mt-metadata 0.3.3__tar.gz → 0.3.5__tar.gz

{mt_metadata-0.3.3 → mt_metadata-0.3.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: mt_metadata
-Version: 0.3.3
+Version: 0.3.5
 Summary: Metadata for magnetotelluric data
 Home-page: https://github.com/kujaku11/mt_metadata
 Author: Jared Peacock
@@ -22,7 +22,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 License-File: AUTHORS.rst
 
-# mt_metadata version 0.3.3
+# mt_metadata version 0.3.5
  Standard MT metadata
 
 [![PyPi version](https://img.shields.io/pypi/v/mt_metadata.svg)](https://pypi.python.org/pypi/mt-metadata)
@@ -52,7 +52,7 @@ 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**: 0.3.3
+* **Version**: 0.3.5
 * **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**
@@ -63,7 +63,7 @@ Most people will be using the transfer functions, but a lot of that metadata com
 
 ## From Source
 
-`git clone git://github.com/kujaku11/mt_metadata`
+`git clone https://github.com/kujaku11/mt_metadata.git`
 
 `python setup.py install`
 

{mt_metadata-0.3.3 → mt_metadata-0.3.5}/README.md

@@ -1,4 +1,4 @@
-# mt_metadata version 0.3.3
+# mt_metadata version 0.3.5
  Standard MT metadata
 
 [![PyPi version](https://img.shields.io/pypi/v/mt_metadata.svg)](https://pypi.python.org/pypi/mt-metadata)
@@ -28,7 +28,7 @@ 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**: 0.3.3
+* **Version**: 0.3.5
 * **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**
@@ -39,7 +39,7 @@ Most people will be using the transfer functions, but a lot of that metadata com
 
 ## From Source
 
-`git clone git://github.com/kujaku11/mt_metadata`
+`git clone https://github.com/kujaku11/mt_metadata.git`
 
 `python setup.py install`
 

{mt_metadata-0.3.3 → mt_metadata-0.3.5}/mt_metadata/__init__.py

@@ -39,7 +39,7 @@ you should only have to changes these dictionaries.
 
 __author__ = """Jared Peacock"""
 __email__ = "jpeacock@usgs.gov"
-__version__ = "0.3.3"
+__version__ = "0.3.5"
 
 # =============================================================================
 # Imports
@@ -82,6 +82,14 @@ REQUIRED_KEYS = [
     "default",
 ]
 
+DEFAULT_CHANNEL_NOMENCLATURE = {
+    "hx": "hx",
+    "hy": "hy",
+    "hz": "hz",
+    "ex": "ex",
+    "ey": "ey",
+}
+
 # =============================================================================
 # Initiate loggers
 # =============================================================================
@@ -152,19 +160,13 @@ TF_POOR_XML = DATA_DIR.joinpath("data/transfer_functions/tf_poor_xml.xml")
 TF_XML_MULTIPLE_ATTACHMENTS = DATA_DIR.joinpath(
     "data/transfer_functions/tf_xml_multiple_attachments.xml"
 )
-TF_EDI_PHOENIX = DATA_DIR.joinpath(
-    "data/transfer_functions/tf_edi_phoenix.edi"
-)
-TF_EDI_EMPOWER = DATA_DIR.joinpath(
-    "data/transfer_functions/tf_edi_empower.edi"
-)
+TF_EDI_PHOENIX = DATA_DIR.joinpath("data/transfer_functions/tf_edi_phoenix.edi")
+TF_EDI_EMPOWER = DATA_DIR.joinpath("data/transfer_functions/tf_edi_empower.edi")
 TF_EDI_METRONIX = DATA_DIR.joinpath(
     "data/transfer_functions/tf_edi_metronix.edi"
 )
 TF_EDI_CGG = DATA_DIR.joinpath("data/transfer_functions/tf_edi_cgg.edi")
-TF_EDI_QUANTEC = DATA_DIR.joinpath(
-    "data/transfer_functions/tf_edi_quantec.edi"
-)
+TF_EDI_QUANTEC = DATA_DIR.joinpath("data/transfer_functions/tf_edi_quantec.edi")
 TF_EDI_RHO_ONLY = DATA_DIR.joinpath(
     "data/transfer_functions/tf_edi_rho_only.edi"
 )

{mt_metadata-0.3.3 → mt_metadata-0.3.5}/mt_metadata/base/metadata.py

@@ -2,7 +2,7 @@
 """
 Created on Wed Dec 23 20:41:16 2020
 
-:copyright: 
+:copyright:
     Jared Peacock (jpeacock@usgs.gov)
 
