general code clean-up

autoPyLoT.py

@@ -8,11 +8,11 @@ import glob
 
 import matplotlib.pyplot as plt
 from obspy.core import read
-from pylot.core.util import _getVersionString
 from pylot.core.read.data import Data
 from pylot.core.read.inputs import AutoPickParameter
 from pylot.core.util.structure import DATASTRUCTURE
 from pylot.core.pick.autopick import autopickevent
+from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
 

icons.qrc

@@ -1,10 +1,10 @@
 <RCC>
     <qresource>
-		<file>icons/pylot.ico</file>
+        <file>icons/pylot.ico</file>
-		<file>icons/pylot.png</file>
+        <file>icons/pylot.png</file>
         <file>icons/printer.png</file>
         <file>icons/delete.png</file>
-		<file>icons/key_E.png</file>
+        <file>icons/key_E.png</file>
         <file>icons/key_N.png</file>
         <file>icons/key_P.png</file>
         <file>icons/key_Q.png</file>
@@ -14,7 +14,7 @@
         <file>icons/key_U.png</file>
         <file>icons/key_V.png</file>
         <file>icons/key_W.png</file>
-		<file>icons/key_Z.png</file>
+        <file>icons/key_Z.png</file>
         <file>icons/filter.png</file>
         <file>icons/sync.png</file>
         <file>icons/zoom_0.png</file>

pylot/core/__init__.py

@@ -0,0 +1 @@
+# -*- coding: utf-8 -*-

pylot/core/active/__init__.py

@@ -1 +1,2 @@
+# -*- coding: utf-8 -*-
 __author__ = 'sebastianw'

pylot/core/active/activeSeismoPick.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import sys
 import numpy as np
 from pylot.core.active import seismicshot
@@ -144,8 +145,8 @@ class Survey(object):
 
     def countAllTraces(self):
         numtraces = 0
-        for line in self.getShotlist():
+        for shot in self.getShotlist():
-            for line in self.getReceiverlist():
+            for rec in self.getReceiverlist():
                 numtraces += 1
         return numtraces
 

pylot/core/active/fmtomo2vtk.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import numpy as np
 
 def vgrids2VTK(inputfile = 'vgrids.in', outputfile = 'vgrids.vtk'):

pylot/core/active/picking_script.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import sys
 from obspy import read
 from obspy import Stream

pylot/core/active/seismicArrayPreparation.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import sys
 import numpy as np
 from scipy.interpolate import griddata

pylot/core/active/seismicArrayPreperation.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import sys
 import numpy as np
 from scipy.interpolate import griddata

pylot/core/active/seismicshot.py

@@ -35,8 +35,7 @@ class SeismicShot(object):
         self.snr = {}
         self.snrthreshold = {}
         self.timeArray = {}
-        self.paras = {}
+        self.paras = {'shotname': obsfile}
-        self.paras['shotname'] = obsfile
 
     def removeEmptyTraces(self):
         traceIDs = []

pylot/core/active/surveyPlotTools.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import matplotlib.pyplot as plt
 plt.interactive(True)
 

pylot/core/analysis/__init__.py

@@ -0,0 +1 @@
+# -*- coding: utf-8 -*-

pylot/core/analysis/coinctimes.py

@@ -6,7 +6,7 @@ from obspy.signal.trigger import coincidenceTrigger
 
 
 
-class CoincidenceTimes():
+class CoincidenceTimes(object):
 
     def __init__(self, st, comp='Z', coinum=4, sta=1., lta=10., on=5., off=1.):
         _type = 'recstalta'

pylot/core/analysis/magnitude.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
 Created August/September 2015.
@@ -142,7 +143,7 @@ class DCfc(Magnitude):
     '''
 
     def calcsourcespec(self):
-    	print ("Calculating source spectrum ....")
+        print ("Calculating source spectrum ....")
 
         self.w0 = None # DC-value
         self.fc = None # corner frequency

pylot/core/pick/CharFuns.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
 Created Oct/Nov 2014
@@ -315,7 +316,7 @@ class ARZcf(CharacteristicFunction):
         cf = np.zeros(len(xnp))
         loopstep = self.getARdetStep()
         arcalci = ldet + self.getOrder() #AR-calculation index
-	for i in range(ldet + self.getOrder(), tend - lpred - 1):
+        for i in range(ldet + self.getOrder(), tend - lpred - 1):
             if i == arcalci:
                 #determination of AR coefficients
                 #to speed up calculation, AR-coefficients are calculated only every i+loopstep[1]!
@@ -362,7 +363,7 @@ class ARZcf(CharacteristicFunction):
         rhs = np.zeros(self.getOrder())
         for k in range(0, self.getOrder()):
             for i in range(rind, ldet+1):
-		ki = k + 1
+                ki = k + 1
                 rhs[k] = rhs[k] + data[i] * data[i - ki]
 
