From be74318a2b269ec0c1e16981e7286679746f1a49 Mon Sep 17 00:00:00 2001 From: Mario Mulansky Date: Mon, 17 Aug 2015 11:57:53 +0200 Subject: fix #15 add test case and fix for Issue #15 closes #15 --- test/test_regression/test_regression_15.py | 78 ++++++++++++++++++++++++++++++ 1 file changed, 78 insertions(+) create mode 100644 test/test_regression/test_regression_15.py (limited to 'test/test_regression/test_regression_15.py') diff --git a/test/test_regression/test_regression_15.py b/test/test_regression/test_regression_15.py new file mode 100644 index 0000000..1ce1290 --- /dev/null +++ b/test/test_regression/test_regression_15.py @@ -0,0 +1,78 @@ +""" test_regression_15.py + +Regression test for Issue #15 + +Copyright 2015, Mario Mulansky + +Distributed under the BSD License + +""" + +import numpy as np +from numpy.testing import assert_equal, assert_almost_equal, \ + assert_array_almost_equal + +import pyspike as spk + + +def test_regression_15_isi(): + # load spike trains + spike_trains = spk.load_spike_trains_from_txt("test/SPIKE_Sync_Test.txt", + edges=[0, 4000]) + + N = len(spike_trains) + + dist_mat = spk.isi_distance_matrix(spike_trains) + assert_equal(dist_mat.shape, (N, N)) + + ind = np.arange(N/2) + dist_mat = spk.isi_distance_matrix(spike_trains, ind) + assert_equal(dist_mat.shape, (N/2, N/2)) + + ind = np.arange(N/2, N) + dist_mat = spk.isi_distance_matrix(spike_trains, ind) + assert_equal(dist_mat.shape, (N/2, N/2)) + + +def test_regression_15_spike(): + # load spike trains + spike_trains = spk.load_spike_trains_from_txt("test/SPIKE_Sync_Test.txt", + edges=[0, 4000]) + + N = len(spike_trains) + + dist_mat = spk.spike_distance_matrix(spike_trains) + assert_equal(dist_mat.shape, (N, N)) + + ind = np.arange(N/2) + dist_mat = spk.spike_distance_matrix(spike_trains, ind) + assert_equal(dist_mat.shape, (N/2, N/2)) + + ind = np.arange(N/2, N) + dist_mat = spk.spike_distance_matrix(spike_trains, ind) + assert_equal(dist_mat.shape, (N/2, N/2)) + + +def test_regression_15_sync(): + # load spike trains + spike_trains = spk.load_spike_trains_from_txt("test/SPIKE_Sync_Test.txt", + edges=[0, 4000]) + + N = len(spike_trains) + + dist_mat = spk.spike_sync_matrix(spike_trains) + assert_equal(dist_mat.shape, (N, N)) + + ind = np.arange(N/2) + dist_mat = spk.spike_sync_matrix(spike_trains, ind) + assert_equal(dist_mat.shape, (N/2, N/2)) + + ind = np.arange(N/2, N) + dist_mat = spk.spike_sync_matrix(spike_trains, ind) + assert_equal(dist_mat.shape, (N/2, N/2)) + + +if __name__ == "__main__": + test_regression_15_isi() + test_regression_15_spike() + test_regression_15_sync() -- cgit v1.2.3 From fe1f6179cce645df2511bfedae3af90167308f5f Mon Sep 17 00:00:00 2001 From: Igor Gnatenko Date: Sun, 13 Dec 2015 11:01:34 +0100 Subject: py3: division Signed-off-by: Igor Gnatenko --- pyspike/generic.py | 5 +++-- test/test_regression/test_regression_15.py | 26 ++++++++++++++------------ 2 files changed, 17 insertions(+), 14 deletions(-) (limited to 'test/test_regression/test_regression_15.py') diff --git a/pyspike/generic.py b/pyspike/generic.py index 81ae660..5ad06f1 100644 --- a/pyspike/generic.py +++ b/pyspike/generic.py @@ -7,6 +7,7 @@ Copyright 2015, Mario Mulansky 