Merge branch 'develop' into feature/refactor
This commit is contained in:
Darius Arnold
@@ -2,3 +2,4 @@
|
||||
*~
|
||||
pylot/RELEASE-VERSION
|
||||
*.idea
|
||||
autopylot.sh*
|
||||
|
||||
@@ -110,21 +110,8 @@ class MainWindow(QMainWindow):
|
||||
def __init__(self, parent=None, infile=None):
|
||||
super(MainWindow, self).__init__(parent)
|
||||
|
||||
# check for default pylot.in-file
|
||||
if not infile:
|
||||
infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
|
||||
print('Using default input file {}'.format(infile))
|
||||
if os.path.isfile(infile) == False:
|
||||
infile = QFileDialog().getOpenFileName(caption='Choose PyLoT-input file')
|
||||
self.init_config_files(infile)
|
||||
|
||||
if not os.path.exists(infile[0]):
|
||||
QMessageBox.warning(self, "PyLoT Warning",
|
||||
"No PyLoT-input file declared!")
|
||||
sys.exit(0)
|
||||
self.infile = infile[0]
|
||||
else:
|
||||
self.infile = infile
|
||||
self._inputs = PylotParameter(infile)
|
||||
self._props = None
|
||||
|
||||
self.dirty = False
|
||||
@@ -208,6 +195,22 @@ class MainWindow(QMainWindow):
|
||||
|
||||
self.loc = False
|
||||
|
||||
|
||||
def init_config_files(self, infile):
|
||||
pylot_config_dir = os.path.join(os.path.expanduser('~'), '.pylot')
|
||||
if not os.path.exists(pylot_config_dir):
|
||||
os.mkdir(pylot_config_dir)
|
||||
|
||||
self._inputs = PylotParameter(infile)
|
||||
if not infile:
|
||||
self._inputs.reset_defaults()
|
||||
# check for default pylot.in-file
|
||||
infile = os.path.join(pylot_config_dir, '.pylot.in')
|
||||
print('Using default input file {}'.format(infile))
|
||||
self._inputs.export2File(infile)
|
||||
self.infile = infile
|
||||
|
||||
|
||||
def setupUi(self):
|
||||
try:
|
||||
self.startTime = min(
|
||||
@@ -1058,9 +1061,12 @@ class MainWindow(QMainWindow):
|
||||
eventlist = ed.selectedFiles()
|
||||
basepath = eventlist[0].split(os.path.basename(eventlist[0]))[0]
|
||||
if check_obspydmt_structure(basepath):
|
||||
print('Recognized obspyDMT structure in selected files.')
|
||||
print('Recognized obspyDMT structure in selected files. Settings Datastructure to ObspyDMT')
|
||||
self.dataStructure = DATASTRUCTURE['obspyDMT']()
|
||||
eventlist = check_all_obspy(eventlist)
|
||||
else:
|
||||
print('Settings Datastructure to PILOT')
|
||||
self.dataStructure = DATASTRUCTURE['PILOT']()
|
||||
eventlist = check_all_pylot(eventlist)
|
||||
if not eventlist:
|
||||
print('No events found! Expected structure for event folders: [eEVID.DOY.YR],\n'
|
||||
@@ -1407,7 +1413,7 @@ class MainWindow(QMainWindow):
|
||||
self.get_data().resetPicks()
|
||||
return self.saveData(event, directory, outformats)
|
||||
|
||||
fcheck = ['manual', 'origins', 'magnitude']
|
||||
fcheck = ['auto', 'manual', 'origins', 'magnitude']
|
||||
|
||||
saved_as = str()
|
||||
for outformat in outformats:
|
||||
@@ -2631,17 +2637,20 @@ class MainWindow(QMainWindow):
|
||||
elif type == 'auto':
|
||||
event.addAutopicks(picksdict['auto'])
|
||||
|
||||
def drawPicks(self, station=None, picktype=None):
|
||||
def drawPicks(self, station=None, picktype=None, stime=None):
|
||||
# if picktype not specified, draw both
|
||||
if not stime:
|
||||
stime = self.getStime()
|
||||
|
||||
if not picktype:
|
||||
self.drawPicks(station, 'manual')
|
||||
self.drawPicks(station, 'auto')
|
||||
self.drawPicks(station, 'manual', stime)
|
||||
self.drawPicks(station, 'auto', stime)
|
||||
return
|
||||
|
||||
# if picks to draw not specified, draw all picks available
|
||||
if not station:
|
||||
for station in self.getPicks(type=picktype):
|
||||
self.drawPicks(station, picktype=picktype)
|
||||
self.drawPicks(station, picktype=picktype, stime=stime)
|
||||
return
|
||||
|
||||
# check for station key in dictionary, else return
|
||||
@@ -2659,7 +2668,6 @@ class MainWindow(QMainWindow):
|
||||
ylims = np.array([-.5, +.5]) + plotID
|
||||
|
||||
stat_picks = self.getPicks(type=picktype)[station]
|
||||
stime = self.getStime()
|
||||
|
||||
for phase in stat_picks:
|
||||
if phase == 'SPt': continue # wadati SP time
|
||||
|
||||
+2
-2
@@ -314,7 +314,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
|
||||
ttpat)
|
||||
|
||||
# locate the event
|
||||
nll.locate(ctrfile, inputfile)
|
||||
nll.locate(ctrfile, parameter)
