diff options
author | Mario Mulansky <mario.mulansky@gmx.net> | 2016-03-29 12:40:04 +0200 |
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committer | Mario Mulansky <mario.mulansky@gmx.net> | 2016-03-29 12:40:04 +0200 |
commit | 9cf75c9f72a5bea6ed636d9624eff951a473dcde (patch) | |
tree | 5b288389f8794e94de7c76d89482329f88dc6305 /pyspike | |
parent | ad29154d8c152996d16c012dcc5798c5f1957aed (diff) | |
parent | d9e2125dcc76693056ab04264add29227f398f4f (diff) |
Merge branch 'develop' into new_directionality
Diffstat (limited to 'pyspike')
-rw-r--r-- | pyspike/DiscreteFunc.py | 9 | ||||
-rw-r--r-- | pyspike/__init__.py | 4 | ||||
-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 | 41 |
7 files changed, 82 insertions, 53 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 7f578b0..25e13eb 100644 --- a/pyspike/__init__.py +++ b/pyspike/__init__.py @@ -24,8 +24,8 @@ from .spike_sync import spike_sync_profile, spike_sync,\ filter_by_spike_sync from .psth import psth -from .spikes import load_spike_trains_from_txt, spike_train_from_string, \ - merge_spike_trains, generate_poisson_spikes +from .spikes import load_spike_trains_from_txt, save_spike_trains_to_txt, \ + spike_train_from_string, merge_spike_trains, generate_poisson_spikes from .spike_directionality import spike_directionality, \ spike_directionality_profiles, spike_directionality_matrix, \ 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 f50700f..d4070ae 100644 --- a/pyspike/cython/cython_distances.pyx +++ b/pyspike/cython/cython_distances.pyx @@ -628,9 +628,4 @@ 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 11fbe62..a4a0c9e 100644 --- a/pyspike/cython/python_backend.py +++ b/pyspike/cython/python_backend.py @@ -591,7 +591,9 @@ 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 @@ -612,20 +614,21 @@ 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 37590b4..28e252c 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..ab6d4c4 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, @@ -47,17 +48,41 @@ 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 ############################################################ +# 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 ############################################################ def merge_spike_trains(spike_trains): |