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

Browse Source 
Conflicts:
	autoPyLoT.py
This commit is contained in:
Ludger Küperkoch
2015-11-05 08:47:06 +01:00
parent 3fa4a31978 223902f2d4
commit f738160a8b
8 changed files with 208 additions and 83 deletions
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2
pylot/RELEASE-VERSION
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@@ -1 +1 @@
ac7d-dirty
a31e-dirty

38
pylot/core/active/fmtomo2vtk.py
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@@ -1,7 +1,7 @@
# -*- coding: utf-8 -*-
import numpy as np
def vgrids2VTK(inputfile = 'vgrids.in', outputfile = 'vgrids.vtk'):
def vgrids2VTK(inputfile = 'vgrids.in', outputfile = 'vgrids.vtk', absOrRel = 'abs', inputfileref = 'vgridsref.in'):
'''
Generate a vtk-file readable by e.g. paraview from FMTOMO output vgrids.in
'''
@@ -19,6 +19,8 @@ def vgrids2VTK(inputfile = 'vgrids.in', outputfile = 'vgrids.vtk'):
nTheta = int(vglines[1].split()[1])
nPhi = int(vglines[1].split()[2])
print('readNumberOf Points: Awaiting %d grid points in %s'
%(nR*nTheta*nPhi, filename))
fin.close()
return nR, nTheta, nPhi
@@ -91,13 +93,39 @@ def vgrids2VTK(inputfile = 'vgrids.in', outputfile = 'vgrids.vtk'):
outfile.writelines('SPACING %f %f %f\n' %(dX, dY, dZ))
outfile.writelines('POINT_DATA %15d\n' %(nPoints))
outfile.writelines('SCALARS velocity float %d\n' %(1))
if absOrRel == 'abs':
outfile.writelines('SCALARS velocity float %d\n' %(1))
elif absOrRel == 'rel':
outfile.writelines('SCALARS velChangePercent float %d\n' %(1))
outfile.writelines('LOOKUP_TABLE default\n')
# write velocity
print("Writing velocity values to VTK file...")
for velocity in vel:
outfile.writelines('%10f\n' %velocity)
if absOrRel == 'abs':
print("Writing velocity values to VTK file...")
for velocity in vel:
outfile.writelines('%10f\n' %velocity)
elif absOrRel == 'rel':
velref = readVelocity(inputfileref)
if not len(velref) == len(vel):
print('ERROR: Number of gridpoints mismatch for %s and %s'%(inputfile, inputfileref))
return
#velrel = [((vel - velref) / velref * 100) for vel, velref in zip(vel, velref)]
velrel = []
for velocities in zip(vel, velref):
v, vref = velocities
if not vref == 0:
velrel.append((v - vref) / vref * 100)
else:
velrel.append(0)
nR_ref, nTheta_ref, nPhi_ref = readNumberOfPoints(inputfileref)
if not nR_ref == nR and nTheta_ref == nTheta and nPhi_ref == nPhi:
print('ERROR: Dimension mismatch of grids %s and %s'%(inputfile, inputfileref))
return
print("Writing velocity values to VTK file...")
for velocity in velrel:
outfile.writelines('%10f\n' %velocity)
print('Pertubations: min: %s, max: %s'%(min(velrel), max(velrel)))
outfile.close()
print("Wrote velocity grid for %d points to file: %s" %(nPoints, outputfile))

