Support SpikeTrainList object and deprecate RecordingChannel in Eleph…

…ant (#447)

* Handle SpikeTrainList as input for BinnedSpikeTrain

* Add corresponding regression test

* PEP 8; avoid universal try-except clause

* Fixed SpikeTrainList issue in spike train synchrony class

* Fixed SpikeTrainList issue in SPADE

* Pep8 issue

* This removes support of RrcordingChannelGroup in CSD methods.

* Changed requirements to Neo >=0.10.0

* Fix spiketrain lists in instantaneous rate.

elephant/conversion.py

@@ -1223,14 +1223,14 @@ def __init__(self, t_start, t_stop, bin_size, units, sparse_matrix,
         self.tolerance = tolerance
 
 
-def _check_neo_spiketrain(matrix):
+def _check_neo_spiketrain(query):
     """
     Checks if given input contains neo.SpikeTrain objects
 
     Parameters
     ----------
-    matrix
-        Object to test for `neo.SpikeTrain`s
+    query
+        Object to test for `neo.SpikeTrain` objects
 
     Returns
     -------
@@ -1240,11 +1240,14 @@ def _check_neo_spiketrain(matrix):
 
     """
     # Check for single spike train
-    if isinstance(matrix, neo.SpikeTrain):
+    if isinstance(query, neo.SpikeTrain):
         return True
-    # Check for list or tuple
-    if isinstance(matrix, (list, tuple)):
-        return all(map(_check_neo_spiketrain, matrix))
+    # Check for list, tuple, or SpikeTrainList
+    try:
+        return all(map(_check_neo_spiketrain, query))
+    except TypeError:
+        pass
+
     return False
 
 

elephant/current_source_density.py

@@ -62,7 +62,7 @@
 
 
 @deprecated_alias(coords='coordinates')
-def estimate_csd(lfp, coordinates=None, method=None,
+def estimate_csd(lfp, coordinates='coordinates', method=None,
                  process_estimate=True, **kwargs):
     """
     Function call to compute the current source density (CSD) from
@@ -72,12 +72,16 @@ def estimate_csd(lfp, coordinates=None, method=None,
     Parameters
     ----------
     lfp : neo.AnalogSignal
-        positions of electrodes can be added as neo.RecordingChannel
-        coordinate or sent externally as a func argument (See coords)
-    coordinates : [Optional] corresponding spatial coordinates of the
-        electrodes.
-        Defaults to None
-        Otherwise looks for ChannelIndex coordinate
+        Positions of electrodes can be added as an array annotation
+    coordinates : array-like Quantity or string
+        Specifies the corresponding spatial coordinates of the electrodes.
+        Coordinates can be directly supplied by a NxM array-like Quantity
+        with dimension of space, where M is the number of signals in 'lfp',
+        and N is equal to the dimensionality of the method.
+        Alternatively, if coordinates is a string, the function will fetch the
+        coordinates, supplied in the same format, as annotation of 'lfp' by that
+        name.
+        Default: 'coordinates'
     method : string
         Pick a method corresponding to the setup, in this implementation
         For Laminar probe style (1D), use 'KCSD1D' or 'StandardCSD',
@@ -114,17 +118,19 @@ def estimate_csd(lfp, coordinates=None, method=None,
     """
     if not isinstance(lfp, neo.AnalogSignal):
         raise TypeError('Parameter `lfp` must be a neo.AnalogSignal object')
-    if coordinates is None:
-        coordinates = lfp.channel_index.coordinates
-    else:
-        scaled_coords = []
-        for coord in coordinates:
-            try:
-                scaled_coords.append(coord.rescale(pq.mm))
-            except AttributeError:
-                raise AttributeError('No units given for electrode spatial \
-                coordinates')
-        coordinates = scaled_coords
+    if isinstance(coordinates, str):
+        coordinates = lfp.annotations[coordinates]
+
+    # Scale all coordinates to mm as common basis
+    scaled_coords = []
+    for coord in coordinates:
+        try:
+            scaled_coords.append(coord.rescale(pq.mm))
+        except AttributeError:
+            raise AttributeError('No units given for electrode spatial \
+            coordinates')
+    coordinates = scaled_coords
+
     if method is None:
         raise ValueError('Must specify a method of CSD implementation')
     if len(coordinates) != lfp.shape[1]:
@@ -249,7 +255,8 @@ def generate_lfp(csd_profile, x_positions, y_positions=None, z_positions=None,
     -------
     LFP : neo.AnalogSignal
        The potentials created by the csd profile at the electrode positions.
-       The electrode positions are attached as RecordingChannel's coordinate.
+       The electrode positions are attached as an annotation named
+       'coordinates'.
     """
 
