mt-metadata 0.3.6__py2.py3-none-any.whl → 0.3.8__py2.py3-none-any.whl

mt_metadata/transfer_functions/io/emtfxml/emtfxml.py

@@ -358,14 +358,20 @@ class EMTFXML(emtf_xml.EMTF):
             if hasattr(value, "to_xml") and callable(getattr(value, "to_xml")):
                 if key == "processing_info":
                     if skip_field_notes:
-                        value.remote_info._order.remove("field_notes")
+                        try:
+                            value.remote_info._order.remove("field_notes")
+                        except ValueError:
+                            self.logger.debug("No field notes to skip.")
                     if value.remote_info.site.id in [
                         None,
                         "",
                         "None",
                         "none",
                     ]:
-                        value.remote_info._order.remove("site")
+                        try:
+                            value.remote_info._order.remove("site")
+                        except ValueError:
+                            self.logger.debug("No remote field notes to skip.")
                 element = value.to_xml()
                 if isinstance(element, list):
                     for item in element:

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

@@ -432,7 +432,7 @@ class TransferFunction(Base):
                 pass
 
             comp_element = et.SubElement(
-                period_element, key.replace("_", ".").capitalize(), attr_dict
+                period_element, key.replace("_", ".").upper(), attr_dict
             )
             idx_dict = self.write_dict[key]
             shape = arr.shape

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

@@ -56,7 +56,7 @@ class Estimate(Base):
 
         root = et.Element(
             self.__class__.__name__.capitalize(),
-            {"name": self.name, "type": self.type},
+            {"name": self.name.upper(), "type": self.type},
         )
 
         et.SubElement(root, "Description").text = self.description

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

@@ -20,6 +20,8 @@ from mt_metadata.transfer_functions.io.emtfxml.metadata import helpers
 
 # =============================================================================
 attr_dict = get_schema("period_range", SCHEMA_FN_PATHS)
+
+
 # =============================================================================
 class PeriodRange(Base):
     __doc__ = write_lines(attr_dict)
@@ -45,7 +47,10 @@ class PeriodRange(Base):
 
         root = et.Element(
             self.__class__.__name__,
-            {"min": f"{self.min:.9f}", "max": f"{self.max:.9f}"},
+            {
+                "min": f"{self.min:<16.5E}".strip(),
+                "max": f"{self.max:<16.5E}".strip(),
+            },
         )
         if string:
             return element_to_string(root)

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

@@ -11,7 +11,11 @@ Created on Wed Dec 23 21:30:36 2020
 # =============================================================================
 # Imports
 # =============================================================================
-from mt_metadata.base.helpers import write_lines, dict_to_xml, element_to_string
+from mt_metadata.base.helpers import (
+    write_lines,
+    dict_to_xml,
+    element_to_string,
+)
 from mt_metadata.base import get_schema, Base
 from .standards import SCHEMA_FN_PATHS
 from . import Person
@@ -40,7 +44,7 @@ class Provenance(Base):
 
     @property
     def create_time(self):
-        return self._creation_dt.iso_str
+        return self._creation_dt.iso_str.split(".")[0]
 
     @create_time.setter
     def create_time(self, dt_str):

mt_metadata/transfer_functions/io/emtfxml/metadata/standards/copyright.json

@@ -21,7 +21,8 @@
             "Restricted release",
             "Paper Citation Required",
             "Academic Use Only",
-            "Conditions Apply"
+            "Conditions Apply",
+            "Data Citation Required"
         ],
         "alias": [],
         "example": "Unrestricted release",

mt_metadata/transfer_functions/processing/aurora/channel_nomenclature.py

@@ -10,53 +10,11 @@ from mt_metadata.base.helpers import write_lines
 from mt_metadata.base import get_schema, Base
 from .standards import SCHEMA_FN_PATHS
 
+from mt_metadata.transfer_functions import CHANNEL_MAPS
+
 # =============================================================================
 attr_dict = get_schema("channel_nomenclature", SCHEMA_FN_PATHS)
 
