Bug fix in pseudo-inverse computation in the case of hydrogen.

Matgenix · Aug 21, 2024 · 6c46406 · 6c46406
1 parent af57a94
commit 6c46406
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Showing 3 changed files with 10 additions and 4 deletions.
diff --git a/matminer/featurizers/composition/tests/test_composite.py b/matminer/featurizers/composition/tests/test_composite.py
@@ -318,7 +318,7 @@ def test_elem_optical(self):
             self.df_nans, col_id="composition"
         )
         self.assertEqual(df_elem.isna().sum().sum(), 0)
-        self.assertAlmostEqual(df_elem.drop(columns="composition").sum().sum(), 201.3255, 4)
+        self.assertAlmostEqual(df_elem.drop(columns="composition").sum().sum(), 204.4712, 4)
 
     def test_elem_transport(self):
         df_elem = ElementProperty.from_preset("mp_transport", impute_nan=False).featurize_dataframe(
@@ -343,7 +343,7 @@ def test_elem_transport(self):
         df_elem = ElementProperty.from_preset("mp_transport", impute_nan=True).featurize_dataframe(
             self.df_nans, col_id="composition"
         )
-        self.assertAlmostEqual(df_elem.drop(columns="composition").sum().sum(), 9798095.622017656, 4)
+        self.assertAlmostEqual(df_elem.drop(columns="composition").sum().sum(), 10029874.1567, 4)
 
 
 if __name__ == "__main__":

diff --git a/matminer/utils/tests/test_data.py b/matminer/utils/tests/test_data.py
@@ -283,7 +283,7 @@ def test_get_data(self):
         c_k = self.data_source_imputed.get_elemental_property(elem="C", property_name="k_760.0")
         self.assertAlmostEqual(c_k, 0.7462931865379264)
         og_r = self.data_source_imputed.get_elemental_property(elem="Og", property_name="R_400.0")
-        self.assertAlmostEqual(og_r, 0.4624005395190695)
+        self.assertAlmostEqual(og_r, 0.46962554794905487)
 
 
 class TestTransportData(TestCase):
@@ -308,7 +308,7 @@ def test_get_data(self):
         cu_kappan = self.data_source_imputed.get_elemental_property(elem="Cu", property_name="kappa_n")
         self.assertAlmostEqual(cu_kappan, 1814544.75663, places=5)
         og_mn = self.data_source_imputed.get_elemental_property(elem="Og", property_name="m_n")
-        self.assertAlmostEqual(og_mn, 0.03237036761677134)
+        self.assertAlmostEqual(og_mn, 0.03293018092682478)
 
 
 if __name__ == "__main__":

diff --git a/matminer/utils/utils.py b/matminer/utils/utils.py
@@ -137,5 +137,11 @@ def get_pseudo_inverse(df_init, cols=None):
     res_pi = np.vstack([res_pi, np.nan * np.ones([len(elems_not_in_df), len(df.T) - 1])])
 
     df_pi = pd.DataFrame(res_pi, columns=cols, index=pd.Index(elems_in_df + elems_not_in_df))
+    # Handle the case of hydrogen, deuterium, and tritium
+    # If all are present, there contributions are summed
+    # and given to hydrogen only. Others are removed.
+    if all(e in df_pi.index for e in ["H", "D", "T"]):
+        df_pi.loc["H"] = df_pi.loc["H"] + df_pi.loc["D"] + df_pi.loc["T"]
+        df_pi.drop(index=["T", "D"], inplace=True)
 
     return df_pi