Merge branch 'develop'

QtPyLoT.py

@@ -55,9 +55,9 @@ except ImportError:
 from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar    
 from matplotlib.figure import Figure
 
-from pylot.core.analysis.magnitude import RichterMagnitude, MomentMagnitude
+from pylot.core.analysis.magnitude import LocalMagnitude, MomentMagnitude
 from pylot.core.io.data import Data
-from pylot.core.io.inputs import FilterOptions, AutoPickParameter
+from pylot.core.io.inputs import FilterOptions, PylotParameter
 from autoPyLoT import autoPyLoT
 from pylot.core.pick.compare import Comparison
 from pylot.core.pick.utils import symmetrize_error
@@ -73,7 +73,7 @@ from pylot.core.util.utils import fnConstructor, getLogin, \
 from pylot.core.io.location import create_creation_info, create_event
 from pylot.core.util.widgets import FilterOptionsDialog, NewEventDlg, \
     WaveformWidget, WaveformWidgetPG, PropertiesDlg, HelpForm, createAction, PickDlg, \
-    getDataType, ComparisonDialog, TuneAutopicker, AutoPickParaBox
+    getDataType, ComparisonDialog, TuneAutopicker, PylotParaBox
 from pylot.core.util.map_projection import map_projection
 from pylot.core.util.structure import DATASTRUCTURE
 from pylot.core.util.thread import AutoPickThread, Thread
@@ -103,7 +103,7 @@ class MainWindow(QMainWindow):
             self.infile = infile[0]
         else:
              self.infile = infile
-        self._inputs = AutoPickParameter(infile)
+        self._inputs = PylotParameter(infile)
         self._props = None
 
         self.dirty = False
@@ -799,7 +799,7 @@ class MainWindow(QMainWindow):
                 self.paraBox.setValue(box, dirs[directory])
                 #show needed parameter in box
                 self.paraBox.show_parameter(directory)
-            dirs_box = self.paraBox.get_groupbox_exclusive('Directories')
+            dirs_box = self.paraBox.get_groupbox_dialog('Directories')
             if not dirs_box.exec_():
                 return
             self.project.rootpath = dirs['rootpath']
@@ -2150,7 +2150,7 @@ class MainWindow(QMainWindow):
         # if not rest_flag:
         #     raise ProcessingError('Restitution of waveform data failed!')
         if type == 'ML':
-            local_mag = RichterMagnitude(corr_wf, self.get_data().get_evt_data(), self.inputs.get('sstop'), verbosity = True)
+            local_mag = LocalMagnitude(corr_wf, self.get_data().get_evt_data(), self.inputs.get('sstop'), verbosity = True)
             return local_mag.updated_event()
         elif type == 'Mw':
             moment_mag = MomentMagnitude(corr_wf, self.get_data().get_evt_data(), self.inputs.get('vp'), self.inputs.get('Qp'), self.inputs.get('rho'), verbosity = True)
@@ -2331,7 +2331,7 @@ class MainWindow(QMainWindow):
 
     def setParameter(self, show=True):
         if not self.paraBox:
-            self.paraBox = AutoPickParaBox(self._inputs)
+            self.paraBox = PylotParaBox(self._inputs)
             self.paraBox._apply.clicked.connect(self._setDirty)
             self.paraBox._okay.clicked.connect(self._setDirty)
         if show:

autoPyLoT.py

@@ -16,9 +16,9 @@ import pylot.core.loc.focmec as focmec
 import pylot.core.loc.hash as hash
 import pylot.core.loc.nll as nll
 #from PySide.QtGui import QWidget, QInputDialog
-from pylot.core.analysis.magnitude import MomentMagnitude, RichterMagnitude
+from pylot.core.analysis.magnitude import MomentMagnitude, LocalMagnitude
 from pylot.core.io.data import Data
-from pylot.core.io.inputs import AutoPickParameter
+from pylot.core.io.inputs import PylotParameter
 from pylot.core.pick.autopick import autopickevent, iteratepicker
 from pylot.core.util.dataprocessing import restitute_data, read_metadata, \
     remove_underscores
@@ -35,7 +35,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
 
