def __init__(self, claw, fmin=0.2, fmax=5., order=4.0, dt=1. / 12.):
"""
:param claw: Claw object, phase velocity dispersion laws
:param fmin: lower frequency for butterworth or central freq for gaussian bandpass, (Hz)
:param fmax: upper frequency for butterworth or central freq for gaussian bandpass, (Hz)
:param order: filter order for butterworth or gaussian bandpass
:param dt: sampling interval (s)
"""
self.c = claw #
self.fmin = fmin # 0.2
self.fmax = fmax # 5.
self.order = order # 4.
self.dt = dt # 1. / 12.
assert self.fmax <= 0.5 / self.dt # nyquist criterion
if self.fmin < self.fmax:
f = freqspace(self.fmin, self.fmax, 100, 'flog')
c = self.c(f)
self.cmin, self.cmax = np.min(c), np.max(c)
else:
self.cmin = self.cmax = self.c(self.fmin)
def __init__(self,
claws,
fmin=0.2,
fmax=5.,
order=4.0,
dt=1. / 12.): # , proj = mp):
"""
:param claws: list of Claw objects, phase velocity dispersion laws, first one must have interpolationmode = to 0
:param fmin: lower frequency for butterworth or central freq for gaussian bandpass, (Hz)
:param fmax: upper frequency for butterworth or central freq for gaussian bandpass, (Hz)
:param order: filter order for butterworth or gaussian bandpass
:param dt: sampling interval (s)
"""
self.claws = claws #
self.fmin = fmin # 0.2
self.fmax = fmax # 5.
self.order = order # 4.
self.dt = dt # 1. / 12.
assert self.fmax <= 0.5 / self.dt # nyquist criterion
assert 0. < self.fmin < self.fmax
# find lowest group velocities
self.umin, self.umax = np.inf, -np.inf
for claw in self.claws:
ftmp = freqspace(self.fmin, self.fmax, 100, 'flog')
utmp = claw.to_ulaw()(ftmp)
utmp = utmp[~np.isnan(utmp)]
if len(utmp):
self.umin = np.min([self.umin, utmp.min()])
self.umax = np.max([self.umax, utmp.max()])
assert isfloat(self.umin)
assert isfloat(self.umax)
assert 0. <= self.umin <= self.umax
print "group velocity range : %f - %fkm/s" % (self.umin, self.umax)
def target(argv, verbose):
for k in argv.keys():
if k in ['main', "_keyorder"]:
continue # private keys
if k not in authorized_keys:
raise Exception('option %s is not recognized' % k)
# determine root names from target filess
rootnames = []
for s96 in argv['main']:
rootname = "_HerrMet_" + s96.split('/')[-1].split('.s96')[0].split(
'.surf96')[0]
rootnames.append(rootname)
assert len(np.unique(rootnames)) == len(
rootnames) # make sure all rootnames are distinct
# handle already existing files
if "-ot" not in argv.keys():
for rootname in rootnames:
if os.path.exists('%s/_HerrMet.target' % rootname):
raise Exception(
'file %s/_HerrMet.target exists already, use -ot to overwrite'
% rootname)
# loop over targets
for rootname, s96 in zip(rootnames, argv['main']):
# create directory
if not os.path.isdir(rootname):
os.mkdir(rootname)
os.system('cp %s %s/%s.copy' % (s96, rootname, s96.split('/')[-1]))
s = surf96reader(s96)
# -------------------
if "-resamp" in argv.keys():
news = s.copy()
news.clear() # clear all entries
newf = freqspace(freqmin=float(argv["-resamp"][0]),
freqmax=float(argv["-resamp"][1]),
nfreq=int(argv["-resamp"][2]),
