mt-metadata 0.3.9__py2.py3-none-any.whl → 0.4.0__py2.py3-none-any.whl

mt_metadata/timeseries/station.py

@@ -2,7 +2,7 @@
 """
 Created on Wed Dec 23 21:30:36 2020
 
-:copyright: 
+:copyright:
     Jared Peacock (jpeacock@usgs.gov)
 
 :license: MIT
@@ -21,6 +21,7 @@ from . import (
     Fdsn,
     Orientation,
     Person,
+    provenance,
     Provenance,
     Location,
     TimePeriod,
@@ -46,8 +47,9 @@ attr_dict.add_dict(
     keys=["name", "comments", "organization"],
 )
 attr_dict.add_dict(get_schema("orientation", SCHEMA_FN_PATHS), "orientation")
+
 attr_dict.add_dict(
-    Provenance()._attr_dict,
+    provenance.attr_dict,
     "provenance",
 )
 

mt_metadata/timeseries/stationxml/__init__.py

@@ -3,6 +3,11 @@
 Tools to translate StationXML to MT Metadata
 """
 
+try:
+    import obspy
+except ImportError:
+    raise ImportError("StationXML requires obspy to be installed.")
+
 from .xml_network_mt_survey import XMLNetworkMTSurvey
 from .xml_equipment_mt_run import XMLEquipmentMTRun
 from .xml_station_mt_station import XMLStationMTStation

mt_metadata/timeseries/stationxml/xml_channel_mt_channel.py

@@ -42,7 +42,7 @@ class XMLChannelMTChannel(BaseTranslator):
         "induction coil",
         "coil",
         "dipole",
-        "electrode"
+        "electrode",
     ]
 
     def __init__(self):
@@ -121,8 +121,10 @@ class XMLChannelMTChannel(BaseTranslator):
         # fill channel filters
         mt_channel.filter.name = list(mt_filters.keys())
         mt_channel.filter.applied = [True] * len(list(mt_filters.keys()))
-        if UTCDateTime(mt_channel.time_period.end) < UTCDateTime(mt_channel.time_period.start):
-            mt_channel.time_period.end = '2200-01-01T00:00:00+00:00'
+        if UTCDateTime(mt_channel.time_period.end) < UTCDateTime(
+            mt_channel.time_period.start
+        ):
+            mt_channel.time_period.end = "2200-01-01T00:00:00+00:00"
         return mt_channel, mt_filters
 
     def mt_to_xml(self, mt_channel, filters_dict, hard_code=True):
@@ -190,12 +192,8 @@ class XMLChannelMTChannel(BaseTranslator):
         xml_channel.types = ["geophysical".upper()]
         xml_channel.sensor = self._mt_to_sensor(mt_channel)
         xml_channel.comments = self._make_xml_comments(mt_channel.comments)
-        xml_channel.restricted_status = release_dict[
-            xml_channel.restricted_status
-        ]
-        xml_channel = self._mt_to_xml_response(
-            mt_channel, filters_dict, xml_channel
-        )
+        xml_channel.restricted_status = release_dict[xml_channel.restricted_status]
+        xml_channel = self._mt_to_xml_response(mt_channel, filters_dict, xml_channel)
 
         for mt_key, xml_key in self.mt_translator.items():
             if xml_key is None:
@@ -211,9 +209,7 @@ class XMLChannelMTChannel(BaseTranslator):
                 xml_channel.dip = mt_channel.measurement_tilt % 360
 
             else:
-                setattr(
-                    xml_channel, xml_key, mt_channel.get_attr_from_name(mt_key)
-                )
+                setattr(xml_channel, xml_key, mt_channel.get_attr_from_name(mt_key))
 
         return xml_channel
 
@@ -272,9 +268,7 @@ class XMLChannelMTChannel(BaseTranslator):
             mt_channel.negative.model = sensor.model
             mt_channel.negative.type = "electrode"
 
-            mt_channel.dipole_length = self._parse_dipole_length(
-                sensor.description
-            )
+            mt_channel.dipole_length = self._parse_dipole_length(sensor.description)
 
             return mt_channel
 
@@ -434,7 +428,10 @@ class XMLChannelMTChannel(BaseTranslator):
         :rtype: TYPE
 
