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[task] reformatting activeSeismoPick and editing pool mapping to work properly

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This commit is contained in:
Sebastian Wehling-Benatelli 2016-05-23 11:53:22 +02:00
parent 3cc77f4868
commit 41b7ca6968
2 changed files with 92 additions and 59 deletions
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140
pylot/core/active/activeSeismoPick.py
View File

@ -4,6 +4,7 @@ import numpy as np
from pylot.core.active import seismicshot from pylot.core.active import seismicshot
from pylot.core.active.surveyUtils import cleanUp from pylot.core.active.surveyUtils import cleanUp
class Survey(object): class Survey(object):
def __init__(self, path, sourcefile, receiverfile, useDefaultParas=False): def __init__(self, path, sourcefile, receiverfile, useDefaultParas=False):
''' '''
@ -21,13 +22,13 @@ class Survey(object):
self._sourcefile = sourcefile self._sourcefile = sourcefile
self._obsdir = path self._obsdir = path
self._generateSurvey() self._generateSurvey()
self._initiateFilenames() self._initiate_fnames()
if useDefaultParas == True: if useDefaultParas == True:
self.setParametersForAllShots() self.setParametersForAllShots()
self._removeAllEmptyTraces() self._removeAllEmptyTraces()
self._updateShots() self._updateShots()
def _initiateFilenames(self): def _initiate_fnames(self):
for shot in self.data.values(): for shot in self.data.values():
shot.setRecfile(self.getPath() + self.getReceiverfile()) shot.setRecfile(self.getPath() + self.getReceiverfile())
shot.setSourcefile(self.getPath() + self.getSourcefile()) shot.setSourcefile(self.getPath() + self.getSourcefile())
@ -74,7 +75,7 @@ class Survey(object):
but were set in the input files. but were set in the input files.
''' '''
logfile = 'updateShots.out' logfile = 'updateShots.out'
count = 0; count = 0
countTraces = 0 countTraces = 0
for shot in self.data.values(): for shot in self.data.values():
del_traceIDs = shot.updateTraceList() del_traceIDs = shot.updateTraceList()
@ -93,15 +94,8 @@ class Survey(object):
"on removed traces." % (logfile)) "on removed traces." % (logfile))
outfile.close() outfile.close()
def setArtificialPick(self, traceID, pick): def setParametersForAllShots(self, cutwindow=(0, 0.2), tmovwind=0.3,
''' tsignal=0.03, tgap=0.0007):
Sets an artificial pick for a traceID of all shots in the survey object.
(Commonly used to generate a travel time t = 0 at the source origin)
'''
for shot in self.data.values():
shot.setPick(traceID, pick)
def setParametersForAllShots(self, cutwindow=(0, 0.2), tmovwind=0.3, tsignal=0.03, tgap=0.0007):
if (cutwindow == (0, 0.2) and tmovwind == 0.3 and if (cutwindow == (0, 0.2) and tmovwind == 0.3 and
tsignal == 0.03 and tgap == 0.0007): tsignal == 0.03 and tgap == 0.0007):
print ("Warning: Standard values used for " print ("Warning: Standard values used for "
@ -136,8 +130,10 @@ class Survey(object):
if not shot in diffs.keys(): if not shot in diffs.keys():
diffs[shot] = {} diffs[shot] = {}
for traceID in shot.getTraceIDlist(): for traceID in shot.getTraceIDlist():
if shot.getPickFlag(traceID) == 1 and shot.getManualPickFlag(traceID) == 1: if shot.getPickFlag(traceID) == 1 and shot.getManualPickFlag(
diffs[shot][traceID] = shot.getPick(traceID) - shot.getManualPick(traceID) traceID) == 1:
diffs[shot][traceID] = shot.getPick(
traceID) - shot.getManualPick(traceID)
return diffs return diffs
def plotDiffs(self): def plotDiffs(self):
@ -146,14 +142,15 @@ class Survey(object):
difference between automatic and manual pick. difference between automatic and manual pick.
