Merge pull request #174 from kujaku11/fix_mt_metadata_issue_173

- Fix issue #173 (filter logic: `units_in`, `units_out`,  and `applied`)
  - There is now a defined direction of filters
  - Filters are only for instrument response

.github/workflows/tests.yml

@@ -34,7 +34,7 @@ jobs:
         conda install pytest=7.1.2
         conda install pytest-cov
         conda install pytest-subtests
-        pip install git+https://github.com/kujaku11/mt_metadata.git@patches
+        pip install git+https://github.com/kujaku11/mt_metadata.git@fix_issue_173
         
     - name: Install Our Package
       shell: bash

mth5/groups/channel_dataset.py

@@ -20,7 +20,7 @@
 from mt_metadata import timeseries as metadata
 from mt_metadata.utils.mttime import MTime
 from mt_metadata.base import Base
-from mt_metadata.timeseries.filters import ChannelResponseFilter
+from mt_metadata.timeseries.filters import ChannelResponse
 
 from mth5 import CHANNEL_DTYPE
 from mth5.utils.exceptions import MTH5Error
@@ -248,7 +248,7 @@ def survey_id(self):
         return self.hdf5_dataset.parent.parent.parent.parent.attrs["id"]
 
     @property
-    def channel_response_filter(self):
+    def channel_response(self):
         # get the filters to make a channel response
         filters_group = FiltersGroup(
             self.hdf5_dataset.parent.parent.parent.parent["Filters"]
@@ -261,7 +261,7 @@ def channel_response_filter(self):
             except KeyError:
                 self.logger.warning(f"Could not locate filter {name}")
                 continue
-        return ChannelResponseFilter(filters_list=f_list)
+        return ChannelResponse(filters_list=f_list)
 
     @property
     def start(self):
@@ -686,7 +686,7 @@ def to_channel_ts(self):
             run_metadata=self.run_metadata.copy(),
             station_metadata=self.station_metadata.copy(),
             survey_metadata=self.survey_metadata.copy(),
-            channel_response_filter=self.channel_response_filter,
+            channel_response=self.channel_response,
         )
 
     def to_xarray(self):
@@ -1079,7 +1079,7 @@ def time_slice(
                 self.metadata.type,
                 data=self.hdf5_dataset[regional_ref],
                 channel_metadata={self.metadata.type: meta_dict},
-                channel_response_filter=self.channel_response_filter,
+                channel_response=self.channel_response,
             )
         else:
             msg = "return_type not understood, must be [ pandas | numpy | channel_ts ]"

mth5/groups/filters.py

@@ -5,7 +5,7 @@
 Need to make a group for FAP and FIR filters.
 
 
-:copyright: 
+:copyright:
     Jared Peacock ([email protected])
 
 :license: MIT
@@ -143,8 +143,8 @@ def to_filter_object(self, name):
         try:
             f_type = self.filter_dict[name]["type"]
         except KeyError:
-            msg = "Could not find %s in the filter dictionary"
-            self.logger.error(msg, name)
+            msg = f"Could not find {name} in the filter dictionary"
+            self.logger.error(msg)
             raise KeyError(msg, name)
         if f_type in ["zpk"]:
             return self.zpk_group.to_object(name)

mth5/groups/run.py

@@ -678,11 +678,11 @@ def from_channel_ts(self, channel_ts_obj):
             self.logger.error(msg)
             raise MTH5Error(msg)
         ## Need to add in the filters
-        if channel_ts_obj.channel_response_filter.filters_list != []:
+        if channel_ts_obj.channel_response.filters_list != []:
             from mth5.groups import FiltersGroup
 
             fg = FiltersGroup(self.hdf5_group.parent.parent.parent["Filters"])
-            for ff in channel_ts_obj.channel_response_filter.filters_list:
+            for ff in channel_ts_obj.channel_response.filters_list:
                 fg.add_filter(ff)
         ch_obj = self.add_channel(
             channel_ts_obj.component,

mth5/io/nims/nims.py

@@ -321,7 +321,7 @@ def hx(self):
                 channel_metadata=self.hx_metadata,
                 run_metadata=self.run_metadata,
                 station_metadata=self.station_metadata,
-                channel_response_filter=self.get_channel_response("hx"),
+                channel_response=self.get_channel_response("hx"),
             )
         return None
 
