Exemple #1
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 def test_mean_firing_rate_typical_use_case(self):
     np.random.seed(92)
     st = homogeneous_poisson_process(rate=100 * pq.Hz, t_stop=100 * pq.s)
     rate1 = statistics.mean_firing_rate(st)
     rate2 = statistics.mean_firing_rate(st,
                                         t_start=st.t_start,
                                         t_stop=st.t_stop)
     self.assertEqual(rate1.units, rate2.units)
     self.assertAlmostEqual(rate1.item(), rate2.item())
Exemple #2
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 def test_mean_firing_rate_with_spiketrain_set_ends(self):
     st = neo.SpikeTrain(self.test_array_1d, units='ms', t_stop=10.0)
     target = pq.Quantity(2 / 0.5, '1/ms')
     res = statistics.mean_firing_rate(st,
                                       t_start=0.4 * pq.ms,
                                       t_stop=0.9 * pq.ms)
     assert_array_almost_equal(res, target, decimal=9)
Exemple #3
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def spike_statistics(idx, row):
    from elephant.statistics import mean_firing_rate, cv, isi
    from elephant.conversion import BinnedSpikeTrain
    from elephant.spike_train_correlation import corrcoef

    print(idx)
    results = {}

    # read spike trains from file
    io = get_io(row["output_file"])
    data_block = io.read()[0]
    spiketrains = data_block.segments[0].spiketrains

    # calculate mean firing rate
    results["spike_counts"] = sum(st.size for st in spiketrains)
    rates = [mean_firing_rate(st) for st in spiketrains]
    results["firing_rate"] = Quantity(rates, units=rates[0].units).rescale("1/s").mean()

    # calculate coefficient of variation of the inter-spike interval
    cvs = [cv(isi(st)) for st in spiketrains if st.size > 1]
    if len(cvs) > 0:
        results["cv_isi"] = sum(cvs)/len(cvs)
    else:
        results["cv_isi"] = 0

    # calculate global cross-correlation
    #cc_matrix = corrcoef(BinnedSpikeTrain(spiketrains, binsize=5*ms))
    #results["cc_min"] = cc_matrix.min()
    #results["cc_max"] = cc_matrix.max()
    #results["cc_mean"] = cc_matrix.mean()

    io.close()
    return results
 def compute_elephant_mean_firing_rate(self, spikes_times,
                                       **elephant_kwargs):
     """A method to compute mean (across time) rate from an input of spikes' events or spikes' times
        using the elephant.statistics.mean_firing_rate method.
        Arguments:
         - spikes: a neo.core.SpikeTrain or
                   an array of spikes' times or a dict with a key-value pair of "times" and spikes' times array
         - number_of_neurons=1: the number (integer) of neurons
         - duration: Default=None, in which case it is computed by start_time and end_time
        Returns:
         - the mean rate (float)
         - the neo.core.SpikeTrain used for the computation
     """
     from quantities import ms
     from elephant.statistics import mean_firing_rate
     t_start, t_stop = self._assert_start_end_times_from_spikes_times(
         spikes_times)
     spikes_train = self._assert_spike_train(spikes_times)
     elephant_kwargs["t_start"] = elephant_kwargs.get(
         "t_start", t_start - self._fmin_resolution) * ms
     elephant_kwargs["t_stop"] = elephant_kwargs.get(
         "t_stop", t_stop + self._fmin_resolution) * ms
     if len(spikes_train):
         return mean_firing_rate(spikes_train,
                                 **elephant_kwargs), spikes_train
     else:
         return 0.0, spikes_train
Exemple #5
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 def generate_prediction(self, model, **kwargs):
     rates = self.get_prediction(model)
     if rates is None:
         if kwargs:
             self.params.update(kwargs)
         spiketrains = model.produce_spiketrains(**self.params)
         rates = [mean_firing_rate(st).rescale('Hz') for st in spiketrains]
         self.set_prediction(model, rates)
     return rates
Exemple #6
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 def test_mean_firing_rate_with_plain_array_2d_1_set_ends(self):
     st = self.test_array_2d
     target = np.array([4, 1, 3]) / (1.23 - 0.14)
     res = statistics.mean_firing_rate(st,
                                       axis=1,
                                       t_start=0.14,
                                       t_stop=1.23)
     assert not isinstance(res, pq.Quantity)
     assert_array_almost_equal(res, target, decimal=9)
Exemple #7
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def spikes_to_rate( spikes,t_start,t_stop, windows=0.0):
    """
    #WARNING function unused but keep it for idea
    Compute the rate of one spike train or multiple of spike trains