-# Define allowed sets of channel labellings
-STANDARD_INPUT_NAMES = [
-    "hx",
-    "hy",
-]
-STANDARD_OUTPUT_NAMES = [
-    "ex",
-    "ey",
-    "hz",
-]
-
-def load_channel_maps():
-    """
-    :return: Keys are the channel_nomenclature schema keywords.
-     Values are dictionaries which map the STANDARD_INPUT_NAMES, \
-     STANDARD_OUTPUT_NAMES to the channel names associated with a given
-     channel nomenclature
-    :rtype: dict
-    """
-    import json
-    import pathlib
-    fn = pathlib.Path(__file__).parent.joinpath("standards", "channel_nomenclatures.json")
-    with open(fn) as f:
-        channel_maps = json.loads(f.read())
-    return channel_maps
-
-CHANNEL_MAPS = load_channel_maps()
-
-def get_allowed_channel_names(standard_names):
-    """
-    :param standard_names: one of STANDARD_INPUT_NAMES, or STANDARD_OUTPUT_NAMES
-    :type standard_names: list
-    :return: allowed_names: list of channel names that are supported
-    :rtype: list
-    """
-    allowed_names = []
-    for ch in standard_names:
-        for _, channel_map in CHANNEL_MAPS.items():
-            allowed_names.append(channel_map[ch])
-    allowed_names = list(set(allowed_names))
-    return allowed_names
-
-ALLOWED_INPUT_CHANNELS = get_allowed_channel_names(STANDARD_INPUT_NAMES)
-ALLOWED_OUTPUT_CHANNELS = get_allowed_channel_names(STANDARD_OUTPUT_NAMES)
 
 # =============================================================================
 class ChannelNomenclature(Base):

mt_metadata/transfer_functions/processing/aurora/decimation_level.py

@@ -31,7 +31,7 @@ attr_dict.add_dict(get_schema("estimator", SCHEMA_FN_PATHS), "estimator")
 # =============================================================================
 
 
-def df_from_bands(band_list):
+def df_from_bands(band_list: list) -> pd.DataFrame:
     """
     Utility function that transforms a list of bands into a dataframe
 
@@ -70,13 +70,13 @@ def df_from_bands(band_list):
     out_df.reset_index(inplace=True, drop=True)
     return out_df
 
-def get_fft_harmonics(samples_per_window, sample_rate):
+def get_fft_harmonics(samples_per_window: int, sample_rate: float) -> np.ndarray:
     """
     Works for odd and even number of points.
 
-    Could be midified with kwargs to support one_sided, two_sided, ignore_dc
-    ignore_nyquist, and etc.  Could actally take FrequencyBands as an argument
-    if we wanted as well.
+    Development notes:
+    Could be modified with kwargs to support one_sided, two_sided, ignore_dc
+    ignore_nyquist, and etc.  Consider taking FrequencyBands as an argument.
 
     Parameters
     ----------

mt_metadata/transfer_functions/processing/aurora/standards/regression.json

@@ -31,5 +31,50 @@
         "alias": [],
         "example": "2",
 		"default": 2
+    },
+    "r0": {
+        "type": "float",
+        "required": true,
+        "style": "number",
+        "units": null,
+        "description": "The number of standard deviations where the influence function changes from linear to quadratic",
+        "options": [],
+        "alias": [],
+        "example": "1.4",
+		"default": 1.5
+    },
+	"u0": {
+        "type": "float",
+        "required": true,
+        "style": "number",
+        "units": null,
+        "description": "Control for redescending Huber regression weights.",
+        "options": [],
+        "alias": [],
+        "example": "2.8",
+		"default": 2.8
+    },
+	"tolerance": {
+        "type": "float",
+        "required": true,
+        "style": "number",
+        "units": null,
+        "description": "Control for convergence of RME algorithm.  Lower means more iterations",
+        "options": [],
+        "alias": [],
+        "example": "0.005",
+		"default": 0.005
+    },
+	"verbosity": {
+        "type": "int",
+        "required": true,
+        "style": "number",
+        "units": null,
+        "description": "Control for logging messages during regression -- Higher means more messages",
+        "options": [0, 1, 2],
+        "alias": [],
+        "example": "1",
+		"default": 0
+
     }
-}
+}

mt_metadata/transfer_functions/processing/aurora/station.py

@@ -17,6 +17,8 @@ from .run import Run
 
 # =============================================================================
 attr_dict = get_schema("station", SCHEMA_FN_PATHS)
+
+
 # =============================================================================
 class Station(Base):
     __doc__ = write_lines(attr_dict)
@@ -88,8 +90,8 @@ class Station(Base):
         processing
 
