Merge pull request #247 from kujaku11/fix_issue_238_housekeeping

remove anti_alias_filter accessors from FCDecimation and AuroraDecima…

mt_metadata/transfer_functions/processing/aurora/decimation_level.py

@@ -96,29 +96,6 @@ def __init__(self, **kwargs):
 
         super().__init__(attr_dict=attr_dict, **kwargs)
 
-        # if self.decimation.level == 0:
-        #     self.anti_alias_filter = None
-
-    @property
-    def window(self) -> Window:
-        """
-            Convenience access to STFT window metadata.
-
-            This was placed here to allow access to legacy Decimation's window attribute.
-
-            Note: This maybe deprecated in future to use only direct access via self.stft.window.
-
-        """
-        return self.stft.window
-
-    @property
-    def anti_alias_filter(self) -> str:
-        """
-        get anti_alais_filter from TimeSeriesDecimation.
-
-        """
-        return self.decimation.anti_alias_filter
-
     @property
     def bands(self) -> list:
         """
@@ -224,7 +201,7 @@ def frequency_sample_interval(self) -> float:
             Returns the delta_f in frequency domain df = 1 / (N * dt)
             Here dt is the sample interval after decimation
         """
-        return self.sample_rate_decimation / self.window.num_samples
+        return self.decimation.sample_rate / self.stft.window.num_samples
 
     @property
     def band_edges(self) -> np.ndarray:
@@ -239,7 +216,7 @@ def band_edges(self) -> np.ndarray:
         ).T
         return band_edges
 
-    def frequency_bands_obj(self) -> FrequencyBands:  #  TODO: FIXME circular import when correctly dtyped -> FrequencyBands:
+    def frequency_bands_obj(self) -> FrequencyBands:
         """
         Gets a FrequencyBands object that is used as input to processing.
 
@@ -256,33 +233,6 @@ def frequency_bands_obj(self) -> FrequencyBands:  #  TODO: FIXME circular import
         frequency_bands = FrequencyBands(band_edges=self.band_edges)
         return frequency_bands
 
-    # # TODO: FIXME WIP
-    # def to_frequency_bands_obj(self):
-    #     """
-    #         Define band_edges array from decimation_level object,
-    #
-    #     Development Notes.
-    #       This function was originally in FrequencyBands class, it was called:
-    #        from_decimation_object.  Circular imports were encountered when it was correctly dtyped.
-    #        There is no reason to have FrequencyBands.from_decimation_object(decimation_level)
-    #        _and_ decimation_level.to_frequency_bands_obj()
-    #        The function above already does the task of generating a frequency bands.
-    #        Keeping this commented until documentation improves.
-    #        Below looks like an alternative, and more readable way to get band_edges,
-    #        without passing through the dataframe.  At a minimum a test should be created
-    #        that makes band edges both ways and asserts equal.
-    #        (a few command line tests showed that they are, Dec 2024).
-    #
-    #     """
-    #     df = self.frequency_sample_interval
-    #     half_df = df / 2.0
-    #
-    #     lower_edges = (self.lower_bounds * df) - half_df
-    #     upper_edges = (self.upper_bounds * df) + half_df
-    #     band_edges = np.vstack((lower_edges, upper_edges)).T
-    #     return FrequencyBands(band_edges=band_edges)
-
-
     @property
     def fft_frequencies(self) -> np.ndarray:
         """
@@ -291,18 +241,9 @@ def fft_frequencies(self) -> np.ndarray:
             :return freqs: The frequencies at which the stft will be available.
             :rtype freqs: np.ndarray
         """
-        freqs = self.window.fft_harmonics(self.decimation.sample_rate)
+        freqs = self.stft.window.fft_harmonics(self.decimation.sample_rate)
         return freqs
 
-    @property
-    def sample_rate_decimation(self) -> float:
-        """
-            Returns the sample rate of the data after decimation.
-            TODO: Delete this method and replace calls to self.sample_rate_decimation with self.decimation.sample_rate
-
-        """
-        return self.decimation.sample_rate
-
     @property
     def harmonic_indices(self) -> List[int]:
         """
@@ -344,15 +285,15 @@ def is_consistent_with_archived_fc_parameters(
 
             Iterates over FCDecimation attributes:
                 "channels_estimated": to ensure all expected channels are in the group
-                "anti_alias_filter": check that the expected AAF was applied
-                "sample_rate,
-                "method",
-                "prewhitening_type",
-                "recoloring",
-                "pre_fft_detrend_type",
-                "min_num_stft_windows",
-                "window",
-                "harmonic_indices",
+                "decimation.anti_alias_filter": check that the expected AAF was applied
+                "decimation.sample_rate,
+                "decimation.method",
+                "stft.prewhitening_type",
+                "stft.recoloring",
+                "stft.pre_fft_detrend_type",
+                "stft.min_num_stft_windows",
+                "stft.window",
+                "stft.harmonic_indices",
         Returns
         -------
 