     :param inputfile: path to the input file containing all parameter
     information for automatic picking (for formatting details, see.
-    `~pylot.core.io.inputs.AutoPickParameter`
+    `~pylot.core.io.inputs.PylotParameter`
     :type inputfile: str
     :return:
 
@@ -71,13 +71,13 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
 
     if not parameter:
         if inputfile:
-            parameter = AutoPickParameter(inputfile)
+            parameter = PylotParameter(inputfile)
             iplot = parameter['iplot']
         else:
             print('No parameters set and no input file given. Choose either of both.')
             return
     else:
-        if not type(parameter) == AutoPickParameter:
+        if not type(parameter) == PylotParameter:
             print('Wrong input type for parameter: {}'.format(type(parameter)))
             return
         if inputfile:
@@ -252,9 +252,9 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                         for station, props in moment_mag.moment_props.items():
                             picks[station]['P'].update(props)
                         evt = moment_mag.updated_event()
-                        local_mag = RichterMagnitude(corr_dat, evt,
+                        local_mag = LocalMagnitude(corr_dat, evt,
-                                                     parameter.get('sstop'), True,\
+                                                   parameter.get('sstop'), parameter.get('WAscaling'), \
-                                                     iplot)
+                                                   True, iplot)
                         for station, amplitude in local_mag.amplitudes.items():
                             picks[station]['S']['Ao'] = amplitude.generic_amplitude
                         evt = local_mag.updated_event()
@@ -310,9 +310,9 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                             for station, props in moment_mag.moment_props.items():
                                 picks[station]['P'].update(props)
                             evt = moment_mag.updated_event()
-                            local_mag = RichterMagnitude(corr_dat, evt,
+                            local_mag = LocalMagnitude(corr_dat, evt,
-                                                         parameter.get('sstop'), True, \
+                                                       parameter.get('sstop'), parameter.get('WAscaling'), \
-                                                         iplot)
+                                                       True, iplot)
                             for station, amplitude in local_mag.amplitudes.items():
                                 picks[station]['S']['Ao'] = amplitude.generic_amplitude
                             evt = local_mag.updated_event()

pylot/RELEASE-VERSION

@@ -1 +1 @@
-6feff-dirty
+f91e1-dirty

pylot/core/analysis/magnitude.py

@@ -38,10 +38,10 @@ class Magnitude(object):
 
     def __init__(self, stream, event, verbosity=False, iplot=0):
         self._type = "M"
+        self._stream = stream
         self._plot_flag = iplot
         self._verbosity = verbosity
         self._event = event
-        self._stream = stream
         self._magnitudes = dict()
 
     def __str__(self):
@@ -136,7 +136,7 @@ class Magnitude(object):
         return None
 
 
-class RichterMagnitude(Magnitude):
+class LocalMagnitude(Magnitude):
     """
     Method to derive peak-to-peak amplitude as seen on a Wood-Anderson-
     seismograph. Has to be derived from instrument corrected traces!
@@ -153,10 +153,11 @@ class RichterMagnitude(Magnitude):
 
     _amplitudes = dict()
 
-    def __init__(self, stream, event, calc_win, verbosity=False, iplot=0):
+    def __init__(self, stream, event, calc_win, wascaling=None, verbosity=False, iplot=0):
-        super(RichterMagnitude, self).__init__(stream, event, verbosity, iplot)
+        super(LocalMagnitude, self).__init__(stream, event, verbosity, iplot)
 
         self._calc_win = calc_win
+        self._wascaling = wascaling
         self._type = 'ML'
         self.calc()
 
@@ -168,6 +169,10 @@ class RichterMagnitude(Magnitude):
     def calc_win(self, value):
         self._calc_win = value
 