     def integrate_1D(x0, csd_x, csd, h):
@@ -327,10 +334,8 @@ def integrate_3D(x, y, z, csd, xlin, ylin, zlin, X, Y, Z):
         pots /= 4 * np.pi * sigma
         ele_pos = np.vstack((x_positions, y_positions, z_positions)).T
     ele_pos = ele_pos * pq.mm
-    ch = neo.ChannelIndex(index=range(len(pots)))
+
     asig = neo.AnalogSignal(np.expand_dims(pots, axis=0),
                             sampling_rate=pq.kHz, units='mV')
-    ch.coordinates = ele_pos
-    ch.analogsignals.append(asig)
-    ch.create_relationship()
+    asig.annotate(coordinates=ele_pos)
     return asig

elephant/spade.py

@@ -97,6 +97,7 @@
 from itertools import chain, combinations
 
 import neo
+from neo.core.spiketrainlist import SpikeTrainList
 import numpy as np
 import quantities as pq
 from scipy import sparse
@@ -614,7 +615,7 @@ def concepts_mining(spiketrains, bin_size, winlen, min_spikes=2, min_occ=2,
             "report has to assume of the following values:" +
             "  'a', '#' and '3d#,' got {} instead".format(report))
     # if spiketrains is list of neo.SpikeTrain convert to conv.BinnedSpikeTrain
-    if isinstance(spiketrains, list) and \
+    if isinstance(spiketrains, (list, SpikeTrainList)) and \
             isinstance(spiketrains[0], neo.SpikeTrain):
         spiketrains = conv.BinnedSpikeTrain(
             spiketrains, bin_size=bin_size, tolerance=None)

elephant/spike_train_synchrony.py

@@ -349,7 +349,11 @@ def delete_synchrofacts(self, threshold, in_place=False, mode='delete'):
                     # replace link to spiketrain in segment
                     new_index = self._get_spiketrain_index(
                         segment.spiketrains, st)
-                    segment.spiketrains[new_index] = new_st
+                    # Todo: Simplify following lines once Neo SpikeTrainList
+                    # implments indexed assignment of entries (i.e., stl[i]=st)
+                    spiketrainlist = list(segment.spiketrains)
+                    spiketrainlist[new_index] = new_st
+                    segment.spiketrains = spiketrainlist
                 except ValueError:
                     # st is not in this segment even though it points to it
                     warnings.warn(f"The SpikeTrain at index {idx} of the "

elephant/statistics.py

@@ -70,6 +70,7 @@
 import warnings
 
 import neo
+from neo.core.spiketrainlist import SpikeTrainList
 import numpy as np
 import quantities as pq
 import scipy.stats
@@ -769,7 +770,7 @@ def optimal_kernel(st):
         if kernel == 'auto':
             kernel = optimal_kernel(spiketrains)
         spiketrains = [spiketrains]
-    elif not isinstance(spiketrains, (list, tuple)):
+    elif not isinstance(spiketrains, (list, tuple, SpikeTrainList)):
         raise TypeError(
             "'spiketrains' must be a list of neo.SpikeTrain's or a single "
             "neo.SpikeTrain. Found: '{}'".format(type(spiketrains)))

elephant/test/test_conversion.py

@@ -9,6 +9,7 @@
 import unittest
 
 import neo
+from neo.core.spiketrainlist import SpikeTrainList
 import numpy as np
 import quantities as pq
 from numpy.testing import (assert_array_almost_equal, assert_array_equal)
@@ -185,6 +186,28 @@ def test_bin_edges_empty_binned_spiketrain(self):
         assert_array_equal(bst.spike_indices, [[]])  # no binned spikes
         self.assertEqual(bst.get_num_of_spikes(), 0)
 
+    def test_regression_431(self):
+        """
+        Addresses issue 431
+        This unittest addresses an issue where a SpikeTrainList obejct was not
+        correctly handled by the constructor
+        """
+        st1 = neo.SpikeTrain(
+            times=np.array([1, 2, 3]) * pq.ms,
+            t_start=0 * pq.ms, t_stop=10 * pq.ms)
+        st2 = neo.SpikeTrain(
+            times=np.array([4, 5, 6]) * pq.ms,
+            t_start=0 * pq.ms, t_stop=10 * pq.ms)
+        real_list = [st1, st2]
+        spiketrainlist = SpikeTrainList([st1, st2])
+
+        real_list_binary = cv.BinnedSpikeTrain(real_list, bin_size=1*pq.ms)
+        spiketrainlist_binary = cv.BinnedSpikeTrain(
+            spiketrainlist, bin_size=1 * pq.ms)
+
+        assert_array_equal(
+            real_list_binary.to_array(), spiketrainlist_binary.to_array())
+
 
