/
e3d_classes.py
509 lines (429 loc) · 17.6 KB
/
e3d_classes.py
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import csv
import glob
import os
import pickle
import smtplib
import subprocess
import warnings
import matplotlib as plt
from pylab import *
from numpy import *
from scipy import signal
import matplotlib.animation as animation
from matplotlib.patches import Patch
from time import localtime, strftime
#--------------------------------------------------------------------
# Configuration Data
#--------------------------------------------------------------------
class Config:
def __init__(self):
try:
self.load('./e3d_default.pkl')
except:
self.default()
self.save()
def addmaterial(self, N):
self.material.insert(N, Material())
def addsource(self, N):
self.source.insert(N, Source())
#self.source = self.source + [Source()]
def default(self):
self.basic = Basic()
self.boundary = Boundary()
self.material = [Material()]
self.model = Model()
self.path = Path()
self.source = [Source()]
self.output = Output()
def delmaterial(self, N):
self.material.pop(N)
def delsource(self, N):
self.source.pop(N)
def load(self, name):
back = open(name, 'rb')
tmp = pickle.load(back)
back.close()
self.__dict__.update(tmp)
def save(self, name='./e3d_default.pkl'):
back = open(name, 'wb')
pickle.dump(self.__dict__, back, 2)
back.close()
class Basic:
def __init__(self):
#Basic Configuration
self.acoust = 1
self.atten = 0
self.degrees_free = 1
self.loopnum = 1
self.multicore = [1, 1, 1]
self.multimodel = 0
self.newmodel = 0
self.run = 1
self.units = 1
class Boundary:
def __init__(self):
#Boundary Configuration
self.type = 3
self.sponge = 0
self.atten = 1
self.atten_thick = 25
self.atten_val = 5
self.rand = 1
class Material():
def __init__(self):
self.mn = [3.0, 1.73, 2.7, 40.0, 40.0]
self.sd = [0.01, 0.01, 0.0, 0.0, 0.0]
self.dist = [0.0, 1.0, 1.0, 1.0, 0.0]
self.type = 7
self.geo = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
class Model:
def __init__(self):
self.dims = 3
self.size = [1.0, 1.0, 1.0]
self.spacing = [0.005, 0.005, 0.005]
self.number = [200, 200, 200]
self.origin = [0.0, 0.0, 0.0]
self.time = 1.0
self.dt = 1e-3
self.timesteps = 1e3
self.max_dtct = 0.1
self.v_avg = [0, 0, 0, 0, 0]
self.v_min = [0, 0, 0, 0, 0]
self.v_max = [0, 0, 0, 0, 0]
class Movies:
def __init__(self):
self.dir = 'z'
self.loc = 0.5
self.type = 13
class Output:
def __init__(self):
self.filt = 0
self.bandpass = [0.0, 1.0e5]
self.dec_space = 5
self.dec_time = 10
self.model = 1
self.movie = 1
self.trace = 1
self.font = 'Helvetica'
self.fontsize = '12'
self.hres = 480 # Horizontal resolution
self.hratio = 4.0 / 3.0 # Widescreen = 16.0/9.0
self.sres = 50 # Screen resolution
self.dpi = 150 # Print resolution
self.fsize = (4, 3) # Print size
self.scale_sat = 1 # Colorbar saturation
#Add one trace and movie by default
self.movies = [Movies()]
self.traces = [Traces()]
def addmovie(self, N):
self.movies.insert(N, Movies())
def delmovie(self, N):
self.movies.pop(N)
def addtrace(self, N):
self.traces.insert(N, Traces())
def deltrace(self, N):
self.traces.pop(N)
class Path:
def __init__(self):
self.usr = str(raw_input('Input Username: '))
self.bin = os.path.expanduser('/usr/local/SeismicTools/E3D/bin/')
self.fin = 'E3D_in.txt'
self.firstmodel = ''
self.link = os.path.expanduser('~/SeismicTools/E3D/Link/')
self.log = os.path.expanduser('~/Dropbox/Python/PyE3D/')
self.log_msg = 'Test Model'
self.oldmodel = os.path.expanduser('~/SeismicTools/E3D/')
self.out = os.path.expanduser('~/SeismicTools/E3D/Results/')
self.email = 'youremail@gmail.com'
class Region:
def __init__(self, model):
