Source code for ibllib.tests.extractors.test_ephys_fpga

"""Tests for ephys FPGA sync and FPGA wheel extraction."""
import unittest
import tempfile
from pathlib import Path
import pickle

import numpy as np
import spikeglx

from ibllib.io.extractors import ephys_fpga
from ibllib.io.extractors.training_wheel import extract_first_movement_times, infer_wheel_units
from ibllib.io.extractors.training_wheel import extract_wheel_moves
import brainbox.behavior.wheel as wh


[docs] class TestsFolderStructure(unittest.TestCase):
[docs] def setUp(self): self.dir = tempfile.TemporaryDirectory() pl = Path(self.dir.name) / 'raw_ephys_data' / 'probe_left' pr = Path(self.dir.name) / 'raw_ephys_data' / 'probe_right' pl.mkdir(parents=True) pr.mkdir(parents=True) (pl / 'iblrig_ephysData.raw_g0_t0.imec.lf.bin').touch() (pl / 'iblrig_ephysData.raw_g0_t0.imec.ap.bin').touch() (pr / 'iblrig_ephysData.raw_g0_t0.imec.lf.bin').touch() (pr / 'iblrig_ephysData.raw_g0_t0.imec.ap.bin').touch()
[docs] def test_get_ephys_files(self): # first test at the root directory level, with a string input ephys_files = spikeglx.glob_ephys_files(self.dir.name) for ef in ephys_files: self.assertTrue(ef.label in ['probe_right', 'probe_left']) self.assertTrue(ef.ap.exists() and ef.lf.exists()) # second test at the ephys directory level, with a pathlib.Path input ephys_files = spikeglx.glob_ephys_files(Path(self.dir.name) / 'raw_ephys_data') for ef in ephys_files: self.assertTrue(ef.label in ['probe_right', 'probe_left']) self.assertTrue(ef.ap.exists() and ef.lf.exists())
[docs] def tearDown(self): self.dir.cleanup()
[docs] class TestSyncExtraction(unittest.TestCase):
[docs] def setUp(self): self.workdir = Path(__file__).parents[1] / 'fixtures' / 'sync_ephys_fpga' self.meta_files = list(Path.glob(self.workdir, '*.meta'))
[docs] def test_sync_nidq(self): self.sync_gen(fn='sample3B_g0_t0.nidq.meta', ns=32, nc=2, sync_depth=8)
[docs] def test_sync_3B(self): self.sync_gen(fn='sample3B_g0_t0.imec1.ap.meta', ns=32, nc=385, sync_depth=16)
[docs] def test_sync_3A(self): self.sync_gen(fn='sample3A_g0_t0.imec.ap.meta', ns=32, nc=385, sync_depth=16)
[docs] def sync_gen(self, fn, ns, nc, sync_depth): # nidq has 1 analog and 1 digital sync channels with tempfile.TemporaryDirectory() as tdir: ses_path = Path(tdir).joinpath('raw_ephys_data') ses_path.mkdir(parents=True, exist_ok=True) bin_file = ses_path.joinpath(fn).with_suffix('.bin') nidq = spikeglx._mock_spikeglx_file(bin_file, self.workdir / fn, ns=ns, nc=nc, sync_depth=sync_depth) syncs, files = ephys_fpga.extract_sync(tdir) self.assertTrue(np.all(syncs[0].channels[slice(1, None, 2)] == np.arange(0, nidq['sync_depth']))) with self.assertLogs(level='INFO') as log: ephys_fpga.extract_sync(tdir) self.assertEqual(1, len(log.output)) self.assertIn('SGLX sync found', log.output[0])
[docs] class TestIBLChannelMaps(unittest.TestCase):
[docs] def setUp(self): self.workdir = Path(__file__).parents[1] / 'fixtures'
[docs] def test_ibl_sync_maps(self): s = ephys_fpga.get_ibl_sync_map({'ap': 'toto', 'path': self.workdir}, '3A') self.assertEqual(s, ephys_fpga.CHMAPS['3A']['ap']) s = ephys_fpga.get_ibl_sync_map({'nidq': 'toto', 'path': self.workdir}, '3B') self.assertEqual(s, ephys_fpga.CHMAPS['3B']['nidq']) s = ephys_fpga.get_ibl_sync_map({'ap': 'toto', 'path': self.workdir}, '3B') self.assertEqual(s, ephys_fpga.CHMAPS['3B']['ap'])
[docs] class TestTTLsExtraction(unittest.TestCase):
