Merge branch 'develop' of ariadne.geophysik.ruhr-uni-bochum.de:/data/git/pylot into develop

pylot/core/active/activeSeismoPick.py

@@ -19,7 +19,8 @@ class Survey(object):
             self.setParametersForShots()
         self._removeAllEmptyTraces()
         self._updateShots()
-
+        self.setArtificialPick(0, 0) # artificial pick at source origin
+        
     def _generateSurvey(self):
         from obspy.core import read
 
@@ -34,17 +35,23 @@ class Survey(object):
             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)
@@ -121,14 +128,13 @@ 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)    
-                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
@@ -138,6 +144,22 @@ 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)
@@ -195,7 +217,7 @@ 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,
@@ -236,7 +258,7 @@ class Survey(object):
             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)
@@ -253,14 +275,87 @@ 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, 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)
@@ -268,38 +363,50 @@ 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}
 
-        return ax, region
+        if refreshPlot is False:
+            ax = self.createPlot(dist, pick, color[colorByVal], label = '%s'%colorByVal)
+            region = regions(ax, self)
+            ax.legend()
+            return ax, region
+        elif refreshPlot is True:
+            ax = self.createPlot(dist, pick, color[colorByVal], label = '%s'%colorByVal, ax = ax)
+            ax.legend()
+            return ax
 
-    def createPlot(self, dist, pick, inkByVal, label):
+    def createPlot(self, dist, pick, inkByVal, label, ax = None):
         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)
+            fig = ax.scatter(dist, pick, cmap = cm, c = inkByVal, s = 5, edgecolors = 'none', label = label)
-        cbar.set_label(label)
+            cbar = plt.colorbar(fig, fraction = 0.05)
-        plt.title('Plot of all Picks')
+            cbar.set_label(label)
-        plt.xlabel('Distance [m]')
+            plt.title('Plot of all Picks')
-        plt.ylabel('Time [s]')
+            plt.xlabel('Distance [m]')
+            plt.ylabel('Time [s]')
+        else:
+            ax.scatter(dist, pick, cmap = cm, c = inkByVal, s = 5, edgecolors = 'none', label = label)
 
         return ax
 

pylot/core/active/fmtomo2vtk.py

@@ -128,7 +128,12 @@ def rays2VTK(fnin, fdirout = './vtk_files/', nthPoint = 50):
         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

@@ -1,107 +0,0 @@
-# -*- coding: utf-8 -*-
-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

@@ -491,7 +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

pylot/core/active/seismicArrayPreperation.py

@@ -1,666 +0,0 @@
-# -*- coding: utf-8 -*-
-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 = {}
@@ -132,17 +131,27 @@ 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))
@@ -217,7 +226,7 @@ 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):
         '''
@@ -240,7 +249,7 @@ 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 ? ##########
         '''
@@ -305,16 +314,17 @@ class SeismicShot(object):
                      '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):
         '''
@@ -464,7 +474,10 @@ class SeismicShot(object):
         #    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
@@ -475,7 +488,14 @@ class SeismicShot(object):
         #        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
@@ -580,7 +600,39 @@ 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 not traceID 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
 
@@ -588,33 +640,48 @@ class SeismicShot(object):
         stime = getGlobalTimes(stream)[0]
         timeaxis = prepTimeAxis(stime, stream[0])
         timeaxis -= stime
+        
+        ax = self.traces4plot[traceID]['ax1']
 
-        plt.interactive('True')
+        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')
+                 [min(np.minimum(hoscf.getCF(), aiccf.getCF())), 
-        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):
         '''
@@ -632,7 +699,6 @@ 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
@@ -641,13 +707,13 @@ 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)
 
@@ -671,8 +737,8 @@ class SeismicShot(object):
         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
 
@@ -682,27 +748,32 @@ 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')
 
@@ -710,14 +781,28 @@ 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

@@ -1,49 +1,191 @@
 # -*- 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.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
+
+    '''
+    def __init__(self, ax, survey):
         self.ax = ax
-        self.shot_dict = shot_dict
+        self.survey = survey
+        self.shot_dict = self.survey.getShotDict()
         self._x0 = []
         self._y0 = []
         self._x1 = []
         self._y1 = []
+        self._polyx = []
+        self._polyy = []
+        self._allpicks = None
         self.shots_found = {}
         self.shots_for_deletion = {}
+        self._generateList()
 
