def test_npz(self, tmpdir, capsys):
io.save(tmpdir+'/test.npz', **self.data)
outstr, _ = capsys.readouterr()
assert 'Data saved to «' in outstr
assert emg3d.__version__ in outstr
# Save it with other verbosity.
_, _ = capsys.readouterr()
io.save(tmpdir+'/test.npz', **self.data, verb=0)
outstr, _ = capsys.readouterr()
assert outstr == ""
out = io.save(tmpdir+'/test.npz', **self.data, verb=-1)
assert 'Data saved to «' in out
# Load it.
out_npz = io.load(str(tmpdir+'/test.npz'), allow_pickle=True)
outstr, _ = capsys.readouterr()
assert 'Data loaded from «' in outstr
assert 'test.npz' in outstr
assert emg3d.__version__ in outstr
assert out_npz['Model'] == self.model
assert_allclose(out_npz['a'], self.a)
assert out_npz['b'] == self.b
assert_allclose(self.field.fx, out_npz['Field'].fx)
assert_allclose(self.grid.cell_volumes, out_npz['Grid'].cell_volumes)
# Load it with other verbosity.
_, _ = capsys.readouterr()
out = io.load(tmpdir+'/test.npz', verb=0)
outstr, _ = capsys.readouterr()
assert outstr == ""
out, out_str = io.load(tmpdir+'/test.npz', verb=-1)
assert 'Data loaded from «' in out_str
def test_json(self, tmpdir):
io.save(tmpdir+'/test.json', **self.data)
out_json = io.load(str(tmpdir+'/test.json'))
assert out_json['Model'] == self.model
assert_allclose(out_json['a'], self.a)
assert out_json['b'] == self.b
assert_allclose(self.field.fx, out_json['Field'].fx)
assert_allclose(self.grid.cell_volumes, out_json['Grid'].cell_volumes)
def test_h5(self, tmpdir):
if h5py:
io.save(tmpdir+'/test.h5', **self.data)
out_h5 = io.load(str(tmpdir+'/test.h5'))
assert out_h5['Model'] == self.model
assert_allclose(out_h5['a'], self.a)
assert out_h5['b'] == self.b
assert_allclose(self.field.fx, out_h5['Field'].fx)
assert_allclose(self.grid.cell_volumes,
out_h5['Grid'].cell_volumes)
else:
with pytest.warns(UserWarning, match='emg3d: This feature requir'):
io.save(tmpdir+'/test.h5', grid=self.grid)
def test_warnings(self, tmpdir, capsys):
# Check message from loading another file
data = io._dict_serialize({'meshes': self.grid})
fdata = io._dict_flatten(data)
np.savez_compressed(tmpdir+'/test2.npz', **fdata)
_ = io.load(str(tmpdir+'/test2.npz'), allow_pickle=True)
outstr, _ = capsys.readouterr()
assert "[version/format/date unknown; not created by emg" in outstr
# Unknown keyword.
with pytest.raises(TypeError, match="Unexpected "):
io.load('ttt.npz', stupidkeyword='a')
# Unknown extension.
with pytest.raises(ValueError, match="Unknown extension '.abc'"):
io.save(tmpdir+'/testwrongextension.abc', something=1)
with pytest.raises(ValueError, match="Unknown extension '.abc'"):
io.load(tmpdir+'/testwrongextension.abc')
def to_file(self, fname, name='survey', **kwargs):
"""Store Survey to a file.
Parameters
----------
fname : str
Absolute or relative file name including ending, which defines the
used data format. See :func:`emg3d.io.save` for the options.
name : str, default: 'survey'
Name with which the survey is stored in the file.
kwargs : Keyword arguments, optional
Passed through to :func:`emg3d.io.save`.
"""
kwargs[name] = self # Add survey to dict.
return io.save(fname, **kwargs)
}
model_l = models.Model(**input_model_l)
input_source_l = {
'grid': grid_l,
'source': [0, 0, 250., 30, 10], # A rotated source to include all
'frequency': freq
}
# Fields
sfield_l = fields.get_source_field(**input_source_l)
# F-cycle
fefield_l = solver.solve(model_l, sfield_l, plain=True)
# BiCGSTAB; F-cycle
bicefield_l = solver.solve(model_l, sfield_l, sslsolver='bicgstab', plain=True)
out_l = {
'input_grid': input_grid_l,
'input_model': input_model_l,
'input_source': input_source_l,
'grid': grid_l,
'model': model_l,
'sfield': sfield_l,
'Fresult': fefield_l,
'bicresult': bicefield_l,
}
io.save('../data/regression.npz', res=out, reg_2=reg_2, grid=mesh, lap=out_l)
def simulation(args_dict):
"""Run `emg3d` invoked by CLI.
