ax, trace, time_ax, nth_sample)
def plot_additional_data(self, ax, trace, time_ax, nth_sample):
times = [time for index, time in enumerate(time_ax) if not index % nth_sample]
p_data = trace.data
for index in range(3):
ax.plot(times, p_data, color='red', alpha=0.5, linewidth=0.7)
p_data += 1
def finalize_plot(self, ax, wfstart, wfend, nmax, zoomx, zoomy, iniPick, title, snr):
if iniPick: if iniPick:
ax.vlines(iniPick, ax.get_ylim()[0], ax.get_ylim()[1], ax.vlines(iniPick, ax.get_ylim()[0], ax.get_ylim()[1], colors='m', linestyles='dashed', linewidth=2)
colors='m', linestyles='dashed', xlabel = f'seconds since {wfstart}'
linewidth=2)
xlabel = 'seconds since {0}'.format(wfstart)
ylabel = '' ylabel = ''
self.updateWidget(xlabel, ylabel, title) self.updateWidget(xlabel, ylabel, title)
self.setXLims(ax, [0, wfend - wfstart]) self.setXLims(ax, [0, wfend - wfstart])
@ -1486,15 +1500,14 @@ class PylotCanvas(FigureCanvas):
if zoomy is not None: if zoomy is not None:
self.setYLims(ax, zoomy) self.setYLims(ax, zoomy)
if snr is not None: if snr is not None:
if snr < 2: self.plot_snr_warning(ax, snr)
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() self.draw()
def plot_snr_warning(self, ax, snr):
if snr < 2:
warning = 'LOW SNR' if snr >= 1.5 else 'VERY LOW SNR'
ax.text(0.1, 0.9, f'WARNING - {warning}', ha='center', va='center', transform=ax.transAxes, color='red')
@staticmethod @staticmethod
def getXLims(ax): def getXLims(ax):
return ax.get_xlim() return ax.get_xlim()
@ -1846,8 +1859,8 @@ class PhaseDefaults(QtWidgets.QDialog):
class PickDlg(QDialog): class PickDlg(QDialog):
update_picks = QtCore.Signal(dict) update_picks = QtCore.Signal(dict)
def __init__(self, parent=None, data=None, station=None, network=None, location=None, picks=None, def __init__(self, parent=None, data=None, data_compare=None, station=None, network=None, location=None, picks=None,
autopicks=None, rotate=False, parameter=None, embedded=False, metadata=None, autopicks=None, rotate=False, parameter=None, embedded=False, metadata=None, show_comp_data=False,
event=None, filteroptions=None, model=None, wftype=None): event=None, filteroptions=None, model=None, wftype=None):
super(PickDlg, self).__init__(parent, Qt.Window) super(PickDlg, self).__init__(parent, Qt.Window)
self.orig_parent = parent self.orig_parent = parent
@ -1856,6 +1869,7 @@ class PickDlg(QDialog):
# initialize attributes # initialize attributes
self.parameter = parameter self.parameter = parameter
self._embedded = embedded self._embedded = embedded
self.showCompData = show_comp_data
self.station = station self.station = station
self.network = network self.network = network
self.location = location self.location = location
@ -1894,11 +1908,32 @@ class PickDlg(QDialog):
else: else:
self.filteroptions = FILTERDEFAULTS self.filteroptions = FILTERDEFAULTS
self.pick_block = False self.pick_block = False
# set attribute holding data
if data is None or not data:
try:
data = parent.get_data().get_wf_data().copy()
self.data = data.select(station=station)
except AttributeError as e:
errmsg = 'You either have to put in a data or an appropriate ' \
'parent (PyLoT MainWindow) object: {0}'.format(e)
raise Exception(errmsg)
else:
self.data = data
self.data_compare = data_compare