-    def _onselect(self, eclick, erelease):
+    def _onselect_clicks(self, eclick, erelease):
-        'eclick and erelease are matplotlib events at press and release'                                                                                            #print ' startposition : (%f, %f)' % (eclick.xdata, eclick.ydata)
+        'eclick and erelease are matplotlib events at press and release'
-        #print ' endposition   : (%f, %f)' % (erelease.xdata, erelease.ydata)
+        #print ' startposition : (%f, %f)' % (eclick.xdata, eclick.ydata)     
-        print 'region selected x0, y0 = (%3s, %3s), x1, y1 = (%3s, %3s)'%(eclick.xdata, eclick.ydata, erelease.xdata, erelease.ydata)
+        #print ' endposition   : (%f, %f)' % (erelease.xdata, erelease.ydata)        
+        print 'region selected x0, y0 = (%3s, %3s), x1, y1 = (%3s, %3s)'%(eclick.xdata, eclick.ydata, 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)
-        self._x0.append(x0)
+
-        self._x1.append(x1)
+        shots, numtraces = self.findTracesInShotDict((x0, x1), (y0, y1))
-        self._y0.append(y0)
+        print('Found %d traces in rectangle: %s' %(numtraces, shots))
-        self._y1.append(y1)
+
-        self.markCurrentRegion(x0, x1, y0, y1)
+        key = self.getKey()
+        self.shots_found[key] = {'shots': shots,
+                                 'selection': 'rect',
+                                 'xvalues': (x0, x1),
+                                 'yvalues': (y0, y1)}
+        self.markRectangle((x0, x1), (y0, y1), key)
+        
+    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()
+
+    def getKey(self):
+        if self.shots_found.keys() == []:
+            key = 1
+        else:
+            key = max(self.shots_found.keys()) + 1
+        return key
+
+    def drawPolyLine(self):
+        x = self._polyx
+        y = self._polyy
+        if len(x) >= 2 and len(y) >= 2:
+            plt.plot(x[-2:], y[-2:], 'k')
+
+    def drawLastPolyLine(self):
+        x = self._polyx
+        y = self._polyy
+        if len(x) >= 2 and len(y) >= 2:
+            plt.plot((x[-1], x[0]), (y[-1], y[0]), 'k')
+
+    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}
+
+        print('Found %d traces in polygon: %s' %(numtraces, shots))
+
+    def markPolygon(self, x, y, key = None, color = 'grey', alpha = 0.1, linewidth = 1):
+        from matplotlib.patches import Polygon
+        poly = Polygon(np.array(zip(x, y)), color = color, alpha = alpha, lw = linewidth)
+        self.ax.add_patch(poly)
+        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()
+
+    def disconnectPoly(self):
+        self.ax.figure.canvas.mpl_disconnect(self._cid)
+        del self._cid
+        self.finishPolygon()
+        self._lasso.disconnect_events()
+        print('disconnected poly selection\n')
+
+    def disconnectRect(self):
+        self.ax.figure.canvas.mpl_disconnect(self._cid)
+        del self._cid
+        self._rectangle.disconnect_events()
+        print('disconnected rectangle selection\n')
 
     def chooseRectangles(self):
+        '''
+        Activates matplotlib widget RectangleSelector.
+        '''
         from matplotlib.widgets import RectangleSelector
 
-        print 'Select rectangle is active'
+        print('Select rectangle is active')
-        return RectangleSelector(self.ax, self._onselect)
+        self._cid = self.ax.figure.canvas.mpl_connect('button_press_event', self._onpress)
+        self._rectangle = RectangleSelector(self.ax, self._onselect_clicks)
+        return self._rectangle
 
-    def _getx0(self):
+    def choosePolygon(self):
-        return self._x0
+        '''
+        Activates matplotlib widget LassoSelector.
+        '''
+        from matplotlib.widgets import LassoSelector
 
-    def _getx1(self):
+        print('Select polygon is active')
-        return self._x1
+        self._cid = self.ax.figure.canvas.mpl_connect('button_press_event', self._onpress)        
+        self._lasso = LassoSelector(self.ax, self._onselect_verts)
+        return self._lasso
+    
+    def deselectLastSelection(self):
+        if self.shots_found.keys() == []:
+            print('No selection found.')
+            return
+        key = max(self.shots_found.keys())
+        self.deselectSelection(key)
 
-    def _gety0(self):
+    def deselectSelection(self, key, color = 'green', alpha = 0.1):
-        return self._y0
+        if not key in self.shots_found.keys():
+            print('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)
+        print('Deselected selection number %d'% key)
+        return
 
-    def _gety1(self):
+    def _generateList(self):
-        return self._y1
+        allpicks = []
+        for shot in self.shot_dict.values():
+            for traceID in shot.getTraceIDlist():                           
+                allpicks.append((shot.getDistance(traceID), shot.getPickIncludeRemoved(traceID),
+                                 shot.getShotnumber(), traceID, shot.getFlag(traceID)))
+        allpicks.sort()
+        self._allpicks = allpicks
 
     def getShotDict(self):
         return self.shot_dict
@@ -51,119 +193,216 @@ class regions(object):
     def getShotsForDeletion(self):
         return self.shots_for_deletion
 
-    def findTracesInShotDict(self, picks = 'normal'):
+    def findTracesInPoly(self, x, y, picks = 'normal', highlight = True):
-        '''
+        def dotproduct(v1, v2):
-        Returns traces corresponding to a certain area in a plot with all picks over the distances.
+            return sum((a*b) for a, b in zip(v1, v2))
-        '''
-        print "findTracesInShotDict: Searching for marked traces in the shot dictionary... "
 