         #recursive calculation of data array (second sum at left part of eq. 6.5 in Kueperkoch et al. 2012)

pylot/core/pick/Picker.py

@@ -312,7 +312,7 @@ class PragPicker(AutoPicking):
             else:
                 for i in range(1, len(self.cf)):
                     if i > ismooth:
-                        ii1 = i - ismooth;
+                        ii1 = i - ismooth
                         cfsmooth[i] = cfsmooth[i - 1] + (self.cf[i] - self.cf[ii1]) / ismooth
                     else:
                         cfsmooth[i] = np.mean(self.cf[1 : i])

pylot/core/pick/__init__.py

@@ -1 +1,2 @@
+# -*- coding: utf-8 -*-
 #

pylot/core/pick/autopick.py

@@ -317,29 +317,29 @@ def autopickstation(wfstream, pickparam):
                 data = Data()
                 [corzdat, restflag] = data.restituteWFData(invdir, zdat)
                 if restflag == 1:
-                        # integrate to displacement
+                    # integrate to displacement
-                        corintzdat = integrate.cumtrapz(corzdat[0], None, corzdat[0].stats.delta)
+                    corintzdat = integrate.cumtrapz(corzdat[0], None, corzdat[0].stats.delta)
-                        # class needs stream object => build it
+                    # class needs stream object => build it
-                        z_copy = zdat.copy()
+                    z_copy = zdat.copy()
-                        z_copy[0].data = corintzdat
+                    z_copy[0].data = corintzdat
-                        # largest detectable period == window length
+                    # largest detectable period == window length
-                        # after P pulse for calculating source spectrum
+                    # after P pulse for calculating source spectrum
-                        winzc = (1 / bpz2[0]) * z_copy[0].stats.sampling_rate  
+                    winzc = (1 / bpz2[0]) * z_copy[0].stats.sampling_rate
-                        impickP = mpickP * z_copy[0].stats.sampling_rate
+                    impickP = mpickP * z_copy[0].stats.sampling_rate
-                        wfzc = z_copy[0].data[impickP : impickP + winzc]
+                    wfzc = z_copy[0].data[impickP : impickP + winzc]
-                        # calculate spectrum using only first cycles of
+                    # calculate spectrum using only first cycles of
-                        # waveform after P onset!
+                    # waveform after P onset!
-                        zc = crossings_nonzero_all(wfzc)
+                    zc = crossings_nonzero_all(wfzc)
-                        if np.size(zc) == 0:
+                    if np.size(zc) == 0:
-                            print ("Something is wrong with the waveform, " \
+                        print ("Something is wrong with the waveform, " \
-                                   "no zero crossings derived!")
+                               "no zero crossings derived!")
-                            print ("Cannot calculate source spectrum!")
+                        print ("Cannot calculate source spectrum!")
-                        else:
+                    else:
-                            calcwin = (zc[3] - zc[0]) * z_copy[0].stats.delta
+                        calcwin = (zc[3] - zc[0]) * z_copy[0].stats.delta
-                	    # calculate source spectrum and get w0 and fc
+                    # calculate source spectrum and get w0 and fc
-                	    specpara = DCfc(z_copy, mpickP, calcwin, iplot)
+                    specpara = DCfc(z_copy, mpickP, calcwin, iplot)
-                            w0 = specpara.getw0()
+                    w0 = specpara.getw0()
-                            fc = specpara.getfc()
+                    fc = specpara.getfc()
 
                 print ("autopickstation: P-weight: %d, SNR: %f, SNR[dB]: %f, " \
                        "Polarity: %s" % (Pweight, SNRP, SNRPdB, FM))

pylot/core/pick/utils.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+# -*- coding: utf-8 -*-
 #
 # -*- coding: utf-8 -*-
 """
@@ -493,9 +494,9 @@ def wadaticheck(pickdic, dttolerance, iplot):
 
 
     if len(SPtimes) >= 3:
-    	# calculate slope
+        # calculate slope
-    	p1 = np.polyfit(Ppicks, SPtimes, 1)
+        p1 = np.polyfit(Ppicks, SPtimes, 1)
-    	wdfit = np.polyval(p1, Ppicks)
+        wdfit = np.polyval(p1, Ppicks)
         wfitflag = 0
 
