refactor for numpy 2.0 compatibility

int-brain-lab · Nov 18, 2024 · d66f612 · d66f612
1 parent 02862b1
commit d66f612
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/iblatlas/genomics/merfish_scrapping/01_ingest_zhuang.py b/iblatlas/genomics/merfish_scrapping/01_ingest_zhuang.py
@@ -45,7 +45,7 @@ def int_after_colon(text):
         captured_integer = int(match.group(1))
         return float(captured_integer)
     else:
-        return np.NaN
+        return np.nan
 
 
 def fcn_groupby_check_unique(df_cells, group, fields):
@@ -79,7 +79,7 @@ def reindex_missing_rows(df):
         elif isinstance(missing_rec[k], int | np.uint32 | np.int32 | np.uint64 | np.int64):
             missing_rec[k] = 0
         elif isinstance(missing_rec[k], float | np.float32 | np.float64):
-            missing_rec[k] = np.NaN
+            missing_rec[k] = np.nan
     df = df.reindex(pd.Index(np.arange(np.max(df.index) + 1), name=df.index.name), fill_value=0)
     df.iloc[imiss, :] = missing_rec
     return df

diff --git a/iblatlas/regions.py b/iblatlas/regions.py
@@ -658,7 +658,7 @@ def propagate_down(self, acronyms, values):
         _, user_indices = ismember(user_aids, self.id)
         self.compute_hierarchy()
         ia, ib = ismember(self.hierarchy, user_indices)
-        v = np.zeros_like(ia, dtype=np.float64) * np.NaN
+        v = np.zeros_like(ia, dtype=np.float64) * np.nan
         v[ia] = values[ib]
         all_values = np.nanmedian(v, axis=0)
         indices = np.where(np.any(ia, axis=0))[0]

diff --git a/iblatlas/tests/test_atlas.py b/iblatlas/tests/test_atlas.py
@@ -527,7 +527,7 @@ def test_init_from_dict(self):
 
         brain_atlas = _create_mock_atlas()
         brain_atlas.compute_surface()
-        brain_atlas.top = brain_atlas.top * np.NaN
+        brain_atlas.top = brain_atlas.top * np.nan
         ins = Insertion.from_dict(d, brain_atlas=brain_atlas)
         # eval the entry point, should be super close
         dxyz = ins.trajectory.eval_x(d['x'] / 1e6) - np.array((d['x'], d['y'], d['z'])) / 1e6
@@ -562,7 +562,7 @@ def test_init_from_track(self):
         brain_exit = insertion.get_brain_exit(insertion.trajectory, brain_atlas)
         self.assertTrue(brain_exit[2] == brain_atlas.bc.i2z(104))
         # test getting no intersection with the brain surface
-        brain_atlas.srf_xyz *= np.NaN
+        brain_atlas.srf_xyz *= np.nan
         with self.assertRaises(ValueError):
             insertion.get_brain_entry(insertion.trajectory, brain_atlas)
         self.assertIsNone(insertion.get_brain_entry(insertion.trajectory, brain_atlas, mode='none'))