         [
-            "station_id",
-            "run_id",
+            "station",
+            "run",
             "start",
             "end",
             "mth5_path",
@@ -106,8 +108,8 @@ class Station(Base):
         for run in self.runs:
             for tp in run.time_periods:
                 entry = {
-                    "station_id": self.id,
-                    "run_id": run.id,
+                    "station": self.id,
+                    "run": run.id,
                     "start": tp.start,
                     "end": tp.end,
                     "mth5_path": self.mth5_path,
@@ -130,8 +132,8 @@ class Station(Base):
         set a data frame
 
         [
-            "station_id",
-            "run_id",
+            "station",
+            "run",
             "start",
             "end",
             "mth5_path",
@@ -150,15 +152,17 @@ class Station(Base):
 
         self.runs = []
 
-        self.id = df.station_id.unique()[0]
+        self.id = df.station.unique()[0]
         self.mth5_path = df.mth5_path.unique()[0]
         self.remote = df.remote.unique()[0]
 
         for entry in df.itertuples():
             try:
-                r = self.run_dict[entry.run_id]
+                r = self.run_dict[entry.run]
                 r.time_periods.append(
-                    TimePeriod(start=entry.start.isoformat(), end=entry.end.isoformat())
+                    TimePeriod(
+                        start=entry.start.isoformat(), end=entry.end.isoformat()
+                    )
                 )
 
             except KeyError:
@@ -167,7 +171,7 @@ class Station(Base):
                 else:
                     channel_scale_factors = {}
                 r = Run(
-                    id=entry.run_id,
+                    id=entry.run,
                     sample_rate=entry.sample_rate,
                     input_channels=entry.input_channels,
                     output_channels=entry.output_channels,
@@ -175,6 +179,8 @@ class Station(Base):
                 )
 
                 r.time_periods.append(
-                    TimePeriod(start=entry.start.isoformat(), end=entry.end.isoformat())
+                    TimePeriod(
+                        start=entry.start.isoformat(), end=entry.end.isoformat()
+                    )
                 )
                 self.runs.append(r)

mt_metadata/transfer_functions/processing/aurora/stations.py

@@ -117,14 +117,14 @@ class Stations(Base):
 
         """
 
-        station = df[df.remote == False].station_id.unique()[0]
-        rr_stations = df[df.remote == True].station_id.unique()
+        station = df[df.remote == False].station.unique()[0]
+        rr_stations = df[df.remote == True].station.unique()
 
-        self.local.from_dataset_dataframe(df[df.station_id == station])
+        self.local.from_dataset_dataframe(df[df.station == station])
 
         for rr_station in rr_stations:
             rr = Station()
-            rr.from_dataset_dataframe(df[df.station_id == rr_station])
+            rr.from_dataset_dataframe(df[df.station == rr_station])
             self.add_remote(rr)
 
     def to_dataset_dataframe(self):

mt_metadata/utils/list_dict.py

@@ -44,18 +44,14 @@ class ListDict:
 
     def _get_key_from_index(self, index):
         try:
-            return next(
-                key for ii, key in enumerate(self._home) if ii == index
-            )
+            return next(key for ii, key in enumerate(self._home) if ii == index)
 
         except StopIteration:
             raise KeyError(f"Could not find {index}")
 
     def _get_index_from_key(self, key):
         try:
-            return next(
-                index for index, k in enumerate(self._home) if k == key
-            )
+            return next(index for index, k in enumerate(self._home) if k == key)
 
         except StopIteration:
             raise KeyError(f"Could not find {key}")
@@ -75,9 +71,7 @@ class ListDict:
         elif hasattr(obj, "component"):
             return obj.component
         else:
-            raise TypeError(
-                "could not identify an appropriate key from object"
-            )
+            raise TypeError("could not identify an appropriate key from object")
 
     def __deepcopy__(self, memodict={}):
         """
@@ -230,9 +224,7 @@ class ListDict:
                 raise (KeyError("Could not find None in keys."))
 
