Merge pull request #431 from cmu-delphi/change-smooth-refactor

Refactor CHC to use smoothing utils

Author: krivard

changehc/delphi_changehc/__init__.py

@@ -12,7 +12,6 @@
 from . import load_data
 from . import run
 from . import sensor
-from . import smooth
 from . import update_sensor
 from . import weekday
 

changehc/delphi_changehc/sensor.py

@@ -12,15 +12,19 @@
 # third party
 import numpy as np
 import pandas as pd
+from delphi_utils import Smoother
 
 # first party
 from .config import Config
-from .smooth import left_gauss_linear
+
 
 
 class CHCSensor:
     """Sensor class to fit a signal using Covid counts from Change HC outpatient data.
     """
+    smoother = Smoother("savgol",
+                        poly_fit_degree=1,
+                        gaussian_bandwidth=Config.SMOOTHER_BANDWIDTH)
 
     @staticmethod
     def gauss_smooth(count,total):
@@ -29,8 +33,8 @@ def gauss_smooth(count,total):
         Args:
             count, total: array
             """
-        count_smooth = left_gauss_linear(count)
-        total_smooth = left_gauss_linear(total)
+        count_smooth = CHCSensor.smoother.smooth(count)
+        total_smooth = CHCSensor.smoother.smooth(total)
         total_clip = np.clip(total_smooth, 0, None)
         count_clip = np.clip(count_smooth, 0, total_clip)
         return count_clip, total_clip

changehc/delphi_changehc/smooth.py

@@ -2,7 +2,7 @@
 import pytest
 
 # third party
-from delphi_utils import read_params
+from delphi_utils import read_params, Smoother
 import numpy as np
 import numpy.random as nr
 import pandas as pd
@@ -20,7 +20,12 @@
 
 class TestLoadData:
     combined_data = load_combined_data(DENOM_FILEPATH, COVID_FILEPATH, DROP_DATE,
-                                            "fips")
+                                       "fips")
+    # change smoother window length for test data
+    CHCSensor.smoother = Smoother("savgol",
+                                  poly_fit_degree=1,
+                                  gaussian_bandwidth=Config.SMOOTHER_BANDWIDTH,
+                                  window_length=20)
 
     def test_backfill(self):
         num0 = np.array([0, 1, 2, 3, 4, 5, 6, 7, 8], dtype=float).reshape(-1, 1)