Merge branch 'develop' of ariadne.geophysik.rub.de:/data/git/pylot into develop

Conflicts:
	autoPyLoT.py
	pylot/core/analysis/magnitude.py
	pylot/core/pick/utils.py

QtPyLoT.py

@@ -273,8 +273,7 @@ class MainWindow(QMainWindow):
                                       slot=self.autoPick, shortcut='Alt+Ctrl+A',
                                       icon=auto_icon, tip='Automatically pick'
                                                           ' the entire dataset'
-                                                          ' displayed!',
+                                                          ' displayed!')
-                                      checkable=False)
 
         autoPickToolBar = self.addToolBar("autoPyLoT")
         autoPickActions = (auto_pick,)

autoPyLoT.py

@@ -8,12 +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.pick.utils import writephases
+from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
 
@@ -86,9 +85,6 @@ def autoPyLoT(inputfile):
                 # !automated picking starts here!
                 picks = autopickevent(wfdat, parameter)
 
-                # write phases to NLLoc-phase file
-                writephases(wd_checked_onsets, 'NLLoc', phasefile) 
-
                 print '------------------------------------------'
                 print '-----Finished event %s!-----' % event
                 print '------------------------------------------'
@@ -104,9 +100,6 @@ def autoPyLoT(inputfile):
             # !automated picking starts here!
             picks = autopickevent(wfdat, parameter)
 
-            # write phases to NLLoc-phase file
-            writephases(wd_checked_onsets, 'NLLoc', phasefile) 
-
             print '------------------------------------------'
             print '-------Finished event %s!-------' % parameter.getParam('eventID')
             print '------------------------------------------'

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
@@ -14,11 +15,12 @@ class Survey(object):
         self._sourcefile = sourcefile
         self._obsdir = path
         self._generateSurvey()
-        if useDefaultParas == True: 
+        if useDefaultParas == True:
             self.setParametersForShots()
         self._removeAllEmptyTraces()
         self._updateShots()
-        
+        self.setArtificialPick(0, 0)
+
     def _generateSurvey(self):
         from obspy.core import read
 
@@ -27,23 +29,28 @@ class Survey(object):
         for shotnumber in shotlist:       # loop over data files
             # generate filenames and read manual picks to a list
             obsfile = self._obsdir + str(shotnumber) + '_pickle.dat'
-
+            if obsfile not in shot_dict.keys():
-            if not obsfile in shot_dict.keys():
                 shot_dict[shotnumber] = []
             shot_dict[shotnumber] = seismicshot.SeismicShot(obsfile)
             shot_dict[shotnumber].setParameters('shotnumber', shotnumber)
 
-        self.setArtificialPick(0, 0) # artificial pick at source origin
-
         self.data = shot_dict
         print ("Generated Survey object for %d shots" % len(shotlist))
         print ("Total number of traces: %d \n" %self.countAllTraces())
 
+    def setArtificialPick(self, traceID, pick):
+        '''
+        Sets an artificial pick for a traceID of all shots in the survey object.
+        (This can be used to create a pick with t = 0 at the source origin)
+        '''
+        for shot in self.data.values():
+            shot.setPick(traceID, pick)
+
     def setParametersForShots(self, cutwindow = (0, 0.2), tmovwind = 0.3, tsignal = 0.03, tgap = 0.0007):
         if (cutwindow == (0, 0.2) and tmovwind == 0.3 and
             tsignal == 0.03 and tgap == 0.0007):
             print ("Warning: Standard values used for "
-                   "setParamters. This may not be clever.")
+                   "setParamters. This might not be clever.")
         # CHANGE this later. Parameters only needed for survey, not for each shot.
         for shot in self.data.values():
             shot.setCut(cutwindow)
@@ -65,7 +72,7 @@ class Survey(object):
             if removed is not None:
                 if count == 0: outfile = open(filename, 'w')
                 count += 1
-                outfile.writelines('shot: %s, removed empty traces: %s\n' 
+                outfile.writelines('shot: %s, removed empty traces: %s\n'
                                    %(shot.getShotnumber(), removed))
         print ("\nremoveEmptyTraces: Finished! Removed %d traces" %count)
         if count > 0:
@@ -83,7 +90,7 @@ class Survey(object):
                 count += 1
                 countTraces += len(del_traceIDs)
                 outfile.writelines("shot: %s, removed traceID(s) %s because "
-                                   "they were not found in the corresponding stream\n" 
+                                   "they were not found in the corresponding stream\n"
                                    %(shot.getShotnumber(), del_traceIDs))
 
         print ("\nupdateShots: Finished! Updated %d shots and removed "
@@ -120,14 +127,13 @@ class Survey(object):
                 shot.setPickwindow(traceID, pickwin_used)
                 shot.pickTraces(traceID, windowsize, folm, HosAic) # picker
 
-                # ++ TEST: set and check SNR before adding to distance bin ############################
                 shot.setSNR(traceID)    
                 #if shot.getSNR(traceID)[0] < snrthreshold:
                 if shot.getSNR(traceID)[0] < shot.getSNRthreshold(traceID):
                         shot.removePick(traceID)
-                # -- TEST: set and check SNR before adding to distance bin ############################
+                        
-
+                # set epp and lpp if SNR > 1 (else earllatepicker cant set values)
-                if shot.getPick(traceID) is not None:
+                if shot.getSNR(traceID)[0] > 1:
                     shot.setEarllatepick(traceID)
 
             tpicksum += (datetime.now() - tstartpick); tpick = tpicksum/count
@@ -137,6 +143,22 @@ class Survey(object):
             self._update_progress(shot.getShotname(), tend, progress)
         print('\npickAllShots: Finished\n')
 
+    def recover(self):
+        '''
+        Recovers all (accidently) removed picks. Still regards SNR threshold.
+        '''
+        print('Recovering survey...')
+        numpicks = 0
+        for shot in self.data.values():
+            for traceID in shot.getTraceIDlist():
+                if shot.getFlag(traceID) == 0:
+                    shot.setFlag(traceID, 1)
+                    if shot.getSNR(traceID)[0] < shot.getSNRthreshold(traceID):
+                        shot.removePick(traceID)
+                    else:
+                        numpicks += 1
+        print('Recovered %d picks'%numpicks)
+
     def setArtificialPick(self, traceID, pick):
         for shot in self.data.values():
             shot.setPick(traceID, pick)
@@ -144,8 +166,8 @@ 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(): ### shot.getReceiverlist etc.
                 numtraces += 1
         return numtraces
 
@@ -180,7 +202,7 @@ class Survey(object):
 
     def getReceiverfile(self):
         return self._recfile
-    
+
     def getPath(self):
         return self._obsdir
 
@@ -194,7 +216,7 @@ class Survey(object):
             for traceID in shot.getTraceIDlist():
                 snrlist.append(shot.getSNR(traceID)[0])
                 dist.append(shot.getDistance(traceID))
-                if shot.getPick(traceID) is not None:
+                if shot.getFlag(traceID) is not 0:
                     pickedTraces += 1
             info_dict[shot.getShotnumber()] = {'numtraces': numtraces,
                                                'picked traces': [pickedTraces,
@@ -228,14 +250,14 @@ class Survey(object):
             (x, y, z) = shot.getSrcLoc() # getSrcLoc returns (x, y, z)
             srcfile.writelines('%10s %10s %10s\n' %(getAngle(y), getAngle(x), (-1)*z)) # lat, lon, depth
             LatAll.append(getAngle(y)); LonAll.append(getAngle(x)); DepthAll.append((-1)*z)
-            srcfile.writelines('%10s\n' %1) # 
+            srcfile.writelines('%10s\n' %1) #
             srcfile.writelines('%10s %10s %10s\n' %(1, 1, ttfilename))
             ttfile = open(directory + '/' + ttfilename, 'w')
             traceIDlist = shot.getTraceIDlist()
             traceIDlist.sort()
             ttfile.writelines(str(self.countPickedTraces(shot)) + '\n')
             for traceID in traceIDlist:
-                if shot.getPick(traceID) is not None:
+                if shot.getFlag(traceID) is not 0:
                     pick = shot.getPick(traceID) * fmtomo_factor
                     delta = shot.getPickError(traceID) * fmtomo_factor
                     (x, y, z) = shot.getRecLoc(traceID)
@@ -243,7 +265,7 @@ class Survey(object):
                     LatAll.append(getAngle(y)); LonAll.append(getAngle(x)); DepthAll.append((-1)*z)
                     count += 1
             ttfile.close()
-        srcfile.close()       
+        srcfile.close()
         print 'Wrote output for %s traces' %count
         print 'WARNING: output generated for FMTOMO-obsdata. Obsdata seems to take Lat, Lon, Depth and creates output for FMTOMO as Depth, Lat, Lon'
         print 'Dimensions of the seismic Array, transformed for FMTOMO, are Depth(%s, %s), Lat(%s, %s), Lon(%s, %s)'%(
@@ -252,14 +274,87 @@ class Survey(object):
     def countPickedTraces(self, shot):
         count = 0
         for traceID in shot.getTraceIDlist():
-            if shot.getPick(traceID) is not None:
+            if shot.getFlag(traceID) is not 0:
                 count += 1
         return count
 
-    def plotAllPicks(self, plotDeleted = False):
+    def countAllPickedTraces(self):
+        count = 0
+        for shot in self.data.values():
+            for traceID in shot.getTraceIDlist():
+                if shot.getFlag(traceID) is not 0:
+                    count += 1
+        return count
+
+    def plotAllShots(self, rows = 3, columns = 4):
         '''
-        Plots all picks over the distance between source and receiver. Returns (ax, region)
+        Plots all shots as Matrices with the color corresponding to the traveltime for each receiver.
+        IMPORTANT NOTE: Topography (z - coordinate) is not considered in the diagrams!
         '''
+        import matplotlib.pyplot as plt
+        from mpl_toolkits.mplot3d import Axes3D
+        plt.interactive(True)
+
+        fig = plt.figure()
+        ax = fig.add_subplot(111)
+
+        figPerSubplot = columns * rows
+
+        index = 1
+        #shotnames = []
+        #shotnumbers = []
+
+        # for shot in self.data.values():
+        #     shotnames.append(shot.getShotname())
+        #     shotnumbers.append(shot.getShotnumber())
+
+        # shotnumbers = [shotnumbers for (shotnumbers, shotnames) in sorted(zip(shotnumbers, shotnames))]
+        
+        for shotnumber in self.getShotlist():
+            if index <= figPerSubplot:
+                #ax = fig.add_subplot(3,3,i, projection = '3d', title = 'shot:' 
+                #+str(shot_dict[shotnumber].getShotnumber()), xlabel = 'X', ylabel = 'Y', zlabel = 'traveltime')
+                #shot_dict[shotnumber].plot3dttc(ax = ax, plotpicks = True)
+                ax = fig.add_subplot(3, 4, index)
+                self.getShot(shotnumber).matshow(ax = ax, colorbar = False, annotations = True)
+                index += 1
+            if index > figPerSubplot:
+                fig.subplots_adjust(left = 0, bottom = 0, right = 1, top = 1, wspace = 0, hspace = 0)
+                fig = plt.figure()
+                index = 1
+
+        fig.subplots_adjust(left = 0, bottom = 0, right = 1, top = 1, wspace = 0, hspace = 0)
+
+    def plotAllPicks(self, plotRemoved = False, colorByVal = 'log10SNR', ax = None, cbar = None, refreshPlot = False):
+        '''
+        Plots all picks over the distance between source and receiver. Returns (ax, region).
+        Picks can be checked and removed by using region class (pylot.core.active.surveyPlotTools.regions)
+
+        :param: plotRemoved, if True plots traces that were picked but removed from the survey (flag = 0)
+        :type: logical
+
+        :param: colorByVal, can be "log10SNR", "pickerror", or "spe"
+        :type: str
+
+        Examples:
+
+        regions.chooseRectangles():
+         - lets the user choose several rectangular regions in the plot
+
+        regions.plotTracesInRegions():
+         - creates plots (shot.plot_traces) for all traces in the active regions (i.e. chosen by e.g. chooseRectangles)
+
+        regions.setActiveRegionsForDeletion():
+         - highlights all shots in a the active regions for deletion
+
+        regions.deleteMarkedPicks():
+         - deletes the picks (pick flag set to 0) for all shots set for deletion
+
+        regions.deselectSelection(number):
+         - deselects the region of number = number
+
+        '''
+
         import matplotlib.pyplot as plt
         import math
         plt.interactive(True)
@@ -267,44 +362,63 @@ class Survey(object):
 
         dist = []
         pick = []
-        snrloglist = []
+        snrlog = []
+        pickerror = []
+        spe = []
+
         for shot in self.data.values():
             for traceID in shot.getTraceIDlist():
-                if plotDeleted == False:
+                if plotRemoved == False:
-                    if shot.getPick(traceID) is not None: 
+                    if shot.getFlag(traceID) is not 0 or plotRemoved == True: 
                         dist.append(shot.getDistance(traceID))
                         pick.append(shot.getPick(traceID))
-                        snrloglist.append(math.log10(shot.getSNR(traceID)[0]))
+                        snrlog.append(math.log10(shot.getSNR(traceID)[0]))
-                elif plotDeleted == True:
+                        pickerror.append(shot.getPickError(traceID))
-                    dist.append(shot.getDistance(traceID))
+                        spe.append(shot.getSymmetricPickError(traceID))
-                    pick.append(shot.getPick(traceID))
-                    snrloglist.append(math.log10(shot.getSNR(traceID)[0]))
 
-        ax = self.createPlot(dist, pick, snrloglist, label = 'log10(SNR)')
+        color = {'log10SNR': snrlog,
-        region = regions(ax, self.data)
+         'pickerror': pickerror,
-        ax.legend()
+         'spe': spe}
+        self.color = color
+        if refreshPlot is False:
+            ax, cbar = self.createPlot(dist, pick, color[colorByVal], label='%s' % colorByVal)
+            region = regions(ax, cbar, self)
+            ax.legend()
+            return (ax, region)
+        if refreshPlot is True:
+            ax, cbar = self.createPlot(dist, pick, color[colorByVal], label='%s' % colorByVal, ax=ax, cbar=cbar)
+            ax.legend()
+            return ax
 
-        return ax, region
+    def createPlot(self, dist, pick, inkByVal, label, ax = None, cbar = None):
-
-    def createPlot(self, dist, pick, inkByVal, label):
         import matplotlib.pyplot as plt
         plt.interactive(True)
         cm = plt.cm.jet
-
+        if ax is None:
-        fig = plt.figure()
+            print('Generating new plot...')
-        ax = fig.add_subplot(111)
+            fig = plt.figure()
-        fig = ax.scatter(dist, pick, cmap = cm, c = inkByVal, s = 5, edgecolors = 'none', label = label)
+            ax = fig.add_subplot(111)
-        cbar = plt.colorbar(fig, fraction = 0.05)
+            sc = ax.scatter(dist, pick, cmap=cm, c=inkByVal, s=5, edgecolors='none', label=label)
-        cbar.set_label(label)
+            cbar = plt.colorbar(sc, fraction=0.05)
-        plt.title('Plot of all Picks')
+            cbar.set_label(label)
-        plt.xlabel('Distance [m]')
+            ax.set_xlabel('Distance [m]')
-        plt.ylabel('Time [s]')
+            ax.set_ylabel('Time [s]')
-
+            ax.text(0.5, 0.95, 'Plot of all picks', transform=ax.transAxes, horizontalalignment='center')
-        return ax
+        else:
+            sc = ax.scatter(dist, pick, cmap=cm, c=inkByVal, s=5, edgecolors='none', label=label)
+            cbar = plt.colorbar(sc, cax=cbar.ax)
+            cbar.set_label(label)
+            ax.set_xlabel('Distance [m]')
+            ax.set_ylabel('Time [s]')
+            ax.text(0.5, 0.95, 'Plot of all picks', transform=ax.transAxes, horizontalalignment='center')
+        return (ax, cbar)
 
     def _update_progress(self, shotname, tend, progress):
-        sys.stdout.write("Working on shot %s. ETC is %02d:%02d:%02d [%2.2f %%]\r" 
+        sys.stdout.write('Working on shot %s. ETC is %02d:%02d:%02d [%2.2f %%]\r' % (shotname,
-                         %(shotname, tend.hour, tend.minute, tend.second, progress))
+         tend.hour,
+         tend.minute,
+         tend.second,
+         progress))
         sys.stdout.flush()
 
     def saveSurvey(self, filename = 'survey.pickle'):
@@ -313,8 +427,8 @@ class Survey(object):
 
         cPickle.dump(self, outfile, -1)
         print('saved Survey to file %s'%(filename))
-        
+
-    @staticmethod    
+    @staticmethod
     def from_pickle(filename):
         import cPickle
         infile = open(filename, 'rb')

pylot/core/active/fmtomo2vtk.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import numpy as np
 
 def vgrids2VTK(inputfile = 'vgrids.in', outputfile = 'vgrids.vtk'):
@@ -73,7 +74,7 @@ def vgrids2VTK(inputfile = 'vgrids.in', outputfile = 'vgrids.vtk'):
 
     dX = getDistance(np.rad2deg(dPhi))
     dY = getDistance(np.rad2deg(dTheta))
-    
+
     nPoints = nX * nY * nZ
 
     dZ = dR
@@ -114,7 +115,7 @@ def rays2VTK(fnin, fdirout = './vtk_files/', nthPoint = 50):
         R = 6371.
         distance = angle / 180 * (PI * R)
         return distance
-    
+
     infile = open(fnin, 'r')
     R = 6371
     rays = {}
@@ -124,10 +125,15 @@ def rays2VTK(fnin, fdirout = './vtk_files/', nthPoint = 50):
     ### NOTE: rays.dat seems to be in km and radians
 
     while True:
-        raynumber += 1 
+        raynumber += 1
         firstline = infile.readline()
         if firstline == '': break # break at EOF
+        raynumber = int(firstline.split()[0])
         shotnumber = int(firstline.split()[1])
+        rayValid = int(firstline.split()[4]) # is zero if the ray is invalid
+        if rayValid == 0:
+            print('Invalid ray number %d for shot number %d'%(raynumber, shotnumber))
+            continue
         nRayPoints = int(infile.readline().split()[0])
         if not shotnumber in rays.keys():
             rays[shotnumber] = {}