         else:
-            raise TypeError(
-                "could not identify an appropriate key from object"
-            )
+            raise TypeError("could not identify an appropriate key from object")
 
     def extend(self, other, skip_keys=[]):
         """
@@ -282,3 +274,18 @@ class ListDict:
             )
 
         self._home.update(other)
+
+    def pop(self, key):
+        """
+        pop item off of dictionary.  The key must be verbatim
+
+        :param key: key of item to be popped off of dictionary
+        :type key: string
+        :return: item popped
+
+        """
+
+        if key in self.keys():
+            return dict([self._home.popitem(key)])
+        else:
+            raise KeyError(f"{key} is not in ListDict keys.")

mt_metadata/utils/mttime.py

@@ -400,7 +400,7 @@ class MTime:
 
         """
         t_min_max = False
-        if dt_str in [None, "", "none", "None", "NONE"]:
+        if dt_str in [None, "", "none", "None", "NONE", "Na"]:
             self.logger.debug(
                 "Time string is None, setting to 1980-01-01:00:00:00"
             )

mt_metadata/utils/validators.py

@@ -378,6 +378,15 @@ def validate_default(value_dict):
 
 def validate_value_type(value, v_type, style=None):
     """
+
+    :param value:
+    :type value:
+    :param v_type:
+    :type v_type:
+    :param style:
+    :type style:
+    :return:
+
     validate type from standards
 
     """
@@ -469,7 +478,7 @@ def validate_value_type(value, v_type, style=None):
 
         # if a number convert to appropriate type
         elif isinstance(
-            value, (float, np.float_, np.float16, np.float32, np.float64)
+            value, (float, np.float16, np.float32, np.float64)
         ):
             if v_type is int:
                 return int(value)
@@ -481,7 +490,7 @@ def validate_value_type(value, v_type, style=None):
         elif isinstance(value, Iterable):
             if v_type is str:
                 if isinstance(value, np.ndarray):
-                    value = value.astype(np.unicode_)
+                    value = value.astype(np.str_)
                 value = [
                     f"{v}".replace("'", "").replace('"', "") for v in value
                 ]

{mt_metadata-0.3.6.dist-info → mt_metadata-0.3.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: mt-metadata
-Version: 0.3.6
+Version: 0.3.8
 Summary: Metadata for magnetotelluric data
 Home-page: https://github.com/kujaku11/mt_metadata
 Author: Jared Peacock
@@ -28,7 +28,7 @@ Requires-Dist: matplotlib
 Requires-Dist: xarray
 Requires-Dist: loguru
 
-# mt_metadata version 0.3.6
+# mt_metadata version 0.3.8
  Standard MT metadata
 
 [![PyPi version](https://img.shields.io/pypi/v/mt_metadata.svg)](https://pypi.python.org/pypi/mt-metadata)
@@ -58,7 +58,7 @@ MT Metadata is a project led by [IRIS-PASSCAL MT Software working group](https:/
 
 Most people will be using the transfer functions, but a lot of that metadata comes from the time series metadata.  This module supports both and has tried to make them more or less seamless to reduce complication.
 
-* **Version**: 0.3.6
+* **Version**: 0.3.8
 * **Free software**: MIT license
 * **Documentation**: https://mt-metadata.readthedocs.io.
 * **Examples**: Click the `Binder` badge above and Jupyter Notebook examples are in **mt_metadata/examples/notebooks** and **docs/source/notebooks**
@@ -377,3 +377,60 @@ History
 -----------------------
 