@@ -373,18 +314,18 @@ def is_consistent_with_archived_fc_parameters(
             self.logger.info(msg)
             return False
 
-        # anti_alias_filter: Check that the data were
+        # anti_alias_filter: Check that the data were filtered the same way
         try:
-            assert fc_decimation.decimation_anti_alias_filter == self.decimation.anti_alias_filter
+            assert fc_decimation.time_series_decimation.anti_alias_filter == self.decimation.anti_alias_filter
         except AssertionError:
-            cond1 = self.anti_alias_filter == "default"
-            cond2 = fc_decimation.decimation_anti_alias_filter is None
+            cond1 = self.time_series_decimation.anti_alias_filter == "default"
+            cond2 = fc_decimation.time_series_decimation.anti_alias_filter is None
             if cond1 & cond2:
                 pass
             else:
                 msg = (
                     "Antialias Filters Not Compatible -- need to add handling for "
-                    f"{msg} FCdec {fc_decimation.decimation_anti_alias_filter} and "
+                    f"{msg} FCdec {fc_decimation.time_series_decimation.anti_alias_filter} and "
                     f"{msg} processing config:{self.decimation.anti_alias_filter}"
                 )
                 raise NotImplementedError(msg)
@@ -478,6 +419,8 @@ def is_consistent_with_archived_fc_parameters(
             # if harmonic_indices is -1, it means the archive kept all so we can skip this check.
             pass
         else:
+            msg = "WIP: harmonic indices in AuroraDecimationlevel are derived from processing bands -- Not robustly tested to compare with FCDecimation"
+            self.logger.debug(msg)
             harmonic_indices_requested = self.harmonic_indices
             fcdec_group_set = set(fc_decimation.harmonic_indices)
             processing_set = set(harmonic_indices_requested)
@@ -542,7 +485,7 @@ def to_fc_decimation(
         fc_dec_obj.stft.pre_fft_detrend_type = self.stft.pre_fft_detrend_type
         fc_dec_obj.stft.prewhitening_type = self.stft.prewhitening_type
         fc_dec_obj.stft.recoloring = self.stft.recoloring
-        fc_dec_obj.time_series_decimation.sample_rate = self.sample_rate_decimation
+        fc_dec_obj.time_series_decimation.sample_rate = self.decimation.sample_rate
         fc_dec_obj.stft.window = self.stft.window
 
         return fc_dec_obj

mt_metadata/transfer_functions/processing/aurora/processing.py

@@ -216,7 +216,7 @@ def assign_bands(
             )  # self.decimations_dict[key]
             decimation_obj.decimation.factor = d
             decimation_obj.decimation.sample_rate = sr
-            decimation_obj.window.num_samples = num_samples_window[i_level]
+            decimation_obj.stft.window.num_samples = num_samples_window[i_level]
             frequencies = decimation_obj.fft_frequencies
 
             for low, high in band_edges:

mt_metadata/transfer_functions/processing/fourier_coefficients/decimation.py

@@ -70,13 +70,6 @@ def __init__(self, **kwargs):
             logger.debug(msg)
             self.short_time_fourier_transform.per_window_detrend_type = ""
 
-        # if self.time_series_decimation.level == 0:
-        #     self.time_series_decimation.anti_alias_filter = None
-
-    @property
-    def window(self):
-        return self.stft.window
-
     def __len__(self) -> int:
         return len(self.channels)
 
@@ -96,6 +89,14 @@ def __add__(self, other):
             raise TypeError(msg)
 
     #----- Begin (Possibly Temporary) methods for integrating TimeSeriesDecimation Class -----#
+
+    @property
+    def decimation(self) -> TimeSeriesDecimation:
+        """
+            Passthrough method to access self.time_series_decimation
+        """
+        return self.time_series_decimation
+
     @property
     def factor(self):
         """
@@ -158,22 +159,6 @@ def decimation_method(self, value: str) -> None:
         """
         self.time_series_decimation.method = value
 
-    @property
-    def decimation_anti_alias_filter(self) -> str:
-        """
-            Access the decimation anti_alias_filter description from the TSDecimation
-            :return: Description of how anti_alias_filtering is performed
-            :rtype: str
-        """
-        return self.time_series_decimation.anti_alias_filter
-
-    @decimation_method.setter
-    def decimation_anti_alias_filter(self, value: str) -> None:
-        """
-            Set the decimation_anti_alias_filter in the TSDecimation
-        """
-        self.time_series_decimation.anti_alias_filter = value
-
     @property
     def decimation_sample_rate(self) -> float:
         """
@@ -183,29 +168,6 @@ def decimation_sample_rate(self) -> float:
         """
         return self.time_series_decimation.sample_rate
 