         """
+
         comments = []
+        if mt_comment is None:
+            return comments
         clist = mt_comment.split("run_ids:")
         for item in clist:
             if ":" in item:
@@ -479,9 +476,7 @@ class XMLChannelMTChannel(BaseTranslator):
     def _get_mt_units(self, xml_channel, mt_channel):
         """ """
         name = xml_channel.response.response_stages[-1].output_units
-        description = xml_channel.response.response_stages[
-            -1
-        ].output_units_description
+        description = xml_channel.response.response_stages[-1].output_units_description
         if description and name:
             if len(description) > len(name):
                 mt_channel.units = description
@@ -545,9 +540,9 @@ class XMLChannelMTChannel(BaseTranslator):
                     return f_obj.name, False
 
         try:
-            last = sorted(
-                [k for k in existing_filters.keys() if mt_filter.type in k]
-            )[-1]
+            last = sorted([k for k in existing_filters.keys() if mt_filter.type in k])[
+                -1
+            ]
         except IndexError:
             return f"{mt_filter.type}_{0:02}", True
         try:
@@ -582,7 +577,6 @@ class XMLChannelMTChannel(BaseTranslator):
 
         return xml_channel
 
-
     def _deduce_sensor_type(self, sensor):
         """
 
@@ -606,11 +600,12 @@ class XMLChannelMTChannel(BaseTranslator):
         else:
             sensor_description = copy.deepcopy(original_sensor_type)
 
-
         if sensor_type.lower() in self.understood_sensor_types:
             return sensor_type
         else:
-            self.logger.warning(f" sensor {sensor} type {sensor.type} not in {self.understood_sensor_types}")
+            self.logger.warning(
+                f" sensor {sensor} type {sensor.type} not in {self.understood_sensor_types}"
+            )
 
         #  Try handling Bartington FGM at Earthscope ... this is a place holder for handling non-standard cases
         if sensor_type.lower() == "bartington":
@@ -619,12 +614,15 @@ class XMLChannelMTChannel(BaseTranslator):
             if sensor_description == "Bartington 3-Axis Fluxgate Sensor":
                 sensor_type = "magnetometer"
             if sensor_description:
-                if ("bf-4" in sensor_description.lower()) & ("schlumberger" in sensor_description.lower()):  # BSL-NCEDC
+                if ("bf-4" in sensor_description.lower()) & (
+                    "schlumberger" in sensor_description.lower()
+                ):  # BSL-NCEDC
                     sensor_type = "magnetometer"
-                elif ("electric" in sensor_description.lower()) & ("dipole" in sensor_description.lower()):  # BSL-NCEDC
+                elif ("electric" in sensor_description.lower()) & (
+                    "dipole" in sensor_description.lower()
+                ):  # BSL-NCEDC
                     sensor_type = "dipole"
 
-
         # reset sensor_type to None it it was not handled
         if not sensor_type:
             sensor_type = original_sensor_type

mt_metadata/timeseries/stationxml/xml_inventory_mt_experiment.py

@@ -85,9 +85,7 @@ class XMLInventoryMTExperiment:
                             run_channel = deepcopy(mt_channel)
                             mt_run = mt_station.get_run(run_id)
                             # need to set the start and end time to the run
-                            run_channel.time_period.start = (
-                                mt_run.time_period.start
-                            )
+                            run_channel.time_period.start = mt_run.time_period.start
                             run_channel.time_period.end = mt_run.time_period.end
                             mt_run.add_channel(run_channel)
                     # if there are runs already try to match by start, end, sample_rate
@@ -105,16 +103,13 @@ class XMLInventoryMTExperiment:
                                     mt_run.time_period.start
                                     >= mt_channel.time_period.start
                                 ) and (
-                                    mt_run.time_period.end
-                                    <= mt_channel.time_period.end
+                                    mt_run.time_period.end <= mt_channel.time_period.end
                                 ):
                                     mt_run.channels.append(mt_channel)
                                     mt_run.sample_rate = mt_channel.sample_rate
                     # make a new run with generic information
                     else:
-                        mt_run = metadata.Run(
-                            id=f"{len(mt_station.runs)+1:03d}"
-                        )
+                        mt_run = metadata.Run(id=f"{len(mt_station.runs)+1:03d}")
                         mt_run.time_period.start = mt_channel.time_period.start
                         mt_run.time_period.end = mt_channel.time_period.end
                         mt_run.sample_rate = mt_channel.sample_rate
@@ -128,18 +123,14 @@ class XMLInventoryMTExperiment:
             # need to check if the network/survey already exists, the files
             # from make_mth5_from_iris have multiples of the same network
             if mt_survey.id in mt_experiment.surveys.keys():
-                mt_experiment.surveys[mt_survey.id].stations.update(
-                    mt_survey.stations
-                )
+                mt_experiment.surveys[mt_survey.id].stations.update(mt_survey.stations)
             else:
                 mt_experiment.surveys.append(mt_survey)
         if mt_fn:
             mt_experiment.to_xml(fn=mt_fn)
         return mt_experiment
 
