def setUp(self):
self.mth5_obj = mth5.MTH5()
pd_series = pd.Series({
'station': 'MT test',
'latitude': 40.90,
'longitude': -115.78,
'elevation': 1234,
'declination': -15.5,
'start_date': '2018-01-01 12:00:00.00',
'end_date': '2018-02-01 12:00:00.00',
'datum': 'WGS84',
'coordinate_system': 'Geographic North',
'units': 'mV',
'instrument_id': 'ZEN_test',
'ex_azimuth': 0,
'ex_length': 50.0,
'ex_sensor': 1,
'ex_num': 1,
'ey_azimuth': 90,
'ey_length': 52.0,
'ey_sensor': 2,
'ey_num': 2,
'hx_azimuth': 0,
'hx_sensor': 2274,
'hx_num': 3,
'hy_azimuth': 90,
'hy_sensor': 2284,
'hy_num': 4,
'hz_azimuth': 0,
'hz_sensor': 2294,
'hz_num': 5
})
self.mth5_obj.update_metadata_from_series(pd_series)
def setUp(self):
self.maxDiff = None
self.fn = fn_path.joinpath("test.h5")
self.mth5_obj = mth5.MTH5(file_version="0.1.0")
self.mth5_obj.open_mth5(self.fn, mode="w")
self.experiment = Experiment()
self.experiment.from_xml(fn=MT_EXPERIMENT_SINGLE_STATION)
self.mth5_obj.from_experiment(self.experiment)
def setUp(self):
self.translator = stationxml.XMLInventoryMTExperiment()
self.experiment = self.translator.xml_to_mt(
stationxml_fn=STATIONXML_01)
self.fn = fn_path.joinpath("from_stationxml.h5")
if self.fn.exists():
self.fn.unlink()
self.m = mth5.MTH5(file_version="0.1.0")
self.m.open_mth5(self.fn)
self.m.from_experiment(self.experiment, 0)
def setUp(self):
self.translator = stationxml.XMLInventoryMTExperiment()
self.experiment = self.translator.xml_to_mt(
stationxml_fn=STATIONXML_01)
self.experiment.surveys[0].id = "test"
self.base_path = "Experiment/Surveys/test"
self.fn = fn_path.joinpath("from_stationxml.h5")
self.m = mth5.MTH5(file_version="0.2.0")
self.m.open_mth5(self.fn)
self.m.from_experiment(self.experiment)
def setUp(self):
self.maxDiff = None
self.fn = fn_path.joinpath("test.h5")
self.mth5_obj = mth5.MTH5(file_version="0.1.0")
self.mth5_obj.open_mth5(self.fn, mode="w")
self.experiment = Experiment()
self.experiment.from_xml(fn=MT_EXPERIMENT_SINGLE_STATION)
self.mth5_obj.from_experiment(self.experiment)
self.experiment_02 = Experiment()
self.experiment_02.from_xml(fn=MT_EXPERIMENT_SINGLE_STATION)
self.experiment_02.surveys[0].id = "different_survey_name"
self.experiment_02.surveys[0].stations[0].location.latitude = 10
def setUp(self):
self.fn = fn_path.joinpath("filter_test.h5")
self.m_obj = mth5.MTH5(file_version="0.1.0")
self.m_obj.open_mth5(self.fn, "w")
self.filter_group = self.m_obj.filters_group
self.zpk = PoleZeroFilter()
self.zpk.units_in = "counts"
self.zpk.units_out = "mv"
self.zpk.name = "zpk_test"
self.zpk.poles = np.array([1 + 2j, 0, 1 - 2j])
self.zpk.zeros = np.array([10 - 1j, 10 + 1j])
self.coefficient = CoefficientFilter()
self.coefficient.units_in = "volts"
self.coefficient.units_out = "millivolts per meter"
self.coefficient.name = "coefficient_test"
self.coefficient.gain = 10.0
self.zpk_group = self.filter_group.add_filter(self.zpk)
self.coefficient_group = self.filter_group.add_filter(self.coefficient)
os.mkdir(station_save_dir)
print('--> Archiving Station {0} ...'.format(station))
### capture output to put into a log file
with archive.Capturing() as output:
station_st = datetime.datetime.now()
### copy edi and png into archive director
# if not os.path.isfile(os.path.join(station_save_dir, '{0}.edi'.format(station))):
# shutil.copy(os.path.join(edi_path, '{0}.edi'.format(station)),
# os.path.join(station_save_dir, '{0}.edi'.format(station)))
# if not os.path.isfile(os.path.join(station_save_dir, '{0}.png'.format(station))):
# shutil.copy(os.path.join(png_path, '{0}.png'.format(station)),
# os.path.join(station_save_dir, '{0}.png'.format(station)))
### Make MTH5 File
m = mth5.MTH5()
