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

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This commit is contained in:
Darius Arnold
2018-07-13 09:28:50 +02:00
parent 1ff50c000e 9f1672d793
commit 2c92f6f2fd
25 changed files with 306 additions and 88 deletions
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93
pylot/core/util/dataprocessing.py
View File

@@ -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)

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

@@ -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}

17
pylot/core/util/utils.py
View File

@@ -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):

14
pylot/core/util/widgets.py
View File

@@ -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)