|
||||
|
||||
# !iterative picking if traces remained unpicked or occupied with bad picks!
|
||||
# get theoretical onset times for picks with weights >= 4
|
||||
@@ -402,7 +402,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
|
||||
# remove actual NLLoc-location file to keep only the last
|
||||
os.remove(nllocfile)
|
||||
# locate the event
|
||||
nll.locate(ctrfile, inputfile)
|
||||
nll.locate(ctrfile, parameter)
|
||||
print("autoPyLoT: Iteration No. %d finished." % nlloccounter)
|
||||
# get updated NLLoc-location file
|
||||
nllocfile = max(glob.glob(locsearch), key=os.path.getctime)
|
||||
|
||||
@@ -0,0 +1 @@
|
||||
python ./autoPyLoT.py -i /home/marcel/.pylot/pylot_global.in -dmt processed -c 80
|
||||
@@ -733,6 +733,22 @@ class PilotDataStructure(GenericDataStructure):
|
||||
self.setExpandFields(['root', 'database'])
|
||||
|
||||
|
||||
class ObspyDMTdataStructure(GenericDataStructure):
|
||||
"""
|
||||
Object containing the data access information for the old PILOT data
|
||||
structure.
|
||||
"""
|
||||
|
||||
def __init__(self, **fields):
|
||||
if not fields:
|
||||
fields = {'database': '',
|
||||
'root': ''}
|
||||
|
||||
GenericDataStructure.__init__(self, **fields)
|
||||
|
||||
self.setExpandFields(['root', 'database'])
|
||||
|
||||
|
||||
class SeiscompDataStructure(GenericDataStructure):
|
||||
"""
|
||||
Dictionary containing the data access information for an SDS data archive:
|
||||
|
||||
@@ -63,7 +63,7 @@ defaults = {'rootpath': {'type': str,
|
||||
|
||||
'ctrfile': {'type': str,
|
||||
'tooltip': 'name of autoPyLoT-output control file for NLLoc',
|
||||
'value': 'Insheim_min1d2015_auto.in',
|
||||
'value': '',
|
||||
'namestring': 'Control filename'},
|
||||
|
||||
'ttpatter': {'type': str,
|
||||
|
||||
@@ -48,6 +48,7 @@ class PylotParameter(object):
|
||||
self.__init_default_paras()
|
||||
self.__init_subsettings()
|
||||
self.__filename = fnin
|
||||
self.__parameter = {}
|
||||
self._verbosity = verbosity
|
||||
self._parFileCont = {}
|
||||
# io from parsed arguments alternatively
|
||||
@@ -273,8 +274,8 @@ class PylotParameter(object):
|
||||
:rtype: None
|
||||
"""
|
||||
defaults = self.get_defaults()
|
||||
for param in defaults:
|
||||
self.setParamKV(param, defaults[param]['value'])
|
||||
for param_name, param in defaults.items():
|
||||
self.setParamKV(param_name, param['value'])
|
||||
|
||||
def from_file(self, fnin=None):
|
||||
"""
|
||||
|
||||
@@ -73,17 +73,14 @@ def modify_inputs(ctrfn, root, nllocoutn, phasefn, tttn):
|
||||
nllfile.close()
|
||||
|
||||
|
||||
def locate(fnin, infile=None):
|
||||
def locate(fnin, parameter=None):
|
||||
"""
|
||||
takes an external program name and tries to run it
|
||||
:param fnin: external program name
|
||||
:return: None
|
||||
"""
|
||||
|
||||
if infile is None:
|
||||
exe_path = which('NLLoc')
|
||||
else:
|
||||
exe_path = which('NLLoc', infile)
|
||||
exe_path = which('NLLoc', parameter)
|
||||
if exe_path is None:
|
||||
raise NLLocError('NonLinLoc executable not found; check your '
|
||||
'environment variables')
|
||||
|
||||
@@ -89,14 +89,22 @@ def autopickevent(data, param, iplot=0, fig_dict=None, fig_dict_wadatijack=None,
|
||||
'stations on {} cores.'.format(len(input_tuples), ncores_str))
|
||||
|
||||
pool = gen_Pool(ncores)
|
||||
result = pool.map(call_autopickstation, input_tuples)
|
||||
results = pool.map(call_autopickstation, input_tuples)
|
||||
pool.close()
|
||||
|
||||
for pick in result:
|
||||
if pick:
|
||||
station = pick['station']
|
||||
pick.pop('station')
|
||||
all_onsets[station] = pick
|
||||
for result, wfstream in results:
|
||||
if type(result) == dict:
|
||||
station = result['station']
|
||||
result.pop('station')
|
||||
all_onsets[station] = result
|
||||
else:
|
||||
if result == None:
|
||||
result = 'Picker exited unexpectedly.'
