Merge pull request #236 from kujaku11/fix_issue_235

Fix issue 235, and other PR's above.

MANIFEST.in

@@ -18,6 +18,7 @@ recursive-include mt_metadata/transfer_functions/io/edi/metadata/standards *.jso
 recursive-include mt_metadata/transfer_functions/io/zfiles/metadata/standards *.json
 recursive-include mt_metadata/transfer_functions/io/jfiles/metadata/standards *.json
 recursive-include mt_metadata/transfer_functions/io/zonge/metadata/standards *.json
+recursive-include mt_metadata/transfer_functions/processing/standards *.json
 recursive-include mt_metadata/transfer_functions/processing/aurora/standards *.json
 recursive-include mt_metadata/transfer_functions/processing/fourier_coefficients/standards *.json
 recursive-include mt_metadata/data/mt_xml *.xml

mt_metadata/transfer_functions/processing/__init__.py

@@ -1 +1 @@
-
+from .time_series_decimation import TimeSeriesDecimation

mt_metadata/transfer_functions/processing/aurora/__init__.py

@@ -1,16 +1,15 @@
 from .band import Band
 from .channel import Channel
 from .channel_nomenclature import ChannelNomenclature
-from .window import Window
-from .decimation import Decimation
 from .decimation_level import DecimationLevel
 from .estimator import Estimator
+from .frequency_bands import FrequencyBands
 from .processing import Processing
 from .regression import Regression
 from .run import Run
 from .station import Station
 from .stations import Stations
-
+from .window import Window
 
 __all__ = [
     "Band",

mt_metadata/transfer_functions/processing/aurora/band.py

@@ -12,6 +12,7 @@
 from mt_metadata.base.helpers import write_lines
 from mt_metadata.base import get_schema, Base
 from .standards import SCHEMA_FN_PATHS
+from typing import Optional
 
 # =============================================================================
 attr_dict = get_schema("band", SCHEMA_FN_PATHS)
@@ -22,28 +23,33 @@ class Band(Base):
     __doc__ = write_lines(attr_dict)
 
     def __init__(self, **kwargs):
+        """
+            Constructor.
+
+            :param kwargs: TODO description here
+        """
 
         super().__init__(attr_dict=attr_dict, **kwargs)
         self._name = None
 
     @property
-    def lower_bound(self):
+    def lower_bound(self) -> float:
         return self.frequency_min
 
     @property
-    def upper_bound(self):
+    def upper_bound(self) -> float:
         return self.frequency_max
 
     @property
-    def lower_closed(self):
+    def lower_closed(self) -> bool:
         return self.to_interval().closed_left
 
     @property
-    def upper_closed(self):
+    def upper_closed(self) -> bool:
         return self.to_interval().closed_right
 
     @property
-    def name(self):
+    def name(self) -> str:
         """
         :return: The name of the frequency band (currently defaults to fstring with 6 decimal places.
         :rtype: str
@@ -57,7 +63,7 @@ def name(self):
     def name(self, value):
         self._name = value
 
-    def _indices_from_frequencies(self, frequencies):
+    def _indices_from_frequencies(self, frequencies: np.ndarray) -> np.ndarray:
         """
 
         Parameters
@@ -84,7 +90,7 @@ def _indices_from_frequencies(self, frequencies):
         indices = np.where(cond1 & cond2)[0]
         return indices
 
-    def set_indices_from_frequencies(self, frequencies):
+    def set_indices_from_frequencies(self, frequencies: np.ndarray) -> None:
         """assumes min/max freqs are defined"""
         indices = self._indices_from_frequencies(frequencies)
         self.index_min = indices[0]
@@ -98,15 +104,15 @@ def to_interval(self):
     @property
     def harmonic_indices(self):
         """
-        Assumes all harmincs between min and max are present in the band
+        Assumes all harmoincs between min and max are present in the band
 
         Returns
         -------
         numpy array of integers corresponding to harminic indices
         """
         return np.arange(self.index_min, self.index_max + 1)
 
-    def in_band_harmonics(self, frequencies):
+    def in_band_harmonics(self, frequencies: np.ndarray):
         """
         Parameters
         ----------
@@ -122,7 +128,7 @@ def in_band_harmonics(self, frequencies):
         return harmonics
 