self.r = zeros(model.number)
def load(self, rnumber):
fid = open('region_' + str(rnumber) + '.pkl', 'rb')
self.r = pickle.load(fid)
fid.close()
def copy(self, source, target):
target = (1 - self.r) * target + self.r * source
return target
def scale(self, source, target, mn, sd):
target = (1 - self.r) * target + self.r * (sd * source + 1) * mn
return target
class Source:
def __init__(self):
self.type = 5
self.amp = 1e20
self.freq = 10.0
self.off = 0.2
self.loc = [0.5, 0.5, 0.0]
self.wav = 1
self.F = [0.0, 0.0, 1.0]
self.M = [1.0, 1.0, 1.0, 0.0, 0.0, 0.0]
self.orient = [56.0, 41.0, 106.0, 0.0, 0.0, 0.0, 0.0, 0.0, 3.0]
class Traces:
def __init__(self):
self.dir = 'z'
self.loc = [0.5, 0.5, 0.0]
self.N = 200
self.space = 0.005
self.corr = 1
#--------------------------------------------------------------------
# Output/Input Files
#--------------------------------------------------------------------
# Model files (velocity, density, attenuation)
class Mfile:
def __init__(self, model):
self.v = zeros(model.number)
self.name = ''
def read(self, model, target):
ft = {'pvel': 'P-wave Velocity', 'svel': 'S-wave Velocity', 'rden': 'Density', 'patn': 'P-wave Attenuation',
'satn': 'S-wave Attenuation'}
self.type = target[-7:-3]
self.name = ft[self.type]
nelements = model.number[0] * model.number[1] * model.number[2]
mshape = (model.number[0], model.number[2], model.number[1])
with open(target, 'rb') as fid:
tmp = fromfile(fid, dtype='float32', count=nelements)
self.v = swapaxes(reshape(tmp, mshape, order='F'), 1, 2).astype('float')
def readfromcsv(self, model, target, type):
# Read data from csv file (format = X, Y, Z, Vp, Vs, Dens)
interp_data = genfromtxt(target, delimiter=',')
# If file looks 1D, choose nearest neighbor interpolation, otherwise choose linear interpolation
dx = amax(interp_data[:, 0]) - amin(interp_data[:, 0])
dy = amax(interp_data[:, 1]) - amin(interp_data[:, 1])
dz = amax(interp_data[:, 2]) - amin(interp_data[:, 2])
test = sorted([dx, dy, dz])
if (test[0] >= 10*test[1]):
imethod = 'nearest'
else:
imethod = 'linear'
# Interpolate
grid_x, grid_y, grid_z = meshgrid(linspace(model.origin[0], model.origin[0]+model.size[0], model.number[0]),
linspace(model.origin[1], model.origin[1]+model.size[1], model.number[1]),
linspace(model.origin[2], model.origin[2]+model.size[2], model.number[2]))
self.v = interpolate.griddat(interp_data[:, :3], interp_data[type+3], (grid_x, grid_y, grid_z), method=imethod)
def write(self, model, target):
nelements = model.number[0] * model.number[1] * model.number[2]
tmp = reshape(swapaxes(self.v, 1, 2), nelements, order='F')
with open(target, 'wb') as fid:
tmp.astype('float32').tofile(fid)
def plot(self, model, output):
Z = linspace(0, model.number[2] * model.spacing[2], model.number[2]) + model.spacing[2]
imsize = [model.origin[0], model.size[0] + model.origin[0], model.origin[1], model.size[1] + model.origin[1]]
fig = plt.figure(figsize=(output.hres / output.sres, output.hres / (output.sres * output.hratio)),
dpi=output.sres)
vimg = plt.imshow(transpose(self.v[:, :, 0]), extent=imsize, vmin=round(amin(self.v), 1) - 0.05, vmax=round(amax(self.v) + 0.05, 1),
cmap=cm.jet)
vtitle = plt.title('')
plt.xlabel('X')
plt.ylabel('Y')
plt.colorbar()
def animate(ii):
vimg.set_array(transpose(self.v[:, :, ii]))
vtitle.set_text("%s Plot (Z = %1.2fkm)" % (self.name, Z[ii]))
return vimg, vtitle
try:
ani = animation.FuncAnimation(fig, animate, frames=len(Z), interval=20, blit=False, repeat=False)
ani.save("./%s.mp4" % self.type, fps=30, codec='libx264', bitrate=1800)
except IndexError:
print 'To render movies, make sure that ffmpeg is installed!'