|
||||
if len(wfstream) > 0:
|
||||
station = wfstream[0].stats.station
|
||||
else:
|
||||
station = None
|
||||
print('Could not pick a station: {}\nReason: {}'.format(station, result))
|
||||
|
||||
# quality control
|
||||
# median check and jackknife on P-onset times
|
||||
@@ -116,7 +124,10 @@ def call_autopickstation(input_tuple):
|
||||
"""
|
||||
wfstream, pickparam, verbose, metadata, origin = input_tuple
|
||||
# multiprocessing not possible with interactive plotting
|
||||
return autopickstation(wfstream, pickparam, verbose, iplot=0, metadata=metadata, origin=origin)
|
||||
try:
|
||||
return autopickstation(wfstream, pickparam, verbose, iplot=0, metadata=metadata, origin=origin), wfstream
|
||||
except Exception as e:
|
||||
return e, wfstream
|
||||
|
||||
|
||||
def get_source_coords(parser, station_id):
|
||||
|
||||
+21
-17
@@ -23,7 +23,7 @@ import warnings
|
||||
|
||||
import matplotlib.pyplot as plt
|
||||
import numpy as np
|
||||
from scipy.signal import argrelmax
|
||||
from scipy.signal import argrelmax, argrelmin
|
||||
from pylot.core.pick.charfuns import CharacteristicFunction
|
||||
from pylot.core.pick.utils import getnoisewin, getsignalwin
|
||||
|
||||
@@ -197,10 +197,15 @@ class AICPicker(AutoPicker):
|
||||
|
||||
# find minimum in AIC-CF front of maximum of HOS/AR-CF
|
||||
lpickwindow = int(round(self.PickWindow / self.dt))
|
||||
for i in range(icfmax - 1, max([icfmax - lpickwindow, 2]), -1):
|
||||
if aicsmooth[i - 1] >= aicsmooth[i]:
|
||||
self.Pick = self.Tcf[i]
|
||||
break
|
||||
tsafety = self.TSNR[1] # safety gap, AIC is usually a little bit too late
|
||||
left_corner_ind = max([icfmax - lpickwindow, 2])
|
||||
right_corner_ind = icfmax + int(tsafety / self.dt)
|
||||
aic_snip = aicsmooth[left_corner_ind : right_corner_ind]
|
||||
minima = argrelmin(aic_snip)[0] # 0th entry of tuples for axes
|
||||
if len(minima) > 0:
|
||||
pickindex = minima[-1] + left_corner_ind
|
||||
self.Pick = self.Tcf[pickindex]
|
||||
|
||||
# if no minimum could be found:
|
||||
# search in 1st derivative of AIC-CF
|
||||
if self.Pick is None:
|
||||
@@ -215,17 +220,12 @@ class AICPicker(AutoPicker):
|
||||
for i in range(icfmax - 1, max([icfmax - lpickwindow, 2]), -1):
|
||||
if diffcf[i - 1] >= diffcf[i]:
|
||||
self.Pick = self.Tcf[i]
|
||||
pickindex = i
|
||||
break
|
||||
|
||||
if self.Pick is not None:
|
||||
# get noise window
|
||||
inoise = getnoisewin(self.Tcf, self.Pick, self.TSNR[0], self.TSNR[1])
|
||||
# check, if these are counts or m/s, important for slope estimation!
|
||||
# this is quick and dirty, better solution? #Todo wtf
|
||||
if max(self.Data[0].data < 1e-3) and max(self.Data[0].data >= 1e-6):
|
||||
self.Data[0].data = self.Data[0].data * 1000000.
