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

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This commit is contained in:
Sebastian Wehling-Benatelli 2015-11-13 14:05:39 +01:00
commit bb3e068232
3 changed files with 283 additions and 64 deletions
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46
autoPyLoT.py
View File

@ -88,7 +88,9 @@ def autoPyLoT(inputfile):
nllocoutpatter = parameter.getParam('outpatter')
else:
locflag = 0
print ("!!No location routine available, autoPyLoT just picks the events without locating them!!")
print (" !!! ")
print ("!!No location routine available, autoPyLoT is running in non-location mode!!")
print (" !!! ")
# multiple event processing
@ -130,20 +132,28 @@ def autoPyLoT(inputfile):
# locate the event
subprocess.call([nlloccall, locfile])
# !iterative picking if traces remained unpicked or with bad picks!
# get theoretical onset times for picks with weights >= 4
# in order to reprocess them using smaller time windows
##########################################################
# write phase files for various location routines
# HYPO71
hypo71file = '%s/%s/autoPyLoT_HYPO71.pha' % (datapath, evID)
writephases(picks, 'HYPO71', hypo71file)
print '------------------------------------------'
print '-----Finished event %s!-----' % event
print '------------------------------------------'
endsplash = '''------------------------------------------\n'
-----Finished event %s!-----\n'
------------------------------------------'''.format \
(version=_getVersionString()) % evID
print(endsplash)
if locflag == 0:
print("autoPyLoT was running in non-location mode!")
# single event processing
else:
data.setWFData(glob.glob(os.path.join(datapath, parameter.getParam('eventID'), '*')))
print 'Working on event ', parameter.getParam('eventID')
print("Working on event "), parameter.getParam('eventID')
print data
wfdat = data.getWFData() # all available streams
@ -175,22 +185,30 @@ def autoPyLoT(inputfile):
# locate the event
subprocess.call([nlloccall, locfile])
# !iterative picking if traces remained unpicked or with bad picks!
# get theoretical onset times for picks with weights >= 4
# in order to reprocess them using smaller time windows
##########################################################
# write phase files for various location routines
# HYPO71
hypo71file = '%s/%s/autoPyLoT_HYPO71.pha' % (datapath, parameter.getParam('eventID'))
writephases(picks, 'HYPO71', hypo71file)
endsplash = '''------------------------------------------\n'
-----Finished event %s!-----\n'
------------------------------------------'''.format \
(version=_getVersionString()) % parameter.getParam('eventID')
print(endsplash)
if locflag == 0:
print("autoPyLoT was running in non-location mode!")
print '------------------------------------------'
print '-------Finished event %s!-------' % parameter.getParam('eventID')
print '------------------------------------------'
print '####################################'
print '************************************'
print '*********autoPyLoT terminates*******'
print 'The Python picking and Location Tool'
print '************************************'
endsp = '''####################################\n
************************************\n
*********autoPyLoT terminates*******\n
The Python picking and Location Tool\n
************************************'''.format(version=_getVersionString())
print(endsp)
if __name__ == "__main__":
# parse arguments

7
pylot/core/active/fmtomo2vtk.py
View File

@ -47,6 +47,9 @@ def vgrids2VTK(inputfile = 'vgrids.in', outputfile = 'vgrids.vtk', absOrRel = 'a
return sR, sTheta, sPhi
def readVelocity(filename):
'''
Reads in velocity from vgrids file and returns a list containing all values in the same order
'''
vel = []; count = 0
fin = open(filename, 'r')
vglines = fin.readlines()
@ -59,7 +62,7 @@ def vgrids2VTK(inputfile = 'vgrids.in', outputfile = 'vgrids.vtk', absOrRel = 'a
print("Read %d points out of file: %s" %(count - 4, filename))
return vel
R = 6371 # earth radius
R = 6371. # earth radius
outfile = open(outputfile, 'w')
# Theta, Phi in radians, R in km
@ -167,7 +170,7 @@ def rays2VTK(fnin, fdirout = './vtk_files/', nthPoint = 50):
rays[shotnumber] = {}
rays[shotnumber][raynumber] = []
for index in range(nRayPoints):
if index%nthPoint is 0 or index == nRayPoints:
if index % nthPoint is 0 or index == (nRayPoints - 1):
rad, lat, lon = infile.readline().split()
rays[shotnumber][raynumber].append([getDistance(np.rad2deg(float(lon))), getDistance(np.rad2deg(float(lat))), float(rad) - R])
else:

294
pylot/core/active/seismicArrayPreparation.py
View File

@ -303,9 +303,9 @@ class SeisArray(object):
self._interpolateXY4rec()
self.interpZcoords4rec()
def interpolateTopography(self, nTheta, nPhi, thetaSN, phiWE, method = 'linear', filename = 'interface1.in'):
def interpolateTopography(self, nTheta, nPhi, thetaSN, phiWE, elevation = 0.25, method = 'linear'):
'''
Interpolate Z values on a regular grid with cushion nodes to use it as FMTOMO topography interface.