-    def mt_to_xml(
-        self, mt_experiment, mt_fn=None, stationxml_fn=None, ns_dict=None
-    ):
+    def mt_to_xml(self, mt_experiment, mt_fn=None, stationxml_fn=None, ns_dict=None):
         """
         Convert from MT :class:`mt_metadata.timeseries.Experiment` to
         :class:`obspy.core.inventory.Inventory`
@@ -176,9 +167,7 @@ class XMLInventoryMTExperiment:
                     )
                 # need to sort the runs by time
                 for mt_run in mt_station.runs:
-                    xml_station = self.add_run(
-                        xml_station, mt_run, mt_survey.filters
-                    )
+                    xml_station = self.add_run(xml_station, mt_run, mt_survey.filters)
                 xml_network.stations.append(xml_station)
             xml_inventory.networks.append(xml_network)
         if stationxml_fn:
@@ -204,19 +193,13 @@ class XMLInventoryMTExperiment:
         """
 
         for mt_channel in mt_run.channels:
-            xml_channel = self.channel_translator.mt_to_xml(
-                mt_channel, filters_dict
-            )
-            existing_channels = xml_station.select(
-                channel=xml_channel.code
-            ).channels
+            xml_channel = self.channel_translator.mt_to_xml(mt_channel, filters_dict)
+            existing_channels = xml_station.select(channel=xml_channel.code).channels
 
             if existing_channels:
                 find = False
                 start_list = [c.start_date for c in existing_channels]
-                existing_channel = existing_channels[
-                    start_list.index(max(start_list))
-                ]
+                existing_channel = existing_channels[start_list.index(max(start_list))]
                 # should only compare the last channel
                 # for existing_channel in existing_channels:
                 run_list = [c.value for c in existing_channel.comments]
@@ -231,9 +214,7 @@ class XMLInventoryMTExperiment:
                         f"Matched {xml_channel.code}={existing_channel.code}"
                     )
                     if not mt_run.id in run_list:
-                        self.logger.debug(
-                            f"adding run id {mt_run.id} to {run_list}"
-                        )
+                        self.logger.debug(f"adding run id {mt_run.id} to {run_list}")
                         existing_channel.comments.append(
                             inventory.Comment(mt_run.id, subject="mt.run.id")
                         )
@@ -250,22 +231,16 @@ class XMLInventoryMTExperiment:
                     )
                     run_list = [c.value for c in xml_channel.comments]
                     if not mt_run.id in run_list:
-                        self.logger.debug(
-                            f"adding run id {mt_run.id} to {run_list}"
-                        )
+                        self.logger.debug(f"adding run id {mt_run.id} to {run_list}")
                         xml_channel.comments.append(
                             inventory.Comment(mt_run.id, subject="mt.run.id")
                         )
                     xml_station.channels.append(xml_channel)
             else:
-                self.logger.debug(
-                    f"no existing channels for {xml_channel.code}"
-                )
+                self.logger.debug(f"no existing channels for {xml_channel.code}")
                 run_list = [c.value for c in xml_channel.comments]
                 if not mt_run.id in run_list:
-                    self.logger.debug(
-                        f"adding run id {mt_run.id} to {run_list}"
-                    )
+                    self.logger.debug(f"adding run id {mt_run.id} to {run_list}")
                     xml_channel.comments.append(
                         inventory.Comment(mt_run.id, subject="mt.run.id")
                     )
@@ -294,20 +269,14 @@ class XMLInventoryMTExperiment:
             )
             return False
         if xml_channel_01.sensor != xml_channel_02.sensor:
-            self.logger.debug(
-                f"{xml_channel_01.sensor} != {xml_channel_02.sensor}"
-            )
+            self.logger.debug(f"{xml_channel_01.sensor} != {xml_channel_02.sensor}")
             return False
-        if round(xml_channel_01.latitude, 3) != round(
-            xml_channel_02.latitude, 3
-        ):
+        if round(xml_channel_01.latitude, 3) != round(xml_channel_02.latitude, 3):
             self.logger.debug(
                 f"{round(xml_channel_01.latitude, 3)} != {round(xml_channel_02.latitude, 3)}"
             )
             return False
-        if round(xml_channel_01.longitude, 3) != round(
-            xml_channel_02.longitude, 3
-        ):
+        if round(xml_channel_01.longitude, 3) != round(xml_channel_02.longitude, 3):
             self.logger.debug(
                 f"{round(xml_channel_01.longitude, 3)} != {round(xml_channel_02.longitude, 3)}"
             )