|
||||
elif max(self.Data[0].data < 1e-6):
|
||||
self.Data[0].data = self.Data[0].data * 1e13
|
||||
# get signal window
|
||||
isignal = getsignalwin(self.Tcf, self.Pick, self.TSNR[2])
|
||||
if len(isignal) == 0:
|
||||
@@ -244,7 +244,6 @@ class AICPicker(AutoPicker):
|
||||
# calculate slope from CF after initial pick
|
||||
# get slope window
|
||||
tslope = self.TSNR[3] # slope determination window
|
||||
tsafety = self.TSNR[1] # safety gap, AIC is usually a little bit too late
|
||||
if tsafety >= 0:
|
||||
islope = np.where((self.Tcf <= min([self.Pick + tslope + tsafety, self.Tcf[-1]])) \
|
||||
& (self.Tcf >= self.Pick)) # TODO: put this in a seperate function like getsignalwin
|
||||
@@ -263,7 +262,6 @@ class AICPicker(AutoPicker):
|
||||
return
|
||||
try:
|
||||
imaxs, = argrelmax(dataslope)
|
||||
imaxs.size
|
||||
imax = imaxs[0]
|
||||
except ValueError as e:
|
||||
print(e, 'picker: argrelmax not working!')
|
||||
@@ -280,7 +278,7 @@ class AICPicker(AutoPicker):
|
||||
if self.iplot > 1:
|
||||
if self.fig == None or self.fig == 'None':
|
||||
fig = plt.figure()
|
||||
plt_flag = 1
|
||||
plt_flag = iplot
|
||||
else:
|
||||
fig = self.fig
|
||||
ax = fig.add_subplot(111)
|
||||
@@ -291,7 +289,7 @@ class AICPicker(AutoPicker):
|
||||
ax.set_xlabel('Time [s] since %s' % self.Data[0].stats.starttime)
|
||||
ax.set_yticks([])
|
||||
ax.set_title(self.Data[0].stats.station)
|
||||
if plt_flag == 1:
|
||||
if plt_flag in [1, 2]:
|
||||
fig.show()
|
||||
try: input()
|
||||
except SyntaxError: pass
|
||||
@@ -307,6 +305,8 @@ class AICPicker(AutoPicker):
|
||||
print('AICPicker: Negative slope, bad onset skipped!')
|
||||
else:
|
||||
self.slope = 1 / (len(dataslope) * self.Data[0].stats.delta) * (datafit[-1] - datafit[0])
|
||||
# normalize slope to maximum of cf to make it unit independent
|
||||
self.slope /= self.Data[0].data[icfmax]
|
||||
|
||||
else:
|
||||
self.SNR = None
|
||||
@@ -315,7 +315,7 @@ class AICPicker(AutoPicker):
|
||||
if iplot > 1:
|
||||
if self.fig == None or self.fig == 'None':
|
||||
fig = plt.figure() # self.iplot)
|
||||
plt_flag = 1
|
||||
plt_flag = iplot
|
||||
else:
|
||||
fig = self.fig
|
||||
fig._tight = True
|
||||
@@ -359,11 +359,15 @@ class AICPicker(AutoPicker):
|
||||
else:
|
||||
ax1.set_title(self.Data[0].stats.station)
|
||||
|
||||
if plt_flag == 1:
|
||||
if plt_flag in [1, 2]:
|
||||
fig.show()
|
||||
try: input()
|
||||
except SyntaxError: pass
|
||||
plt.close(fig)
|
||||
if plt_flag == 3:
|
||||
stats = self.Data[0].stats
|
||||
netstlc = '{}.{}.{}'.format(stats.network, stats.station, stats.location)
|
||||
fig.savefig('aicfig_{}_{}.png'.format(netstlc, stats.channel))
|
||||
|
||||
if self.Pick == None:
|
||||
print('AICPicker: Could not find minimum, picking window too short?')
