[add] docstrings in pylot/core/io

pylot/core/io/data.py

@@ -99,6 +99,11 @@ class Data(object):
         return self
 
     def getPicksStr(self):
+        """
+        Return picks in event data
+        :return: picks seperated by newlines
+        :rtype: str
+        """
         picks_str = ''
         for pick in self.get_evt_data().picks:
             picks_str += str(pick) + '\n'
@@ -106,18 +111,11 @@ class Data(object):
 
     def getParent(self):
         """
-
+        Get PySide.QtGui.QWidget parent object
-
-        :return:
         """
         return self._parent
 
     def isNew(self):
-        """
-
-
-        :return:
-        """
         return self._new
 
     def setNew(self):
@@ -125,9 +123,9 @@ class Data(object):
 
     def getCutTimes(self):
         """
-
+        Returns earliest start and latest end of all waveform data
-
+        :return: minimum start time and maximum end time as a tuple
-        :return:
+        :rtype: (UTCDateTime, UTCDateTime)
         """
         if self.cuttimes is None:
             self.updateCutTimes()
@@ -135,22 +133,34 @@ class Data(object):
 
     def updateCutTimes(self):
         """
-
+        Update cuttimes to contain earliest start and latest end time
-
+        of all waveform data
+        :rtype: None
         """
         self.cuttimes = full_range(self.getWFData())
 
     def getEventFileName(self):
-        """
-
-
-        :return:
-        """
         ID = self.getID()
         # handle forbidden filenames especially on windows systems
         return fnConstructor(str(ID))
 
     def checkEvent(self, event, fcheck, forceOverwrite=False):
+        """
+        Check information in supplied event and own event and replace own
+        information with supplied information if own information not exiisting
+        or forced by forceOverwrite
+        :param event: Event that supplies information for comparison
+        :type event: pylot.core.util.event.Event
+        :param fcheck: check and delete existing information
+        can be a str or a list of strings of ['manual', 'auto', 'origin', 'magnitude']
+        :type fcheck: str, [str]
+        :param forceOverwrite: Set to true to force overwrite own information. If false,
+        supplied information from event is only used if there is no own information in that
+        category (given in fcheck: manual, auto, origin, magnitude)
+        :type forceOverwrite: bool
+        :return:
+        :rtype: None
+        """
         if 'origin' in fcheck:
             self.replaceOrigin(event, forceOverwrite)
         if 'magnitude' in fcheck:
@@ -161,18 +171,47 @@ class Data(object):
             self.replacePicks(event, 'manual')
 
     def replaceOrigin(self, event, forceOverwrite=False):
+        """
+        Replace own origin with the one supplied in event if own origin is not
+        existing or forced by forceOverwrite = True
+        :param event: Event that supplies information for comparison
+        :type event: pylot.core.util.event.Event
+        :param forceOverwrite: always replace own information with supplied one if true
+        :type forceOverwrite: bool
+        :return:
+        :rtype: None
+        """
         if self.get_evt_data().origins or forceOverwrite:
             if event.origins:
                 print("Found origin, replace it by new origin.")
             event.origins = self.get_evt_data().origins
 
     def replaceMagnitude(self, event, forceOverwrite=False):
+        """
+        Replace own magnitude with the one supplied in event if own magnitude is not
+        existing or forced by forceOverwrite = True
+        :param event: Event that supplies information for comparison
+        :type event: pylot.core.util.event.Event
+        :param forceOverwrite: always replace own information with supplied one if true
+        :type forceOverwrite: bool
+        :return:
+        :rtype: None
+        """
         if self.get_evt_data().magnitudes or forceOverwrite:
             if event.magnitudes:
                 print("Found magnitude, replace it by new magnitude")
             event.magnitudes = self.get_evt_data().magnitudes
 
     def replacePicks(self, event, picktype):
+        """
+        Replace own picks with the one in event
+        :param event: Event that supplies information for comparison
+        :type event: pylot.core.util.event.Event
+        :param picktype: 'auto' or 'manual' picks
+        :type picktype: str
+        :return:
+        :rtype: None
+        """
         checkflag = 0
         picks = event.picks
         # remove existing picks
@@ -189,10 +228,10 @@ class Data(object):
                 picks.append(pick)
 