138
pylot/core/active/seismicArrayPreparation.py
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@@ -16,13 +16,14 @@ class SeisArray(object):
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.recfile = recfile
self._receiverlines = {}
self._receiverCoords = {}
self._measuredReceivers = {}
self._measuredTopo = {}
self._sourceLocs = {}
self._geophoneNumbers = {}
self._receiverlist = open(recfile, 'r').readlines()
self._receiverlist = open(self.recfile, 'r').readlines()
self._generateReceiverlines()
self._setReceiverCoords()
self._setGeophoneNumbers()
@@ -363,9 +364,9 @@ class SeisArray(object):
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' ):
Rbt = (-62.0, 6.0), thetaSN = None,
phiWE = None, outfilename = 'vgrids.in',
method = 'linear', infilename = 'mygrid.in'):
'''
Generate a velocity grid for fmtomo regarding topography with a linear gradient starting at the topography with 0.34 [km/s].
@@ -386,9 +387,12 @@ class SeisArray(object):
:param: Rbt (bot, top) extensions of the model in km
type: tuple
:param: vbot, velocity at the bottom of the model
type: real
:param: method, interpolation method for topography
type: str
'''
def getRad(angle):
@@ -396,16 +400,48 @@ class SeisArray(object):
rad = angle / 180 * PI
return rad
def getZmax(surface):
z = []
for point in surface:
z.append(point[2])
return max(z)
def readMygridNlayers(filename):
infile = open(filename, 'r')
nlayers = len(infile.readlines()) / 2
infile.close()
return nlayers
def readMygrid(filename):
ztop = []; zbot = []; vtop = []; vbot = []
infile = open(filename, 'r')
nlayers = readMygridNlayers(filename)
for index in range(nlayers):
line1 = infile.readline()
line2 = infile.readline()
ztop.append(float(line1.split()[0]))
vtop.append(float(line1.split()[1]))
zbot.append(float(line2.split()[0]))
vbot.append(float(line2.split()[1]))
if not ztop[0] == 0:
print('ERROR: there must be a velocity set for z = 0 in the file %s'%filename)
print('e.g.:\n0 0.33\n-5 1.0\netc.')
infile.close()
return ztop, zbot, vtop, vbot
R = 6371
vmin = 0.34
cushionfactor = 0.1 # add some extra space to the model
decm = 0.3 # diagonal elements of the covariance matrix (grid3dg's default value is 0.3)
outfile = open(filename, 'w')
outfile = open(outfilename, 'w')
# generate dimensions of the grid from array
if thetaSN is None and phiWE is None:
x, y, z = self.getAllMeasuredPointsLists()
phi_min, phi_max = (self._getAngle(min(x)), self._getAngle(max(x)))
theta_min, theta_max = (self._getAngle(min(y)), self._getAngle(max(y)))
cushionPhi = abs(phi_max - phi_min) * cushionfactor
cushionTheta = abs(theta_max - theta_min) * cushionfactor
phiWE = (phi_min - cushionPhi, phi_max + cushionPhi)
thetaSN = (theta_min - cushionTheta, theta_max + cushionTheta)
thetaS, thetaN = thetaSN
phiW, phiE = phiWE
@@ -413,9 +449,9 @@ class SeisArray(object):
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)
thetaDelta = abs(thetaN - thetaS) / float((nTheta - 1))
phiDelta = abs(phiE - phiW) / float((nPhi - 1))
rDelta = abs(rbot - rtop) / float((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
@@ -432,11 +468,14 @@ class SeisArray(object):
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 "\nGenerating velocity grid for FMTOMO. Output filename = %s, interpolation method = %s"%(outfilename, method)
print "nTheta = %s, nPhi = %s, nR = %s, thetaSN = %s, phiWE = %s, Rbt = %s"%(nTheta, nPhi, nR, thetaSN, phiWE, Rbt)
count = 0
nlayers = readMygridNlayers(infilename)
ztop, zbot, vtop, vbot = readMygrid(infilename)
for radius in rGrid:
for theta in thetaGrid:
