diff options
Diffstat (limited to 'pyspike')
| -rw-r--r-- | pyspike/DiscreteFunc.py | 9 | ||||
| -rw-r--r-- | pyspike/__init__.py | 3 | ||||
| -rw-r--r-- | pyspike/cython/cython_add.pyx | 33 | ||||
| -rw-r--r-- | pyspike/cython/cython_distances.pyx | 5 | ||||
| -rw-r--r-- | pyspike/cython/python_backend.py | 33 | ||||
| -rw-r--r-- | pyspike/spike_sync.py | 10 | ||||
| -rw-r--r-- | pyspike/spikes.py | 66 |
7 files changed, 107 insertions, 52 deletions
diff --git a/pyspike/DiscreteFunc.py b/pyspike/DiscreteFunc.py index fe97bc2..caad290 100644 --- a/pyspike/DiscreteFunc.py +++ b/pyspike/DiscreteFunc.py @@ -170,10 +170,6 @@ expected." start_ind, end_ind = get_indices(ival) value += np.sum(self.y[start_ind:end_ind]) multiplicity += np.sum(self.mp[start_ind:end_ind]) - if multiplicity == 0.0: - # empty profile, return spike sync of 1 - value = 1.0 - multiplicity = 1.0 return (value, multiplicity) def avrg(self, interval=None, normalize=True): @@ -190,7 +186,10 @@ expected." """ val, mp = self.integral(interval) if normalize: - return val/mp + if mp > 0: + return val/mp + else: + return 1.0 else: return val diff --git a/pyspike/__init__.py b/pyspike/__init__.py index 069090b..08253fb 100644 --- a/pyspike/__init__.py +++ b/pyspike/__init__.py @@ -23,7 +23,8 @@ from .spike_sync import spike_sync_profile, spike_sync,\ spike_sync_profile_multi, spike_sync_multi, spike_sync_matrix from .psth import psth -from .spikes import load_spike_trains_from_txt, spike_train_from_string, \ +from .spikes import load_spike_trains_from_txt, save_spike_trains_to_txt, \ + spike_train_from_string, import_spike_trains_from_time_series, \ merge_spike_trains, generate_poisson_spikes # define the __version__ following diff --git a/pyspike/cython/cython_add.pyx b/pyspike/cython/cython_add.pyx index 8da1e53..25f1181 100644 --- a/pyspike/cython/cython_add.pyx +++ b/pyspike/cython/cython_add.pyx @@ -182,8 +182,8 @@ def add_discrete_function_cython(double[:] x1, double[:] y1, double[:] mp1, cdef int index1 = 0 cdef int index2 = 0 cdef int index = 0 - cdef int N1 = len(y1) - cdef int N2 = len(y2) + cdef int N1 = len(y1)-1 + cdef int N2 = len(y2)-1 x_new[0] = x1[0] while (index1+1 < N1) and (index2+1 < N2): if x1[index1+1] < x2[index2+1]: @@ -206,20 +206,21 @@ def add_discrete_function_cython(double[:] x1, double[:] y1, double[:] mp1, y_new[index] = y1[index1] + y2[index2] mp_new[index] = mp1[index1] + mp2[index2] # one array reached the end -> copy the contents of the other to the end - if index1+1 < len(y1): - x_new[index+1:index+1+len(x1)-index1-1] = x1[index1+1:] - y_new[index+1:index+1+len(x1)-index1-1] = y1[index1+1:] - mp_new[index+1:index+1+len(x1)-index1-1] = mp1[index1+1:] - index += len(x1)-index1-1 - elif index2+1 < len(y2): - x_new[index+1:index+1+len(x2)-index2-1] = x2[index2+1:] - y_new[index+1:index+1+len(x2)-index2-1] = y2[index2+1:] - mp_new[index+1:index+1+len(x2)-index2-1] = mp2[index2+1:] - index += len(x2)-index2-1 - # else: # both arrays reached the end simultaneously - # x_new[index+1] = x1[-1] - # y_new[index+1] = y1[-1] + y2[-1] - # mp_new[index+1] = mp1[-1] + mp2[-1] + if index1+1 < N1: + x_new[index+1:index+1+N1-index1] = x1[index1+1:] + y_new[index+1:index+1+N1-index1] = y1[index1+1:] + mp_new[index+1:index+1+N1-index1] = mp1[index1+1:] + index += N1-index1 + elif index2+1 < N2: + x_new[index+1:index+1+N2-index2] = x2[index2+1:] + y_new[index+1:index+1+N2-index2] = y2[index2+1:] + mp_new[index+1:index+1+N2-index2] = mp2[index2+1:] + index += N2-index2 + else: # both arrays reached the end simultaneously + x_new[index+1] = x1[index1+1] + y_new[index+1] = y1[index1+1] + y2[index2+1] + mp_new[index+1] = mp1[index1+1] + mp2[index2+1] + index += 1 y_new[0] = y_new[1] mp_new[0] = mp_new[1] diff --git a/pyspike/cython/cython_distances.pyx b/pyspike/cython/cython_distances.pyx index 7dc9cb9..ac5f226 100644 --- a/pyspike/cython/cython_distances.pyx +++ b/pyspike/cython/cython_distances.pyx @@ -428,9 +428,4 @@ def coincidence_value_cython(double[:] spikes1, double[:] spikes2, mp += 2 coinc += 2 - if coinc == 0 and mp == 0: - # empty spike trains -> spike sync = 1 by definition - coinc = 1 - mp = 1 - return coinc, mp diff --git a/pyspike/cython/python_backend.py b/pyspike/cython/python_backend.py index a1e3a65..6b7209a 100644 --- a/pyspike/cython/python_backend.py +++ b/pyspike/cython/python_backend.py @@ -560,7 +560,9 @@ def add_discrete_function_python(x1, y1, mp1, x2, y2, mp2): index1 = 0 index2 = 0 index = 0 - while (index1+1 < len(y1)) and (index2+1 < len(y2)): + N1 = len(x1)-1 + N2 = len(x2)-1 + while (index1+1 < N1) and (index2+1 < N2): if x1[index1+1] < x2[index2+1]: index1 += 1 index += 1 @@ -581,20 +583,21 @@ def add_discrete_function_python(x1, y1, mp1, x2, y2, mp2): y_new[index] = y1[index1] + y2[index2] mp_new[index] = mp1[index1] + mp2[index2] # one array reached the end -> copy the contents of the other to the end - if index1+1 < len(y1): - x_new[index+1:index+1+len(x1)-index1-1] = x1[index1+1:] - y_new[index+1:index+1+len(x1)-index1-1] = y1[index1+1:] - mp_new[index+1:index+1+len(x1)-index1-1] = mp1[index1+1:] - index += len(x1)-index1-1 - elif index2+1 < len(y2): - x_new[index+1:index+1+len(x2)-index2-1] = x2[index2+1:] - y_new[index+1:index+1+len(x2)-index2-1] = y2[index2+1:] - mp_new[index+1:index+1+len(x2)-index2-1] = mp2[index2+1:] - index += len(x2)-index2-1 - # else: # both arrays reached the end simultaneously - # x_new[index+1] = x1[-1] - # y_new[index+1] = y1[-1] + y2[-1] - # mp_new[index+1] = mp1[-1] + mp2[-1] + if index1+1 < N1: + x_new[index+1:index+1+N1-index1] = x1[index1+1:] + y_new[index+1:index+1+N1-index1] = y1[index1+1:] + mp_new[index+1:index+1+N1-index1] = mp1[index1+1:] + index += N1-index1 + elif index2+1 < N2: + x_new[index+1:index+1+N2-index2] = x2[index2+1:] + y_new[index+1:index+1+N2-index2] = y2[index2+1:] + mp_new[index+1:index+1+N2-index2] = mp2[index2+1:] + index += N2-index2 + else: # both arrays reached the end simultaneously + x_new[index+1] = x1[-1] + y_new[index+1] = y1[-1] + y2[-1] + mp_new[index+1] = mp1[-1] + mp2[-1] + index += 1 y_new[0] = y_new[1] mp_new[0] = mp_new[1] diff --git a/pyspike/spike_sync.py b/pyspike/spike_sync.py index 617dd86..80f7805 100644 --- a/pyspike/spike_sync.py +++ b/pyspike/spike_sync.py @@ -215,7 +215,10 @@ def spike_sync_bi(spike_train1, spike_train2, interval=None, max_tau=None): """ c, mp = _spike_sync_values(spike_train1, spike_train2, interval, max_tau) - return 1.0*c/mp + if mp == 0: + return 1.0 + else: + return 1.0*c/mp ############################################################ @@ -257,7 +260,10 @@ def spike_sync_multi(spike_trains, indices=None, interval=None, max_tau=None): coincidence += c mp += m - return coincidence/mp + if mp == 0.0: + return 1.0 + else: + return coincidence/mp ############################################################ diff --git a/pyspike/spikes.py b/pyspike/spikes.py index b18d7eb..486a4a0 100644 --- a/pyspike/spikes.py +++ b/pyspike/spikes.py @@ -2,6 +2,7 @@ # Copyright 2014, Mario Mulansky <mario.mulansky@gmx.net> # Distributed under the BSD License + import numpy as np from pyspike import SpikeTrain @@ -25,7 +26,7 @@ def spike_train_from_string(s, edges, sep=' ', is_sorted=False): ############################################################ -# load_spike_trains_txt +# load_spike_trains_from_txt ############################################################ def load_spike_trains_from_txt(file_name, edges, separator=' ', comment='#', is_sorted=False, @@ -47,16 +48,65 @@ def load_spike_trains_from_txt(file_name, edges, :returns: list of :class:`.SpikeTrain` """ spike_trains = [] - spike_file = open(file_name, 'r') - for line in spike_file: - if len(line) > 1 and not line.startswith(comment): - # use only the lines with actual data and not commented - spike_train = spike_train_from_string(line, edges, - separator, is_sorted) - spike_trains.append(spike_train) + with open(file_name, 'r') as spike_file: + for line in spike_file: + if not line.startswith(comment): # ignore comments + if len(line) > 1: + # ignore empty lines + spike_train = spike_train_from_string(line, edges, + separator, is_sorted) + spike_trains.append(spike_train) + elif not(ignore_empty_lines): + # add empty spike train + spike_trains.append(SpikeTrain([], edges)) return spike_trains +def import_spike_trains_from_time_series(file_name, start_time, time_bin, + separator=None, comment='#'): + """ Imports spike trains from time series consisting of 0 and 1 denoting + the absence or presence of a spike. Each line in the data file represents + one spike train. + + :param file_name: The name of the data file containing the time series. + :param edges: A pair (T_start, T_end) of values representing the + start and end time of the spike train measurement + or a single value representing the end time, the + T_start is then assuemd as 0. + :param separator: The character used to seprate the values in the text file + :param comment: Lines starting with this character are ignored. + + """ + data = np.loadtxt(file_name, comments=comment, delimiter=separator) + time_points = start_time + time_bin + np.arange(len(data[0, :]))*time_bin + spike_trains = [] + for time_series in data: + spike_trains.append(SpikeTrain(time_points[time_series > 0], + edges=[start_time, + time_points[-1]])) + return spike_trains + + +############################################################ +# save_spike_trains_to_txt +############################################################ +def save_spike_trains_to_txt(spike_trains, file_name, + separator=' ', precision=8): + """ Saves the given spike trains into a file with the given file name. + Each spike train will be stored in one line in the text file with the times + separated by `separator`. + + :param spike_trains: List of :class:`.SpikeTrain` objects + :param file_name: The name of the text file. + """ + # format string to print the spike times with given precision + format_str = "{0:.%de}" % precision + with open(file_name, 'w') as spike_file: + for st in spike_trains: + s = separator.join(map(format_str.format, st.spikes)) + spike_file.write(s+'\n') + + ############################################################ # merge_spike_trains ############################################################ |