|
||||
|
||||
@@ -705,7 +705,7 @@ def wadaticheck(pickdic, dttolerance, iplot=0, fig_dict=None):
|
||||
wfitflag = 1
|
||||
|
||||
# plot results
|
||||
if iplot > 0:
|
||||
if iplot > 0 or fig_dict:
|
||||
if fig_dict:
|
||||
fig = fig_dict['wadati']
|
||||
linecolor = fig_dict['plot_style']['linecolor']['rgba_mpl']
|
||||
@@ -947,7 +947,7 @@ def checkPonsets(pickdic, dttolerance, jackfactor=5, iplot=0, fig_dict=None):
|
||||
|
||||
checkedonsets = pickdic
|
||||
|
||||
if iplot > 0:
|
||||
if iplot > 0 or fig_dict:
|
||||
if fig_dict:
|
||||
fig = fig_dict['jackknife']
|
||||
plt_flag = 0
|
||||
|
||||
@@ -15,33 +15,81 @@ from pylot.core.util.utils import key_for_set_value, find_in_list, \
|
||||
class Metadata(object):
|
||||
def __init__(self, inventory=None):
|
||||
self.inventories = []
|
||||
if os.path.isdir(inventory):
|
||||
self.add_inventory(inventory)
|
||||
if os.path.isfile(inventory):
|
||||
self.add_inventory_file(inventory)
|
||||
self.seed_ids = {}
|
||||
# saves read metadata objects (Parser/inventory) for a filename
|
||||
self.inventory_files = {}
|
||||
# saves filenames holding metadata for a seed_id
|
||||
self.seed_ids = {}
|
||||
if inventory:
|
||||
if os.path.isdir(inventory):
|
||||
self.add_inventory(inventory)
|
||||
if os.path.isfile(inventory):
|
||||
self.add_inventory_file(inventory)
|
||||
|
||||
|
||||
def __str__(self):
|
||||
repr = 'PyLoT Metadata object including the following inventories:\n\n'
|
||||
ntotal = len(self.inventories)
|
||||
for index, inventory in enumerate(self.inventories):
|
||||
if index < 2 or (ntotal - index) < 3:
|
||||
repr += '{}\n'.format(inventory)
|
||||
if ntotal > 4 and int(ntotal/2) == index:
|
||||
repr += '...\n'
|
||||
if ntotal > 4:
|
||||
repr += '\nTotal of {} inventories. Use Metadata.inventories to see all.'.format(ntotal)
|
||||
return repr
|
||||
|
||||
|
||||
def __repr__(self):
|
||||
return self.__str__()
|
||||
|
||||
|
||||
def add_inventory(self, path_to_inventory):
|
||||
# add paths to list of inventories
|
||||
'''
|
||||
add paths to list of inventories
|
||||
|
||||
:param path_to_inventory:
|
||||
:return:
|
||||
'''
|
||||
assert (os.path.isdir(path_to_inventory)), '{} is no directory'.format(path_to_inventory)
|
||||
if not path_to_inventory in self.inventories:
|
||||
self.inventories.append(path_to_inventory)
|
||||
|
||||
|
||||
def add_inventory_file(self, path_to_inventory_file):
|
||||
assert (os.path.isfile(path_to_inventory_file)), '{} is no directory'.format(path_to_inventory_file)
|
||||
'''
|
||||
add a single file to inventory files
|
||||
|
||||
:param path_to_inventory_file:
|
||||
:return:
|
||||
|
||||
'''
|
||||
assert (os.path.isfile(path_to_inventory_file)), '{} is no file'.format(path_to_inventory_file)
|
||||
self.add_inventory(os.path.split(path_to_inventory_file)[0])
|
||||
if not path_to_inventory_file in self.inventory_files.keys():
|
||||
self.read_single_file(path_to_inventory_file)
|
||||
|
||||
|
||||
def remove_all_inventories(self):
|
||||
self.__init__()
|
||||
|
||||
|
||||
def remove_inventory(self, path_to_inventory):
|
||||
'''
|
||||
remove a path from inventories list
|
||||
|
||||
:param path_to_inventory:
|
||||
:return:
|
||||
'''
|
||||
if not path_to_inventory in self.inventories:
|
||||
print('Path {} not in inventories list.'.format(path_to_inventory))
|
||||
return
|
||||
self.inventories.remove(path_to_inventory)
|
||||
for filename in self.inventory_files.keys():
|
||||
if filename.startswith(path_to_inventory):
|
||||
del(self.inventory_files[filename])
|
||||
for seed_id in self.seed_ids.keys():
|
||||
if self.seed_ids[seed_id].startswith(path_to_inventory):
|
||||
del(self.seed_ids[seed_id])
|
||||
|
