Udpdate channel nomenclature to be in config

-Added ChannelNomenclature and channel_nomenclature to config
-weave ChannelNomenclature class into synthetic tests
-added methods for setting default input/output/reference channels to processing
 config (may need mod for 4 channel stations)
-changed channel_nomenclature from kwarg to ard in process_mth5
-modified TTFZ to use ChannelNomenclature class
-removed dependencies on aurora.channel_nomenclature

[Issue(s): #74]

aurora/config/metadata/__init__.py

@@ -1,6 +1,7 @@
 from .window import Window
 from .station import Station
 from .channel import Channel
+from .channel_nomenclature import ChannelNomenclature
 from .run import Run
 from .stations import Stations
 from .band import Band
@@ -14,6 +15,7 @@
     "Window",
     "Station",
     "Channel",
+    "ChannelNomenclature",
     "Run",
     "Stations",
     "Band",

aurora/config/metadata/processing.py

@@ -13,12 +13,14 @@
 from mt_metadata.base import get_schema, Base
 from .standards import SCHEMA_FN_PATHS
 
-from . import DecimationLevel, Stations, Band
+from . import DecimationLevel, Stations, Band, ChannelNomenclature
 
 
 # =============================================================================
 attr_dict = get_schema("processing", SCHEMA_FN_PATHS)
 attr_dict.add_dict(Stations()._attr_dict, "stations")
+attr_dict.add_dict(ChannelNomenclature()._attr_dict, "channel_nomenclature")
+
 
 # =============================================================================
 class Processing(Base):
@@ -28,6 +30,7 @@ def __init__(self, **kwargs):
 
         self.stations = Stations()
         self._decimations = []
+        self.channel_nomenclature = ChannelNomenclature()
 
         super().__init__(attr_dict=attr_dict, **kwargs)
 
@@ -179,6 +182,27 @@ def drop_reference_channels(self):
             decimation.reference_channels = []
         return
 
+    def set_input_channels(self, channels):
+        for decimation in self.decimations:
+            decimation.input_channels = channels
+
+    def set_output_channels(self, channels):
+        for decimation in self.decimations:
+            decimation.output_channels = channels
+
+    def set_reference_channels(self, channels):
+        for decimation in self.decimations:
+            decimation.reference_channels = channels
+
+    def set_default_input_output_channels(self):
+        self.set_input_channels(self.channel_nomenclature.default_input_channels)
+        self.set_output_channels(self.channel_nomenclature.default_output_channels)
+
+    def set_default_reference_channels(self):
+        self.set_reference_channels(
+            self.channel_nomenclature.default_reference_channels
+        )
+
     def validate(self):
         """
         Placeholder.  Some of the checks and methods here maybe better placed in

aurora/config/metadata/standards/processing.json

@@ -20,16 +20,5 @@
         "alias": [],
         "example": "0",
 		"default": null
-    },
-    "channel_nomenclature": {
-        "type": "string",
-        "required": true,
-        "style": "free form",
-        "units": null,
-        "description": "key to a dict of how channels are named",
-        "options": [],
-        "alias": [],
-        "example": "LEMI12",
-        "default": "default"
     }
 }

aurora/pipelines/process_mth5.py

@@ -202,9 +202,9 @@ def process_tf_decimation_level(
 
 def export_tf(
     tf_collection,
+    channel_nomenclature,
     station_metadata_dict={},
     survey_dict={},
-    channel_nomenclature="default",
 ):
     """
     This method may wind up being embedded in the TF class
@@ -429,9 +429,7 @@ def process_mth5(
             local_merged_stft_obj,
             remote_merged_stft_obj,
         )
-        tf_obj.apparent_resistivity(
-            units=units, channel_nomenclature=processing_config.channel_nomenclature
-        )
+        tf_obj.apparent_resistivity(processing_config.channel_nomenclature, units=units)
         tf_dict[i_dec_level] = tf_obj
 
         if show_plot:
@@ -476,9 +474,9 @@ def process_mth5(
 
         tf_cls = export_tf(
             tf_collection,
+            processing_config.channel_nomenclature,
             station_metadata_dict=station_metadata.to_dict(),
             survey_dict=survey_dict,
-            channel_nomenclature=processing_config.channel_nomenclature,
         )
         close_mths_objs(dataset_df)
         return tf_cls

aurora/test_utils/synthetic/make_mth5_from_asc.py

@@ -18,7 +18,7 @@
 from mth5.timeseries import ChannelTS, RunTS
 from mth5.mth5 import MTH5
 