self.nextStation = QtWidgets.QCheckBox('Continue with next station ') self.nextStation = QtWidgets.QCheckBox('Continue with next station ')
# comparison channel # comparison channel
self.compareChannel = QtWidgets.QComboBox() self.referenceChannel = QtWidgets.QComboBox()
self.compareChannel.activated.connect(self.resetPlot) self.referenceChannel.activated.connect(self.resetPlot)
# comparison channel
self.compareCB = QtWidgets.QCheckBox()
self.compareCB.setChecked(self.showCompData)
self.compareCB.clicked.connect(self.switchCompData)
self.compareCB.clicked.connect(self.resetPlot)
self.compareCB.setVisible(bool(self.data_compare))
# scale channel # scale channel
self.scaleChannel = QtWidgets.QComboBox() self.scaleChannel = QtWidgets.QComboBox()
@ -1911,19 +1946,7 @@ class PickDlg(QDialog):
self.cur_xlim = None self.cur_xlim = None
self.cur_ylim = None self.cur_ylim = None
# set attribute holding data self.stime, self.etime = full_range(self.get_wf_data())
if data is None or not data:
try:
data = parent.get_data().getWFData().copy()
self.data = data.select(station=station)
except AttributeError as e:
errmsg = 'You either have to put in a data or an appropriate ' \
'parent (PyLoT MainWindow) object: {0}'.format(e)
raise Exception(errmsg)
else:
self.data = data
self.stime, self.etime = full_range(self.getWFData())
# initialize plotting widget # initialize plotting widget
self.multicompfig = PylotCanvas(parent=self, multicursor=True) self.multicompfig = PylotCanvas(parent=self, multicursor=True)
@ -1934,12 +1957,12 @@ class PickDlg(QDialog):
self.setupUi() self.setupUi()
# fill compare and scale channels # fill compare and scale channels
self.compareChannel.addItem('-', None) self.referenceChannel.addItem('-', None)
self.scaleChannel.addItem('individual', None) self.scaleChannel.addItem('individual', None)
for trace in self.getWFData(): for trace in self.get_wf_data():
channel = trace.stats.channel channel = trace.stats.channel
self.compareChannel.addItem(channel, trace) self.referenceChannel.addItem(channel, trace)
if not channel[-1] in ['Z', 'N', 'E', '1', '2', '3']: if not channel[-1] in ['Z', 'N', 'E', '1', '2', '3']:
print('Skipping unknown channel for scaling: {}'.format(channel)) print('Skipping unknown channel for scaling: {}'.format(channel))
continue continue
@ -1956,7 +1979,7 @@ class PickDlg(QDialog):
if self.wftype is not None: if self.wftype is not None:
title += ' | ({})'.format(self.wftype) title += ' | ({})'.format(self.wftype)
self.multicompfig.plotWFData(wfdata=self.getWFData(), self.multicompfig.plotWFData(wfdata=self.get_wf_data(), wfdata_compare=self.get_wf_dataComp(),
title=title) title=title)
self.multicompfig.setZoomBorders2content() self.multicompfig.setZoomBorders2content()
@ -2132,8 +2155,11 @@ class PickDlg(QDialog):
_dialtoolbar.addWidget(est_label) _dialtoolbar.addWidget(est_label)
_dialtoolbar.addWidget(self.plot_arrivals_button) _dialtoolbar.addWidget(self.plot_arrivals_button)
_dialtoolbar.addSeparator() _dialtoolbar.addSeparator()
_dialtoolbar.addWidget(QtWidgets.QLabel('Compare to channel: ')) _dialtoolbar.addWidget(QtWidgets.QLabel('Plot reference channel: '))
_dialtoolbar.addWidget(self.compareChannel) _dialtoolbar.addWidget(self.referenceChannel)
_dialtoolbar.addSeparator()
_dialtoolbar.addWidget(QtWidgets.QLabel('Compare: '))
_dialtoolbar.addWidget(self.compareCB)