scale=argv["-resamp"][3])
for law in s.get_all():
law.set_extrapolationmode(1)
stdlaw = Claw(freq=law.freq,
value=law.dvalue,
extrapolationmode=0)
newvalues = law(newf)
newdvalues = stdlaw(newf)
I = ~np.isnan(newvalues)
if I.any():
N = I.sum()
news.data['WAVE'] = np.concatenate(
(news.data['WAVE'], np.array([law.wave]).repeat(N)))
news.data['TYPE'] = np.concatenate(
(news.data['TYPE'], np.array([law.type]).repeat(N)))
news.data['FLAG'] = np.concatenate(
(news.data['FLAG'], np.array([law.flag]).repeat(N)))
news.data['MODE'] = np.concatenate(
(news.data['MODE'], np.array([law.mode]).repeat(N)))
news.data['PERIOD'] = np.concatenate(
(news.data['PERIOD'], 1. / newf[I]))
news.data['VALUE'] = np.concatenate(
(news.data['VALUE'], newvalues[I]))
news.data['DVALUE'] = np.concatenate(
(news.data['DVALUE'], newdvalues[I]))
s = news
# print news
# -------------------
if "-lunc" in argv.keys():
# set uncertainties to constant in log domain
lunc = float(argv["-lunc"][0])
s.data['DVALUE'] = s.data['VALUE'] * lunc
elif "-unc" in argv.keys():
# set uncertainties to constant in lin domain
unc = float(argv["-unc"][0])
s.data['DVALUE'] = np.ones(len(s.data['VALUE'])) * unc
# -------------------
if verbose:
print "writing %s/_HerrMet.target" % rootname
s.write96('%s/_HerrMet.target' % rootname)
# -------------------
print "please keep only datapoints to invert in */_HerrMet.target"
print "use option --display to see the target data"
def _display_function(rootname, argv, verbose, mapkwargs):
"""private"""
targetfile = "%s/_HerrMet.target" % rootname
paramfile = "%s/_HerrMet.param" % rootname
runfile = '%s/_HerrMet.run' % rootname
pngfile = '%s/_HerrMet.png' % rootname
#HerrLininitfile = '%s/_HerrLin.init' % rootname
# ------ Initiate the displayer using the target data if exists
if "-compact" in argv.keys(): # compact mode
which_displayer = DepthDispDisplayCompact
else:
which_displayer = DepthDispDisplay
if os.path.exists(targetfile):
rd = which_displayer(targetfile=targetfile)
d = makedatacoder(
targetfile, which=Datacoder_log) # datacoder based on observations
dobs, _ = d.target()
else:
print "no target file found in %s" % rootname
rd = which_displayer()
# ------ Display run results if exist
if os.path.exists(runfile) and ("-plot" in argv.keys()
or "-pdf" in argv.keys()):
with RunFile(runfile, verbose=verbose) as rundb:
s = rundb.select('select MODELID from MODELS limit 1')
if s is not None:
# --- display best models
if "-plot" in argv.keys():
assert argv["-plot"] == [] or len(
argv["-plot"]) == 4 # unexpected argument number
if argv["-plot"] == []:
plot_mode, plot_limit, plot_llkmin, plot_step = \
default_plot_mode, default_plot_limit, \
default_plot_llkmin, default_plot_step
elif len(argv['-plot']) == 4:
plot_mode, plot_limit, plot_llkmin, plot_step = argv[
'-plot']
else:
raise Exception()
print "plot : %s, limit %d, llkmin %f, step %d" % (
plot_mode, plot_limit, plot_llkmin, plot_step),
if plot_mode == "best":
chainids, weights, llks, ms, ds = \
rundb.getzip(limit=plot_limit,
llkmin=plot_llkmin,