 :license: MIT
@@ -113,14 +113,25 @@ class Base:
                 try:
                     other_value = other_dict[key]
                     if isinstance(value, np.ndarray):
+                        if value.size != other_value.size:
+                            msg = f"Array sizes for {key} differ: {value.size} != {other_value.size}"
+                            self.logger.info(msg)
+                            fail=True
+                            continue
                         if not (value == other_value).all():
                             msg = f"{key}: {value} != {other_value}"
                             self.logger.info(msg)
                             fail = True
-                    elif value != other_value:
-                        msg = f"{key}: {value} != {other_value}"
-                        self.logger.info(msg)
-                        fail = True
+                    elif isinstance(value, (float, int, complex)):
+                        if not np.isclose(value, other_value):
+                            msg = f"{key}: {value} != {other_value}"
+                            self.logger.info(msg)
+                            fail = True
+                    else:
+                        if value != other_value:
+                            msg = f"{key}: {value} != {other_value}"
+                            self.logger.info(msg)
+                            fail = True
                 except KeyError:
                     msg = "Cannot find {0} in other".format(key)
                     self.logger.info(msg)
@@ -289,7 +300,7 @@ class Base:
             self.logger.exception(error)
             raise MTSchemaError(error)
 
-    def _validate_option(self, name, option_list):
+    def _validate_option(self, name, value, option_list):
         """
         validate the given attribute name agains possible options and check
         for aliases
@@ -304,21 +315,21 @@ class Base:
         :rtype: TYPE
 
         """
-        if name is None:
+        if value is None:
             return True, False, None
         options = [ss.lower() for ss in option_list]
         other_possible = False
         if "other" in options:
             other_possible = True
-        if name.lower() in options:
+        if value.lower() in options:
             return True, other_possible, None
-        elif name.lower() not in options and other_possible:
+        elif value.lower() not in options and other_possible:
             msg = (
-                "{0} not found in options list {1}, but other options"
-                + " are allowed.  Allowing {2} to be set to {0}."
+                f"Value '{value}' not found for metadata field '{name}' in options list {option_list}, but other options"
+                + f" are allowed.  Allowing {option_list} to be set to {value}."
             )
             return True, other_possible, msg
-        return False, other_possible, "{0} not found in options list {1}"
+        return False, other_possible, f"Value '{value}' for metadata field '{name}' not found in options list {option_list}"
 
     def __setattr__(self, name, value):
         """
@@ -388,7 +399,7 @@ class Base:
                 # check options
                 if v_dict["style"] == "controlled vocabulary":
                     options = v_dict["options"]
-                    accept, other, msg = self._validate_option(value, options)
+                    accept, other, msg = self._validate_option(name, value, options)
                     if not accept:
                         self.logger.error(msg.format(value, options))
                         raise MTSchemaError(msg.format(value, options))

{mt_metadata-0.3.3 → mt_metadata-0.3.5}/mt_metadata/data/transfer_functions/tf_zmm.zmm

@@ -1,5 +1,5 @@
  TRANSFER FUNCTIONS IN MEASUREMENT COORDINATES
- ********** WITH FULL ERROR COVARINCE*********
+ ********** WITH FULL ERROR COVARIANCE*********
                                                                                 
 300                 
 coordinate    34.727  -115.735 declination    13.10

{mt_metadata-0.3.3 → mt_metadata-0.3.5}/mt_metadata/timeseries/channel.py

@@ -2,7 +2,7 @@
 """
 Created on Wed Dec 23 21:30:36 2020
 
-:copyright: 
+:copyright:
     Jared Peacock (jpeacock@usgs.gov)
 
 :license: MIT
@@ -16,7 +16,7 @@ from mt_metadata.base.helpers import write_lines
 from mt_metadata.base import get_schema, Base
 from .standards import SCHEMA_FN_PATHS
 from . import DataQuality, Filtered, Location, TimePeriod, Instrument, Fdsn
-from mt_metadata.timeseries.filters import ChannelResponseFilter
+from mt_metadata.timeseries.filters import ChannelResponse
 
 # =============================================================================
 attr_dict = get_schema("channel", SCHEMA_FN_PATHS)
@@ -79,4 +79,9 @@ class Channel(Base):
                 self.logger.error(msg)
                 continue
         # compute instrument sensitivity and units in/out
-        return ChannelResponseFilter(filters_list=mt_filter_list)
+        return ChannelResponse(filters_list=mt_filter_list)
+
+    @property
+    def unit_object(self):
+        from mt_metadata.utils.units import get_unit_object
+        return get_unit_object(self.units)