-        for shot in self.shot_dict.values():
+        def getlength(v):
-            whichpicks = {'normal': shot.getPick,
+            return math.sqrt(dotproduct(v, v))
-                          'includeCutOut': shot.getPick_backup}
+
-            for index in range(len(self._getx1())):
+        def getangle(v1, v2):
-                distancebin = (self._getx0()[index], self._getx1()[index])
+            return np.rad2deg(math.acos(dotproduct(v1, v2) / (getlength(v1) * getlength(v2))))
-                pickbin = (self._gety0()[index], self._gety1()[index])
+
-                if shot.getTraceIDs4Dist(distancebin = distancebin) is not None:
+        def insidePoly(x, y, pickX, pickY):
-                    for traceID in shot.getTraceIDs4Dist(distancebin = distancebin):
+            angle = 0
-                        if pickbin[0] < whichpicks[picks](traceID) < pickbin[1]:
+            epsilon = 10e-8
+            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:
+            print('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 not shotnumber 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 not shotnumber 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.set_ylim(shot.getCut())
 
-    def plotTracesInRegion(self):
+    def highlightAllRegions(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 plotTracesInRegions(self, 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)
+            print('No picks defined in that region(s)')
 
-    def plotTracesInRegion_withCutOutTraces(self):
+    def setActiveRegionsForDeletion(self):
-        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)
 
+        for key in keys:
+            for shotnumber in self.shots_found[key]['shots'].keys():
+                if not shotnumber in self.shots_for_deletion:
+                    self.shots_for_deletion[shotnumber] = []
+                for traceID in self.shots_found[key]['shots'][shotnumber]:
+                    if not traceID in self.shots_for_deletion[shotnumber]:
+                        self.shots_for_deletion[shotnumber].append(traceID)
+            self.deselectSelection(key, color = 'red', alpha = 0.2)
 
-    def setCurrentRegionsForDeletion(self):
+        print 'Set region(s) %s for deletion'%keys
-        # if len(self.shots_found) == 0:
-        self.findTracesInShotDict()
 
-        for shotnumber in self.shots_found:
+    def markAllActiveRegions(self):
-            if not shotnumber in self.shots_for_deletion:
+        for key in self.shots_found.keys():
-                self.shots_for_deletion[shotnumber] = []
+            if self.shots_found[key]['selection'] == 'rect':
-            for traceID in self.shots_found[shotnumber]:
+                self.markRectangle(self.shots_found[key]['xvalues'],
-                if not traceID in self.shots_for_deletion[shotnumber]:
+                                   self.shots_found[key]['yvalues'], key = key)
-                    self.shots_for_deletion[shotnumber].append(traceID)
+            if self.shots_found[key]['selection'] == 'poly':
-        self.markAllRegions(color = 'red')
+                self.markPolygon(self.shots_found[key]['xvalues'],
-        print 'Marked regions for deletion'
+                                 self.shots_found[key]['yvalues'], key = key)
+            
 
-    def markAllRegions(self, color = 'grey'):
+    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
 
-        for index in range(len(self._getx0())):
+        self.ax.add_patch(Rectangle((x0, y0), (x1 - x0), (y1 - y0),
-            x0 = self._getx0()[index]
+                                    alpha = alpha, facecolor = color, linewidth = linewidth))
-            y0 = self._gety0()[index]
+        if key is not None: 
-            x1 = self._getx1()[index]
+            self.ax.text((x0 + (x1 - x0) / 2), (y0 + (y1 - y0) / 2), str(key))
-            y1 = self._gety1()[index]
+        self.drawFigure()
 
-            self.ax.add_patch(Rectangle((x0, y0), (x1 - x0), (y1 - y0), alpha=0.5, facecolor = color))
+    def refreshFigure(self):
-            self.refreshFigure()
+        print('Refreshing figure...')
+        self.ax.clear()
+        self.ax = self.survey.plotAllPicks(ax = self.ax, refreshPlot = True)
+        self.markAllActiveRegions()
+        self.drawFigure()
+        print('Done!')
 
-    def markCurrentRegion(self, x0, x1, y0, y1, color = 'grey'):
+    def clearShotsForDeletion(self):
-        from matplotlib.patches import Rectangle
+        '''
-
+        Clears the list of shots marked for deletion.
-        self.ax.add_patch(Rectangle((x0, y0), (x1 - x0), (y1 - y0), alpha=0.1, facecolor = color))
+        '''
-        self.refreshFigure()
+        self.shots_for_deletion = {}
+        print('Cleared all shots that were set for deletion.')
 
+    def getShotsForDeletion(self):
+        return self.shots_for_deletion
+            
     def deleteMarkedPicks(self):
+        '''
+        Deletes all shots set for deletion.
+        '''
+        if len(self.getShotsForDeletion()) is 0:
+            print('No shots set for deletion.')
+            return
+
         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 drawFigure(self):
         plt.draw()

pylot/core/active/surveyUtils.py

@@ -73,7 +73,7 @@ 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)

pylot/core/pick/CharFuns.py

@@ -25,7 +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.
@@ -62,6 +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
@@ -135,6 +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)
@@ -219,7 +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)
@@ -257,11 +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)
 

pylot/core/pick/utils.py

@@ -15,7 +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,
@@ -44,7 +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,
@@ -75,8 +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("\nearllatepicker: 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))