_dialtoolbar.addSeparator() _dialtoolbar.addSeparator()
_dialtoolbar.addWidget(QtWidgets.QLabel('Scaling: ')) _dialtoolbar.addWidget(QtWidgets.QLabel('Scaling: '))
_dialtoolbar.addWidget(self.scaleChannel) _dialtoolbar.addWidget(self.scaleChannel)
@ -2470,7 +2496,7 @@ class PickDlg(QDialog):
def activatePicking(self): def activatePicking(self):
self.leave_rename_phase() self.leave_rename_phase()
self.renamePhaseAction.setEnabled(False) self.renamePhaseAction.setEnabled(False)
self.compareChannel.setEnabled(False) self.referenceChannel.setEnabled(False)
self.scaleChannel.setEnabled(False) self.scaleChannel.setEnabled(False)
phase = self.currentPhase phase = self.currentPhase
phaseID = self.getPhaseID(phase) phaseID = self.getPhaseID(phase)
@ -2488,7 +2514,7 @@ class PickDlg(QDialog):
if self.autoFilterAction.isChecked(): if self.autoFilterAction.isChecked():
for filteraction in [self.filterActionP, self.filterActionS]: for filteraction in [self.filterActionP, self.filterActionS]:
filteraction.setChecked(False) filteraction.setChecked(False)
self.filterWFData() self.filter_wf_data()
self.draw() self.draw()
else: else:
self.draw() self.draw()
@ -2502,7 +2528,7 @@ class PickDlg(QDialog):
self.disconnectPressEvent() self.disconnectPressEvent()
self.multicompfig.connectEvents() self.multicompfig.connectEvents()
self.renamePhaseAction.setEnabled(True) self.renamePhaseAction.setEnabled(True)
self.compareChannel.setEnabled(True) self.referenceChannel.setEnabled(True)
self.scaleChannel.setEnabled(True) self.scaleChannel.setEnabled(True)
self.connect_pick_delete() self.connect_pick_delete()
self.draw() self.draw()
@ -2572,9 +2598,15 @@ class PickDlg(QDialog):
def getGlobalLimits(self, ax, axis): def getGlobalLimits(self, ax, axis):
return self.multicompfig.getGlobalLimits(ax, axis) return self.multicompfig.getGlobalLimits(ax, axis)
def getWFData(self): def get_wf_data(self):
return self.data return self.data
def get_wf_dataComp(self):
if self.showCompData:
return self.data_compare
else:
return Stream()
def selectWFData(self, channel): def selectWFData(self, channel):
component = channel[-1].upper() component = channel[-1].upper()
wfdata = Stream() wfdata = Stream()
@ -2584,17 +2616,17 @@ class PickDlg(QDialog):
return tr return tr
if component == 'E' or component == 'N': if component == 'E' or component == 'N':
for trace in self.getWFData(): for trace in self.get_wf_data():
trace = selectTrace(trace, 'NE') trace = selectTrace(trace, 'NE')
if trace: if trace:
wfdata.append(trace) wfdata.append(trace)
elif component == '1' or component == '2': elif component == '1' or component == '2':
for trace in self.getWFData(): for trace in self.get_wf_data():
trace = selectTrace(trace, '12') trace = selectTrace(trace, '12')
if trace: if trace:
wfdata.append(trace) wfdata.append(trace)
else: else:
wfdata = self.getWFData().select(component=component) wfdata = self.get_wf_data().select(component=component)
return wfdata return wfdata
def getPicks(self, picktype='manual'): def getPicks(self, picktype='manual'):
@ -2696,11 +2728,16 @@ class PickDlg(QDialog):
stime = self.getStartTime() stime = self.getStartTime()
# copy data for plotting # copy wfdata for plotting
data = self.getWFData().copy() wfdata = self.get_wf_data().copy()
