slimmed down the code

This commit is contained in:
Marcel Paffrath 2015-11-17 10:29:32 +01:00
parent b700940f54
commit f192a72ad7

View File

@ -6,83 +6,27 @@ def vgrids2VTK(inputfile = 'vgrids.in', outputfile = 'vgrids.vtk', absOrRel = 'a
''' '''
Generate a vtk-file readable by e.g. paraview from FMTOMO output vgrids.in Generate a vtk-file readable by e.g. paraview from FMTOMO output vgrids.in
''' '''
def getDistance(angle):
PI = np.pi
R = 6371.
distance = angle / 180 * (PI * R)
return distance
def readNumberOfPoints(filename):
fin = open(filename, 'r')
vglines = fin.readlines()
nR = int(vglines[1].split()[0])
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
def readDelta(filename):
fin = open(filename, 'r')
vglines = fin.readlines()
dR = float(vglines[2].split()[0])
dTheta = float(vglines[2].split()[1])
dPhi = float(vglines[2].split()[2])
fin.close()
return dR, dTheta, dPhi
def readStartpoints(filename):
fin = open(filename, 'r')
vglines = fin.readlines()
sR = float(vglines[3].split()[0])
sTheta = float(vglines[3].split()[1])
sPhi = float(vglines[3].split()[2])
fin.close()
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()
for line in vglines:
count += 1
if count > 4:
vel.append(float(line.split()[0]))
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') outfile = open(outputfile, 'w')
# Theta, Phi in radians, R in km number, delta, start, vel = _readVgrid(inputfile)
nR, nTheta, nPhi = readNumberOfPoints(inputfile)
dR, dTheta, dPhi = readDelta(inputfile) nR, nTheta, nPhi = number
sR, sTheta, sPhi = readStartpoints(inputfile) dR, dTheta, dPhi = delta
vel = readVelocity(inputfile) sR, sTheta, sPhi = start
thetaGrid, phiGrid, rGrid = _generateGrids(number, delta, start)
nPoints = nR * nTheta * nPhi
nX = nPhi; nY = nTheta; nZ = nR nX = nPhi; nY = nTheta; nZ = nR
sZ = sR - R sZ = sR - R
sX = getDistance(np.rad2deg(sPhi)) sX = _getDistance(sPhi)
sY = getDistance(np.rad2deg(sTheta)) sY = _getDistance(sTheta)
dX = getDistance(np.rad2deg(dPhi))
dY = getDistance(np.rad2deg(dTheta))
nPoints = nX * nY * nZ
dX = _getDistance(dPhi)
dY = _getDistance(dTheta)
dZ = dR dZ = dR
# write header # write header
@ -109,7 +53,8 @@ def vgrids2VTK(inputfile = 'vgrids.in', outputfile = 'vgrids.vtk', absOrRel = 'a
for velocity in vel: for velocity in vel:
outfile.writelines('%10f\n' %velocity) outfile.writelines('%10f\n' %velocity)
elif absOrRel == 'rel': elif absOrRel == 'rel':
velref = readVelocity(inputfileref) nref, dref, sref, velref = _readVgrid(inputfileref)
nR_ref, nTheta_ref, nPhi_ref = nref
if not len(velref) == len(vel): if not len(velref) == len(vel):
print('ERROR: Number of gridpoints mismatch for %s and %s'%(inputfile, inputfileref)) print('ERROR: Number of gridpoints mismatch for %s and %s'%(inputfile, inputfileref))
return return
@ -122,7 +67,6 @@ def vgrids2VTK(inputfile = 'vgrids.in', outputfile = 'vgrids.vtk', absOrRel = 'a
else: else:
velrel.append(0) velrel.append(0)
nR_ref, nTheta_ref, nPhi_ref = readNumberOfPoints(inputfileref)
if not nR_ref == nR and nTheta_ref == nTheta and nPhi_ref == nPhi: if not nR_ref == nR and nTheta_ref == nTheta and nPhi_ref == nPhi:
print('ERROR: Dimension mismatch of grids %s and %s'%(inputfile, inputfileref)) print('ERROR: Dimension mismatch of grids %s and %s'%(inputfile, inputfileref))
return return
@ -142,12 +86,6 @@ def rays2VTK(fnin, fdirout = './vtk_files/', nthPoint = 50):
:param: nthPoint, plot every nth point of the ray :param: nthPoint, plot every nth point of the ray
:type: integer :type: integer
''' '''
def getDistance(angle):
PI = np.pi
R = 6371.