pylot/core/active/picking_script.py

@@ -1,106 +0,0 @@
-import sys
-from obspy import read
-from obspy import Stream
-from obspy import Trace
-from datetime import datetime
-import numpy as np
-
-from pylot.core.active import surveyUtils
-from pylot.core.active import seismicshot
-import activeSeismoPick
-reload(seismicshot)
-reload(surveyUtils)
-
-#####################################################################################
-# parameter definitions:#############################################################
-#traceslist = list(np.arange(1, 49, 1))      # traces (1-48)
-#shotlist = list(np.arange(302, 352, 1))   # shot-files(.dat) (Paffrath: 302-352) (Hauburg: 353-401) (arange+1!)
-cutwindow = (0, 0.2)              # cut out a part of the trace [seconds]
-tmovwind = 0.3                     # size of the moving window
-windowsize = (5, 0)               # windowsize for AIC picker (indices around HOS picks!!)
-pickwindow = cutwindow              # for local max and threshold picker: fraction of the seismogram used (0...1) TO BE DONE: depends on cutwindow!!!!
-folm = 0.6
-
-rockeskyll = False
-if rockeskyll == True:
-    receiverfile = "Geophone_interpoliert_rockes"
-    sourcefile = "Schusspunkte_rockes"
-    obsdir = "/rscratch/minos22/marcel/flachseismik/rockeskyll_200615_270615/"
-    filename = 'survey_rockes.pickle'
-else:
-    receiverfile = "Geophone_interpoliert_GZB" 
-    sourcefile = "Schusspunkte_GZB"
-    obsdir = "/rscratch/minos22/marcel/flachseismik/GZB_26_06_15_01/"
-    filename = 'survey_GZB.pickle'
-
-# SNR
-tsignal = 0.03
-tgap = 0.0007
-snrthreshold = 1
-######################################################################################
-
-vmin = 333
-vmax = 5500
-distBinSize = 2
-
-###########################################
-############# Settings: ###################
-thresholdpick=True
-localmaxpick=False
-
-if thresholdpick == True: pickmethod = "threshold"
-if localmaxpick == True: pickmethod = "localmax"
-
-HosAic = 'hos' # can be 'hos' or 'aic'
-###########################################
-
-starttime = datetime.now()
-
-print '\n--------------------Starting Script at %s -------------------\n' %starttime.time()
-if thresholdpick == True: print 'Using treshold pickmethod!\n'
-elif localmaxpick == True: print 'Using local maximum pick method!\n'
-if HosAic == 'aic': print 'picking with AIC\n'
-if HosAic == 'hos': print 'picking with HOS\n'
-
-survey = activeSeismoPick.Survey(obsdir, sourcefile, receiverfile, True)
-surveyUtils.setFittedSNR(survey.getShotDict())
-print '\nDone after %s seconds!\n------------------------------------------------------------------------------\n' % (datetime.now() - starttime).seconds
-
-count = 0; tpicksum = starttime - starttime
-
-for shot in survey.data.values():
-    tstartpick = datetime.now(); count += 1
-    for traceID in shot.getTraceIDlist():
-        distance = shot.getDistance(traceID) # receive distance
-
-        pickwin_used = pickwindow # use pickwindow set in the parameter section
-        # for higher distances use a linear vmin/vmax to cut out late/early regions with high noise
-        if distance > 5.:
-            pwleft = distance/vmax ################## TEST
-            pwright = distance/vmin
-            if pwright > cutwindow[1]:
-                pwright = cutwindow[1]
-        pickwin_used = (pwleft, pwright)
-
-        shot.setPickwindow(traceID, pickwin_used)
-        shot.pickTraces(traceID, windowsize, folm, HosAic) # picker
-        #shot.setManualPicks(traceID, picklist) # set manual picks if given (yet used on 2D only)
-        
-        # ++ TEST: set and check SNR before adding to distance bin ############################
-        shot.setSNR(traceID)    
-        #if shot.getSNR(traceID)[0] < snrthreshold:
-        if shot.getSNR(traceID)[0] < shot.getSNRthreshold(traceID):
-                shot.removePick(traceID)
-        # -- TEST: set and check SNR before adding to distance bin ############################
-
-        if shot.getPick(traceID) is not None:
-            shot.setEarllatepick(traceID)
-
-    tpicksum += (datetime.now() - tstartpick); tpick = tpicksum/count
-    tremain = (tpick * (len(survey.getShotDict()) - count))
-    tend = datetime.now() + tremain
-    print 'shot: %s, est. time to be finished is %s:%s:%s' % (shot.getShotname(), tend.hour, tend.minute, tend.second)
-
-survey.saveSurvey(filename)
-print '\n--- Finished script ---'
-print 'Elapsed time:', datetime.now()-starttime

pylot/core/active/seismicArrayPreparation.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import sys
 import numpy as np
 from scipy.interpolate import griddata
@@ -28,12 +29,12 @@ class SeisArray(object):
 
     def _generateReceiverlines(self):
         '''
-        Connects the traceIDs to the lineIDs 
+        Connects the traceIDs to the lineIDs
         for each receiverline in a dictionary.
         '''
         for receiver in self._receiverlist:
-            traceID = int(receiver.split()[0]) 
+            traceID = int(receiver.split()[0])
-            lineID =  int(receiver.split()[1]) 
+            lineID =  int(receiver.split()[1])
             if not lineID in self._receiverlines.keys():
                 self._receiverlines[lineID] = []
             self._receiverlines[lineID].append(traceID)
@@ -43,16 +44,16 @@ class SeisArray(object):
         Fills the three x, y, z dictionaries with measured coordinates
         '''
         for line in self._getReceiverlist():
-            traceID = int(line.split()[0]) 
+            traceID = int(line.split()[0])
-            x = float(line.split()[3]) 
+            x = float(line.split()[3])
-            y = float(line.split()[4]) 
+            y = float(line.split()[4])
-            z = float(line.split()[5]) 
+            z = float(line.split()[5])
             self._receiverCoords[traceID] = (x, y, z)
             self._measuredReceivers[traceID] = (x, y, z)
 
     def _setGeophoneNumbers(self):
         for line in self._getReceiverlist():
-            traceID = int(line.split()[0]) 
+            traceID = int(line.split()[0])
             gphoneNum = float(line.split()[2])
             self._geophoneNumbers[traceID] = gphoneNum
 
@@ -93,7 +94,7 @@ class SeisArray(object):
         return self._geophoneNumbers[traceID]
 
     def getMeasuredReceivers(self):
-        return self._measuredReceivers 
+        return self._measuredReceivers
 
     def getMeasuredTopo(self):
         return self._measuredTopo
@@ -139,11 +140,11 @@ class SeisArray(object):
         if self._getReceiverValue(traceID1, coordinate) < self._getReceiverValue(traceID2, coordinate):
             direction = +1
             return direction
-        if self._getReceiverValue(traceID1, coordinate) > self._getReceiverValue(traceID2, coordinate): 
+        if self._getReceiverValue(traceID1, coordinate) > self._getReceiverValue(traceID2, coordinate):
             direction = -1
             return direction
         print "Error: Same Value for traceID1 = %s and traceID2 = %s" %(traceID1, traceID2)
-                        
+
     def _interpolateMeanDistances(self, traceID1, traceID2, coordinate):
         '''
         Returns the mean distance between two traceID's depending on the number of geophones in between
@@ -186,7 +187,7 @@ class SeisArray(object):
             x = float(line[1])
             y = float(line[2])
             z = float(line[3])
-            self._measuredTopo[pointID] = (x, y, z)        
+            self._measuredTopo[pointID] = (x, y, z)
 
     def addSourceLocations(self, filename):
         '''
@@ -202,7 +203,7 @@ class SeisArray(object):
             x = float(line[1])
             y = float(line[2])
             z = float(line[3])
-            self._sourceLocs[pointID] = (x, y, z)        
+            self._sourceLocs[pointID] = (x, y, z)
 
     def interpZcoords4rec(self, method = 'linear'):
         '''
@@ -239,9 +240,9 @@ class SeisArray(object):
         '''
         x = []; y = []; z = []
         for traceID in self.getMeasuredReceivers().keys():
-            x.append(self.getMeasuredReceivers()[traceID][0])        
+            x.append(self.getMeasuredReceivers()[traceID][0])
             y.append(self.getMeasuredReceivers()[traceID][1])
-            z.append(self.getMeasuredReceivers()[traceID][2])        
+            z.append(self.getMeasuredReceivers()[traceID][2])
         return x, y, z
 
     def getMeasuredTopoLists(self):
@@ -250,9 +251,9 @@ class SeisArray(object):
         '''
         x = []; y = []; z = []
         for pointID in self.getMeasuredTopo().keys():
-            x.append(self.getMeasuredTopo()[pointID][0])        
+            x.append(self.getMeasuredTopo()[pointID][0])
             y.append(self.getMeasuredTopo()[pointID][1])
-            z.append(self.getMeasuredTopo()[pointID][2])        
+            z.append(self.getMeasuredTopo()[pointID][2])
         return x, y, z
 
     def getSourceLocsLists(self):
@@ -261,9 +262,9 @@ class SeisArray(object):
         '''
         x = []; y = []; z = []
         for pointID in self.getSourceLocations().keys():
-            x.append(self.getSourceLocations()[pointID][0])        
+            x.append(self.getSourceLocations()[pointID][0])
             y.append(self.getSourceLocations()[pointID][1])
-            z.append(self.getSourceLocations()[pointID][2])        
+            z.append(self.getSourceLocations()[pointID][2])
         return x, y, z
 
     def getAllMeasuredPointsLists(self):
@@ -289,7 +290,7 @@ class SeisArray(object):
             y.append(self.getReceiverCoordinates()[traceID][1])
             z.append(self.getReceiverCoordinates()[traceID][2])
         return x, y, z
-       
+
     def _interpolateXY4rec(self):
         '''
         Interpolates the X and Y coordinates for all receivers.
@@ -317,7 +318,7 @@ class SeisArray(object):
 
         :param: phiWE (W, E) extensions of the model in degree
         type: tuple
-        '''                                       
+        '''
 
         surface = []
         elevation = 0.25 # elevate topography so that no source lies above the surface
@@ -356,9 +357,9 @@ class SeisArray(object):
                 progress = float(count) / float(nTotal) * 100
                 self._update_progress(progress)
 
-                if filename is not None: 
+                if filename is not None:
                     outfile.writelines('%10s\n'%(z + elevation))
-                
+
         return surface
 
     def generateVgrid(self, nTheta = 80, nPhi = 80, nR = 120,
@@ -415,7 +416,7 @@ class SeisArray(object):
         thetaDelta = abs(thetaN - thetaS) / (nTheta - 1)
         phiDelta = abs(phiE - phiW) / (nPhi - 1)
         rDelta = abs(rbot - rtop) / (nR - 1)
-        
+
         # create a regular grid including +2 cushion nodes in every direction
         thetaGrid = np.linspace(thetaS - thetaDelta, thetaN + thetaDelta, num = nTheta + 2) # +2 cushion nodes
         phiGrid = np.linspace(phiW - phiDelta, phiE + phiDelta, num = nPhi + 2) # +2 cushion nodes
@@ -455,7 +456,7 @@ class SeisArray(object):
 
                     progress = float(count) / float(nTotal) * 100
                     self._update_progress(progress)
-                    
+
         outfile.close()
 
     def exportAll(self, filename = 'interpolated_receivers.out'):
@@ -463,7 +464,7 @@ class SeisArray(object):
         count = 0
         for traceID in self.getReceiverCoordinates().keys():
             count += 1
-            x, y, z = self.getReceiverCoordinates()[traceID] 
+            x, y, z = self.getReceiverCoordinates()[traceID]
             recfile_out.writelines('%5s %15s %15s %15s\n' %(traceID, x, y, z))
         print "Exported coordinates for %s traces to file > %s" %(count, filename)
         recfile_out.close()
@@ -472,15 +473,15 @@ class SeisArray(object):
         import matplotlib.pyplot as plt
         plt.interactive(True)
         plt.figure()
-        xmt, ymt, zmt = self.getMeasuredTopoLists() 
+        xmt, ymt, zmt = self.getMeasuredTopoLists()
         xsc, ysc, zsc = self.getSourceLocsLists()
-        xmr, ymr, zmr = self.getMeasuredReceiverLists() 
+        xmr, ymr, zmr = self.getMeasuredReceiverLists()
-        xrc, yrc, zrc = self.getReceiverLists() 
+        xrc, yrc, zrc = self.getReceiverLists()
 
         plt.plot(xrc, yrc, 'k.', markersize = 10, label = 'all receivers')
         plt.plot(xsc, ysc, 'b*', markersize = 10, label = 'shot locations')
 
-        if plot_topo == True: 
+        if plot_topo == True:
             plt.plot(xmt, ymt, 'b', markersize = 10, label = 'measured topo points')
         if highlight_measured == True:
             plt.plot(xmr, ymr, 'ro', label = 'measured receivers')
@@ -490,7 +491,11 @@ class SeisArray(object):
         plt.legend()
         if annotations == True:
             for traceID in self.getReceiverCoordinates().keys():
-                plt.annotate(str(traceID), xy = (self._getXreceiver(traceID), self._getYreceiver(traceID)), fontsize = 'x-small')
+                plt.annotate((' ' + str(traceID)), xy = (self._getXreceiver(traceID), self._getYreceiver(traceID)), fontsize = 'x-small', color = 'k')
+            for shotnumber in self.getSourceLocations().keys():
+                plt.annotate(('  ' + str(shotnumber)), xy = (self._getXshot(shotnumber), self._getYshot(shotnumber)), fontsize = 'x-small', color = 'b')
+
+
 
     def plotArray3D(self, ax = None):
         import matplotlib.pyplot as plt
@@ -501,9 +506,9 @@ class SeisArray(object):
             fig = plt.figure()
             ax = plt.axes(projection = '3d')
 
-        xmt, ymt, zmt = self.getMeasuredTopoLists() 
+        xmt, ymt, zmt = self.getMeasuredTopoLists()
-        xmr, ymr, zmr = self.getMeasuredReceiverLists() 
+        xmr, ymr, zmr = self.getMeasuredReceiverLists()
-        xin, yin, zin = self.getReceiverLists() 
+        xin, yin, zin = self.getReceiverLists()
 
         ax.plot(xmt, ymt, zmt, 'b*', markersize = 10, label = 'measured topo points')
         ax.plot(xin, yin, zin, 'k.', markersize = 10, label = 'interpolated receivers')
@@ -512,8 +517,8 @@ class SeisArray(object):
         ax.legend()
 
         return ax
-            
+
-        
+
     def plotSurface3D(self, ax = None, step = 0.5, method = 'linear'):
         from matplotlib import cm
         import matplotlib.pyplot as plt
@@ -657,8 +662,8 @@ class SeisArray(object):
 
         cPickle.dump(self, outfile, -1)
         print('saved SeisArray to file %s'%(filename))
-        
+
-    @staticmethod    
+    @staticmethod
     def from_pickle(filename):
         import cPickle
         infile = open(filename, 'rb')