data = self.getPickPhases(data, phase) wfdata_comp = self.get_wf_dataComp().copy()
data.normalize() wfdata = self.getPickPhases(wfdata, phase)
if not data: wfdata_comp = self.getPickPhases(wfdata_comp, phase)
for wfd in [wfdata, wfdata_comp]:
if wfd:
wfd.normalize()
if not wfdata:
QtWidgets.QMessageBox.warning(self, 'No channel to plot', QtWidgets.QMessageBox.warning(self, 'No channel to plot',
'No channel to plot for phase: {}. ' 'No channel to plot for phase: {}. '
'Make sure to select the correct channels for P and S ' 'Make sure to select the correct channels for P and S '
@ -2708,14 +2745,16 @@ class PickDlg(QDialog):
self.leave_picking_mode() self.leave_picking_mode()
return return
# filter data and trace on which is picked prior to determination of SNR # filter wfdata and trace on which is picked prior to determination of SNR
filterphase = self.currentFilterPhase() filterphase = self.currentFilterPhase()
if filterphase: if filterphase:
filteroptions = self.getFilterOptions(filterphase).parseFilterOptions() filteroptions = self.getFilterOptions(filterphase).parseFilterOptions()
try: try:
data.detrend('linear') for wfd in [wfdata, wfdata_comp]:
data.filter(**filteroptions) if wfd:
# wfdata.filter(**filteroptions)# MP MP removed filtering of original data wfd.detrend('linear')
wfd.filter(**filteroptions)
# wfdata.filter(**filteroptions)# MP MP removed filtering of original wfdata
except ValueError as e: except ValueError as e:
self.qmb = QtWidgets.QMessageBox(QtWidgets.QMessageBox.Icon.Information, self.qmb = QtWidgets.QMessageBox(QtWidgets.QMessageBox.Icon.Information,
'Denied', 'Denied',
@ -2725,8 +2764,8 @@ class PickDlg(QDialog):
snr = [] snr = []
noiselevels = {} noiselevels = {}
# determine SNR and noiselevel # determine SNR and noiselevel
for trace in data.traces: for trace in wfdata.traces:
st = data.select(channel=trace.stats.channel) st = wfdata.select(channel=trace.stats.channel)
stime_diff = trace.stats.starttime - stime stime_diff = trace.stats.starttime - stime
result = getSNR(st, (noise_win, gap_win, signal_win), ini_pick - stime_diff) result = getSNR(st, (noise_win, gap_win, signal_win), ini_pick - stime_diff)
snr.append(result[0]) snr.append(result[0])
@ -2737,23 +2776,25 @@ class PickDlg(QDialog):
noiselevel = nfac noiselevel = nfac
noiselevels[trace.stats.channel] = noiselevel noiselevels[trace.stats.channel] = noiselevel
# prepare plotting of data # prepare plotting of wfdata
for trace in data: for wfd in [wfdata, wfdata_comp]:
t = prep_time_axis(trace.stats.starttime - stime, trace) if wfd:
inoise = getnoisewin(t, ini_pick, noise_win, gap_win) for trace in wfd:
trace = demeanTrace(trace, inoise) t = prep_time_axis(trace.stats.starttime - stime, trace)
# upscale trace data in a way that each trace is vertically zoomed to noiselevel*factor inoise = getnoisewin(t, ini_pick, noise_win, gap_win)
channel = trace.stats.channel trace = demeanTrace(trace, inoise)
noiselevel = noiselevels[channel] # upscale trace wfdata in a way that each trace is vertically zoomed to noiselevel*factor
noiseScaleFactor = self.calcNoiseScaleFactor(noiselevel, zoomfactor=5.) channel = trace.stats.channel
trace.data *= noiseScaleFactor noiselevel = noiselevels[channel]
noiselevels[channel] *= noiseScaleFactor noiseScaleFactor = self.calcNoiseScaleFactor(noiselevel, zoomfactor=5.)
