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Merge remote-tracking branch 'origin/develop' into feature/refactor

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This commit is contained in:
Darius Arnold
2018-08-03 11:55:13 +02:00
parent b9cf219b39 5c74160710
commit a45e817213
35 changed files with 1708 additions and 1056 deletions
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pylot/core/util/utils.py
+124 -114
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@@ -22,11 +22,7 @@ from pylot.styles import style_settings
from scipy.interpolate import splrep, splev
from PySide import QtCore, QtGui
try:
import pyqtgraph as pg
except Exception as e:
print('PyLoT: Could not import pyqtgraph. {}'.format(e))
pg = None
import pyqtgraph as pg
def _pickle_method(m):
if m.im_self is None:
@@ -34,6 +30,7 @@ def _pickle_method(m):
else:
return getattr, (m.im_self, m.im_func.func_name)
def getAutoFilteroptions(phase, parameter):
filtername = {'P': 'bpz2',
'S': 'bph2'}
@@ -41,9 +38,10 @@ def getAutoFilteroptions(phase, parameter):
print('autoPickParameter: No filter options for phase {}.'.format(phase))
return
freqmin, freqmax = parameter.get(filtername[phase])
filteroptions = FilterOptions(type='bandpass', freq=[freqmin, freqmax], order=4) # order=4 default from obspy
filteroptions = FilterOptions(type='bandpass', freq=[freqmin, freqmax], order=4) # order=4 default from obspy
return filteroptions
def readDefaultFilterInformation(fname):
"""
Read default filter information from pylot.in file
@@ -118,8 +116,12 @@ def gen_Pool(ncores=0):
"""
import multiprocessing
if ncores == 0:
ncores = multiprocessing.cpu_count()
ncores_max = multiprocessing.cpu_count()
if ncores == 0 or ncores > ncores_max:
ncores = ncores_max
if ncores > ncores_max:
print('Reduced number of requested CPU slots to available number: {}'.format(ncores))
print('gen_Pool: Generated multiprocessing Pool with {} cores\n'.format(ncores))
@@ -397,6 +399,10 @@ def full_range(stream):
:return: minimum start time and maximum end time
:rtype: (`~maximum start time and minimum end time`, maximum start time and minimum end time)
"""
if not stream:
print('full_range: Empty Stream!')
return None, None
min_start = min([trace.stats.starttime for trace in stream])
max_end = max([trace.stats.endtime for trace in stream])
@@ -537,7 +543,7 @@ def isSorted(iterable):
False
"""
assert isIterable(iterable), 'object is not iterable; object: {' \
'0}'.format(iterable)
'}'.format(iterable)
if type(iterable) is str:
iterable = [s for s in iterable]
return sorted(iterable) == iterable
@@ -675,7 +681,7 @@ def pick_color(picktype, phase, quality=0):
bpc = base_phase_colors(picktype, phase) # returns dict like {'modifier': 'g', 'rgba': (0, 0, 255, 255)}
rgba = bpc['rgba']
modifier = bpc['modifier']
intensity = 255.*quality/min_quality
intensity = 255. * quality / min_quality
rgba = modify_rgba(rgba, modifier, intensity)
return rgba
@@ -787,6 +793,7 @@ def base_phase_colors(picktype, phase):
phasecolors = style_settings.phasecolors
return phasecolors[picktype][phase]
def transform_colors_mpl_str(colors, no_alpha=False):
"""
Transforms rgba color values to a matplotlib string of color values with a range of [0, 1]
@@ -805,6 +812,7 @@ def transform_colors_mpl_str(colors, no_alpha=False):
colors_mpl = '({}, {}, {}, {})'.format(*colors_mpl)
return colors_mpl
def transform_colors_mpl(colors):
"""
Transform rgba colors from [0, 255] to [0, 1]
@@ -817,6 +825,7 @@ def transform_colors_mpl(colors):
colors_mpl = tuple([color / 255. for color in colors])
return colors_mpl
def remove_underscores(data):
"""
takes a `obspy.core.stream.Stream` object and removes all underscores
@@ -826,9 +835,9 @@ def remove_underscores(data):
:return: data stream
:rtype: `~obspy.core.stream.Stream`
"""
for tr in data:
# remove underscores
tr.stats.station = tr.stats.station.strip('_')
#for tr in data:
# # remove underscores
# tr.stats.station = tr.stats.station.strip('_')
return data
@@ -926,7 +935,10 @@ def get_stations(data):
def check4rotated(data, 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
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
side effect.