#plt.ion()
#plt.show() # Showing plot prevents other files from rendering
#plt.close()
# Trace files
class Tfile:
def __init__(self):
self.comp = ''
self.x = []
self.v = []
self.t = []
def all(self, target, traces, source, output):
self.read(target, traces)
self.correct(source)
self.output(output)
def read(self, target, traces):
self.comp = target[-1]
self.x = []
self.v = []
self.dir = []
self.loc = []
self.corr = []
with open(target, 'rb') as fid:
# File information
self.N = fromfile(fid, dtype='int32', count=1)
self.timesteps = fromfile(fid, dtype='int32', count=1)
self.dt = fromfile(fid, dtype='float32', count=1)
self.t = linspace(0, self.timesteps * self.dt, self.timesteps)
# Read traces
multiplex = []
while (1):
multiplex.append(fromfile(fid, dtype='int32', count=1))
if (multiplex[-1] == -1):
break
ntraces = len(multiplex) - 1
tmp = array(fromfile(fid, dtype='float32', count=self.timesteps * ntraces))
tmp = reshape(tmp, (ntraces, self.timesteps), order='F')
tmp2 = zeros((self.N, self.timesteps))
# Sort traces (if missing pad with zeros)
for ii in range(0, self.N):
try:
loc = multiplex.index(ii)
tmp2[ii, :] = tmp[loc, :]
except:
tmp2[ii, :] = zeros((1, self.timesteps))
# Separate traces
off = 0
for trace in traces:
self.v.append(tmp2[off:off + trace.N])
self.x.append(array(linspace(0, trace.N * trace.space, trace.N)))
self.loc.append(trace.loc)
self.dir.append(trace.dir.lower())
self.corr.append(trace.corr)
def correct(self, source, ctype='time'):
if (ctype == 'body') or (ctype == 'surface'):
comp = {'x': [0, 1, 2], 'y': [1, 0, 2], 'z': [2, 0, 1]}
for ii in range(0, len(self.v)):
r = sqrt((self.x[ii] - source.loc[comp[self.dir[ii]][0]]) ** 2
+ (self.loc[ii][comp[self.dir[ii]][1]] - source.loc[comp[self.dir[ii]][0]]) ** 2
+ (self.loc[ii][comp[self.dir[ii]][2]] - source.loc[comp[self.dir[ii]][0]]) ** 2)
if (ctype == 'surface'):
r = sqrt(r)
for jj in range(0, size(self.v[ii], 0)):
self.v[ii][jj][:] = self.v[ii][jj][:] * r[jj]
elif (ctype == 'time'):
Vcorr = 0.92
corr = reshape(array(sqrt(abs(self.t - source.off) / Vcorr)), (1, 1, len(self.t)))
for ii in range(0, len(self.v)):
for jj in range(0, size(self.v[ii], 0)):
self.v[ii][jj][:] = self.v[ii][jj][:]*corr
def plot(self, output):
plt.figure(figsize=output.fsize, dpi=output.dpi)
for ii in range(0, len(self.v)):
imsize = [self.t[0], self.t[-1], self.x[ii][-1], self.x[ii][0]]
lim = amax(absolute(self.v[ii])) / output.scale_sat
plt.imshow(self.v[ii], extent=imsize, vmin=-lim, vmax=lim, cmap=cm.gray, origin='upper', aspect='auto')
plt.title("%s-Velocity for Trace #%i" % (self.comp.upper(), ii))
plt.xlabel('Time (s)')
plt.ylabel('Offset (km)')
#plt.colorbar()
plt.savefig("Trace_%i_v%s.pdf" % (ii, self.comp))
plt.clf()
# Movie files
class Vfile:
def __init__(self):
self.dir = ''
self.x = []
self.y = []
self.v = []
self.t = []
def load(self, model, multicore, target):
# File information
ftype = {'.Vx': ['Vx', -3], '.Vy': ['Vy', -3], '.Vz': ['Vz', -3], 'Txx': ['Txx', -4],
'Tyy': ['Tyy', -4], 'Tzz': ['Tzz', -4], 'Txy': ['Txy', -4], 'Txz': ['Txz', -4],
'Tyz': ['Tyz', -4], '.FP': ['PP', -3], '.FS': ['SP', -3]}
comp = {'x': [1, 2], 'y': [0, 2], 'z': [0, 1]}
self.type = ftype[target[-3:]][0]
off = ftype[target[-3:]][1]
self.dir = target[0]
self.loc = target[2:off]
self.ngrids = multicore[comp[self.dir][0]] * multicore[comp[self.dir][1]]
# Global Grid information
self.fid = open(target, 'rb')
gx = fromfile(self.fid, dtype='int32', count=1)
gy = fromfile(self.fid, dtype='int32', count=1)
self.timesteps = fromfile(self.fid, dtype='int32', count=1)
self.dt = fromfile(self.fid, dtype='float32', count=1)
self.fid.seek(8 * 4)
f = fromfile(self.fid, dtype='int32', count=1)
self.fid.seek(4 * 4)