trace.data *= noiseScaleFactor
noiselevels[channel] *= noiseScaleFactor
mean_snr = np.mean(snr) mean_snr = np.mean(snr)
x_res = getResolutionWindow(mean_snr, parameter.get('extent')) x_res = getResolutionWindow(mean_snr, parameter.get('extent'))
xlims = [ini_pick - x_res, ini_pick + x_res] xlims = [ini_pick - x_res, ini_pick + x_res]
ylims = list(np.array([-.5, .5]) + [0, len(data) - 1]) ylims = list(np.array([-.5, .5]) + [0, len(wfdata) - 1])
title = self.getStation() + ' picking mode' title = self.getStation() + ' picking mode'
title += ' | SNR: {}'.format(mean_snr) title += ' | SNR: {}'.format(mean_snr)
@ -2761,9 +2802,10 @@ class PickDlg(QDialog):
filtops_str = transformFilteroptions2String(filteroptions) filtops_str = transformFilteroptions2String(filteroptions)
title += ' | Filteroptions: {}'.format(filtops_str) title += ' | Filteroptions: {}'.format(filtops_str)
plot_additional = bool(self.compareChannel.currentText()) plot_additional = bool(self.referenceChannel.currentText())
additional_channel = self.compareChannel.currentText() additional_channel = self.referenceChannel.currentText()
self.multicompfig.plotWFData(wfdata=data, self.multicompfig.plotWFData(wfdata=wfdata,
wfdata_compare=wfdata_comp,
title=title, title=title,
zoomx=xlims, zoomx=xlims,
zoomy=ylims, zoomy=ylims,
@ -2797,7 +2839,7 @@ class PickDlg(QDialog):
filteroptions = None filteroptions = None
# copy and filter data for earliest and latest possible picks # copy and filter data for earliest and latest possible picks
wfdata = self.getWFData().copy().select(channel=channel) wfdata = self.get_wf_data().copy().select(channel=channel)
if filteroptions: if filteroptions:
try: try:
wfdata.detrend('linear') wfdata.detrend('linear')
@ -2844,7 +2886,7 @@ class PickDlg(QDialog):
minFMSNR = parameter.get('minFMSNR') minFMSNR = parameter.get('minFMSNR')
quality = get_quality_class(spe, parameter.get('timeerrorsP')) quality = get_quality_class(spe, parameter.get('timeerrorsP'))
if quality <= minFMweight and snr >= minFMSNR: if quality <= minFMweight and snr >= minFMSNR:
FM = fmpicker(self.getWFData().select(channel=channel).copy(), wfdata.copy(), parameter.get('fmpickwin'), FM = fmpicker(self.get_wf_data().select(channel=channel).copy(), wfdata.copy(), parameter.get('fmpickwin'),
pick - stime_diff) pick - stime_diff)
# save pick times for actual phase # save pick times for actual phase
@ -3136,7 +3178,7 @@ class PickDlg(QDialog):
def togglePickBlocker(self): def togglePickBlocker(self):
return not self.pick_block return not self.pick_block
def filterWFData(self, phase=None): def filter_wf_data(self, phase=None):
if not phase: if not phase:
phase = self.currentPhase phase = self.currentPhase
if self.getPhaseID(phase) == 'P': if self.getPhaseID(phase) == 'P':
@ -3154,7 +3196,8 @@ class PickDlg(QDialog):
self.cur_xlim = self.multicompfig.axes[0].get_xlim() self.cur_xlim = self.multicompfig.axes[0].get_xlim()
self.cur_ylim = self.multicompfig.axes[0].get_ylim() self.cur_ylim = self.multicompfig.axes[0].get_ylim()
# self.multicompfig.updateCurrentLimits() # self.multicompfig.updateCurrentLimits()
data = self.getWFData().copy() wfdata = self.get_wf_data().copy()
wfdata_comp = self.get_wf_dataComp().copy()
title = self.getStation() title = self.getStation()
if filter: if filter:
filtoptions = None filtoptions = None
@ -3162,19 +3205,22 @@ class PickDlg(QDialog):
filtoptions = self.getFilterOptions(self.getPhaseID(phase), gui_filter=True).parseFilterOptions() filtoptions = self.getFilterOptions(self.getPhaseID(phase), gui_filter=True).parseFilterOptions()
if filtoptions is not None: if filtoptions is not None:
data.detrend('linear') for wfd in [wfdata, wfdata_comp]:
data.taper(0.02, type='cosine') if wfd:
data.filter(**filtoptions) wfd.detrend('linear')
wfd.taper(0.02, type='cosine')
wfd.filter(**filtoptions)
filtops_str = transformFilteroptions2String(filtoptions) filtops_str = transformFilteroptions2String(filtoptions)
title += ' | Filteroptions: {}'.format(filtops_str) title += ' | Filteroptions: {}'.format(filtops_str)
if self.wftype is not None: if self.wftype is not None:
title += ' | ({})'.format(self.wftype) title += ' | ({})'.format(self.wftype)