     def exportEvent(self, fnout, fnext='.xml', fcheck='auto', upperErrors=None):
-
         """
+        Export event to file
         :param fnout: basename of file
-        :param fnext: file extension
+        :param fnext: file extension, xml, cnv, obs
         :param fcheck: check and delete existing information
         can be a str or a list of strings of ['manual', 'auto', 'origin', 'magnitude']
         """
@@ -304,17 +343,13 @@ class Data(object):
 
     def getComp(self):
         """
-
+        Get component (ZNE)
-
-        :return:
         """
         return self.comp
 
     def getID(self):
         """
-
+        Get unique resource id
-
-        :return:
         """
         try:
             return self.evtdata.get('resource_id').id
@@ -323,16 +358,17 @@ class Data(object):
 
     def filterWFData(self, kwargs):
         """
-
+        Filter waveform data
-        :param kwargs:
+        :param kwargs: arguments to pass through to filter function
         """
         self.getWFData().filter(**kwargs)
         self.dirty = True
 
     def setWFData(self, fnames):
         """
-
+        Clear current waveform data and set given waveform data
-        :param fnames:
+        :param fnames: waveform data names to append
+        :type fnames: list
         """
         self.wfdata = Stream()
         self.wforiginal = None
@@ -346,8 +382,9 @@ class Data(object):
 
     def appendWFData(self, fnames):
         """
-
+        Read waveform data from fnames and append it to current wf data
-        :param fnames:
+        :param fnames: waveform data to append
+        :type fnames: list
         """
         assert isinstance(fnames, list), "input parameter 'fnames' is " \
                                          "supposed to be of type 'list' " \
@@ -372,54 +409,42 @@ class Data(object):
             print(warnmsg)
 
     def getWFData(self):
-        """
-
-
-        :return:
-        """
         return self.wfdata
 
     def getOriginalWFData(self):
-        """
-
-
-        :return:
-        """
         return self.wforiginal
 
     def resetWFData(self):
         """
-
+        Set waveform data to original waveform data
-
         """
         self.wfdata = self.getOriginalWFData().copy()
         self.dirty = False
 
     def resetPicks(self):
         """
-
+        Clear all picks from event
-
         """
         self.get_evt_data().picks = []
 
     def get_evt_data(self):
-        """
-
-
-        :return:
-        """
         return self.evtdata
 
     def setEvtData(self, event):
         self.evtdata = event
 
     def applyEVTData(self, data, typ='pick', authority_id='rub'):
-
         """
-
+        Either takes an `obspy.core.event.Event` object and applies all new
-        :param data:
+        information on the event to the actual data if typ is 'event or
-        :param typ:
+        creates ObsPy pick objects and append it to the picks list from the
-        :param authority_id:
+        PyLoT dictionary contain all picks if type is pick
+        :param data: data to apply, either picks or complete event
+        :type data:
+        :param typ: which event data to apply, 'pick' or 'event'
+        :type typ: str
+        :param authority_id: (currently unused)
+        :type: str
         :raise OverwriteError:
         """
 

pylot/core/io/default_parameters.py

@@ -1,6 +1,10 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+"""
+Default parameters used for picking
+"""
+
 defaults = {'rootpath': {'type': str,
                          'tooltip': 'project path',
                          'value': '',

pylot/core/io/inputs.py

@@ -70,6 +70,7 @@ class PylotParameter(object):
 
     # Set default values of parameter names
     def __init_default_paras(self):
+        """set default values of parameter names"""
         parameters = default_parameters.defaults
         self.__defaults = parameters
 
@@ -104,15 +105,34 @@ class PylotParameter(object):
         return len(self.__parameter.keys())
 
     def iteritems(self):
+        """
+        Iterate over parameters
+        :return: key, value tupel
+        :rtype:
+        """
         for key, value in self.__parameter.items():
             yield key, value
 
     def hasParam(self, parameter):
+        """
+        Check if parameter is in keys
+        :param parameter: parameter to look for in keys
+        :type parameter:
+        :return:
+        :rtype: bool
+        """
         if parameter in self.__parameter.keys():
             return True
         return False
 
     def get(self, *args):
+        """
+        Get first available parameter in args
+        :param args:
+        :type args:
+        :return:
+        :rtype:
+        """
         try:
             for param in args:
                 try:
@@ -128,15 +148,35 @@ class PylotParameter(object):
                 raise ParameterError(e)
 
     def get_defaults(self):
+        """
+        get default parameters
+        :return:
+        :rtype: dict
+        """
         return self.__defaults
 
