Polished up Example 15. Fixed some small errors here and there, inclu…

…ding: error in the GeneralizedLibrary that was not allowing for feature_names to be passed to this library properly. Added tests for GeneralizedLibrary with feature_names parameter passed or not passed.
OP-Luffy · Nov 29, 2021 · 8cbaa74 · 8cbaa74
1 parent 13a7143
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diff --git a/examples/15_pysindy_lectures.ipynb b/examples/15_pysindy_lectures.ipynb
diff --git a/examples/1_feature_overview.ipynb b/examples/1_feature_overview.ipynb
diff --git a/pysindy/feature_library/base.py b/pysindy/feature_library/base.py
@@ -474,16 +474,25 @@ def get_feature_names(self, input_features=None):
         feature_names = list()
         for i in range(len(self.libraries_)):
             lib_i = self.libraries_[i]
-            input_features_i = [
-                "x%d" % k for k in np.unique(self.inputs_per_library_[i, :])
-            ]
+            if input_features is None:
+                input_features_i = [
+                    "x%d" % k for k in np.unique(self.inputs_per_library_[i, :])
+                ]
+            else:
+                input_features_i = np.asarray(input_features)[
+                    np.unique(self.inputs_per_library_[i, :])
+                ].tolist()
             lib_i_feat_names = lib_i.get_feature_names(input_features_i)
             for j in range(i + 1, len(self.libraries_)):
                 lib_j = self.libraries_[j]
-                # Need to overwrite input feature names
-                input_features_j = [
-                    "x%d" % k for k in np.unique(self.inputs_per_library_[j, :])
-                ]
+                if input_features is None:
+                    input_features_j = [
+                        "x%d" % k for k in np.unique(self.inputs_per_library_[j, :])
+                    ]
+                else:
+                    input_features_j = np.asarray(input_features)[
+                        np.unique(self.inputs_per_library_[j, :])
+                    ].tolist()
                 lib_j_feat_names = lib_j.get_feature_names(input_features_j)
                 feature_names += self._name_combinations(
                     lib_i_feat_names, lib_j_feat_names

diff --git a/pysindy/feature_library/generalized_library.py b/pysindy/feature_library/generalized_library.py
@@ -283,14 +283,22 @@ def get_feature_names(self, input_features=None):
         feature_names = list()
         for i, lib in enumerate(self.libraries_):
             if i < self.inputs_per_library_.shape[0]:
-                input_features = [
-                    "x%d" % k for k in np.unique(self.inputs_per_library_[i, :])
-                ]
+                if input_features is None:
+                    input_features_i = [
+                        "x%d" % k for k in np.unique(self.inputs_per_library_[i, :])
+                    ]
+                else:
+                    input_features_i = np.asarray(input_features)[
+                        np.unique(self.inputs_per_library_[i, :])
+                    ].tolist()
             else:
                 # Tensor libraries need all the inputs and then internally
                 # handle the subsampling of the input variables
-                input_features = [
-                    "x%d" % k for k in range(self.inputs_per_library_.shape[0])
-                ]
-            feature_names += lib.get_feature_names(input_features)
+                if input_features is None:
+                    input_features_i = [
+                        "x%d" % k for k in range(self.inputs_per_library_.shape[1])
+                    ]
+                else:
+                    input_features_i = input_features
+            feature_names += lib.get_feature_names(input_features_i)
         return feature_names
diff --git a/test/feature_library/test_feature_library.py b/test/feature_library/test_feature_library.py
@@ -488,6 +488,16 @@ def test_generalized_library(data_lorenz):
     model.get_feature_names()
     assert len(model.get_feature_names()) == 24
 
+    # Repeat with feature names
+    feature_names = ["x", "y", "z"]
+    model = SINDy(
+        optimizer=sindy_opt, feature_library=sindy_library, feature_names=feature_names
+    )
+    model.fit(x, t=t)
+    model.print()
+    model.get_feature_names()
+    assert len(model.get_feature_names()) == 24
+
     # Next try with tensor libraries but still all the input variables
     sindy_library = GeneralizedLibrary(
         [poly_library, fourier_library, custom_library], tensor_array=tensor_array
@@ -501,6 +511,18 @@ def test_generalized_library(data_lorenz):
     # 24 + (9 * 6) = 54 + (9 * 9) = 81
     assert len(model.get_feature_names()) == 159
 
+    # Repeat with feature_names
+    sindy_library = GeneralizedLibrary(
+        [poly_library, fourier_library, custom_library], tensor_array=tensor_array
+    )
+    model = SINDy(
+        optimizer=sindy_opt, feature_library=sindy_library, feature_names=feature_names
+    )
+    model.fit(x, t=t)
+    model.print()
+    # 24 + (9 * 6) = 54 + (9 * 9) = 81
+    assert len(model.get_feature_names()) == 159
+
     sindy_library = GeneralizedLibrary(
         [poly_library, fourier_library, custom_library],
         tensor_array=tensor_array,
@@ -513,6 +535,18 @@ def test_generalized_library(data_lorenz):
     model.fit(x, t=t)
     assert len(model.get_feature_names()) == 29
 
+    # Repeat with feature names
+    sindy_library = GeneralizedLibrary(
+        [poly_library, fourier_library, custom_library],
+        tensor_array=tensor_array,
+        inputs_per_library=inputs_per_library,
+    )
+    model = SINDy(
+        optimizer=sindy_opt, feature_library=sindy_library, feature_names=feature_names
+    )
+    model.fit(x, t=t)
+    assert len(model.get_feature_names()) == 29
+
 
 # Helper function for testing PDE libraries
 def pde_library_helper(library, u_flattened, u_dot_flattened, coef_first_dim):