-    @property
-    def sample_rate_decimation(self) -> float:
-        """
-            TODO: Delete this function in 2025.
-
-            Access the decimation sample rate from the TSDecimation
-            :return:Time series sample rate after decimation (from the TSDecimation)
-            :rtype: str
-        """
-        msg = "sample_rate_decimation is deprecated -- use self.time_series_decimation.sample_rate"
-        logger.warning(msg)
-        return self.time_series_decimation.sample_rate
-
-    @sample_rate_decimation.setter
-    def sample_rate_decimation(self, value: float) -> None:
-        """
-            TODO: Delete this function in 2025.
-
-            Set the decimation sample_rate_decimation in the TSDecimation
-        """
-        msg = "sample_rate_decimation is deprecated -- use self.time_series_decimation.sample_rate"
-        logger.warning(msg)
-        self.time_series_decimation.sample_rate = value
 
     #----- End (Possibly Temporary) methods for integrating TimeSeriesDecimation Class -----#
 
@@ -446,14 +408,14 @@ def is_valid_for_time_series_length(self, n_samples_ts: int) -> bool:
 
         """
         required_num_samples = (
-            self.window.num_samples
-            + (self.stft.min_num_stft_windows - 1) * self.window.num_samples_advance
+            self.stft.window.num_samples
+            + (self.stft.min_num_stft_windows - 1) * self.stft.window.num_samples_advance
         )
         if n_samples_ts < required_num_samples:
             msg = (
                 f"{n_samples_ts} not enough samples for minimum of "
                 f"{self.stft.min_num_stft_windows} stft windows of length "
-                f"{self.window.num_samples} and overlap {self.window.overlap}"
+                f"{self.stft.window.num_samples} and overlap {self.stft.window.overlap}"
             )
             self.logger.warning(msg)
             return False
@@ -463,7 +425,7 @@ def is_valid_for_time_series_length(self, n_samples_ts: int) -> bool:
     @property
     def fft_frequencies(self) -> np.ndarray:
         """ Returns the one-sided fft frequencies (without Nyquist)"""
-        return self.window.fft_harmonics(self.sample_rate)
+        return self.stft.window.fft_harmonics(self.sample_rate)
 
 
 def fc_decimations_creator(

mt_metadata/transfer_functions/processing/time_series_decimation.py

@@ -10,7 +10,7 @@
     ["level", "factor", "method", "sample_rate", "anti_alias_filter"],
 
     TODO: Consider adding a parent_sample_rate attribute to this class
-    
+
 Created on Thu Dec 26 12:00:00 2024
 
 @author: kkappler
@@ -45,28 +45,6 @@ def __init__(self, **kwargs):
 
         super().__init__(attr_dict=attr_dict, **kwargs)
 
-    # Temporary workarounds while replacing legacy Decimation class
-    # @property
-    # def level(self):
-    #     return self.decimation_level
-    #
-    # @property
-    # def factor(self):
-    #     return self.decimation_factor
-    #
-    # @property
-    # def method(self):
-    #     return self.decimation_method
-    #
-    # @property
-    # def sample_rate(self):
-    #     return self.sample_rate_decimation
-
-
-#
-# def main():
-#     pass
-#
-#
-# if __name__ == "__main__":
-#     main()
+    # TODO: add this logic to __init__ and a test
+    # if self.level == 0:
+    #     self.anti_alias_filter = None

tests/tf/processing/fcs/test_decimation.py

@@ -116,7 +116,7 @@ def test_update(self):
     def test_fft_frequencies(self):
         dl1 = self.dl.copy()
         freqs = dl1.fft_frequencies
-        assert (len(freqs) == dl1.window.num_samples/2)
+        assert (len(freqs) == dl1.stft.window.num_samples/2)
 
 
     def test_update_with_match(self):
@@ -203,7 +203,7 @@ def setUp(self):
         self.dl.decimation_factor = 4
         self.dl.decimation_level = 1
         self.dl.id = 1
-        self.dl.sample_rate_decimation = 16
+        self.dl.time_series_decimation.sample_rate = 16
         for ch in ["ex", "ey", "hx", "hy", "hz"]:
             self.dl.add_channel(Channel(component=ch))
 
@@ -253,7 +253,7 @@ def test_pre_fft_detrend_type_false(self):
         )
 
     def test_window_false(self):
-        self.adl.window.type = "dpss"
+        self.adl.stft.window.type = "dpss"
         self.assertEqual(
             False, self.adl.is_consistent_with_archived_fc_parameters(self.dl, None)
         )