''' '''
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
diffs = []; diffs = []
dists = []; dists = []
mpicks = []; mpicks = []
picks = [] picks = []
diffsDic = self.getDiffsFromManual() diffsDic = self.getDiffsFromManual()
for shot in self.data.values(): for shot in self.data.values():
for traceID in shot.getTraceIDlist(): for traceID in shot.getTraceIDlist():
if shot.getPickFlag(traceID) == 1 and shot.getManualPickFlag(traceID) == 1: if shot.getPickFlag(traceID) == 1 and shot.getManualPickFlag(
traceID) == 1:
dists.append(shot.getDistance(traceID)) dists.append(shot.getDistance(traceID))
mpicks.append(shot.getManualPick(traceID)) mpicks.append(shot.getManualPick(traceID))
picks.append(shot.getPick(traceID)) picks.append(shot.getPick(traceID))
@ -165,13 +162,16 @@ class Survey(object):
fig = plt.figure() fig = plt.figure()
ax = fig.add_subplot(111) ax = fig.add_subplot(111)
sc_a = ax.scatter(dists, picks, c='0.5', s=10, edgecolors='none', label=labela, alpha=0.3) sc_a = ax.scatter(dists, picks, c='0.5', s=10, edgecolors='none',
sc = ax.scatter(dists, mpicks, c=diffs, s=5, edgecolors='none', label=labelm) label=labela, alpha=0.3)
sc = ax.scatter(dists, mpicks, c=diffs, s=5, edgecolors='none',
label=labelm)
cbar = plt.colorbar(sc, fraction=0.05) cbar = plt.colorbar(sc, fraction=0.05)
cbar.set_label(labelm) cbar.set_label(labelm)
ax.set_xlabel('Distance [m]') ax.set_xlabel('Distance [m]')
ax.set_ylabel('Time [s]') ax.set_ylabel('Time [s]')
ax.text(0.5, 0.95, 'Plot of all MANUAL picks', transform=ax.transAxes, horizontalalignment='center') ax.text(0.5, 0.95, 'Plot of all MANUAL picks', transform=ax.transAxes,
horizontalalignment='center')
plt.legend() plt.legend()
def plotHist(self, nbins=20, ax=None): def plotHist(self, nbins=20, ax=None):
@ -186,14 +186,18 @@ class Survey(object):
ax = fig.add_subplot(111) ax = fig.add_subplot(111)
for shot in self.data.values(): for shot in self.data.values():
for traceID in shot.getTraceIDlist(): for traceID in shot.getTraceIDlist():
if shot.getPickFlag(traceID) == 1 and shot.getManualPickFlag(traceID) == 1: if shot.getPickFlag(traceID) == 1 and shot.getManualPickFlag(
traceID) == 1:
diffs.append(self.getDiffsFromManual()[shot][traceID]) diffs.append(self.getDiffsFromManual()[shot][traceID])
hist = plt.hist(diffs, nbins, histtype='step', normed=True, stacked=True) hist = plt.hist(diffs, nbins, histtype='step', normed=True,
plt.title('Histogram of the differences between automatic and manual pick') stacked=True)
plt.title(
'Histogram of the differences between automatic and manual pick')
plt.xlabel('Difference in time (auto - manual) [s]') plt.xlabel('Difference in time (auto - manual) [s]')
return diffs return diffs
def pickAllShots(self, vmin=333, vmax=5500, folm=0.6, HosAic='hos', aicwindow=(10, 0)): def pickAllShots(self, vmin=333, vmax=5500, folm=0.6, HosAic='hos',
aicwindow=(10, 0)):
''' '''
Automatically pick all traces of all shots of the survey. Automatically pick all traces of all shots of the survey.
