better distance validation

settylab · Jun 3, 2024 · f311bc9 · f311bc9
1 parent 6627774
commit f311bc9
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Showing 6 changed files with 689 additions and 32 deletions.
diff --git a/mellon/base_model.py b/mellon/base_model.py
@@ -35,6 +35,7 @@
     _validate_bool,
     _validate_array,
     _validate_float_or_iterable_numerical,
+    _validate_nn_distances,
 )
 from .parameter_validation import (
     _validate_params,
@@ -240,19 +241,7 @@ def _compute_nn_distances(self):
         x = self.x
         logger.info("Computing nearest neighbor distances.")
         nn_distances = compute_nn_distances(x)
-
-        # Check for invalid values
-        nan_count = np.isnan(nn_distances).sum()
-        inf_count = np.isinf(nn_distances).sum()
-        negative_count = (nn_distances < 0).sum()
-        if nan_count > 0 or inf_count > 0 or negative_count > 0:
-            total_invalid = nan_count + inf_count + negative_count
-            logger.warning(
-                "The computed nearest neighbor distances (`nn_distances` attribute) contain "
-                f"{total_invalid:,} invalid values: "
-                f"{nan_count:,} NaN, {inf_count:,} infinite, {negative_count:,} less than 0. "
-                "Please check the input data."
-            )
+        nn_distances = _validate_nn_distances(nn_distances)
         return nn_distances
 
     def _compute_ls(self):