     def get_main_para_names(self):
+        """
+        Get main parameter names
+        :return: list of keys available in parameters
+        :rtype:
+        """
         return self._settings_main
 
     def get_special_para_names(self):
+        """
+        Get pick parameter names
+        :return: list of keys available in parameters
+        :rtype:
+        """
         return self._settings_special_pick
 
     def get_all_para_names(self):
+        """
+        Get all parameter names
+        :return:
+        :rtype: list
+        """
         all_names = []
         all_names += self.get_main_para_names()['dirs']
         all_names += self.get_main_para_names()['nlloc']
@@ -151,6 +191,16 @@ class PylotParameter(object):
         return all_names
 
     def checkValue(self, param, value):
+        """
+        Check type of value against expected type of param.
+        Print warning message if type check fails
+        :param param:
+        :type param:
+        :param value:
+        :type value:
+        :return:
+        :rtype:
+        """
         is_type = type(value)
         expect_type = self.get_defaults()[param]['type']
         if not is_type == expect_type and not is_type == tuple:
@@ -159,9 +209,25 @@ class PylotParameter(object):
             print(Warning(message))
 
     def setParamKV(self, param, value):
+        """
+        set parameter param to value
+        :param param:
+        :type param:
+        :param value:
+        :type value:
+        :return:
+        :rtype: None
+        """
         self.__setitem__(param, value)
 
     def setParam(self, **kwargs):
+        """
+        Set multiple parameters
+        :param kwargs:
+        :type kwargs:
+        :return:
+        :rtype: None
+        """
         for key in kwargs:
             self.__setitem__(key, kwargs[key])
 
@@ -170,11 +236,23 @@ class PylotParameter(object):
         print('ParameterError:\n non-existent parameter %s' % errmsg)
 
     def reset_defaults(self):
+        """
+        Reset current parameters to default parameters
+        :return:
+        :rtype: None
+        """
         defaults = self.get_defaults()
         for param in defaults:
             self.setParamKV(param, defaults[param]['value'])
 
     def from_file(self, fnin=None):
+        """
+        read parameters from file and set values to read values
+        :param fnin: filename
+        :type fnin:
+        :return:
+        :rtype: None
+        """
         if not fnin:
             if self.__filename is not None:
                 fnin = self.__filename
@@ -221,6 +299,13 @@ class PylotParameter(object):
         self.__parameter = self._parFileCont
 
     def export2File(self, fnout):
+        """
+        Export parameters to file
+        :param fnout: Filename of export file
+        :type fnout: str
+        :return:
+        :rtype:
+        """
         fid_out = open(fnout, 'w')
         lines = []
         # for key, value in self.iteritems():
@@ -257,6 +342,19 @@ class PylotParameter(object):
                            'quality assessment', None)
 
     def write_section(self, fid, names, title, separator):
+        """
+        write a section of parameters to file
+        :param fid: File object to write to
+        :type fid:
+        :param names: which parameter names to write to file
+        :type names:
+        :param title: title of section
+        :type title: str
+        :param separator: section separator, written at start of section
+        :type separator: str
+        :return:
+        :rtype:
+        """
         if separator:
             fid.write(separator)
         fid.write('#{}#\n'.format(title))

pylot/core/io/location.py

@@ -54,7 +54,7 @@ def create_arrival(pickresID, cinfo, phase, azimuth=None, dist=None):
 
 def create_creation_info(agency_id=None, creation_time=None, author=None):
     '''
-
+    get creation info of obspy event
     :param agency_id:
     :param creation_time:
     :param author:
@@ -197,9 +197,9 @@ def create_pick(origintime, picknum, picktime, eventnum, cinfo, phase, station,
 
 def create_resourceID(timetohash, restype, authority_id=None, hrstr=None):
     '''
-
+    create unique resource id
-    :param timetohash:
+    :param timetohash: event origin time to hash
-    :type timetohash
+    :type timetohash: class: `~obspy.core.utcdatetime.UTCDateTime` object
     :param restype: type of the resource, e.g. 'orig', 'earthquake' ...
     :type restype: str
     :param authority_id: name of the institution carrying out the processing

pylot/core/io/phases.py

@@ -118,6 +118,13 @@ def readPILOTEvent(phasfn=None, locfn=None, authority_id='RUB', **kwargs):
 