step=plot_step,
algo="METROPOLIS")
elif plot_mode == "last":
chainids, weights, llks, ms, ds = \
rundb.getlastszip(limit=plot_limit,
llkmin=plot_llkmin,
step=plot_step,
algo="METROPOLIS")
else:
raise Exception('unexpected plot mode %s' % plot_mode)
vmin, vmax = llks.min(), llks.max()
# colors = values2colors(llks, vmin=vmin, vmax=vmax, cmap=argv['-cmap'])
if "-overdisp" in argv.keys():
"""note : recomputing dispersion with another frequency array might
result in a completely different dispersion curve in case
of root search failure """
waves, types, modes, freqs, _ = ds[0]
overwaves, overtypes, overmodes, _, _ = zip(*list(
groupbywtm(waves, types, modes, freqs,
np.arange(len(freqs)), None, True)))
overfreqs = [
freqspace(0.6 * min(freqs), 1.4 * max(freqs), 100,
"plog") for _ in xrange(len(overwaves))
]
overwaves, overtypes, overmodes, overfreqs = \
igroupbywtm(overwaves, overtypes, overmodes, overfreqs)
for llk, (mms, dds) in zip(
llks[::-1],
overdisp(ms[::-1],
overwaves,
overtypes,
overmodes,
overfreqs,
verbose=verbose,
**mapkwargs)):
# rd.plotmodel(color=clr, alpha=1.0, linewidth=3, *mms)
rd.addmodel(colorvalue=llk, *mms)
try:
# rd.plotdisp(color=clr, alpha=1.0, linewidth=3, *dds)
rd.adddisp(colorvalue=llk, *dds)
except KeyboardInterrupt:
raise
except Exception as e:
print "Error : could not plot dispersion curve (%s)" % str(
e)
# cb = makecolorbar(vmin=vmin, vmax=vmax, cmap=argv['-cmap'])
# pos = rd.axdisp[-1].get_position()
# cax = rd.fig.add_axes((pos.x0, 0.12, pos.width, 0.01))
# rd.fig.colorbar(cb, cax=cax, label="log likelyhood", orientation="horizontal")
else:
"display the dispersion curves as stored in the database"
for i in range(len(llks))[::-1]:
# rd.plotmodel(color=colors[i], alpha=1.0, linewidth=3, *ms[i])
# rd.plotdisp(color=colors[i], alpha=1.0, linewidth=3, *ds[i])
rd.addmodel(colorvalue=llks[i], *ms[i])
rd.adddisp(colorvalue=llks[i], *ds[i])
# cb = makecolorbar(vmin=vmin, vmax=vmax, cmap=argv['-cmap'])
# pos = rd.axdisp[-1].get_position()
# cax = rd.fig.add_axes((pos.x0, 0.12, pos.width, 0.01))
# rd.fig.colorbar(cb, cax=cax, label="log likelyhood", orientation="horizontal")
# cax.set_xticklabels(cax.get_xticklabels(), rotation=90., horizontalalignment="center")
rd.showdispcoll(vmin=vmin,
vmax=vmax,
cmap=argv['-cmap'],
alpha=1.0,
linewidth=3)
rd.showdepthcoll(vmin=vmin,
vmax=vmax,
cmap=argv['-cmap'],
alpha=1.0,
linewidth=3)
rd.colorbar(vmin=vmin,
vmax=vmax,
cmap=argv['-cmap'],
label="log likelyhood",
orientation="horizontal")
print rd.cax.get_position()
rd.cax.set_xticklabels(rd.cax.get_xticklabels(),
rotation=90.,
horizontalalignment="center")
# ---- display posterior pdf
if "-pdf" in argv.keys():
assert argv["-pdf"] == [] or len(
argv["-pdf"]) == 4 # unexpected argument number
if argv["-pdf"] == []:
pdf_mode, pdf_limit, pdf_llkmin, pdf_step = \
default_pdf_mode, default_pdf_limit, default_pdf_llkmin, default_pdf_step
elif len(argv['-pdf']) == 4:
pdf_mode, pdf_limit, pdf_llkmin, pdf_step = argv[
'-pdf']
else:
raise Exception()
print "pdf : %s, limit %d, llkmin %f, step %d" % (