@@ -357,7 +357,7 @@ def hy(self):
                 channel_metadata=self.hy_metadata,
                 run_metadata=self.run_metadata,
                 station_metadata=self.station_metadata,
-                channel_response_filter=self.get_channel_response("hy"),
+                channel_response=self.get_channel_response("hy"),
             )
         return None
 
@@ -394,7 +394,7 @@ def hz(self):
                 channel_metadata=self.hz_metadata,
                 run_metadata=self.run_metadata,
                 station_metadata=self.station_metadata,
-                channel_response_filter=self.get_channel_response("hz"),
+                channel_response=self.get_channel_response("hz"),
             )
         return None
 
@@ -432,7 +432,7 @@ def ex(self):
                 channel_metadata=self.ex_metadata,
                 run_metadata=self.run_metadata,
                 station_metadata=self.station_metadata,
-                channel_response_filter=self.get_channel_response("ex", self.ex_length),
+                channel_response=self.get_channel_response("ex", self.ex_length),
             )
         return None
 
@@ -470,7 +470,7 @@ def ey(self):
                 channel_metadata=self.ey_metadata,
                 run_metadata=self.run_metadata,
                 station_metadata=self.station_metadata,
-                channel_response_filter=self.get_channel_response("ey", self.ey_length),
+                channel_response=self.get_channel_response("ey", self.ey_length),
             )
         return None
 

mth5/io/nims/response_filters.py

@@ -12,7 +12,7 @@
     PoleZeroFilter,
     TimeDelayFilter,
     CoefficientFilter,
-    ChannelResponseFilter,
+    ChannelResponse,
 )
 
 # =============================================================================
@@ -273,12 +273,12 @@ def get_channel_response(self, channel, dipole_length=1):
         """
 
         if channel[0] in ["e"]:
-            return ChannelResponseFilter(
+            return ChannelResponse(
                 filters_list=self._get_electric_filter(channel, dipole_length)
             )
 
         elif channel[0] in ["b", "h"]:
-            return ChannelResponseFilter(
+            return ChannelResponse(
                 filters_list=self._get_magnetic_filter(channel)
             )
 

mth5/io/phoenix/readers/base.py

@@ -1,13 +1,13 @@
 """
-Module to read and parse native Phoenix Geophysics data formats of the 
+Module to read and parse native Phoenix Geophysics data formats of the
 MTU-5C Family.
 
 This module implements Streamed readers for segmented-decimated continuus-decimated
 and native sampling rate time series formats of the MTU-5C family.
 
 :author: Jorge Torres-Solis
 
-Revised 2022 by J. Peacock 
+Revised 2022 by J. Peacock
 """
 
 # =============================================================================
@@ -21,7 +21,7 @@
 
 from mt_metadata.timeseries.filters import (
     CoefficientFilter,
-    ChannelResponseFilter,
+    ChannelResponse,
 )
 
 from loguru import logger
@@ -463,7 +463,7 @@ def get_v_to_mv_filter(self):
 
         return conversion
 
-    def get_channel_response_filter(self, rxcal_fn=None, scal_fn=None):
+    def get_channel_response(self, rxcal_fn=None, scal_fn=None):
         """
         Get the channel response filter
 
@@ -489,4 +489,4 @@ def get_channel_response_filter(self, rxcal_fn=None, scal_fn=None):
         if ch_metadata.type in ["electric"]:
             filter_list.append(self.get_dipole_filter())
 