||||
|
||||
def get_metadata(self, seed_id):
|
||||
@@ -54,9 +102,12 @@ class Metadata(object):
|
||||
self.read_all()
|
||||
for inv_fname, metadata in self.inventory_files.items():
|
||||
# use get_coordinates to check for seed_id
|
||||
if metadata['data'].get_coordinates(seed_id):
|
||||
try:
|
||||
metadata['data'].get_coordinates(seed_id)
|
||||
self.seed_ids[seed_id] = inv_fname
|
||||
return metadata
|
||||
except Exception as e:
|
||||
continue
|
||||
print('Could not find metadata for station {}'.format(seed_id))
|
||||
return None
|
||||
fname = self.seed_ids[seed_id]
|
||||
@@ -64,6 +115,10 @@ class Metadata(object):
|
||||
|
||||
|
||||
def read_all(self):
|
||||
'''
|
||||
read all metadata files found in all inventories
|
||||
:return:
|
||||
'''
|
||||
for inventory in self.inventories:
|
||||
for inv_fname in os.listdir(inventory):
|
||||
inv_fname = os.path.join(inventory, inv_fname)
|
||||
@@ -93,17 +148,18 @@ class Metadata(object):
|
||||
|
||||
def get_coordinates(self, seed_id):
|
||||
metadata = self.get_metadata(seed_id)
|
||||
if not metadata:
|
||||
return
|
||||
return metadata['data'].get_coordinates(seed_id)
|
||||
|
||||
|
||||
def get_paz(self, seed_id, time=None):
|
||||
def get_paz(self, seed_id, time):
|
||||
metadata = self.get_metadata(seed_id)
|
||||
if not metadata:
|
||||
return
|
||||
if metadata['invtype'] in ['dless', 'dseed']:
|
||||
return metadata['data'].get_paz(seed_id)
|
||||
return metadata['data'].get_paz(seed_id, time)
|
||||
elif metadata['invtype'] in ['resp', 'xml']:
|
||||
if not time:
|
||||
print('Time needed to extract metadata from station inventory.')
|
||||
return None
|
||||
resp = metadata['data'].get_response(seed_id, time)
|
||||
return resp.get_paz(seed_id)
|
||||
|
||||
@@ -404,11 +460,16 @@ def read_metadata(path_to_inventory):
|
||||
|
||||
|
||||
def restitute_trace(input_tuple):
|
||||
tr, invtype, inobj, unit, force = input_tuple
|
||||
tr, metadata, unit, force = input_tuple
|
||||
|
||||
remove_trace = False
|
||||
|
||||
seed_id = tr.get_id()
|
||||
|
||||
mdata = metadata.get_metadata(seed_id)
|
||||
invtype = mdata['invtype']
|
||||
inobj = mdata['data']
|
||||
|
||||
# check, whether this trace has already been corrected
|
||||
if 'processing' in tr.stats.keys() \
|
||||
and np.any(['remove' in p for p in tr.stats.processing]) \
|
||||
@@ -476,7 +537,7 @@ def restitute_trace(input_tuple):
|
||||
return tr, remove_trace
|
||||
|
||||
|
||||
def restitute_data(data, invtype, inobj, unit='VEL', force=False, ncores=0):
|
||||
def restitute_data(data, metadata, unit='VEL', force=False, ncores=0):
|
||||
"""
|
||||
takes a data stream and a path_to_inventory and returns the corrected
|
||||
waveform data stream
|
||||
@@ -497,7 +558,7 @@ def restitute_data(data, invtype, inobj, unit='VEL', force=False, ncores=0):
|
||||
# loop over traces
|
||||
input_tuples = []
|
||||
for tr in data:
|
||||
input_tuples.append((tr, invtype, inobj, unit, force))
|
||||
input_tuples.append((tr, metadata, unit, force))
|
||||
data.remove(tr)
|
||||
|
||||
pool = gen_Pool(ncores)
|
||||
|
||||
@@ -6,7 +6,7 @@ Created on Wed Jan 26 17:47:25 2015
|
||||
@author: sebastianw
|
||||
"""
|
||||
|
||||
from pylot.core.io.data import SeiscompDataStructure, PilotDataStructure
|
||||
from pylot.core.io.data import SeiscompDataStructure, PilotDataStructure, ObspyDMTdataStructure
|
||||
|
||||
DATASTRUCTURE = {'PILOT': PilotDataStructure, 'SeisComP': SeiscompDataStructure,
|
||||
'obspyDMT': None, None: None}
|
||||
'obspyDMT': ObspyDMTdataStructure, None: PilotDataStructure}
|
||||
|
||||
@@ -1024,7 +1024,7 @@ def check4rotated(data, metadata=None, verbosity=1):
|
||||
for trace_id in trace_ids:
|
||||