         # calculate vp/vs ratio before check
@@ -532,40 +533,40 @@ def wadaticheck(pickdic, dttolerance, iplot):
                 pickdic[key]['S']['marked'] = marker
 
         if len(checkedPpicks) >= 3:
-    		# calculate new slope
+            # calculate new slope
-    		p2 = np.polyfit(checkedPpicks, checkedSPtimes, 1)
+            p2 = np.polyfit(checkedPpicks, checkedSPtimes, 1)
-    		wdfit2 = np.polyval(p2, checkedPpicks)
+            wdfit2 = np.polyval(p2, checkedPpicks)
 
-        	# calculate vp/vs ratio after check
+            # calculate vp/vs ratio after check
-        	cvpvsr = p2[0] + 1
+            cvpvsr = p2[0] + 1
-        	print ("wadaticheck: Average Vp/Vs ratio after check: %f" % cvpvsr)
+            print ("wadaticheck: Average Vp/Vs ratio after check: %f" % cvpvsr)
-                print ("wadatacheck: Skipped %d S pick(s)" % ibad)
+            print ("wadatacheck: Skipped %d S pick(s)" % ibad)
         else:
-                print ("###############################################")
+            print ("###############################################")
-        	print ("wadatacheck: Not enough checked S-P times available!")
+            print ("wadatacheck: Not enough checked S-P times available!")
-                print ("Skip Wadati check!")
+            print ("Skip Wadati check!")
 
         checkedonsets = pickdic
 
     else:
-    	print ("wadaticheck: Not enough S-P times available for reliable regression!")
+        print ("wadaticheck: Not enough S-P times available for reliable regression!")
         print ("Skip wadati check!")
         wfitflag = 1
 
     # plot results
     if iplot > 1:
-    	plt.figure(iplot)
+        plt.figure(iplot)
-    	f1, = plt.plot(Ppicks, SPtimes, 'ro')
+        f1, = plt.plot(Ppicks, SPtimes, 'ro')
         if wfitflag == 0:
-        	f2, = plt.plot(Ppicks, wdfit, 'k')
+            f2, = plt.plot(Ppicks, wdfit, 'k')
-                f3, = plt.plot(checkedPpicks, checkedSPtimes, 'ko')
+            f3, = plt.plot(checkedPpicks, checkedSPtimes, 'ko')
-                f4, = plt.plot(checkedPpicks, wdfit2, 'g')
+            f4, = plt.plot(checkedPpicks, wdfit2, 'g')
-                plt.title('Wadati-Diagram, %d S-P Times, Vp/Vs(raw)=%5.2f,' \
+            plt.title('Wadati-Diagram, %d S-P Times, Vp/Vs(raw)=%5.2f,' \
-                          'Vp/Vs(checked)=%5.2f' % (len(SPtimes), vpvsr, cvpvsr))
+                      'Vp/Vs(checked)=%5.2f' % (len(SPtimes), vpvsr, cvpvsr))
-                plt.legend([f1, f2, f3, f4], ['Skipped S-Picks', 'Wadati 1', \
+            plt.legend([f1, f2, f3, f4], ['Skipped S-Picks', 'Wadati 1', \
-                           'Reliable S-Picks', 'Wadati 2'], loc='best')
+                       'Reliable S-Picks', 'Wadati 2'], loc='best')
         else:
-        	plt.title('Wadati-Diagram, %d S-P Times' % len(SPtimes))
+            plt.title('Wadati-Diagram, %d S-P Times' % len(SPtimes))
 
         plt.ylabel('S-P Times [s]')
         plt.xlabel('P Times [s]')
@@ -612,7 +613,7 @@ def checksignallength(X, pick, TSNR, minsiglength, nfac, minpercent, iplot):
     print ("Checking signal length ...")
 