[docs] def test_audio_ttl_wiring_camera(self): """ Test ephys_fpga._clean_audio function. Test removal of spurious TTLs due to a wrong wiring of the camera onto the soundcard example eid: e349a2e7-50a3-47ca-bc45-20d1899854ec """ # on this example it's business as usual and the clean up should not change anything audio = { 'times': np.array([1740.1032, 1740.20176667, 1741.0786, 1741.57713333, 1744.78716667, 1744.88573333]), 'polarities': np.array([1., -1., 1., -1., 1., -1.]), } audio_ = ephys_fpga._clean_audio(audio) self.assertEqual(audio, audio_) # on that example audio = {'times': np.array([3399.4090251, 3399.4110249, 3399.4156911, 3399.4176909, 3399.42232377, 3399.42432357, 3399.42898977, 3399.43095624, 3399.43562244, 3399.43762224, 3399.44228844, 3399.44425491, 3399.44892111, 3399.45092091, 3399.45558711, 3399.45755358, 3399.46221978, 3399.46421958, 3399.46888578, 3399.47085225, 3399.47551845, 3399.47751825, 3399.48215112, 3399.48415092, 3399.48881712, 3399.49081692, 3399.49544979, 3399.49744959, 3399.50211579, 3399.50411559, 3400.306602, 3400.3086018, 3400.313268, 3400.3152678, 3400.31990067, 3400.32190047, 3400.32656667, 3400.32856647, 3400.33319934, 3400.33519914, 3400.33986534, 3400.34186514, 3400.34649801, 3400.34849781, 3400.35316401, 3400.35516381, 3400.35979668, 3400.36179648, 3400.36646268, 3400.36846248, 3400.37309535, 3400.37509515, 3400.37976135, 3400.38172782, 3400.38639402, 3400.38839382, 3400.39306002, 3400.39502649, 3400.39969269, 3400.40169249, 3400.40635869, 3400.40832516, 3400.41299136, 3400.41499116, 3400.41962403, 3400.42162383, 3400.42629003, 3400.42828983, 3400.4329227, 3400.4349225, 3400.4395887, 3400.4415885, 3400.44622137, 3400.44822117, 3400.45288737, 3400.45488717, 3400.45952004, 3400.46151984, 3400.46618604, 3400.46818584, 3400.47281871, 3400.47481851, 3400.47948471, 3400.48148451, 3400.48611738, 3400.48811718, 3400.49278338, 3400.49478318, 3400.49941605, 3400.50141585, 3400.50608205, 3400.50808185, 3400.51271472, 3400.51471452, 3400.51938072, 3400.52138052, 3400.52601339, 3400.52801319, 3400.53267939, 3400.53467919, 3400.53931206, 3400.54131186, 3400.54597806, 3400.54797786, 3400.55261073, 3400.55461053, 3400.55927673, 3400.5612432, 3400.5659094, 3400.5679092, 3400.5725754, 3400.57454187, 3400.57920807, 3400.58120787, 3400.58587407, 3400.58784054, 3400.59250674, 3400.59450654, 3400.59917274, 3400.60113921, 3400.60580541, 3400.60780521, 3400.61243808, 3400.61443788, 3400.61910408, 3400.62110388, 3400.62573675, 3400.62773655, 3400.63240275, 3400.63440255, 3400.63903542, 3400.64103522, 3400.64570142, 3400.64770122, 3400.65233409, 3400.65433389, 3400.65900009, 3400.66099989, 3400.66563276, 3400.66763256, 3400.67229876, 3400.67429856, 3400.67893143, 3400.68093123, 3400.68559743, 3400.68759723, 3400.6922301, 3400.6942299, 3400.6988961, 3400.7008959, 3400.70552877, 3400.70752857, 3400.71219477, 3400.71419457, 3400.71882744, 3400.72082724, 3400.72549344, 3400.72749324, 3400.73212611, 3400.73412591, 3400.73879211, 3400.74079191, 3400.74542478, 3400.74742458, 3400.75209078, 3400.75405725, 3400.75872345, 3400.76072325, 3400.76538945, 3400.76735592, 3400.77202212, 3400.77402192, 3400.77868812, 3400.78065459, 3400.78532079, 3400.78732059, 3400.79198679, 3400.79395326, 3400.79861946, 3400.80061926]), 'polarities': np.array([1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1.]) } audio_ = ephys_fpga._clean_audio(audio) expected = {'times': np.array([3399.4090251, 3399.50411559, 3400.306602, 3400.80061926]), 'polarities': np.array([1., -1., 1., -1.])} assert all(np.all(audio_[k] == expected[k]) for k in audio_)