{mt_metadata-0.3.3 → mt_metadata-0.3.5}/mt_metadata/timeseries/filters/__init__.py

@@ -3,7 +3,7 @@ from .fir_filter import FIRFilter
 from .pole_zero_filter import PoleZeroFilter
 from .time_delay_filter import TimeDelayFilter
 from .frequency_response_table_filter import FrequencyResponseTableFilter
-from .channel_response_filter import ChannelResponseFilter
+from .channel_response import ChannelResponse
 
 
 __all__ = [
@@ -12,5 +12,5 @@ __all__ = [
     "PoleZeroFilter",
     "TimeDelayFilter",
     "FrequencyResponseTableFilter",
-    "ChannelResponseFilter",
+    "ChannelResponse",
 ]

mt_metadata-0.3.3/mt_metadata/timeseries/filters/channel_response_filter.py → mt_metadata-0.3.5/mt_metadata/timeseries/filters/channel_response.py

@@ -3,11 +3,11 @@
 Channel Response Filter
 ==========================
 
-Combines all filters for a given channel into a total response that can be used in 
+Combines all filters for a given channel into a total response that can be used in
 the frequency domain.
 
-.. note:: Time Delay filters should be applied in the time domain 
-    otherwise bad things can happen.   
+.. note:: Time Delay filters should be applied in the time domain
+    otherwise bad things can happen.
 """
 # =============================================================================
 # Imports
@@ -24,6 +24,7 @@ from mt_metadata.timeseries.filters import (
     FrequencyResponseTableFilter,
     FIRFilter,
 )
+from mt_metadata.timeseries.filters.filter_base import FilterBase
 from mt_metadata.utils.units import get_unit_object
 from mt_metadata.timeseries.filters.plotting_helpers import plot_response
 from obspy.core import inventory
@@ -33,9 +34,11 @@ attr_dict = get_schema("channel_response", SCHEMA_FN_PATHS)
 # =============================================================================
 
 
-class ChannelResponseFilter(Base):
+class ChannelResponse(Base):
     """
     This class holds a list of all the filters associated with a channel.
+    The list should be ordered to match the order in which the filters are applied to the signal.
+
     It has methods for combining the responses of all the filters into a total
     response that we will apply to a data segment.
     """
@@ -60,6 +63,7 @@ class ChannelResponseFilter(Base):
     def __repr__(self):
         return self.__str__()
 
+
     @property
     def filters_list(self):
         """filters list"""
@@ -106,7 +110,7 @@ class ChannelResponseFilter(Base):
 
     def _validate_filters_list(self, filters_list):
         """
-        make sure the filters list is valid
+        make sure the filters list is valid.
 
         :param filters_list: DESCRIPTION
         :type filters_list: TYPE
@@ -114,7 +118,7 @@ class ChannelResponseFilter(Base):
         :rtype: TYPE
 
         """
-        ACCEPTABLE_FILTERS = [
+        supported_filters = [
             PoleZeroFilter,
             CoefficientFilter,
             TimeDelayFilter,
@@ -122,8 +126,8 @@ class ChannelResponseFilter(Base):
             FIRFilter,
         ]
 
-        def is_acceptable_filter(item):
-            if isinstance(item, tuple(ACCEPTABLE_FILTERS)):
+        def is_supported_filter(item):
+            if isinstance(item, tuple(supported_filters)):
                 return True
             else:
                 return False
@@ -139,11 +143,11 @@ class ChannelResponseFilter(Base):
         fails = []
         return_list = []
         for item in filters_list:
-            if is_acceptable_filter(item):
+            if is_supported_filter(item):
                 return_list.append(item)
             else:
                 fails.append(
-                    f"Item is not an acceptable filter type, {type(item)}"
+                    f"Item is not a supported filter type, {type(item)}"
                 )
 
         if fails:
@@ -222,15 +226,46 @@ class ChannelResponseFilter(Base):
             total_delay += delay_filter.delay
         return total_delay
 
+    def get_indices_of_filters_to_remove(self, include_decimation=False, include_delay=False):
+        indices = list(np.arange(len(self.filters_list)))
+
+        if not include_delay:
+            indices = [i for i in indices if self.filters_list[i].type != "time delay"]
+
+        if not include_decimation:
+            indices = [i for i in indices if not self.filters_list[i].decimation_active]
+
+        return indices
+
+    def get_list_of_filters_to_remove(self, include_decimation=False, include_delay=False):
+        """
+
+        :param include_decimation: bool
+        :param include_delay: bool
+        :return:
+
+        # Experimental snippet if we want to allow filters with the opposite convention
+        # into channel response -- I don't think we do.
+        # if self.correction_operation == "multiply":
+        #     inverse_filters = [x.inverse() for x in self.filters_list]
+        #     self.filters_list = inverse_filters
+        """
+        indices = self.get_indices_of_filters_to_remove(include_decimation=include_decimation,
+                                                        include_delay=include_delay)
+        return [self.filters_list[i] for i in indices]
+
     def complex_response(
         self,
         frequencies=None,
+        filters_list=None,
+        include_decimation=False,
         include_delay=False,
         normalize=False,
-        include_decimation=True,
         **kwargs,
     ):
         """
+        Computes the complex response of self.
+        Allows the user to optionally supply a subset of filters
 
