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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.surveyUtils import cleanUp
class Survey(object):
def __init__(self, path, sourcefile, receiverfile, useDefaultParas=False):
'''
@ -21,13 +22,13 @@ class Survey(object):
self._sourcefile = sourcefile
self._obsdir = path
self._generateSurvey()
self._initiateFilenames()
self._initiate_fnames()
if useDefaultParas == True:
self.setParametersForAllShots()
self._removeAllEmptyTraces()
self._updateShots()
def _initiateFilenames(self):
def _initiate_fnames(self):
for shot in self.data.values():
shot.setRecfile(self.getPath() + self.getReceiverfile())
shot.setSourcefile(self.getPath() + self.getSourcefile())
@ -74,7 +75,7 @@ class Survey(object):
but were set in the input files.
'''
logfile = 'updateShots.out'
count = 0;
count = 0
countTraces = 0
for shot in self.data.values():
del_traceIDs = shot.updateTraceList()
@ -93,15 +94,8 @@ class Survey(object):
"on removed traces." % (logfile))
outfile.close()
def setArtificialPick(self, traceID, pick):
'''
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):
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
tsignal == 0.03 and tgap == 0.0007):
print ("Warning: Standard values used for "
@ -136,8 +130,10 @@ class Survey(object):
if not shot in diffs.keys():
diffs[shot] = {}
for traceID in shot.getTraceIDlist():
if shot.getPickFlag(traceID) == 1 and shot.getManualPickFlag(traceID) == 1:
diffs[shot][traceID] = shot.getPick(traceID) - shot.getManualPick(traceID)
if shot.getPickFlag(traceID) == 1 and shot.getManualPickFlag(
traceID) == 1:
diffs[shot][traceID] = shot.getPick(
traceID) - shot.getManualPick(traceID)
return diffs
def plotDiffs(self):
@ -146,14 +142,15 @@ class Survey(object):
difference between automatic and manual pick.
'''
import matplotlib.pyplot as plt
diffs = [];
dists = [];
mpicks = [];
diffs = []
dists = []
mpicks = []
picks = []
diffsDic = self.getDiffsFromManual()
for shot in self.data.values():
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))
mpicks.append(shot.getManualPick(traceID))
picks.append(shot.getPick(traceID))
@ -165,13 +162,16 @@ class Survey(object):
fig = plt.figure()
ax = fig.add_subplot(111)
sc_a = ax.scatter(dists, picks, c='0.5', s=10, edgecolors='none', label=labela, alpha=0.3)
sc = ax.scatter(dists, mpicks, c=diffs, s=5, edgecolors='none', label=labelm)
sc_a = ax.scatter(dists, picks, c='0.5', s=10, edgecolors='none',
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.set_label(labelm)
ax.set_xlabel('Distance [m]')
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()
def plotHist(self, nbins=20, ax=None):
@ -186,14 +186,18 @@ class Survey(object):
ax = fig.add_subplot(111)
for shot in self.data.values():
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])
hist = plt.hist(diffs, nbins, histtype='step', normed=True, stacked=True)
plt.title('Histogram of the differences between automatic and manual pick')
hist = plt.hist(diffs, nbins, histtype='step', normed=True,
stacked=True)
plt.title(
'Histogram of the differences between automatic and manual pick')
plt.xlabel('Difference in time (auto - manual) [s]')
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.
@ -211,11 +215,11 @@ class Survey(object):
'''
from datetime import datetime
starttime = datetime.now()
count = 0;
count = 0
tpicksum = starttime - starttime
for shot in self.data.values():
tstartpick = datetime.now();
tstartpick = datetime.now()
shot.setVmin(vmin)
shot.setVmax(vmax)
count += 1
@ -235,7 +239,8 @@ class Survey(object):
ntraces = self.countAllTraces()
pickedtraces = self.countAllPickedTraces()
print('Picked %s / %s traces (%d %%)\n'
% (pickedtraces, ntraces, float(pickedtraces) / float(ntraces) * 100.))
% (pickedtraces, ntraces,
float(pickedtraces) / float(ntraces) * 100.))
def setSNR(self):
for shot in self.data.values():
@ -373,8 +378,11 @@ class Survey(object):
pickedTraces += 1
info_dict[shot.getShotnumber()] = {'numtraces': numtraces,
'picked traces': [pickedTraces,
'%2.2f %%' % (float(pickedTraces) /
float(numtraces) * 100)],
'%2.2f %%' % (
float(
pickedTraces) /
float(
numtraces) * 100)],
'mean SNR': np.mean(snrlist),
'mean distance': np.mean(dist)}
@ -388,10 +396,12 @@ class Survey(object):
if shot.getShotnumber() == shotnumber:
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.
'''
def getAngle(distance):
PI = np.pi
R = 6371.