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]]) diff --git a/test/test_regression/test_regression_15.py b/test/test_regression/test_regression_15.py index 1ce1290..42a39ea 100644 --- a/test/test_regression/test_regression_15.py +++ b/test/test_regression/test_regression_15.py @@ -8,6 +8,8 @@ Distributed under the BSD License """ +from __future__ import division + import numpy as np from numpy.testing import assert_equal, assert_almost_equal, \ assert_array_almost_equal @@ -25,13 +27,13 @@ def test_regression_15_isi(): dist_mat = spk.isi_distance_matrix(spike_trains) assert_equal(dist_mat.shape, (N, N)) - ind = np.arange(N/2) + ind = np.arange(N//2) dist_mat = spk.isi_distance_matrix(spike_trains, ind) - assert_equal(dist_mat.shape, (N/2, N/2)) + assert_equal(dist_mat.shape, (N//2, N//2)) - ind = np.arange(N/2, N) + ind = np.arange(N//2, N) dist_mat = spk.isi_distance_matrix(spike_trains, ind) - assert_equal(dist_mat.shape, (N/2, N/2)) + assert_equal(dist_mat.shape, (N//2, N//2)) def test_regression_15_spike(): @@ -44,13 +46,13 @@ def test_regression_15_spike(): dist_mat = spk.spike_distance_matrix(spike_trains) assert_equal(dist_mat.shape, (N, N)) - ind = np.arange(N/2) + ind = np.arange(N//2) dist_mat = spk.spike_distance_matrix(spike_trains, ind) - assert_equal(dist_mat.shape, (N/2, N/2)) + assert_equal(dist_mat.shape, (N//2, N//2)) - ind = np.arange(N/2, N) + ind = np.arange(N//2, N) dist_mat = spk.spike_distance_matrix(spike_trains, ind) - assert_equal(dist_mat.shape, (N/2, N/2)) + assert_equal(dist_mat.shape, (N//2, N//2)) def test_regression_15_sync(): @@ -63,13 +65,13 @@ def test_regression_15_sync(): dist_mat = spk.spike_sync_matrix(spike_trains) assert_equal(dist_mat.shape, (N, N)) - ind = np.arange(N/2) + ind = np.arange(N//2) dist_mat = spk.spike_sync_matrix(spike_trains, ind) - assert_equal(dist_mat.shape, (N/2, N/2)) + assert_equal(dist_mat.shape, (N//2, N//2)) - ind = np.arange(N/2, N) + ind = np.arange(N//2, N) dist_mat = spk.spike_sync_matrix(spike_trains, ind) - assert_equal(dist_mat.shape, (N/2, N/2)) + assert_equal(dist_mat.shape, (N//2, N//2)) if __name__ == "__main__": -- cgit v1.2.3 From 45d4fac7b207bb5ce98f17433a443837fce0455a Mon Sep 17 00:00:00 2001 From: Igor Gnatenko Date: Mon, 14 Dec 2015 01:53:21 +0100 Subject: tests: allow to run out-of-tree Signed-off-by: Igor Gnatenko --- test/test_distance.py | 14 ++++++++------ test/test_regression/test_regression_15.py | 12 ++++++------ test/test_spikes.py | 9 +++++---- 3 files changed, 19 insertions(+), 16 deletions(-) (limited to 'test/test_regression/test_regression_15.py') diff --git a/test/test_distance.py b/test/test_distance.py index d5bce30..d405839 100644 --- a/test/test_distance.py +++ b/test/test_distance.py @@ -17,6 +17,8 @@ from numpy.testing import assert_equal, assert_almost_equal, \ import pyspike as spk from pyspike import SpikeTrain +import os +TEST_PATH = os.path.dirname(os.path.realpath(__file__)) def test_isi(): # generate two spike trains: @@ -275,8 +277,8 @@ def test_multi_spike_sync(): expected, decimal=15) # multivariate regression test - spike_trains = spk.load_spike_trains_from_txt("test/SPIKE_Sync_Test.txt", - edges=[0, 4000]) + spike_trains = spk.load_spike_trains_from_txt( + os.path.join(TEST_PATH, "SPIKE_Sync_Test.txt"), edges=[0, 