distance = angle / 180 * (PI * R)
return distance
infile = open(fnin, 'r') infile = open(fnin, 'r')
R = 6371 R = 6371
rays = {} rays = {}
@ -155,7 +93,6 @@ def rays2VTK(fnin, fdirout = './vtk_files/', nthPoint = 50):
nPoints = 0 nPoints = 0
### NOTE: rays.dat seems to be in km and radians ### NOTE: rays.dat seems to be in km and radians
while True: while True:
raynumber += 1 raynumber += 1
firstline = infile.readline() firstline = infile.readline()
@ -173,7 +110,7 @@ def rays2VTK(fnin, fdirout = './vtk_files/', nthPoint = 50):
for index in range(nRayPoints): for index in range(nRayPoints):
if index % nthPoint is 0 or index == (nRayPoints - 1): if index % nthPoint is 0 or index == (nRayPoints - 1):
rad, lat, lon = infile.readline().split() rad, lat, lon = infile.readline().split()
rays[shotnumber][raynumber].append([getDistance(np.rad2deg(float(lon))), getDistance(np.rad2deg(float(lat))), float(rad) - R]) rays[shotnumber][raynumber].append([_getDistance(np.rad2deg(float(lon))), _getDistance(np.rad2deg(float(lat))), float(rad) - R])
else: else:
dummy = infile.readline() dummy = infile.readline()
@ -199,7 +136,6 @@ def rays2VTK(fnin, fdirout = './vtk_files/', nthPoint = 50):
# write coordinates # write coordinates
#print("Writing coordinates to VTK file...") #print("Writing coordinates to VTK file...")
for raynumber in rays[shotnumber].keys(): for raynumber in rays[shotnumber].keys():
for raypoint in rays[shotnumber][raynumber]: for raypoint in rays[shotnumber][raynumber]:
outfile.writelines('%10f %10f %10f \n' %(raypoint[0], raypoint[1], raypoint[2])) outfile.writelines('%10f %10f %10f \n' %(raypoint[0], raypoint[1], raypoint[2]))
@ -208,7 +144,6 @@ def rays2VTK(fnin, fdirout = './vtk_files/', nthPoint = 50):
# write indices # write indices
#print("Writing indices to VTK file...") #print("Writing indices to VTK file...")
count = 0 count = 0
for raynumber in rays[shotnumber].keys(): for raynumber in rays[shotnumber].keys():
outfile.writelines('%d ' %(len(rays[shotnumber][raynumber]))) outfile.writelines('%d ' %(len(rays[shotnumber][raynumber])))
@ -217,29 +152,7 @@ def rays2VTK(fnin, fdirout = './vtk_files/', nthPoint = 50):
count += 1 count += 1
outfile.writelines('\n') outfile.writelines('\n')
# outfile.writelines('POINT_DATA %15d\n' %(nPoints)) def _readVgrid(filename):
# outfile.writelines('SCALARS rays 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)
# outfile.close()
# print("Wrote velocity grid for %d points to file: %s" %(nPoints, outputfile))
def addCheckerboard(spacing = 10., pertubation = 0.1, inputfile = 'vgrids.in',
outputfile = 'vgrids_cb.in', ampmethod = 'linear', rect = (None, None)):
'''
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): def readNumberOfPoints(filename):
fin = open(filename, 'r') fin = open(filename, 'r')
vglines = fin.readlines() vglines = fin.readlines()
@ -291,6 +204,46 @@ def addCheckerboard(spacing = 10., pertubation = 0.1, inputfile = 'vgrids.in',
print("Read %d points out of file: %s" %(count - 4, filename)) print("Read %d points out of file: %s" %(count - 4, filename))
return vel return vel
# Theta, Phi in radians, R in km
nR, nTheta, nPhi = readNumberOfPoints(filename)
dR, dThetaRad, dPhiRad = readDelta(filename)
sR, sThetaRad, sPhiRad = readStartpoints(filename)
vel = readVelocity(filename)
dTheta, dPhi = np.rad2deg((dThetaRad, dPhiRad))
sTheta, sPhi = np.rad2deg((sThetaRad, sPhiRad))
number = (nR, nTheta, nPhi)
delta = (dR, dTheta, dPhi)
start = (sR, sTheta, sPhi)