pylot/core/active/seismicArrayPreperation.py

@@ -1,665 +0,0 @@
-import sys
-import numpy as np
-from scipy.interpolate import griddata
-
-class SeisArray(object):
-    '''
-    Can be used to interpolate missing values of a receiver grid, if only support points were measured.
-    Input file should contain in each line: ('traceID' 'receiverLineID' 'number of the geophone on recLine'  'X'  'Y'  'Z')
-
-    Can be used to generate a velocity grid file (vgrids.in) for FMTOMO with a topography adapting gradient.
-
-    Can be used to generate an interface file for FMTOMO (right now only interface.z used by grid3dg) for the topography.
-
-    Supports vtk output for sources and receivers.
-    Note: Source and Receiver files for FMTOMO will be generated by the Survey object (because traveltimes will be added directly).
-    '''
-    def __init__(self, recfile):
-        self._receiverlines = {}
-        self._receiverCoords = {}
-        self._measuredReceivers = {}
-        self._measuredTopo = {}
-        self._sourceLocs = {}
-        self._geophoneNumbers = {}
-        self._receiverlist = open(recfile, 'r').readlines()
-        self._generateReceiverlines()
-        self._setReceiverCoords()
-        self._setGeophoneNumbers()
-
-    def _generateReceiverlines(self):
-        '''
-        Connects the traceIDs to the lineIDs 
-        for each receiverline in a dictionary.
-        '''
-        for receiver in self._receiverlist:
-            traceID = int(receiver.split()[0]) 
-            lineID =  int(receiver.split()[1]) 
-            if not lineID in self._receiverlines.keys():
-                self._receiverlines[lineID] = []
-            self._receiverlines[lineID].append(traceID)
-
-    def _setReceiverCoords(self):
-        '''
-        Fills the three x, y, z dictionaries with measured coordinates
-        '''
-        for line in self._getReceiverlist():
-            traceID = int(line.split()[0]) 
-            x = float(line.split()[3]) 
-            y = float(line.split()[4]) 
-            z = float(line.split()[5]) 
-            self._receiverCoords[traceID] = (x, y, z)
-            self._measuredReceivers[traceID] = (x, y, z)
-
-    def _setGeophoneNumbers(self):
-        for line in self._getReceiverlist():
-            traceID = int(line.split()[0]) 
-            gphoneNum = float(line.split()[2])
-            self._geophoneNumbers[traceID] = gphoneNum
-
-    def _getReceiverlines(self):
-        return self._receiverlines
-
-    def _getReceiverlist(self):
-        return self._receiverlist
-
-    def getReceiverCoordinates(self):
-        return self._receiverCoords
-
-    def _getXreceiver(self, traceID):
-        return self._receiverCoords[traceID][0]
-
-    def _getYreceiver(self, traceID):
-        return self._receiverCoords[traceID][1]
-
-    def _getZreceiver(self, traceID):
-        return self._receiverCoords[traceID][2]
-
-    def _getXshot(self, shotnumber):
-        return self._sourceLocs[shotnumber][0]
-
-    def _getYshot(self, shotnumber):
-        return self._sourceLocs[shotnumber][1]
-
-    def _getZshot(self, shotnumber):
-        return self._sourceLocs[shotnumber][2]
-
-    def _getReceiverValue(self, traceID, coordinate):
-        setCoordinate = {'X': self._getXreceiver,
-                         'Y': self._getYreceiver,
-                         'Z': self._getZreceiver}
-        return setCoordinate[coordinate](traceID)
-
-    def _getGeophoneNumber(self, traceID):
-        return self._geophoneNumbers[traceID]
-
-    def getMeasuredReceivers(self):
-        return self._measuredReceivers 
-
-    def getMeasuredTopo(self):
-        return self._measuredTopo
-
-    def getSourceLocations(self):
-        return self._sourceLocs
-
-    def _setXvalue(self, traceID, value):
-        self._checkKey(traceID)
-        self._receiverCoords[traceID][0] = value
-
-    def _setYvalue(self, traceID, value):
-        self._checkKey(traceID)
-        self._receiverCoords[traceID][1] = value
-
-    def _setZvalue(self, traceID, value):
-        self._checkKey(traceID)
-        self._receiverCoords[traceID][2] = value
-
-    def _setValue(self, traceID, coordinate, value):
-        setCoordinate = {'X': self._setXvalue,
-                         'Y': self._setYvalue,
-                         'Z': self._setZvalue}
-        setCoordinate[coordinate](traceID, value)
-
-    def _checkKey(self, traceID):
-        if not traceID in self._receiverCoords.keys():
-            self._receiverCoords[traceID] = [None, None, None]
-
-    def _checkTraceIDdirection(self, traceID1, traceID2):
-        if traceID2 > traceID1:
-            direction = +1
-            return direction
-        if traceID2 < traceID1:
-            direction = -1
-            return direction
-        print "Error: Same Value for traceID1 = %s and traceID2 = %s" %(traceID1, traceID2)
-
-    def _checkCoordDirection(self, traceID1, traceID2, coordinate):
-        '''
-        Checks whether the interpolation direction is positive or negative
-        '''
-        if self._getReceiverValue(traceID1, coordinate) < self._getReceiverValue(traceID2, coordinate):
-            direction = +1
-            return direction
-        if self._getReceiverValue(traceID1, coordinate) > self._getReceiverValue(traceID2, coordinate): 
-            direction = -1
-            return direction
-        print "Error: Same Value for traceID1 = %s and traceID2 = %s" %(traceID1, traceID2)
-                        
-    def _interpolateMeanDistances(self, traceID1, traceID2, coordinate):
-        '''
-        Returns the mean distance between two traceID's depending on the number of geophones in between
-        '''
-        num_spaces = abs(self._getGeophoneNumber(traceID1) - self._getGeophoneNumber(traceID2))
-        mean_distance =  abs(self._getReceiverValue(traceID1, coordinate) - self._getReceiverValue(traceID2, coordinate))/num_spaces
-        return mean_distance
-
-    def interpolateValues(self, coordinate):
-        '''
-        Interpolates and sets all values (linear) for coordinate = 'X', 'Y' or 'Z'
-        '''
-        for lineID in self._getReceiverlines().keys():
-                number_measured = len(self._getReceiverlines()[lineID])
-                for index, traceID1 in enumerate(self._getReceiverlines()[lineID]):
-                    if index + 1 < number_measured:
-                        traceID2 = self._getReceiverlines()[lineID][index + 1]
-
-                        traceID_dir = self._checkTraceIDdirection(traceID1, traceID2)
-                        traceID_interp = traceID1 + traceID_dir
-
-                        coord_dir = self._checkCoordDirection(traceID1, traceID2, coordinate)
-                        mean_distance = self._interpolateMeanDistances(traceID1, traceID2, coordinate)
-
-                        while (traceID_dir * traceID_interp) < (traceID_dir * traceID2):
-                            self._setValue(traceID_interp, coordinate,
-                                          (self._getReceiverValue(traceID_interp - traceID_dir, coordinate)
-                                           + coord_dir * (mean_distance)))
-                            traceID_interp += traceID_dir
-
-    def addMeasuredTopographyPoints(self, filename):
-        '''
-        Use more measured points for a higher precision of height interpolation.
-        Input file should contain in each line: ('point ID'  'X'  'Y'  'Z')
-        '''
-        topolist = open(filename, 'r').readlines()
-        for line in topolist:
-            line = line.split()
-            pointID = int(line[0])
-            x = float(line[1])
-            y = float(line[2])
-            z = float(line[3])
-            self._measuredTopo[pointID] = (x, y, z)        
-
-    def addSourceLocations(self, filename):
-        '''
-        Use source locations for a higher precision of height interpolation.
-        Input file should contain in each line: ('point ID'  'X'  'Y'  'Z')
-
-        Source locations must be added before they can be written to vtk files.
-        '''
-        topolist = open(filename, 'r').readlines()
-        for line in topolist:
-            line = line.split()
-            pointID = int(line[0])
-            x = float(line[1])
-            y = float(line[2])
-            z = float(line[3])
-            self._sourceLocs[pointID] = (x, y, z)        
-
-    def interpZcoords4rec(self, method = 'linear'):
-        '''
-        Interpolates z values for all receivers.
-        '''
-        measured_x, measured_y, measured_z = self.getAllMeasuredPointsLists()
-
-        for traceID in self.getReceiverCoordinates().keys():
-            if type(self.getReceiverCoordinates()[traceID]) is not tuple:
-                z = griddata((measured_x, measured_y), measured_z, (self._getXreceiver(traceID), self._getYreceiver(traceID)), method = method)
-                self._setZvalue(traceID, float(z))
-
-    def _getAngle(self, distance):
-        '''
-        Function returns the angle on a Sphere of the radius R = 6371 [km] for a distance [km].
-        '''
-        PI = np.pi
-        R = 6371.
-        angle = distance * 180 / (PI * R)
-        return angle
-
-    def _getDistance(self, angle):
-        '''
-        Function returns the distance [km] on a Sphere of the radius R = 6371 [km] for an angle.
-        '''
-        PI = np.pi
-        R = 6371.
-        distance = angle / 180 * (PI * R)
-        return distance
-
-    def getMeasuredReceiverLists(self):
-        '''
-        Returns a list of all measured receivers known to SeisArray.
-        '''
-        x = []; y = []; z = []
-        for traceID in self.getMeasuredReceivers().keys():
-            x.append(self.getMeasuredReceivers()[traceID][0])        
-            y.append(self.getMeasuredReceivers()[traceID][1])
-            z.append(self.getMeasuredReceivers()[traceID][2])        
-        return x, y, z
-
-    def getMeasuredTopoLists(self):
-        '''
-        Returns a list of all measured topography points known to the SeisArray.
-        '''
-        x = []; y = []; z = []
-        for pointID in self.getMeasuredTopo().keys():
-            x.append(self.getMeasuredTopo()[pointID][0])        
-            y.append(self.getMeasuredTopo()[pointID][1])
-            z.append(self.getMeasuredTopo()[pointID][2])        
-        return x, y, z
-
-    def getSourceLocsLists(self):
-        '''
-        Returns a list of all measured source locations known to SeisArray.
-        '''
-        x = []; y = []; z = []
-        for pointID in self.getSourceLocations().keys():
-            x.append(self.getSourceLocations()[pointID][0])        
-            y.append(self.getSourceLocations()[pointID][1])
-            z.append(self.getSourceLocations()[pointID][2])        
-        return x, y, z
-
-    def getAllMeasuredPointsLists(self):
-        '''
-        Returns a list of all measured points known to SeisArray.
-        '''
-        mtopo_x, mtopo_y, mtopo_z = self.getMeasuredTopoLists()
-        msource_x, msource_y, msource_z = self.getSourceLocsLists()
-        mrec_x, mrec_y, mrec_z = self.getMeasuredReceiverLists()
-
-        x = mtopo_x + mrec_x + msource_x
-        y = mtopo_y + mrec_y + msource_y
-        z = mtopo_z + mrec_z + msource_z
-        return x, y, z
-
-    def getReceiverLists(self):
-        '''
-        Returns a list of all receivers (measured and interpolated).
-        '''
-        x = []; y =[]; z = []
-        for traceID in self.getReceiverCoordinates().keys():
-            x.append(self.getReceiverCoordinates()[traceID][0])
-            y.append(self.getReceiverCoordinates()[traceID][1])
-            z.append(self.getReceiverCoordinates()[traceID][2])
-        return x, y, z
-       
-    def _interpolateXY4rec(self):
-        '''
-        Interpolates the X and Y coordinates for all receivers.
-        '''
-        for coordinate in ('X', 'Y'):
-            self.interpolateValues(coordinate)
-
-    def interpolateAll(self):
-        self._interpolateXY4rec()
-        self.interpZcoords4rec()
-
-    def interpolateTopography(self, nTheta, nPhi, thetaSN, phiWE, method = 'linear', filename = 'interface1.in'):
-        '''
-        Interpolate Z values on a regular grid with cushion nodes to use it as FMTOMO topography interface.
-        Returns a surface in form of a list of points [[x1, y1, z1], [x2, y2, y2], ...] (cartesian).
-
-        :param: nTheta, number of points in theta (NS)
-        type: integer
-
-        :param: nPhi, number of points in phi (WE)
-        type: integer
-
-        :param: thetaSN (S, N) extensions of the model in degree
-        type: tuple
-
-        :param: phiWE (W, E) extensions of the model in degree
-        type: tuple
-        '''                                       
-
-        surface = []
-        elevation = 0.25 # elevate topography so that no source lies above the surface
-
-        if filename is not None:
-            outfile = open(filename, 'w')
-
-        print "Interpolating topography on regular grid with the dimensions:"
-        print "nTheta = %s, nPhi = %s, thetaSN = %s, phiWE = %s"%(nTheta, nPhi, thetaSN, phiWE)
-        print "method = %s, filename = %s" %(method, filename)
-
-        thetaS, thetaN = thetaSN
-        phiW, phiE = phiWE
-
-        measured_x, measured_y, measured_z = self.getAllMeasuredPointsLists()
-
-        # need to determine the delta to add two cushion nodes around the min/max values
-        thetaDelta = (thetaN - thetaS) / (nTheta - 1)
-        phiDelta = (phiE - phiW) / (nPhi - 1)
-
-        thetaGrid = np.linspace(thetaS - thetaDelta, thetaN + thetaDelta, num = nTheta + 2) # +2 cushion nodes
-        phiGrid = np.linspace(phiW - phiDelta, phiE + phiDelta, num = nPhi + 2) # +2 cushion nodes
-
-        nTotal = len(thetaGrid) * len(phiGrid); count = 0
-        for theta in thetaGrid:
-            for phi in phiGrid:
-                xval = self._getDistance(phi)
-                yval = self._getDistance(theta)
-                z = griddata((measured_x, measured_y), measured_z, (xval, yval), method = method)
-                # in case the point lies outside, nan will be returned. Find nearest:
-                if np.isnan(z) == True:
-                    z = griddata((measured_x, measured_y), measured_z, (xval, yval), method = 'nearest')
-                z = float(z)
-                surface.append((xval, yval, z))
-                count += 1
-                progress = float(count) / float(nTotal) * 100
-                self._update_progress(progress)
-
-                if filename is not None: 
-                    outfile.writelines('%10s\n'%(z + elevation))
-                
-        return surface
-
-    def generateVgrid(self, nTheta = 80, nPhi = 80, nR = 120,
-                      thetaSN = (-0.2, 1.2), phiWE = (-0.2, 1.2),
-                      Rbt = (-62.0, 6.0), vbot = 5.5, filename = 'vgrids.in',
-                      method = 'linear' ):
-        '''
-        Generate a velocity grid for fmtomo regarding topography with a linear gradient starting at the topography with 0.34 [km/s].
-
-        :param: nTheta, number of points in theta (NS)
-        type: integer
-
-        :param: nPhi, number of points in phi (WE)
-        type: integer
-
-        :param: nR, number of points in depth
-        type: integer
-
-        :param: thetaSN (S, N) extensions of the model in degree
-        type: tuple
-
-        :param: phiWE (W, E) extensions of the model in degree
-        type: tuple
-
-        :param: Rbt (bot, top) extensions of the model in km
-        type: tuple
-
-        :param: vbot, velocity at the bottom of the model
-        type: real
-        '''
-
-        def getRad(angle):
-            PI = np.pi
-            rad = angle / 180 * PI
-            return rad
-
-        def getZmax(surface):
-            z = []
-            for point in surface:
-                z.append(point[2])
-            return max(z)
-
-        R = 6371
-        vmin = 0.34
-        decm = 0.3 # diagonal elements of the covariance matrix (grid3dg's default value is 0.3)
-        outfile = open(filename, 'w')
-
-        thetaS, thetaN = thetaSN
-        phiW, phiE = phiWE
-        rbot = Rbt[0] + R
-        rtop = Rbt[1] + R
-
-        # need to determine the delta to add two cushion nodes around the min/max values
-        thetaDelta = abs(thetaN - thetaS) / (nTheta - 1)
-        phiDelta = abs(phiE - phiW) / (nPhi - 1)
-        rDelta = abs(rbot - rtop) / (nR - 1)
-        
-        # create a regular grid including +2 cushion nodes in every direction
-        thetaGrid = np.linspace(thetaS - thetaDelta, thetaN + thetaDelta, num = nTheta + 2) # +2 cushion nodes
-        phiGrid = np.linspace(phiW - phiDelta, phiE + phiDelta, num = nPhi + 2) # +2 cushion nodes
-        rGrid = np.linspace(rbot - rDelta, rtop + rDelta, num = nR + 2) # +2 cushion nodes
-
-        nTotal = len(rGrid) * len(thetaGrid) * len(phiGrid)
-        print "Total number of grid nodes: %s"%nTotal
-
-        # write header for velocity grid file (in RADIANS)
-        outfile.writelines('%10s %10s \n' %(1, 1))
-        outfile.writelines('%10s %10s %10s\n' %(nR + 2, nTheta + 2, nPhi + 2))
-        outfile.writelines('%10s %10s %10s\n' %(rDelta, getRad(thetaDelta), getRad(phiDelta)))
-        outfile.writelines('%10s %10s %10s\n' %(rbot - rDelta, getRad(thetaS - thetaDelta), getRad(phiW - phiDelta)))
-
-        surface = self.interpolateTopography(nTheta, nPhi, thetaSN, phiWE, method = method, filename = None)
-        zmax = getZmax(surface)
-
-        print "\nGenerating velocity grid for FMTOMO. Output filename = %s, interpolation method = %s"%(filename, method)
-        print "nTheta = %s, nPhi = %s, nR = %s, thetaSN = %s, phiWE = %s, Rbt = %s"%(nTheta, nPhi, nR, thetaSN, phiWE, Rbt)
-        count = 0
-        for radius in rGrid:
-            for theta in thetaGrid:
-                for phi in phiGrid:
-                    xval = self._getDistance(phi)
-                    yval = self._getDistance(theta)
-                    for point in surface:
-                        if point[0] == xval and point[1] == yval:
-                            z = point[2]
-                    if radius > (R + z + 1):
-                        vel = 0.0
-                    # elif radius > (R + z - 15): ########### TESTING
-                    #     vel = (radius - z - R) / (Rbt[0] - rDelta - zmax) * 1.0 + vmin     ##########################
-                    else:
-                        vel = (radius - z - R) / (Rbt[0] - rDelta - zmax) * vbot + vmin     ##########################
-                    count += 1
-                    outfile.writelines('%10s %10s\n'%(vel, decm))
-
-                    progress = float(count) / float(nTotal) * 100
-                    self._update_progress(progress)
-                    
-        outfile.close()
-
-    def exportAll(self, filename = 'interpolated_receivers.out'):
-        recfile_out = open(filename, 'w')
-        count = 0
-        for traceID in self.getReceiverCoordinates().keys():
-            count += 1
-            x, y, z = self.getReceiverCoordinates()[traceID] 
-            recfile_out.writelines('%5s %15s %15s %15s\n' %(traceID, x, y, z))
-        print "Exported coordinates for %s traces to file > %s" %(count, filename)
-        recfile_out.close()
-
-    def plotArray2D(self, plot_topo = False, highlight_measured = False, annotations = True):
-        import matplotlib.pyplot as plt
-        plt.interactive(True)
-        plt.figure()
-        xmt, ymt, zmt = self.getMeasuredTopoLists() 
-        xsc, ysc, zsc = self.getSourceLocsLists()
-        xmr, ymr, zmr = self.getMeasuredReceiverLists() 
-        xrc, yrc, zrc = self.getReceiverLists() 
-
-        plt.plot(xrc, yrc, 'k.', markersize = 10, label = 'all receivers')
-        plt.plot(xsc, ysc, 'b*', markersize = 10, label = 'shot locations')
-
-        if plot_topo == True: 
-            plt.plot(xmt, ymt, 'b', markersize = 10, label = 'measured topo points')
-        if highlight_measured == True:
-            plt.plot(xmr, ymr, 'ro', label = 'measured receivers')
-
-        plt.xlabel('X [m]')
-        plt.ylabel('Y [m]')
-        plt.legend()
-        if annotations == True:
-            for traceID in self.getReceiverCoordinates().keys():
-                plt.annotate(str(traceID), xy = (self._getXreceiver(traceID), self._getYreceiver(traceID)), fontsize = 'x-small')
-
-    def plotArray3D(self, ax = None):
-        import matplotlib.pyplot as plt
-        from mpl_toolkits.mplot3d import Axes3D
-        plt.interactive(True)
-
-        if ax == None:
-            fig = plt.figure()
-            ax = plt.axes(projection = '3d')
-
-        xmt, ymt, zmt = self.getMeasuredTopoLists() 
-        xmr, ymr, zmr = self.getMeasuredReceiverLists() 
-        xin, yin, zin = self.getReceiverLists() 
-
-        ax.plot(xmt, ymt, zmt, 'b*', markersize = 10, label = 'measured topo points')
-        ax.plot(xin, yin, zin, 'k.', markersize = 10, label = 'interpolated receivers')
-        ax.plot(xmr, ymr, zmr, 'ro', label = 'measured receivers')
-        ax.set_xlabel('X'); ax.set_ylabel('Y'); ax.set_zlabel('elevation')
-        ax.legend()
-
-        return ax
-            
-        
-    def plotSurface3D(self, ax = None, step = 0.5, method = 'linear'):
-        from matplotlib import cm
-        import matplotlib.pyplot as plt
-        from mpl_toolkits.mplot3d import Axes3D
-        plt.interactive(True)
-
-        if ax == None:
-            fig = plt.figure()
-            ax = plt.axes(projection = '3d')
-
-        xmt, ymt, zmt = self.getMeasuredTopoLists()
-        xmr, ymr, zmr = self.getMeasuredReceiverLists()
-
-        x = xmt + xmr
-        y = ymt + ymr
-        z = zmt + zmr
-
-        xaxis = np.arange(min(x)+1, max(x), step)
-        yaxis = np.arange(min(y)+1, max(y), step)
-
-        xgrid, ygrid = np.meshgrid(xaxis, yaxis)
-
-        zgrid = griddata((x, y), z, (xgrid, ygrid), method = method)
-
-        ax.plot_surface(xgrid, ygrid, zgrid, linewidth = 0, cmap = cm.jet, vmin = min(z), vmax = max(z))
-
-        ax.set_zlim(-(max(x) - min(x)/2),(max(x) - min(x)/2))
-        ax.set_aspect('equal')
-
-        ax.set_xlabel('X'); ax.set_ylabel('Y'); ax.set_zlabel('elevation')
-        ax.legend()
-
-        return ax
-
-    def _update_progress(self, progress):
-        sys.stdout.write("%d%% done   \r" % (progress) )
-        sys.stdout.flush()
-
-    def receivers2VTK(self, filename = 'receivers.vtk'):
-        '''
-        Generates vtk files from all receivers of the SeisArray object.
-        '''
-        outfile = open(filename, 'w')
-        traceIDs = []
-
-        for traceID in self.getReceiverCoordinates():
-            traceIDs.append(traceID)
-
-        nPoints = len(traceIDs)
-
-        # write header
-        print("Writing header for VTK file...")
-        outfile.writelines('# vtk DataFile Version 3.1\n')
-        outfile.writelines('Receivers with traceIDs\n')
-        outfile.writelines('ASCII\n')
-        outfile.writelines('DATASET POLYDATA\n')
-        outfile.writelines('POINTS %15d float\n' %(nPoints))
-
-        # write coordinates
-        print("Writing coordinates to VTK file...")
-        for traceID in traceIDs:
-            x = self._getXreceiver(traceID)
-            y = self._getYreceiver(traceID)
-            z = self._getZreceiver(traceID)
-
-            outfile.writelines('%10f %10f %10f \n' %(x, y, z))
-
-        outfile.writelines('VERTICES %15d %15d\n' %(nPoints, 2 * nPoints))
-
-        # write indices
-        print("Writing indices to VTK file...")
-        for index in range(nPoints):
-            outfile.writelines('%10d %10d\n' %(1, index))
-
-        outfile.writelines('POINT_DATA %15d\n' %(nPoints))
-        outfile.writelines('SCALARS traceIDs int %d\n' %(1))
-        outfile.writelines('LOOKUP_TABLE default\n')
-
-        # write traceIDs
-        print("Writing traceIDs to VTK file...")
-        for traceID in traceIDs:
-            outfile.writelines('%10d\n' %traceID)
-
-        outfile.close()
-        print("Wrote receiver grid for %d points to file: %s" %(nPoints, filename))
-        return
-
-    def sources2VTK(self, filename = 'sources.vtk'):
-        '''
-        Generates vtk-files for all source locations in the SeisArray object.
-        '''
-        outfile = open(filename, 'w')
-        shotnumbers = []
-
-        for shotnumber in self.getSourceLocations():
-            shotnumbers.append(shotnumber)
-
-        nPoints = len(shotnumbers)
-
-        # write header
-        print("Writing header for VTK file...")
-        outfile.writelines('# vtk DataFile Version 3.1\n')
-        outfile.writelines('Shots with shotnumbers\n')
-        outfile.writelines('ASCII\n')
-        outfile.writelines('DATASET POLYDATA\n')
-        outfile.writelines('POINTS %15d float\n' %(nPoints))
-
-        # write coordinates
-        print("Writing coordinates to VTK file...")
-        for shotnumber in shotnumbers:
-            x = self._getXshot(shotnumber)
-            y = self._getYshot(shotnumber)
-            z = self._getZshot(shotnumber)
-
-            outfile.writelines('%10f %10f %10f \n' %(x, y, z))
-
-        outfile.writelines('VERTICES %15d %15d\n' %(nPoints, 2 * nPoints))
-
-        # write indices
-        print("Writing indices to VTK file...")
-        for index in range(nPoints):
-            outfile.writelines('%10d %10d\n' %(1, index))
-
-        outfile.writelines('POINT_DATA %15d\n' %(nPoints))
-        outfile.writelines('SCALARS shotnumbers int %d\n' %(1))
-        outfile.writelines('LOOKUP_TABLE default\n')
-
-        # write shotnumber
-        print("Writing shotnumbers to VTK file...")
-        for shotnumber in shotnumbers:
-            outfile.writelines('%10d\n' %shotnumber)
-
-        outfile.close()
-        print("Wrote receiver grid for %d points to file: %s" %(nPoints, filename))
-        return
-
-
-    def saveSeisArray(self, filename = 'seisArray.pickle'):
-        import cPickle
-        outfile = open(filename, 'wb')
-
-        cPickle.dump(self, outfile, -1)
-        print('saved SeisArray to file %s'%(filename))
-        
-    @staticmethod    
-    def from_pickle(filename):
-        import cPickle
-        infile = open(filename, 'rb')
-        return cPickle.load(infile)