@ -211,11 +215,11 @@ class Survey(object):
''' '''
from datetime import datetime from datetime import datetime
starttime = datetime.now() starttime = datetime.now()
count = 0; count = 0
tpicksum = starttime - starttime tpicksum = starttime - starttime
for shot in self.data.values(): for shot in self.data.values():
tstartpick = datetime.now(); tstartpick = datetime.now()
shot.setVmin(vmin) shot.setVmin(vmin)
shot.setVmax(vmax) shot.setVmax(vmax)
count += 1 count += 1
@ -235,7 +239,8 @@ class Survey(object):
ntraces = self.countAllTraces() ntraces = self.countAllTraces()
pickedtraces = self.countAllPickedTraces() pickedtraces = self.countAllPickedTraces()
print('Picked %s / %s traces (%d %%)\n' print('Picked %s / %s traces (%d %%)\n'
% (pickedtraces, ntraces, float(pickedtraces) / float(ntraces) * 100.)) % (pickedtraces, ntraces,
float(pickedtraces) / float(ntraces) * 100.))
def setSNR(self): def setSNR(self):
for shot in self.data.values(): for shot in self.data.values():
@ -373,8 +378,11 @@ class Survey(object):
pickedTraces += 1 pickedTraces += 1
info_dict[shot.getShotnumber()] = {'numtraces': numtraces, info_dict[shot.getShotnumber()] = {'numtraces': numtraces,
'picked traces': [pickedTraces, 'picked traces': [pickedTraces,
'%2.2f %%' % (float(pickedTraces) / '%2.2f %%' % (
float(numtraces) * 100)], float(
pickedTraces) /
float(
numtraces) * 100)],
'mean SNR': np.mean(snrlist), 'mean SNR': np.mean(snrlist),
'mean distance': np.mean(dist)} 'mean distance': np.mean(dist)}
@ -388,10 +396,12 @@ class Survey(object):
if shot.getShotnumber() == shotnumber: if shot.getShotnumber() == shotnumber:
return shot return shot
def exportFMTOMO(self, directory='FMTOMO_export', sourcefile='input_sf.in', ttFileExtension='.tt'): def exportFMTOMO(self, directory='FMTOMO_export', sourcefile='input_sf.in',
ttFileExtension='.tt'):
''' '''
Exports all picks into a directory as travel time files readable by FMTOMO obsdata. Exports all picks into a directory as travel time files readable by FMTOMO obsdata.
''' '''
def getAngle(distance): def getAngle(distance):
PI = np.pi PI = np.pi
R = 6371. R = 6371.
@ -400,18 +410,20 @@ class Survey(object):
count = 0 count = 0
fmtomo_factor = 1000 # transforming [m/s] -> [km/s] fmtomo_factor = 1000 # transforming [m/s] -> [km/s]
LatAll = []; LatAll = []
LonAll = []; LonAll = []
DepthAll = [] DepthAll = []
srcfile = open(directory + '/' + sourcefile, 'w') srcfile = open(directory + '/' + sourcefile, 'w')
srcfile.writelines('%10s\n' % len(self.data)) # number of sources srcfile.writelines('%10s\n' % len(self.data)) # number of sources
for shotnumber in self.getShotlist(): for shotnumber in self.getShotlist():
shot = self.getShotForShotnumber(shotnumber) shot = self.getShotForShotnumber(shotnumber)
ttfilename = str(shotnumber) + ttFileExtension # filename of travel time file for this shot ttfilename = str(
shotnumber) + ttFileExtension # filename of travel time file for this shot
(x, y, z) = shot.getSrcLoc() # getSrcLoc returns (x, y, z) (x, y, z) = shot.getSrcLoc() # getSrcLoc returns (x, y, z)
srcfile.writelines('%10s %10s %10s\n' % (getAngle(y), getAngle(x), (-1) * z)) # transform to lat, lon, depth srcfile.writelines('%10s %10s %10s\n' % (
LatAll.append(getAngle(y)); getAngle(y), getAngle(x), (-1) * z)) # transform to lat, lon, depth
LonAll.append(getAngle(x)); LatAll.append(getAngle(y))
LonAll.append(getAngle(x))
DepthAll.append((-1) * z) DepthAll.append((-1) * z)
srcfile.writelines('%10s\n' % 1) srcfile.writelines('%10s\n' % 1)