return number, delta, start, vel
def _generateGrids(number, delta, start):
nR, nTheta, nPhi = number
dR, dTheta, dPhi = delta
sR, sTheta, sPhi = start
eR = sR + (nR - 1) * dR
ePhi = sPhi + (nPhi - 1) * dPhi
eTheta = sTheta + (nTheta - 1) * dTheta
thetaGrid = np.linspace(sTheta, eTheta, num = nTheta)
phiGrid = np.linspace(sPhi, ePhi, num = nPhi)
rGrid = np.linspace(sR, eR, num = nR)
return (thetaGrid, phiGrid, rGrid)
def addCheckerboard(spacing = 10., pertubation = 0.1, inputfile = 'vgrids.in',
outputfile = 'vgrids_cb.in', ampmethod = 'linear', rect = (None, None)):
'''
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 correctSpacing(spacing, delta, disttype = None): def correctSpacing(spacing, delta, disttype = None):
if spacing > delta: if spacing > delta:
spacing_corr = round(spacing / delta) * delta spacing_corr = round(spacing / delta) * delta
@ -320,35 +273,24 @@ def addCheckerboard(spacing = 10., pertubation = 0.1, inputfile = 'vgrids.in',
else: else:
print('ampFunc: Could not amplify cb pattern') print('ampFunc: Could not amplify cb pattern')
R = 6371. # earth radius
decm = 0.3 # diagonal elements of the covariance matrix (grid3dg's default value is 0.3) decm = 0.3 # diagonal elements of the covariance matrix (grid3dg's default value is 0.3)
outfile = open(outputfile, 'w') outfile = open(outputfile, 'w')
# Theta, Phi in radians, R in km number, delta, start, vel = _readVgrid(inputfile)
nR, nTheta, nPhi = readNumberOfPoints(inputfile)
dR, dThetaRad, dPhiRad = readDelta(inputfile)
sR, sThetaRad, sPhiRad = readStartpoints(inputfile)
vel = readVelocity(inputfile)
dTheta, dPhi = np.rad2deg((dThetaRad, dPhiRad)) nR, nTheta, nPhi = number
sTheta, sPhi = np.rad2deg((dThetaRad, dPhiRad)) dR, dTheta, dPhi = delta
sR, sTheta, sPhi = start
eR = sR + (nR - 1) * dR
ePhi = sPhi + (nPhi - 1) * dPhi thetaGrid, phiGrid, rGrid = _generateGrids(number, delta, start)
eTheta = sTheta + (nTheta - 1) * dTheta
nPoints = nR * nTheta * nPhi nPoints = nR * nTheta * nPhi
thetaGrid = np.linspace(sTheta, eTheta, num = nTheta)
phiGrid = np.linspace(sPhi, ePhi, num = nPhi)
rGrid = np.linspace(sR, eR, num = nR)
# write header for velocity grid file (in RADIANS) # write header for velocity grid file (in RADIANS)
outfile.writelines('%10s %10s \n' %(1, 1)) outfile.writelines('%10s %10s \n' %(1, 1))
outfile.writelines('%10s %10s %10s\n' %(nR, nTheta, nPhi)) outfile.writelines('%10s %10s %10s\n' %(nR, nTheta, nPhi))
outfile.writelines('%10s %10s %10s\n' %(dR, dThetaRad, dPhiRad)) outfile.writelines('%10s %10s %10s\n' %(dR, np.deg2rad(dTheta), np.deg2rad(dPhi)))
outfile.writelines('%10s %10s %10s\n' %(sR, sThetaRad, sPhiRad)) outfile.writelines('%10s %10s %10s\n' %(sR, np.deg2rad(sTheta), np.deg2rad(sPhi)))
spacR = correctSpacing(spacing, dR, '[meter], R') spacR = correctSpacing(spacing, dR, '[meter], R')
spacTheta = correctSpacing(_getAngle(spacing), dTheta, '[degree], Theta') spacTheta = correctSpacing(_getAngle(spacing), dTheta, '[degree], Theta')
@ -402,6 +344,85 @@ def addCheckerboard(spacing = 10., pertubation = 0.1, inputfile = 'vgrids.in',
'Outputfile: %s.'%(inputfile, spacing, pertubation, outputfile)) 'Outputfile: %s.'%(inputfile, spacing, pertubation, outputfile))
outfile.close() outfile.close()
def addBox(x = (None, None), y = (None, None), z = (None, None),
boxvelocity = 1.0, inputfile = 'vgrids.in',
outputfile = 'vgrids_box.in'):
'''
Add a box with constant velocity to an existing vgrids.in velocity model.