+    @property
+    def wascaling(self):
+        return self._wascaling
+
     @property
     def amplitudes(self):
         return self._amplitudes
@@ -251,10 +256,16 @@ class RichterMagnitude(Magnitude):
             self.event.amplitudes.append(amplitude)
             self.amplitudes = (station, amplitude)
             # using standard Gutenberg-Richter relation
-            # TODO make the ML calculation more flexible by allowing
+            # or scale WA amplitude with given scaling relation
-            # use of custom relation functions
+            if self.wascaling == None:
-            magnitude = ope.StationMagnitude(
+                print("Calculating original Richter magnitude ...")
-                mag=np.log10(a0) + richter_magnitude_scaling(delta))
+                magnitude = ope.StationMagnitude(mag=np.log10(a0) \
+                            + richter_magnitude_scaling(delta))
+            else:
+                print("Calculating scaled local magnitude ...")
+                magnitude = ope.StationMagnitude(mag=np.log10(a0) \
+                            + self.wascaling[0] * np.log10(delta) + self.wascaling[1] 
+                            * delta + self.wascaling[2])
             magnitude.origin_id = self.origin_id
             magnitude.waveform_id = pick.waveform_id
             magnitude.amplitude_id = amplitude.resource_id

pylot/core/io/default_parameters.py

@@ -277,13 +277,13 @@ defaults = {'rootpath': {'type': str,
                              'tooltip': 'maximum allowed deviation from Wadati-diagram',
                              'value': 1.0},
             
-            'WAscaling': {'type': float,
+            'WAscaling': {'type': (float, float, float),
-                         'tooltip': 'Scaling relation of Wood-Anderson amplitude [nm]',
+                         'tooltip': 'Scaling relation (log(Ao)+Alog(r)+Br+C) of Wood-Anderson amplitude Ao [nm]',
-                         'value': 1.0},
+                         'value': (1.0, 1.0, 1.0)},
 
-            'magscaling': {'type': float,
+            'magscaling': {'type': (float, float),
                          'tooltip': 'Scaling relation for derived local magnitude [a*Ml+b]',
-                         'value': 1.0}
+                         'value': (1.0, 1.0)}
 }
 
 settings_main={

pylot/core/io/inputs.py

@@ -4,9 +4,9 @@
 from pylot.core.util.errors import ParameterError
 import default_parameters
 
-class AutoPickParameter(object):
+class PylotParameter(object):
     '''
-    AutoPickParameters is a parameter type object capable to read and/or write
+    PylotParameter is a parameter type object capable to read and/or write
     parameter ASCII.
 
     :param fn str: Filename of the input file
@@ -78,7 +78,7 @@ class AutoPickParameter(object):
         
     # String representation of the object
     def __repr__(self):
-        return "AutoPickParameter('%s')" % self.__filename
+        return "PylotParameter('%s')" % self.__filename
 
     # Boolean test
     def __nonzero__(self):

pylot/core/io/phases.py

@@ -8,7 +8,7 @@ import scipy.io as sio
 import warnings
 from obspy.core import UTCDateTime
 
-from pylot.core.io.inputs import AutoPickParameter
+from pylot.core.io.inputs import PylotParameter
 from pylot.core.io.location import create_arrival, create_event, \
     create_magnitude, create_origin, create_pick
 from pylot.core.pick.utils import select_for_phase
@@ -116,7 +116,7 @@ def picksdict_from_pilot(fn):
     picks = dict()
     phases_pilot = sio.loadmat(fn)
     stations = stations_from_pilot(phases_pilot['stat'])
-    params = AutoPickParameter(TIMEERROR_DEFAULTS)
+    params = PylotParameter(TIMEERROR_DEFAULTS)
     timeerrors = dict(P=params.get('timeerrorsP'),
                       S=params.get('timeerrorsS'))
     for n, station in enumerate(stations):
@@ -295,14 +295,14 @@ def reassess_pilot_db(root_dir, db_dir, out_dir=None, fn_param=None, verbosity=0
 def reassess_pilot_event(root_dir, db_dir, event_id, out_dir=None, fn_param=None, verbosity=0):
     from obspy import read
 
-    from pylot.core.io.inputs import AutoPickParameter
+    from pylot.core.io.inputs import PylotParameter
     from pylot.core.pick.utils import earllatepicker
 
     if fn_param is None:
         import pylot.core.util.defaults as defaults
         fn_param = defaults.AUTOMATIC_DEFAULTS
 