pylot/core/active/seismicshot.py

@@ -10,6 +10,8 @@ from pylot.core.pick.CharFuns import HOScf
 from pylot.core.pick.CharFuns import AICcf
 from pylot.core.pick.utils import getSNR
 from pylot.core.pick.utils import earllatepicker
+import matplotlib.pyplot as plt
+plt.interactive('True')
 
 class SeismicShot(object):
     '''
@@ -27,9 +29,6 @@ class SeismicShot(object):
         self.srcCoordlist = None
         self.traceIDs = None
         self.pick = {}
-        self.pick_backup = {}
-        self.earliest = {}
-        self.latest = {}
         self.pickwindow= {}
         self.manualpicks= {}
         self.snr = {}
@@ -44,14 +43,14 @@ class SeismicShot(object):
         removed = []
         for i in range(0, len(coordlist)):
             traceIDs.append(int(coordlist[i].split()[0]))
-            
+
         for trace in self.traces:
             try:
                 traceIDs.index(int(trace.stats.channel))
             except:
-                self.traces.remove(trace)        
+                self.traces.remove(trace)
                 removed.append(int(trace.stats.channel))
-                
+
         if len(removed) > 0:
             return removed
 
@@ -59,7 +58,7 @@ class SeismicShot(object):
         for trace in self.traces:
             if traceID == trace.stats.channel:
                 self.traces.remove(trace)
-        
+
         # for traceID in TraceIDs:
         #     traces = [trace for trace in self.traces if int(trace.stats.channel) == traceID]
         #     if len(traces) is not 1:
@@ -133,24 +132,34 @@ class SeismicShot(object):
     def getSourcefile(self):
         return self.paras['sourcefile']
 
-    def getPick(self, traceID):
+    def getPick(self, traceID, returnRemoved = False):
-        return self.pick[traceID]
+        if not self.getFlag(traceID) == 0:
+            return self.pick[traceID]['mpp']
+        if returnRemoved == True:
+            #print('getPick: Returned removed pick for shot %d, traceID %d' %(self.getShotnumber(), traceID))
+            return self.pick[traceID]['mpp']
 
-    def getPick_backup(self, traceID):
+    def getPickIncludeRemoved(self, traceID):
-        return self.pick_backup[traceID]
+        return self.getPick(traceID, returnRemoved = True)
 
     def getEarliest(self, traceID):
-        return self.earliest[traceID]
+        return self.pick[traceID]['epp']
 
     def getLatest(self, traceID):
-        return self.latest[traceID]
+        return self.pick[traceID]['lpp']
+
+    def getSymmetricPickError(self, traceID):
+        pickerror = self.pick[traceID]['spe']
+        if np.isnan(pickerror) == True: 
+            print "SPE is NaN for shot %s, traceID %s"%(self.getShotnumber(), traceID)
+        return pickerror
 
     def getPickError(self, traceID):
         pickerror = abs(self.getEarliest(traceID) - self.getLatest(traceID))
-        if np.isnan(pickerror) == True: 
+        if np.isnan(pickerror) == True:
             print("SPE is NaN for shot %s, traceID %s"%(self.getShotnumber(), traceID))
-        return pickerror 
+        return pickerror
-  
+
     def getStreamTraceIDs(self):
         traceIDs = []
         for trace in self.traces:
@@ -172,15 +181,15 @@ class SeismicShot(object):
 
     def getPickwindow(self, traceID):
         try:
-            self.pickwindow[traceID]    
+            self.pickwindow[traceID]
         except KeyError as e:
             print('no pickwindow for trace %s, set to %s' % (traceID, self.getCut()))
             self.setPickwindow(traceID, self.getCut())
         return self.pickwindow[traceID]
-    
+
     def getSNR(self, traceID):
         return self.snr[traceID]
-    
+
     def getSNRthreshold(self, traceID):
         return self.snrthreshold[traceID]
 
@@ -218,7 +227,7 @@ class SeismicShot(object):
         :type: int
         '''
         return HOScf(self.getSingleStream(traceID), self.getCut(),
-                     self.getTmovwind(), self.getOrder())
+                     self.getTmovwind(), self.getOrder(), stealthMode = True)
 
     def getAICcf(self, traceID):
         '''
@@ -241,7 +250,7 @@ class SeismicShot(object):
         tr_cf = Trace()
         tr_cf.data = self.getHOScf(traceID).getCF()
         st_cf += tr_cf
-        return AICcf(st_cf, self.getCut(), self.getTmovwind())
+        return AICcf(st_cf, self.getCut(), self.getTmovwind(), stealthMode = True)
 
     def getSingleStream(self, traceID):  ########## SEG2 / SEGY ? ##########
         '''
@@ -254,19 +263,19 @@ class SeismicShot(object):
         traces = [trace for trace in self.traces if int(trace.stats.channel) == traceID]
         if len(traces) == 1:
             return Stream(traces)
-        else:
+        self.setPick(traceID, None)
-            self.setPick(traceID, None)
+        print 'Warning: ambigious or empty traceID: %s' % traceID
-            print('Warning: ambigious or empty traceID: %s' % traceID)
+
-        
         #raise ValueError('ambigious or empty traceID: %s' % traceID)
-        
+
     def pickTraces(self, traceID, windowsize, folm = 0.6, HosAic = 'hos'): ########## input variables ##########
+        # LOCALMAX NOT IMPLEMENTED!
         '''
         Intitiate picking for a trace.
 
         :param: traceID
         :type: int
-
+        
         :param: cutwindow (equals HOScf 'cut' variable)
         :type: tuple
 
@@ -289,29 +298,28 @@ class SeismicShot(object):
         aiccf = self.getAICcf(traceID)
 
         self.timeArray[traceID] = hoscf.getTimeArray()
-
         aiccftime, hoscftime = self.threshold(hoscf, aiccf, windowsize, self.getPickwindow(traceID), folm)
-
         setHosAic = {'hos': hoscftime,
                      'aic': aiccftime}
 
         self.setPick(traceID, setHosAic[HosAic])
-        self.pick_backup[traceID] = setHosAic[HosAic] ### verbessern (vor allem weil ueberschrieben bei 2tem mal picken)
 
     def setEarllatepick(self, traceID, nfac = 1.5):
         tgap = self.getTgap()
         tsignal = self.getTsignal()
-        tnoise = self.getPick(traceID) - tgap
+        tnoise = self.getPickIncludeRemoved(traceID) - tgap
 
-        (self.earliest[traceID], self.latest[traceID], tmp) = earllatepicker(self.getSingleStream(traceID), 
+        (self.pick[traceID]['epp'], self.pick[traceID]['lpp'],
-                                                                             nfac, (tnoise, tgap, tsignal), 
+         self.pick[traceID]['spe']) = earllatepicker(self.getSingleStream(traceID),
-                                                                             self.getPick(traceID))
+                                                     nfac, (tnoise, tgap, tsignal), 
+                                                     self.getPickIncludeRemoved(traceID),
+                                                     stealthMode = True)
 
     def threshold(self, hoscf, aiccf, windowsize, pickwindow, folm = 0.6):
         '''
-        Threshold picker, using the local maximum in a pickwindow to find the time at 
+        Threshold picker, using the local maximum in a pickwindow to find the time at
         which a fraction of the local maximum is reached for the first time.
-        
+
         :param: hoscf, Higher Order Statistics Characteristic Function
         :type: 'Characteristic Function'
 
@@ -337,34 +345,34 @@ class SeismicShot(object):
         threshold = folm * max(hoscflist[leftb : rightb]) # combination of local maximum and threshold
 
         m = leftb
-        
+
         while hoscflist[m] < threshold:
             m += 1
- 
+
         hoscftime = list(hoscf.getTimeArray())[m]
 
         lb = max(0, m - windowsize[0]) # if window exceeds t = 0
         aiccfcut = list(aiccf.getCF())[lb : m + windowsize[1]]
         n = aiccfcut.index(min(aiccfcut))
- 
+
         m = lb + n
- 
+
         aiccftime = list(hoscf.getTimeArray())[m]
-       
+
         return aiccftime, hoscftime
 
     def getDistance(self, traceID):
         '''
         Returns the distance of the receiver with the ID == traceID to the source location (shot location).
         Uses getSrcLoc and getRecLoc.
-        
+
         :param: traceID
         :type: int
         '''
         shotX, shotY, shotZ = self.getSrcLoc()
         recX, recY, recZ = self.getRecLoc(traceID)
         dist = np.sqrt((shotX-recX)**2 + (shotY-recY)**2 + (shotZ-recZ)**2)
-        
+
         if np.isnan(dist) == True:
             raise ValueError("Distance is NaN for traceID %s" %traceID)
 
@@ -375,7 +383,7 @@ class SeismicShot(object):
         '''
         Returns the location (x, y, z) of the receiver with the ID == traceID.
         RECEIVEIVER FILE MUST BE SET FIRST, TO BE IMPROVED.
-        
+
         :param: traceID
         :type: int
         '''
@@ -389,7 +397,7 @@ class SeismicShot(object):
                 y = coordlist[i].split()[2]
                 z = coordlist[i].split()[3]
                 return float(x), float(y), float(z)
-            
+
         #print "WARNING: traceID %s not found" % traceID
         raise ValueError("traceID %s not found" % traceID)
         #return float(self.getSingleStream(traceID)[0].stats.seg2['RECEIVER_LOCATION'])
@@ -412,7 +420,7 @@ class SeismicShot(object):
         '''
         Returns the traceID(s) for a certain distance between source and receiver.
         Used for 2D Tomography. TO BE IMPROVED.
-        
+
         :param: distance
         :type: real
 
@@ -428,7 +436,7 @@ class SeismicShot(object):
                     if self.getDistance(traceID) == distance:
                         traceID_list.append(traceID)
                 if distancebin[0] >= 0 and distancebin[1] > 0:
-                    if self.getDistance(traceID) > distancebin[0] and self.getDistance(traceID) < distancebin[1]:
+                    if distancebin[0] < self.getDistance(traceID) < distancebin[1]:
                         traceID_list.append(traceID)
 
         if len(traceID_list) > 0:
@@ -437,7 +445,7 @@ class SeismicShot(object):
     def setManualPicks(self, traceID, picklist): ########## picklist momentan nicht allgemein, nur testweise benutzt ##########
         '''
         Sets the manual picks for a receiver with the ID == traceID for comparison.
-        
+
         :param: traceID
         :type: int
 
@@ -452,21 +460,31 @@ class SeismicShot(object):
         if not self.manualpicks.has_key(traceID):
             self.manualpicks[traceID] = (mostlikely, earliest, latest)
         #else:
-        #    raise KeyError('MANUAL pick to be set more than once for traceID %s' % traceID) 
+        #    raise KeyError('MANUAL pick to be set more than once for traceID %s' % traceID)
-        
+
     def setPick(self, traceID, pick): ########## siehe Kommentar ##########
-        self.pick[traceID] = pick
+        if not traceID in self.pick.keys():
+            self.pick[traceID] = {}
+        self.pick[traceID]['mpp'] = pick
+        self.pick[traceID]['flag'] = 1
         # ++++++++++++++ Block raus genommen, da Error beim 2ten Mal picken! (Ueberschreiben von erstem Pick!)
         # if not self.pick.has_key(traceID):
         #     self.getPick(traceID) = picks
         # else:
-        #     raise KeyError('pick to be set more than once for traceID %s' % traceID) 
+        #     raise KeyError('pick to be set more than once for traceID %s' % traceID)
 
         #    def readParameter(self, parfile):
         #        parlist = open(parfile,'r').readlines()
 
     def removePick(self, traceID):
-        self.setPick(traceID, None)
+        self.setFlag(traceID, 0)
+
+    def setFlag(self, traceID, flag):
+        'Set flag = 0 if pick is invalid, else flag = 1'
+        self.pick[traceID]['flag'] = flag
+
+    def getFlag(self, traceID):
+        return self.pick[traceID]['flag']
 
     def setPickwindow(self, traceID, pickwindow):
         self.pickwindow[traceID] = pickwindow
@@ -474,12 +492,13 @@ class SeismicShot(object):
     def setSNR(self, traceID):  ########## FORCED HOS PICK ##########
         '''
         Gets the SNR using pylot and then sets the SNR for the traceID.
-        
+
         :param: traceID
         :type: int
 
         :param: (tnoise, tgap, tsignal), as used in pylot SNR
         '''
+
         from pylot.core.pick.utils import getSNR
 
         tgap = self.getTgap()
@@ -509,7 +528,7 @@ class SeismicShot(object):
     # def plot2dttc(self, dist_med = 0):  ########## 2D ##########
     #     '''
     #     Function to plot the traveltime curve for automated picks (AIC & HOS) of a shot. 2d only!
-        
+
     #     :param: dist_med (optional)
     #     :type: 'dictionary'
     #     '''
@@ -517,7 +536,7 @@ class SeismicShot(object):
     #     plt.interactive('True')
     #     aictimearray = []
     #     hostimearray = []
-    #     if dist_med is not 0: 
+    #     if dist_med is not 0:
     #         dist_medarray = []
 
     #     i = 1
@@ -570,42 +589,89 @@ class SeismicShot(object):
     #     plt.plot(self.getDistArray4ttcPlot(), pickwindowarray_upperb, ':k')
 
     def plot_traces(self, traceID, folm = 0.6): ########## 2D, muss noch mehr verbessert werden ##########
-        import matplotlib.pyplot as plt
+        from matplotlib.widgets import Button
+
+        def onclick(event):
+            self.setPick(traceID, event.xdata)
+            self._drawStream(traceID, refresh = True)
+            self._drawCFs(traceID, folm, refresh = True)
+            fig.canvas.mpl_disconnect(self.traces4plot[traceID]['cid'])
+            plt.draw()
+
+        def connectButton(event = None):
+            cid = fig.canvas.mpl_connect('button_press_event', onclick)
+            self.traces4plot[traceID]['cid'] = cid
+            
+        fig = plt.figure()
+        ax1 = fig.add_subplot(2,1,1)
+        ax2 = fig.add_subplot(2,1,2, sharex = ax1)
+        axb = fig.add_axes([0.15, 0.91, 0.05, 0.03])
+        button = Button(axb, 'repick', color = 'red', hovercolor = 'grey')
+        button.on_clicked(connectButton)
+
+        self.traces4plot = {}
+        if traceID not in self.traces4plot.keys():
+            self.traces4plot[traceID] = {'fig': fig,
+                                         'ax1': ax1,
+                                         'ax2': ax2,
+                                         'axb': axb,
+                                         'button': button,
+                                         'cid': None}
+
+        self._drawStream(traceID)
+        self._drawCFs(traceID, folm)
+
+    def _drawStream(self, traceID, refresh = False):
         from pylot.core.util.utils import getGlobalTimes
         from pylot.core.util.utils import prepTimeAxis
-        
+
         stream = self.getSingleStream(traceID)
         stime = getGlobalTimes(stream)[0]
-        timeaxis = prepTimeAxis(stime, stream[0]) 
+        timeaxis = prepTimeAxis(stime, stream[0])
         timeaxis -= stime
-
-        plt.interactive('True')
         
+        ax = self.traces4plot[traceID]['ax1']
+
+        if refresh == True:
+            xlim, ylim = ax.get_xlim(), ax.get_ylim()
+        ax.clear()
+        if refresh == True:
+            ax.set_xlim(xlim)
+            ax.set_ylim(ylim)
+
+        ax.set_title('Shot: %s, traceID: %s, pick: %s'
+                     %(self.getShotnumber(), traceID, self.getPick(traceID)))
+        ax.plot(timeaxis, stream[0].data, 'k', label = 'trace')
+        ax.plot([self.getPick(traceID), self.getPick(traceID)], 
+                [min(stream[0].data), 
+                 max(stream[0].data)],
+                'r', label = 'mostlikely')
+        ax.legend()
+
+    def _drawCFs(self, traceID, folm, refresh = False):
         hoscf = self.getHOScf(traceID)
         aiccf = self.getAICcf(traceID)
+        ax = self.traces4plot[traceID]['ax2']
 