pdf_mode, pdf_limit, pdf_llkmin, pdf_step),
if pdf_mode == "best":
chainids, weights, llks, ms, ds = \
rundb.getzip(limit=pdf_limit,
llkmin=pdf_llkmin,
step=pdf_step,
algo="METROPOLIS")
elif pdf_mode == "last":
chainids, weights, llks, ms, ds = \
rundb.getlastszip(limit=pdf_limit,
llkmin=pdf_llkmin,
step=pdf_step,
algo="METROPOLIS")
else:
raise Exception('unexpected pdf mode %s' % pdf_mode)
dms = [
depthmodel_from_arrays(ztop, vp, vs, rh)
for ztop, vp, vs, rh in ms
]
# display percentiles of model and data pdfs
clr = "b" if "-plot" not in argv.keys() else "k"
alp = 1.0 if "-plot" not in argv.keys() else 0.5
for p, (vppc, vspc, rhpc, prpc) in \
dmstats1(dms,
percentiles=[0.01, 0.16, 0.5, 0.84, 0.99],
Ndepth=100,
Nvalue=100,
weights=weights,
**mapkwargs):
try:
l = 3 if p == 0.5 else 1
for what, where in zip([vppc, vspc, rhpc, prpc], [
rd.axdepth['VP'], rd.axdepth['VS'],
rd.axdepth['RH'], rd.axdepth['PR']
]):
if where is not None:
what.show(where,
color=clr,
linewidth=l,
alpha=alp)
except KeyboardInterrupt:
raise
except Exception as e:
print "Error", str(e)
# display the disp pdf
for p, (wpc, tpc, mpc, fpc, vpc) in \
dispstats(ds,
percentiles=[0.01, 0.16, 0.5, 0.84, 0.99],
Ndisp=100,
weights=weights,
**mapkwargs):
try:
l = 3 if p == 0.5 else 1
rd.plotdisp(wpc,
tpc,
mpc,
fpc,
vpc,
dvalues=None,
color=clr,
alpha=alp,
linewidth=l)
except KeyboardInterrupt:
raise
except Exception as e:
print "Error", str(e)
# ------
if os.path.exists(paramfile):
p, _ = load_paramfile(paramfile)
showvp, showvs, showrh, showpr = True, True, True, True
if isinstance(p, Parameterizer_mZVSVPRH):
showpr = False
elif isinstance(p, Parameterizer_mZVSPRRH):
showvp = False
elif isinstance(p, Parameterizer_mZVSPRzRHvp):
showvp = showpr = showrh = False
elif isinstance(p, Parameterizer_mZVSPRzRHz):
showvp = showpr = showrh = False
else:
raise Exception('')
#
vplow, vphgh, vslow, vshgh, rhlow, rhhgh, prlow, prhgh = p.boundaries()
for what, where in zip(\
[vplow, vphgh, vslow, vshgh, rhlow, rhhgh, prlow, prhgh],
[rd.axdepth['VP'], rd.axdepth['VP'], rd.axdepth['VS'], rd.axdepth['VS'], rd.axdepth['RH'], rd.axdepth['RH'], rd.axdepth['PR'], rd.axdepth['PR']]):
if where is not None:
what.show(where,
alpha=1.0,
color="k",
marker="o--",
linewidth=1,
markersize=3)
zmax = 1.1 * p.inv(p.MINF)[0][-1]
if isinstance(p, Parameterizer_mZVSPRzRHvp):
rd.axdepth['PR'].plot(p.PRz(np.linspace(0., zmax, 100)),
np.linspace(0., zmax, 100),
"r--",
linewidth=3)
legendtext(rd.axdepth['PR'], p.PRzName, loc=4)
legendtext(rd.axdepth['RH'], p.RHvpName, loc=4)
elif isinstance(p, Parameterizer_mZVSPRzRHz):
rd.axdepth['PR'].plot(p.PRz(np.linspace(0., zmax, 100)),
np.linspace(0., zmax, 100),
"r--",
linewidth=3)
rd.axdepth['RH'].plot(p.RHz(np.linspace(0., zmax, 100)),
np.linspace(0., zmax, 100),
"r--",
linewidth=3)
legendtext(rd.axdepth['PR'], p.PRzName, loc=4)
legendtext(rd.axdepth['RH'], p.RHzName, loc=4)
rd.set_zlim(np.array([0, zmax]))
else:
print "call option --param to see prior depth boundaries"
# --------------------
if "-m96" in argv.keys(): # plot user data on top