dip, az = get_dip_azimut(parser, trace_id)
|
||||
trace = wfstream.select(id=trace_id)[0]
|
||||
if az > 315 and az <= 45 or az > 135 and az <= 225:
|
||||
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:
|
||||
@@ -1094,7 +1094,7 @@ def runProgram(cmd, parameter=None):
|
||||
subprocess.check_output('{} | tee /dev/stderr'.format(cmd), shell=True)
|
||||
|
||||
|
||||
def which(program, infile=None):
|
||||
def which(program, parameter):
|
||||
"""
|
||||
takes a program name and returns the full path to the executable or None
|
||||
modified after: http://stackoverflow.com/questions/377017/test-if-executable-exists-in-python
|
||||
@@ -1109,16 +1109,9 @@ def which(program, infile=None):
|
||||
for key in settings.allKeys():
|
||||
if 'binPath' in key:
|
||||
os.environ['PATH'] += ':{0}'.format(settings.value(key))
|
||||
if infile is None:
|
||||
# use default parameter-file name
|
||||
bpath = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
|
||||
else:
|
||||
bpath = os.path.join(os.path.expanduser('~'), '.pylot', infile)
|
||||
|
||||
if os.path.exists(bpath):
|
||||
nllocpath = ":" + PylotParameter(bpath).get('nllocbin')
|
||||
os.environ['PATH'] += nllocpath
|
||||
except ImportError as e:
|
||||
nllocpath = ":" + parameter.get('nllocbin')
|
||||
os.environ['PATH'] += nllocpath
|
||||
except Exception as e:
|
||||
print(e.message)
|
||||
|
||||
def is_exe(fpath):
|
||||
|
||||
@@ -2832,10 +2832,20 @@ class MultiEventWidget(QWidget):
|
||||
self.rb_layout.insertWidget(index, rb)
|
||||
self.rb_layout.setStretch(index, 0)
|
||||
|
||||
self.pb = QtGui.QProgressBar()
|
||||
self.pb.setRange(0, 0)
|
||||
self.pb.setVisible(False)
|
||||
|
||||
#space holder for progressbar
|
||||
self._pb_space = QtGui.QWidget()
|
||||
|
||||
self.rb_layout.addWidget(self.start_button)
|
||||
|
||||
self.rb_layout.addWidget(QtGui.QWidget())
|
||||
self.rb_layout.addWidget(self.pb)
|
||||
self.rb_layout.addWidget(self._pb_space)
|
||||
|
||||
self.rb_layout.setStretch(len(self.options) + 1, 1)
|
||||
self.rb_layout.setStretch(len(self.options) + 2, 1)
|
||||
|
||||
self.main_layout.insertLayout(0, self.rb_layout)
|
||||
|
||||
@@ -2866,6 +2876,8 @@ class MultiEventWidget(QWidget):
|
||||
for rb in self.rb_dict.values():
|
||||
rb.setEnabled(bool)
|
||||
self.start_button.setEnabled(bool)
|
||||
self.pb.setVisible(not(bool))
|
||||
self._pb_space.setVisible(bool)
|
||||
self.eventbox.setEnabled(bool)
|
||||
self.button_clear.setEnabled(bool)
|
||||
|
||||
|
||||
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
@@ -0,0 +1,104 @@
|
||||
import unittest
|
||||
import os
|
||||
|
||||
from pylot.core.util.dataprocessing import Metadata
|
||||
|
||||
class TestMetadata(unittest.TestCase):
|
||||
|
||||
def setUp(self):
|
||||
self.station_id = 'BW.WETR..HH'
|
||||
metadata_folder = 'metadata1'
|
||||
self.m = Metadata(metadata_folder)
|
||||
|
||||
def test_get_coordinates_sucess(self):
|
||||
expected = {'Z': {u'elevation': 607.0, u'longitude': 12.87571, u'local_depth': 0.0, u'azimuth': 0.0, u'latitude': 49.14502, u'dip': -90.0},
|
||||
'E': {u'azimuth': 90.0, u'dip': 0.0, u'elevation': 607.0, u'latitude': 49.14502, u'local_depth': 0.0, u'longitude': 12.87571},
|
||||
'N': {u'azimuth': 0.0, u'dip': 0.0, u'elevation': 607.0, u'latitude': 49.14502, u'local_depth': 0.0, u'longitude': 12.87571}
|
||||
}
|
||||
result = {}
|
||||
for channel in ('Z', 'N', 'E'):
|
||||
coords = self.m.get_coordinates(self.station_id+channel)
|
||||
result[channel] = coords
|
||||
self.assertDictEqual(result[channel], expected[channel])
|
||||
|
||||
class TestMetadataAdding(unittest.TestCase):
|
||||
"""Tests if adding files and directories to a metadata object works."""
