Merge pull request #132 from rmarkello/normwarn

[REF] Adds option to suppress norm warnings
rmarkello · Nov 26, 2019 · 991226e · 991226e
2 parents fc91343 + 01a051a
commit 991226e
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Showing 2 changed files with 13 additions and 7 deletions.
diff --git a/abagen/allen.py b/abagen/allen.py
@@ -341,10 +341,12 @@ def get_expression_data(atlas, atlas_info=None, *,
 
         if sample_norm is not None:
             microarray[subj] = correct.normalize_expression(microarray[subj].T,
-                                                            norm=sample_norm).T
+                                                            norm=sample_norm,
+                                                            ignore_warn=True).T
         if gene_norm is not None:
             microarray[subj] = correct.normalize_expression(microarray[subj],
-                                                            norm=gene_norm)
+                                                            norm=gene_norm,
+                                                            ignore_warn=True)
 
         # get counts of samples collapsed into each ROI
         labs, num = np.unique(labels, return_counts=True)

diff --git a/abagen/correct.py b/abagen/correct.py
@@ -124,8 +124,7 @@ def _rs(data, axis=0):
     # calculate sigmoid normalization
     med = np.median(data, axis=axis, keepdims=True)
     iqr = sstats.iqr(data, axis=axis, scale='normal', keepdims=True)
-    with np.errstate(divide='ignore', invalid='ignore'):
-        rs = 1 / (1 + np.exp(-(data - med) / iqr))
+    rs = 1 / (1 + np.exp(-(data - med) / iqr))
 
     return rs
 
@@ -166,7 +165,7 @@ def _srs(data, low=0, high=1, axis=0):
 )
 
 
-def normalize_expression(expression, norm='srs'):
+def normalize_expression(expression, norm='srs', ignore_warn=False):
     """
     Performs normalization on `expression` data
 
@@ -178,6 +177,9 @@ def normalize_expression(expression, norm='srs'):
     norm : {'rs', 'srs', 'center', 'zscore', 'minmax', 'batch'}, optional
         Function with which to normalize expression data. See Notes for more
         information. Default: 'srs'
+    ignore_warn : bool, optional
+        Whether to suppress potential warnings raised by normalization.
+        Default: False
 
     Returns
     -------
@@ -248,8 +250,10 @@ def normalize_expression(expression, norm='srs'):
         notna = np.logical_not(exp.isna().all(axis=1))
         data = np.asarray(exp)[notna]
 
-        # normalize the data (however was specified)
-        normed = normfunc(data) if norm != 'batch' else corrected[n]
+        kwargs = dict(divide='ignore', invalid='ignore') if ignore_warn else {}
+        with np.errstate(**kwargs):
+            # normalize the data (however was specified)
+            normed = normfunc(data) if norm != 'batch' else corrected[n]
 
         # recreate dataframe and fill non-NaN values
         normalized = pd.DataFrame(np.nan, columns=exp.columns, index=exp.index)