@ -400,18 +410,20 @@ class Survey(object):
count = 0
fmtomo_factor = 1000 # transforming [m/s] -> [km/s]
LatAll = [];
LonAll = [];
LatAll = []
LonAll = []
DepthAll = []
srcfile = open(directory + '/' + sourcefile, 'w')
srcfile.writelines('%10s\n' % len(self.data)) # number of sources
for shotnumber in self.getShotlist():
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)
srcfile.writelines('%10s %10s %10s\n' % (getAngle(y), getAngle(x), (-1) * z)) # transform to lat, lon, depth
LatAll.append(getAngle(y));
LonAll.append(getAngle(x));
srcfile.writelines('%10s %10s %10s\n' % (
getAngle(y), getAngle(x), (-1) * z)) # transform to lat, lon, depth
LatAll.append(getAngle(y))
LonAll.append(getAngle(x))
DepthAll.append((-1) * z)
srcfile.writelines('%10s\n' % 1)
srcfile.writelines('%10s %10s %10s\n' % (1, 1, ttfilename))
@ -424,9 +436,10 @@ class Survey(object):
pick = shot.getPick(traceID) * fmtomo_factor
delta = shot.getSymmetricPickError(traceID) * fmtomo_factor
(x, y, z) = shot.getRecLoc(traceID)
ttfile.writelines('%20s %20s %20s %10s %10s\n' % (getAngle(y), getAngle(x), (-1) * z, pick, delta))
LatAll.append(getAngle(y));
LonAll.append(getAngle(x));
ttfile.writelines('%20s %20s %20s %10s %10s\n' % (
getAngle(y), getAngle(x), (-1) * z, pick, delta))
LatAll.append(getAngle(y))
LonAll.append(getAngle(x))
DepthAll.append((-1) * z)
count += 1
ttfile.close()
@ -486,19 +499,24 @@ class Survey(object):
if index <= figPerSubplot:
ax = fig.add_subplot(rows, columns, index)
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':
self.getShot(shotnumber).plot2dttc(ax)
self.getShot(shotnumber).plotmanual2dttc(ax)
index += 1
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()
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).
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 traceID in shot.getTraceIDlist():
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))
pick.append(shot.getPick(traceID))
snrlog.append(math.log10(shot.getSNR(traceID)[0]))
@ -554,12 +573,15 @@ class Survey(object):
'spe': spe}
self.color = color
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)
ax.legend()
return (ax, region)
if refreshPlot is True:
ax, cbar = self.createPlot(dist, pick, color[colorByVal], label='%s' % colorByVal, ax=ax, cbar=cbar)
ax, cbar = self.createPlot(dist, pick, color[colorByVal],
label='%s' % colorByVal, ax=ax,
cbar=cbar)
ax.legend()
return ax
@ -574,27 +596,33 @@ class Survey(object):
print('Generating new plot...')
fig = plt.figure()
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.set_label(label)
ax.set_xlabel('Distance [m]')
ax.set_ylabel('Time [s]')
ax.text(0.5, 0.95, 'Plot of all picks', transform=ax.transAxes, horizontalalignment='center')
ax.text(0.5, 0.95, 'Plot of all picks', transform=ax.transAxes,
horizontalalignment='center')
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.set_label(label)
ax.set_xlabel('Distance [m]')
ax.set_ylabel('Time [s]')
ax.text(0.5, 0.95, 'Plot of all picks', transform=ax.transAxes, horizontalalignment='center')
ax.text(0.5, 0.95, 'Plot of all picks', transform=ax.transAxes,
horizontalalignment='center')
return (ax, cbar)
def _update_progress(self, shotname, tend, progress):
sys.stdout.write('Working on shot %s. ETC is %02d:%02d:%02d [%2.2f %%]\r' % (shotname,
tend.hour,
tend.minute,
tend.second,
progress))
sys.stdout.write(
'Working on shot %s. ETC is %02d:%02d:%02d [%2.2f %%]\r' % (
shotname,
tend.hour,
tend.minute,
tend.second,
progress))
sys.stdout.flush()
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 earllatepicker
import matplotlib.pyplot as plt
import warnings
plt.interactive('True')
@ -322,7 +323,7 @@ class SeismicShot(object):
if len(traces) == 1:
return Stream(traces)
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)):
import multiprocessing
@ -336,7 +337,11 @@ class SeismicShot(object):
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):
'''
@ -373,7 +378,7 @@ class SeismicShot(object):
setHosAic = {'hos': hoscftime,
'aic': aiccftime}
self.setPick(traceID, setHosAic[self.getMethod()])
return traceID, setHosAic[self.getMethod()]
def setEarllatepick(self, traceID, nfac=1.5):
tgap = self.getTgap()