-        fig = plt.figure()
+        if refresh == True:
-        ax1 = plt.subplot(2,1,1)
+            xlim, ylim = ax.get_xlim(), ax.get_ylim()
-        plt.title('Shot: %s, traceID: %s, pick: %s' %(self.getShotnumber(), traceID, self.getPick(traceID)))
+        ax.clear()
-        ax1.plot(timeaxis, stream[0].data, 'k', label = 'trace')
+        if refresh == True:
-        ax1.plot([self.getPick(traceID), self.getPick(traceID)], 
+            ax.set_xlim(xlim)
-                 [min(stream[0].data), 
+            ax.set_ylim(ylim)
-                  max(stream[0].data)],
+
-                 'r', label = 'mostlikely')
+        ax.plot(hoscf.getTimeArray(), hoscf.getCF(), 'b', label = 'HOS')
-        plt.legend()
+        ax.plot(hoscf.getTimeArray(), aiccf.getCF(), 'g', label = 'AIC')
-        ax2 = plt.subplot(2,1,2, sharex = ax1)
+        ax.plot([self.getPick(traceID), self.getPick(traceID)], 
-        ax2.plot(hoscf.getTimeArray(), hoscf.getCF(), 'b', label = 'HOS')
-        ax2.plot(hoscf.getTimeArray(), aiccf.getCF(), 'g', label = 'AIC')
-        ax2.plot([self.getPick(traceID), self.getPick(traceID)], 
                  [min(np.minimum(hoscf.getCF(), aiccf.getCF())), 
                   max(np.maximum(hoscf.getCF(), aiccf.getCF()))],
                  'r', label = 'mostlikely')
-        ax2.plot([0, self.getPick(traceID)],
+        ax.plot([0, self.getPick(traceID)],
                  [folm * max(hoscf.getCF()), folm * max(hoscf.getCF())],
                  'm:', label = 'folm = %s' %folm)
-        plt.xlabel('Time [s]')
+        ax.set_xlabel('Time [s]')
-        plt.legend()
+        ax.legend()
-        
+
     def plot3dttc(self, step = 0.5, contour = False, plotpicks = False, method = 'linear', ax = None):
         '''
         Plots a 3D 'traveltime cone' as surface plot by interpolating on a regular grid over the traveltimes, not yet regarding the vertical offset of the receivers.
@@ -622,7 +688,6 @@ class SeismicShot(object):
         :param: method (optional), interpolation method; can be 'linear' (default) or 'cubic'
         :type: 'string'
         '''
-        import matplotlib.pyplot as plt
         from scipy.interpolate import griddata
         from matplotlib import cm
         from mpl_toolkits.mplot3d import Axes3D
@@ -631,20 +696,20 @@ class SeismicShot(object):
         y = []
         z = []
         for traceID in self.pick.keys():
-            if self.getPick(traceID) != None:
+            if self.getFlag(traceID) != 0:
                 x.append(self.getRecLoc(traceID)[0])
                 y.append(self.getRecLoc(traceID)[1])
                 z.append(self.getPick(traceID))
 
-        xaxis = np.arange(min(x)+1, max(x), step)
+        xaxis = np.arange(min(x), max(x), step)
-        yaxis = np.arange(min(y)+1, max(y), step)
+        yaxis = np.arange(min(y), max(y), step)
         xgrid, ygrid = np.meshgrid(xaxis, yaxis)
         zgrid = griddata((x, y), z, (xgrid, ygrid), method = method)
 
         if ax == None:
             fig = plt.figure()
             ax = plt.axes(projection = '3d')
-        
+
         xsrc, ysrc, zsrc = self.getSrcLoc()
 
         if contour == True:
@@ -656,13 +721,13 @@ class SeismicShot(object):
 
         if plotpicks == True:
             ax.plot(x, y, z, 'k.')
-    
+
     def plotttc(self, method, *args):
         plotmethod = {'2d': self.plot2dttc, '3d': self.plot3dttc}
-        
+
         plotmethod[method](*args)
         
-    def matshow(self, step = 0.5, method = 'linear', ax = None, plotRec = False, annotations = False):
+    def matshow(self, ax = None, step = 0.5, method = 'linear', plotRec = True, annotations = True, colorbar = True):
         '''
         Plots a 2D matrix of the interpolated traveltimes. This needs less performance than plot3dttc
 
@@ -672,27 +737,32 @@ class SeismicShot(object):
         :param: method (optional), interpolation method; can be 'linear' (default) or 'cubic'
         :type: 'string'
 
-        :param: plotRec (optional), plot the receiver positions
+        :param: plotRec (optional), plot the receiver positions (colored scatter plot, should not be
+        deactivated because there might be receivers that are not inside the interpolated area)
         :type: 'logical'
 
         :param: annotations (optional), displays traceIDs as annotations
         :type: 'logical'
         '''
-        import matplotlib.pyplot as plt
         from scipy.interpolate import griddata
-#        plt.interactive('True')
 
-        x = []
+        x = []; xcut = []
-        y = []
+        y = []; ycut = []
-        z = []
+        z = []; zcut = []
+        tmin, tmax = self.getCut()
+
         for traceID in self.pick.keys():
-            if self.getPick(traceID) != None:
+            if self.getFlag(traceID) != 0:
                 x.append(self.getRecLoc(traceID)[0])
                 y.append(self.getRecLoc(traceID)[1])
                 z.append(self.getPick(traceID))
+            if self.getFlag(traceID) == 0 and self.getPickIncludeRemoved(traceID) is not None:
+                xcut.append(self.getRecLoc(traceID)[0])
+                ycut.append(self.getRecLoc(traceID)[1])
+                zcut.append(self.getPickIncludeRemoved(traceID))
 
-        xaxis = np.arange(min(x)+1, max(x), step)
+        xaxis = np.arange(min(x), max(x), step)
-        yaxis = np.arange(min(y)+1, max(y), step)
+        yaxis = np.arange(min(y), max(y), step)
         xgrid, ygrid = np.meshgrid(xaxis, yaxis)
         zgrid = griddata((x, y), z, (xgrid, ygrid), method='linear')
 
@@ -700,14 +770,28 @@ class SeismicShot(object):
             fig = plt.figure()
             ax = plt.axes()
 
-        ax.imshow(zgrid, interpolation = 'none', extent = [min(x), max(x), min(y), max(y)])
+        ax.matshow(zgrid, extent = [min(x), max(x), min(y), max(y)], origin = 'lower')
-               
+        plt.text(0.45, 0.9, 'shot: %s' %self.getShotnumber(), transform = ax.transAxes)
-        if annotations == True:
+        sc = ax.scatter(x, y, c = z, s = 30, label = 'picked shots', vmin = tmin, vmax = tmax, linewidths = 1.5)
-            for i, traceID in enumerate(self.pick.keys()):
+        sccut = ax.scatter(xcut, ycut, c = zcut, s = 30, edgecolor = 'm', label = 'cut out shots', vmin = tmin, vmax = tmax, linewidths = 1.5)
-                if shot.picks[traceID] != None:
+        if colorbar == True:
-                    ax.annotate('%s' % traceID, xy=(x[i], y[i]), fontsize = 'x-small')
+            plt.colorbar(sc)
+        ax.set_xlabel('X')
+        ax.set_ylabel('Y')
+        ax.plot(self.getSrcLoc()[0], self.getSrcLoc()[1],'*k', markersize = 15) # plot source location
 
         if plotRec == True:
-            ax.plot(x, y, 'k.')
+            ax.scatter(x, y, c = z, s = 30)
+
+        if annotations == True:
+            for traceID in self.getTraceIDlist():
+                if self.getFlag(traceID) is not 0:
+                    ax.annotate(' %s' %traceID , xy = (self.getRecLoc(traceID)[0], self.getRecLoc(traceID)[1]),
+                                fontsize = 'x-small', color = 'k')
+                else:
+                    ax.annotate(' %s' %traceID , xy = (self.getRecLoc(traceID)[0], self.getRecLoc(traceID)[1]),
+                                fontsize = 'x-small', color = 'r')
 
         plt.show()
+
+

pylot/core/active/surveyPlotTools.py

@@ -1,48 +1,69 @@
+# -*- coding: utf-8 -*-
 import matplotlib.pyplot as plt
+import math
+import numpy as np
 plt.interactive(True)
 
 class regions(object):
-    def __init__(self, ax, shot_dict):
+    '''
+    A class used for manual inspection and processing of all picks for the user.
+
+    Examples:
+
+    regions.chooseRectangles():
+     - lets the user choose several rectangular regions in the plot
+    
+    regions.plotTracesInActiveRegions():
+     - creates plots (shot.plot_traces) for all traces in the active regions (i.e. chosen by e.g. chooseRectangles)
+    
+    regions.setAllActiveRegionsForDeletion():
+     - highlights all shots in a the active regions for deletion
+    
+    regions.deleteAllMarkedPicks():
+     - deletes the picks (pick flag set to 0) for all shots set for deletion
+
+    regions.deselectSelection(number):
+     - deselects the region of number = number
+    
+    '''
+
+    def __init__(self, ax, cbar, survey):
         self.ax = ax
-        self.shot_dict = shot_dict
+        self.cbar = cbar
+        self.cbv = 'log10SNR'
+        self._xlim0 = self.ax.get_xlim()
+        self._ylim0 = self.ax.get_ylim()
+        self._xlim = self.ax.get_xlim()
+        self._ylim = self.ax.get_ylim()
+        self.survey = survey
+        self.shot_dict = self.survey.getShotDict()
         self._x0 = []
         self._y0 = []
         self._x1 = []
         self._y1 = []
+        self._polyx = []
+        self._polyy = []
+        self.buttons = {}
+        self._allpicks = None
         self.shots_found = {}
         self.shots_for_deletion = {}
+        self._generateList()
+        self._addButtons()
+        self.addTextfield()
+        self.drawFigure()
 
-    def _onselect(self, eclick, erelease):
+    def _generateList(self):
-        'eclick and erelease are matplotlib events at press and release'                                                                                            #print ' startposition : (%f, %f)' % (eclick.xdata, eclick.ydata)     
+        allpicks = []
-        #print ' endposition   : (%f, %f)' % (erelease.xdata, erelease.ydata) 
+        for shot in self.shot_dict.values():
-        print 'region selected x0, y0 = (%3s, %3s), x1, y1 = (%3s, %3s)'%(eclick.xdata, eclick.ydata, erelease.xdata, erelease.ydata)      
+            for traceID in shot.getTraceIDlist():
-        x0 = min(eclick.xdata, erelease.xdata)
+                allpicks.append((shot.getDistance(traceID),
-        x1 = max(eclick.xdata, erelease.xdata)
+                 shot.getPickIncludeRemoved(traceID),
-        y0 = min(eclick.ydata, erelease.ydata)
+                 shot.getShotnumber(),
-        y1 = max(eclick.ydata, erelease.ydata)
+                 traceID,
-        self._x0.append(x0)
+                 shot.getFlag(traceID)))
-        self._x1.append(x1)
-        self._y0.append(y0)
-        self._y1.append(y1)
-        self.markCurrentRegion(x0, x1, y0, y1)
 
-    def chooseRectangles(self):
+        allpicks.sort()
-        from matplotlib.widgets import RectangleSelector
+        self._allpicks = allpicks
-
-        print 'Select rectangle is active'
-        return RectangleSelector(self.ax, self._onselect)
-
-    def _getx0(self):
-        return self._x0
-
-    def _getx1(self):
-        return self._x1
-
-    def _gety0(self):
-        return self._y0
-
-    def _gety1(self):
-        return self._y1
 
     def getShotDict(self):
         return self.shot_dict
@@ -50,119 +71,439 @@ class regions(object):
     def getShotsForDeletion(self):
         return self.shots_for_deletion
 
-    def findTracesInShotDict(self, picks = 'normal'):
+    def _onselect_clicks(self, eclick, erelease):
-        '''                                                                                                               
+        '''eclick and erelease are matplotlib events at press and release'''
-        Returns traces corresponding to a certain area in a plot with all picks over the distances.
+        print 'region selected x0, y0 = (%3s, %3s), x1, y1 = (%3s, %3s)' % (eclick.xdata,
-        '''
+         eclick.ydata,
-        print "findTracesInShotDict: Searching for marked traces in the shot dictionary... "
+         erelease.xdata,
+         erelease.ydata)
+        x0 = min(eclick.xdata, erelease.xdata)
+        x1 = max(eclick.xdata, erelease.xdata)
+        y0 = min(eclick.ydata, erelease.ydata)
+        y1 = max(eclick.ydata, erelease.ydata)
 
-        for shot in self.shot_dict.values():
+        shots, numtraces = self.findTracesInShotDict((x0, x1), (y0, y1))
-            whichpicks = {'normal': shot.getPick,
+        self.printOutput('Found %d traces in rectangle: %s' % (numtraces, shots))
-                          'includeCutOut': shot.getPick_backup}
+        key = self.getKey()
-            for index in range(len(self._getx1())):
+        self.shots_found[key] = {'shots': shots,
-                distancebin = (self._getx0()[index], self._getx1()[index])
+                                 'selection': 'rect',
-                pickbin = (self._gety0()[index], self._gety1()[index])
+                                 'xvalues': (x0, x1),
-                if shot.getTraceIDs4Dist(distancebin = distancebin) is not None:
+                                 'yvalues': (y0, y1)}
-                    for traceID in shot.getTraceIDs4Dist(distancebin = distancebin):
+        self.markRectangle((x0, x1), (y0, y1), key)
-                        if pickbin[0] < whichpicks[picks](traceID) < pickbin[1]:
+        self.disconnectRect()
+
+    def _onselect_verts(self, verts):
+        x = verts[0][0]
+        y = verts[0][1]
+        self._polyx.append(x)
+        self._polyy.append(y)
+
+        self.drawPolyLine()
+
+    def _onpress(self, event):
+        if event.button == 3:
+            self.disconnectPoly()
+            self.printOutput('Disconnected polygon selection')
+
+    def addTextfield(self, xpos = 0, ypos = 0.95, width = 1, height = 0.03):
+        self.axtext = self.ax.figure.add_axes([xpos,
+         ypos,
+         width,
+         height])
+        self.axtext.xaxis.set_visible(False)
+        self.axtext.yaxis.set_visible(False)
+
+    def writeInTextfield(self, text = None):
+        self.setXYlim(self.ax.get_xlim(), self.ax.get_ylim())
+        self.axtext.clear()
+        self.axtext.text(0.01, 0.5, text, verticalalignment='center', horizontalalignment='left')
+        self.drawFigure()
+
+    def _addButtons(self):
+        xpos1 = 0.13
+        xpos2 = 0.6
+        dx = 0.06
+        self.addButton('Rect', self.chooseRectangles, xpos=xpos1, color='white')
+        self.addButton('Poly', self.choosePolygon, xpos=xpos1 + dx, color='white')
+        self.addButton('Plot', self.plotTracesInActiveRegions, xpos=xpos1 + 2 * dx, color='yellow')
+        self.addButton('SNR', self.refreshLog10SNR, xpos=xpos1 + 3 * dx, color='cyan')
+        self.addButton('PE', self.refreshPickerror, xpos=xpos1 + 4 * dx, color='cyan')
+        self.addButton('SPE', self.refreshSPE, xpos=xpos1 + 5 * dx, color='cyan')
+        self.addButton('DesLst', self.deselectLastSelection, xpos=xpos2 + dx, color='green')
+        self.addButton('SelAll', self.setAllActiveRegionsForDeletion, xpos=xpos2 + 2 * dx)
+        self.addButton('DelAll', self.deleteAllMarkedPicks, xpos=xpos2 + 3 * dx, color='red')
+
+    def addButton(self, name, action, xpos, ypos = 0.91, color = None):
+        from matplotlib.widgets import Button
+        self.buttons[name] = {'ax': None,
+         'button': None,
+         'action': action,
+         'xpos': xpos}
+        ax = self.ax.figure.add_axes([xpos,
+         ypos,
+         0.05,
+         0.03])
+        button = Button(ax, name, color=color, hovercolor='grey')
+        button.on_clicked(action)
+        self.buttons[name]['ax'] = ax
+        self.buttons[name]['button'] = button
+        self.buttons[name]['xpos'] = xpos
+
+    def getKey(self):
+        if self.shots_found.keys() == []:
+            key = 1
+        else:
+            key = max(self.shots_found.keys()) + 1
+        return key
+
+    def drawPolyLine(self):
+        self.setXYlim(self.ax.get_xlim(), self.ax.get_ylim())
+        x = self._polyx
+        y = self._polyy
+        if len(x) >= 2 and len(y) >= 2:
+            self.ax.plot(x[-2:], y[-2:], 'k', alpha=0.1)
+        self.drawFigure()
+
+    def drawLastPolyLine(self):
+        self.setXYlim(self.ax.get_xlim(), self.ax.get_ylim())
+        x = self._polyx
+        y = self._polyy
+        if len(x) >= 2 and len(y) >= 2:
+            self.ax.plot((x[-1], x[0]), (y[-1], y[0]), 'k', alpha=0.1)
+        self.drawFigure()
+
+    def finishPolygon(self):
+        self.drawLastPolyLine()
+        x = self._polyx
+        y = self._polyy
+        self._polyx = []; self._polyy = []
+
+        key = self.getKey()
+        self.markPolygon(x, y, key = key)
+
+        shots, numtraces = self.findTracesInPoly(x, y)
+        self.shots_found[key] = {'shots': shots,
+         'selection': 'poly',
+         'xvalues': x,
+         'yvalues': y}
+        self.printOutput('Found %d traces in polygon: %s' % (numtraces, shots))
+
+    def printOutput(self, text):
+        print text
+        self.writeInTextfield(text)
+
+    def chooseRectangles(self, event = None):
+        '''
+        Activates matplotlib widget RectangleSelector.
+        '''
+        from matplotlib.widgets import RectangleSelector
+        if hasattr(self, '_cidPoly'):
+            self.disconnectPoly()
+        self.printOutput('Select rectangle is active. Press and hold left mousebutton.')
+        self._cidRect = None
+        self._cidRect = self.ax.figure.canvas.mpl_connect('button_press_event', self._onpress)
+        self._rectangle = RectangleSelector(self.ax, self._onselect_clicks)
+        return self._rectangle
+
+    def choosePolygon(self, event = None):
+        '''
+        Activates matplotlib widget LassoSelector.
+        '''
+        from matplotlib.widgets import LassoSelector
+        if hasattr(self, '_cidRect'):
+            self.disconnectRect()
+        self.printOutput('Select polygon is active. Add points with leftclick. Finish with rightclick.')
+        self._cidPoly = None
+        self._cidPoly = self.ax.figure.canvas.mpl_connect('button_press_event', self._onpress)
+        self._lasso = LassoSelector(self.ax, self._onselect_verts)
+        return self._lasso
+
+    def disconnectPoly(self, event = None):
+        if not hasattr(self, '_cidPoly'):
+            self.printOutput('no poly selection found')
+            return
+        self.ax.figure.canvas.mpl_disconnect(self._cidPoly)
+        del self._cidPoly
+        self.finishPolygon()
+        self._lasso.disconnect_events()
+        print 'disconnected poly selection\n'
+
+    def disconnectRect(self, event = None):
+        if not hasattr(self, '_cidRect'):
+            self.printOutput('no rectangle selection found')
+            return
+        self.ax.figure.canvas.mpl_disconnect(self._cidRect)
+        del self._cidRect
+        self._rectangle.disconnect_events()
+        print 'disconnected rectangle selection\n'
+
+    def deselectLastSelection(self, event = None):
+        if self.shots_found.keys() == []:
+            self.printOutput('No selection found.')
+            return
+        key = max(self.shots_found.keys())
+        self.deselectSelection(key)
+
+    def deselectSelection(self, key, color = 'green', alpha = 0.1):
+        if key not in self.shots_found.keys():
+            self.printOutput('No selection found.')
+            return
+        if color is not None:
+            if self.shots_found[key]['selection'] == 'rect':
+                self.markRectangle(self.shots_found[key]['xvalues'],
+                                   self.shots_found[key]['yvalues'],
+                                   key = key, color = color, alpha = alpha,
+                                   linewidth = 1)
+            elif self.shots_found[key]['selection'] == 'poly':
+                self.markPolygon(self.shots_found[key]['xvalues'],
+                                 self.shots_found[key]['yvalues'],
+                                 key = key, color = color, alpha = alpha,
+                                 linewidth = 1)                    
+        value = self.shots_found.pop(key)
+        self.printOutput('Deselected selection number %d' % key)
+
+    def findTracesInPoly(self, x, y, picks = 'normal', highlight = True):
+        def dotproduct(v1, v2):
+            return sum((a * b for a, b in zip(v1, v2)))
+
+        def getlength(v):
+            return math.sqrt(dotproduct(v, v))
+
+        def getangle(v1, v2):
+            return np.rad2deg(math.acos(dotproduct(v1, v2) / (getlength(v1) * getlength(v2))))
+
+        def insidePoly(x, y, pickX, pickY):
+            angle = 0
+            epsilon = 1e-07
+            for index in range(len(x)):
+                xval1 = x[index - 1]; yval1 = y[index - 1]
+                xval2 = x[index]; yval2 = y[index]
+                angle += getangle([xval1 - pickX, yval1 - pickY], [xval2 - pickX, yval2 - pickY])
+            if 360 - epsilon <= angle <= 360 + epsilon: ### IMPROVE THAT??
+                return True
+
+        if len(x) == 0 or len(y) == 0:
+            self.printOutput('No polygon defined.')
+            return
+
+        shots_found = {}; numtraces = 0
+        x0 = min(x); x1 = max(x)
+        y0 = min(y); y1 = max(y)
+
+        shots, numtracesrect = self.findTracesInShotDict((x0, x1), (y0, y1), highlight = False)
+        for shotnumber in shots.keys():
+            shot = self.shot_dict[shotnumber]
+            for traceID in shots[shotnumber]:
+                if shot.getFlag(traceID) is not 0:
+                    pickX = shot.getDistance(traceID)
+                    pickY = shot.getPick(traceID)
+                    if insidePoly(x, y, pickX, pickY):
+                        if shotnumber not in shots_found.keys():
+                            shots_found[shotnumber] = []
+                        shots_found[shotnumber].append(traceID)
+                        if highlight == True:
                             self.highlightPick(shot, traceID)
-                            if shot.getShotnumber() not in self.shots_found.keys():
+                        numtraces += 1
-                                self.shots_found[shot.getShotnumber()] = []
+
-                            if traceID not in self.shots_found[shot.getShotnumber()]:
+        self.drawFigure()
-                                self.shots_found[shot.getShotnumber()].append(traceID)
+        return shots_found, numtraces
-        self.refreshFigure()
+        
-        print self.shots_found
+    def findTracesInShotDict(self, (x0, x1), (y0, y1), picks = 'normal', highlight = True):
+        '''
+        Returns traces corresponding to a certain area in the plot with all picks over the distances.
+        '''
+        shots_found = {}; numtraces = 0
+        if picks == 'normal': pickflag = 0
+        elif picks == 'includeCutOut': pickflag = None
+
+        for line in self._allpicks:
+            dist, pick, shotnumber, traceID, flag = line
+            if flag == pickflag: continue ### IMPROVE THAT
+            if (x0 <= dist <= x1 and y0 <= pick <= y1):
+                if shotnumber not in shots_found.keys():
+                    shots_found[shotnumber] = []
+                shots_found[shotnumber].append(traceID)
+                if highlight == True:
+                    self.highlightPick(self.shot_dict[shotnumber], traceID)
+                numtraces += 1
+
+        self.drawFigure()
+        return shots_found, numtraces
 