:param data: stream object containing seismic traces
:type data: `~obspy.core.stream.Stream`
:param metadata: tuple containing metadata type string and metadata parser object
@@ -943,100 +955,59 @@ def check4rotated(data, metadata=None, verbosity=1):
Azimut and dip are fetched from metadata. To be rotated, traces of a station have to be cut to the same length.
Returns unrotated traces of no metadata is provided
:param wfstream: stream containing seismic traces
:param wfstream: stream containing seismic traces of a station
:type wfstream: `~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`
"""
try:
# indexing fails if metadata is None
metadata[0]
except TypeError:
if verbosity:
msg = 'Warning: could not rotate traces since no metadata was given\nset Inventory file!'
print(msg)
return wfstream
if metadata[0] is None:
# sometimes metadata is (None, (None,))
if verbosity:
msg = 'Warning: could not rotate traces since no metadata was given\nCheck inventory directory!'
print(msg)
return wfstream
else:
parser = metadata[1]
def get_dip_azimut(parser, trace_id):
"""
Gets azimuth and dip by trace id out of the metadata parser
:param parser: metadata parser object
:type parser: `~obspy.io.xseed.parser.Parser`
:param trace_id: eg. 'BW.RJOB..EHZ',
:type trace_id: str
:return: tuple containing dip and azimuth of the trace corresponding to trace_id
:rtype: (float, float)
"""
dip = None
azimut = None
try:
blockettes = parser._select(trace_id)
except SEEDParserException as e:
print(e)
raise ValueError
for blockette_ in blockettes:
if blockette_.id != 52:
continue
dip = blockette_.dip
azimut = blockette_.azimuth
break
if (dip is None or azimut is None) or (dip == 0 and azimut == 0):
error_msg = 'Dip and azimuth not available for trace_id {}'.format(trace_id)
raise ValueError(error_msg)
return dip, azimut
# check if any traces in this station need to be rotated
trace_ids = [trace.id for trace in wfstream]
for trace_id in trace_ids:
orientation = trace_id[-1] # last letter if trace id is orientation code, ZNE or 123
if orientation.isnumeric():
# misaligned channels have a number as orientation
azimuts = []
dips = []
for trace_id in trace_ids:
try:
dip, azimut = get_dip_azimut(parser, trace_id)
except ValueError as e:
print(e)
print('Failed to rotate station {}, no azimuth or dip available in metadata'.format(trace_id))
return wfstream
azimuts.append(azimut)
dips.append(dip)
# to rotate all traces must have same length
wfstream = trim_station_components(wfstream, trim_start=True, trim_end=True)
z, n, e = rotate2zne(wfstream[0], azimuts[0], dips[0],
wfstream[1], azimuts[1], dips[1],
wfstream[2], azimuts[2], dips[2])
print('check4rotated: rotated station {} to ZNE'.format(trace_id))
z_index = dips.index(min(dips)) # get z-trace index (dip is measured from 0 to -90)
wfstream[z_index].data = z
wfstream[z_index].stats.channel = wfstream[z_index].stats.channel[0:-1] + 'Z'
del trace_ids[z_index]
for trace_id in trace_ids:
dip, az = get_dip_azimut(parser, trace_id)
trace = wfstream.select(id=trace_id)[0]
if az > 315 or az <= 45 or az > 135 and az <= 225:
trace.data = n
trace.stats.channel = trace.stats.channel[0:-1] + 'N'
elif az > 45 and az <= 135 or az > 225 and az <= 315:
trace.data = e
trace.stats.channel = trace.stats.channel[0:-1] + 'E'
break
else:
continue
orientations = [trace_id[-1] for trace_id in trace_ids]
rotation_required = [orientation.isnumeric() for orientation in orientations]
if any(rotation_required):
t_start = full_range(wfstream)
try:
azimuts = [metadata.get_coordinates(tr_id, t_start)['azimuth'] for tr_id in trace_ids]
dips = [metadata.get_coordinates(tr_id, t_start)['dip'] for tr_id in trace_ids]
except (KeyError, TypeError) as e:
print('Failed to rotate trace {}, no azimuth or dip available in metadata'.format(trace_id))
return wfstream
if len(wfstream) < 3:
print('Failed to rotate Stream {}, not enough components available.'.format(wfstream))
return wfstream
# to rotate all traces must have same length, so trim them
wfstream = trim_station_components(wfstream, trim_start=True, trim_end=True)
z, n, e = rotate2zne(wfstream[0], azimuts[0], dips[0],
wfstream[1], azimuts[1], dips[1],
wfstream[2], azimuts[2], dips[2])
print('check4rotated: rotated trace {} to ZNE'.format(trace_id))
# replace old data with rotated data, change the channel code to ZNE
z_index = dips.index(min(
dips)) # get z-trace index, z has minimum dip of -90 (dip is measured from 0 to -90, with -90 being vertical)
wfstream[z_index].data = z
wfstream[z_index].stats.channel = wfstream[z_index].stats.channel[0:-1] + 'Z'
del trace_ids[z_index]
for trace_id in trace_ids:
coordinates = metadata.get_coordinates(trace_id, t_start)
dip, az = coordinates['dip'], coordinates['azimuth']
trace = wfstream.select(id=trace_id)[0]
if az > 315 or az <= 45 or az > 135 and az <= 225:
trace.data = n
trace.stats.channel = trace.stats.channel[0:-1] + 'N'
elif az > 45 and az <= 135 or az > 225 and az <= 315:
trace.data = e
trace.stats.channel = trace.stats.channel[0:-1] + 'E'
return wfstream
if metadata is None:
if verbosity:
msg = 'Warning: could not rotate traces since no metadata was given\nset Inventory file!'