         :param frequencies: frequencies to compute complex response,
          defaults to None
@@ -238,35 +273,31 @@ class ChannelResponseFilter(Base):
         :param include_delay: include delay in complex response,
          defaults to False
         :type include_delay: bool, optional
-        :param normalize: normalize the response to 1, defaults to False
-        :type normalize: bool, optional
         :param include_decimation: Include decimation in response,
          defaults to True
         :type include_decimation: bool, optional
+        :param normalize: normalize the response to 1, defaults to False
+        :type normalize: bool, optional
         :return: complex response along give frequency array
         :rtype: np.ndarray
 
         """
-
         if frequencies is not None:
             self.frequencies = frequencies
 
-        if include_delay:
-            filters_list = deepcopy(self.filters_list)
-        else:
-            filters_list = deepcopy(self.non_delay_filters)
-
-        if not include_decimation:
-            filters_list = deepcopy(
-                [x for x in filters_list if not x.decimation_active]
-            )
+        # make filters list if not supplied
+        if filters_list is None:
+            self.logger.warning("Filters list not provided, building list assuming all are applied")
+            filters_list = self.get_list_of_filters_to_remove(
+                include_decimation=include_decimation,
+            include_delay=include_delay)
 
         if len(filters_list) == 0:
-            # warn that there are no filters associated with channel?
+            self.logger.warning(f"No filters associated with {self.__class__}, returning 1")
             return np.ones(len(self.frequencies), dtype=complex)
 
+        # define the product of all filters as the total response function
         result = filters_list[0].complex_response(self.frequencies)
-
         for ff in filters_list[1:]:
             result *= ff.complex_response(self.frequencies)
 
@@ -274,6 +305,7 @@ class ChannelResponseFilter(Base):
             result /= np.max(np.abs(result))
         return result
 
+
     def compute_instrument_sensitivity(
         self, normalization_frequency=None, sig_figs=6
     ):
@@ -310,8 +342,8 @@ class ChannelResponseFilter(Base):
         """
         if self.filters_list is [] or len(self.filters_list) == 0:
             return None
-
-        return self.filters_list[0].units_in
+        else:
+            return self.filters_list[0].units_in
 
     @property
     def units_out(self):
@@ -320,8 +352,9 @@ class ChannelResponseFilter(Base):
         """
         if self.filters_list is [] or len(self.filters_list) == 0:
             return None
+        else:
+            return self.filters_list[-1].units_out
 
-        return self.filters_list[-1].units_out
 
     def _check_consistency_of_units(self):
         """
@@ -409,7 +442,7 @@ class ChannelResponseFilter(Base):
         pb_tol=1e-1,
         interpolation_method="slinear",
         include_delay=False,
-        include_decimation=True,
+        include_decimation=False,
     ):
         """
         Plot the response

{mt_metadata-0.3.3 → mt_metadata-0.3.5}/mt_metadata/timeseries/filters/coefficient_filter.py

@@ -4,11 +4,10 @@ from obspy.core import inventory
 
 from mt_metadata.base import get_schema
 from mt_metadata.timeseries.filters.filter_base import FilterBase
-from mt_metadata.timeseries.filters.filter_base import OBSPY_MAPPING
+from mt_metadata.timeseries.filters.filter_base import get_base_obspy_mapping
 from mt_metadata.timeseries.filters.standards import SCHEMA_FN_PATHS
 from mt_metadata.base.helpers import write_lines
 
-obspy_mapping = copy.deepcopy(OBSPY_MAPPING)
 
 # =============================================================================
 attr_dict = get_schema("filter_base", SCHEMA_FN_PATHS)
@@ -24,7 +23,6 @@ class CoefficientFilter(FilterBase):
 
         super(FilterBase, self).__init__(attr_dict=attr_dict, **kwargs)
         self.type = "coefficient"
-        self.obspy_mapping = obspy_mapping
 
         if self.gain == 0.0:
             self.gain = 1.0