 * update pandas.append to concat
+
+0.3.4 ()
+-----------------------
+
+* Update HISTORY.rst by @kujaku11 in https://github.com/kujaku11/mt_metadata/pull/179
+* Remove filter direction attributes by @kkappler in https://github.com/kujaku11/mt_metadata/pull/181
+* Fix issue 173 by @kkappler in https://github.com/kujaku11/mt_metadata/pull/182
+* Patch 173 by @kkappler in https://github.com/kujaku11/mt_metadata/pull/183
+* Add some common helper functions by @kkappler in https://github.com/kujaku11/mt_metadata/pull/185
+* Bug fix in FC layer by @kkappler in https://github.com/kujaku11/mt_metadata/pull/186
+* Fix mth5 issue 187 by @kkappler in https://github.com/kujaku11/mt_metadata/pull/187
+* bug fixes by @kujaku11 in https://github.com/kujaku11/mt_metadata/pull/180
+* updating how a TF is initiated, initialize xarray is expensive by @kujaku11 in https://github.com/kujaku11/mt_metadata/pull/188
+* Change default value of `get_elevation` to False by @kujaku11 in https://github.com/kujaku11/mt_metadata/pull/191
+* Updating git clone address in the readme by @xandrd in https://github.com/kujaku11/mt_metadata/pull/189
+* Fix how Z-files read/write by @kujaku11 in https://github.com/kujaku11/mt_metadata/pull/192
+* Adjust how TF._initialize_transfer_function is setup by @kujaku11 in https://github.com/kujaku11/mt_metadata/pull/193
+* Add Ability to store processing configuration in TF by @kujaku11 in https://github.com/kujaku11/mt_metadata/pull/196
+* Bump version: 0.3.3 → 0.3.4 by @kujaku11 in https://github.com/kujaku11/mt_metadata/pull/198
+
+
+0.3.5 ()
+---------------------
+
+* Patches by @kujaku11 in https://github.com/kujaku11/mt_metadata/pull/200
+* Fix issue #202 by @kujaku11 in https://github.com/kujaku11/mt_metadata/pull/203
+* Patches by @kkappler in https://github.com/kujaku11/mt_metadata/pull/205
+* Bump version: 0.3.4 → 0.3.5 by @kujaku11 in https://github.com/kujaku11/mt_metadata/pull/206
+
+0.3.6 ()
+---------------------
+
+* add method for accessing mag channel names by @kkappler in https://github.com/kujaku11/mt_metadata/pull/210
+* Patches by @kujaku11 in https://github.com/kujaku11/mt_metadata/pull/208
+* Fix mth5 issue 207 by @kkappler in https://github.com/kujaku11/mt_metadata/pull/209
+* Minor changes  by @kkappler in https://github.com/kujaku11/mt_metadata/pull/211
+* Patches by @kujaku11 in https://github.com/kujaku11/mt_metadata/pull/212
+
+0.3.7 (2024-08-16)
+---------------------
+
+* Minor fixes numpy 2.0 by @kkappler in https://github.com/kujaku11/mt_metadata/pull/213
+* Fix issue 216 by @kkappler in https://github.com/kujaku11/mt_metadata/pull/218
+* Patches  by @kujaku11 in https://github.com/kujaku11/mt_metadata/pull/219
+* add u0 and r0 as regression parameters by @kkappler in https://github.com/kujaku11/mt_metadata/pull/220
+* Updating EMTF XML and StationXML writers by @kujaku11 in https://github.com/kujaku11/mt_metadata/pull/217
+* Patches by @kkappler in https://github.com/kujaku11/mt_metadata/pull/221
+* Patches by @kkappler in https://github.com/kujaku11/mt_metadata/pull/223
+* Bump version: 0.3.6 → 0.3.7 by @kujaku11 in https://github.com/kujaku11/mt_metadata/pull/225 
+
+0.3.8 (2024-09-30)
+----------------------
+
+* Add pop to ListDict by @kujaku11 in https://github.com/kujaku11/mt_metadata/pull/226
+* Fix EDI Tipper flip by @kujaku11 in https://github.com/kujaku11/mt_metadata/pull/228
+* Patches by @kujaku11 in https://github.com/kujaku11/mt_metadata/pull/227
+* Bump version: 0.3.7 → 0.3.8 by @kujaku11 in https://github.com/kujaku11/mt_metadata/pull/229