     def highlightPick(self, shot, traceID, annotations = True):
+        '''
+        Highlights a single pick for a shot(object)/shotnumber and traceID.
+        If annotations == True: Displays shotnumber and traceID in the plot.
+        '''
+        if type(shot) == int:
+            shot = self.survey.getShotDict()[shot]
+
         self.ax.scatter(shot.getDistance(traceID), shot.getPick(traceID), s = 50, marker = 'o', facecolors = 'none', edgecolors = 'm', alpha = 1)
         if annotations == True:
-            self.ax.annotate(s = 's%s|t%s'%(shot.getShotnumber(), traceID), xy = (shot.getDistance(traceID), shot.getPick(traceID)), fontsize = 'xx-small')
+            self.ax.annotate(s='s%s|t%s' % (shot.getShotnumber(), traceID), xy=(shot.getDistance(traceID), shot.getPick(traceID)), fontsize='xx-small')
-        self.ax.set_ylim(shot.getCut())
 
-    def plotTracesInRegion(self):
+    def highlightAllActiveRegions(self):
+        '''
+        Highlights all picks in all active regions.
+        '''
+        for key in self.shots_found.keys():
+            for shotnumber in self.shots_found[key]['shots'].keys():
+                for traceID in self.shots_found[key]['shots'][shotnumber]:
+                    self.highlightPick(self.shot_dict[shotnumber], traceID)
+        self.drawFigure()
+
+    def plotTracesInActiveRegions(self, event = None, keys = 'all', maxfigures = 20):
+        '''
+        Plots all traces in the active region or for all specified keys.
+
+        :param: keys
+        :type: int or list
+
+        :param: maxfigures, maximum value of figures opened
+        :type: int
+        '''
         count = 0
-        maxfigures = 20
+        if keys == 'all':
-        # if len(self.shots_found) == 0:
+            keys = self.shots_found.keys()
-        self.findTracesInShotDict()
+        elif type(keys) == int:
+            keys = [keys]
 
         if len(self.shots_found) > 0:
             for shot in self.shot_dict.values():
-                for shotnumber in self.shots_found:
+                for key in keys:
-                    if shot.getShotnumber() == shotnumber:
+                    for shotnumber in self.shots_found[key]['shots']:
-                        for traceID in self.shots_found[shotnumber]:
+                        if shot.getShotnumber() == shotnumber:
-                            count += 1
+                            for traceID in self.shots_found[key]['shots'][shotnumber]:
-                            if count > maxfigures:
+                                count += 1
-                                print 'Maximum number of figures (%s) reached. %sth figure was not opened.' %(maxfigures, count)
+                                if count > maxfigures:
-                                break
+                                    print 'Maximum number of figures (%s) reached. %sth figure was not opened.' %(maxfigures, count)
-                            shot.plot_traces(traceID)
+                                    break
+                                shot.plot_traces(traceID)
         else:
-            print 'No picks yet defined in the regions x = (%s, %s), y = (%s, %s)' %(self._x0, self._x1, self._y0, self._y1)
+            self.printOutput('No picks defined in that region(s)')
 
-    def plotTracesInRegion_withCutOutTraces(self):
+    def setAllActiveRegionsForDeletion(self, event = None):
-        count = 0
+        keys = []
-        maxfigures = 20
+        for key in self.shots_found.keys():
-        # if len(self.shots_found) == 0:
+            keys.append(key)
-        self.findTracesInShotDict(picks = 'includeCutOut')
+        self.setRegionForDeletion(keys)
 
-        if len(self.shots_found) > 0:
+    def setRegionForDeletion(self, keys):
-            for shot in self.shot_dict.values():
+        if type(keys) == int:
-                for shotnumber in self.shots_found:
+            keys = [keys]
-                    if shot.getShotnumber() == shotnumber:
-                        for traceID in self.shots_found[shotnumber]:
-                            count += 1
-                            if count > maxfigures:
-                                print 'Maximum number of figures (%s) reached. %sth figure was not opened.' %(maxfigures, count)
-                                break
-                            shot.plot_traces(traceID)
-        else:
-            print 'No picks yet defined in the regions x = (%s, %s), y = (%s, %s)' %(self._x0, self._x1, self._y0, self._y1)
-           
 
-    def setCurrentRegionsForDeletion(self):
+        for key in keys:
-        # if len(self.shots_found) == 0:
+            for shotnumber in self.shots_found[key]['shots'].keys():
-        self.findTracesInShotDict()
+                if shotnumber not in self.shots_for_deletion:
+                    self.shots_for_deletion[shotnumber] = []
+                for traceID in self.shots_found[key]['shots'][shotnumber]:
+                    if traceID not in self.shots_for_deletion[shotnumber]:
+                        self.shots_for_deletion[shotnumber].append(traceID)
+            self.deselectSelection(key, color = 'red', alpha = 0.2)
 
-        for shotnumber in self.shots_found:
+            self.deselectSelection(key, color='red', alpha=0.2)
-            if not shotnumber in self.shots_for_deletion:
-                self.shots_for_deletion[shotnumber] = []
-            for traceID in self.shots_found[shotnumber]:
-                if not traceID in self.shots_for_deletion[shotnumber]:
-                    self.shots_for_deletion[shotnumber].append(traceID)
-        self.markAllRegions(color = 'red')
-        print 'Marked regions for deletion'
 
-    def markAllRegions(self, color = 'grey'):
+        self.printOutput('Set region(s) %s for deletion' % keys)
+
+    def markAllActiveRegions(self):
+        for key in self.shots_found.keys():
+            if self.shots_found[key]['selection'] == 'rect':
+                self.markRectangle(self.shots_found[key]['xvalues'],
+                                   self.shots_found[key]['yvalues'], key = key)
+            if self.shots_found[key]['selection'] == 'poly':
+                self.markPolygon(self.shots_found[key]['xvalues'],
+                                 self.shots_found[key]['yvalues'], key = key)
+            
+
+    def markRectangle(self, (x0, x1), (y0, y1), key = None, color = 'grey', alpha = 0.1, linewidth = 1):
+        '''
+        Mark a rectangular region on the axes.
+        '''
         from matplotlib.patches import Rectangle
+        self.ax.add_patch(Rectangle((x0, y0), x1 - x0, y1 - y0, alpha=alpha, facecolor=color, linewidth=linewidth))
+        if key is not None:
+            self.ax.text(x0 + (x1 - x0) / 2, y0 + (y1 - y0) / 2, str(key))
+        self.drawFigure()
 
-        for index in range(len(self._getx0())):
+    def markPolygon(self, x, y, key = None, color = 'grey', alpha = 0.1, linewidth = 1):
-            x0 = self._getx0()[index]
+        from matplotlib.patches import Polygon
-            y0 = self._gety0()[index]
+        poly = Polygon(np.array(zip(x, y)), color=color, alpha=alpha, lw=linewidth)
-            x1 = self._getx1()[index]
+        self.ax.add_patch(poly)
-            y1 = self._gety1()[index]
+        if key is not None:
+            self.ax.text(min(x) + (max(x) - min(x)) / 2, min(y) + (max(y) - min(y)) / 2, str(key))
+        self.drawFigure()
 
-            self.ax.add_patch(Rectangle((x0, y0), (x1 - x0), (y1 - y0), alpha=0.5, facecolor = color))
+    def clearShotsForDeletion(self):
-            self.refreshFigure()
+        '''
+        Clears the list of shots marked for deletion.
+        '''
+        self.shots_for_deletion = {}
+        print('Cleared all shots that were set for deletion.')
 
-    def markCurrentRegion(self, x0, x1, y0, y1, color = 'grey'):
+    def getShotsForDeletion(self):
-        from matplotlib.patches import Rectangle
+        return self.shots_for_deletion
 
-        self.ax.add_patch(Rectangle((x0, y0), (x1 - x0), (y1 - y0), alpha=0.1, facecolor = color))
+    def deleteAllMarkedPicks(self, event = None):
-        self.refreshFigure()
+        '''
+        Deletes all shots set for deletion.
+        '''
+        if len(self.getShotsForDeletion()) is 0:
+            self.printOutput('No shots set for deletion.')
+            return
 
-    def deleteMarkedPicks(self):
         for shot in self.getShotDict().values():
             for shotnumber in self.getShotsForDeletion():
                 if shot.getShotnumber() == shotnumber:
                     for traceID in self.getShotsForDeletion()[shotnumber]:
                         shot.removePick(traceID)
                         print "Deleted the pick for traceID %s on shot number %s" %(traceID, shotnumber)
-        self.shots_for_deletion = {} # clear dictionary
+        self.clearShotsForDeletion()
-
-    def highlightPicksForShot(self, shot, annotations = False):
-        for traceID in shot.getTraceIDlist():
-            if shot.getPick(traceID) is not None:
-                self.highlightPick(shot, traceID, annotations)
         self.refreshFigure()
 
-    def refreshFigure(self):
+    def highlightPicksForShot(self, shot, annotations = False):
+        '''
+        Highlight all picks for a given shot.
+        '''
+        if type(shot) is int:
+            shot = self.survey.getShotDict()[shotnumber]
+
+        for traceID in shot.getTraceIDlist():
+            if shot.getFlag(traceID) is not 0:
+                self.highlightPick(shot, traceID, annotations)
+
+        self.drawFigure()
+
+    def setXYlim(self, xlim, ylim):
+        self._xlim, self._ylim = xlim, ylim
+
+    def refreshLog10SNR(self, event = None):
+        cbv = 'log10SNR'
+        self.refreshFigure(self, colorByVal=cbv)
+
+    def refreshPickerror(self, event = None):
+        cbv = 'pickerror'
+        self.refreshFigure(self, colorByVal=cbv)
+
+    def refreshSPE(self, event = None):
+        cbv = 'spe'
+        self.refreshFigure(self, colorByVal=cbv)
+
+    def refreshFigure(self, event = None, colorByVal = None):
+        if colorByVal == None:
+            colorByVal = self.cbv
+        else:
+            self.cbv = colorByVal
+        self.printOutput('Refreshing figure...')
+        self.ax.clear()
+        self.ax = self.survey.plotAllPicks(ax=self.ax, cbar=self.cbar, refreshPlot=True, colorByVal=colorByVal)
+        self.setXYlim(self.ax.get_xlim(), self.ax.get_ylim())
+        self.markAllActiveRegions()
+        self.highlightAllActiveRegions()
+        self.drawFigure()
+        self.printOutput('Done!')
+
+    def drawFigure(self, resetAxes = True):
+        if resetAxes == True:
+            self.ax.set_xlim(self._xlim)
+            self.ax.set_ylim(self._ylim)
         plt.draw()

pylot/core/active/surveyUtils.py

@@ -1,19 +1,21 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
 import numpy as np
 
 def readParameters(parfile, parameter):
     from ConfigParser import ConfigParser
     parameterConfig = ConfigParser()
     parameterConfig.read('parfile')
-    
+
-    value = parameterConfig.get('vars', parameter).split('#')[0]
+    value = parameterConfig.get('vars', parameter).split('\t')[0]
-    value = value.replace(" ", "")
 
     return value
 
+def setArtificialPick(shot_dict, traceID, pick):
+    for shot in shot_dict.values():
+        shot.setPick(traceID, pick)
+        shot.setPickwindow(traceID, shot.getCut())
+
 def fitSNR4dist(shot_dict, shiftdist = 5):
+    import numpy as np
     dists = []
     picks = []
     snrs = []
@@ -23,7 +25,7 @@ def fitSNR4dist(shot_dict, shiftdist = 5):
         for traceID in shot.getTraceIDlist():
             if shot.getSNR(traceID)[0] >= 1:
                 dists.append(shot.getDistance(traceID))
-                picks.append(shot.getPick_backup(traceID))
+                picks.append(shot.getPickIncludeRemoved(traceID))
                 snrs.append(shot.getSNR(traceID)[0])
                 snr_sqrt_inv.append(1/np.sqrt(shot.getSNR(traceID)[0]))
     fit = np.polyfit(dists, snr_sqrt_inv, 1)
@@ -34,6 +36,7 @@ def fitSNR4dist(shot_dict, shiftdist = 5):
     plotFittedSNR(dists, snrthresholds, snrs)
     return fit_fn #### ZU VERBESSERN, sollte fertige funktion wiedergeben
 
+
 def plotFittedSNR(dists, snrthresholds, snrs):
     import matplotlib.pyplot as plt
     plt.interactive(True)
@@ -45,25 +48,28 @@ def plotFittedSNR(dists, snrthresholds, snrs):
     plt.legend()
 
 def setFittedSNR(shot_dict, shiftdist = 5, p1 = 0.004, p2 = -0.004):
+    import numpy as np
     #fit_fn = fitSNR4dist(shot_dict)
     fit_fn = np.poly1d([p1, p2])
     for shot in shot_dict.values():
         for traceID in shot.getTraceIDlist(): ### IMPROVE
             shot.setSNRthreshold(traceID, 1/(fit_fn(shot.getDistance(traceID) + shiftdist)**2)) ### s.o.
-    print "\nsetFittedSNR: Finished setting of fitted SNR-threshold"
+    print "setFittedSNR: Finished setting of fitted SNR-threshold"
+
 
 def findTracesInRanges(shot_dict, distancebin, pickbin):
     '''
     Returns traces corresponding to a certain area in a plot with all picks over the distances.
-    
+
     :param: shot_dict, dictionary containing all shots that are used
     :type: dictionary
-                                                                                     
+
     :param: distancebin
     :type: tuple, (dist1[m], dist2[m])
-                                                                                     
+
     :param: pickbin
     :type: tuple, (t1[s], t2[s])
+
     '''
     shots_found = {}
     for shot in shot_dict.values():

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'
@@ -54,4 +54,4 @@ def main():
 
 
 if __name__ == '__main__':
-    main()
+    main()

pylot/core/analysis/magnitude.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
 Created August/September 2015.
@@ -34,7 +35,7 @@ class Magnitude(object):
         :type: integer
 
         '''
-        
+
         assert isinstance(wfstream, Stream), "%s is not a stream object" % str(wfstream)
 
         self.setwfstream(wfstream)
@@ -62,7 +63,7 @@ class Magnitude(object):
 
     def setpwin(self, pwin):
         self.pwin = pwin
-   
+
     def getiplot(self):
         return self.iplot
 
