Merge pull request #154 from aidh-ms/issue/fix-warnings

Fix warnings
aidh-ms · Feb 3, 2025 · 86f68ac · 86f68ac
2 parents 9c57d68 + aa26b59
commit 86f68ac
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Showing 2 changed files with 15 additions and 3 deletions.
diff --git a/pyaki/preprocessors.py b/pyaki/preprocessors.py
@@ -134,7 +134,7 @@ def process(self, df: pd.DataFrame) -> pd.DataFrame:
             The processed urine output dataset as a pandas DataFrame.
         """
 
-        df = df.groupby(self._stay_identifier).resample("1H").sum()  # type: ignore
+        df = df.groupby(self._stay_identifier).resample("1h").sum()  # type: ignore
         df[df["urineoutput"] == 0] = None
 
         if not self._interpolate:
@@ -195,7 +195,7 @@ def process(self, df: pd.DataFrame) -> pd.DataFrame:
         pd.DataFrame
             The processed creatinine dataset as a pandas DataFrame.
         """
-        df = df.groupby(self._stay_identifier).resample("1H").mean()  # type: ignore
+        df = df.groupby(self._stay_identifier).resample("1h").mean()  # type: ignore
         if not self._ffill:
             return df
 
@@ -244,5 +244,5 @@ def process(self, df: pd.DataFrame) -> pd.DataFrame:
         pd.DataFrame
             The processed RRT dataset as a pandas DataFrame.
         """
-        df = df.groupby(self._stay_identifier).resample("1H").last()  # type: ignore
+        df = df.groupby(self._stay_identifier).resample("1h").last()  # type: ignore
         return df.ffill()
diff --git a/pyaki/probes.py b/pyaki/probes.py
@@ -9,6 +9,7 @@
 
 import numpy as np
 import pandas as pd
+from pandas import PeriodIndex
 
 from pyaki.utils import Dataset, DatasetType, approx_gte, dataset_as_df, df_to_dataset
 
@@ -164,6 +165,8 @@ def probe(
         if self._patient_weight_column not in patient:
             raise ValueError("Missing weight for stay")
 
+        df = df.copy()
+
         weight: pd.Series = patient[self._patient_weight_column]
         # fmt: off
         df.loc[:, self.RESNAME] = np.nan  # set all urineoutput_stage values to NaN
@@ -316,6 +319,9 @@ def creatinine_baseline(self, df: pd.DataFrame, patient: pd.DataFrame) -> pd.Ser
         pd.Series
             The calculated creatinine baseline values.
         """
+        if isinstance(df.index, PeriodIndex):
+            df.index = df.index.to_timestamp()
+
         if self._method == CreatinineBaselineMethod.ROLLING_FIRST:
             return (
                 df[df[self._column] > 0]
@@ -547,6 +553,8 @@ def probe(
         pd.DataFrame
             The modified DataFrame with the absolute creatinine stage column added.
         """
+        df = df.copy()
+
         baseline_values: pd.Series = self.creatinine_baseline(df, patient)
 
         df.loc[:, self.RESNAME] = 0
@@ -623,6 +631,8 @@ def probe(self, df: pd.DataFrame, patient: pd.DataFrame, **kwargs: Any) -> pd.Da
         pd.DataFrame
             The modified DataFrame with the relative creatinine stage column added.
         """
+        df = df.copy()
+
         baseline_values: pd.Series = self.creatinine_baseline(df, patient)
 
         df.loc[:, self.RESNAME] = 0
@@ -676,6 +686,8 @@ def probe(self, df: pd.DataFrame) -> pd.DataFrame:
         pd.DataFrame
             The modified DataFrame with the RRT stage column added.
         """
+        df = df.copy()
+
         df.loc[:, self.RESNAME] = 0
         df.loc[df[self._column] == 1, self.RESNAME] = 3