 class BinnedSpikeTrainTestCase(unittest.TestCase):
     def setUp(self):

elephant/test/test_kcsd.py

@@ -32,11 +32,7 @@ def setUp(self):
             temp_signals.append(self.pots[ii])
         self.an_sigs = neo.AnalogSignal(np.array(temp_signals).T * pq.mV,
                                         sampling_rate=1000 * pq.Hz)
-        chidx = neo.ChannelIndex(range(len(self.pots)))
-        chidx.analogsignals.append(self.an_sigs)
-        chidx.coordinates = self.ele_pos * pq.mm
-
-        chidx.create_relationship()
+        self.an_sigs.annotate(coordinates=self.ele_pos * pq.mm)
 
     def test_kcsd1d_estimate(self, cv_params={}):
         self.test_params.update(cv_params)
@@ -86,11 +82,7 @@ def setUp(self):
             temp_signals.append(self.pots[ii])
         self.an_sigs = neo.AnalogSignal(np.array(temp_signals).T * pq.mV,
                                         sampling_rate=1000 * pq.Hz)
-        chidx = neo.ChannelIndex(range(len(self.pots)))
-        chidx.analogsignals.append(self.an_sigs)
-        chidx.coordinates = self.ele_pos * pq.mm
-
-        chidx.create_relationship()
+        self.an_sigs.annotate(coordinates=self.ele_pos * pq.mm)
 
     def test_kcsd2d_estimate(self, cv_params={}):
         self.test_params.update(cv_params)
@@ -149,11 +141,7 @@ def setUp(self):
             temp_signals.append(self.pots[ii])
         self.an_sigs = neo.AnalogSignal(np.array(temp_signals).T * pq.mV,
                                         sampling_rate=1000 * pq.Hz)
-        chidx = neo.ChannelIndex(range(len(self.pots)))
-        chidx.analogsignals.append(self.an_sigs)
-        chidx.coordinates = self.ele_pos * pq.mm
-
-        chidx.create_relationship()
+        self.an_sigs.annotate(coordinates=self.ele_pos * pq.mm)
 
     def test_kcsd3d_estimate(self, cv_params={}):
         self.test_params.update(cv_params)

elephant/test/test_spade.py

@@ -10,6 +10,7 @@
 import random
 
 import neo
+from neo.core.spiketrainlist import SpikeTrainList
 import numpy as np
 import quantities as pq
 from numpy.testing.utils import assert_array_equal
@@ -180,6 +181,35 @@ def test_spade_msip(self):
         # check the lags
         assert_array_equal(lags_msip, self.lags_msip)
 
+    # Testing with multiple patterns input
+    def test_spade_msip_spiketrainlist(self):
+        output_msip = spade.spade(
+            SpikeTrainList(self.msip), self.bin_size, self.winlen,
+            approx_stab_pars=dict(
+            n_subsets=self.n_subset,
+            stability_thresh=self.stability_thresh),
+            n_surr=self.n_surr, alpha=self.alpha,
+            psr_param=self.psr_param,
+            stat_corr='no',
+            output_format='patterns')['patterns']
+        elements_msip = []
+        occ_msip = []
+        lags_msip = []
+        # collecting spade output
+        for out in output_msip:
+            elements_msip.append(out['neurons'])
+            occ_msip.append(list(out['times'].magnitude))
+            lags_msip.append(list(out['lags'].magnitude))
+        elements_msip = sorted(elements_msip, key=len)
+        occ_msip = sorted(occ_msip, key=len)
+        lags_msip = sorted(lags_msip, key=len)
+        # check neurons in the patterns
+        assert_array_equal(elements_msip, self.elements_msip)
+        # check the occurrences time of the patters
+        assert_array_equal(occ_msip, self.occ_msip)
+        # check the lags
+        assert_array_equal(lags_msip, self.lags_msip)
+
     def test_parameters(self):
         """
         Test under different configuration of parameters than the default one

elephant/utils.py

@@ -16,6 +16,7 @@
 from functools import wraps
 
 import neo
+from neo.core.spiketrainlist import SpikeTrainList
 import numpy as np
 import quantities as pq
 
@@ -188,7 +189,7 @@ def check_neo_consistency(neo_objects, object_type, t_start=None,
     ValueError
         If input object units, t_start, or t_stop do not match across trials.
     """
-    if not isinstance(neo_objects, (list, tuple)):
+    if not isinstance(neo_objects, (list, tuple, SpikeTrainList)):
         neo_objects = [neo_objects]
     try:
         units = neo_objects[0].units

requirements/requirements.txt

@@ -1,4 +1,4 @@
-neo>=0.9.0,<0.10.0
+neo>=0.10.0
 numpy>=1.18.1
 quantities>=0.12.1
 scipy<1.7.0