 
 def picksdict_from_pilot(fn):
+    """
+    Create pick dictionary from matlab file
+    :param fn: matlab file
+    :type fn:
+    :return: pick dictionary
+    :rtype: dict
+    """
     from pylot.core.util.defaults import TIMEERROR_DEFAULTS
     picks = dict()
     phases_pilot = sio.loadmat(fn)
@@ -147,6 +154,13 @@ def picksdict_from_pilot(fn):
 
 
 def stations_from_pilot(stat_array):
+    """
+    Create stations list from pilot station array
+    :param stat_array:
+    :type stat_array:
+    :return:
+    :rtype: list
+    """
     stations = list()
     cur_stat = None
     for stat in stat_array:
@@ -164,6 +178,13 @@ def stations_from_pilot(stat_array):
 
 
 def convert_pilot_times(time_array):
+    """
+    Convert pilot times to UTCDateTimes
+    :param time_array: pilot times
+    :type time_array:
+    :return:
+    :rtype:
+    """
     times = [int(time) for time in time_array]
     microseconds = int((time_array[-1] - times[-1]) * 1e6)
     times.append(microseconds)
@@ -171,6 +192,13 @@ def convert_pilot_times(time_array):
 
 
 def picksdict_from_obs(fn):
+    """
+    create pick dictionary from obs file
+    :param fn: filename
+    :type fn:
+    :return:
+    :rtype:
+    """
     picks = dict()
     station_name = str()
     for line in open(fn, 'r'):
@@ -240,6 +268,16 @@ def picksdict_from_picks(evt):
 
 
 def picks_from_picksdict(picks, creation_info=None):
+    """
+    Create a list of picks out of a pick dictionary
+    :param picks: pick dictionary
+    :type picks: dict
+    :param creation_info: obspy creation information to apply to picks
+    :type creation_info:
+    :param creation_info: obspy creation information to apply to picks
+    :return: list of picks
+    :rtype: list
+    """
     picks_list = list()
     for station, onsets in picks.items():
         for label, phase in onsets.items():
@@ -410,25 +448,24 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
 
     HYPO71, NLLoc, VELEST, HYPOSAT, and hypoDD
 
-    :param: arrivals
+    :param arrivals:dictionary containing all phase information including
-    :type: dictionary containing all phase information including
+     station ID, phase, first motion, weight (uncertainty), ...
-           station ID, phase, first motion, weight (uncertainty),
+    :type arrivals: dict
-           ....
 
-    :param: fformat
+    :param fformat: chosen file format (location routine),
-    :type:  string, chosen file format (location routine),
+    choose between NLLoc, HYPO71, HYPOSAT, VELEST,
-            choose between NLLoc, HYPO71, HYPOSAT, VELEST,
+    HYPOINVERSE, and hypoDD
-            HYPOINVERSE, and hypoDD
+    :type fformat: str
 
-    :param: filename, full path and name of phase file
+    :param filename: full path and name of phase file
-    :type:  string
+    :type filename:  string
 
-    :param: parameter, all input information
+    :param parameter: all input information
-    :type:  object
+    :type parameter:  object
 
-    :param: eventinfo, optional, needed for VELEST-cnv file 
+    :param eventinfo: optional, needed for VELEST-cnv file
             and FOCMEC- and HASH-input files 
-    :type:  `obspy.core.event.Event` object
+    :type eventinfo: `obspy.core.event.Event` object
     """
 
     if fformat == 'NLLoc':
@@ -874,10 +911,20 @@ def merge_picks(event, picks):
 
 def getQualitiesfromxml(xmlnames, ErrorsP, ErrorsS, plotflag=1):
     """
-   Script to get onset uncertainties from Quakeml.xml files created by PyLoT.
+    Script to get onset uncertainties from Quakeml.xml files created by PyLoT.
    Uncertainties are tranformed into quality classes and visualized via histogram if desired.
    Ludger Küperkoch, BESTEC GmbH, 07/2017
-   """
+    :param xmlnames: list of xml obspy event files containing picks
+    :type xmlnames: list
+    :param ErrorsP: time errors of P waves for the four discrete quality classes
+    :type ErrorsP:
+    :param ErrorsS: time errors of S waves for the four discrete quality classes
+    :type ErrorsS:
+    :param plotflag:
+    :type plotflag:
+    :return:
+    :rtype:
+    """
 
     from pylot.core.pick.utils import getQualityFromUncertainty
     from pylot.core.util.utils import loopIdentifyPhase, identifyPhase