diff options
Diffstat (limited to 'pyspike')
-rw-r--r-- | pyspike/DiscreteFunc.py | 10 | ||||
-rw-r--r-- | pyspike/PieceWiseConstFunc.py | 6 | ||||
-rw-r--r-- | pyspike/PieceWiseLinFunc.py | 8 | ||||
-rw-r--r-- | pyspike/__init__.py | 22 | ||||
-rw-r--r-- | pyspike/directionality/__init__.py | 4 | ||||
-rw-r--r-- | pyspike/directionality/spike_train_order.py | 16 | ||||
-rw-r--r-- | pyspike/generic.py | 9 | ||||
-rw-r--r-- | pyspike/isi_distance.py | 8 | ||||
-rw-r--r-- | pyspike/psth.py | 2 | ||||
-rw-r--r-- | pyspike/spike_distance.py | 8 | ||||
-rw-r--r-- | pyspike/spike_sync.py | 8 |
11 files changed, 57 insertions, 44 deletions
diff --git a/pyspike/DiscreteFunc.py b/pyspike/DiscreteFunc.py index 9cc7bd5..fe97bc2 100644 --- a/pyspike/DiscreteFunc.py +++ b/pyspike/DiscreteFunc.py @@ -2,7 +2,7 @@ # Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net> # Distributed under the BSD License -from __future__ import print_function +from __future__ import absolute_import, print_function import numpy as np import collections @@ -80,7 +80,7 @@ class DiscreteFunc(object): expected_mp = (averaging_window_size+1) * int(self.mp[0]) y_plot = np.zeros_like(self.y) # compute the values in a loop, could be done in cython if required - for i in xrange(len(y_plot)): + for i in range(len(y_plot)): if self.mp[i] >= expected_mp: # the current value contains already all the wanted @@ -206,7 +206,7 @@ expected." # cython version try: - from cython.cython_add import add_discrete_function_cython as \ + from .cython.cython_add import add_discrete_function_cython as \ add_discrete_function_impl except ImportError: if not(pyspike.disable_backend_warning): @@ -215,7 +215,7 @@ 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_discrete_function_python as \ + from .cython.python_backend import add_discrete_function_python as \ add_discrete_function_impl self.x, self.y, self.mp = \ @@ -244,7 +244,7 @@ def average_profile(profiles): assert len(profiles) > 1 avrg_profile = profiles[0].copy() - for i in xrange(1, len(profiles)): + for i in range(1, len(profiles)): avrg_profile.add(profiles[i]) avrg_profile.mul_scalar(1.0/len(profiles)) # normalize diff --git a/pyspike/PieceWiseConstFunc.py b/pyspike/PieceWiseConstFunc.py index 23ff536..5ce5f27 100644 --- a/pyspike/PieceWiseConstFunc.py +++ b/pyspike/PieceWiseConstFunc.py @@ -2,7 +2,7 @@ # Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net> # Distributed under the BSD License -from __future__ import print_function +from __future__ import absolute_import, print_function import numpy as np import collections @@ -189,7 +189,7 @@ class PieceWiseConstFunc(object): # cython version try: - from cython.cython_add import add_piece_wise_const_cython as \ + from .cython.cython_add import add_piece_wise_const_cython as \ add_piece_wise_const_impl except ImportError: if not(pyspike.disable_backend_warning): @@ -198,7 +198,7 @@ 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 \ + from .cython.python_backend import add_piece_wise_const_python as \ add_piece_wise_const_impl self.x, self.y = add_piece_wise_const_impl(self.x, self.y, f.x, f.y) diff --git a/pyspike/PieceWiseLinFunc.py b/pyspike/PieceWiseLinFunc.py index 0d51c76..8145e63 100644 --- a/pyspike/PieceWiseLinFunc.py +++ b/pyspike/PieceWiseLinFunc.py @@ -2,7 +2,7 @@ # Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net> # Distributed under the BSD License -from __future__ import print_function +from __future__ import absolute_import, print_function import numpy as np import collections @@ -222,13 +222,13 @@ class PieceWiseLinFunc: assert self.x[-1] == f.x[-1], "The functions have different intervals" # python implementation - # from python_backend import add_piece_wise_lin_python + # from .python_backend