[move] pseudo method restituteWFData changed to function restitute_data and moved to dataprocessing

pylot/core/analysis/magnitude.py

@@ -14,6 +14,7 @@ from pylot.core.util.utils import getPatternLine
 from scipy.optimize import curve_fit
 from scipy import integrate, signal
 from pylot.core.io.data import Data
+from pylot.core.util.dataprocessing import restitute_data
 
 
 class Magnitude(object):
@@ -354,7 +355,7 @@ def calcsourcespec(wfstream, onset, inventory, vp, delta, azimuth, incidence, Qp
     data = Data()
     wf_copy = wfstream.copy()
 
-    [cordat, restflag] = data.restituteWFData(inventory, wf_copy)
+    [cordat, restflag] = restitute_data(wf_copy, inventory)
     if restflag == 1:
         zdat = cordat.select(component="Z")
         if len(zdat) == 0:

pylot/core/io/data.py

@@ -2,12 +2,10 @@
 # -*- coding: utf-8 -*-
 
 import copy
-import glob
 import os
-from obspy import read_events, read_inventory
+from obspy import read_events
 from obspy.core import read, Stream, UTCDateTime
 from obspy.core.event import Event
-from obspy.io.xseed import Parser
 
 from pylot.core.io.phases import readPILOTEvent, picks_from_picksdict, \
     picksdict_from_pilot, merge_picks
@@ -269,139 +267,6 @@ class Data(object):
         """
         self.get_evt_data().picks = []
 
-    def restituteWFData(self, invdlpath, streams=None):
-        """
-
-        :param invdlpath:
-        :param streams:
-        :return:
-        """
-
-        restflag = 0
-
-        if streams is None:
-            st_raw = self.getWFData()
-            st = st_raw.copy()
-        else:
-            st = streams
-
-        for tr in st:
-            # remove underscores
-            if len(tr.stats.station) > 3 and tr.stats.station[3] == '_':
-                tr.stats.station = tr.stats.station[0:3]
-        dlp = '%s/*.dless' % invdlpath
-        invp = '%s/*.xml' % invdlpath
-        respp = '%s/*.resp' % invdlpath
-        dlfile = glob.glob(dlp)
-        invfile = glob.glob(invp)
-        respfile = glob.glob(respp)
-
-        # check for dataless-SEED file
-        if len(dlfile) >= 1:
-            print("Found dataless-SEED file(s)!")
-            print("Reading meta data information ...")
-            for j in range(len(dlfile)):
-                print("Found dataless-SEED file %s" % dlfile[j])
-                parser = Parser('%s' % dlfile[j])
-                for i in range(len(st)):
-                    # check, whether this trace has already been corrected
-                    try:
-                        st[i].stats.processing
-                    except:
-                        try:
-                            print(
-                                "Correcting %s, %s for instrument response "
-                                "..." % (st[i].stats.station,
-                                         st[i].stats.channel))
-                            # get corner frequencies for pre-filtering
-                            fny = st[i].stats.sampling_rate / 2
-                            fc21 = fny - (fny * 0.05)
-                            fc22 = fny - (fny * 0.02)
-                            prefilt = [0.5, 0.9, fc21, fc22]
-                            # instrument correction
-                            st[i].simulate(pre_filt=prefilt,
-                                           seedresp={'filename': parser,
-                                                     'date': st[
-                                                         i].stats.starttime,
-                                                     'units': "VEL"})
-                            restflag = 1
-                        except ValueError as e:
-                            vmsg = '{0}'.format(e)
-                            print(vmsg)
-                    else:
-                        print("Trace has already been corrected!")
-        # check for inventory-xml file
-        if len(invfile) >= 1:
-            print("Found inventory-xml file(s)!")
-            print("Reading meta data information ...")
-            for j in range(len(invfile)):
-                print("Found inventory-xml file %s" % invfile[j])
-                inv = read_inventory(invfile[j], format="STATIONXML")
-                for i in range(len(st)):
-                    # check, whether this trace has already been corrected
-                    try:
-                        st[i].stats.processing
-                    except:
-                        try:
-                            print("Correcting %s, %s for instrument response "
-                                  "..." % (st[i].stats.station,
-                                           st[i].stats.channel))
-                            # get corner frequencies for pre-filtering
-                            fny = st[i].stats.sampling_rate / 2
-                            fc21 = fny - (fny * 0.05)
-                            fc22 = fny - (fny * 0.02)
-                            prefilt = [0.5, 0.9, fc21, fc22]
-                            # instrument correction
-                            st[i].attach_response(inv)
-                            st[i].remove_response(output='VEL',
-                                                  pre_filt=prefilt)
-                            restflag = 1
-                        except ValueError as e:
-                            vmsg = '{0}'.format(e)
-                            print(vmsg)
-                    else:
-                        print("Trace has already been corrected!")
-        # check for RESP-file
-        if len(respfile) >= 1:
-            print("Found response file(s)!")
-            print("Reading meta data information ...")
-            for j in range(len(respfile)):
-                print("Found RESP-file %s" % respfile[j])
-                for i in range(len(st)):
-                    # check, whether this trace has already been corrected
-                    try:
-                        st[i].stats.processing
-                    except:
-                        try:
-                            print("Correcting %s, %s for instrument response "
-                                  "..." % (st[i].stats.station,
-                                           st[i].stats.channel))
-                            # get corner frequencies for pre-filtering
-                            fny = st[i].stats.sampling_rate / 2
-                            fc21 = fny - (fny * 0.05)
-                            fc22 = fny - (fny * 0.02)
-                            prefilt = [0.5, 0.9, fc21, fc22]
-                            # instrument correction
-                            seedresp = {'filename': respfile[0],
-                                        'date': st[0].stats.starttime,
-                                        'units': "VEL"}
-                            st[i].simulate(paz_remove=None, pre_filt=prefilt,
-                                           seedresp=seedresp)
-                            restflag = 1
-                        except ValueError as e:
-                            vmsg = '{0}'.format(e)
-                            print(vmsg)
-                    else:
-                        print("Trace has already been corrected!")
-
-        if len(respfile) < 1 and len(invfile) < 1 and len(dlfile) < 1:
-            print("No dataless-SEED file,inventory-xml file nor RESP-file "
-                  "found!")
-            print("Go on processing data without source parameter "
-                  "determination!")
-
-        return st, restflag
-
     def get_evt_data(self):
         """
 