Interpolate Z values on a regular grid with cushion nodes e.g. 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)
@ -319,17 +319,38 @@ class SeisArray(object):
:param: phiWE (W, E) extensions of the model in degree
type: tuple
:param: elevation, default: 0.25 (elevate topography so that no source lies above the surface)
type: float
'''
return self.interpolateOnRegularGrid(nTheta, nPhi, thetaSN, phiWE, elevation, method)
def interpolateOnRegularGrid(self, nTheta, nPhi, thetaSN, phiWE, elevation, method = 'linear'):
'''
Interpolate Z values on a regular grid with cushion nodes e.g. 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
:param: elevation, default: 0.25 (elevate topography so that no source lies above the surface)
type: float
'''
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 "Interpolating interface 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)
print "method = %s, elevation = %s" %(method, elevation)
thetaS, thetaN = thetaSN
phiW, phiE = phiWE
@ -337,11 +358,11 @@ class SeisArray(object):
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)
deltaTheta = (thetaN - thetaS) / (nTheta - 1)
deltaPhi = (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
thetaGrid = np.linspace(thetaS - deltaTheta, thetaN + deltaTheta, num = nTheta + 2) # +2 cushion nodes
phiGrid = np.linspace(phiW - deltaPhi, phiE + deltaPhi, num = nPhi + 2) # +2 cushion nodes
nTotal = len(thetaGrid) * len(phiGrid); count = 0
for theta in thetaGrid:
@ -352,21 +373,183 @@ class SeisArray(object):
# 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)
z = float(z) + elevation
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,
Rbt = (-62.0, 6.0), thetaSN = None,
phiWE = None, outfilename = 'vgrids.in',
method = 'linear', infilename = 'mygrid.in'):
def generateFMTOMOinputFromArray(self, nRP, nThetaP, nPhiP, nRI, nThetaI, nPhiI,
Rbt, cushionfactor, interpolationMethod = 'linear',
customgrid = 'mygrid.in'):
print('\n------------------------------------------------------------')
print('Automatically generating input for FMTOMO from array size.')
print('Propgrid: nR = %s, nTheta = %s, nPhi = %s'%(nRP, nThetaP, nPhiP))
print('Interpolation Grid and Interfaces Grid: nR = %s, nTheta = %s, nPhi = %s'%(nRI, nThetaI, nPhiI))
print('Bottom and Top of model: (%s, %s)'%(Rbt[0], Rbt[1]))
print('Method: %s, customgrid = %s'%(interpolationMethod, customgrid))
print('------------------------------------------------------------')
def getZmin(surface):
z = []
for point in surface:
z.append(point[2])
return min(z)
self.generatePropgrid(nThetaP, nPhiP, nRP, Rbt, cushionfactor = cushionfactor,
cushionpropgrid = 0.05)
surface = self.generateVgrid(nThetaI, nPhiI, nRI, Rbt, method = interpolationMethod,
cushionfactor = cushionfactor, infilename = customgrid,
returnTopo = True)
depthmax = abs(Rbt[0] - getZmin(surface)) - 1.0 # cushioning for the bottom interface
self.generateInterfaces(nThetaI, nPhiI, depthmax, cushionfactor = cushionfactor,
returnInterfaces = False, method = interpolationMethod)
def generateInterfaces(self, nTheta, nPhi, depthmax, cushionfactor = 0.1,
outfilename = 'interfaces.in', method = 'linear',
returnInterfaces = False):
'''
Create an interfaces.in file for FMTOMO from the SeisArray boundaries.
:param: nTheta, number of points in Theta
type: int
:param: nPhi, number of points in Phi
type: int
:param: depthmax, maximum depth of the model (below topography)
type: float
:param: cushionfactor, add some extra space to the model (default: 0.1 = 10%)
type: float
'''
print('\n------------------------------------------------------------')
print('Generating interfaces...')
nInterfaces = 2
# generate dimensions of the grid from array
thetaSN, phiWE = self.getThetaPhiFromArray(cushionfactor)
thetaS, thetaN = thetaSN
phiW, phiE = phiWE
R = 6371.