srcfile.writelines('%10s %10s %10s\n' % (1, 1, ttfilename)) srcfile.writelines('%10s %10s %10s\n' % (1, 1, ttfilename))
@ -424,9 +436,10 @@ class Survey(object):
pick = shot.getPick(traceID) * fmtomo_factor pick = shot.getPick(traceID) * fmtomo_factor
delta = shot.getSymmetricPickError(traceID) * fmtomo_factor delta = shot.getSymmetricPickError(traceID) * fmtomo_factor
(x, y, z) = shot.getRecLoc(traceID) (x, y, z) = shot.getRecLoc(traceID)
ttfile.writelines('%20s %20s %20s %10s %10s\n' % (getAngle(y), getAngle(x), (-1) * z, pick, delta)) ttfile.writelines('%20s %20s %20s %10s %10s\n' % (
LatAll.append(getAngle(y)); getAngle(y), getAngle(x), (-1) * z, pick, delta))
LonAll.append(getAngle(x)); LatAll.append(getAngle(y))
LonAll.append(getAngle(x))
DepthAll.append((-1) * z) DepthAll.append((-1) * z)
count += 1 count += 1
ttfile.close() ttfile.close()
@ -486,19 +499,24 @@ class Survey(object):
if index <= figPerSubplot: if index <= figPerSubplot:
ax = fig.add_subplot(rows, columns, index) ax = fig.add_subplot(rows, columns, index)
if mode == '3d': if mode == '3d':
self.getShot(shotnumber).matshow(ax=ax, colorbar=False, annotations=True, legend=False) self.getShot(shotnumber).matshow(ax=ax, colorbar=False,
annotations=True,
legend=False)
elif mode == '2d': elif mode == '2d':
self.getShot(shotnumber).plot2dttc(ax) self.getShot(shotnumber).plot2dttc(ax)
self.getShot(shotnumber).plotmanual2dttc(ax) self.getShot(shotnumber).plotmanual2dttc(ax)
index += 1 index += 1
if index > figPerSubplot: if index > figPerSubplot:
fig.subplots_adjust(left=0, bottom=0, right=1, top=1, wspace=0, hspace=0) fig.subplots_adjust(left=0, bottom=0, right=1, top=1, wspace=0,
hspace=0)
fig = plt.figure() fig = plt.figure()
index = 1 index = 1
fig.subplots_adjust(left=0, bottom=0, right=1, top=1, wspace=0, hspace=0) 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): 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). 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) Picks can be checked and removed by using region class (pylot.core.active.surveyPlotTools.regions)
@ -542,7 +560,8 @@ class Survey(object):
for shot in self.data.values(): for shot in self.data.values():
for traceID in shot.getTraceIDlist(): for traceID in shot.getTraceIDlist():
if plotRemoved == False: if plotRemoved == False:
if shot.getPickFlag(traceID) is not 0 or plotRemoved == True: if shot.getPickFlag(
traceID) is not 0 or plotRemoved == True:
dist.append(shot.getDistance(traceID)) dist.append(shot.getDistance(traceID))
pick.append(shot.getPick(traceID)) pick.append(shot.getPick(traceID))
snrlog.append(math.log10(shot.getSNR(traceID)[0])) snrlog.append(math.log10(shot.getSNR(traceID)[0]))
@ -554,12 +573,15 @@ class Survey(object):
'spe': spe} 'spe': spe}
self.color = color self.color = color
if refreshPlot is False: if refreshPlot is False:
ax, cbar = self.createPlot(dist, pick, color[colorByVal], label='%s' % colorByVal) ax, cbar = self.createPlot(dist, pick, color[colorByVal],
label='%s' % colorByVal)
region = regions(ax, cbar, self) region = regions(ax, cbar, self)
ax.legend() ax.legend()
return (ax, region) return (ax, region)
if refreshPlot is True: if refreshPlot is True:
ax, cbar = self.createPlot(dist, pick, color[colorByVal], label='%s' % colorByVal, ax=ax, cbar=cbar) ax, cbar = self.createPlot(dist, pick, color[colorByVal],
label='%s' % colorByVal, ax=ax,
cbar=cbar)
ax.legend() ax.legend()
return ax return ax
@ -574,27 +596,33 @@ class Survey(object):
print('Generating new plot...') print('Generating new plot...')
