[MRG] Nans in view connectome (nilearn#2166)

* nan_to_num in view_connectome

* update warning test

* whatsnew

doc/whats_new.rst

@@ -62,6 +62,9 @@ Changes
   colormap. These arguments were already accepted in `kwargs` but not documented
   before.
 
+- :func:`nilearn.plotting.view_connectome` now converts NaNs in the adjacency
+  matrix to 0.
+
 Fixes
 -----
 

nilearn/plotting/html_connectome.py

@@ -31,7 +31,7 @@ def _get_connectome(adjacency_matrix, coords, threshold=None,
                     marker_size=None, cmap=cm.cold_hot, symmetric_cmap=True):
     connectome = {}
     coords = np.asarray(coords, dtype='<f4')
-    adjacency_matrix = adjacency_matrix.copy()
+    adjacency_matrix = np.nan_to_num(adjacency_matrix, copy=True)
     colors = colorscale(
         cmap, adjacency_matrix.ravel(), threshold=threshold,
         symmetric_cmap=symmetric_cmap)

nilearn/plotting/tests/test_html_connectome.py

@@ -47,6 +47,11 @@ def test_get_connectome():
     assert {'_con_x', '_con_y', '_con_z', '_con_w', 'colorscale'
             }.issubset(connectome.keys())
     assert (connectome['cmin'], connectome['cmax']) == (-2.5, 2.5)
+    adj[adj == 0] = np.nan
+    connectome = html_connectome._get_connectome(adj, coord)
+    con_x = decode(connectome['_con_x'], '<f4')
+    assert (con_x == expected_x).all()
+    assert (connectome['cmin'], connectome['cmax']) == (-2.5, 2.5)
 
 
 def test_view_connectome():
@@ -129,10 +134,11 @@ def test_params_deprecation_view_connectome():
                                         )
     old_params = ['coords', 'threshold', 'cmap', 'marker_size']
 
-    assert len(raised_warnings) == 4
-    for old_param_, raised_warning_ in zip(old_params, raised_warnings):
-        assert warning_msgs[old_param_] == str(raised_warning_.message)
-        assert raised_warning_.category is DeprecationWarning
+    raised_warning_messages = ''.join(
+        str(warning.message) for warning in raised_warnings)
+    print(raised_warning_messages)
+    for old_param_ in old_params:
+        assert warning_msgs[old_param_] in raised_warning_messages
 
 
 def test_get_markers():