mth5_fn = os.path.join(station_save_dir, '{0}.mth5'.format(station))
m.open_mth5(mth5_fn)
if not m.h5_is_write:
raise mth5.MTH5Error('Something is wrong')
### update metadata from csv and cfg files
m.update_metadata_from_cfg(cfg_fn)
if csv_fn is not None:
try:
station_df = archive.get_station_info_from_csv(csv_fn,
station)
m.update_metadata_from_series(station_df)
except archive.ArchiveError as err:
print('{0} {1} {0}'.format('*'*4, err))
m.write_metadata()
def setUp(self):
self.fn = fn_path.joinpath("test.mth5")
self.mth5_obj = mth5.MTH5(file_version="0.2.0")
self.mth5_obj.open_mth5(self.fn, mode="w")
self.survey_group = self.mth5_obj.add_survey("test")
h5_fn.unlink()
print(f"INFO: Removed existing file {h5_fn}")
# need to unzip the data
with zipfile.ZipFile(zen_dir.joinpath("zen.zip"), "r") as zip_ref:
zip_ref.extractall(zen_dir)
# write some simple metadata for the survey
survey = metadata.Survey()
survey.acquired_by.author = "MT Master"
survey.fdsn.id = "TST01"
survey.fdsn.network = "MT"
survey.name = "test"
# open mth5 file
m = mth5.MTH5(h5_fn)
m.open_mth5()
# add survey metadata
m.survey_group.metadata.from_dict(survey.to_dict())
# add station metadata from z3d files
ch_list = []
for fn in zip_ref.filelist:
mtts_obj = read_file(zen_dir.joinpath(fn.filename))
station_group = m.add_station(
mtts_obj.station_metadata.id,
station_metadata=mtts_obj.station_metadata,
)
def test_make_stationxml_from_mt():
fn_path = Path(__file__).parent
fn = fn_path.joinpath("example.h5")
if fn.exists():
fn.unlink()
xml_fn = fn_path.joinpath("example.xml")
if fn.exists():
fn.unlink()
survey = metadata.Survey()
survey.from_dict({
"survey": {
"acquired_by.author": "MT",
"acquired_by.comments": "tired",
"archive_id": "MT01",
"fdsn.network": "EM",
"citation_dataset.doi": "http://doi.####",
"citation_journal.doi": None,
"comments": None,
"country": None,
"datum": "WGS84",
"geographic_name": "earth",
"name": "entire survey of the earth",
"northwest_corner.latitude": 80.0,
"northwest_corner.longitude": 179.9,
"project": "EM-EARTH",
"project_lead.author": "T. Lurric",
"project_lead.email": "*****@*****.**",
"project_lead.organization": "mt rules",
"release_license": "CC-0",
"southeast_corner.latitude": -80.0,
"southeast_corner.longitude": -179.9,
"summary": None,
"time_period.end_date": "1980-01-01T00:00:00.000000Z",
"time_period.start_date": "2020-01-01T00:00:00.000000Z",
}
})
station = metadata.Station()
station.from_dict({
"station": {
"acquired_by.author": "mt",
"acquired_by.comments": None,
"archive_id": "MT012",
"channel_layout": "L",
"comments": None,
"data_type": "MT",
"geographic_name": "london",
"id": "mt012",
"fdsn.id": "mt012",
"location.declination.comments": None,
"location.declination.model": "WMM",
"location.declination.value": 12.3,
"location.elevation": 1234.0,
"location.latitude": 10.0,
"location.longitude": -112.98,
"orientation.method": "compass",
"orientation.reference_frame": "geomagnetic",
"provenance.comments": None,
"provenance.creation_time": "1980-01-01T00:00:00+00:00",
"provenance.log": None,
"provenance.software.author": "test",
"provenance.software.name": "name",
"provenance.software.version": "1.0a",
"provenance.submitter.author": "name",
"provenance.submitter.email": "*****@*****.**",
"provenance.submitter.organization": None,
"time_period.end": "1980-01-01T00:00:00+00:00",
"time_period.start": "1980-01-01T00:00:00+00:00",
}
})
run = metadata.Run()