     if len(X) > 1:
-    	# all three components available
+        # all three components available
         # make sure, all components have equal lengths
         ilen = min([len(X[0].data), len(X[1].data), len(X[2].data)])
         x1 = X[0][0:ilen]
@@ -639,7 +640,7 @@ def checksignallength(X, pick, TSNR, minsiglength, nfac, minpercent, iplot):
     numoverthr = len(np.where(rms[isignal] >= minsiglevel)[0])
 
     if numoverthr >= minnum:
-    	print ("checksignallength: Signal reached required length.")
+        print ("checksignallength: Signal reached required length.")
         returnflag = 1
     else:
         print ("checksignallength: Signal shorter than required minimum signal length!")
@@ -649,7 +650,7 @@ def checksignallength(X, pick, TSNR, minsiglength, nfac, minpercent, iplot):
 
     if iplot == 2:
         plt.figure(iplot)
-    	p1, = plt.plot(t,rms, 'k')
+        p1, = plt.plot(t,rms, 'k')
         p2, = plt.plot(t[inoise], rms[inoise], 'c')
         p3, = plt.plot(t[isignal],rms[isignal], 'r')
         p4, = plt.plot([t[isignal[0]], t[isignal[len(isignal)-1]]], \
@@ -729,27 +730,27 @@ def checkPonsets(pickdic, dttolerance, iplot):
     badjkmarker = 'badjkcheck'
     for i in range(0, len(goodstations)):
         # mark P onset as checked and keep P weight
-    	pickdic[goodstations[i]]['P']['marked'] = goodmarker
+        pickdic[goodstations[i]]['P']['marked'] = goodmarker
     for i in range(0, len(badstations)):
-       	# mark P onset and downgrade P weight to 9
+        # mark P onset and downgrade P weight to 9
-       	# (not used anymore)
+        # (not used anymore)
-    	pickdic[badstations[i]]['P']['marked'] = badmarker
+        pickdic[badstations[i]]['P']['marked'] = badmarker
-      	pickdic[badstations[i]]['P']['weight'] = 9
+        pickdic[badstations[i]]['P']['weight'] = 9
     for i in range(0, len(badjkstations)):
-       	# mark P onset and downgrade P weight to 9
+        # mark P onset and downgrade P weight to 9
-       	# (not used anymore)
+        # (not used anymore)
-    	pickdic[badjkstations[i]]['P']['marked'] = badjkmarker
+        pickdic[badjkstations[i]]['P']['marked'] = badjkmarker
-      	pickdic[badjkstations[i]]['P']['weight'] = 9
+        pickdic[badjkstations[i]]['P']['weight'] = 9
 
     checkedonsets = pickdic
 
     if iplot > 1:
-    	p1, = plt.plot(np.arange(0, len(Ppicks)), Ppicks, 'r+', markersize=14)
+        p1, = plt.plot(np.arange(0, len(Ppicks)), Ppicks, 'r+', markersize=14)
         p2, = plt.plot(igood, np.array(Ppicks)[igood], 'g*', markersize=14)
         p3, = plt.plot([0, len(Ppicks) - 1], [pmedian, pmedian], 'g', \
                         linewidth=2)
         for i in range(0, len(Ppicks)):
-        	plt.text(i, Ppicks[i] + 0.2, stations[i])
+            plt.text(i, Ppicks[i] + 0.2, stations[i])
 
         plt.xlabel('Number of P Picks')
         plt.ylabel('Onset Time [s] from 1.1.1970')
@@ -789,37 +790,37 @@ def jackknife(X, phi, h):
     g = len(X) / h
 
     if type(g) is not int:
-    	print ("jackknife: Cannot divide quantity X in equal sized subgroups!")
+        print ("jackknife: Cannot divide quantity X in equal sized subgroups!")
         print ("Choose another size for subgroups!")
         return PHI_jack, PHI_pseudo, PHI_sub
     else:
-    	# estimator of undisturbed spot check
+        # estimator of undisturbed spot check
-    	if phi == 'MEA':
+        if phi == 'MEA':
-        	phi_sc = np.mean(X)
+            phi_sc = np.mean(X)
         elif phi == 'VAR':
-        	phi_sc = np.var(X)
+            phi_sc = np.var(X)
         elif phi == 'MED':
-        	phi_sc = np.median(X)
+            phi_sc = np.median(X)
 