import add_piece_wise_lin_python # self.x, self.y1, self.y2 = add_piece_wise_lin_python( # self.x, self.y1, self.y2, f.x, f.y1, f.y2) # cython version try: - from cython.cython_add import add_piece_wise_lin_cython as \ + from .cython.cython_add import add_piece_wise_lin_cython as \ add_piece_wise_lin_impl except ImportError: if not(pyspike.disable_backend_warning): @@ -237,7 +237,7 @@ 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 \ + from .cython.python_backend import add_piece_wise_lin_python as \ add_piece_wise_lin_impl self.x, self.y1, self.y2 = add_piece_wise_lin_impl( diff --git a/pyspike/__init__.py b/pyspike/__init__.py index 8d92ea4..335b1d3 100644 --- a/pyspike/__init__.py +++ b/pyspike/__init__.py @@ -4,27 +4,29 @@ Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net> Distributed under the BSD License """ +from __future__ import absolute_import + __all__ = ["isi_distance", "spike_distance", "spike_sync", "psth", "spikes", "SpikeTrain", "PieceWiseConstFunc", "PieceWiseLinFunc", "DiscreteFunc", "directionality"] -from PieceWiseConstFunc import PieceWiseConstFunc -from PieceWiseLinFunc import PieceWiseLinFunc -from DiscreteFunc import DiscreteFunc -from SpikeTrain import SpikeTrain +from .PieceWiseConstFunc import PieceWiseConstFunc +from .PieceWiseLinFunc import PieceWiseLinFunc +from .DiscreteFunc import DiscreteFunc +from .SpikeTrain import SpikeTrain -from isi_distance import isi_profile, isi_distance, isi_profile_multi,\ +from .isi_distance import isi_profile, isi_distance, isi_profile_multi,\ isi_distance_multi, isi_distance_matrix -from spike_distance import spike_profile, spike_distance, spike_profile_multi,\ +from .spike_distance import spike_profile, spike_distance, spike_profile_multi,\ spike_distance_multi, spike_distance_matrix -from spike_sync import spike_sync_profile, spike_sync,\ +from .spike_sync import spike_sync_profile, spike_sync,\ spike_sync_profile_multi, spike_sync_multi, spike_sync_matrix -from psth import psth +from .psth import psth -from spikes import load_spike_trains_from_txt, spike_train_from_string, \ +from .spikes import load_spike_trains_from_txt, spike_train_from_string, \ merge_spike_trains, generate_poisson_spikes -import directionality as drct +from . import directionality as drct # define the __version__ following # http://stackoverflow.com/questions/17583443 diff --git a/pyspike/directionality/__init__.py b/pyspike/directionality/__init__.py index 6f74c50..6ea38b2 100644 --- a/pyspike/directionality/__init__.py +++ b/pyspike/directionality/__init__.py @@ -4,9 +4,11 @@ Copyright 2015, Mario Mulansky <mario.mulansky@gmx.net> Distributed under the BSD License """ +from __future__ import absolute_import + __all__ = ["spike_train_order"] -from spike_train_order import spike_train_order_profile, \ +from .spike_train_order import spike_train_order_profile, \ spike_train_order, spike_train_order_profile_multi, \ spike_train_order_matrix, spike_order_values, \ optimal_spike_train_order, optimal_spike_train_order_from_matrix, \ diff --git a/pyspike/directionality/spike_train_order.py b/pyspike/directionality/spike_train_order.py index 892ffd0..e6c9830 100644 --- a/pyspike/directionality/spike_train_order.py +++ b/pyspike/directionality/spike_train_order.py @@ -2,6 +2,8 @@ # Copyright 2015, Mario Mulansky <mario.mulansky@gmx.net> # Distributed under the BSD License +from __future__ import absolute_import + import numpy as np from math import exp from functools import partial @@ -35,7 +37,7 @@ def spike_train_order_profile(spike_train1, spike_train2, max_tau=None): # cython implementation try: - from cython.cython_directionality import \ + from .cython.cython_directionality import \ spike_train_order_profile_cython as \ spike_train_order_profile_impl except ImportError: @@ -45,7 +47,7 @@ def spike_train_order_profile(spike_train1, spike_train2, max_tau=None): PySpike is installed by running\n 'python setup.py build_ext --inplace'!