[docs] def test_audio_ttl_start_up_down(self): """ If the behaviour starts before FPGA, it is very unlikely but possible that the FPGA starts on up state and that the first front of the audio is a downgoing one. The extraction should handle both cases seamlessly: cf eid d839491f-55d8-4cbe-a298-7839208ba12b """ def _test_audio(audio, audio_intervals): for tone, intervals in audio_intervals.items(): if tone == 'unassigned': self.assertFalse(len(intervals)) else: np.testing.assert_array_almost_equal( intervals[:, 0], audio['times'][audio[tone]], err_msg=tone) audio = { 'times': np.array([1740.1032, 1740.20176667, 1741.0786, 1741.57713333, 1744.78716667, 1744.88573333]), 'polarities': np.array([1., -1., 1., -1., 1., -1.]), 'error_tone': np.array([False, False, True, False, False, False]), 'ready_tone': np.array([True, False, False, False, True, False]), 'channels': np.zeros(6, dtype=int) } extractor = ephys_fpga.FpgaTrials('subject/2023-01-01/000') # placeholder session path unused _audio, audio_intervals = extractor.get_audio_event_times(audio, {'audio': 0}) _test_audio(audio, audio_intervals) # this tests the usual pulses audio['channels'][0] = 1 # this tests when it starts in upstate audio['ready_tone'][0] = False # the first ready tone should now be skipped _audio, audio_intervals = extractor.get_audio_event_times(audio, {'audio': 0}) _test_audio(audio, audio_intervals) np.testing.assert_array_equal(_audio['times'], audio['times'][1:])
[docs] def test_frame2ttl_flickers(self): """ Frame2ttl can flicker abnormally. One way to detect this is to remove consecutive polarity switches under a given threshold """ DISPLAY = False # for debug purposes F2TTL_THRESH = 0.01 diff = F2TTL_THRESH * np.array([0.5, 10]) # flicker ends with a polarity switch - downgoing pulse is removed t = np.r_[0, np.cumsum(diff[np.array([1, 1, 0, 0, 1])])] + 1 frame2ttl = {'times': t, 'polarities': np.mod(np.arange(t.size) + 1, 2) * 2 - 1} expected = {'times': np.array([1., 1.1, 1.2, 1.31]), 'polarities': np.array([1, -1, 1, -1])} frame2ttl_ = ephys_fpga._clean_frame2ttl(frame2ttl, display=DISPLAY, threshold=F2TTL_THRESH) assert all(np.all(frame2ttl_[k] == expected[k]) for k in frame2ttl_) # stand-alone flicker t = np.r_[0, np.cumsum(diff[np.array([1, 1, 0, 0, 0, 1])])] + 1 frame2ttl = {'times': t, 'polarities': np.mod(np.arange(t.size) + 1, 2) * 2 - 1} expected = {'times': np.array([1., 1.1, 1.2, 1.215, 1.315]), 'polarities': np.array([1, -1, 1, -1, 1])} frame2ttl_ = ephys_fpga._clean_frame2ttl(frame2ttl, display=DISPLAY) assert all(np.all(frame2ttl_[k] == expected[k]) for k in frame2ttl_)
[docs] def test_bpod_trace_extraction(self): """Test FpgaTrials.get_bpod_event_times method.""" expected = { 'trial_start': np.array([0, 4, 8, 12, 14, 16, 20, 24, 26, 28, 32, 34, 38, 42, 46, 48, 52, 56]), 'valve_open': np.array([2, 6, 10, 18, 22, 30, 36, 40, 44, 50, 54]) } bpod_fronts_ = np.array([1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1., 1., -1.]) bpod_times_ = np.array([6.75033333, 109.7648, 117.12136667, 117.27136667, 118.51416667, 118.51426667, 122.3873, 122.5373, 123.7964, 123.7965, 127.82903333, 127.97903333, 129.24503333, 129.24513333, 132.97976667, 132.97986667, 136.8624, 136.8625, 140.56083333, 140.71083333, 141.95523333, 141.95533333, 143.55326667, 143.70326667, 144.93636667, 144.93646667, 149.5042, 149.5043, 153.08273333, 153.08283333, 155.29713333, 155.44713333, 156.70316667, 156.70326667, 164.0096, 164.0097, 164.9186, 165.0686, 166.30633333, 166.30643333, 167.91133333, 168.06133333, 169.28373333, 169.28386667, 171.39736667, 171.54736667, 172.77786667, 172.77796667, 176.7828, 176.7829, 178.0305, 178.1805, 179.41063333, 179.41073333, 181.70343333, 181.85343333, 183.12896667, 183.12906667]) extractor = ephys_fpga.FpgaTrials('subject/2023-01-01/000') # placeholder session path unused sync = {'times': bpod_times_, 'polarities': bpod_fronts_, 'channels': np.zeros_like(bpod_times_, dtype=int)} _, bpod_intervals = extractor.get_bpod_event_times(sync, {'bpod': 0}) for k in expected: np.testing.assert_array_equal(bpod_intervals[k][:, 0], bpod_times_[expected[k]])