    #TODO : need to have add the overlapping of windows
    :param spikes: one spike train or multiple spike train
    :param t_start: time to start to compute rate
    :param t_stop: time to stop to compute rate
    :param windows: the window for compute rate
    # :param overlaps: FUTURE overlap of window
    :return: rates or variation of rates
    """

    if windows == 0.0:
        #case without variation of rate
        if len(spikes[0].shape) ==0:
            # with only one rate
            result = [mean_firing_rate(spiketrain=spikes,t_start=t_start,t_stop=t_stop).rescale(Hz)]
        else:
            # with multiple rate
            result = []
            for spike in spikes:
                result.append(mean_firing_rate(spiketrain=spike,t_start=t_start,t_stop=t_stop).rescale(Hz))
        return np.array(result)
    else:
        # case with variation of rate
        rate = []
        for time in np.arange(t_start,t_stop,windows):
            t_start_window = time*t_start.units
            t_stop_window = t_start_window+windows
            if len(spikes[0].shape) == 0:
                # for only one spike train
                result = [mean_firing_rate(spiketrain=spikes, t_start=t_start_window, t_stop=t_stop_window).rescale(Hz)]
            else:
                # for multiple spike train
                result = []
                for spike in spikes:
                    result.append(mean_firing_rate(spiketrain=spike, t_start=t_start_window, t_stop=t_stop_window).rescale(Hz))
            rate.append(result)
        return np.array(rate)
Exemple #8
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def calculate_neuron_mfr_elephant(col, num_mins_per_bin, total_time):
    num_bins = np.int(total_time / num_mins_per_bin)
    col_bins = np.array_split(col, num_bins)
    mfrs = pd.Series(np.zeros(num_bins))

    for ind, col_bin in enumerate(col_bins):
        spike_times = pd.to_numeric(col_bin[col_bin.notnull()].index.values)
        try:
            spike_train = SpikeTrain(times=spike_times,
                                     t_stop=spike_times[-1],
                                     units=ns)
            mfr = mean_firing_rate(spike_train)
        except IndexError:
            mfr = np.nan
        mfrs[ind] = mfr
    mfrs *= 10**10
    return mfrs
Exemple #9
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def compute_spontan_rate(chxs, stim_off_epoch):
    # TODO: test
    '''
    Calculates spontaneous firing rate
    Parameters
    ----------
    chxs : list
        list of neo.core.ChannelIndex
    stim_off_epoch : neo.core.Epoch
        stimulus epoch
    Returns
    -------
    out : defaultdict(dict)
        rates[channel_index_name][unit_id] = spontaneous rate
    '''
    from collections import defaultdict
    from elephant.statistics import mean_firing_rate

    rates = defaultdict(dict)
    unit_rates = pq.Hz

    for chx in chxs:
        for un in chx.units:
            cluster_group = un.annotations.get('cluster_group') or 'noise'
            if cluster_group.lower() != "noise":
                sptr = un.spiketrains[0]
                unit_id = un.annotations["cluster_id"]
                trials = make_spiketrain_trials(
                    epoch=stim_off_epoch,
                    t_start=0 * pq.s,
                    t_stop=stim_off_epoch.durations,
                    spike_train=sptr)
                rate = 0 * unit_rates
                for trial in trials:
                    rate += mean_firing_rate(trial, trial.t_start,
                                             trial.t_stop)

                rates[chx.name][unit_id] = rate / len(trials)