\n \ Falling back to slow python backend.") # use python backend - from cython.directionality_python_backend import \ + from .cython.directionality_python_backend import \ spike_train_order_python as spike_train_order_profile_impl if max_tau is None: @@ -72,7 +74,7 @@ def spike_train_order(spike_train1, spike_train2, normalize=True, # distance over the whole interval is requested: use specific function # for optimal performance try: - from cython.cython_directionality import \ + from .cython.cython_directionality import \ spike_train_order_cython as spike_train_order_impl if max_tau is None: max_tau = 0.0 @@ -170,7 +172,7 @@ def spike_order_values(spike_trains, indices=None, # cython implementation try: - from cython.cython_directionality import \ + from .cython.cython_directionality import \ spike_order_values_cython as spike_order_values_impl except ImportError: raise NotImplementedError() @@ -179,7 +181,7 @@ def spike_order_values(spike_trains, indices=None, # 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 coincidence_python \ +# from .cython.python_backend import coincidence_python \ # as coincidence_profile_impl if max_tau is None: @@ -258,7 +260,7 @@ def optimal_spike_train_order(spike_trains, indices=None, interval=None, def permutate_matrix(D, p): N = len(D) D_p = np.empty_like(D) - for n in xrange(N): - for m in xrange(N): + for n in range(N): + for m in range(N): D_p[n, m] = D[p[n], p[m]] return D_p diff --git a/pyspike/generic.py b/pyspike/generic.py index 904c3c2..5ad06f1 100644 --- a/pyspike/generic.py +++ b/pyspike/generic.py @@ -7,6 +7,7 @@ Copyright 2015, Mario Mulansky <mario.mulansky@gmx.net> Distributed under the BSD License """ +from __future__ import division import numpy as np @@ -38,14 +39,14 @@ def _generic_profile_multi(spike_trains, pair_distance_func, indices=None): L1 = len(pairs1) if L1 > 1: dist_prof1 = divide_and_conquer(pairs1[:L1//2], - pairs1[int(L1//2):]) + pairs1[L1//2:]) else: dist_prof1 = pair_distance_func(spike_trains[pairs1[0][0]], spike_trains[pairs1[0][1]]) L2 = len(pairs2) if L2 > 1: dist_prof2 = divide_and_conquer(pairs2[:L2//2], - pairs2[int(L2//2):]) + pairs2[L2//2:]) else: dist_prof2 = pair_distance_func(spike_trains[pairs2[0][0]], spike_trains[pairs2[0][1]]) @@ -137,8 +138,8 @@ def _generic_distance_matrix(spike_trains, dist_function, assert (indices < len(spike_trains)).all() and (indices >= 0).all(), \ "Invalid index list." # generate a list of possible index pairs - pairs = [(i, j) for i in xrange(len(indices)) - for j in xrange(i+1, len(indices))] + pairs = [(i, j) for i in range(len(indices)) + for j in range(i+1, len(indices))] distance_matrix = np.zeros((len(indices), len(indices))) for i, j in pairs: diff --git a/pyspike/isi_distance.py b/pyspike/isi_distance.py index e50f203..0ae7393 100644 --- a/pyspike/isi_distance.py +++ b/pyspike/isi_distance.py @@ -2,6 +2,8 @@ # Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net> # Distributed under the BSD License +from __future__ import absolute_import + import pyspike from pyspike import PieceWiseConstFunc from pyspike.generic import _generic_profile_multi, _generic_distance_multi, \ @@ -32,7 +34,7 @@ def isi_profile(spike_train1, spike_train2): # load cython implementation try: - from cython.cython_profiles import isi_profile_cython \ + from .cython.cython_profiles import isi_profile_cython \ as isi_profile_impl except ImportError: if not(pyspike.disable_backend_warning): @@ -40,7 +42,7 @@ def isi_profile(spike_train1, spike_train2): 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 \ + from .cython.python_backend import isi_distance_python \ as isi_profile_impl times, values = isi_profile_impl(spike_train1.get_spikes_non_empty(), @@ -74,7 +76,7 @@ def isi_distance(spike_train1, spike_train2, interval=None): # distance over the whole interval is requested: use specific function # for optimal performance try: - from cython.cython_distances import isi_distance_cython \ + from .cython.cython_distances import isi_distance_cython \ as isi_distance_impl return isi_distance_impl(spike_train1.get_spikes_non_empty(), diff --git a/pyspike/psth.py b/pyspike/psth.py index 4027215..7cf1140 100644 --- a/pyspike/psth.py +++ b/pyspike/psth.py @@ -24,7 +24,7 @@ def psth(spike_trains, bin_size): # N = len(spike_trains) combined_spike_train = spike_trains[0].spikes - for i in xrange(1, len(spike_trains)): + for i in range(1, len(spike_trains)): combined_spike_train = np.append(combined_spike_train, spike_trains[i].spikes) diff --git a/pyspike/spike_distance.py b/pyspike/spike_distance.py index feea0c1..e418283 100644 --- a/pyspike/spike_distance.py +++ b/pyspike/spike_distance.py @@ -2,6 +2,8 @@ # Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net> # Distributed under the BSD License +from __future__ import absolute_import + import pyspike from pyspike import PieceWiseLinFunc from pyspike.generic import _generic_profile_multi, _generic_distance_multi, \ @@ -32,7 +34,7 @@ def spike_profile(spike_train1, spike_train2): # cython implementation try: - from cython.cython_profiles import spike_profile_cython \ + from .cython.cython_profiles import spike_profile_cython \ as spike_profile_impl except ImportError: if not(pyspike.disable_backend_warning): @@ -40,7 +42,7 @@ def spike_profile(spike_train1, spike_train2): 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 spike_distance_python \ + from .cython.python_backend import spike_distance_python \ as spike_profile_impl times, y_starts, y_ends = spike_profile_impl( @@ -76,7 +78,7 @@ def spike_distance(spike_train1, spike_train2, interval=None): # distance over the whole interval is requested: use specific function # for optimal performance try: - from cython.cython_distances import spike_distance_cython \ + from .cython.cython_distances import spike_distance_cython \ as spike_distance_impl return spike_distance_impl(spike_train1.get_spikes_non_empty(), spike_train2.get_spikes_non_empty(), diff --git a/pyspike/spike_sync.py b/pyspike/spike_sync.py index 10ebdc7..3dc29ff 100644 --- a/pyspike/spike_sync.py +++ b/pyspike/spike_sync.py @@ -3,6 +3,8 @@ # Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net> # Distributed under the BSD License +from __future__ import absolute_import + import numpy as np from functools import partial import pyspike @@ -37,7 +39,7 @@ def spike_sync_profile(spike_train1, spike_train2, max_tau=None): # cython implementation try: - from cython.cython_profiles import coincidence_profile_cython \ + from .cython.cython_profiles import coincidence_profile_cython \ as coincidence_profile_impl except ImportError: if not(pyspike.disable_backend_warning): @@ -45,7 +47,7 @@ def spike_sync_profile(spike_train1, spike_train2, max_tau=None): 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 coincidence_python \ + from .cython.python_backend import coincidence_python \ as coincidence_profile_impl if max_tau is None: @@ -73,7 +75,7 @@ def _spike_sync_values(spike_train1, spike_train2, interval, max_tau): # distance over the whole interval is requested: use specific function # for optimal performance try: - from cython.cython_distances import coincidence_value_cython \ + from .cython.cython_distances import coincidence_value_cython \ as coincidence_value_impl if max_tau is None: max_tau = 0.0 |