[Bug fix] Fix bug of synchrotool index out of bounds

doc/authors.rst

@@ -51,6 +51,8 @@ contribution, and may not be the current affiliation of a contributor.
 * Florian Porrmann [13]
 * Sarah Pilz [13]
 * Oliver Kloß [1]
+* Jonas Oberste-Frielinghaus [1]
+* Sven Krausse [1]
 * Felician Richter [12]
 
 1. Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany

elephant/statistics.py

@@ -1357,6 +1357,11 @@ class Complexity(object):
     bin edge into the following bin. This can be adjusted using the tolerance
     parameter and turned off by setting `tolerance=None`.
 
+    Due to the rounding error correction an indexing error would occur if 
+    spikes were in the last bin. To avoid the t_stop of the original spike 
+    trains is modified to add one more bin in the cases where a spike is found
+    at the last time bin.
+
     See also
     --------
     elephant.conversion.BinnedSpikeTrain
@@ -1445,6 +1450,15 @@ def __init__(self, spiketrains,
         if bin_size is None and sampling_rate is not None:
             self.bin_size = 1 / self.sampling_rate
 
+        # Check if spikes happen in the last bin
+        for st in self.input_spiketrains:
+            # Extend t_stop to avoid indexing problems
+            if np.isclose(self.t_stop.magnitude, st.times[-1].magnitude):
+                self.t_stop += self.bin_size
+                for st in self.input_spiketrains:
+                    st.t_stop = self.t_stop
+                break
+
         if spread == 0:
             self.time_histogram, self.complexity_histogram = \
                 self._histogram_no_spread()
@@ -1555,6 +1569,7 @@ def _epoch_no_spread(self):
             if left_edges[0] < self.t_start:
                 left_edges[0] = self.t_start
                 durations[0] -= bin_shift
+
         else:
             warnings.warn('No sampling rate specified. '
                           'Note that using the complexity epoch to get '

elephant/test/test_spike_train_synchrony.py

@@ -193,6 +193,8 @@ def _test_template(self, spiketrains, correct_complexities, sampling_rate,
                        spread, deletion_threshold=2, mode='delete',
                        in_place=False, binary=True):
 
+        intial_t_stop = spiketrains[0].t_stop.magnitude
+
         synchrofact_obj = Synchrotool(
             spiketrains,
             sampling_rate=sampling_rate,
@@ -233,6 +235,9 @@ def _test_template(self, spiketrains, correct_complexities, sampling_rate,
                                           cleaned_spike_times):
             assert_array_almost_equal(cleaned_st, correct_st)
 
+        assert_array_almost_equal(spiketrains[0].t_stop.magnitude,
+                                  intial_t_stop)
+
     def test_no_synchrofacts(self):
 
         # nothing to find here
@@ -390,16 +395,16 @@ def test_binning_for_input_with_rounding_errors(self):
 
         sampling_rate = 30000 / pq.s
 
-        spiketrains = [neo.SpikeTrain(np.arange(1000) * pq.s / 30000,
+        spiketrains = [neo.SpikeTrain(np.arange(10) * pq.s / 30000,
                                       t_stop=.1 * pq.s),
-                       neo.SpikeTrain(np.arange(2000, step=2) * pq.s / 30000,
+                       neo.SpikeTrain(np.arange(20, step=2) * pq.s / 30000,
                                       t_stop=.1 * pq.s)]
 
-        first_annotations = np.ones(1000)
+        first_annotations = np.ones(10)
         first_annotations[::2] = 2
 
-        second_annotations = np.ones(1000)
-        second_annotations[:500] = 2
+        second_annotations = np.ones(10)
+        second_annotations[:5] = 2
 
         correct_annotations = np.array([first_annotations,
                                         second_annotations])
@@ -408,6 +413,28 @@ def test_binning_for_input_with_rounding_errors(self):
                             spread=0, mode='delete', in_place=True,
                             deletion_threshold=2)
 
+    def test_binning_indexing_last_bin_synchrofact(self):
+
+        # a test with inputs divided by 30000 which leads to rounding errors
+        # these errors have to be accounted for by proper binning;
+        # check if we still get the correct result
+        # If there is a synchrofact in the last bin there was an indexing
+        # error due to the rounding error correction
+
+        sampling_rate = 30000 / pq.s
+
+        st = neo.SpikeTrain(np.arange(10) * pq.s / 30000, t_stop=.1 * pq.s)
+
+        spiketrains = [st, st]
+
+        annotations = 2*np.ones(10)
+
+        correct_annotations = np.array([annotations, annotations])
+
+        self._test_template(spiketrains, correct_annotations, sampling_rate,
+                            spread=0, mode='delete', in_place=True,
+                            deletion_threshold=2)
+
     def test_correct_transfer_of_spiketrain_attributes(self):
 
         # for delete=True the spiketrains in the block are changed,

requirements/environment.yml

@@ -13,6 +13,6 @@ dependencies:
   - statsmodels
   - jinja2
   - pip:
-    - neo>=0.10.0
+    - neo>=0.13.0
     - viziphant
     # neo, viziphant can be removed once it is integrated into requirements-tutorials.txt