    return rates
Exemple #10
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def compute_orientation_tuning(orient_trials):
    from exana.stimulus.tools import (make_orientation_trials,
                                      _convert_string_to_quantity_scalar)
    '''
    Calculates the mean firing rate for each orientation
    Parameters
    ----------
    trials : collections.OrderedDict
        OrderedDict with orients as keys and trials as values.
    Returns
    -------
    rates : quantity array
        average rates
    orients : quantity array
        sorted stimulus orientations
    '''
    from elephant.statistics import mean_firing_rate

    unit_orients = pq.deg
    unit_rates = pq.Hz
    orient_count = len(orient_trials)

    rates = np.zeros((orient_count)) * unit_rates
    orients = np.zeros((orient_count)) * unit_orients

    for i, (orient, trials) in enumerate(orient_trials.items()):
        orient = _convert_string_to_quantity_scalar(orient)
        rate = 0 * unit_rates

        for trial in trials:
            rate += mean_firing_rate(trial, trial.t_start, trial.t_stop)

        rates[i] = rate / len(trials)
        orients[i] = orient.rescale(unit_orients)

    return rates, orients
Exemple #11
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 def test_mean_firing_rate_with_plain_array_2d_None(self):
     st = self.test_array_2d
     target = self.targ_array_2d_None/self.max_array_2d_None
     res = es.mean_firing_rate(st, axis=None)
     assert not isinstance(res, pq.Quantity)
     assert_array_almost_equal(res, target, decimal=9)
Exemple #12
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 def test_mean_firing_rate_with_plain_array_2d_1_set_ends(self):
     st = self.test_array_2d
     target = np.array([4, 1, 3])/(1.23-0.14)
     res = es.mean_firing_rate(st, axis=1, t_start=0.14, t_stop=1.23)
     assert not isinstance(res, pq.Quantity)
     assert_array_almost_equal(res, target, decimal=9)
Exemple #13
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 def test_mean_firing_rate_with_plain_array_3d_2(self):
     st = self.test_array_3d
     target = np.sum(self.test_array_3d, 2)/5.
     res = es.mean_firing_rate(st, axis=2, t_stop=5.)
     assert not isinstance(res, pq.Quantity)
     assert_array_almost_equal(res, target, decimal=9)
Exemple #14
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 def test_mean_firing_rate_with_plain_array_1d_set_ends(self):
     st = self.test_array_1d
     target = self.targ_array_1d/(1.23-0.3)
     res = es.mean_firing_rate(st, t_start=0.3, t_stop=1.23)
     assert not isinstance(res, pq.Quantity)
     assert_array_almost_equal(res, target, decimal=9)
 def statistic_mean_firing_rates(self, spiketrain, t_start=None,
                                 t_stop=None, axis=None):
     mean_firing_rate(spiketrain, t_start, t_stop, axis)
Exemple #16
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 def test_mean_firing_rate_with_plain_array_3d_2(self):
     st = self.test_array_3d
     target = np.sum(self.test_array_3d, 2)/5.
     res = es.mean_firing_rate(st, axis=2, t_stop=5.)
     assert not isinstance(res, pq.Quantity)
     assert_array_almost_equal(res, target, decimal=9)
Exemple #17
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 def test_mean_firing_rate_with_quantities_1d_set_ends(self):
     st = pq.Quantity(self.test_array_1d, units='ms')
     target = pq.Quantity(2/0.6, '1/ms')
     res = es.mean_firing_rate(st, t_start=400*pq.us, t_stop=1.)
     assert_array_almost_equal(res, target, decimal=9)
Exemple #18
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 def test_mean_firing_rate_with_spiketrain(self):
     st = neo.SpikeTrain(self.test_array_1d, units='ms', t_stop=10.0)
     target = pq.Quantity(self.targ_array_1d/10., '1/ms')
     res = es.mean_firing_rate(st)
     assert_array_almost_equal(res, target, decimal=9)
Exemple #19