@@ -71,7 +72,7 @@ class Magnitude(object):
 
     def getwapp(self):
         return self.wapp
-  
+
     def getw0(self):
         return self.w0
 
@@ -103,7 +104,7 @@ class WApp(Magnitude):
             'poles': [5.6089 - 5.4978j, -5.6089 - 5.4978j],
             'zeros': [0j, 0j],
             'gain': 2080,
-            'sensitivity': 1} 
+            'sensitivity': 1}
 
         stream.simulate(paz_remove=None, paz_simulate=paz_wa)
 
@@ -133,19 +134,19 @@ class WApp(Magnitude):
             raw_input()
             plt.close(f)
 
-    
+
 class DCfc(Magnitude):
     '''
-    Method to calculate the source spectrum and to derive from that the plateau 
+    Method to calculate the source spectrum and to derive from that the plateau
-    (so-called DC-value) and the corner frequency assuming Aki's omega-square 
+    (so-called DC-value) and the corner frequency assuming Aki's omega-square
     source model. Has to be derived from instrument corrected displacement traces!
     '''
 
     def calcsourcespec(self):
-    	print ("Calculating source spectrum ....")
+        print ("Calculating source spectrum ....")
 
         self.w0 = None # DC-value
-        self.fc = None # corner frequency 
+        self.fc = None # corner frequency
 
         stream = self.getwfstream()
         tr = stream[0]
@@ -155,7 +156,7 @@ class DCfc(Magnitude):
         iwin = getsignalwin(t, self.getTo(), self.getpwin())
         xdat = tr.data[iwin]
 
-        # fft 
+        # fft
         fny = tr.stats.sampling_rate / 2
         l = len(xdat) / tr.stats.sampling_rate
         n = tr.stats.sampling_rate * l # number of fft bins after Bath
@@ -167,7 +168,7 @@ class DCfc(Magnitude):
         L = (N - 1) / tr.stats.sampling_rate
         f = np.arange(0, fny, 1/L)
 
-        # remove zero-frequency and frequencies above 
+        # remove zero-frequency and frequencies above
         # corner frequency of seismometer (assumed
         # to be 100 Hz)
         fi = np.where((f >= 1) & (f < 100))
@@ -184,18 +185,16 @@ class DCfc(Magnitude):
         [optspecfit, pcov] = curve_fit(synthsourcespec, F, YY.real, [DCin, Fcin])
         self.w0 = optspecfit[0]
         self.fc = optspecfit[1]
-        print ("DCfc: Determined DC-value: %e m/Hz, \n" \
+        print ("DCfc: Determined DC-value: %e m/Hz, \n"
-               "Determined corner frequency: %f Hz" % (self.w0, self.fc)) 
+               "Determined corner frequency: %f Hz" % (self.w0, self.fc))
-        
+
-        
+
-        #if self.getiplot() > 1:
+        if self.getiplot() > 1:
-        iplot=2
-        if iplot > 1:
             f1 = plt.figure()
             plt.subplot(2,1,1)
             # show displacement in mm
-            plt.plot(t, np.multiply(tr, 1000), 'k') 
+            plt.plot(t, np.multiply(tr, 1000), 'k')
-            plt.plot(t[iwin], np.multiply(xdat, 1000), 'g') 
+            plt.plot(t[iwin], np.multiply(xdat, 1000), 'g')
             plt.title('Seismogram and P pulse, station %s' % tr.stats.station)
             plt.xlabel('Time since %s' % tr.stats.starttime)
             plt.ylabel('Displacement [mm]')
@@ -216,8 +215,8 @@ class DCfc(Magnitude):
 
 def synthsourcespec(f, omega0, fcorner):
     '''
-    Calculates synthetic source spectrum from given plateau and corner 
+    Calculates synthetic source spectrum from given plateau and corner
-    frequency assuming Akis omega-square model.  
+    frequency assuming Akis omega-square model.
 
     :param: f, frequencies
     :type:  array
@@ -228,7 +227,7 @@ def synthsourcespec(f, omega0, fcorner):
     :param: fcorner, corner frequency of source spectrum
     :type:  float
     '''
-        
+
     #ssp = omega0 / (pow(2, (1 + f / fcorner)))
     ssp = omega0 / (1 + pow(2, (f / fcorner)))
 

pylot/core/pick/CharFuns.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
 Created Oct/Nov 2014
@@ -24,7 +25,7 @@ class CharacteristicFunction(object):
     '''
     SuperClass for different types of characteristic functions.
     '''
-    def __init__(self, data, cut, t2=None, order=None, t1=None, fnoise=None):
+    def __init__(self, data, cut, t2=None, order=None, t1=None, fnoise=None, stealthMode=False):
         '''
         Initialize data type object with information from the original
         Seismogram.
@@ -61,6 +62,7 @@ class CharacteristicFunction(object):
         self.calcCF(self.getDataArray())
         self.arpara = np.array([])
         self.xpred = np.array([])
+        self._stealthMode = stealthMode
 
     def __str__(self):
         return '''\n\t{name} object:\n
@@ -119,7 +121,7 @@ class CharacteristicFunction(object):
 
     def getTimeArray(self):
         incr = self.getIncrement()
-        self.TimeArray = np.arange(0, len(self.getCF()) * incr, incr) + self.getCut()[0] 
+        self.TimeArray = np.arange(0, len(self.getCF()) * incr, incr) + self.getCut()[0]
         return self.TimeArray
 
     def getFnoise(self):
@@ -134,6 +136,9 @@ class CharacteristicFunction(object):
     def getXCF(self):
         return self.xcf
 
+    def _getStealthMode(self):
+        return self._stealthMode()
+
     def getDataArray(self, cut=None):
         '''
         If cut times are given, time series is cut from cut[0] (start time)
@@ -164,31 +169,31 @@ class CharacteristicFunction(object):
                    stop = min([len(self.orig_data[0]), len(self.orig_data[1])])
                 elif self.cut[0] == 0 and self.cut[1] is not 0:
                    start = 0
-                   stop = min([self.cut[1] / self.dt, len(self.orig_data[0]), \
+                   stop = min([self.cut[1] / self.dt, len(self.orig_data[0]),
-                              len(self.orig_data[1])])
+                               len(self.orig_data[1])])
                 else:
                    start = max([0, self.cut[0] / self.dt])
-                   stop = min([self.cut[1] / self.dt, len(self.orig_data[0]), \
+                   stop = min([self.cut[1] / self.dt, len(self.orig_data[0]),
-                              len(self.orig_data[1])])
+                               len(self.orig_data[1])])
                 hh = self.orig_data.copy()
                 h1 = hh[0].copy()
                 h2 = hh[1].copy()
                 hh[0].data = h1.data[int(start):int(stop)]
                 hh[1].data = h2.data[int(start):int(stop)]
-                data = hh 
+                data = hh
                 return data
             elif len(self.orig_data) == 3:
                 if self.cut[0] == 0 and self.cut[1] == 0:
                    start = 0
-                   stop = min([self.cut[1] / self.dt, len(self.orig_data[0]), \
+                   stop = min([self.cut[1] / self.dt, len(self.orig_data[0]),
-                              len(self.orig_data[1]), len(self.orig_data[2])])
+                               len(self.orig_data[1]), len(self.orig_data[2])])
                 elif self.cut[0] == 0 and self.cut[1] is not 0:
                    start = 0
                    stop = self.cut[1] / self.dt
                 else:
                    start = max([0, self.cut[0] / self.dt])
-                   stop = min([self.cut[1] / self.dt, len(self.orig_data[0]), \
+                   stop = min([self.cut[1] / self.dt, len(self.orig_data[0]),
-                              len(self.orig_data[1]), len(self.orig_data[2])])
+                               len(self.orig_data[1]), len(self.orig_data[2])])
                 hh = self.orig_data.copy()
                 h1 = hh[0].copy()
                 h2 = hh[1].copy()
@@ -196,12 +201,12 @@ class CharacteristicFunction(object):
                 hh[0].data = h1.data[int(start):int(stop)]
                 hh[1].data = h2.data[int(start):int(stop)]
                 hh[2].data = h3.data[int(start):int(stop)]
-                data = hh 
+                data = hh
                 return data
         else:
             data = self.orig_data.copy()
             return data
-       
+
     def calcCF(self, data=None):
         self.cf = data
 
@@ -218,7 +223,8 @@ class AICcf(CharacteristicFunction):
 
     def calcCF(self, data):
 
-        #print 'Calculating AIC ...'  ## MP MP output suppressed
+        #if self._getStealthMode() is False:
+        #    print 'Calculating AIC ...'
         x = self.getDataArray()
         xnp = x[0].data
         nn = np.isnan(xnp)
@@ -230,7 +236,7 @@ class AICcf(CharacteristicFunction):
         cumsumcf = np.cumsum(np.power(xnp, 2))
         i = np.where(cumsumcf == 0)
         cumsumcf[i] = np.finfo(np.float64).eps
-        cf[k] = ((k - 1) * np.log(cumsumcf[k] / k) + (datlen - k + 1) * \
+        cf[k] = ((k - 1) * np.log(cumsumcf[k] / k) + (datlen - k + 1) *
                  np.log((cumsumcf[datlen - 1] - cumsumcf[k - 1]) / (datlen - k + 1)))
         cf[0] = cf[1]
         inf = np.isinf(cf)
@@ -256,11 +262,13 @@ class HOScf(CharacteristicFunction):
         if len(nn) > 1:
            xnp[nn] = 0
         if self.getOrder() == 3:  # this is skewness
-            print 'Calculating skewness ...'
+            #if self._getStealthMode() is False:
+            #    print 'Calculating skewness ...'
             y = np.power(xnp, 3)
             y1 = np.power(xnp, 2)
         elif self.getOrder() == 4:  # this is kurtosis
-            #print 'Calculating kurtosis ...'  ## MP MP output suppressed
+            #if self._getStealthMode() is False:
+            #    print 'Calculating kurtosis ...'
             y = np.power(xnp, 4)
             y1 = np.power(xnp, 2)
 
@@ -285,7 +293,7 @@ class HOScf(CharacteristicFunction):
                 LTA[j] = lta / np.power(lta1, 1.5)
             elif self.getOrder() == 4:
                 LTA[j] = lta / np.power(lta1, 2)
-        
+
         nn = np.isnan(LTA)
         if len(nn) > 1:
            LTA[nn] = 0
@@ -315,7 +323,7 @@ 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 +370,7 @@ 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)
@@ -382,7 +390,7 @@ class ARZcf(CharacteristicFunction):
     def arPredZ(self, data, arpara, rind, lpred):
         '''
         Function to predict waveform, assuming an autoregressive process of order
-        p (=size(arpara)), with AR parameters arpara calculated in arDet. After 
+        p (=size(arpara)), with AR parameters arpara calculated in arDet. After
         Thomas Meier (CAU), published in Kueperkoch et al. (2012).
         :param: data, time series to be predicted
         :type: array
@@ -400,9 +408,9 @@ class ARZcf(CharacteristicFunction):
         '''
         #be sure of the summation indeces
         if rind < len(arpara):
-            rind = len(arpara) 
+            rind = len(arpara)
         if rind > len(data) - lpred :
-            rind = len(data) - lpred 
+            rind = len(data) - lpred
         if lpred < 1:
             lpred = 1
         if lpred > len(data) - 2:
@@ -422,7 +430,7 @@ class ARHcf(CharacteristicFunction):
     def calcCF(self, data):
 
         print 'Calculating AR-prediction error from both horizontal traces ...'
-        
+
         xnp = self.getDataArray(self.getCut())
         n0 = np.isnan(xnp[0].data)
         if len(n0) > 1:
@@ -430,7 +438,7 @@ class ARHcf(CharacteristicFunction):
         n1 = np.isnan(xnp[1].data)
         if len(n1) > 1:
            xnp[1].data[n1] = 0
-        
+
         #some parameters needed
         #add noise to time series
         xenoise = xnp[0].data + np.random.normal(0.0, 1.0, len(xnp[0].data)) * self.getFnoise() * max(abs(xnp[0].data))
@@ -441,7 +449,7 @@ class ARHcf(CharacteristicFunction):
         #Time2: length of AR-prediction window [sec]
         ldet = int(round(self.getTime1() / self.getIncrement()))    #length of AR-determination window [samples]
         lpred = int(np.ceil(self.getTime2() / self.getIncrement())) #length of AR-prediction window [samples]
-              
+
         cf = np.zeros(len(xenoise))
         loopstep = self.getARdetStep()
         arcalci = lpred + self.getOrder() - 1 #AR-calculation index
@@ -515,7 +523,7 @@ class ARHcf(CharacteristicFunction):
     def arPredH(self, data, arpara, rind, lpred):
         '''
         Function to predict waveform, assuming an autoregressive process of order
-        p (=size(arpara)), with AR parameters arpara calculated in arDet. After 
+        p (=size(arpara)), with AR parameters arpara calculated in arDet. After
         Thomas Meier (CAU), published in Kueperkoch et al. (2012).
         :param: data, horizontal component seismograms to be predicted
         :type: structured array
@@ -558,7 +566,7 @@ class AR3Ccf(CharacteristicFunction):
     def calcCF(self, data):
 
         print 'Calculating AR-prediction error from all 3 components ...'
-        
+
         xnp = self.getDataArray(self.getCut())
         n0 = np.isnan(xnp[0].data)
         if len(n0) > 1:
@@ -569,7 +577,7 @@ class AR3Ccf(CharacteristicFunction):
         n2 = np.isnan(xnp[2].data)
         if len(n2) > 1:
            xnp[2].data[n2] = 0
-        
+
         #some parameters needed
         #add noise to time series
         xenoise = xnp[0].data + np.random.normal(0.0, 1.0, len(xnp[0].data)) * self.getFnoise() * max(abs(xnp[0].data))
@@ -581,7 +589,7 @@ class AR3Ccf(CharacteristicFunction):
         #Time2: length of AR-prediction window [sec]
         ldet = int(round(self.getTime1() / self.getIncrement()))    #length of AR-determination window [samples]
         lpred = int(np.ceil(self.getTime2() / self.getIncrement())) #length of AR-prediction window [samples]
-              
+
         cf = np.zeros(len(xenoise))
         loopstep = self.getARdetStep()
         arcalci = ldet + self.getOrder() - 1 #AR-calculation index
@@ -616,7 +624,7 @@ class AR3Ccf(CharacteristicFunction):
         Function to calculate AR parameters arpara after Thomas Meier (CAU), published
         in  Kueperkoch et al. (2012). This function solves SLE using the Moore-
         Penrose inverse, i.e. the least-squares approach. "data" is a structured array.
-        AR parameters are calculated based on both horizontal components and vertical 
+        AR parameters are calculated based on both horizontal components and vertical
         componant.
         :param: data, horizontal component seismograms to calculate AR parameters from
         :type: structured array
@@ -658,7 +666,7 @@ class AR3Ccf(CharacteristicFunction):
     def arPred3C(self, data, arpara, rind, lpred):
         '''
         Function to predict waveform, assuming an autoregressive process of order
-        p (=size(arpara)), with AR parameters arpara calculated in arDet3C. After 
+        p (=size(arpara)), with AR parameters arpara calculated in arDet3C. After
         Thomas Meier (CAU), published in Kueperkoch et al. (2012).
         :param: data, horizontal and vertical component seismograms to be predicted
         :type: structured array

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

@@ -204,27 +204,27 @@ def autopickstation(wfstream, pickparam):
             if len(ndat) == 0 or len(edat) == 0:
                 print ("One or more horizontal components missing!")
                 print ("Signal length only checked on vertical component!")
-                print ("Decreasing minsiglengh from %f to %f" \
+                print ("Decreasing minsiglengh from %f to %f"
-                        % (minsiglength, minsiglength / 2))
+                       % (minsiglength, minsiglength / 2))
                 Pflag = checksignallength(zne, aicpick.getpick(), tsnrz,
-                                          minsiglength / 2, \
+                                          minsiglength / 2,
                                           nfacsl, minpercent, iplot)
             else:
                 # filter and taper horizontal traces
                 trH1_filt = edat.copy()
                 trH2_filt = ndat.copy()
                 trH1_filt.filter('bandpass', freqmin=bph1[0],
-                                  freqmax=bph1[1], \
+                                  freqmax=bph1[1],
-                                  zerophase=False)
+                                 zerophase=False)
                 trH2_filt.filter('bandpass', freqmin=bph1[0],
-                                  freqmax=bph1[1], \
+                                  freqmax=bph1[1],
-                                  zerophase=False)
+                                 zerophase=False)
                 trH1_filt.taper(max_percentage=0.05, type='hann')
                 trH2_filt.taper(max_percentage=0.05, type='hann')
                 zne += trH1_filt
                 zne += trH2_filt
                 Pflag = checksignallength(zne, aicpick.getpick(), tsnrz,
-                                          minsiglength, \
+                                          minsiglength,
                                           nfacsl, minpercent, iplot)
 
             if Pflag == 1:
@@ -234,7 +234,7 @@ def autopickstation(wfstream, pickparam):
                     print 'One or more horizontal components missing!'
                     print 'Skipping control function checkZ4S.'
                 else:
-                    Pflag = checkZ4S(zne, aicpick.getpick(), zfac, \
+                    Pflag = checkZ4S(zne, aicpick.getpick(), zfac,
                                      tsnrz[3], iplot)
                     if Pflag == 0:
                         Pmarker = 'SinsteadP'
@@ -317,31 +317,31 @@ 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, " \
+                print ("autopickstation: P-weight: %d, SNR: %f, SNR[dB]: %f, "
                        "Polarity: %s" % (Pweight, SNRP, SNRPdB, FM))
                 Sflag = 1
 
@@ -352,7 +352,7 @@ def autopickstation(wfstream, pickparam):
             Sflag = 0
 
     else:
-        print ("autopickstation: No vertical component data available!, " \
+        print ("autopickstation: No vertical component data available!, "
                "Skipping station!")
 