outfile = open(outfilename, 'w')
# determine the deltas
deltaTheta = abs(thetaN - thetaS) / float((nTheta - 1))
deltaPhi = abs(phiE - phiW) / float((nPhi - 1))
# write header for interfaces grid file (in RADIANS)
outfile.writelines('%10s\n' %(nInterfaces))
outfile.writelines('%10s %10s\n' %(nTheta + 2, nPhi + 2)) # +2 cushion nodes
outfile.writelines('%10s %10s\n' %(np.deg2rad(deltaTheta), np.deg2rad(deltaPhi)))
outfile.writelines('%10s %10s\n' %(np.deg2rad(thetaS - deltaTheta), np.deg2rad(phiW - deltaPhi)))
interface1 = self.interpolateTopography(nTheta, nPhi, thetaSN, phiWE, method = method)
interface2 = self.interpolateOnRegularGrid(nTheta, nPhi, thetaSN, phiWE, -depthmax, method = method)
for point in interface1:
z = point[2]
outfile.writelines('%10s\n'%(z + R))
outfile.writelines('\n')
for point in interface2:
z = point[2]
outfile.writelines('%10s\n'%(z + R))
outfile.close()
if returnInterfaces == True:
return interface1, interface2
print('Finished generating interfaces.')
print('------------------------------------------------------------')
def getThetaPhiFromArray(self, cushionfactor = 0.1):
'''
Determine and returns PhiWE (tuple: (West, East)) and thetaSN (tuple (South, North)) from the SeisArray boundaries.
:param: cushionfactor, add some extra space to the model (default: 0.1 = 10%)
type: float
'''
x, y, _ = 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)
return thetaSN, phiWE
def generatePropgrid(self, nTheta, nPhi, nR, Rbt, cushionfactor, cushionpropgrid = 0.05,
refinement = (5, 5), outfilename = 'propgrid.in'):
'''
Create a propergation grid file for FMTOMO using SeisArray boundaries
:param: nTheta, number of points in Theta
type: int
:param: nPhi, number of points in Phi
type: int
:param: nR, number of points in R
type: int
:param: Rbt (bot, top) extensions of the model in m
type: tuple
:param: cushionfactor, add some extra space to the model (default: 0.1 = 10%)
type: float
:param: cushionpropogrid, cushionfactor for the propagationgrid (cushion direction
opposing to vgrids cushionfactor)
type: float
:param: refinement, (refinement factor, number of local cells for refinement) used by FMTOMO
type: tuple
'''
outfile = open(outfilename, 'w')
print('\n------------------------------------------------------------')
print('Generating Propagation Grid for nTheta = %s, nPhi'
' = %s, nR = %s and a cushioning of %s'
%(nTheta, nPhi, nR, cushionpropgrid))
print('Bottom of the grid: %s, top of the grid %s'
%(Rbt[0], Rbt[1]))
thetaSN, phiWE = self.getThetaPhiFromArray(cushionfactor)
thetaS = thetaSN[0] + cushionpropgrid
thetaN = thetaSN[1] - cushionpropgrid
phiW = phiWE[0] + cushionpropgrid
phiE = phiWE[1] - cushionpropgrid
rbot = Rbt[0]
rtop = Rbt[1]
deltaTheta = abs(thetaN - thetaS) / float(nTheta - 1)
deltaPhi = abs(phiE - phiW) / float(nPhi - 1)
deltaR = abs(rbot - rtop) / float(nR - 1)
outfile.writelines('%10s %10s %10s\n' %(nR, nTheta, nPhi))
outfile.writelines('%10s %10s %10s\n' %(deltaR, deltaTheta, deltaPhi))
outfile.writelines('%10s %10s %10s\n' %(rtop, thetaS, phiW))
outfile.writelines('%10s %10s\n' %refinement)
outfile.close()
print('Created Propagation Grid and saved it to %s' %outfilename)
print('------------------------------------------------------------')
def generateVgrid(self, nTheta, nPhi, nR, Rbt, thetaSN = None,
phiWE = None, cushionfactor = 0.1,
outfilename = 'vgrids.in', method = 'linear',
infilename = 'mygrid.in', returnTopo = False):
'''
Generate a velocity grid for fmtomo regarding topography with a linear gradient starting at the topography with 0.34 [km/s].
@ -385,7 +568,7 @@ class SeisArray(object):
:param: phiWE (W, E) extensions of the model in degree
type: tuple
:param: Rbt (bot, top) extensions of the model in km
:param: Rbt (bot, top) extensions of the model in m
type: tuple
:param: vbot, velocity at the bottom of the model
@ -394,11 +577,13 @@ class SeisArray(object):
:param: method, interpolation method for topography
type: str
'''
print('\n------------------------------------------------------------')
print('generateVgrid: Starting...')