-    	# estimators of subgroups
+        # estimators of subgroups
         PHI_pseudo = []
         PHI_sub = []
         for i in range(0, g - 1):
-        	# subgroup i, remove i-th sample
+            # subgroup i, remove i-th sample
-                xx = X[:]
+            xx = X[:]
-                del xx[i]
+            del xx[i]
-                # calculate estimators of disturbed spot check
+            # calculate estimators of disturbed spot check
-        	if phi == 'MEA':
+            if phi == 'MEA':
-                	phi_sub = np.mean(xx)
+                phi_sub = np.mean(xx)
-                elif phi == 'VAR':
+            elif phi == 'VAR':
-                	phi_sub = np.var(xx)
+                phi_sub = np.var(xx)
-                elif phi == 'MED':
+            elif phi == 'MED':
-                	phi_sub = np.median(xx)
+                phi_sub = np.median(xx)
 
-                PHI_sub.append(phi_sub)
+            PHI_sub.append(phi_sub)
-                # pseudo values
+            # pseudo values
-                phi_pseudo = g * phi_sc - ((g - 1) * phi_sub)
+            phi_pseudo = g * phi_sc - ((g - 1) * phi_sub)
-                PHI_pseudo.append(phi_pseudo)
+            PHI_pseudo.append(phi_pseudo)
         # jackknife estimator
         PHI_jack = np.mean(PHI_pseudo)
 
@@ -899,17 +900,17 @@ def checkZ4S(X, pick, zfac, checkwin, iplot):
     # vertical P-coda level must exceed horizontal P-coda level
     # zfac times encodalevel
     if zcodalevel < minsiglevel:
-    	print ("checkZ4S: Maybe S onset? Skip this P pick!")
+        print ("checkZ4S: Maybe S onset? Skip this P pick!")
     else:
         print ("checkZ4S: P onset passes checkZ4S test!")
         returnflag = 1
 
     if iplot > 1:
-    	te = np.arange(0, edat[0].stats.npts / edat[0].stats.sampling_rate,
+        te = np.arange(0, edat[0].stats.npts / edat[0].stats.sampling_rate,
                   edat[0].stats.delta)
-    	tn = np.arange(0, ndat[0].stats.npts / ndat[0].stats.sampling_rate,
+        tn = np.arange(0, ndat[0].stats.npts / ndat[0].stats.sampling_rate,
                   ndat[0].stats.delta)
-    	plt.plot(tz, z / max(z), 'k')
+        plt.plot(tz, z / max(z), 'k')
         plt.plot(tz[isignal], z[isignal] / max(z), 'r')
         plt.plot(te, edat[0].data / max(edat[0].data) + 1, 'k')
         plt.plot(te[isignal], edat[0].data[isignal] / max(edat[0].data) + 1, 'r')

pylot/core/read/__init__.py

@@ -1 +1 @@
-
+# -*- coding: utf-8 -*-

pylot/core/read/inputs.py

@@ -208,8 +208,7 @@ class FilterOptions(object):
 
     def parseFilterOptions(self):
         if self.getFilterType():
-            robject = {'type':self.getFilterType()}
+            robject = {'type': self.getFilterType(), 'corners': self.getOrder()}
-            robject['corners'] = self.getOrder()
             if len(self.getFreq()) > 1:
                 robject['freqmin'] = self.getFreq()[0]
                 robject['freqmax'] = self.getFreq()[1]

pylot/core/util/__init__.py

@@ -1 +1,2 @@
+# -*- coding: utf-8 -*-
 from pylot.core.util.version import get_git_version as _getVersionString

pylot/core/util/testUtils.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 Created on 10.11.2014
 

pylot/core/util/testWidgets.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 Created on 10.11.2014
 

pylot/core/util/thread.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import sys
 from PySide.QtCore import QThread, Signal
 

pylot/core/util/utils.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+# -*- coding: utf-8 -*-
 #
 # -*- coding: utf-8 -*-
 

testHelpForm.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+# -*- coding: utf-8 -*-
 
 import sys, time
 from PySide.QtGui import QApplication

testPickDlg.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+# -*- coding: utf-8 -*-
 
 import sys
 import matplotlib

testPropDlg.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+# -*- coding: utf-8 -*-
 
 import sys, time
 from PySide.QtGui import QApplication

testUIcomponents.py

@@ -1,4 +1,6 @@
 #!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
 
 import sys, time
 from PySide.QtGui import QApplication
@@ -9,7 +11,7 @@ dialogs = [FilterOptionsDialog, PropertiesDlg, HelpForm]
 app = QApplication(sys.argv)
 
 for dlg in dialogs:
-	win = dlg()
+    win = dlg()
-	win.show()
+    win.show()
-	time.sleep(1)
+    time.sleep(1)
-	win.destroy()
+    win.destroy()