for m96 in argv['-m96']:
try:
dm = depthmodel_from_mod96(m96)
dm.vp.show(rd.axdepth['VP'], "m", linewidth=3, label=m96)
dm.vs.show(rd.axdepth['VS'], "m", linewidth=3)
dm.rh.show(rd.axdepth['RH'], "m", linewidth=3)
dm.pr().show(rd.axdepth['PR'], "m", linewidth=3)
except KeyboardInterrupt:
raise
except: #Exception as e:
print 'could not read or display %s (reason : %s)' % (m96,
str(e))
rd.axdepth['VP'].legend(loc=3)
if "-ritt" in argv.keys():
a = AsciiFile('/mnt/labex2/home/max/data/boreholes/GRT1/GRT1.logsonic')
for what, where in zip(
[a.data['VS'], a.data['VP'], a.data['VP'] / a.data['VS']],
[rd.axdepth['VS'], rd.axdepth['VP'], rd.axdepth['PR']]):
if where is not None:
where.plot(what, a.data['TVD'] / 1000., "m", alpha=0.5)
# --------------------
if os.path.exists(targetfile):
# plot data on top
rd.plotdisp(d.waves,
d.types,
d.modes,
d.freqs,
d.inv(dobs),
dvalues=d.dvalues,
alpha=.5,
color="r",
linewidth=2)
if "-overdisp" in argv.keys():
rd.set_vlim((0.5 * d.values.min(), 1.5 * d.values.max()))
rd.set_plim((0.8 / overfreqs.max(), 1.2 / overfreqs.min()))
else:
rd.set_vlim((0.8 * d.values.min(), 1.2 * d.values.max()))
rd.set_plim((0.8 / d.freqs.max(), 1.2 / d.freqs.min()))
rd.tick()
rd.grid()
rd.fig.suptitle(rootname.split('_HerrMet_')[-1])
if "-ftsz" in argv.keys():
chftsz(rd.fig, argv["-ftsz"][0])
else:
chftsz(rd.fig, default_fontsize)
if "-png" in argv.keys():
dpi = argv['-png'][0] if len(argv['-png']) else default_dpi
if verbose:
print "writing %s" % pngfile
rd.fig.savefig(pngfile, dpi=dpi)
elif "-inline" in argv.keys():
plt.show()
else:
showme()
plt.close(rd.fig)
if I.any():
s = "\n".join([fmt.format(\
wave = law.wave,
type = law.type,
flag = law.flag,
mode = law.mode,
period = 1./ff,
value = vv,
dvalue = ss) for ff, vv, ss in zip(newf[I], newv[I], news[I])])
return s
return ""
sfx = argv["sfx"][0] if "sfx" in argv.keys() else "resamp"
print argv['fspace']
newf = freqspace(
float(argv['fspace'][0]), float(argv['fspace'][1]),
int(argv['fspace'][2]),
argv['fspace'][3]) #np.sort(np.unique(np.abs(argv['newf'])))
print newf
for f in argv['resamp']:
s = surf96reader(f)
fout = ".".join(
f.split('/')[-1].split('.')[:-1] + [sfx] +
[f.split('/')[-1].split('.')[-1]])
print fout
out = ""
for law in s.get_all():
out += "\n" + tostr(law, newf)
out = out.strip('\n').strip()
with open(fout, 'w') as fid:
fid.write(out)
from srfpython.Herrmann.Herrmann import HerrmannCaller, Curve
for m in argv['disp']:
dm = depthmodel_from_mod96(m)
ztop = dm.vp.ztop()
vp = dm.vp.values
vs = dm.vs.values
rh = dm.rh.values
#Waves, Types, Modes, Freqs = [], [], [], []
curves = []
for k in argv.keys():
if k[0].upper() in "RL" and k[1].upper(
) in "UC" and k[2] in "0123456789":
fstart, fend, nfreq, fspace = argv[k]
freqs = freqspace(float(fstart), float(fend), int(nfreq),
fspace)
curve = Curve(
wave=k[0], # Waves.append(k[0])
type=k[1], # Types.append(k[1])
mode=int(k[2:]), # Modes.append(int(k[2:]))
freqs=freqs) # Freqs.append(freq)
curves.append(curve)
hc = HerrmannCaller(curves=curves)
