def test_from_CMTSOLUTION_file(cmt):
origin_time = obspy.UTCDateTime(2001, 9, 9, 23, 59, 17.78)
cmt_time = origin_time + 2.0
cmt_true = \
CMTSource(origin_time=origin_time,
pde_latitude=34.0745, pde_longitude=-118.3792,
pde_depth_in_m=6400, mb=4.2, ms=4.2, region_tag="Hollywood",
eventname="9703873", cmt_time=cmt_time, half_duration=1.0,
latitude=34.1745, longitude=-118.4792, depth_in_m=5400.0,
m_rr=1.0e22, m_tt=-1.0e22)
assert cmt == cmt_true
def get_stats_json(filename):
"""Reads the stats json and outputs dictionary with
all the necessary data
"""
d = load_json(os.path.abspath(filename))
data_container = {
"sta_lon": np.array(d["sta_lon"]),
"sta_lat": np.array(d["sta_lat"]),
"nwindows": d["nwindows"],
"nwin_on_trace": d["nwin_on_trace"]
}
cmtsource = CMTSource.from_dictionary(d["oldcmt"])
new_cmtsource = CMTSource.from_dictionary(d["newcmt"])
config = Struct(**d["config"])
nregions = d["nregions"]
bootstrap_mean = np.array(d["bootstrap_mean"])
bootstrap_std = np.array(d["bootstrap_std"])
var_reduction = d["var_reduction"]
mode = d["mode"]
G = d["G"]
stats = d["stats"]
return (data_container, cmtsource, new_cmtsource, config, nregions,
bootstrap_mean, bootstrap_std, var_reduction, mode, G, stats)
def test_pycmt3d():
npar = 9
cmtsource = CMTSource.from_CMTSOLUTION_file(cmtfile)
# modify the flexwin output file by adding the absolute path
flexwin_output = modify_input_winfile(original_flexwin_output)
data_con = DataContainer(PAR_LIST[0:npar])
data_con.add_measurements_from_sac(flexwin_output)
config = Config(npar, dlocation=0.03, ddepth=3.0, dmoment=2.0e+23,
weight_data=True, weight_function=None,
normalize_window=True, station_correction=True,
zero_trace=True, double_couple=False, lamda_damping=0.0,
bootstrap=True)
srcinv = Cmt3D(cmtsource, data_con, config)
srcinv.source_inversion()
def gradient(cmt_file_db, param_path):
"""Runs the actual inversion.
:param cmt_file_db:
:param param_path:
:return: Nothing, inversion results are written to file.
"""
# Inversion Params
inversionparam_path = os.path.join(param_path,
"CMTInversion/InversionParams.yml")
INV_params = read_yaml_file(inversionparam_path)
# Weight Params
weightparam_path = os.path.join(param_path,
"CMTInversion/WeightParams.yml")
weight_params = read_yaml_file(weightparam_path)
# Check if grid search should be performed from the parameters file
if not bool(INV_params["gridsearch"]):
return
# Get processing path from cmt_filename in database
cmt_dir = os.path.dirname(os.path.abspath(cmt_file_db))
# Create cmt source:
cmtsource = CMTSource.from_CMTSOLUTION_file(cmt_file_db)
# Inversion dictionary directory
inv_dict_dir = os.path.join(cmt_dir, "inversion", "inversion_dicts")
# Inversion dictionaries
inv_dict_files = glob.glob(os.path.join(inv_dict_dir, "grid*"))
# Inversion output directory
inv_out_dir = os.path.join(cmt_dir, "inversion", "inversion_output", "g3d")
# WRite start of inversion process
logger.info(" ")
logger.info("#######################################################")
logger.info("# #")
logger.info("# Starting inversion ... #")
logger.info("# #")
logger.info("#######################################################")
logger.info(" ")
# Creating Data container
dcon = DataContainer()
for _i, inv_dict_file in enumerate(inv_dict_files):
# Get processing band
bandstring1 = str(os.path.basename(inv_dict_file).split(".")[1])
if "surface" in bandstring1 or "body" in bandstring1:
bandstring = bandstring1.split("#")[0]
else:
bandstring = bandstring1
band = [float(x) for x in bandstring.split("_")]
logger.info(" ")
logger.info(" " + 54 * "*")
logger.info(" Getting data for inversion from period band:")
logger.info(" Low: %d s || High: %d s" % tuple(band))
logger.info(" " + 54 * "*")
logger.info(" ")
# Load inversion file dictionary
inv_dict = read_yaml_file(inv_dict_file)
asdf_dict = inv_dict["asdf_dict"]
window_file = inv_dict["window_file"]
# Adding measurements
# Print Inversion parameters:
logger.info(" Adding measurements to data container:")