mt_metadata/timeseries/stationxml/xml_station_mt_station.py

@@ -2,7 +2,7 @@
 """
 Created on Thu Feb 18 12:49:13 2021
 
-:copyright: 
+:copyright:
     Jared Peacock (jpeacock@usgs.gov)
 
 :license: MIT
@@ -142,9 +142,7 @@ class XMLStationMTStation(BaseTranslator):
                 mt_station.id = mt_station.fdsn.id
 
         # read in equipment information
-        mt_station = self._equipments_to_runs(
-            xml_station.equipments, mt_station
-        )
+        mt_station = self._equipments_to_runs(xml_station.equipments, mt_station)
         mt_station = self._add_run_comments(run_comments, mt_station)
 
         return mt_station
@@ -175,37 +173,46 @@ class XMLStationMTStation(BaseTranslator):
             mt_station.fdsn.id = mt_station.id
 
         xml_station = inventory.Station(
-            code,
+            code.upper(),
             mt_station.location.latitude,
             mt_station.location.longitude,
             mt_station.location.elevation,
         )
 
         for xml_key, mt_key in self.xml_translator.items():
-            if xml_key in ["alternate_code"]:
-                xml_station.alternate_code = mt_station.id
+            # need to skip code because we just set it above and it needs to be upper.
+
             if mt_key is None:
-                msg = "cannot currently map mt_key.station to inventory.station.{0}".format(
-                    xml_key
+                self.logger.debug(
+                    f"Cannot currently map mt_key.station to inventory.station.{xml_key}"
                 )
-                self.logger.debug(msg)
                 continue
 
-            if xml_key == "operators":
+            if xml_key in ["code"]:
+                continue
+            elif xml_key in ["alternate_code"]:
+                xml_station.alternate_code = mt_station.id.upper()
+
+            elif xml_key == "operators":
                 if mt_station.acquired_by.name:
                     if mt_station.acquired_by.organization is None:
                         mt_station.acquired_by.organization = " "
                     operator = inventory.Operator(
                         agency=mt_station.acquired_by.organization
                     )
-                    person = inventory.Person(
-                        names=[mt_station.acquired_by.name]
-                    )
+                    person = inventory.Person(names=[mt_station.acquired_by.name])
                     operator.contacts = [person]
                     xml_station.operators = [operator]
 
             elif xml_key == "site":
-                xml_station.site.name = mt_station.geographic_name
+                if mt_station.geographic_name is None:
+                    xml_station.site.name = mt_station.id.upper()
+                    self.logger.warning(
+                        f"Station.geographic_name is None, using Station.id = {mt_station.id}."
+                        "Check StationXML site.name."
+                    )
+                else:
+                    xml_station.site.name = mt_station.geographic_name
 
             elif xml_key == "comments":
                 if mt_station.comments is not None:
@@ -216,9 +223,7 @@ class XMLStationMTStation(BaseTranslator):
                     xml_station.restricted_status
                 ]
             else:
-                setattr(
-                    xml_station, xml_key, mt_station.get_attr_from_name(mt_key)
-                )
+                setattr(xml_station, xml_key, mt_station.get_attr_from_name(mt_key))
 