pylot/core/pick/autopick.py

@@ -17,6 +17,7 @@ from pylot.core.pick.charfuns import CharacteristicFunction
 from pylot.core.pick.charfuns import HOScf, AICcf, ARZcf, ARHcf, AR3Ccf
 from pylot.core.pick.utils import checksignallength, checkZ4S, earllatepicker, \
     getSNR, fmpicker, checkPonsets, wadaticheck
+from pylot.core.util.dataprocessing import restitute_data
 from pylot.core.util.utils import getPatternLine
 from pylot.core.io.data import Data
 from pylot.core.analysis.magnitude import WApp
@@ -564,7 +565,7 @@ def autopickstation(wfstream, pickparam, verbose=False):
                 hdat = edat.copy()
                 hdat += ndat
                 h_copy = hdat.copy()
-                [cordat, restflag] = data.restituteWFData(invdir, h_copy)
+                [cordat, restflag] = restitute_data(h_copy, invdir)
                 # calculate WA-peak-to-peak amplitude
                 # using subclass WApp of superclass Magnitude
                 if restflag == 1:
@@ -598,7 +599,7 @@ def autopickstation(wfstream, pickparam, verbose=False):
             hdat = edat.copy()
             hdat += ndat
             h_copy = hdat.copy()
-            [cordat, restflag] = data.restituteWFData(invdir, h_copy)
+            [cordat, restflag] = restitute_data(h_copy, invdir)
             if restflag == 1:
                 # calculate WA-peak-to-peak amplitude
                 # using subclass WApp of superclass Magnitude

pylot/core/util/dataprocessing.py

@@ -3,8 +3,10 @@
 
 import os
 import glob
-from obspy import UTCDateTime
+from obspy import UTCDateTime, read_inventory
 import sys
+from obspy.io.xseed import Parser
+
 
 def time_from_header(header):
     """
@@ -148,6 +150,140 @@ def evt_head_check(root_dir, out_dir = None):
     print(nfiles)
 
