""" Tests of neo.io.exampleio """ import warnings import unittest import quantities as pq import numpy as np from neo.io.nestio import ColumnIO from neo.io.nestio import NestIO from neo.test.iotest.common_io_test import BaseTestIO from neo.test.iotest.tools import get_test_file_full_path class TestNestIO_Analogsignals(BaseTestIO, unittest.TestCase): ioclass = NestIO files_to_test = [] files_to_download = ['0gid-1time-2gex-3Vm-1261-0.dat', '0gid-1time-2gex-1262-0.dat', '0gid-1time-2Vm-3gex-4gin-1260-0.dat', '0gid-1time-2Vm-3Iex-4Iin-1264-0.dat', '0gid-1time-2Vm-1259-0.dat', '0gid-1time-1256-0.gdf', '0gid-1time_in_steps-2Vm-1263-0.dat', '0gid-1time_in_steps-1258-0.gdf', '0time-1255-0.gdf', '0time_in_steps-1257-0.gdf', 'brunel-delta-nest_mod.py', 'N1-0gid-1time-2Vm-1265-0.dat', 'N1-0time-1Vm-1266-0.dat', 'N1-0Vm-1267-0.dat'] def test_read_analogsignal(self): """ Tests reading files in the 2 different formats: - with GIDs, with times as floats - with GIDs, with time as integer """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-2gex-3Vm-1261-0.dat', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) r.read_analogsignal(gid=1, t_stop=1000. * pq.ms, sampling_period=pq.ms, lazy=False, id_column=0, time_column=1, value_column=2, value_type='V_m') r.read_segment(gid_list=[1], t_stop=1000. * pq.ms, sampling_period=pq.ms, lazy=False, id_column_dat=0, time_column_dat=1, value_columns_dat=2, value_types='V_m') filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time_in_steps-2Vm-1263-0.dat', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) r.read_analogsignal(gid=1, t_stop=1000. * pq.ms, time_unit=pq.CompoundUnit('0.1*ms'), sampling_period=pq.ms, lazy=False, id_column=0, time_column=1, value_column=2, value_type='V_m') r.read_segment(gid_list=[1], t_stop=1000. * pq.ms, time_unit=pq.CompoundUnit('0.1*ms'), sampling_period=pq.ms, lazy=False, id_column_dat=0, time_column_dat=1, value_columns_dat=2, value_types='V_m') filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-2Vm-1259-0.dat', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) r.read_analogsignal(gid=1, t_stop=1000. * pq.ms, time_unit=pq.CompoundUnit('0.1*ms'), sampling_period=pq.ms, lazy=False, id_column=0, time_column=1, value_column=2, value_type='V_m') r.read_segment(gid_list=[1], t_stop=1000. * pq.ms, time_unit=pq.CompoundUnit('0.1*ms'), sampling_period=pq.ms, lazy=False, id_column_dat=0, time_column_dat=1, value_columns_dat=2, value_types='V_m') def test_id_column_none_multiple_neurons(self): """ Tests if function correctly raises an error if the user tries to read from a file which does not contain unit IDs, but data for multiple units. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0time-1255-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) with self.assertRaises(ValueError): r.read_analogsignal(t_stop=1000. * pq.ms, lazy=False, sampling_period=pq.ms, id_column=None, time_column=0, value_column=1) r.read_segment(t_stop=1000. * pq.ms, lazy=False, sampling_period=pq.ms, id_column_gdf=None, time_column_gdf=0) def test_values(self): """ Tests if the function returns the correct values. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-2gex-3Vm-1261-0.dat', directory=self.local_test_dir, clean=False) id_to_test = 1 r = NestIO(filenames=filename) seg = r.read_segment(gid_list=[id_to_test], t_stop=1000. * pq.ms, sampling_period=pq.ms, lazy=False, id_column_dat=0, time_column_dat=1, value_columns_dat=2, value_types='V_m') dat = np.loadtxt(filename) target_data = dat[:, 2][np.where(dat[:, 0] == id_to_test)] target_data = target_data[:, None] st = seg.analogsignals[0] np.testing.assert_array_equal(st.magnitude, target_data) def test_read_segment(self): """ Tests if signals are correctly stored in a segment. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-2gex-1262-0.dat', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) id_list_to_test = range(1, 10) seg = r.read_segment(gid_list=id_list_to_test, t_stop=1000. * pq.ms, sampling_period=pq.ms, lazy=False, id_column_dat=0, time_column_dat=1, value_columns_dat=2, value_types='V_m') self.assertTrue(len(seg.analogsignals) == len(id_list_to_test)) id_list_to_test = [] seg = r.read_segment(gid_list=id_list_to_test, t_stop=1000. * pq.ms, sampling_period=pq.ms, lazy=False, id_column_dat=0, time_column_dat=1, value_columns_dat=2, value_types='V_m') self.assertEqual(len(seg.analogsignals), 50) def test_read_block(self): """ Tests if signals are correctly stored in a block. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-2gex-1262-0.dat', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) id_list_to_test = range(1, 10) blk = r.read_block(gid_list=id_list_to_test, t_stop=1000. * pq.ms, sampling_period=pq.ms, lazy=False, id_column_dat=0, time_column_dat=1, value_columns_dat=2, value_types='V_m') self.assertTrue(len(blk.segments[0].analogsignals) == len(id_list_to_test)) def test_wrong_input(self): """ Tests two cases of wrong user input, namely - User does not specify a value column - User does not make any specifications - User does not define sampling_period as a unit - User specifies a non-default value type without specifying a value_unit - User specifies t_start < 1.*sampling_period """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-2gex-1262-0.dat', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) with self.assertRaises(ValueError): r.read_segment(t_stop=1000. * pq.ms, lazy=False, id_column_dat=0, time_column_dat=1) with self.assertRaises(ValueError): r.read_segment() with self.assertRaises(ValueError): r.read_segment(gid_list=[1], t_stop=1000. * pq.ms, sampling_period=1. * pq.ms, lazy=False, id_column_dat=0, time_column_dat=1, value_columns_dat=2, value_types='V_m') with self.assertRaises(ValueError): r.read_segment(gid_list=[1], t_stop=1000. * pq.ms, sampling_period=pq.ms, lazy=False, id_column_dat=0, time_column_dat=1, value_columns_dat=2, value_types='U_mem') def test_t_start_t_stop(self): """ Test for correct t_start and t_stop values of AnalogSignalArrays. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-2gex-1262-0.dat', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) t_start_targ = 450. * pq.ms t_stop_targ = 480. * pq.ms seg = r.read_segment(gid_list=[], t_start=t_start_targ, t_stop=t_stop_targ, lazy=False, id_column_dat=0, time_column_dat=1, value_columns_dat=2, value_types='V_m') anasigs = seg.analogsignals for anasig in anasigs: self.assertTrue(anasig.t_start == t_start_targ) self.assertTrue(anasig.t_stop == t_stop_targ) def test_notimeid(self): """ Test for warning, when no time column id was provided. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-2gex-1262-0.dat', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) t_start_targ = 450. * pq.ms t_stop_targ = 460. * pq.ms sampling_period = pq.CompoundUnit('5*ms') with warnings.catch_warnings(record=True) as w: # Cause all warnings to always be triggered. warnings.simplefilter("always") seg = r.read_segment(gid_list=[], t_start=t_start_targ, sampling_period=sampling_period, t_stop=t_stop_targ, lazy=False, id_column_dat=0, time_column_dat=None, value_columns_dat=2, value_types='V_m') # Verify number and content of warning self.assertEqual(len(w), 1) self.assertIn("no time column id", str(w[0].message)) sts = seg.analogsignals for st in sts: self.assertTrue(st.t_start == 1 * 5 * pq.ms) self.assertTrue( st.t_stop == len(st) * sampling_period + 1 * 5 * pq.ms) def test_multiple_value_columns(self): """ Test for simultaneous loading of multiple columns from dat file. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-2Vm-3Iex-4Iin-1264-0.dat', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) sampling_period = pq.CompoundUnit('5*ms') seg = r.read_segment(gid_list=[1001], value_columns_dat=[2, 3], sampling_period=sampling_period) anasigs = seg.analogsignals self.assertEqual(len(anasigs), 2) def test_single_gid(self): filename = get_test_file_full_path( ioclass=NestIO, filename='N1-0gid-1time-2Vm-1265-0.dat', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) anasig = r.read_analogsignal(gid=1, t_stop=1000. * pq.ms, time_unit=pq.CompoundUnit('0.1*ms'), sampling_period=pq.ms, lazy=False, id_column=0, time_column=1, value_column=2, value_type='V_m') assert anasig.annotations['id'] == 1 def test_no_gid(self): filename = get_test_file_full_path( ioclass=NestIO, filename='N1-0time-1Vm-1266-0.dat', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) anasig = r.read_analogsignal(gid=None, t_stop=1000. * pq.ms, time_unit=pq.CompoundUnit('0.1*ms'), sampling_period=pq.ms, lazy=False, id_column=None, time_column=0, value_column=1, value_type='V_m') self.assertEqual(anasig.annotations['id'], None) self.assertEqual(len(anasig), 19) def test_no_gid_no_time(self): filename = get_test_file_full_path( ioclass=NestIO, filename='N1-0Vm-1267-0.dat', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) anasig = r.read_analogsignal(gid=None, sampling_period=pq.ms, lazy=False, id_column=None, time_column=None, value_column=0, value_type='V_m') self.assertEqual(anasig.annotations['id'], None) self.assertEqual(len(anasig), 19) class TestNestIO_Spiketrains(BaseTestIO, unittest.TestCase): ioclass = NestIO files_to_test = [] files_to_download = [] def test_read_spiketrain(self): """ Tests reading files in the 4 different formats: - without GIDs, with times as floats - without GIDs, with times as integers in time steps - with GIDs, with times as floats - with GIDs, with times as integers in time steps """ filename = get_test_file_full_path( ioclass=NestIO, filename='0time-1255-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) r.read_spiketrain(t_start=400. * pq.ms, t_stop=500. * pq.ms, lazy=False, id_column=None, time_column=0) r.read_segment(t_start=400. * pq.ms, t_stop=500. * pq.ms, lazy=False, id_column_gdf=None, time_column_gdf=0) filename = get_test_file_full_path( ioclass=NestIO, filename='0time_in_steps-1257-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) r.read_spiketrain(t_start=400. * pq.ms, t_stop=500. * pq.ms, time_unit=pq.CompoundUnit('0.1*ms'), lazy=False, id_column=None, time_column=0) r.read_segment(t_start=400. * pq.ms, t_stop=500. * pq.ms, time_unit=pq.CompoundUnit('0.1*ms'), lazy=False, id_column_gdf=None, time_column_gdf=0) filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-1256-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) r.read_spiketrain(gdf_id=1, t_start=400. * pq.ms, t_stop=500. * pq.ms, lazy=False, id_column_gdf=0, time_column_gdf=1) r.read_segment(gid_list=[1], t_start=400. * pq.ms, t_stop=500. * pq.ms, lazy=False, id_column_gdf=0, time_column_gdf=1) filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time_in_steps-1258-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) r.read_spiketrain(gdf_id=1, t_start=400. * pq.ms, t_stop=500. * pq.ms, time_unit=pq.CompoundUnit('0.1*ms'), lazy=False, id_column=0, time_column=1) r.read_segment(gid_list=[1], t_start=400. * pq.ms, t_stop=500. * pq.ms, time_unit=pq.CompoundUnit('0.1*ms'), lazy=False, id_column_gdf=0, time_column_gdf=1) def test_read_integer(self): """ Tests if spike times are actually stored as integers if they are stored in time steps in the file. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0time_in_steps-1257-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) st = r.read_spiketrain(gdf_id=None, t_start=400. * pq.ms, t_stop=500. * pq.ms, time_unit=pq.CompoundUnit('0.1*ms'), lazy=False, id_column=None, time_column=0) self.assertTrue(st.magnitude.dtype == np.int32) seg = r.read_segment(gid_list=[None], t_start=400. * pq.ms, t_stop=500. * pq.ms, time_unit=pq.CompoundUnit('0.1*ms'), lazy=False, id_column_gdf=None, time_column_gdf=0) sts = seg.spiketrains self.assertTrue(all([st.magnitude.dtype == np.int32 for st in sts])) filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time_in_steps-1258-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO( filenames=filename) st = r.read_spiketrain(gdf_id=1, t_start=400. * pq.ms, t_stop=500. * pq.ms, time_unit=pq.CompoundUnit('0.1*ms'), lazy=False, id_column=0, time_column=1) self.assertTrue(st.magnitude.dtype == np.int32) seg = r.read_segment(gid_list=[1], t_start=400. * pq.ms, t_stop=500. * pq.ms, time_unit=pq.CompoundUnit('0.1*ms'), lazy=False, id_column_gdf=0, time_column_gdf=1) sts = seg.spiketrains self.assertTrue(all([st.magnitude.dtype == np.int32 for st in sts])) def test_read_float(self): """ Tests if spike times are stored as floats if they are stored as floats in the file. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-1256-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) st = r.read_spiketrain(gdf_id=1, t_start=400. * pq.ms, t_stop=500. * pq.ms, lazy=False, id_column=0, time_column=1) self.assertTrue(st.magnitude.dtype == np.float) seg = r.read_segment(gid_list=[1], t_start=400. * pq.ms, t_stop=500. * pq.ms, lazy=False, id_column_gdf=0, time_column_gdf=1) sts = seg.spiketrains self.assertTrue(all([s.magnitude.dtype == np.float for s in sts])) def test_values(self): """ Tests if the routine loads the correct numbers from the file. """ id_to_test = 1 filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-1256-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) seg = r.read_segment(gid_list=[id_to_test], t_start=400. * pq.ms, t_stop=500. * pq.ms, lazy=False, id_column_gdf=0, time_column_gdf=1) dat = np.loadtxt(filename) target_data = dat[:, 1][np.where(dat[:, 0] == id_to_test)] st = seg.spiketrains[0] np.testing.assert_array_equal(st.magnitude, target_data) def test_read_segment(self): """ Tests if spiketrains are correctly stored in a segment. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-1256-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) id_list_to_test = range(1, 10) seg = r.read_segment(gid_list=id_list_to_test, t_start=400. * pq.ms, t_stop=500. * pq.ms, lazy=False, id_column_gdf=0, time_column_gdf=1) self.assertTrue(len(seg.spiketrains) == len(id_list_to_test)) id_list_to_test = [] seg = r.read_segment(gid_list=id_list_to_test, t_start=400. * pq.ms, t_stop=500. * pq.ms, lazy=False, id_column_gdf=0, time_column_gdf=1) self.assertTrue(len(seg.spiketrains) == 50) def test_read_segment_accepts_range(self): """ Tests if spiketrains can be retrieved by specifying a range of GDF IDs. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-1256-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) seg = r.read_segment(gid_list=(10, 39), t_start=400. * pq.ms, t_stop=500. * pq.ms, lazy=False, id_column_gdf=0, time_column_gdf=1) self.assertEqual(len(seg.spiketrains), 30) def test_read_segment_range_is_reasonable(self): """ Tests if error is thrown correctly, when second entry is smaller than the first one of the range. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-1256-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) seg = r.read_segment(gid_list=(10, 10), t_start=400. * pq.ms, t_stop=500. * pq.ms, lazy=False, id_column_gdf=0, time_column_gdf=1) self.assertEqual(len(seg.spiketrains), 1) with self.assertRaises(ValueError): r.read_segment(gid_list=(10, 9), t_start=400. * pq.ms, t_stop=500. * pq.ms, lazy=False, id_column_gdf=0, time_column_gdf=1) def test_read_spiketrain_annotates(self): """ Tests if correct annotation is added when reading a spike train. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-1256-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) ID = 7 st = r.read_spiketrain(gdf_id=ID, t_start=400. * pq.ms, t_stop=500. * pq.ms) self.assertEqual(ID, st.annotations['id']) def test_read_segment_annotates(self): """ Tests if correct annotation is added when reading a segment. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-1256-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) IDs = (5, 11) sts = r.read_segment(gid_list=(5, 11), t_start=400. * pq.ms, t_stop=500. * pq.ms) for ID in np.arange(5, 12): self.assertEqual(ID, sts.spiketrains[ID - 5].annotations['id']) def test_adding_custom_annotation(self): """ Tests if custom annotation is correctly added. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-1256-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) st = r.read_spiketrain(gdf_id=0, t_start=400. * pq.ms, t_stop=500. * pq.ms, layer='L23', population='I') self.assertEqual(0, st.annotations.pop('id')) self.assertEqual('L23', st.annotations.pop('layer')) self.assertEqual('I', st.annotations.pop('population')) self.assertEqual({}, st.annotations) def test_wrong_input(self): """ Tests two cases of wrong user input, namely - User does not specify neuron IDs although the file contains IDs. - User does not make any specifications. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-1256-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) with self.assertRaises(ValueError): r.read_segment(t_start=400. * pq.ms, t_stop=500. * pq.ms, lazy=False, id_column_gdf=0, time_column_gdf=1) with self.assertRaises(ValueError): r.read_segment() def test_t_start_t_stop(self): """ Tests if the t_start and t_stop arguments are correctly processed. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-1256-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) t_stop_targ = 490. * pq.ms t_start_targ = 410. * pq.ms seg = r.read_segment(gid_list=[], t_start=t_start_targ, t_stop=t_stop_targ, lazy=False, id_column_gdf=0, time_column_gdf=1) sts = seg.spiketrains self.assertTrue(np.max([np.max(st.magnitude) for st in sts if len(st) > 0]) < t_stop_targ.rescale(sts[0].times.units).magnitude) self.assertTrue(np.min([np.min(st.magnitude) for st in sts if len(st) > 0]) >= t_start_targ.rescale(sts[0].times.units).magnitude) def test_t_start_undefined_raises_error(self): """ Tests if undefined t_start, i.e., t_start=None raises error. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-1256-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) with self.assertRaises(ValueError): r.read_spiketrain(gdf_id=1, t_stop=500. * pq.ms, lazy=False, id_column=0, time_column=1) with self.assertRaises(ValueError): r.read_segment(gid_list=[1, 2, 3], t_stop=500. * pq.ms, lazy=False, id_column_gdf=0, time_column_gdf=1) def test_t_stop_undefined_raises_error(self): """ Tests if undefined t_stop, i.e., t_stop=None raises error. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-1256-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) with self.assertRaises(ValueError): r.read_spiketrain(gdf_id=1, t_start=400. * pq.ms, lazy=False, id_column=0, time_column=1) with self.assertRaises(ValueError): r.read_segment(gid_list=[1, 2, 3], t_start=400. * pq.ms, lazy=False, id_column_gdf=0, time_column_gdf=1) def test_gdf_id_illdefined_raises_error(self): """ Tests if ill-defined gdf_id in read_spiketrain (i.e., None, list, or empty list) raises error. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-1256-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) with self.assertRaises(ValueError): r.read_spiketrain(gdf_id=[], t_start=400. * pq.ms, t_stop=500. * pq.ms) with self.assertRaises(ValueError): r.read_spiketrain(gdf_id=[1], t_start=400. * pq.ms, t_stop=500. * pq.ms) with self.assertRaises(ValueError): r.read_spiketrain(t_start=400. * pq.ms, t_stop=500. * pq.ms) def test_read_segment_can_return_empty_spiketrains(self): """ Tests if read_segment makes sure that only non-zero spike trains are returned. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-1256-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) seg = r.read_segment(gid_list=[], t_start=400.4 * pq.ms, t_stop=400.5 * pq.ms) for st in seg.spiketrains: self.assertEqual(st.size, 0) def test_read_spiketrain_can_return_empty_spiketrain(self): """ Tests if read_spiketrain returns an empty SpikeTrain if no spikes are in time range. """ filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-1256-0.gdf', directory=self.local_test_dir, clean=False) r = NestIO(filenames=filename) st = r.read_spiketrain(gdf_id=0, t_start=400. * pq.ms, t_stop=410. * pq.ms) self.assertEqual(st.size, 0) class TestNestIO_multiple_signal_types(BaseTestIO, unittest.TestCase): ioclass = NestIO files_to_test = [] files_to_download = ['0gid-1time-2gex-3Vm-1261-0.dat', '0gid-1time_in_steps-1258-0.gdf'] def test_read_analogsignal_and_spiketrain(self): """ Test if spiketrains and analogsignals can be read simultaneously using read_segment """ files = ['0gid-1time-2gex-3Vm-1261-0.dat', '0gid-1time_in_steps-1258-0.gdf'] filenames = [get_test_file_full_path(ioclass=NestIO, filename=file, directory=self.local_test_dir, clean=False) for file in files] r = NestIO(filenames=filenames) seg = r.read_segment(gid_list=[], t_start=400 * pq.ms, t_stop=600 * pq.ms, id_column_gdf=0, time_column_gdf=1, id_column_dat=0, time_column_dat=1, value_columns_dat=2) self.assertEqual(len(seg.spiketrains), 50) self.assertEqual(len(seg.analogsignals), 50) class TestColumnIO(BaseTestIO, unittest.TestCase): ioclass = NestIO files_to_download = ['0gid-1time-2Vm-3gex-4gin-1260-0.dat'] def setUp(self): BaseTestIO.setUp(self) filename = get_test_file_full_path( ioclass=NestIO, filename='0gid-1time-2Vm-3gex-4gin-1260-0.dat', directory=self.local_test_dir, clean=False) self.testIO = ColumnIO(filename=filename) def test_no_arguments(self): """ Test if data can be read using the default keyword arguments. """ columns = self.testIO.get_columns() expected = self.testIO.data np.testing.assert_array_equal(columns, expected) def test_single_column_id(self): """ Test if the column_ids keywords works properly. """ column = self.testIO.get_columns(column_ids=1) expected = self.testIO.data[:, [1]] np.testing.assert_array_equal(column, expected) def test_multiple_column_ids(self): """ Test if multiple columns can be read at the same time. """ columns = self.testIO.get_columns(column_ids=range(2)) expected = self.testIO.data[:, [0, 1]] np.testing.assert_array_equal(columns, expected) def test_no_condition(self): """ Test if a missing condition function leads to a warning """ with warnings.catch_warnings(record=True) as w: # Cause all warnings to always be triggered. warnings.simplefilter("always") self.testIO.get_columns(condition_column=0) # Verify number and content of warning assert len(w) == 1 assert "no condition" in str(w[-1].message) def test_no_condition_column(self): """ Test if a missing condition column leads to an error """ with self.assertRaises(ValueError) as context: self.testIO.get_columns(condition=lambda x: True) self.assertTrue('no condition_column ID provided' in str(context.exception)) def test_correct_condition_selection(self): """ Test if combination of condition function and condition_column works properly. """ condition_column = 0 def condition_function(x): return x > 10 result = self.testIO.get_columns(condition=condition_function, condition_column=0) selected_ids = np.where(condition_function(self.testIO.data[:, condition_column]))[0] expected = self.testIO.data[selected_ids, :] np.testing.assert_array_equal(result, expected) assert all(condition_function(result[:, condition_column])) def test_sorting(self): """ Test if presorting of columns work properly. """ result = self.testIO.get_columns(sorting_columns=0) assert len(result) > 0 assert all(np.diff(result[:, 0]) >= 0) if __name__ == "__main__": unittest.main()