# Vectors for plotting, etc.
self.col = round((gx - 1) / f + 1)
self.row = round((gy - 1) / f + 1)
self.x = linspace(0, self.col, self.col) * model.spacing[comp[self.dir][0]] * f + model.origin[
comp[self.dir][0]]
self.y = linspace(0, self.row, self.row) * model.spacing[comp[self.dir][1]] * f + model.origin[
comp[self.dir][1]]
self.t2 = 0
self.writestep = 0
def read(self, nframes=-1):
if (nframes == -1):
nframes = self.timesteps - self.t2 # Read all remaining frames
self.v = zeros((self.col, self.row, nframes), dtype=float32)
self.t = linspace(self.t2 * self.dt, (self.t2 + nframes) * self.dt, nframes)
self.t2 += nframes
# Read frames by subgrid:
for ii in range(0, nframes):
for jj in range(0, self.ngrids):
sx = fromfile(self.fid, dtype='int32', count=1)
sy = fromfile(self.fid, dtype='int32', count=1)
sxo = fromfile(self.fid, dtype='int32', count=1)
syo = fromfile(self.fid, dtype='int32', count=1)
f = fromfile(self.fid, dtype='int32', count=1)
nx = int(floor((sx - 1) / f + 1))
ny = int(floor((sy - 1) / f + 1))
nxo = int(floor(sxo / f))
nyo = int(floor(syo / f))
tmp = fromfile(self.fid, dtype='float32', count=nx * ny)
self.v[nxo:(nxo + nx), nyo:(nyo + ny), ii] = reshape(tmp, (nx, ny), order='F')
def plot(self, output):
# Create adaptive scale
scale_len = 100
scale_fix = 250
nframes = self.v.shape[2]
scale = zeros((nframes, 1))
win = ones((scale_len, 1))
for ii in range(0, nframes):
scale[ii] = amax(absolute(self.v[:, :, ii]))
scale = convolve(squeeze(scale), squeeze(win), mode='same') / output.scale_sat
if (self.writestep == 0):
scale[:scale_fix] = scale[scale_fix]
# Initialize figure
comp = {'x': ['Y', 'Z'], 'y': ['X', 'Z'], 'z': ['X', 'Y']}
fig = plt.figure(figsize=(output.hres / output.sres, output.hres / (output.sres * output.hratio)),
dpi=output.sres)
imsize = [self.x[0], self.x[-1], self.y[-1], self.y[0]]
vimg = plt.imshow(transpose(self.v[:, :, 0]), extent=imsize, vmin=-scale[0], vmax=scale[0], cmap=cm.RdBu)
vtitle = plt.title('')
plt.xlabel(comp[self.dir][0])
plt.ylabel(comp[self.dir][1])
plt.colorbar()
def animate(ii):
vimg.set_array(transpose(self.v[:, :, ii]))
vimg.set_clim(-scale[ii], scale[ii])
vtitle.set_text("%s for %s=%s km (t=%1.2e s)" % (self.type, self.dir, self.loc, self.t[ii]))
return vimg, vtitle
try:
ani = animation.FuncAnimation(fig, animate, frames=self.v.shape[2], interval=20, blit=False, repeat=False)
if (self.writestep == 0):
ani.save("./%s_%s_%s.mp4" % (self.dir, self.loc, self.type), fps=30, codec='libx264', bitrate=1800)
else:
ani.save("./%s_%s_%s_%i.mp4" % (self.dir, self.loc, self.type, self.writestep), fps=30, codec='libx264', bitrate=1800)
except IndexError:
print 'To render movies, make sure that ffmpeg is installed!'
self.writestep += 1
# SAC File
class Sacfile:
def __init__(self):
self.hd = -12345 * ones(158)
self.V = []
self.dt = 1
def create_header(self):
self.hd[0] = self.dt
self.hd[5] = 0
self.hd[6] = (len(self.V) - 1) * self.dt
self.hd[7] = 0
self.hd[76] = 6
self.hd[79] = len(self.V)
self.hd[85] = 1
self.hd[87] = 11
self.hd[105] = 1
def write(self, fname):
with open(fname, 'wb') as fid:
self.hd[:70].astype('float32').tofile(fid)
self.hd[70:].astype('int32').tofile(fid)
self.V.astype('float32').tofile(fid)
def read(self, fname):
with open(fname, 'wb') as fid:
self.hd[:70] = fromfile(fid, dtype='float32', count=70)
self.hd[70:] = fromfile(fid, dtype='int32', count=88)
self.dt = self.hd[0]
self.V = fromfile(fid, dtype='float32', count=self.hd[79])