-        return ChannelResponseFilter(filters_list=filter_list)
+        return ChannelResponse(filters_list=filter_list)

mth5/io/phoenix/readers/contiguous/decimated_continuous_reader.py

@@ -156,7 +156,7 @@ def to_channel_ts(self, rxcal_fn=None, scal_fn=None):
             channel_metadata=self.channel_metadata,
             run_metadata=self.run_metadata,
             station_metadata=self.station_metadata,
-            channel_response_filter=self.get_channel_response_filter(
+            channel_response=self.get_channel_response(
                 rxcal_fn=rxcal_fn, scal_fn=scal_fn
             ),
         )

mth5/io/phoenix/readers/native/native_reader.py

@@ -288,7 +288,7 @@ def to_channel_ts(self, rxcal_fn=None, scal_fn=None):
             channel_metadata=ch_metadata,
             run_metadata=self.run_metadata,
             station_metadata=self.station_metadata,
-            channel_response_filter=self.get_channel_response_filter(
+            channel_response=self.get_channel_response(
                 rxcal_fn=rxcal_fn, scal_fn=scal_fn
             ),
         )

mth5/io/phoenix/readers/receiver_metadata.py

@@ -140,7 +140,7 @@ def _to_electric_metadata(self, tag):
                 f"{self.lp_filter_base_name}_{int(ch.lp)}hz_low_pass",
                 f"dipole_{int(c.dipole_length)}m",
             ]
-            c.filter.applied = [False, False]
+            c.filter.applied = [True, True]
         return c
 
     def _to_magnetic_metadata(self, tag):
@@ -167,10 +167,10 @@ def _to_magnetic_metadata(self, tag):
             c.filter.name = [
                 f"{self.lp_filter_base_name}_{int(ch.lp)}hz_low_pass"
             ]
-            c.filter.applied = [False]
+            c.filter.applied = [True]
             if c.sensor.id is not None:
                 c.filter.name.append(f"coil_{c.sensor.id}_response")
-                c.filter.applied.append(False)
+                c.filter.applied.append(True)
 
         return c
 

mth5/io/phoenix/readers/segmented/decimated_segmented_reader.py

@@ -245,7 +245,7 @@ def to_channel_ts(self, rxcal_fn=None, scal_fn=None):
             channel_metadata=ch_metadata,
             run_metadata=self.run_metadata,
             station_metadata=self.station_metadata,
-            channel_response_filter=self.get_channel_response_filter(
+            channel_response=self.get_channel_response(
                 rxcal_fn=rxcal_fn, scal_fn=scal_fn
             ),
         )
@@ -331,7 +331,7 @@ def to_channel_ts(self, rxcal_fn=None, scal_fn=None):
                     channel_metadata=ch_metadata,
                     run_metadata=self.run_metadata,
                     station_metadata=self.station_metadata,
-                    channel_response_filter=self.get_channel_response_filter(
+                    channel_response=self.get_channel_response(
                         rxcal_fn=rxcal_fn, scal_fn=scal_fn
                     ),
                 )

mth5/io/zen/zen.py

@@ -7,7 +7,7 @@
     * Tools for reading and writing files for Zen and processing software
     * Tools for copying data from SD cards
     * Tools for copying schedules to SD cards
-    
+
 Created on Tue Jun 11 10:53:23 2013
 Updated August 2020 (JP)
 
@@ -30,7 +30,7 @@
 
 from mt_metadata.utils.mttime import MTime
 from mt_metadata.timeseries.filters import (
-    ChannelResponseFilter,
+    ChannelResponse,
     FrequencyResponseTableFilter,
     CoefficientFilter,
 )
@@ -427,7 +427,7 @@ def channel_metadata(self):
         ch.units = "digital counts"
         ch.channel_number = self.channel_number
         ch.filter.name = self.channel_response.names
-        ch.filter.applied = [False] * len(self.channel_response.names)
+        ch.filter.applied = [True] * len(self.channel_response.names)
 
         return ch
 
@@ -596,7 +596,7 @@ def channel_response(self):
             filter_list.append(self.dipole_filter)
 
         filter_list.append(self.counts2mv_filter)
-        return ChannelResponseFilter(filters_list=filter_list)
+        return ChannelResponse(filters_list=filter_list)
 
     @property
     def dipole_filter(self):
@@ -1127,7 +1127,7 @@ def to_channelts(self):
             channel_metadata=self.channel_metadata,
             station_metadata=self.station_metadata,
             run_metadata=self.run_metadata,
-            channel_response_filter=self.channel_response,
+            channel_response=self.channel_response,
         )