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 def test_mean_firing_rate_with_plain_array_2d_default(self):
     st = self.test_array_2d
     target = self.targ_array_2d_default / self.max_array_2d_default
     res = statistics.mean_firing_rate(st)
     assert not isinstance(res, pq.Quantity)
     assert_array_almost_equal(res, target, decimal=9)
Exemple #20
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 def test_mean_firing_rate_with_spiketrain(self):
     st = neo.SpikeTrain(self.test_array_1d, units='ms', t_stop=10.0)
     target = pq.Quantity(self.targ_array_1d/10., '1/ms')
     res = es.mean_firing_rate(st)
     assert_array_almost_equal(res, target, decimal=9)
Exemple #21
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 def test_mean_firing_rate_with_spiketrain_set_ends(self):
     st = neo.SpikeTrain(self.test_array_1d, units='ms', t_stop=10.0)
     target = pq.Quantity(2/0.5, '1/ms')
     res = es.mean_firing_rate(st, t_start=0.4, t_stop=0.9)
     assert_array_almost_equal(res, target, decimal=9)
Exemple #22
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 def test_mean_firing_rate_with_quantities_1d(self):
     st = pq.Quantity(self.test_array_1d, units='ms')
     target = pq.Quantity(self.targ_array_1d/self.max_array_1d, '1/ms')
     res = es.mean_firing_rate(st)
     assert_array_almost_equal(res, target, decimal=9)
Exemple #23
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 def test_mean_firing_rate_with_quantities_1d(self):
     st = pq.Quantity(self.test_array_1d, units='ms')
     target = pq.Quantity(self.targ_array_1d/self.max_array_1d, '1/ms')
     res = es.mean_firing_rate(st)
     assert_array_almost_equal(res, target, decimal=9)
Exemple #24
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 def test_mean_firing_rate_with_plain_array_1d_set_ends(self):
     st = self.test_array_1d
     target = self.targ_array_1d/(1.23-0.3)
     res = es.mean_firing_rate(st, t_start=0.3, t_stop=1.23)
     assert not isinstance(res, pq.Quantity)
     assert_array_almost_equal(res, target, decimal=9)
Exemple #25
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 def test_mean_firing_rate_with_quantities_1d_set_ends(self):
     st = pq.Quantity(self.test_array_1d, units='ms')
     target = pq.Quantity(2/0.6, '1/ms')
     res = es.mean_firing_rate(st, t_start=400*pq.us, t_stop=1.)
     assert_array_almost_equal(res, target, decimal=9)
Exemple #26
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 def test_mean_firing_rate_with_plain_array_2d_None(self):
     st = self.test_array_2d
     target = self.targ_array_2d_None/self.max_array_2d_None
     res = es.mean_firing_rate(st, axis=None)
     assert not isinstance(res, pq.Quantity)
     assert_array_almost_equal(res, target, decimal=9)
Exemple #27
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plt.show()

os.chdir('Analysis/Noise_spike_rasters')
#plt.savefig('Noise_raster_'+file_name+'.png', bbox_inches='tight')
#plt.close()
os.chdir('../..')
print 'Spike raster for ' + file_name + 'saved'

#%%
#doing FI curve
#finding mean firing rate for entire sweep
from elephant.statistics import mean_firing_rate
firing_rate_list = []
for spiketrain in neospiketrain_list:
    temp_firing_rate = mean_firing_rate(spiketrain.rescale(pq.s),
                                        t_start=0.5,
                                        t_stop=1.5)
    firing_rate_list.append(np.asarray(temp_firing_rate))

# %% conversion of discrete spike times to binary counts
from elephant.conversion import BinnedSpikeTrain
bst_list = BinnedSpikeTrain(del_half_neospiketrain_list,
                            binsize=1.0 * pq.ms,
                            t_start=700.0 * pq.ms,
                            t_stop=3200.0 * pq.ms)

bst_arr = bst_list.to_array()  # export binned spike times to an array
bst_df = pd.DataFrame(bst_arr).T  # turn into a df and transpose (.T)
bst_sum = bst_df.apply(np.sum, axis=1)  # sum by row across columns

# plt.figure()