for phi in phiGrid:
@@ -444,19 +483,29 @@ class SeisArray(object):
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 ##########################
topo = point[2]
z = -(R + topo - radius)
if z > (topo + 1):
vel = vtop[0]
elif (topo + 1) >= z > topo: # cushioning around topography
vel = vtop[0]
else:
vel = (radius - z - R) / (Rbt[0] - rDelta - zmax) * vbot + vmin ##########################
for index in range(nlayers):
if (topo + ztop[index]) >= z > (topo + zbot[index]):
vel = (z - ztop[index]) / (zbot[index] - ztop[index]) * (vbot[index] - vtop[index]) + vtop[index]
break
if not (topo + ztop[index]) >= z > (topo + zbot[index]):
print('ERROR in grid inputfile, could not find velocity for a z-value of %s in the inputfile'%(z - topo))
return
count += 1
if vel < 0:
print('ERROR, vel <0; z, topo, zbot, vbot, vtop:', z, topo, zbot[index], vbot[index], vtop[index])
outfile.writelines('%10s %10s\n'%(vel, decm))
progress = float(count) / float(nTotal) * 100
self._update_progress(progress)
print('Wrote %d points to file %s for %d layers'%(count, outfilename, nlayers))
outfile.close()
def exportAll(self, filename = 'interpolated_receivers.out'):
@@ -469,31 +518,36 @@ class SeisArray(object):
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):
def plotArray2D(self, plot_topo = False, highlight_measured = False, annotations = True, pointsize = 10):
import matplotlib.pyplot as plt
plt.interactive(True)
plt.figure()
fig = plt.figure()
ax = plt.axes()
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 len(xrc) > 0:
ax.plot(xrc, yrc, 'k.', markersize = pointsize, label = 'all receivers')
if len(xsc) > 0:
ax.plot(xsc, ysc, 'b*', markersize = pointsize, label = 'shot locations')
if plot_topo == True:
plt.plot(xmt, ymt, 'b', markersize = 10, label = 'measured topo points')
ax.plot(xmt, ymt, 'b.', markersize = pointsize, label = 'measured topo points')
if highlight_measured == True:
plt.plot(xmr, ymr, 'ro', label = 'measured receivers')
ax.plot(xmr, ymr, 'r.', markersize = pointsize, label = 'measured receivers')
plt.xlabel('X [m]')
plt.ylabel('Y [m]')
plt.title('2D plot of seismic array %s'%self.recfile)
ax.set_xlabel('X [m]')
ax.set_ylabel('Y [m]')
ax.set_aspect('equal')
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', color = 'k')
ax.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')
ax.annotate((' ' + str(shotnumber)), xy = (self._getXshot(shotnumber), self._getYshot(shotnumber)), fontsize = 'x-small', color = 'b')
@@ -508,18 +562,25 @@ class SeisArray(object):
xmt, ymt, zmt = self.getMeasuredTopoLists()
xmr, ymr, zmr = self.getMeasuredReceiverLists()
xin, yin, zin = self.getReceiverLists()
xrc, yrc, zrc = self.getReceiverLists()
xsc, ysc, zsc = self.getSourceLocsLists()
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')
plt.title('3D plot of seismic array %s'%self.recfile)
if len(xmt) > 0:
ax.plot(xmt, ymt, zmt, 'b.', markersize = 10, label = 'measured topo points')
if len(xrc) > 0:
ax.plot(xrc, yrc, zrc, 'k.', markersize = 10, label = 'all receivers')
if len(xmr) > 0:
ax.plot(xmr, ymr, zmr, 'ro', label = 'measured receivers')
if len(xsc) > 0:
ax.plot(xsc, ysc, zsc, 'b*', label = 'shot locations')
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'):
def plotSurface3D(self, ax = None, step = 0.5, method = 'linear', exag = False):
from matplotlib import cm
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
@@ -545,7 +606,8 @@ class SeisArray(object):
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))
if exag == False:
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')