         # add mt comments
         xml_station.comments = self.make_mt_comments(mt_station, "mt.station")
@@ -281,9 +286,7 @@ class XMLStationMTStation(BaseTranslator):
                             if run_attr == "comments":
                                 value = f"{ckey}: {cvalue}"
                                 try:
-                                    station_obj.runs[
-                                        run_index
-                                    ].comments += f", {value}"
+                                    station_obj.runs[run_index].comments += f", {value}"
                                 except TypeError:
                                     station_obj.runs[run_index].comments = value
                             else:
@@ -293,8 +296,6 @@ class XMLStationMTStation(BaseTranslator):
                                     c_attr, cvalue
                                 )
                         else:
-                            station_obj.runs[run_index].set_attr_from_name(
-                                ckey, cvalue
-                            )
+                            station_obj.runs[run_index].set_attr_from_name(ckey, cvalue)
 
         return station_obj

mt_metadata/transfer_functions/__init__.py

@@ -9,6 +9,7 @@ STANDARD_OUTPUT_CHANNELS = [
     "hz",
 ]
 
+# channel nomenclature mappings
 CHANNEL_MAPS = {
     "default": {"hx": "hx", "hy": "hy", "hz": "hz", "ex": "ex", "ey": "ey"},
     "lemi12": {"hx": "bx", "hy": "by", "hz": "bz", "ex": "e1", "ey": "e2"},
@@ -16,6 +17,8 @@ CHANNEL_MAPS = {
     "phoenix123": {"hx": "h1", "hy": "h2", "hz": "h3", "ex": "e1", "ey": "e2"},
     "musgraves": {"hx": "bx", "hy": "by", "hz": "bz", "ex": "ex", "ey": "ey"},
 }
+CHANNEL_MAPS["nims"] = CHANNEL_MAPS["default"]  # Alias NIMS system to use same config as default
+
 
 
 def get_allowed_channel_names(standard_names):

mt_metadata/transfer_functions/core.py

@@ -37,7 +37,7 @@ from mt_metadata.transfer_functions.io.zfiles.metadata import (
 from mt_metadata.base.helpers import validate_name
 from mt_metadata.utils.list_dict import ListDict
 from mt_metadata import DEFAULT_CHANNEL_NOMENCLATURE
-
+from typing import Optional
 # =============================================================================
 
 
@@ -179,12 +179,12 @@ class TF:
 
         return f"TF( {(', ').join(lines)} )"
 
-    def __eq__(self, other):
+    def __eq__(self, other, ignore_station_metadata_keys: Optional[list] = None):
         is_equal = True
         if not isinstance(other, TF):
             self.logger.info(f"Comparing object is not TF, type {type(other)}")
             is_equal = False
-        if self.station_metadata != other.station_metadata:
+        if not self.station_metadata.__eq__(other.station_metadata, ignore_keys=ignore_station_metadata_keys):
             self.logger.info("Station metadata is not equal")
             is_equal = False
         if self.survey_metadata != other.survey_metadata:
@@ -375,9 +375,7 @@ class TF:
         """
 
         if station_metadata is not None:
-            station_metadata = self._validate_station_metadata(
-                station_metadata
-            )
+            station_metadata = self._validate_station_metadata(station_metadata)
 
             runs = ListDict()
             if self.run_metadata.id not in ["0", 0, None]:
@@ -1943,7 +1941,7 @@ class TF:
                     "residual_covariance": "residual_covariance",
                     "transfer_function_error": "tf_err",
                     "survey_metadata": "survey_metadata",
-                    "station_metadata": "station_metadata",
+                    # "station_metadata": "station_metadata",
                     "_rotation_angle": "rotation_angle",
                 }
             )
@@ -1956,7 +1954,7 @@ class TF:
                     "tipper": "t",
                     "tipper_error": "t_err",
                     "survey_metadata": "survey_metadata",
-                    "station_metadata": "station_metadata",
+                    # "station_metadata": "station_metadata",
                     "_rotation_angle": "rotation_angle",
                 }
             )
@@ -2054,7 +2052,7 @@ class TF:
                 f"Input must be a EMTFXML object not {type(emtfxml_obj)}"
             )
         self.survey_metadata = emtfxml_obj.survey_metadata
-        self.station_metadata = emtfxml_obj.station_metadata
+        self.station_metadata = self.survey_metadata.stations[0]
 