-    default = AutoPickParameter(fn_param, verbosity)
+    default = PylotParameter(fn_param, verbosity)
 
     search_base = os.path.join(root_dir, db_dir, event_id)
     phases_file = glob.glob(os.path.join(search_base, 'PHASES.mat'))

pylot/core/pick/autopick.py

@@ -11,7 +11,7 @@ function conglomerate utils.
 
 import matplotlib.pyplot as plt
 import numpy as np
-from pylot.core.io.inputs import AutoPickParameter
+from pylot.core.io.inputs import PylotParameter
 from pylot.core.pick.picker import AICPicker, PragPicker
 from pylot.core.pick.charfuns import CharacteristicFunction
 from pylot.core.pick.charfuns import HOScf, AICcf, ARZcf, ARHcf, AR3Ccf
@@ -81,7 +81,7 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
 
     :param pickparam: container of picking parameters from input file,
            usually autoPyLoT.in
-    :type pickparam: AutoPickParameter
+    :type pickparam: PylotParameter
     :param verbose:
     :type verbose: bool
 

pylot/core/util/utils.py

@@ -10,7 +10,7 @@ import re
 import warnings
 import subprocess
 from obspy import UTCDateTime, read
-from pylot.core.io.inputs import AutoPickParameter
+from pylot.core.io.inputs import PylotParameter
 
 
 def _pickle_method(m):
@@ -497,7 +497,7 @@ def which(program, infile=None):
             bpath = os.path.join(os.path.expanduser('~'), '.pylot', infile)
             
         if os.path.exists(bpath):
-            nllocpath = ":" + AutoPickParameter(bpath).get('nllocbin')
+            nllocpath = ":" + PylotParameter(bpath).get('nllocbin')
             os.environ['PATH'] += nllocpath
     except ImportError as e:
         print(e.message)

pylot/core/util/widgets.py

@@ -36,7 +36,7 @@ from PySide.QtCore import QSettings, Qt, QUrl, Signal, Slot
 from PySide.QtWebKit import QWebView
 from obspy import Stream, UTCDateTime
 from pylot.core.io.data import Data
-from pylot.core.io.inputs import FilterOptions, AutoPickParameter
+from pylot.core.io.inputs import FilterOptions, PylotParameter
 from pylot.core.pick.utils import getSNR, earllatepicker, getnoisewin, \
     getResolutionWindow
 from pylot.core.pick.compare import Comparison
@@ -1662,7 +1662,7 @@ class TuneAutopicker(QWidget):
         self.stb_names = ['aicARHfig', 'refSpick', 'el_S1pick', 'el_S2pick']
 
     def add_parameters(self):
-        self.paraBox = AutoPickParaBox(self.parameter)
+        self.paraBox = PylotParaBox(self.parameter)
         self.paraBox.set_tune_mode(True)
         self.update_eventID()
         self.parameter_layout.addWidget(self.paraBox)
@@ -1968,13 +1968,13 @@ class TuneAutopicker(QWidget):
         self.qmb.show()        
     
                 
-class AutoPickParaBox(QtGui.QWidget):     
+class PylotParaBox(QtGui.QWidget):     
     def __init__(self, parameter, parent=None):
         '''
         Generate Widget containing parameters for automatic picking algorithm.
 
         :param: parameter
-        :type: AutoPickParameter (object)
+        :type: PylotParameter (object)
 
