Cumulative fix for various Neo 0.7.x related issues (NeuralEnsemble#203)

* Change signal's `duplicate_with_new_array` to `duplicate_with_new_data`

For compatibility with Neo 0.7.0

* Fixed error by replacing deprecated pandas function

* Quick fix due to event labels being treated as array annotations

* Quick fix due to event labels being treated as array annotations

* Fixed handling of neo 0.7 array_annotations

* Fixed requirements for neo

* Removed left-over print statement

* Added a hot fix to circumtvent Neo problem in generating fake epochs

* Added fixed Neo Version 0.7.x

* Fixed failing test in spike_train_correlation by alternate numpy construct.

elephant/neo_tools.py

@@ -45,6 +45,17 @@ def extract_neo_attrs(obj, parents=True, child_first=True,
 
     """
     attrs = obj.annotations.copy()
+    if not skip_array:
+        try:
+            for a in obj.array_annotations:
+                # Exclude labels and durations (and maybe other attributes) that are handled as array_annotations
+                # These would be duplicate
+                if a not in [_[0] for _ in obj._necessary_attrs + obj._recommended_attrs]:
+                    if "array_annotations" not in attrs:
+                        attrs["array_annotations"] = {}
+                    attrs["array_annotations"][a] = obj.array_annotations[a].copy()
+        except AttributeError:
+            pass
     for attr in obj._necessary_attrs + obj._recommended_attrs:
         if skip_array and len(attr) >= 3 and attr[2]:
             continue

elephant/pandas_bridge.py

@@ -60,7 +60,7 @@ def _sort_inds(obj, axis=0):
         return obj
 
     obj = obj.reorder_levels(sorted(obj.axes[axis].names), axis=axis)
-    return obj.sortlevel(0, axis=axis, sort_remaining=True)
+    return obj.sort_index(level=0, axis=axis, sort_remaining=True)
 
 
 def _extract_neo_attrs_safe(obj, parents=True, child_first=True):

elephant/signal_processing.py

@@ -118,7 +118,7 @@ def zscore(signal, inplace=True):
         # Create new signal instance
         result = []
         for sig in signal:
-            sig_dimless = sig.duplicate_with_new_array(
+            sig_dimless = sig.duplicate_with_new_data(
                 (sig.magnitude - m.magnitude) / s.magnitude) / sig.units
             result.append(sig_dimless)
     else:
@@ -376,7 +376,7 @@ def _design_butterworth_filter(Fs, hpfreq=None, lpfreq=None, order=4):
         )
 
     if isinstance(signal, neo.AnalogSignal):
-        return signal.duplicate_with_new_array(np.rollaxis(filtered_data, -1, 0))
+        return signal.duplicate_with_new_data(np.rollaxis(filtered_data, -1, 0))
     elif isinstance(signal, pq.quantity.Quantity):
         return filtered_data * signal.units
     else:
@@ -608,6 +608,6 @@ def hilbert(signal, N='nextpow'):
     else:
         raise ValueError("'{}' is an unknown N.".format(N))
 
-    output = signal.duplicate_with_new_array(
+    output = signal.duplicate_with_new_data(
         scipy.signal.hilbert(signal.magnitude, N=n, axis=0)[:n_org])
     return output / output.units

elephant/test/test_neo_tools.py

@@ -26,7 +26,8 @@
                'index',
                'channel_names',
                'channel_ids',
-               'coordinates'
+               'coordinates',
+               'array_annotations'
                ]
 
 
@@ -446,6 +447,26 @@ def test__extract_neo_attrs__spiketrain_parents_empty_array(self):
     def test__extract_neo_attrs__epoch_parents_empty_array(self):
         obj = fake_neo('Epoch', seed=0)
         targ = get_fake_values('Epoch', seed=0)
+
+        # TODO: Circumvent bug in neo 0.7.1, where fake objects are not
+        # properly constructed. Here, the returned fake values do not match
+        # with the corresponding object in terms of the length of the Epoch
+        # object. We introduce a manual fix, cutting the fake Neo object to the
+        # number of items returned by the get_fake_values() function.
+        num_times = len(targ['times'])
+        array_annotation_save = obj.array_annotations
+        obj.array_annotations = {
+            'durations': array_annotation_save['durations'],
+            'labels': array_annotation_save['labels']}
+        obj.durations = obj.durations[:num_times]
+        obj.labels = obj.labels[:num_times]
+        for k in array_annotation_save:
+            obj.array_annotations[k] = array_annotation_save[k][:num_times]
+
+        # TODO: Fix once inconsistencies in handling array annotations
+        # are properly fixed in neo
+        del targ['array_annotations']
+
         del targ['times']
 
         res000 = nt.extract_neo_attrs(obj, parents=False)
@@ -616,6 +637,26 @@ def test__extract_neo_attrs__spiketrain_noparents_array(self):
     def test__extract_neo_attrs__epoch_noparents_array(self):
         obj = self.block.list_children_by_class('Epoch')[0]
         targ = get_fake_values('Epoch', seed=obj.annotations['seed'])
+
+        # TODO: Circumvent bug in neo 0.7.1, where fake objects are not
+        # properly constructed. Here, the returned fake values do not match
+        # with the corresponding object in terms of the length of the Epoch
+        # object. We introduce a manual fix, cutting the fake Neo object to the
+        # number of items returned by the get_fake_values() function.
+        num_times = len(targ['times'])
+        array_annotation_save = obj.array_annotations
+        obj.array_annotations = {
+            'durations': array_annotation_save['durations'],
+            'labels': array_annotation_save['labels']}
+        obj.durations = obj.durations[:num_times]
+        obj.labels = obj.labels[:num_times]
+        for k in array_annotation_save:
+            obj.array_annotations[k] = array_annotation_save[k][:num_times]
+
+        # TODO: Fix once inconsistencies in handling array annotations
+        # are properly fixed in neo
+        del targ['array_annotations']
+
         del targ['times']
 