         self.period = emtfxml_obj.data.period
         self.impedance = emtfxml_obj.data.z
@@ -2116,7 +2114,7 @@ class TF:
                 "tipper": "t",
                 "tipper_error": "t_err",
                 "survey_metadata": "survey_metadata",
-                "station_metadata": "station_metadata",
+                # "station_metadata": "station_metadata",
             }
         )
 
@@ -2377,7 +2375,6 @@ class TF:
         if not isinstance(avg_obj, ZongeMTAvg):
             raise TypeError(f"Input must be a ZMM object not {type(avg_obj)}")
         self.survey_metadata = avg_obj.survey_metadata
-        self.station_metadata = avg_obj.station_metadata
 
         self.period = 1.0 / avg_obj.frequency
         self.impedance = avg_obj.z

mt_metadata/transfer_functions/io/emtfxml/metadata/location.py

@@ -24,6 +24,8 @@ from mt_metadata.transfer_functions.io.emtfxml.metadata import helpers
 # =============================================================================
 attr_dict = get_schema("location", SCHEMA_FN_PATHS)
 attr_dict.add_dict(Declination()._attr_dict, "declination")
+
+
 # =============================================================================
 class Location(Base):
     __doc__ = write_lines(attr_dict)
@@ -31,6 +33,9 @@ class Location(Base):
     def __init__(self, **kwargs):
 
         self.declination = Declination()
+        self._latitude = 0.0
+        self._longitude = 0.0
+        self._elevation = 0.0
 
         super().__init__(attr_dict=attr_dict, **kwargs)
 

mt_metadata/transfer_functions/io/emtfxml/metadata/provenance.py

@@ -25,9 +25,20 @@ from mt_metadata import __version__
 
 # =============================================================================
 attr_dict = get_schema("provenance", SCHEMA_FN_PATHS)
-person_dict = get_schema("person", SCHEMA_FN_PATHS)
-attr_dict.add_dict(person_dict, "creator")
-attr_dict.add_dict(person_dict, "submitter")
+person_dict = get_schema(
+    "person",
+    SCHEMA_FN_PATHS,
+)
+attr_dict.add_dict(
+    person_dict,
+    "creator",
+    keys=["name", "comments", "url", "org", "org_url", "email"],
+)
+attr_dict.add_dict(
+    person_dict,
+    "submitter",
+    keys=["name", "comments", "url", "org", "org_url", "email"],
+)
 # =============================================================================
 
 

mt_metadata/transfer_functions/io/tools.py

@@ -198,7 +198,9 @@ def get_nm_elev(latitude, longitude):
 
     # read the xml response and convert to a float
     try:
+        # unpack the response to a dictionary
         info = json.loads(response.read())
+
     except json.JSONDecodeError:
         logger.error(
             f"Input values (latitude={latitude}, longitude={longitude}) "

mt_metadata/transfer_functions/io/zonge/metadata/header.py

@@ -68,7 +68,7 @@ class Header(Base):
         self.stn = STN()
         self.line = Line()
         self.unit = Unit()
-        self.job = Job
+        self.job = Job()
         self._elevation = 0.0
         super().__init__(attr_dict=attr_dict, **kwargs)
 

mt_metadata/transfer_functions/io/zonge/metadata/standards/header.json

@@ -8,6 +8,6 @@
         "options": [],
         "alias": [],
         "example": "null",
-		"default": null
+		  "default": null
     }	
 }

mt_metadata/transfer_functions/io/zonge/metadata/standards/job.json

@@ -8,7 +8,7 @@
         "options": [],
         "alias": [],
         "example": "yellowstone",
-    	"default": null
+    	  "default": null
     },
 	 "for": {
         "type": "string",
@@ -19,7 +19,7 @@
         "options": [],
         "alias": [],
         "example": "NSF",
-    	"default": null
+    	  "default": null
     }
     
 }