Merge pull request #30 from rmarkello/fix/atlasnum

[FIX] More fixes for atlas numbering
rmarkello · Oct 17, 2018 · 39cb746 · 39cb746
2 parents ab2c232 + 552b24d
commit 39cb746
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Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/abagen/allen.py b/abagen/allen.py
@@ -423,10 +423,11 @@ def get_expression_data(files, atlas, atlas_info=None, *, exact=True,
         if not exact:
             coords = utils.xyz_to_ijk(annotation[['mni_x', 'mni_y', 'mni_z']],
                                       atlas.affine)
-            empty = np.setdiff1d(all_labels, labs)
+            empty = ~np.in1d(all_labels, labs)
             closest, dist = utils.closest_centroid(coords, centroids[empty],
                                                    return_dist=True)
             closest = samples.loc[annotation.iloc[closest].index]
+            empty = all_labels[empty]
             closest.index = pd.Series(empty, name='label')
             missing += [(closest, dict(zip(empty, np.diag(dist))))]
 

diff --git a/abagen/tests/test_allen.py b/abagen/tests/test_allen.py
@@ -48,8 +48,12 @@ def test_missing_labels(testfiles):
     atlas_info = pd.read_csv(ATLAS.info)
     atlas_info = atlas_info[~atlas_info.id.isin(remove)]
     # test get expression
-    out = allen.get_expression_data(testfiles, atlas, atlas_info)
+    out, counts = allen.get_expression_data(testfiles, atlas, atlas_info,
+                                            exact=False, return_counts=True)
     assert isinstance(out, pd.DataFrame)
     assert out.index.name == 'label'
     assert out.columns.name == 'gene_symbol'
     assert len(out) == len(atlas_info)
+
+    assert isinstance(counts, pd.DataFrame)
+    assert counts.shape == (len(atlas_info), len(testfiles.probes))