         '''
         QtGui.QWidget.__init__(self, parent)
@@ -1987,6 +1987,7 @@ class AutoPickParaBox(QtGui.QWidget):
         self.labels = {}
         self.boxes = {}
         self.groupboxes = {}
+        self._exclusive_widgets = []
         self._init_sublayouts()
         self.setLayout(self.layout)
         self.add_main_parameters_tab()
@@ -2034,7 +2035,7 @@ class AutoPickParaBox(QtGui.QWidget):
         
     def _create_advanced_cb(self):
         self._advanced_cb = QtGui.QCheckBox('Enable Advanced Settings')
-        self._advanced_layout.addWidget(self._advanced_cb)
+        self._advanced_layout.insertWidget(0, self._advanced_cb)
         self._advanced_cb.toggled.connect(self._toggle_advanced_settings)
 
     def _toggle_advanced_settings(self):
@@ -2140,13 +2141,13 @@ class AutoPickParaBox(QtGui.QWidget):
 
     def add_special_pick_parameters_tab(self):
         self.add_to_layout(self._advanced_layout, 'Z-component',
-                           self.parameter.get_special_para_names()['z'], 0)
+                           self.parameter.get_special_para_names()['z'], 1)
         self.add_to_layout(self._advanced_layout, 'H-components',
-                           self.parameter.get_special_para_names()['h'], 1)
+                           self.parameter.get_special_para_names()['h'], 2)
         self.add_to_layout(self._advanced_layout, 'First-motion picker',
-                           self.parameter.get_special_para_names()['fm'], 2)
+                           self.parameter.get_special_para_names()['fm'], 3)
         self.add_to_layout(self._advanced_layout, 'Quality assessment',
-                           self.parameter.get_special_para_names()['quality'], 3)
+                           self.parameter.get_special_para_names()['quality'], 4)
         self.add_tab(self._advanced_layout, 'Advanced Settings')
 
     # def gen_h_seperator(self):
@@ -2168,20 +2169,29 @@ class AutoPickParaBox(QtGui.QWidget):
             layout.insertWidget(position, groupbox)
 
     def get_groupbox_exclusive(self, name):
+        widget = QtGui.QWidget(self, 1)
+        layout = QtGui.QVBoxLayout()
+        widget.setLayout(layout)
+        layout.addWidget(self.groupboxes[name])
+        self._exclusive_widgets.append(widget)
+        return widget
+
+    def get_groupbox_dialog(self, name):
+        widget = self.get_groupbox_exclusive(name)
         dialog = QtGui.QDialog(self.parent())
-        buttonbox = QtGui.QDialogButtonBox(QDialogButtonBox.Ok |
-                                           QDialogButtonBox.Cancel)
-        self._exclusive_dialog = dialog
         layout = QtGui.QVBoxLayout()
         dialog.setLayout(layout)
-        layout.addWidget(self.groupboxes[name])
+        buttonbox = QtGui.QDialogButtonBox(QDialogButtonBox.Ok |
-        layout.addWidget(buttonbox)
+                                           QDialogButtonBox.Cancel)
         buttonbox.accepted.connect(dialog.accept)
         buttonbox.accepted.connect(self.refresh)
         buttonbox.accepted.connect(self.params_from_gui)
         buttonbox.rejected.connect(dialog.reject)
         buttonbox.rejected.connect(self.refresh)
         buttonbox.rejected.connect(self.params_to_gui)
+        layout.addWidget(widget)
+        layout.addWidget(buttonbox)
+        self._exclusive_dialog = dialog
         return dialog
         
     def add_to_layout(self, layout, name, items, position):
@@ -2342,6 +2352,7 @@ class AutoPickParaBox(QtGui.QWidget):
         self.show_parameter()
         if hasattr(self, '_exclusive_dialog'):
             self._exclusive_dialog.close()
+        self._exclusive_widgets = []
         QtGui.QWidget.show(self)
             
     def _warn(self, message):
@@ -2510,7 +2521,7 @@ class InputsTab(PropTab):
         return values
 
     def resetValues(self, infile):
-        para = AutoPickParameter(infile)
+        para = PylotParameter(infile)
         datstruct = para.get('datastructure')
         if datstruct == 'SeisComp':
            index = 0
@@ -2766,7 +2777,7 @@ class LocalisationTab(PropTab):
         return values
 
     def resetValues(self, infile):
-        para = AutoPickParameter(infile)
+        para = PylotParameter(infile)
         nllocroot = para.get('nllocroot')
         nllocbin = para.get('nllocbin')
         loctool = self.locToolComboBox.setCurrentIndex(3)