 
+def restitute_data(data, invdlpath):
+    """
+
+    :param invdlpath:
+    :param data:
+    :return:
+    """
+
+    restflag = False
+
+    for tr in data:
+        # remove underscores
+        if len(tr.stats.station) > 3 and tr.stats.station[3] == '_':
+            tr.stats.station = tr.stats.station[0:3]
+    dlfile = list()
+    invfile = list()
+    respfile = list()
+    inv = dict(dless=dlfile, xml=invfile, resp=respfile)
+    if os.path.isfile(invdlpath):
+        ext = os.path.splitext(invdlpath)[1].split('.')[1]
+        inv[ext] += [invdlpath]
+    else:
+        for ext in inv.keys():
+            inv[ext] += glob.glob1(invdlpath,'*.{}'.format(ext))
+
+    # check for dataless-SEED file
+    # TODO ineffective loop -> better concatenate inventory entries and
+    # loop over traces
+    if len(dlfile) >= 1:
+        print("Found dataless-SEED file(s)!")
+        print("Reading meta data information ...")
+        for j in range(len(dlfile)):
+            print("Found dataless-SEED file %s" % dlfile[j])
+            parser = Parser('%s' % dlfile[j])
+            for i in range(len(data)):
+                # check, whether this trace has already been corrected
+                try:
+                    data[i].stats.processing
+                except:
+                    try:
+                        print(
+                            "Correcting %s, %s for instrument response "
+                            "..." % (data[i].stats.station,
+                                     data[i].stats.channel))
+                        # get corner frequencies for pre-filtering
+                        fny = data[i].stats.sampling_rate / 2
+                        fc21 = fny - (fny * 0.05)
+                        fc22 = fny - (fny * 0.02)
+                        prefilt = [0.5, 0.9, fc21, fc22]
+                        # instrument correction
+                        data[i].simulate(pre_filt=prefilt,
+                                       seedresp={'filename': parser,
+                                                 'date': data[
+                                                     i].stats.starttime,
+                                                 'units': "VEL"})
+                        restflag = True
+                    except ValueError as e:
+                        vmsg = '{0}'.format(e)
+                        print(vmsg)
+                else:
+                    print("Trace has already been corrected!")
+    # check for inventory-xml file
+    if len(invfile) >= 1:
+        print("Found inventory-xml file(s)!")
+        print("Reading meta data information ...")
+        for j in range(len(invfile)):
+            print("Found inventory-xml file %s" % invfile[j])
+            inv = read_inventory(invfile[j], format="STATIONXML")
+            for i in range(len(data)):
+                # check, whether this trace has already been corrected
+                try:
+                    data[i].stats.processing
+                except:
+                    try:
+                        print("Correcting %s, %s for instrument response "
+                              "..." % (data[i].stats.station,
+                                       data[i].stats.channel))
+                        # get corner frequencies for pre-filtering
+                        fny = data[i].stats.sampling_rate / 2
+                        fc21 = fny - (fny * 0.05)
+                        fc22 = fny - (fny * 0.02)
+                        prefilt = [0.5, 0.9, fc21, fc22]
+                        # instrument correction
+                        data[i].attach_response(inv)
+                        data[i].remove_response(output='VEL',
+                                              pre_filt=prefilt)
+                        restflag = True
+                    except ValueError as e:
+                        vmsg = '{0}'.format(e)
+                        print(vmsg)
+                else:
+                    print("Trace has already been corrected!")
+    # check for RESP-file
+    if len(respfile) >= 1:
+        print("Found response file(s)!")
+        print("Reading meta data information ...")
+        for j in range(len(respfile)):
+            print("Found RESP-file %s" % respfile[j])
+            for i in range(len(data)):
+                # check, whether this trace has already been corrected
+                try:
+                    data[i].stats.processing
+                except:
+                    try:
+                        print("Correcting %s, %s for instrument response "
+                              "..." % (data[i].stats.station,
+                                       data[i].stats.channel))
+                        # get corner frequencies for pre-filtering
+                        fny = data[i].stats.sampling_rate / 2
+                        fc21 = fny - (fny * 0.05)
+                        fc22 = fny - (fny * 0.02)
+                        prefilt = [0.5, 0.9, fc21, fc22]
+                        # instrument correction
+                        seedresp = {'filename': respfile[0],
+                                    'date': data[0].stats.starttime,
+                                    'units': "VEL"}
+                        data[i].simulate(paz_remove=None, pre_filt=prefilt,
+                                       seedresp=seedresp)
+                        restflag = True
+                    except ValueError as e:
+                        vmsg = '{0}'.format(e)
+                        print(vmsg)
+                else:
+                    print("Trace has already been corrected!")
+
+    if len(respfile) < 1 and len(invfile) < 1 and len(dlfile) < 1:
+        print("No dataless-SEED file,inventory-xml file nor RESP-file "
+              "found!")
+        print("Go on processing data without source parameter "
+              "determination!")
+
+    return data, restflag
+
+
 if __name__ == "__main__":
     import doctest