     @property
-    def center_frequency(self):
+    def center_frequency(self) -> float:
         """
         Returns
         -------
@@ -135,131 +141,6 @@ def center_frequency(self):
             return (self.lower_bound + self.upper_bound) / 2
 
     @property
-    def center_period(self):
+    def center_period(self) -> float:
+        """ Returns the inverse of center frequency."""
         return 1.0 / self.center_frequency
-
-
-class FrequencyBands(object):
-    """
-    This is just collection of objects of class Band.
-    It is intended to be used at a single decimation level
-
-    The core underlying variable is "band_edges", a 2D array, with one row per
-    frequency band and two columns, one for the left-hand (lower bound) of the
-    frequency band and one for the right-hand (upper bound).
-
-    Note there are some "clever" ways to define the bands using a 1-D array but this
-    assumes the bands to be adjacent, and there is no good reason to bake this
-    constriant in -- band edges is thus 2-D.
-    """
-
-    def __init__(self, **kwargs):
-        """
-
-        Parameters
-        ----------
-        kwargs
-        band_edges: 2d numpy array
-        """
-        self.band_edges = kwargs.get("band_edges", None)
-
-    @property
-    def number_of_bands(self):
-        return self.band_edges.shape[0]
-
-    def validate(self):
-        """
-        Placeholder for sanity checks.
-        Main reason for this is in anticipation of an append() method that accepts Band objects.
-        In that case we may wish to re-order the band edges.
-
-        """
-        band_centers = self.band_centers()
-
-        # check band centers are monotonically increasing
-        monotone_condition = np.all(band_centers[1:] > band_centers[:-1])
-        if monotone_condition:
-            pass
-        else:
-            print(
-                "WARNING Band Centers are Not Monotonic.  This probably means that "
-                "the bands are being defined in an adhoc way"
-            )
-            print("This condition untested 20210720")
-            print("Attempting to reorganize bands")
-            # use np.argsort to rorganize the bands
-            self.band_edges = self.band_edges[np.argsort(band_centers), :]
-
-        return
-
-    def bands(self, direction="increasing_frequency"):
-        """
-        make this a generator for iteration over bands
-        Returns
-        -------
-
-        """
-        band_indices = range(self.number_of_bands)
-        if direction == "increasing_period":
-            band_indices = np.flip(band_indices)
-        return (self.band(i_band) for i_band in band_indices)
-
-    def band(self, i_band):
-        """
-        Parameters
-        ----------
-        i_band: integer (zero-indexed)
-            Specifies the band to return
-
-        Returns
-        -------
-        frequency_band: Band()
-            Class that represents a frequency band
-        """
-
-        frequency_band = Band(
-            frequency_min=self.band_edges[i_band, 0],
-            frequency_max=self.band_edges[i_band, 1],
-        )
-        return frequency_band
-
-    def band_centers(self, frequency_or_period="frequency"):
-        """
-        Parameters
-        ----------
-        frequency_or_period : str
-            One of ["frequency" , "period"].  Determines if the vector of band
-            centers is returned in "Hz" or "s"
-
-        Returns
-        -------
-        band_centers : numpy array
-            center frequencies of the bands in Hz or in s
-        """
-        band_centers = np.full(self.number_of_bands, np.nan)
-        for i_band in range(self.number_of_bands):
-            frequency_band = self.band(i_band)
-            band_centers[i_band] = frequency_band.center_frequency
-        if frequency_or_period == "period":
-            band_centers = 1.0 / band_centers
-        return band_centers
-
-    def from_decimation_object(self, decimation_object):
-        """
-        Define band_edges array from config object,
-
-        Parameters
-        ----------
-        decimation_object: mt_metadata.transfer_functions.processing.aurora.Decimation
-        """
-        # replace below with decimation_object.delta_frequency ?
-        df = (
-            decimation_object.decimation.sample_rate
-            / decimation_object.window.num_samples
-        )
-        half_df = df / 2.0
-        # half_df /=100
-        lower_edges = (decimation_object.lower_bounds * df) - half_df
-        upper_edges = (decimation_object.upper_bounds * df) + half_df
-        band_edges = np.vstack((lower_edges, upper_edges)).T
-        self.band_edges = band_edges