fig = plt.figure() fig = plt.figure()
ax = fig.add_subplot(111) ax = fig.add_subplot(111)
sc = ax.scatter(dist, pick, cmap=cm, c=inkByVal, s=5, edgecolors='none', label=label) sc = ax.scatter(dist, pick, cmap=cm, c=inkByVal, s=5,
edgecolors='none', label=label)
cbar = plt.colorbar(sc, fraction=0.05) cbar = plt.colorbar(sc, fraction=0.05)
cbar.set_label(label) cbar.set_label(label)
ax.set_xlabel('Distance [m]') ax.set_xlabel('Distance [m]')
ax.set_ylabel('Time [s]') ax.set_ylabel('Time [s]')
ax.text(0.5, 0.95, 'Plot of all picks', transform=ax.transAxes, horizontalalignment='center') ax.text(0.5, 0.95, 'Plot of all picks', transform=ax.transAxes,
horizontalalignment='center')
else: else:
sc = ax.scatter(dist, pick, cmap=cm, c=inkByVal, s=5, edgecolors='none', label=label) sc = ax.scatter(dist, pick, cmap=cm, c=inkByVal, s=5,
edgecolors='none', label=label)
cbar = plt.colorbar(sc, cax=cbar.ax) cbar = plt.colorbar(sc, cax=cbar.ax)
cbar.set_label(label) cbar.set_label(label)
ax.set_xlabel('Distance [m]') ax.set_xlabel('Distance [m]')
ax.set_ylabel('Time [s]') ax.set_ylabel('Time [s]')
ax.text(0.5, 0.95, 'Plot of all picks', transform=ax.transAxes, horizontalalignment='center') ax.text(0.5, 0.95, 'Plot of all picks', transform=ax.transAxes,
horizontalalignment='center')
return (ax, cbar) return (ax, cbar)
def _update_progress(self, shotname, tend, progress): def _update_progress(self, shotname, tend, progress):
sys.stdout.write('Working on shot %s. ETC is %02d:%02d:%02d [%2.2f %%]\r' % (shotname, sys.stdout.write(
tend.hour, 'Working on shot %s. ETC is %02d:%02d:%02d [%2.2f %%]\r' % (
tend.minute, shotname,
tend.second, tend.hour,
progress)) tend.minute,
tend.second,
progress))
sys.stdout.flush() sys.stdout.flush()
def saveSurvey(self, filename='survey.pickle'): def saveSurvey(self, filename='survey.pickle'):

11
pylot/core/active/seismicshot.py
View File

@ -11,6 +11,7 @@ from pylot.core.pick.charfuns import AICcf
from pylot.core.pick.utils import getSNR from pylot.core.pick.utils import getSNR
from pylot.core.pick.utils import earllatepicker from pylot.core.pick.utils import earllatepicker
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
import warnings
plt.interactive('True') plt.interactive('True')
@ -322,7 +323,7 @@ class SeismicShot(object):
if len(traces) == 1: if len(traces) == 1:
return Stream(traces) return Stream(traces)
self.setPick(traceID, None) self.setPick(traceID, None)
print 'Warning: ambigious or empty traceID: %s' % traceID warnings.warn('ambigious or empty traceID: %s' % traceID)
def pickParallel(self, folm, method = 'hos', aicwindow = (10, 0)): def pickParallel(self, folm, method = 'hos', aicwindow = (10, 0)):
import multiprocessing import multiprocessing
@ -336,7 +337,11 @@ class SeismicShot(object):
traceIDs = self.getTraceIDlist() traceIDs = self.getTraceIDlist()
pool.map(self.pickTrace, traceIDs) picks = pool.map(self.pickTrace, traceIDs)
for traceID, pick in picks:
self.setPick(traceID, pick)
def pickTrace(self, traceID): def pickTrace(self, traceID):
''' '''
@ -373,7 +378,7 @@ class SeismicShot(object):
setHosAic = {'hos': hoscftime, setHosAic = {'hos': hoscftime,
'aic': aiccftime} 'aic': aiccftime}
self.setPick(traceID, setHosAic[self.getMethod()]) return traceID, setHosAic[self.getMethod()]
def setEarllatepick(self, traceID, nfac=1.5): def setEarllatepick(self, traceID, nfac=1.5):
tgap = self.getTgap() tgap = self.getTgap()