plot_additional = bool(self.compareChannel.currentText()) plot_additional = bool(self.referenceChannel.currentText())
additional_channel = self.compareChannel.currentText() additional_channel = self.referenceChannel.currentText()
scale_channel = self.scaleChannel.currentText() scale_channel = self.scaleChannel.currentText()
self.multicompfig.plotWFData(wfdata=data, title=title, self.multicompfig.plotWFData(wfdata=wfdata, wfdata_compare=wfdata_comp,
title=title,
zoomx=self.getXLims(), zoomx=self.getXLims(),
zoomy=self.getYLims(), zoomy=self.getYLims(),
plot_additional=plot_additional, plot_additional=plot_additional,
@ -3188,14 +3234,14 @@ class PickDlg(QDialog):
def filterP(self): def filterP(self):
self.filterActionS.setChecked(False) self.filterActionS.setChecked(False)
if self.filterActionP.isChecked(): if self.filterActionP.isChecked():
self.filterWFData('P') self.filter_wf_data('P')
else: else:
self.refreshPlot() self.refreshPlot()
def filterS(self): def filterS(self):
self.filterActionP.setChecked(False) self.filterActionP.setChecked(False)
if self.filterActionS.isChecked(): if self.filterActionS.isChecked():
self.filterWFData('S') self.filter_wf_data('S')
else: else:
self.refreshPlot() self.refreshPlot()
@ -3247,11 +3293,14 @@ class PickDlg(QDialog):
self.resetZoom() self.resetZoom()
self.refreshPlot() self.refreshPlot()
def switchCompData(self):
self.showCompData = self.compareCB.isChecked()
def refreshPlot(self): def refreshPlot(self):
if self.autoFilterAction.isChecked(): if self.autoFilterAction.isChecked():
self.filterActionP.setChecked(False) self.filterActionP.setChecked(False)
self.filterActionS.setChecked(False) self.filterActionS.setChecked(False)
# data = self.getWFData().copy() # data = self.get_wf_data().copy()
# title = self.getStation() # title = self.getStation()
filter = False filter = False
phase = None phase = None
@ -3751,8 +3800,8 @@ class TuneAutopicker(QWidget):
fnames = self.station_ids[self.get_current_station_id()] fnames = self.station_ids[self.get_current_station_id()]
if not fnames == self.fnames: if not fnames == self.fnames:
self.fnames = fnames self.fnames = fnames
self.data.setWFData(fnames) self.data.set_wf_data(fnames)
wfdat = self.data.getWFData() # all available streams wfdat = self.data.get_wf_data() # all available streams
# remove possible underscores in station names # remove possible underscores in station names
# wfdat = remove_underscores(wfdat) # wfdat = remove_underscores(wfdat)
# rotate misaligned stations to ZNE # rotate misaligned stations to ZNE
@ -3857,12 +3906,14 @@ class TuneAutopicker(QWidget):
network = None network = None
location = None location = None
wfdata = self.data.getWFData() wfdata = self.data.get_wf_data()
wfdata_comp = self.data.get_wf_dataComp()
metadata = self.parent().metadata metadata = self.parent().metadata
event = self.get_current_event() event = self.get_current_event()
filteroptions = self.parent().filteroptions filteroptions = self.parent().filteroptions
wftype = self.wftype if self.obspy_dmt else '' wftype = self.wftype if self.obspy_dmt else ''
self.pickDlg = PickDlg(self.parent(), data=wfdata.select(station=station).copy(), self.pickDlg = PickDlg(self.parent(), data=wfdata.select(station=station).copy(),
data_comp=wfdata_comp.select(station=station).copy(),
station=station, network=network, station=station, network=network,
location=location, parameter=self.parameter, location=location, parameter=self.parameter,
picks=self.get_current_event_picks(station), picks=self.get_current_event_picks(station),
@ -3911,7 +3962,7 @@ class TuneAutopicker(QWidget):
for plotitem in self._manual_pick_plots: for plotitem in self._manual_pick_plots:
self.clear_plotitem(plotitem) self.clear_plotitem(plotitem)
self._manual_pick_plots = [] self._manual_pick_plots = []
st = self.data.getWFData() st = self.data.get_wf_data()
tr = st.select(station=self.get_current_station())[0] tr = st.select(station=self.get_current_station())[0]
starttime = tr.stats.starttime starttime = tr.stats.starttime
# create two lists with figure names and subindices (for subplots) to get the correct axes # create two lists with figure names and subindices (for subplots) to get the correct axes