logger.info(" _____________________________________________________")
logger.info(" ")
# Add measurements from ASDF file and windowfile
logger.info(" Window file:")
logger.info(" " + window_file)
logger.info(" ")
logger.info(" ASDF files:")
for key, value in asdf_dict.items():
logger.info(" " + key + ": " + value)
dcon.add_measurements_from_asdf(window_file, asdf_dict)
logger.info(" _____________________________________________________")
logger.info(" ... ")
logger.info(" ")
logger.info(" ... ")
logger.info(" Setting up inversion classes .... ")
logger.info(" " + 54 * "*")
logger.info(" ... ")
# Setting up weight config
inv_weight_config = weight_params["weight_config"]
grad3d_params = INV_params["grad3d_config"]
weight_config_grad3d = WeightConfig(
normalize_by_energy=inv_weight_config["normalize_by_energy"],
normalize_by_category=inv_weight_config["normalize_by_category"],
azi_bins=inv_weight_config["azi_bins"],
azi_exp_idx=inv_weight_config["azi_exp_idx"])
grad3d_config = Gradient3dConfig(
method=grad3d_params["method"],
weight_data=bool(grad3d_params["weight_data"]),
weight_config=weight_config_grad3d,
# flag to use the gradient method on inverted traces.
taper_type=grad3d_params["taper_type"],
c1=float(grad3d_params["c1"]),
c2=float(grad3d_params["c2"]),
idt=float(grad3d_params["idt"]),
ia=float(grad3d_params["ia"]),
nt=int(grad3d_params["nt"]),
nls=int(grad3d_params["nls"]),
crit=float(grad3d_params["crit"]),
precond=bool(grad3d_params["precond"]),
reg=bool(grad3d_params["reg"]),
bootstrap=bool(grad3d_params["bootstrap"]),
bootstrap_repeat=int(grad3d_params["bootstrap_repeat"]),
bootstrap_subset_ratio=float(grad3d_params["bootstrap_subset_ratio"]),
mpi_env=bool(grad3d_params["mpi_env"]),
parallel=bool(grad3d_params["parallel"]))
logger.info(" PyCMT3D is finding an improved CMTSOLUTION .... ")
logger.info(" " + 54 * "*")
logger.info(" ")
logger.info(" ")
# Create Gradient3d class
g3d = Gradient3d(cmtsource, dcon, grad3d_config)
# Run inversion
g3d.search()
# Plot results
if bool(INV_params["summary_plot"]):
pass
# g3d.plot_summary(inv_out_dir, figure_format="pdf")
if bool(INV_params["statistics_plot"]):
# Plot Statistics for inversion
g3d.plot_stats_histogram(outputdir=inv_out_dir)
if bool(INV_params["summary_json"]):
g3d.write_summary_json(outputdir=inv_out_dir, mode="global")
if bool(INV_params["write_new_cmt"]):
g3d.write_new_cmtfile(outputdir=inv_out_dir)
if bool(INV_params["write_new_synt"]):
g3d.write_new_syn(outputdir=os.path.join(inv_out_dir, "new_synt"),
file_format="asdf")
if bool(INV_params["plot_new_synthetics"]):
g3d.plot_new_synt_seismograms(outputdir=os.path.join(inv_out_dir,
"waveform_plots"),
figure_format="pdf")
from pycmt3d.cmt3d import Cmt3D
from pycmt3d.source import CMTSource
from pycmt3d.config import Config
from pycmt3d.window import *
from pycmt3d.const import PAR_LIST
from pycmt3d.const import NREGIONS
eventname = "010403A"
cmtfile = "/ccs/home/lei/SOURCE_INVERSION/CMT_BIN/from_quakeml/" + eventname
cmtsource = CMTSource.from_CMTSOLUTION_file(cmtfile)
#print cmtsource.depth_in_m
config = Config(9, dlocation=0.03, dmoment=2.0e23, ddepth=3.0,
double_couple=False, station_correction=True,
bootstrap=True, bootstrap_repeat=300,
normalize_window=True)
data_con = DataContainer(PAR_LIST[0:9])
cmt_suffix = "_60_120.win"
flexwinfile = "/lustre/atlas/proj-shared/geo111/Wenjie/DATA_SI/window/cmt3d_input/" + eventname + cmt_suffix
data_con.add_measurements_from_sac(flexwinfile)
cmt_suffix = "_35_60.win"
flexwinfile = "/lustre/atlas/proj-shared/geo111/Wenjie/DATA_SI/window/cmt3d_input/" + eventname + cmt_suffix
data_con.add_measurements_from_sac(flexwinfile)
testcmt = Cmt3D(cmtsource, data_con, config)
testcmt.source_inversion()
def cmtsource():
return CMTSource.from_CMTSOLUTION_file(CMTFILE)
def cmtsource():
return CMTSource.from_CMTSOLUTION_file(CMTFILE)
def invert(cmt_file_db, param_path):
"""Runs the actual inversion.
