add user warning and did refactoring of function

Author: Moritz-Alexander-Kern

elephant/statistics.py

@@ -293,7 +293,7 @@ def fanofactor(spiketrains: Union[List[neo.SpikeTrain], List[pq.Quantity], List[
     spiketrains : list or elephant.trials.Trial
         List of `neo.SpikeTrain` or `pq.Quantity` or `np.ndarray` or list of
         spike times for which to compute the Fano factor of spike counts, or
-        an `elephant.trials.Trial` object, here the behavior can be controlled with the 
+        an `elephant.trials.Trial` object, here the behavior can be controlled with the
         pool_trials and pool_spike_trains parameters.
     warn_tolerance : pq.Quantity
         In case of a list of input neo.SpikeTrains, if their durations vary by
@@ -325,7 +325,7 @@ def fanofactor(spiketrains: Union[List[neo.SpikeTrain], List[pq.Quantity], List[
     Notes
     -----
     The check for the equal duration of the input spike trains is performed
-    only if the input is of type`neo.SpikeTrain`: if you pass a numpy array,
+    only if the input is of type`neo.SpikeTrain`: if you pass e.g. a numpy array,
     please make sure that they all have the same duration manually.
 
     Examples
@@ -346,30 +346,32 @@ def fanofactor(spiketrains: Union[List[neo.SpikeTrain], List[pq.Quantity], List[
     elif not isinstance(pool_spike_trains, bool):
         raise TypeError(f"'pool_spike_trains' must be of type bool, but got {type(pool_spike_trains)}")
     elif not is_time_quantity(warn_tolerance):
-        raise TypeError("'warn_tolerance' must be a time quantity.")
+        raise TypeError(f"'warn_tolerance' must be a time quantity, but got {type(warn_tolerance)}")
+
+    def _check_input_spiketrains_durations(spiketrains: Union[List[neo.SpikeTrain], List[pq.Quantity],
+                                                              List[np.ndarray]]) -> None:
+        if spiketrains and all(isinstance(st, neo.SpikeTrain) for st in spiketrains):
+            durations = np.array(tuple(st.duration for st in spiketrains))
+            if np.max(durations) - np.min(durations) > warn_tolerance:
+                warnings.warn(f"Fano factor calculated for spike trains of "
+                              f"different duration (minimum: {np.min(durations)}s, maximum "
+                              f"{np.max(durations)}s).")
+        else:
+            warnings.warn(f"Spiketrains was of type {type(spiketrains)}, which does not support automatic duration"
+                          f"check. The parameter 'warn_tolerance' will have no effect. Please ensure manually that"
+                          f"all spike trains have the same duration.")
 
-    def _compute_fano(spiketrains: List[neo.SpikeTrain]) -> float:
+    def _compute_fano(spiketrains: Union[List[neo.SpikeTrain], List[pq.Quantity], List[np.ndarray]]) -> float:
+        # Check spike train durations
+        _check_input_spiketrains_durations(spiketrains)
         # Build array of spike counts (one per spike train)
-        spike_counts = np.array([len(st) for st in spiketrains])
-
+        spike_counts = np.array(tuple(len(st) for st in spiketrains))
         # Compute FF
-        if all(count == 0 for count in spike_counts):
+        if np.all(np.array(spike_counts) == 0):
             # empty list of spiketrains reaches this branch, and NaN is returned
             return np.nan
-
-        if all(isinstance(st, neo.SpikeTrain) for st in spiketrains):
-            durations = [(st.t_stop - st.t_start).simplified.item()
-                         for st in spiketrains]
-            durations_min = min(durations)
-            durations_max = max(durations)
-            if durations_max - durations_min > warn_tolerance.simplified.item():
-                warnings.warn("Fano factor calculated for spike trains of "
-                              "different duration (minimum: {_min}s, maximum "
-                              "{_max}s).".format(_min=durations_min,
-                                                 _max=durations_max))
-
-        fano = spike_counts.var() / spike_counts.mean()
-        return fano
+        else:
+            return spike_counts.var()/spike_counts.mean()
 
     if isinstance(spiketrains, elephant.trials.Trials):
         if not pool_trials and not pool_spike_trains:

elephant/test/test_statistics.py

@@ -381,6 +381,11 @@ def test_fanofactor_trials_pool_spike_trains_wrong_type(self):
         self.assertRaises(TypeError, statistics.fanofactor, self.test_trials, pool_spike_trials="Wrong Type",
                           pool_spike_trains="Wrong Type")
 
+    def test_fanofactor_warn_durations_manual_check(self):
+        st1 = [1, 2, 3] * pq.s
+        st2 = [1, 2, 3] * pq.s
+        self.assertWarns(UserWarning, statistics.fanofactor, (st1, st2))
+
 
 class LVTestCase(unittest.TestCase):
     def setUp(self):