Run and log ``emg3d`` given the settings stored in the config file,
overruled by settings passed in ``args_dict`` (which correspond to
command-line arguments).
Results are saved to files according to provided settings.
Parameters
----------
args_dict : dict
Arguments from terminal, see :func:`emg3d.cli.main`. Parameters passed
in ``args_dict`` overrule parameters in the ``config``.
"""
# Start timer.
runtime = utils.Timer()
# Parse configuration file.
cfg, term = parser.parse_config_file(args_dict)
check_files(cfg, term) # Check all files and directories exist.
function, verb = term['function'], term['verbosity']
dry_run = term.get('dry_run', False)
# Start this task: start timing.
logger = initiate_logger(cfg, runtime, verb)
# Log start info, python and emg3d version, and python path.
logger.info(f":: emg3d CLI {function} START :: {time.asctime()} :: "
f"v{utils.__version__}")
logger.debug(f"{utils.Report()}")
# Dump the configuration.
paramdump = json.dumps(cfg, sort_keys=True, indent=4)
logger.debug("\n :: CONFIGURATION ::\n")
logger.debug(f"{term['config_file']}\n{paramdump}")
min_offset = cfg['simulation_options'].pop('min_offset', 0.0)
if cfg['files']['load']:
# Load input.
logger.info("\n :: LOAD SIMULATION ::\n")
sim, sinfo = simulations.Simulation.from_file(
cfg['files']['load'], verb=-1)
logger.info(sinfo.split('\n')[0])
logger.debug(sinfo.split('\n')[1])
else:
# Load input.
logger.info("\n :: LOAD SURVEY AND MODEL ::\n")
sdata, sinfo = io.load(cfg['files']['survey'], verb=-1)
survey = sdata['survey']
logger.info(sinfo.split('\n')[0])
logger.debug(sinfo.split('\n')[1])
model, minfo = io.load(cfg['files']['model'], verb=-1)
logger.info(minfo.split('\n')[0])
logger.debug(minfo.split('\n')[1])
# Select data.
data = cfg['data']
if data:
survey = survey.select(
sources=data.get('sources', None),
receivers=data.get('receivers', None),
frequencies=data.get('frequencies', None),
remove_empty=data.get('remove_empty', False),
)
# Switch-off tqdm if verbosity is zero.
if verb < 1:
cfg['simulation_options']['tqdm_opts'] = {'disable': True}
# Create simulation.
sim = simulations.Simulation(
survey=survey,
model=model['model'],
verb=-1, # Only errors.
**cfg['simulation_options']
)
# Print simulation info.
logger.info("\n :: SIMULATION ::")
logger.info(f"\n{sim}\n")
# Print meshes.
logger.debug(" :: MESHES ::\n")
logger.debug(sim.print_grid_info(return_info=True))
# Initiate output dict, add configuration.
output = {'configuration': cfg}
# Compute forward model (all calls).
logger.info(" :: FORWARD COMPUTATION ::\n")
if dry_run:
output['data'] = np.zeros(sim.survey.shape, dtype=complex)
else:
if function == 'forward':
sim.compute(observed=True, min_offset=min_offset)
output['data'] = sim.data.observed
else:
sim.compute()
output['data'] = sim.data.synthetic
# Print Solver Logs.
if verb in [0, 1]:
sim.print_solver_info('efield', 0)
logger.debug(sim.print_solver_info('efield', 1, True))
# Compute the misfit.
if function in ['misfit', 'gradient']:
if dry_run:
output['misfit'] = 0.0
else:
output['misfit'] = sim.misfit
output['n_observations'] = sim.survey.count
# Compute the gradient.
if function == 'gradient':
logger.info("\n :: BACKWARD COMPUTATION ::\n")
if dry_run:
output['gradient'] = np.zeros(sim.model.grid.shape_cells)
else:
output['gradient'] = sim.gradient
# Print Solver Logs.
if verb in [0, 1]:
sim.print_solver_info('bfield', 0)
logger.debug(sim.print_solver_info('bfield', 1, True))
# Store output to disk.
logger.info(" :: SAVE RESULTS ::\n")
if cfg['files']['save']:
oinfo = sim.to_file(cfg['files']['save'], verb=-1)
logger.info(oinfo.split('\n')[0])
logger.debug(oinfo.split('\n')[1])
oinfo = io.save(cfg['files']['output'], **output, verb=-1)
logger.info(oinfo.split('\n')[0])
logger.debug(oinfo.split('\n')[1])
# Goodbye
logger.info(f"\n:: emg3d CLI {function} END :: {time.asctime()} :: "
f"runtime = {runtime.runtime}")