run.from_dict({
"run": {
"acquired_by.author": "MT guru",
"acquired_by.comments": "lazy",
"channels_recorded_auxiliary": ["temperature"],
"channels_recorded_electric": [],
"channels_recorded_magnetic": [],
"comments": "Cloudy solar panels failed",
"data_logger.firmware.author": "MT instruments",
"data_logger.firmware.name": "FSGMT",
"data_logger.firmware.version": "12.120",
"data_logger.id": "mt091",
"data_logger.manufacturer": "T. Lurric",
"data_logger.model": "Ichiban",
"data_logger.power_source.comments": "rats",
"data_logger.power_source.id": "12",
"data_logger.power_source.type": "pb acid",
"data_logger.power_source.voltage.end": 12.0,
"data_logger.power_source.voltage.start": 14.0,
"data_logger.timing_system.comments": "solid",
"data_logger.timing_system.drift": 0.001,
"data_logger.timing_system.type": "GPS",
"data_logger.timing_system.uncertainty": 0.000001,
"data_logger.type": "broadband",
"data_type": "mt",
"id": "mt01a",
"provenance.comments": None,
"provenance.log": None,
"metadata_by.author": "MT guru",
"metadata_by.comments": "lazy",
"sampling_rate": 256.0,
"time_period.end": "1980-01-01T00:00:00+00:00",
"time_period.start": "1980-01-01T00:00:00+00:00",
}
})
channel = metadata.Auxiliary()
channel.from_dict({
"auxiliary": {
"comments": "great",
"component": "temperature",
"channel_number": 1,
"data_quality.rating.author": "mt",
"data_quality.rating.method": "ml",
"data_quality.rating.value": 4,
"data_quality.warning": None,
"filter.applied": [True, False],
"filter.comments": "test",
"filter.name": ["lowpass", "counts2mv"],
"location.elevation": 1234.0,
"location.latitude": 12.324,
"location.longitude": -112.03,
"measurement_azimuth": 0,
"measurement_tilt": 0,
"sample_rate": 256.0,
"time_period.end": "1980-01-01T00:00:00+00:00",
"time_period.start": "1980-01-01T00:00:00+00:00",
"type": "temperature",
"units": "celsius",
}
})
m = mth5.MTH5()
m.open_mth5(fn)
survey_group = m.survey_group
survey_group.metadata.from_dict(survey.to_dict())
survey_group.write_metadata()
station_group = m.add_station(station.id, station)
run_group = station_group.add_run(run.id, run)
run_group.add_channel(channel.component,
"auxiliary",
None,
channel_metadata=channel)
translator = stationxml.XMLInventoryMTExperiment()
translator.mt_to_xml(m.to_experiment(), stationxml_fn=xml_fn)
def setUp(self):
self.fn = fn_path.joinpath("test.mth5")
self.mth5_obj = mth5.MTH5(file_version="0.1.0")
self.mth5_obj.open_mth5(self.fn, mode="w")
channel.metadata.from_xml(read_xml(directory.joinpath(channel_fn)))
channel.metadata.time_period.start = run.metadata.time_period.start
channel.metadata.time_period.end = run.metadata.time_period.end
channel.write_metadata()
return new_station
xml_root = "path/to/metadata/files.xml"
mth5_filename = "from_xml.mth5"
if mth5_filename.exists():
mth5_filename.unlink()
print(f"--> Rmoved existing file {mth5_filename}")
# initialize mth5 object
mth5_obj = mth5.MTH5()
mth5_obj.open_mth5(mth5_filename, mode="a")
### add survey information
survey_element = read_xml(xml_root.joinpath("survey.xml"))
survey_obj = mth5_obj.survey_group
survey_obj.metadata.from_xml(survey_element)
survey_obj.write_metadata()
for station in ["FL001", "FL002"]:
# add station
new_station = add_station(station, xml_root, mth5_obj)
mth5_obj.close_mth5()
def setUp(self):
self.mth5_obj = mth5.MTH5()
def setUp(self):
self.mth5_obj = mth5.MTH5()
cfg_fn = r"../examples/example_mth5_cfg.txt"
self.assertTrue(os.path.isfile(cfg_fn), "{0} not found".format(cfg_fn))
self.mth5_obj.update_metadata_from_cfg(cfg_fn)