|
||||
|
||||
def setUp(self):
|
||||
self.station_id = 'BW.WETR..HH'
|
||||
self.metadata_folders = ('metadata1', 'metadata2')
|
||||
self.m = Metadata()
|
||||
|
||||
def test_add_inventory_folder(self):
|
||||
"""Test if add_inventory adds the folder to the list of inventories"""
|
||||
self.m.add_inventory(self.metadata_folders[0])
|
||||
# adding an inventory folder should append it to the list of inventories
|
||||
self.assertDictEqual({}, self.m.inventory_files)
|
||||
self.assertDictEqual({}, self.m.seed_ids)
|
||||
self.assertEqual([self.metadata_folders[0]], self.m.inventories)
|
||||
|
||||
def test_add_inventory_file(self):
|
||||
"""Test if add_inventory_file adds the folder containing the file to the list of inventories and
|
||||
if the files is added to inventory_files"""
|
||||
fpath = os.path.join(self.metadata_folders[0], 'DATALESS.BW.WETR..HHZ')
|
||||
self.m.add_inventory_file(fpath)
|
||||
# adding an inventory file should append its folder to the list of inventories and the file to the
|
||||
self.assertEqual(['metadata1/DATALESS.BW.WETR..HHZ'], self.m.inventory_files.keys()) # does the filename exist in inventory files?
|
||||
self.assertEqual(['data', 'invtype'], self.m.inventory_files['metadata1/DATALESS.BW.WETR..HHZ'].keys()) # is the required information attacht to the filename?
|
||||
self.assertDictEqual({}, self.m.seed_ids)
|
||||
self.assertEqual([self.metadata_folders[0]], self.m.inventories)
|
||||
|
||||
def test_add_inventory_invalid_path(self):
|
||||
"""Test if adding an inventory that is not an existing directory fails with an exception"""
|
||||
with self.assertRaises(Exception):
|
||||
self.m.add_inventory('InvalidDirName')
|
||||
self.assertEqual([], self.m.inventories) # inventory list should still be empty
|
||||
|
||||
def test_add_inventory_file_invalid_path(self):
|
||||
"""Test if adding a inventory file with an invalid path fails with an exception"""
|
||||
with self.assertRaises(Exception):
|
||||
self.m.add_inventory_file('/invalid/file/name')
|
||||
self.assertEqual([], self.m.inventories) # inventory list should still be empty
|
||||
|
||||
|
||||
class TestMetadataRemoval(unittest.TestCase):
|
||||
"""Tests if removing files and directories to a metadata object works."""
|
||||
|
||||
def setUp(self):
|
||||
self.station_id = 'BW.WETR..HH'
|
||||
self.metadata_folders = ('metadata1', 'metadata2')
|
||||
self.m = Metadata()
|
||||
|
||||
def test_remove_all_inventories(self):
|
||||
"""Test if function remove_inventory cleans the Metadata object """
|
||||
# add multiple inventories
|
||||
for folder in self.metadata_folders:
|
||||
self.m.add_inventory(folder)
|
||||
self.m.remove_all_inventories()
|
||||
self.isEmpty(self.m)
|
||||
|
||||
def test_remove_inventory(self):
|
||||
"""Test if remove_inventory removes single inventories"""
|
||||
# add multiple inventories
|
||||
for folder in self.metadata_folders:
|
||||
self.m.add_inventory(folder)
|
||||
self.m.remove_inventory(self.metadata_folders[0])
|
||||
self.assertNotIn(self.metadata_folders[0], self.m.inventories)
|
||||
self.m.remove_inventory(self.metadata_folders[1])
|
||||
self.assertNotIn(self.metadata_folders[1], self.m.inventories)
|
||||
self.isEmpty(self.m)
|
||||
|
||||
def test_remove_inventory_not_in_inventory_list(self):
|
||||
"""Test if remove_inventory does not modify the metadata instance if the given inventory to remove does not
|
||||
exist in the instance."""
|
||||
# add multiple inventories
|
||||
self.m.add_inventory(self.metadata_folders[0])
|
||||
self.m.remove_inventory('metadata_not_existing')
|
||||
self.assertIn(self.metadata_folders[0], self.m.inventories)
|
||||
|
||||
def isEmpty(self, metadata):
|
||||
"""Asserts if the given metadata object is empty"""
|
||||
self.assertDictEqual({}, metadata.inventory_files)
|
||||
self.assertDictEqual({}, metadata.seed_ids)
|
||||
self.assertEqual([], metadata.inventories)
|
||||
|
||||
Reference in New Issue
Block a user