:param: x, borders of the box (xleft, xright)
type: tuple
:param: y, borders of the box (yleft, yright)
type: tuple
:param: z, borders of the box (bot, top)
type: tuple
:param: boxvelocity, default: 1.0 km/s
type: float
'''
R = 6371.
decm = 0.3 # diagonal elements of the covariance matrix (grid3dg's default value is 0.3)
outfile = open(outputfile, 'w')
theta1 = _getAngle(y[0])
theta2 = _getAngle(y[1])
phi1 = _getAngle(x[0])
phi2 = _getAngle(x[1])
r1 = R + z[0]
r2 = R + z[1]
print('Adding box to grid with theta = (%s, %s), phi = (%s, %s), '
'r = (%s, %s), velocity = %s [km/s]'
%(theta1, theta2, phi1, phi2, r1, r2, boxvelocity))
number, delta, start, vel = _readVgrid(inputfile)
nR, nTheta, nPhi = number
dR, dTheta, dPhi = delta
sR, sTheta, sPhi = start
thetaGrid, phiGrid, rGrid = _generateGrids(number, delta, start)
nPoints = nR * nTheta * nPhi
# write header for velocity grid file (in RADIANS)
outfile.writelines('%10s %10s \n' %(1, 1))
outfile.writelines('%10s %10s %10s\n' %(nR, nTheta, nPhi))
outfile.writelines('%10s %10s %10s\n' %(dR, np.deg2rad(dTheta), np.deg2rad(dPhi)))
outfile.writelines('%10s %10s %10s\n' %(sR, np.deg2rad(sTheta), np.deg2rad(sPhi)))
count = 0
for radius in rGrid:
if r1 <= radius <= r2:
rFlag = 1
else:
rFlag = 0
for theta in thetaGrid:
if theta1 <= theta <= theta2:
thetaFlag = 1
else:
thetaFlag = 0
for phi in phiGrid:
if phi1 <= phi <= phi2:
phiFlag = 1
else:
phiFlag = 0
velocity = vel[count]
if rFlag * thetaFlag * phiFlag is not 0:
velocity = boxvelocity
outfile.writelines('%10s %10s\n'%(velocity, decm))
count += 1
progress = float(count) / float(nPoints) * 100
_update_progress(progress)
print('Added box to the grid in file %s. '
'Outputfile: %s.'%(inputfile, outputfile))
outfile.close()
def _update_progress(progress): def _update_progress(progress):
sys.stdout.write("%d%% done \r" % (progress) ) sys.stdout.write("%d%% done \r" % (progress) )
sys.stdout.flush() sys.stdout.flush()
@ -415,3 +436,9 @@ def _getAngle(distance):
angle = distance * 180. / (PI * R) angle = distance * 180. / (PI * R)
return angle return angle
def _getDistance(angle):
PI = np.pi
R = 6371.
distance = angle / 180 * (PI * R)
return distance