curves = hc(ztop, vp, vs, rh)
if "save" in argv.keys():
sfx = ""
s96out = ".".join(
m.split('/')[-1].split('.')[:-1]) + sfx + ".surf96"
while os.path.exists(s96out):
s96out = s96out.split(sfx + '.surf96')[0]
def target(argv, verbose):
if '-h' in argv.keys() or "-help" in argv.keys():
print(long_help)
return
for k in argv.keys():
if k in ['main', "_keyorder"]:
continue # private keys
if k not in authorized_keys:
raise Exception('option %s is not recognized' % k)
# determine root names from target filess
rootnames = []
for s96 in argv['main']:
rootname = ROOTNAME.format(node=surf96filename_to_nodename(s96))
rootnames.append(rootname)
assert len(np.unique(rootnames)) == len(
rootnames) # make sure all rootnames are distinct
# handle already existing files
if "-ot" not in argv.keys():
for rootname in rootnames:
target_file = HERRMETTARGETFILE.format(rootname=rootname)
if os.path.exists(target_file):
raise Exception(
'file {} exists already, use -ot to overwrite' %
target_file)
# loop over targets
for rootname, s96 in zip(rootnames, argv['main']):
target_file = HERRMETTARGETFILE.format(rootname=rootname)
target_dir = os.path.dirname(target_file)
# create directory
if not os.path.isdir(target_dir):
if verbose:
print("creating " + target_dir)
os.makedirs(target_dir)
s96copy = os.path.join(target_dir, os.path.basename(s96)) + ".copy"
cpcmd = 'cp {} {}'.format(s96, s96copy)
if verbose:
print(cpcmd)
os.system(cpcmd)
s = surf96reader(s96)
if "-resamp" in argv.keys():
news = s.copy()
news.clear() # clear all entries
newf = freqspace(freqmin=float(argv["-resamp"][0]),
freqmax=float(argv["-resamp"][1]),
nfreq=int(argv["-resamp"][2]),
scale=argv["-resamp"][3])
for law in s.get_all():
law.set_extrapolationmode(1)
stdlaw = Claw(freq=law.freq,
value=law.dvalue,
extrapolationmode=0)
newvalues = law(newf)
newdvalues = stdlaw(newf)
I = ~np.isnan(newvalues)
if I.any():
N = I.sum()
news.data['WAVE'] = np.concatenate(
(news.data['WAVE'], np.array([law.wave]).repeat(N)))
news.data['TYPE'] = np.concatenate(
(news.data['TYPE'], np.array([law.type]).repeat(N)))
news.data['FLAG'] = np.concatenate(
(news.data['FLAG'], np.array([law.flag]).repeat(N)))
news.data['MODE'] = np.concatenate(
(news.data['MODE'], np.array([law.mode]).repeat(N)))
news.data['PERIOD'] = np.concatenate(
(news.data['PERIOD'], 1. / newf[I]))
news.data['VALUE'] = np.concatenate(
(news.data['VALUE'], newvalues[I]))
news.data['DVALUE'] = np.concatenate(
(news.data['DVALUE'], newdvalues[I]))
s = news
# print news
if "-lunc" in argv.keys():
# set uncertainties to constant in log domain
lunc = float(argv["-lunc"][0])
s.data['DVALUE'] = s.data['VALUE'] * lunc
elif "-unc" in argv.keys():
# set uncertainties to constant in lin domain
unc = float(argv["-unc"][0])
s.data['DVALUE'] = np.ones(len(s.data['VALUE'])) * unc
if verbose:
print("writing " + target_file)
s.write96(target_file)
# -------------------
print("please keep only datapoints to invert in " +
HERRMETTARGETFILE.format(rootname="*"))
print("use option --display to see the target data")
