minor fixes after feedback

aidh-ms · Nov 16, 2023 · 36266be · 36266be
1 parent c2384af
commit 36266be
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Showing 3 changed files with 14 additions and 16 deletions.
diff --git a/pyAKI/probes.py b/pyAKI/probes.py
@@ -146,8 +146,6 @@ def probe(
         # fmt: off
         df.loc[:, self.RESNAME] = np.nan # set all urineoutput_stage values to NaN
         df.loc[df.rolling(6).min()[self._column] >= 0, self.RESNAME] = 0
-        for ix in range(5):
-            df.loc[df.index.values[ix], self.RESNAME] = np.nan if np.isnan(df.rolling(ix + 1).min()[self._column].iloc[ix]) else 0
 
         if self._method == UrineOutputMethod.STRICT:
             df.loc[(df.rolling(6).max()[self._column] / weight) < 0.5, self.RESNAME] = 1

diff --git a/test/data/validation_data.csv b/test/data/validation_data.csv
@@ -1456,11 +1456,11 @@ stay_id,charttime,urineoutput,urineoutput_stage,creat,abs_creatinine_stage,rel_c
 35258379,2153-09-21 10:00:00,250.0,0.0,,,,71.1,0.0,0.0,0.0,
 35258379,2153-09-21 11:00:00,120.0,0.0,,,,71.1,0.0,0.0,0.0,
 35258379,2153-09-21 12:00:00,60.0,0.0,,,,71.1,0.0,0.0,0.0,
-35514836,2154-01-02 16:00:00,200.0,0.0,,,,80.2,0.0,0.0,0.0,
-35514836,2154-01-02 17:00:00,45.0,0.0,,,,80.2,0.0,0.0,0.0,
-35514836,2154-01-02 18:00:00,45.0,0.0,,,,80.2,0.0,0.0,0.0,
-35514836,2154-01-02 19:00:00,37.5,0.0,,,,80.2,0.0,0.0,0.0,
-35514836,2154-01-02 20:00:00,37.5,0.0,,,,80.2,0.0,0.0,0.0,
+35514836,2154-01-02 16:00:00,200.0,,,,,80.2,0.0,0.0,0.0,
+35514836,2154-01-02 17:00:00,45.0,,,,,80.2,0.0,0.0,0.0,
+35514836,2154-01-02 18:00:00,45.0,,,,,80.2,0.0,0.0,0.0,
+35514836,2154-01-02 19:00:00,37.5,,,,,80.2,0.0,0.0,0.0,
+35514836,2154-01-02 20:00:00,37.5,,,,,80.2,0.0,0.0,0.0,
 35514836,2154-01-02 21:00:00,35.0,0.0,,,,80.2,0.0,0.0,0.0,
 35514836,2154-01-02 22:00:00,50.0,0.0,,,,80.2,0.0,0.0,0.0,
 35514836,2154-01-02 23:00:00,30.0,1.0,,,,80.2,0.0,0.0,1.0,

diff --git a/test/probes/test_urineoutput_probes.py b/test/probes/test_urineoutput_probes.py
@@ -48,7 +48,7 @@ def test_anuria(self):
         pd.testing.assert_series_equal(
             df["urineoutput_stage"],
             pd.Series(
-                data=[0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 3],
+                data=[np.nan, np.nan, np.nan, np.nan, np.nan, 1, 1, 1, 1, 1, 1, 3],
                 name="urineoutput_stage",
                 index=pd.DatetimeIndex(
                     data=[
@@ -118,11 +118,11 @@ def test_aki(self):
             df["urineoutput_stage"],
             pd.Series(
                 data=[
-                    0,
-                    0,
-                    0,
-                    0,
-                    0,
+                    np.nan,
+                    np.nan,
+                    np.nan,
+                    np.nan,
+                    np.nan,
                     1,
                     1,
                     1,
@@ -222,7 +222,7 @@ def test_aki_strict(self):
         pd.testing.assert_series_equal(
             df["urineoutput_stage"],
             pd.Series(
-                data=[0] * 6 + [1] * 6 + [2] * 12 + [3],
+                data=[np.nan] * 5 + [0] + [1] * 6 + [2] * 12 + [3],
                 name="urineoutput_stage",
                 index=pd.period_range(
                     start="2023-01-01 00:00:00", end="2023-01-02 00:00:00", freq="h"
@@ -259,7 +259,7 @@ def test_nan_values(self):
         pd.testing.assert_series_equal(
             df_mean["urineoutput_stage"],
             pd.Series(
-                data=[0] * 6 + [np.nan] * 11 + [0],
+                data=[np.nan] * 5 + [0] + [np.nan] * 11 + [0],
                 name="urineoutput_stage",
                 index=pd.period_range(
                     start="2023-01-01 00:00:00", end="2023-01-01 17:00:00", freq="h"
@@ -272,7 +272,7 @@ def test_nan_values(self):
         pd.testing.assert_series_equal(
             df_strict["urineoutput_stage"],
             pd.Series(
-                data=[0] * 6 + [np.nan] * 11 + [0],
+                data=[np.nan] * 5 + [0] + [np.nan] * 11 + [0],
                 name="urineoutput_stage",
                 index=pd.period_range(
                     start="2023-01-01 00:00:00", end="2023-01-01 17:00:00", freq="h"