print(msg)
return data
stations = get_stations(data)
for station in stations: # loop through all stations and rotate data if neccessary
wf_station = data.select(station=station)
rotate_components(wf_station, metadata)
@@ -1149,7 +1120,7 @@ def loopIdentifyPhase(phase):
"""
from pylot.core.util.defaults import ALTSUFFIX
if phase == None:
if phase is None:
raise NameError('Can not identify phase that is None')
phase_copy = phase
@@ -1199,20 +1170,6 @@ def identifyPhaseID(phase):
return identifyPhase(loopIdentifyPhase(phase))
def has_spe(pick):
"""
Check for 'spe' key (symmetric picking error) in dict and return its value if found, else return None
:param pick: pick dictionary
:type pick: dict
:return: value of 'spe' key
:rtype: float or None
"""
if not 'spe' in pick.keys():
return None
else:
return pick['spe']
def check_all_obspy(eventlist):
ev_type = 'obspydmt'
return check_event_folders(eventlist, ev_type)
@@ -1245,8 +1202,8 @@ def check_event_folder(path):
folder = path.split('/')[-1]
# for pylot: select only folders that start with 'e', containin two dots and have length 12
if (folder.startswith('e')
and len(folder.split('.')) == 3
and len(folder) == 12):
and len(folder.split('.')) == 3
and len(folder) == 12):
ev_type = 'pylot'
elif check_obspydmt_eventfolder(folder)[0]:
ev_type = 'obspydmt'
@@ -1276,3 +1233,56 @@ if __name__ == "__main__":
import doctest
doctest.testmod()
class SetChannelComponents(object):
def __init__(self):
self.setDefaultCompPosition()
def setDefaultCompPosition(self):
# default component order
self.compPosition_Map = dict(Z=2, N=1, E=0)
self.compName_Map = {'3': 'Z',
'1': 'N',
'2': 'E'}
def _getCurrentPosition(self, component):
for key, value in self.compName_Map.items():
if value == component:
return key, value
errMsg = 'getCurrentPosition: Could not find former position of component {}.'.format(component)
raise ValueError(errMsg)
def _switch(self, component, component_alter):
# Without switching, multiple definitions of the same alter_comp are possible
old_alter_comp, _ = self._getCurrentPosition(component)
old_comp = self.compName_Map[component_alter]
if not old_alter_comp == component_alter and not old_comp == component:
self.compName_Map[old_alter_comp] = old_comp
print('switch: Automatically switched component {} to {}'.format(old_alter_comp, old_comp))
def setCompPosition(self, component_alter, component, switch=True):
component_alter = str(component_alter)
if not component_alter in self.compName_Map.keys():
errMsg = 'setCompPosition: Unrecognized alternative component {}. Expecting one of {}.'
raise ValueError(errMsg.format(component_alter, self.compName_Map.keys()))
if not component in self.compPosition_Map.keys():
errMsg = 'setCompPosition: Unrecognized target component {}. Expecting one of {}.'
raise ValueError(errMsg.format(component, self.compPosition_Map.keys()))
print('setCompPosition: set component {} to {}'.format(component_alter, component))
if switch:
self._switch(component, component_alter)
self.compName_Map[component_alter] = component
def getCompPosition(self, component):
return self._getCurrentPosition(component)[0]
def getPlotPosition(self, component):
component = str(component)
if component in self.compPosition_Map.keys():
return self.compPosition_Map[component]
elif component in self.compName_Map.keys():
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()))