added function to import time series

new function import_spike_trains_from_time_series that loads spike trains
from time series.

3 files changed, 45 insertions, 0 deletions

diff --git a/pyspike/__init__.py b/pyspike/__init__.py
index 069090b..1e879c4 100644
--- a/pyspike/__init__.py
+++ b/pyspike/__init__.py
@@ -24,6 +24,7 @@ from .spike_sync import spike_sync_profile, spike_sync,\
 from .psth import psth
 
 from .spikes import load_spike_trains_from_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/spikes.py b/pyspike/spikes.py
index b18d7eb..1bf474c 100644
--- a/pyspike/spikes.py
+++ b/pyspike/spikes.py
@@ -57,6 +57,31 @@ def load_spike_trains_from_txt(file_name, 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
+
+
 ############################################################
 # merge_spike_trains
 ############################################################
diff --git a/test/test_spikes.py b/test/test_spikes.py
index 609a819..bcface2 100644
--- a/test/test_spikes.py
+++ b/test/test_spikes.py
@@ -17,6 +17,10 @@ import os
 TEST_PATH = os.path.dirname(os.path.realpath(__file__))
 TEST_DATA = os.path.join(TEST_PATH, "PySpike_testdata.txt")
 
+TIME_SERIES_DATA = os.path.join(TEST_PATH, "time_series.txt")
+TIME_SERIES_SPIKES = os.path.join(TEST_PATH, "time_series_spike_trains.txt")
+
+
 def test_load_from_txt():
     spike_trains = spk.load_spike_trains_from_txt(TEST_DATA, edges=(0, 4000))
     assert len(spike_trains) == 40
@@ -33,6 +37,21 @@ def test_load_from_txt():
         assert spike_train.t_end == 4000
 
 
+def test_load_time_series():
+    spike_trains = spk.import_spike_trains_from_time_series(TIME_SERIES_DATA,
+                                                            start_time=0,
+                                                            time_bin=1)
+    assert len(spike_trains) == 40
+    spike_trains_check = spk.load_spike_trains_from_txt(TIME_SERIES_SPIKES,
+                                                        edges=(0, 4000))
+
+    # check spike trains
+    for n in range(len(spike_trains)):
+        assert_equal(spike_trains[n].spikes, spike_trains_check[n].spikes)
+        assert_equal(spike_trains[n].t_start, 0)
+        assert_equal(spike_trains[n].t_end, 4000)
+
+
 def check_merged_spikes(merged_spikes, spike_trains):
     # create a flat array with all spike events
     all_spikes = np.array([])