4000]) # extract all spike times spike_times = np.array([]) for st in spike_trains: @@ -352,8 +354,8 @@ def test_regression_spiky(): # multivariate check - spike_trains = spk.load_spike_trains_from_txt("test/PySpike_testdata.txt", - (0.0, 4000.0)) + spike_trains = spk.load_spike_trains_from_txt( + os.path.join(TEST_PATH, "PySpike_testdata.txt"), (0.0, 4000.0)) isi_dist = spk.isi_distance_multi(spike_trains) # get the full precision from SPIKY assert_almost_equal(isi_dist, 0.17051816816999129656, decimal=15) @@ -371,8 +373,8 @@ def test_regression_spiky(): def test_multi_variate_subsets(): - spike_trains = spk.load_spike_trains_from_txt("test/PySpike_testdata.txt", - (0.0, 4000.0)) + spike_trains = spk.load_spike_trains_from_txt( + os.path.join(TEST_PATH, "PySpike_testdata.txt"), (0.0, 4000.0)) sub_set = [1, 3, 5, 7] spike_trains_sub_set = [spike_trains[i] for i in sub_set] diff --git a/test/test_regression/test_regression_15.py b/test/test_regression/test_regression_15.py index 42a39ea..dcacae2 100644 --- a/test/test_regression/test_regression_15.py +++ b/test/test_regression/test_regression_15.py @@ -16,11 +16,13 @@ from numpy.testing import assert_equal, assert_almost_equal, \ import pyspike as spk +import os +TEST_PATH = os.path.dirname(os.path.realpath(__file__)) +TEST_DATA = os.path.join(TEST_PATH, "..", "SPIKE_Sync_Test.txt") def test_regression_15_isi(): # load spike trains - spike_trains = spk.load_spike_trains_from_txt("test/SPIKE_Sync_Test.txt", - edges=[0, 4000]) + spike_trains = spk.load_spike_trains_from_txt(TEST_DATA, edges=[0, 4000]) N = len(spike_trains) @@ -38,8 +40,7 @@ def test_regression_15_isi(): def test_regression_15_spike(): # load spike trains - spike_trains = spk.load_spike_trains_from_txt("test/SPIKE_Sync_Test.txt", - edges=[0, 4000]) + spike_trains = spk.load_spike_trains_from_txt(TEST_DATA, edges=[0, 4000]) N = len(spike_trains) @@ -57,8 +58,7 @@ def test_regression_15_spike(): def test_regression_15_sync(): # load spike trains - spike_trains = spk.load_spike_trains_from_txt("test/SPIKE_Sync_Test.txt", - edges=[0, 4000]) + spike_trains = spk.load_spike_trains_from_txt(TEST_DATA, edges=[0, 4000]) N = len(spike_trains) diff --git a/test/test_spikes.py b/test/test_spikes.py index d4eb131..609a819 100644 --- a/test/test_spikes.py +++ b/test/test_spikes.py @@ -13,10 +13,12 @@ from numpy.testing import assert_equal import pyspike as spk +import os +TEST_PATH = os.path.dirname(os.path.realpath(__file__)) +TEST_DATA = os.path.join(TEST_PATH, "PySpike_testdata.txt") def test_load_from_txt(): - spike_trains = spk.load_spike_trains_from_txt("test/PySpike_testdata.txt", - edges=(0, 4000)) + spike_trains = spk.load_spike_trains_from_txt(TEST_DATA, edges=(0, 4000)) assert len(spike_trains) == 40 # check the first spike train @@ -48,8 +50,7 @@ def check_merged_spikes(merged_spikes, spike_trains): def test_merge_spike_trains(): # first load the data - spike_trains = spk.load_spike_trains_from_txt("test/PySpike_testdata.txt", - edges=(0, 4000)) + spike_trains = spk.load_spike_trains_from_txt(TEST_DATA, edges=(0, 4000)) merged_spikes = spk.merge_spike_trains([spike_trains[0], spike_trains[1]]) # test if result is sorted -- cgit v1.2.3