56
pylot/core/active/seismicshot.py
View File

@@ -588,6 +588,23 @@ class SeismicShot(object):
# plt.plot(self.getDistArray4ttcPlot(), pickwindowarray_lowerb, ':k')
# plt.plot(self.getDistArray4ttcPlot(), pickwindowarray_upperb, ':k')
def plotTrace(self, traceID, plotSNR = True, lw = 1):
fig = plt.figure()
ax = fig.add_subplot(111)
ax = self._drawStream(traceID, ax = ax)
tgap = self.getTgap()
tsignal = self.getTsignal()
pick = self.getPick(traceID)
tnoise = pick - tgap
snr, snrdb, noiselevel = self.getSNR(traceID)
ax.plot([0, tnoise], [noiselevel, noiselevel], 'm', linewidth = lw, label = 'noise level')
ax.plot([tnoise, pick], [noiselevel, noiselevel], 'g:', linewidth = lw, label = 'gap')
ax.plot([tnoise + tgap, pick + tsignal], [noiselevel * snr, noiselevel * snr], 'b', linewidth = lw, label = 'signal level')
ax.legend()
ax.text(0.05, 0.95, 'SNR: %s' %snr, transform = ax.transAxes)
def plot_traces(self, traceID, folm = 0.6): ########## 2D, muss noch mehr verbessert werden ##########
from matplotlib.widgets import Button
@@ -621,7 +638,7 @@ class SeismicShot(object):
self._drawStream(traceID)
self._drawCFs(traceID, folm)
def _drawStream(self, traceID, refresh = False):
def _drawStream(self, traceID, refresh = False, ax = None):
from pylot.core.util.utils import getGlobalTimes
from pylot.core.util.utils import prepTimeAxis
@@ -630,7 +647,8 @@ class SeismicShot(object):
timeaxis = prepTimeAxis(stime, stream[0])
timeaxis -= stime
ax = self.traces4plot[traceID]['ax1']
if ax is None:
ax = self.traces4plot[traceID]['ax1']
if refresh == True:
xlim, ylim = ax.get_xlim(), ax.get_ylim()
@@ -645,8 +663,9 @@ class SeismicShot(object):
ax.plot([self.getPick(traceID), self.getPick(traceID)],
[min(stream[0].data),
max(stream[0].data)],
'r', label = 'mostlikely')
'r', label = 'most likely')
ax.legend()
return ax
def _drawCFs(self, traceID, folm, refresh = False):
hoscf = self.getHOScf(traceID)
@@ -665,7 +684,7 @@ class SeismicShot(object):
ax.plot([self.getPick(traceID), self.getPick(traceID)],
[min(np.minimum(hoscf.getCF(), aiccf.getCF())),
max(np.maximum(hoscf.getCF(), aiccf.getCF()))],
'r', label = 'mostlikely')
'r', label = 'most likely')
ax.plot([0, self.getPick(traceID)],
[folm * max(hoscf.getCF()), folm * max(hoscf.getCF())],
'm:', label = 'folm = %s' %folm)
@@ -745,11 +764,12 @@ class SeismicShot(object):
:type: 'logical'
'''
from scipy.interpolate import griddata
from matplotlib import cm
cmap = cm.jet
x = []; xcut = []
y = []; ycut = []
z = []; zcut = []
tmin, tmax = self.getCut()
for traceID in self.pick.keys():
if self.getFlag(traceID) != 0:
@@ -761,6 +781,9 @@ class SeismicShot(object):
ycut.append(self.getRecLoc(traceID)[1])
zcut.append(self.getPickIncludeRemoved(traceID))
tmin = 0.8 * min(z) # 20% cushion for colorbar
tmax = 1.2 * max(z)
xaxis = np.arange(min(x), max(x), step)
yaxis = np.arange(min(y), max(y), step)
xgrid, ygrid = np.meshgrid(xaxis, yaxis)
@@ -770,19 +793,28 @@ class SeismicShot(object):
fig = plt.figure()
ax = plt.axes()
ax.matshow(zgrid, extent = [min(x), max(x), min(y), max(y)], origin = 'lower')
count = 0
ax.imshow(zgrid, extent = [min(x), max(x), min(y), max(y)], vmin = tmin, vmax = tmax, cmap = cmap, origin = 'lower', alpha = 0.85)
plt.text(0.45, 0.9, 'shot: %s' %self.getShotnumber(), transform = ax.transAxes)
sc = ax.scatter(x, y, c = z, s = 30, label = 'picked shots', vmin = tmin, vmax = tmax, linewidths = 1.5)
sccut = ax.scatter(xcut, ycut, c = zcut, s = 30, edgecolor = 'm', label = 'cut out shots', vmin = tmin, vmax = tmax, linewidths = 1.5)
sc = ax.scatter(x, y, c = z, s = 30, label = 'picked shots', vmin = tmin, vmax = tmax, cmap = cmap, linewidths = 1.5)
for xyz in zip(xcut, ycut, zcut):
x, y, z = xyz
label = None
if z > tmax:
count += 1
z = 'w'
if count == 1:
label = 'cut out shots'
ax.scatter(x, y, c = z, s = 30, edgecolor = 'm', label = label, vmin = tmin, vmax = tmax, cmap = cmap, linewidths = 1.5)
if colorbar == True:
plt.colorbar(sc)
cbar = plt.colorbar(sc)
cbar.set_label('Time [s]')
ax.legend()
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.scatter(x, y, c = z, s = 30)
if annotations == True:
for traceID in self.getTraceIDlist():
if self.getFlag(traceID) is not 0:

3
pylot/core/pick/autopick.py
View File

@@ -335,7 +335,8 @@ def autopickstation(wfstream, pickparam):
"no zero crossings derived!")
print ("Cannot calculate source spectrum!")
else:
calcwin = (zc[3] - zc[0]) * z_copy[0].stats.delta
index = min([3, len(zc) - 1])
calcwin = (zc[index] - zc[0]) * z_copy[0].stats.delta
# calculate source spectrum and get w0 and fc
specpara = DCfc(z_copy, mpickP, calcwin, iplot)
w0 = specpara.getw0()