:param cmt_file_db:
:param param_path:
:return: Nothing, inversion results are written to file.
"""
# Load Database Parameters
databaseparam_path = os.path.join(param_path,
"Database/DatabaseParameters.yml")
DB_params = read_yaml_file(databaseparam_path)
# Inversion Params
inversionparam_path = os.path.join(param_path,
"CMTInversion/InversionParams.yml")
INV_params = read_yaml_file(inversionparam_path)
# Weight Params
weightparam_path = os.path.join(param_path,
"CMTInversion/WeightParams.yml")
weight_params = read_yaml_file(weightparam_path)
# Get processing path from cmt_filename in database
cmt_dir = os.path.dirname(os.path.abspath(cmt_file_db))
# Create cmt source:
cmtsource = CMTSource.from_CMTSOLUTION_file(cmt_file_db)
# Inversion dictionary directory
inv_dict_dir = os.path.join(cmt_dir, "inversion", "inversion_dicts")
# Inversion dictionaries
inv_dict_files = glob.glob(os.path.join(inv_dict_dir, "inversion*"))
# Inversion output directory
inv_out_dir = os.path.join(cmt_dir, "inversion", "inversion_output",
"cmt3d")
# WRite start of inversion process
logger.info(" ")
logger.info("#######################################################")
logger.info("# #")
logger.info("# Starting CMT3D Inversion ... #")
logger.info("# #")
logger.info("#######################################################")
logger.info(" ")
# Creating Data container
dcon = DataContainer(parlist=PARLIST[:DB_params["npar"]])
for _i, inv_dict_file in enumerate(inv_dict_files):
# Get processing band
bandstring1 = str(os.path.basename(inv_dict_file).split(".")[1])
if "surface" in bandstring1 or "body" in bandstring1:
bandstring = bandstring1.split("#")[0]
else:
bandstring = bandstring1
band = [float(x) for x in bandstring.split("_")]
logger.info(" ")
logger.info(" " + 54 * "*")
logger.info(" Getting data for inversion from period band:")
logger.info(" Low: %d s || High: %d s" % tuple(band))
logger.info(" " + 54 * "*")
logger.info(" ")
# Load inversion file dictionary
inv_dict = read_yaml_file(inv_dict_file)
asdf_dict = inv_dict["asdf_dict"]
window_file = inv_dict["window_file"]
# Adding measurements
# Print Inversion parameters:
logger.info(" Adding measurements to data container:")
logger.info(" _____________________________________________________")
logger.info(" ")
# Add measurements from ASDF file and windowfile
logger.info(" Window file:")
logger.info(" " + window_file)
logger.info(" ")
logger.info(" ASDF files:")
for key, value in asdf_dict.items():
logger.info(" " + key + ": " + value)
dcon.add_measurements_from_asdf(window_file, asdf_dict)
logger.info(" _____________________________________________________")
logger.info(" ... ")
logger.info(" ")
logger.info(" ... ")
logger.info(" Setting up inversion classes .... ")
logger.info(" " + 54 * "*")
logger.info(" ... ")
# Setting up weight config
inv_weight_config = weight_params["weight_config"]
weight_config = WeightConfig(
normalize_by_energy=inv_weight_config["normalize_by_energy"],
normalize_by_category=inv_weight_config["normalize_by_category"],
azi_bins=inv_weight_config["azi_bins"],
azi_exp_idx=inv_weight_config["azi_exp_idx"])
# Setting up general inversion config
inv_params = INV_params["config"]
cmt3d_config = Config(DB_params["npar"],
