Merge pull request #1114 from AllenInstitute/1101/session-analysis-nightly

1101 update 2p session analysis nightly tests for recent scipy

Author: NileGraddis

allensdk/brain_observatory/stimulus_analysis.py

@@ -465,14 +465,14 @@ def get_speed_tuning(self, binsize):
                     nc, start_max * binsize:(start_max + 1) * binsize]
                 other_values = np.delete(celltraces_sorted_sp[nc, :], range(
                     start_max * binsize, (start_max + 1) * binsize))
-                (_, peak_run.ptest_sp[nc]) = st.ks_2samp(
+                (_, peak_run.ptest_sp[nc]) = nonraising_ks_2samp(
                     test_values, other_values)
             else:
                 test_values = celltraces_sorted_sp[
                     nc, start_min * binsize:(start_min + 1) * binsize]
                 other_values = np.delete(celltraces_sorted_sp[nc, :], range(
                     start_min * binsize, (start_min + 1) * binsize))
-                (_, peak_run.ptest_sp[nc]) = st.ks_2samp(
+                (_, peak_run.ptest_sp[nc]) = nonraising_ks_2samp(
                     test_values, other_values)
             temp = binned_cells_vis[nc, :, 0]
             start_max = temp.argmax()
@@ -489,7 +489,7 @@ def get_speed_tuning(self, binsize):
                     nc, start_min * binsize:(start_min + 1) * binsize]
                 other_values = np.delete(celltraces_sorted_vis[nc, :], range(
                     start_min * binsize, (start_min + 1) * binsize))
-            (_, peak_run.ptest_vis[nc]) = st.ks_2samp(
+            (_, peak_run.ptest_vis[nc]) = nonraising_ks_2samp(
                 test_values, other_values)
 
         return binned_dx_sp, binned_cells_sp, binned_dx_vis, binned_cells_vis, peak_run
@@ -581,3 +581,13 @@ def row_from_cell_id(self, csid=None, idx=None):
         else:
             raise Exception("Could not find row for csid(%s) idx(%s)" % (str(csid), str(idx)))
 
+    
+def nonraising_ks_2samp(data1, data2, **kwargs):
+    """ scipy.stats.ks_2samp now raises a ValueError if one of the input arrays 
+    is of length 0. Previously it signaled this case by returning nans. This 
+    function restores the prior behavior.
+    """
+
+    if min(len(data1), len(data2)) == 0:
+        return (np.nan, np.nan)
+    return st.ks_2samp(data1, data2, **kwargs)

allensdk/test/brain_observatory/test_session_analysis.py

@@ -47,13 +47,16 @@ def mock_stimulus_table(dset, name):
     t = _orig_get_stimulus_table(dset, name)
     t.set_value(0, 'end',
                 t.loc[0,'start'] + 10)
-    
+
     return t
 
 
 @pytest.fixture
 def session_a():
-    filename = '/data/informatics/module_test_data/observatory/test_nwb/out_510390912.nwb'
+    filename = os.path.abspath(os.path.join(
+            "/", "allen", "aibs", "informatics", "module_test_data",
+            "observatory", "test_nwb", "out_510390912.nwb"
+    ))
     save_path = 'xyza'
 
     sa = SessionAnalysis(filename, save_path)
@@ -63,7 +66,10 @@ def session_a():
 
 @pytest.fixture
 def session_b():
-    filename = '/data/informatics/module_test_data/observatory/test_nwb/506278598.nwb'
+    filename = os.path.abspath(os.path.join(
+            "/", "allen", "aibs", "informatics", "module_test_data", 
+            "observatory", "test_nwb", "506278598.nwb"
+    ))
     save_path = 'xyzb'
 
     sa = SessionAnalysis(filename, save_path)
@@ -73,7 +79,10 @@ def session_b():
 
 @pytest.fixture
 def session_c():
-    filename = '/data/informatics/module_test_data/observatory/test_nwb/out_510221121.nwb'
+    filename = os.path.abspath(os.path.join(
+            "/", "allen", "aibs", "informatics", "module_test_data",
+            "observatory", "test_nwb", "out_510221121.nwb"
+    ))
     save_path = 'xyzc'
 
     sa = SessionAnalysis(filename, save_path)