new way of smoothing parameter to test

flepimop/gempyor_pkg/src/gempyor/parameters.py

@@ -106,6 +106,10 @@ def __init__(
             else:
                 self.pdata[pn]["stacked_modifier_method"] = "product"
                 logging.debug(f"No 'stacked_modifier_method' for parameter {pn}, assuming multiplicative NPIs")
+
+            if self.pconfig[pn]["rolling_mean_windows"].exists():
+                self.pdata[pn]["rolling_mean_windows"] = self.pconfig[pn]["rolling_mean_windows"].get()
+
             self.stacked_modifier_method[self.pdata[pn]["stacked_modifier_method"]].append(pn.lower())
 
         logging.debug(f"We have {self.npar} parameter: {self.pnames}")
@@ -192,11 +196,14 @@ def parameters_reduce(self, p_draw: ndarray, npi: object) -> ndarray:
         """
         p_reduced = copy.deepcopy(p_draw)
         if npi is not None:
-            for idx, pn in enumerate(self.pnames):
+            for idx, pn in enumerate(self.pnames):  
                 p_reduced[idx] = NPI.reduce_parameter(
                     parameter=p_draw[idx],
                     modification=npi.getReduction(pn.lower()),
                     method=self.pdata[pn]["stacked_modifier_method"],
                 )
+                # apply rolling mean if specified
+                if "rolling_mean_windows" in self.pdata[pn]:
+                    p_reduced[idx] = utils.rolling_mean_pad(data = p_reduced[idx], window=self.pdata[pn]["rolling_mean_windows"])
 
         return p_reduced

flepimop/gempyor_pkg/src/gempyor/seir.py

@@ -7,7 +7,7 @@
 import xarray as xr
 
 from . import NPI, model_info, steps_rk4
-from .utils import Timer, aws_disk_diagnosis, read_df
+from .utils import Timer, print_disk_diagnosis, read_df
 import logging
 
 logger = logging.getLogger(__name__)
@@ -388,7 +388,7 @@ def write_spar_snpi(sim_id, modinf, p_draw, npi):
 
 
 def write_seir(sim_id, modinf, states):
-    # aws_disk_diagnosis()
+    # print_disk_diagnosis()
     out_df = states2Df(modinf, states)
     modinf.write_simID(ftype="seir", sim_id=sim_id, df=out_df)
 

flepimop/gempyor_pkg/src/gempyor/utils.py

@@ -272,7 +272,24 @@ def list_filenames(folder: str = ".", filters: list = []) -> list:
     return fn_list
 
 
-def aws_disk_diagnosis():
+def rolling_mean_pad(data, window):
+  """
+  Calculates rolling mean with centered window and pads the edges.
+
+  Args:
+      data: A NumPy array.
+      window: The window size for the rolling mean.
+
+  Returns:
+      A NumPy array with the padded rolling mean.
+  """
+  padding_size = (window - 1) // 2
+  padded_data = np.pad(data, padding_size, mode='edge')
+  return np.convolve(padded_data, np.ones(window) / window, mode='valid')
+
+
+
+def print_disk_diagnosis():
     import os
     from os import path
     from shutil import disk_usage

flepimop/gempyor_pkg/tests/utils/test_utils.py

@@ -68,8 +68,8 @@ def test_Timer_with_statement_success():
         time.sleep(1)
 
 
-def test_aws_disk_diagnosis_success():
-    utils.aws_disk_diagnosis()
+def test_print_disk_diagnosis_success():
+    utils.print_disk_diagnosis()
 
 
 def test_profile_success():