-from aurora.channel_nomenclature import map_channels
+from aurora.config.metadata.channel_nomenclature import ChannelNomenclature
 from aurora.test_utils.synthetic.synthetic_station_config import make_filters
 from aurora.test_utils.synthetic.synthetic_station_config import make_station_01
 from aurora.test_utils.synthetic.synthetic_station_config import make_station_02
@@ -44,7 +44,9 @@ def create_run_ts_from_synthetic_run(run, df, channel_nomenclature="default"):
     -------
 
     """
-    EX, EY, HX, HY, HZ = map_channels(channel_nomenclature)
+    channel_nomenclature_obj = ChannelNomenclature()
+    channel_nomenclature_obj.keyword = channel_nomenclature
+    EX, EY, HX, HY, HZ = channel_nomenclature_obj.unpack()
     ch_list = []
     for col in df.columns:
         data = df[col].values

aurora/test_utils/synthetic/make_processing_configs.py

@@ -1,4 +1,3 @@
-from aurora.channel_nomenclature import map_channels
 from aurora.config import BANDS_DEFAULT_FILE
 from aurora.config import BANDS_256_FILE
 from aurora.config.config_creator import ConfigCreator
@@ -28,21 +27,16 @@ def create_test_run_config(
 
 
     """
-    EX, EY, HX, HY, HZ = map_channels(channel_nomenclature)
     estimation_engine = "RME"
     local_station_id = test_case_id
     remote_station_id = ""
-    reference_channels = []
-    input_channels = [HX, HY]
-    output_channels = [HZ, EX, EY]
+
     if test_case_id == "test1r2":
         estimation_engine = "RME_RR"
-        reference_channels = [HX, HY]
         local_station_id = "test1"
         remote_station_id = "test2"
     if test_case_id == "test2r1":
         estimation_engine = "RME_RR"
-        reference_channels = [HX, HY]
         local_station_id = "test2"
         remote_station_id = "test1"
 
@@ -67,40 +61,31 @@ def create_test_run_config(
     if test_case_id in ["test1", "test2"]:
         p = cc.create_run_processing_object(
             emtf_band_file=emtf_band_setup_file,
-            input_channels=input_channels,
-            output_channels=output_channels,
         )
         p.id = config_id
-        p.channel_nomenclature = channel_nomenclature
-        p.stations.from_dataset_dataframe(ds_df)
-
-        for decimation in p.decimations:
-            decimation.estimator.engine = estimation_engine
-            decimation.window.type = "hamming"
-            decimation.window.num_samples = num_samples_window
-            decimation.window.overlap = num_samples_overlap
-            decimation.regression.max_redescending_iterations = 2
-
+        p.channel_nomenclature.keyword = channel_nomenclature
+        p.set_default_input_output_channels()
         p.drop_reference_channels()
+        p.stations.from_dataset_dataframe(ds_df)
 
     elif test_case_id in ["test2r1", "test1r2"]:
         config_id = f"{config_id}-RR{remote_station_id}"
         p = cc.create_run_processing_object(
             emtf_band_file=emtf_band_setup_file,
-            input_channels=input_channels,
-            output_channels=output_channels,
         )
         p.id = config_id
-        p.channel_nomenclature = channel_nomenclature
+        p.id = config_id
+        p.channel_nomenclature.keyword = channel_nomenclature
+        p.set_default_input_output_channels()
+        p.set_default_reference_channels()
         p.stations.from_dataset_dataframe(ds_df)
 
-        for decimation in p.decimations:
-            decimation.estimator.engine = estimation_engine
-            decimation.window.type = "hamming"
-            decimation.window.num_samples = num_samples_window
-            decimation.window.overlap = num_samples_overlap
-            decimation.regression.max_redescending_iterations = 2
-            decimation.reference_channels = reference_channels
+    for decimation in p.decimations:
+        decimation.estimator.engine = estimation_engine
+        decimation.window.type = "hamming"
+        decimation.window.num_samples = num_samples_window
+        decimation.window.overlap = num_samples_overlap
+        decimation.regression.max_redescending_iterations = 2
 
     if save == "json":
         cc.to_json(p)

aurora/test_utils/synthetic/synthetic_station_config.py

@@ -18,12 +18,10 @@
 import numpy as np
 import random
 
+from aurora.config.metadata.channel_nomenclature import ChannelNomenclature
 from aurora.test_utils.synthetic.paths import DATA_PATH
 from aurora.time_series.filters.filter_helpers import make_coefficient_filter
 