def getRad(angle):
PI = np.pi
rad = angle / 180 * PI
return rad
# def getRad(angle):
# PI = np.pi
# rad = angle / 180 * PI
# return rad
def readMygridNlayers(filename):
infile = open(filename, 'r')
@ -412,6 +597,7 @@ class SeisArray(object):
infile = open(filename, 'r')
nlayers = readMygridNlayers(filename)
print('\nreadMygrid: Reading file %s.'%filename)
for index in range(nlayers):
line1 = infile.readline()
line2 = infile.readline()
@ -419,6 +605,10 @@ class SeisArray(object):
vtop.append(float(line1.split()[1]))
zbot.append(float(line2.split()[0]))
vbot.append(float(line2.split()[1]))
print('Layer %s:\n[Top: v = %s [km/s], z = %s [m]]'
'\n[Bot: v = %s [km/s], z = %s [m]]'
%(index + 1, vtop[index], ztop[index],
vbot[index], zbot[index]))
if not ztop[0] == 0:
print('ERROR: there must be a velocity set for z = 0 in the file %s'%filename)
@ -429,19 +619,12 @@ class SeisArray(object):
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(outfilename, 'w')
# generate dimensions of the grid from array
if thetaSN is None and phiWE is None:
x, y, _ = 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)
thetaSN, phiWE = self.getThetaPhiFromArray(cushionfactor)
thetaS, thetaN = thetaSN
phiW, phiE = phiWE
@ -449,14 +632,14 @@ 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) / float((nTheta - 1))
phiDelta = abs(phiE - phiW) / float((nPhi - 1))
rDelta = abs(rbot - rtop) / float((nR - 1))
deltaTheta = abs(thetaN - thetaS) / float((nTheta - 1))
deltaPhi = abs(phiE - phiW) / float((nPhi - 1))
deltaR = 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
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
thetaGrid = np.linspace(thetaS - deltaTheta, thetaN + deltaTheta, num = nTheta + 2) # +2 cushion nodes
phiGrid = np.linspace(phiW - deltaPhi, phiE + deltaPhi, num = nPhi + 2) # +2 cushion nodes
rGrid = np.linspace(rbot - deltaR, rtop + deltaR, num = nR + 2) # +2 cushion nodes
nTotal = len(rGrid) * len(thetaGrid) * len(phiGrid)
print("Total number of grid nodes: %s"%nTotal)
@ -464,10 +647,13 @@ class SeisArray(object):
# 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)))
outfile.writelines('%10s %10s %10s\n' %(deltaR, np.deg2rad(deltaTheta), np.deg2rad(deltaPhi)))
outfile.writelines('%10s %10s %10s\n' %(rbot - deltaR, np.deg2rad(thetaS - deltaTheta), np.deg2rad(phiW - deltaPhi)))
surface = self.interpolateTopography(nTheta, nPhi, thetaSN, phiWE, method = method, filename = None)
surface = self.interpolateTopography(nTheta, nPhi, thetaSN, phiWE, method = method)
nlayers = readMygridNlayers(infilename)
ztop, zbot, vtop, vbot = readMygrid(infilename)
print("\nGenerating velocity grid for FMTOMO. "
"Output filename = %s, interpolation method = %s"%(outfilename, method))
@ -475,9 +661,6 @@ class SeisArray(object):
"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:
@ -508,10 +691,23 @@ class SeisArray(object):
progress = float(count) / float(nTotal) * 100
self._update_progress(progress)
print('Wrote %d points to file %s for %d layers'%(count, outfilename, nlayers))
print('\nWrote %d points to file %s for %d layers'%(count, outfilename, nlayers))
print('------------------------------------------------------------')
outfile.close()
def addCheckerboard(self, spacing = 20, pertubation = 1, inputfile = 'vgrids.in', outputfile = 'vgrids_cb.in'):
if returnTopo == True:
return surface
def addCheckerboard(self, spacing = 20., pertubation = 0.1, inputfile = 'vgrids.in', outputfile = 'vgrids_cb.in'):
'''
Add a checkerboard to an existing vgrids.in velocity model.
:param: spacing, size of the tiles
type: float
:param: pertubation, pertubation (default: 0.1 = 10%)
type: float
'''
def readNumberOfPoints(filename):
fin = open(filename, 'r')
vglines = fin.readlines()
@ -631,7 +827,7 @@ class SeisArray(object):
evenOddP = -1
velocity = vel[count]
evenOdd = evenOddR * evenOddT * evenOddP
velocity += evenOdd * pertubation
velocity += evenOdd * pertubation * velocity
outfile.writelines('%10s %10s\n'%(velocity, decm))
count += 1
@ -639,6 +835,8 @@ class SeisArray(object):
progress = float(count) / float(nPoints) * 100
self._update_progress(progress)
print('Added checkerboard to the grid in file %s with a spacing of %s and a pertubation of %s [km/s]. '
'Outputfile: %s.'%(inputfile, spacing, pertubation, outputfile))
outfile.close()
def exportAll(self, filename = 'interpolated_receivers.out'):