dlocation=float(inv_params["dlocation"]),
ddepth=float(inv_params["ddepth"]),
dmoment=float(inv_params["dmoment"]),
weight_data=bool(inv_params["weight_data"]),
station_correction=bool(
inv_params["station_correction"]),
zero_trace=bool(inv_params["zero_trace"]),
double_couple=bool(inv_params["double_couple"]),
bootstrap=bool(inv_params["bootstrap"]),
bootstrap_repeat=int(inv_params["bootstrap_repeat"]),
weight_config=weight_config,
taper_type=inv_params["taper_type"],
damping=float(inv_params["damping"]))
logger.info(" PyCMT3D is finding an improved CMTSOLUTION .... ")
logger.info(" " + 54 * "*")
logger.info(" ")
logger.info(" ")
# Invert for parameters
cmt3d = Cmt3D(cmtsource, dcon, cmt3d_config)
cmt3d.source_inversion()
cmt3d.compute_new_syn()
# Create inversion class
# if bool(INV_params["gridsearch"]):
# inv = Inversion(cmtsource, dcon, cmt3d_config, grad3d_config)
# else:
# inv = Inversion(cmtsource, dcon, cmt3d_config, mt_config=None)
# Run inversion
if bool(INV_params["statistics_plot"]):
cmt3d.plot_stats_histogram(outputdir=inv_out_dir)
# Plot results
if bool(INV_params["summary_plot"]):
cmt3d.plot_summary(inv_out_dir, figure_format="pdf")
#
# if bool(INV_params["statistics_plot"]):
# # Plot Statistics for inversion
# inv.G.plot_stats_histogram(outputdir=inv_out_dir)
#
if bool(INV_params["summary_json"]):
cmt3d.write_summary_json(outputdir=inv_out_dir, mode="global")
if bool(INV_params["write_new_cmt"]):
cmt3d.write_new_cmtfile(outputdir=inv_out_dir)
if bool(INV_params["write_new_synt"]):
cmt3d.write_new_syn(outputdir=os.path.join(inv_out_dir, "new_synt"),
file_format="asdf")
if bool(INV_params["plot_new_synthetics"]):
cmt3d.plot_new_synt_seismograms(outputdir=os.path.join(
inv_out_dir, "waveform_plots"),
figure_format="pdf")
def test_write_CMTSOLUTION_File(tmpdir, cmt):
fn = os.path.join(str(tmpdir), "CMTSOLUTION.temp")
cmt.write_CMTSOLUTION_file(fn)
new_cmt = CMTSource.from_CMTSOLUTION_file(fn)
assert new_cmt == cmt
import os
import conda
os.environ["PROJ_LIB"] = os.path.join(
conda.__file__.split('lib')[0], 'Library', 'share')
from pycmt3d.data_container import DataContainer # NOQA
from pycmt3d.constant import PARLIST # NOQA
from pycmt3d.cmt3d import Cmt3D # NOQA
from pycmt3d.config import Config, DefaultWeightConfig # NOQA
from pycmt3d.source import CMTSource # NOQA
# load cmtsource
cmtfile = os.path.join('..', 'cmt_solutions', 'CMTSOLUTION-syn.txt')
cmtsource = CMTSource.from_CMTSOLUTION_file(cmtfile)
# load data and window from flexwin output file
npar = 9 # read 9 deriv synthetic
data_con = DataContainer(PARLIST[:npar])
flexwin_output = 'windows.txt'
asdf_file_dict = {
'obsd': 'observed.h5',
'synt': 'synthetic_perturbed.h5',
'Mrr': os.path.join('kernels', 'Mrr.h5'),
'Mtt': os.path.join('kernels', 'Mtt.h5'),
'Mpp': os.path.join('kernels', 'Mpp.h5'),
'Mrt': os.path.join('kernels', 'Mrt.h5'),
'Mrp': os.path.join('kernels', 'Mrp.h5'),
'Mtp': os.path.join('kernels', 'Mtp.h5'),
'dep': os.path.join('kernels', 'depth.h5'),
'lat': os.path.join('kernels', 'lat.h5'),
def test_write_CMTSOLUTION_File(tmpdir, cmt):
fn = os.path.join(str(tmpdir), "CMTSOLUTION.temp")
cmt.write_CMTSOLUTION_file(fn)
new_cmt = CMTSource.from_CMTSOLUTION_file(fn)
assert new_cmt == cmt