     if edat is not None and ndat is not None and len(edat) > 0 and len(
@@ -560,7 +560,7 @@ def autopickstation(wfstream, pickparam):
                 hdat += ndat
                 h_copy = hdat.copy()
                 [cordat, restflag] = data.restituteWFData(invdir, h_copy)
-                # calculate WA-peak-to-peak amplitude 
+                # calculate WA-peak-to-peak amplitude
                 # using subclass WApp of superclass Magnitude
                 if restflag == 1:
                     if Sweight < 4:
@@ -591,10 +591,10 @@ def autopickstation(wfstream, pickparam):
             h_copy = hdat.copy()
             [cordat, restflag] = data.restituteWFData(invdir, h_copy)
             if restflag == 1:
-                # calculate WA-peak-to-peak amplitude 
+                # calculate WA-peak-to-peak amplitude
                 # using subclass WApp of superclass Magnitude
-                wapp = WApp(cordat, mpickP, mpickP + sstop + (0.5 * (mpickP \
+                wapp = WApp(cordat, mpickP, mpickP + sstop + (0.5 * (mpickP
-                            + sstop)), iplot)
+                                                                     + sstop)), iplot)
                 Ao = wapp.getwapp()
 
     else:
@@ -771,14 +771,14 @@ def autopickstation(wfstream, pickparam):
     # create dictionary
     # for P phase
     phase = 'P'
-    phasepick = {'lpp': lpickP, 'epp': epickP, 'mpp': mpickP, 'spe': Perror, \
+    phasepick = {'lpp': lpickP, 'epp': epickP, 'mpp': mpickP, 'spe': Perror,
                  'snr': SNRP, 'snrdb': SNRPdB, 'weight': Pweight, 'fm': FM}
     picks = {phase: phasepick}
     # add P marker
     picks[phase]['marked'] = Pmarker
     # add S phase
     phase = 'S'
-    phasepick = {'lpp': lpickS, 'epp': epickS, 'mpp': mpickS, 'spe': Serror, \
+    phasepick = {'lpp': lpickS, 'epp': epickS, 'mpp': mpickS, 'spe': Serror,
                  'snr': SNRS, 'snrdb': SNRSdB, 'weight': Sweight, 'fm': None}
     picks[phase] = phasepick
     # add Wood-Anderson amplitude

pylot/core/pick/run_makeCF.py

@@ -6,8 +6,8 @@
    Only for test purposes!
 """
 
-from obspy.core import read 
+from obspy.core import read
-import matplotlib.pyplot as plt  
+import matplotlib.pyplot as plt
 import numpy as np
 from pylot.core.pick.CharFuns import CharacteristicFunction
 from pylot.core.pick.Picker import AutoPicking
@@ -56,7 +56,7 @@ def run_makeCF(project, database, event, iplot, station=None):
           st_copy = st.copy()
           #filter and taper data
           tr_filt = st[0].copy()
-          tr_filt.filter('bandpass', freqmin=bpz[0], freqmax=bpz[1], zerophase=False) 
+          tr_filt.filter('bandpass', freqmin=bpz[0], freqmax=bpz[1], zerophase=False)
           tr_filt.taper(max_percentage=0.05, type='hann')
           st_copy[0].data = tr_filt.data
           ##############################################################
@@ -120,8 +120,8 @@ def run_makeCF(project, database, event, iplot, station=None):
           #filter and taper data
           trH1_filt = H[0].copy()
           trH2_filt = H[1].copy()
-          trH1_filt.filter('bandpass', freqmin=bph[0], freqmax=bph[1], zerophase=False) 
+          trH1_filt.filter('bandpass', freqmin=bph[0], freqmax=bph[1], zerophase=False)
-          trH2_filt.filter('bandpass', freqmin=bph[0], freqmax=bph[1], zerophase=False) 
+          trH2_filt.filter('bandpass', freqmin=bph[0], freqmax=bph[1], zerophase=False)
           trH1_filt.taper(max_percentage=0.05, type='hann')
           trH2_filt.taper(max_percentage=0.05, type='hann')
           H_copy[0].data = trH1_filt.data
@@ -167,9 +167,9 @@ def run_makeCF(project, database, event, iplot, station=None):
           All1_filt = AllC[0].copy()
           All2_filt = AllC[1].copy()
           All3_filt = AllC[2].copy()
-          All1_filt.filter('bandpass', freqmin=bph[0], freqmax=bph[1], zerophase=False) 
+          All1_filt.filter('bandpass', freqmin=bph[0], freqmax=bph[1], zerophase=False)
-          All2_filt.filter('bandpass', freqmin=bph[0], freqmax=bph[1], zerophase=False) 
+          All2_filt.filter('bandpass', freqmin=bph[0], freqmax=bph[1], zerophase=False)
-          All3_filt.filter('bandpass', freqmin=bpz[0], freqmax=bpz[1], zerophase=False) 
+          All3_filt.filter('bandpass', freqmin=bpz[0], freqmax=bpz[1], zerophase=False)
           All1_filt.taper(max_percentage=0.05, type='hann')
           All2_filt.taper(max_percentage=0.05, type='hann')
           All3_filt.taper(max_percentage=0.05, type='hann')
@@ -209,19 +209,19 @@ def run_makeCF(project, database, event, iplot, station=None):
              plt.ylim([-1.5, 1.5])
              plt.xlabel('Time [s]')
              plt.ylabel('Normalized Counts')
-             plt.title('%s, %s, CF-SNR=%7.2f, CF-Slope=%12.2f' % (tr.stats.station, \
+             plt.title('%s, %s, CF-SNR=%7.2f, CF-Slope=%12.2f' % (tr.stats.station,
-                        tr.stats.channel, aicpick.getSNR(), aicpick.getSlope()))
+                                                                  tr.stats.channel, aicpick.getSNR(), aicpick.getSlope()))
              plt.suptitle(tr.stats.starttime)
-             plt.legend([p1, p2, p3, p4, p5], ['Data', 'HOS-CF', 'HOSAIC-CF', 'ARZ-CF', 'ARZAIC-CF']) 
+             plt.legend([p1, p2, p3, p4, p5], ['Data', 'HOS-CF', 'HOSAIC-CF', 'ARZ-CF', 'ARZAIC-CF'])
              #plot horizontal traces
              plt.figure(2)
              plt.subplot(2,1,1)
-             tsteph = tpredh / 4 
+             tsteph = tpredh / 4
              th1data = np.arange(0, trH1_filt.stats.npts / trH1_filt.stats.sampling_rate, trH1_filt.stats.delta)
              th2data = np.arange(0, trH2_filt.stats.npts / trH2_filt.stats.sampling_rate, trH2_filt.stats.delta)
              tarhcf = np.arange(0, len(arhcf.getCF()) * tsteph, tsteph) + cuttimes[0] + tdeth +tpredh
              p21, = plt.plot(th1data, trH1_filt.data/max(trH1_filt.data), 'k')
-             p22, = plt.plot(arhcf.getTimeArray(), arhcf.getCF()/max(arhcf.getCF()), 'r') 
+             p22, = plt.plot(arhcf.getTimeArray(), arhcf.getCF()/max(arhcf.getCF()), 'r')
              p23, = plt.plot(arhaiccf.getTimeArray(), arhaiccf.getCF()/max(arhaiccf.getCF()))
              plt.plot([aicarhpick.getpick(), aicarhpick.getpick()], [-1, 1], 'b')
              plt.plot([aicarhpick.getpick()-0.5, aicarhpick.getpick()+0.5], [1, 1], 'b')
@@ -238,10 +238,10 @@ def run_makeCF(project, database, event, iplot, station=None):
              plt.ylabel('Normalized Counts')
              plt.title([trH1_filt.stats.station, trH1_filt.stats.channel])
              plt.suptitle(trH1_filt.stats.starttime)
-             plt.legend([p21, p22, p23], ['Data', 'ARH-CF', 'ARHAIC-CF']) 
+             plt.legend([p21, p22, p23], ['Data', 'ARH-CF', 'ARHAIC-CF'])
              plt.subplot(2,1,2)
              plt.plot(th2data, trH2_filt.data/max(trH2_filt.data), 'k')
-             plt.plot(arhcf.getTimeArray(), arhcf.getCF()/max(arhcf.getCF()), 'r') 
+             plt.plot(arhcf.getTimeArray(), arhcf.getCF()/max(arhcf.getCF()), 'r')
              plt.plot(arhaiccf.getTimeArray(), arhaiccf.getCF()/max(arhaiccf.getCF()))
              plt.plot([aicarhpick.getpick(), aicarhpick.getpick()], [-1, 1], 'b')
              plt.plot([aicarhpick.getpick()-0.5, aicarhpick.getpick()+0.5], [1, 1], 'b')
@@ -271,7 +271,7 @@ def run_makeCF(project, database, event, iplot, station=None):
              plt.ylabel('Normalized Counts')
              plt.title([tr.stats.station, tr.stats.channel])
              plt.suptitle(trH1_filt.stats.starttime)
-             plt.legend([p31, p32], ['Data', 'AR3C-CF']) 
+             plt.legend([p31, p32], ['Data', 'AR3C-CF'])
              plt.subplot(3,1,2)
              plt.plot(th1data, trH1_filt.data/max(trH1_filt.data), 'k')
              plt.plot(ar3ccf.getTimeArray(), ar3ccf.getCF()/max(ar3ccf.getCF()), 'r')

pylot/core/pick/utils.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+# -*- coding: utf-8 -*-
 #
 # -*- coding: utf-8 -*-
 """
@@ -14,7 +15,7 @@ from obspy.core import Stream, UTCDateTime
 import warnings
 
 
-def earllatepicker(X, nfac, TSNR, Pick1, iplot=None):
+def earllatepicker(X, nfac, TSNR, Pick1, iplot=None, stealthMode = False):
     '''
     Function to derive earliest and latest possible pick after Diehl & Kissling (2009)
     as reasonable uncertainties. Latest possible pick is based on noise level,
@@ -43,7 +44,8 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None):
     LPick = None
     EPick = None
     PickError = None
-    #print 'earllatepicker: Get earliest and latest possible pick relative to most likely pick ...'
+    if stealthMode is False:
+        print 'earllatepicker: Get earliest and latest possible pick relative to most likely pick ...'
 
     x = X[0].data
     t = np.arange(0, X[0].stats.npts / X[0].stats.sampling_rate,
@@ -74,8 +76,9 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None):
     # if EPick stays NaN the signal window size will be doubled
     while np.isnan(EPick):
         if count > 0:
-            print("earllatepicker: Doubled signal window size %s time(s) "
+            if stealthMode is False:
-                  "because of NaN for earliest pick." %count)
+                print("\nearllatepicker: Doubled signal window size %s time(s) "
+                      "because of NaN for earliest pick." %count)
             isigDoubleWinStart = pis[-1] + 1
             isignalDoubleWin = np.arange(isigDoubleWinStart,
                                      isigDoubleWinStart + len(pis))
@@ -91,7 +94,7 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None):
         T0 = np.mean(np.diff(zc)) * X[0].stats.delta  # this is half wave length
         # T0/4 is assumed as time difference between most likely and earliest possible pick!
         EPick = Pick1 - T0 / 2
-            
+
 
     # get symmetric pick error as mean from earliest and latest possible pick
     # by weighting latest possible pick two times earliest possible pick
@@ -109,7 +112,7 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None):
                        markersize=14)
         plt.legend([p1, p2, p3, p4, p5],
                    ['Data', 'Noise Window', 'Signal Window', 'Noise Level',
-                    'Zero Crossings'], \
+                    'Zero Crossings'],
                    loc='best')
         plt.plot([t[0], t[int(len(t)) - 1]], [-nlevel, -nlevel], '--k')
         plt.plot([Pick1, Pick1], [max(x), -max(x)], 'b', linewidth=2)
@@ -182,10 +185,10 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
         i = 0
         for j in range(ipick[0][1], ipick[0][len(t[ipick]) - 1]):
             i = i + 1
-            if xraw[j - 1] <= 0 and xraw[j] >= 0:
+            if xraw[j - 1] <= 0 <= xraw[j]:
                 zc1.append(t[ipick][i])
                 index1.append(i)
-            elif xraw[j - 1] > 0 and xraw[j] <= 0:
+            elif xraw[j - 1] > 0 >= xraw[j]:
                 zc1.append(t[ipick][i])
                 index1.append(i)
             if len(zc1) == 3:
@@ -224,10 +227,10 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
         i = 0
         for j in range(ipick[0][1], ipick[0][len(t[ipick]) - 1]):
             i = i + 1
-            if xfilt[j - 1] <= 0 and xfilt[j] >= 0:
+            if xfilt[j - 1] <= 0 <= xfilt[j]:
                 zc2.append(t[ipick][i])
                 index2.append(i)
-            elif xfilt[j - 1] > 0 and xfilt[j] <= 0:
+            elif xfilt[j - 1] > 0 >= xfilt[j]:
                 zc2.append(t[ipick][i])
                 index2.append(i)
             if len(zc2) == 3:
@@ -262,15 +265,15 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
         if P1 is not None and P2 is not None:
             if P1[0] < 0 and P2[0] < 0:
                 FM = 'D'
-            elif P1[0] >= 0 and P2[0] < 0:
+            elif P1[0] >= 0 > P2[0]:
                 FM = '-'
-            elif P1[0] < 0 and P2[0] >= 0:
+            elif P1[0] < 0 <= P2[0]:
                 FM = '-'
             elif P1[0] > 0 and P2[0] > 0:
                 FM = 'U'
-            elif P1[0] <= 0 and P2[0] > 0:
+            elif P1[0] <= 0 < P2[0]:
                 FM = '+'
-            elif P1[0] > 0 and P2[0] <= 0:
+            elif P1[0] > 0 >= P2[0]:
                 FM = '+'
 
         print ("fmpicker: Found polarity %s" % FM)
@@ -285,7 +288,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
             p3, = plt.plot(zc1, np.zeros(len(zc1)), '*g', markersize=14)
             p4, = plt.plot(t[islope1], datafit1, '--g', linewidth=2)
             plt.legend([p1, p2, p3, p4],
-                       ['Pick', 'Slope Window', 'Zero Crossings', 'Slope'], \
+                       ['Pick', 'Slope Window', 'Zero Crossings', 'Slope'],
                        loc='best')
             plt.text(Pick + 0.02, max(xraw) / 2, '%s' % FM, fontsize=14)
             ax = plt.gca()
@@ -493,9 +496,9 @@ 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 +535,40 @@ 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]')
@@ -579,8 +582,8 @@ def wadaticheck(pickdic, dttolerance, iplot):
 def checksignallength(X, pick, TSNR, minsiglength, nfac, minpercent, iplot):
     '''
     Function to detect spuriously picked noise peaks.
-    Uses RMS trace of all 3 components (if available) to determine, 
+    Uses RMS trace of all 3 components (if available) to determine,
-    how many samples [per cent] after P onset are below certain 
+    how many samples [per cent] after P onset are below certain
     threshold, calculated from noise level times noise factor.
 
     : param: X, time series (seismogram)
@@ -612,7 +615,7 @@ 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 +642,7 @@ 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!")
@@ -649,15 +652,15 @@ 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]]], \
+        p4, = plt.plot([t[isignal[0]], t[isignal[len(isignal)-1]]],
-                        [minsiglevel, minsiglevel], 'g', linewidth=2)
+                       [minsiglevel, minsiglevel], 'g', linewidth=2)
         p5, = plt.plot([pick, pick], [min(rms), max(rms)], 'b', linewidth=2)
-        plt.legend([p1, p2, p3, p4, p5], ['RMS Data', 'RMS Noise Window', \
+        plt.legend([p1, p2, p3, p4, p5], ['RMS Data', 'RMS Noise Window',
-                    'RMS Signal Window', 'Minimum Signal Level', \
+                                          'RMS Signal Window', 'Minimum Signal Level',
-                    'Onset'], loc='best')
+                                          'Onset'], loc='best')
         plt.xlabel('Time [s] since %s' % X[0].stats.starttime)
         plt.ylabel('Counts')
         plt.title('Check for Signal Length, Station %s' % X[0].stats.station)
@@ -729,32 +732,32 @@ 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', \
+        p3, = plt.plot([0, len(Ppicks) - 1], [pmedian, pmedian], 'g',
-                        linewidth=2)
+                       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')
-        plt.legend([p1, p2, p3], ['Skipped P Picks', 'Good P Picks', 'Median'], \
+        plt.legend([p1, p2, p3], ['Skipped P Picks', 'Good P Picks', 'Median'],
-                    loc='best')
+                   loc='best')
         plt.title('Check P Onsets')
         plt.show()
         raw_input()
@@ -789,37 +792,37 @@ 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)
 
@@ -899,29 +902,29 @@ 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')
         plt.plot(tn, ndat[0].data / max(ndat[0].data) + 2, 'k')
         plt.plot(tn[isignal], ndat[0].data[isignal] / max(ndat[0].data) + 2, 'r')
-        plt.plot([tz[isignal[0]], tz[isignal[len(isignal) - 1]]], \
+        plt.plot([tz[isignal[0]], tz[isignal[len(isignal) - 1]]],
-                  [minsiglevel / max(z), minsiglevel / max(z)], 'g', \
+                 [minsiglevel / max(z), minsiglevel / max(z)], 'g',
-                   linewidth=2)
+                 linewidth=2)
         plt.xlabel('Time [s] since %s' % zdat[0].stats.starttime)
         plt.ylabel('Normalized Counts')
-        plt.yticks([0, 1, 2], [zdat[0].stats.channel, edat[0].stats.channel, \
+        plt.yticks([0, 1, 2], [zdat[0].stats.channel, edat[0].stats.channel,
-                                        ndat[0].stats.channel])
+                               ndat[0].stats.channel])
         plt.title('CheckZ4S, Station %s' % zdat[0].stats.station)
         plt.show()
         raw_input()

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/read/io.py

@@ -73,8 +73,8 @@ def readPILOTEvent(phasfn=None, locfn=None, authority_id=None, **kwargs):
 
         stations = [stat for stat in phases['stat'][0:-1:3]]
 
-        event = createEvent(eventDate, loccinfo, None, 'earthquake', eventNum,
+        event = createEvent(eventDate, loccinfo, etype='earthquake', resID=eventNum,
-                            authority_id)
+                            authority_id=authority_id)
 
         lat = float(loc['LAT'])
         lon = float(loc['LON'])
@@ -130,7 +130,7 @@ def readPILOTEvent(phasfn=None, locfn=None, authority_id=None, **kwargs):
         event.magnitudes.append(magnitude)
         return event
 
-    except AttributeError, e:
+    except AttributeError as e:
         raise AttributeError('{0} - Matlab LOC files {1} and {2} contains \
                               insufficient data!'.format(e, phasfn, locfn))
 

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
 
@@ -23,4 +24,4 @@ class Test(unittest.TestCase):
 
 if __name__ == "__main__":
     #import sys;sys.argv = ['', 'Test.testName']
-    unittest.main()
+    unittest.main()

pylot/core/util/testWidgets.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 Created on 10.11.2014
 
@@ -15,4 +16,4 @@ class Test(unittest.TestCase):
 
 if __name__ == "__main__":
     #import sys;sys.argv = ['', 'Test.testName']
-    unittest.main()
+    unittest.main()

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 -*-
 

pylot/core/util/widgets.py

@@ -814,9 +814,10 @@ class PropertiesDlg(QDialog):
             if values is not None:
                 self.setValues(values)
 
-    def setValues(self, tabValues):
+    @staticmethod
+    def setValues(tabValues):
         settings = QSettings()
-        for setting, value in tabValues.iteritems():
+        for setting, value in tabValues.items():
             settings.setValue(setting, value)
         settings.sync()
 

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
@@ -8,4 +9,4 @@ app = QApplication(sys.argv)
 
 win = PropertiesDlg()
 win.show()
-app.exec_()
+app.exec_()

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()