diff options
Diffstat (limited to 'pyspike')
| -rw-r--r-- | pyspike/DiscreteFunc.py | 4 | ||||
| -rw-r--r-- | pyspike/PieceWiseConstFunc.py | 7 | ||||
| -rw-r--r-- | pyspike/PieceWiseLinFunc.py | 9 | ||||
| -rw-r--r-- | pyspike/SpikeTrain.py | 15 | ||||
| -rw-r--r-- | pyspike/__init__.py | 2 | ||||
| -rw-r--r-- | pyspike/isi_distance.py | 6 | ||||
| -rw-r--r-- | pyspike/spike_distance.py | 7 | ||||
| -rw-r--r-- | pyspike/spike_sync.py | 4 | ||||
| -rw-r--r-- | pyspike/spikes.py | 3 |
9 files changed, 45 insertions, 12 deletions
diff --git a/pyspike/DiscreteFunc.py b/pyspike/DiscreteFunc.py index 17153ee..a8c054e 100644 --- a/pyspike/DiscreteFunc.py +++ b/pyspike/DiscreteFunc.py @@ -6,6 +6,7 @@ from __future__ import print_function import numpy as np import collections +import pyspike ############################################################## @@ -202,7 +203,8 @@ class DiscreteFunc(object): from cython.cython_add import add_discrete_function_cython as \ add_discrete_function_impl except ImportError: - print("Warning: add_discrete_function_cython not found. Make \ + if not(pyspike.disable_backend_warning): + print("Warning: add_discrete_function_cython not found. Make \ sure that PySpike is installed by running\n\ 'python setup.py build_ext --inplace'! \ \n Falling back to slow python backend.") diff --git a/pyspike/PieceWiseConstFunc.py b/pyspike/PieceWiseConstFunc.py index 2705443..23ff536 100644 --- a/pyspike/PieceWiseConstFunc.py +++ b/pyspike/PieceWiseConstFunc.py @@ -6,6 +6,7 @@ from __future__ import print_function import numpy as np import collections +import pyspike ############################################################## @@ -191,8 +192,10 @@ class PieceWiseConstFunc(object): from cython.cython_add import add_piece_wise_const_cython as \ add_piece_wise_const_impl except ImportError: - print("Warning: add_piece_wise_const_cython not found. Make sure \ -that PySpike is installed by running\n 'python setup.py build_ext --inplace'! \ + if not(pyspike.disable_backend_warning): + print("Warning: add_piece_wise_const_cython not found. Make \ +sure that PySpike is installed by running\n \ +'python setup.py build_ext --inplace'! \ \n Falling back to slow python backend.") # use python backend from cython.python_backend import add_piece_wise_const_python as \ diff --git a/pyspike/PieceWiseLinFunc.py b/pyspike/PieceWiseLinFunc.py index c0dd475..0d51c76 100644 --- a/pyspike/PieceWiseLinFunc.py +++ b/pyspike/PieceWiseLinFunc.py @@ -6,6 +6,7 @@ from __future__ import print_function import numpy as np import collections +import pyspike ############################################################## @@ -230,9 +231,11 @@ class PieceWiseLinFunc: from cython.cython_add import add_piece_wise_lin_cython as \ add_piece_wise_lin_impl except ImportError: - print("Warning: add_piece_wise_lin_cython not found. Make sure \ -that PySpike is installed by running\n 'python setup.py build_ext --inplace'! \ -\n Falling back to slow python backend.") + if not(pyspike.disable_backend_warning): + print("Warning: add_piece_wise_lin_cython not found. Make \ +sure that PySpike is installed by running\n \ +'python setup.py build_ext --inplace'! \n \ +Falling back to slow python backend.") # use python backend from cython.python_backend import add_piece_wise_lin_python as \ add_piece_wise_lin_impl diff --git a/pyspike/SpikeTrain.py b/pyspike/SpikeTrain.py index 9127b60..4b59a5d 100644 --- a/pyspike/SpikeTrain.py +++ b/pyspike/SpikeTrain.py @@ -32,6 +32,21 @@ class SpikeTrain(object): self.t_start = 0.0 self.t_end = float(edges) + def __getitem__(self, index): + """ Returns the time of the spike given by index. + + :param index: Index of the spike. + :return: spike time. + """ + return self.spikes[index] + + def __len__(self): + """ Returns the number of spikes. + + :return: Number of spikes. + """ + return len(self.spikes) + def sort(self): """ Sorts the spike times of this spike train using `np.sort` """ diff --git a/pyspike/__init__.py b/pyspike/__init__.py index 3e836bd..2060f73 100644 --- a/pyspike/__init__.py +++ b/pyspike/__init__.py @@ -42,3 +42,5 @@ except DistributionNotFound: __version__ = 'Please install this project with setup.py' else: __version__ = _dist.version + +disable_backend_warning = False diff --git a/pyspike/isi_distance.py b/pyspike/isi_distance.py index 5ea555d..e50f203 100644 --- a/pyspike/isi_distance.py +++ b/pyspike/isi_distance.py @@ -2,6 +2,7 @@ # Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net> # Distributed under the BSD License +import pyspike from pyspike import PieceWiseConstFunc from pyspike.generic import _generic_profile_multi, _generic_distance_multi, \ _generic_distance_matrix @@ -34,8 +35,9 @@ def isi_profile(spike_train1, spike_train2): from cython.cython_profiles import isi_profile_cython \ as isi_profile_impl except ImportError: - print("Warning: isi_distance_cython not found. Make sure that PySpike \ -is installed by running\n 'python setup.py build_ext --inplace'!\n \ + if not(pyspike.disable_backend_warning): + print("Warning: isi_profile_cython not found. Make sure that \ +PySpike is installed by running\n 'python setup.py build_ext --inplace'!\n \ Falling back to slow python backend.") # use python backend from cython.python_backend import isi_distance_python \ diff --git a/pyspike/spike_distance.py b/pyspike/spike_distance.py index ac2d260..feea0c1 100644 --- a/pyspike/spike_distance.py +++ b/pyspike/spike_distance.py @@ -2,6 +2,7 @@ # Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net> # Distributed under the BSD License +import pyspike from pyspike import PieceWiseLinFunc from pyspike.generic import _generic_profile_multi, _generic_distance_multi, \ _generic_distance_matrix @@ -34,7 +35,8 @@ def spike_profile(spike_train1, spike_train2): from cython.cython_profiles import spike_profile_cython \ as spike_profile_impl except ImportError: - print("Warning: spike_profile_cython not found. Make sure that \ + if not(pyspike.disable_backend_warning): + print("Warning: spike_profile_cython not found. Make sure that \ PySpike is installed by running\n 'python setup.py build_ext --inplace'!\n \ Falling back to slow python backend.") # use python backend @@ -54,7 +56,8 @@ Falling back to slow python backend.") ############################################################ def spike_distance(spike_train1, spike_train2, interval=None): """ Computes the spike-distance :math:`D_S` of the given spike trains. The - spike-distance is the integral over the isi distance profile :math:`S(t)`: + spike-distance is the integral over the spike distance profile + :math:`S(t)`: .. math:: D_S = \int_{T_0}^{T_1} S(t) dt. diff --git a/pyspike/spike_sync.py b/pyspike/spike_sync.py index 40d98d2..10ebdc7 100644 --- a/pyspike/spike_sync.py +++ b/pyspike/spike_sync.py @@ -5,6 +5,7 @@ import numpy as np from functools import partial +import pyspike from pyspike import DiscreteFunc from pyspike.generic import _generic_profile_multi, _generic_distance_matrix @@ -39,7 +40,8 @@ def spike_sync_profile(spike_train1, spike_train2, max_tau=None): from cython.cython_profiles import coincidence_profile_cython \ as coincidence_profile_impl except ImportError: - print("Warning: spike_distance_cython not found. Make sure that \ + if not(pyspike.disable_backend_warning): + print("Warning: spike_distance_cython not found. Make sure that \ PySpike is installed by running\n 'python setup.py build_ext --inplace'!\n \ Falling back to slow python backend.") # use python backend diff --git a/pyspike/spikes.py b/pyspike/spikes.py index 35d8533..b18d7eb 100644 --- a/pyspike/spikes.py +++ b/pyspike/spikes.py @@ -28,7 +28,8 @@ def spike_train_from_string(s, edges, sep=' ', is_sorted=False): # load_spike_trains_txt ############################################################ def load_spike_trains_from_txt(file_name, edges, - separator=' ', comment='#', is_sorted=False): + separator=' ', comment='#', is_sorted=False, + ignore_empty_lines=True): """ Loads a number of spike trains from a text file. Each line of the text file should contain one spike train as a sequence of spike times separated by `separator`. Empty lines as well as lines starting with `comment` are |