-from aurora.channel_nomenclature import get_channel_map
-from aurora.channel_nomenclature import map_channels
-
 random.seed(0)
 
 
@@ -61,7 +59,13 @@ def __init__(self, id, **kwargs):
         self.id = id
         self.sample_rate = kwargs.get("sample_rate", 1.0)
         self.raw_data_path = kwargs.get("raw_data_path", None)
-        self.channel_nomenclature = kwargs.get("channel_nomenclature", "default")
+
+        # set channel_map
+        self._channel_map = None
+        self.channel_nomemclature_keyword = kwargs.get(
+            "channel_nomenclature", "default"
+        )
+        self.set_channel_map()
         self.channels = kwargs.get("channels", list(self.channel_map.values()))
         self.noise_scalars = kwargs.get("noise_scalars", None)
         self.nan_indices = kwargs.get("nan_indices", {})
@@ -74,7 +78,15 @@ def __init__(self, id, **kwargs):
 
     @property
     def channel_map(self):
-        return get_channel_map(self.channel_nomenclature)
+        return self._channel_map
+
+    def set_channel_map(self):
+        channel_nomenclature = ChannelNomenclature()
+        channel_nomenclature.keyword = self.channel_nomemclature_keyword
+        channel_map = channel_nomenclature.get_channel_map(
+            self.channel_nomemclature_keyword
+        )
+        self._channel_map = channel_map
 
 
 class SyntheticStation(object):
@@ -92,7 +104,9 @@ def __init__(self, id, **kwargs):
 
 
 def make_station_01(channel_nomenclature="default"):
-    EX, EY, HX, HY, HZ = map_channels(channel_nomenclature)
+    channel_nomenclature_obj = ChannelNomenclature()
+    channel_nomenclature_obj.keyword = channel_nomenclature
+    EX, EY, HX, HY, HZ = channel_nomenclature_obj.unpack()
     station = SyntheticStation("test1")
     station.mth5_path = DATA_PATH.joinpath("test1.h5")
 
@@ -141,10 +155,12 @@ def make_station_02(channel_nomenclature="default"):
 
 
 def make_station_03(channel_nomenclature="default"):
-    EX, EY, HX, HY, HZ = map_channels(channel_nomenclature)
+    channel_nomenclature_obj = ChannelNomenclature()
+    channel_nomenclature_obj.keyword = channel_nomenclature
+    EX, EY, HX, HY, HZ = channel_nomenclature_obj.unpack()
     station = SyntheticStation("test3")
     station.mth5_path = DATA_PATH.joinpath("test3.h5")
-    channels = list(get_channel_map(channel_nomenclature).values())
+    channels = channel_nomenclature_obj.channels
 
     nan_indices = {}
     for ch in channels:

aurora/transfer_function/TTFZ.py

@@ -6,9 +6,6 @@
 
 from aurora.transfer_function.base import TransferFunction
 
-# from mt_metadata.transfer_functions.channel_nomenclature import map_channels
-from aurora.channel_nomenclature import map_channels
-
 
 class TTFZ(TransferFunction):
     """
@@ -26,7 +23,7 @@ class TTFZ(TransferFunction):
     def __init__(self, *args, **kwargs):
         super(TTFZ, self).__init__(*args, **kwargs)
 
-    def apparent_resistivity(self, units="SI", channel_nomenclature="default"):
+    def apparent_resistivity(self, channel_nomenclature, units="SI"):
         """
         ap_res(...) : computes app. res., phase, errors, given imped., cov.
         %USAGE: [rho,rho_se,ph,ph_se] = ap_res(z,sig_s,sig_e,periods) ;
@@ -39,12 +36,12 @@ def apparent_resistivity(self, units="SI", channel_nomenclature="default"):
         ----------
         units: str
             one of ["MT","SI"]
-        channel_nomenclature: str
-            free form, but normally the mt_acquisition system ["MT","SI"]
+        channel_nomenclature:
+        aurora.config.metadata.channel_nomenclature.ChannelNomenclature
+            has a dict that you
 
         """
-
-        ex, ey, hx, hy, hz = map_channels(channel_nomenclature)
+        ex, ey, hx, hy, hz = channel_nomenclature.unpack()
         rad_deg = 180 / np.pi
         # off - diagonal impedances
         self.rho = np.zeros((self.num_bands, 2))