         res00 = nt.extract_neo_attrs(obj, parents=False, skip_array=False)
@@ -627,6 +668,15 @@ def test__extract_neo_attrs__epoch_noparents_array(self):
         res11 = nt.extract_neo_attrs(obj, parents=False, child_first=True)
         res21 = nt.extract_neo_attrs(obj, parents=False, child_first=False)
 
+        for k in res00:
+            print(k,res00[k])
+        print('-=-')
+        for k in res01:
+            print(k,res01[k])
+        print('-=-')
+        for k in targ:
+            print(k,targ[k])
+
         del res00['i']
         del res10['i']
         del res20['i']
@@ -866,6 +916,26 @@ def test__extract_neo_attrs__epoch_parents_childfirst_array(self):
         targ = get_fake_values('Block', seed=blk.annotations['seed'])
         targ.update(get_fake_values('Segment', seed=seg.annotations['seed']))
         targ.update(get_fake_values('Epoch', seed=obj.annotations['seed']))
+
+        # TODO: Circumvent bug in neo 0.7.1, where fake objects are not
+        # properly constructed. Here, the returned fake values do not match
+        # with the corresponding object in terms of the length of the Epoch
+        # object. We introduce a manual fix, cutting the fake Neo object to the
+        # number of items returned by the get_fake_values() function.
+        num_times = len(targ['times'])
+        array_annotation_save = obj.array_annotations
+        obj.array_annotations = {
+            'durations': array_annotation_save['durations'],
+            'labels': array_annotation_save['labels']}
+        obj.durations = obj.durations[:num_times]
+        obj.labels = obj.labels[:num_times]
+        for k in array_annotation_save:
+            obj.array_annotations[k] = array_annotation_save[k][:num_times]
+
+        # TODO: Fix once inconsistencies in handling array annotations
+        # are properly fixed in neo
+        del targ['array_annotations']
+
         del targ['times']
 
         res00 = nt.extract_neo_attrs(obj, parents=True, skip_array=False)
@@ -959,6 +1029,26 @@ def test__extract_neo_attrs__epoch_parents_parentfirst_array(self):
         targ = get_fake_values('Epoch', seed=obj.annotations['seed'])
         targ.update(get_fake_values('Segment', seed=seg.annotations['seed']))
         targ.update(get_fake_values('Block', seed=blk.annotations['seed']))
+
+        # TODO: Circumvent bug in neo 0.7.1, where fake objects are not
+        # properly constructed. Here, the returned fake values do not match
+        # with the corresponding object in terms of the length of the Epoch
+        # object. We introduce a manual fix, cutting the fake Neo object to the
+        # number of items returned by the get_fake_values() function.
+        num_times = len(targ['times'])
+        array_annotation_save = obj.array_annotations
+        obj.array_annotations = {
+            'durations': array_annotation_save['durations'],
+            'labels': array_annotation_save['labels']}
+        obj.durations = obj.durations[:num_times]
+        obj.labels = obj.labels[:num_times]
+        for k in array_annotation_save:
+            obj.array_annotations[k] = array_annotation_save[k][:num_times]
+
+        # TODO: Fix once inconsistencies in handling array annotations
+        # are properly fixed in neo
+        del targ['array_annotations']
+
         del targ['times']
 
         res0 = nt.extract_neo_attrs(obj, parents=True, skip_array=False,

elephant/test/test_spike_train_correlation.py

@@ -521,8 +521,8 @@ def test_border_correction(self):
             border_correction=False, binary=False, kernel=None,
             method='memory')
 
-        self.assertNotEqual(cch.all(), cch_corrected.all())
-        self.assertNotEqual(cch_mem.all(), cch_corrected_mem.all())
+        self.assertEqual(np.any(np.not_equal(cch, cch_corrected)), True)
+        self.assertEqual(np.any(np.not_equal(cch_mem, cch_corrected_mem)), True)
 
     def test_kernel(self):
         '''Test if the smoothing kernel is correctly defined, and wheter it is

elephant/test/test_sta.py

@@ -284,7 +284,7 @@ def test_wrong_input_type(self):
                           self.anasig0, [1, 2, 3])
         self.assertRaises(ValueError,
                           sta.spike_field_coherence,
-                          self.anasig0.duplicate_with_new_array([]), self.bst0)
+                          self.anasig0.duplicate_with_new_data([]), self.bst0)
 
     def test_start_stop_times_out_of_range(self):
         self.assertRaises(ValueError,

requirements.txt

@@ -1,5 +1,5 @@
-neo>=0.5.0
+neo<=0.7.1,<0.8.0
 numpy>=1.8.2
 quantities>=0.10.1
 scipy>=0.14.0
-six>=1.10.0
+six>=1.10.0