[docs] def test_ttl_bpod_gaelle_writes_protocols_but_guido_doesnt_read_them(self): bpod_t = np.array([5.423290950005423, 6.397993470006398, 6.468919710006469, 7.497916800007498, 7.997933460007998, 8.599239990008599, 8.5993399800086, 15.141985650015142, 15.642002310015641, 16.215411630016217, 16.215511620016215, 17.104122750017105, 17.175015660017174, 18.204012750018205, 18.704029410018705, 19.286337840019286, 19.28643783001929, 21.76005711002176, 21.83095002002183, 22.85998044002286]) pol = (np.mod(np.arange(bpod_t.size), 2) - 0.5) * 2 sync = {'times': bpod_t, 'polarities': pol, 'channels': np.zeros_like(bpod_t, dtype=int)} extractor = ephys_fpga.FpgaTrials('subject/2023-01-01/000') # placeholder session path unused _, bpod_intervals = extractor.get_bpod_event_times(sync, {'bpod': 0}) expected = bpod_t[[1, 5, 9, 15]] np.testing.assert_array_equal(bpod_intervals['trial_start'][:, 0], expected) # when the bpod has started before the ephys, the first pulses may have been missed # and the first TTL may be negative/. This needs to yield the same result as if the # bpod was started properly sync['channels'][0] = 1 _, bpod_intervals_ = extractor.get_bpod_event_times(sync, {'bpod': 0}) for event, intervals in bpod_intervals.items(): np.testing.assert_array_equal(intervals, bpod_intervals_[event], err_msg=event)
[docs] def test_align_to_trial(self): """Test ephys_fpga._assign_events_to_trial function.""" # simple test with one missing at the end t_trial_start = np.arange(0, 5) * 10 t_event = np.arange(0, 5) * 10 + 2 t_event_nans = ephys_fpga._assign_events_to_trial(t_trial_start, t_event) self.assertTrue(np.allclose(t_event_nans, t_event, equal_nan=True, atol=0, rtol=0)) # test with missing values t_trial_start = np.array([109, 118, 123, 129, 132, 136, 141, 144, 149, 153]) t_event = np.array([122, 133, 140, 143, 146, 150, 154]) t_event_out_ = np.array([np.nan, 122, np.nan, np.nan, 133, 140, 143, 146, 150, 154]) t_event_nans = ephys_fpga._assign_events_to_trial(t_trial_start, t_event) self.assertTrue(np.allclose(t_event_out_, t_event_nans, equal_nan=True, atol=0, rtol=0)) # test with events before initial start trial t_trial_start = np.arange(0, 5) * 10 t_event = np.arange(0, 5) * 10 - 2 t_event_nans = ephys_fpga._assign_events_to_trial(t_trial_start, t_event) desired_out = np.array([8., 18., 28., 38., np.nan]) self.assertTrue(np.allclose(desired_out, t_event_nans, equal_nan=True, atol=0, rtol=0)) # test with several events per trial, missing events and events before t_trial_start = np.array([0, 10, 20, 30, 40]) t_event = np.array([-1, 2, 4, 12, 35, 42]) t_event_nans = ephys_fpga._assign_events_to_trial(t_trial_start, t_event) desired_out = np.array([4, 12., np.nan, 35, 42]) self.assertTrue(np.allclose(desired_out, t_event_nans, equal_nan=True, atol=0, rtol=0)) # same test above but this time take the first index instead of last t_event_nans = ephys_fpga._assign_events_to_trial(t_trial_start, t_event, take='first') desired_out = np.array([2, 12., np.nan, 35, 42]) self.assertTrue(np.allclose(desired_out, t_event_nans, equal_nan=True, atol=0, rtol=0)) # take second to last t_trial_start = np.array([0, 10, 20, 30, 40]) t_event = np.array([2, 4, 12, 13, 14, 21, 32, 33, 34, 35, 42]) t_event_nans = ephys_fpga._assign_events_to_trial(t_trial_start, t_event, take=-2) desired_out = np.array([2, 13, np.nan, 34, np.nan]) self.assertTrue(np.allclose(desired_out, t_event_nans, equal_nan=True, atol=0, rtol=0)) t_event_nans = ephys_fpga._assign_events_to_trial(t_trial_start, t_event, take=1) desired_out = np.array([4, 13, np.nan, 33, np.nan]) self.assertTrue(np.allclose(desired_out, t_event_nans, equal_nan=True, atol=0, rtol=0)) # test errors self.assertRaises(ValueError, ephys_fpga._assign_events_to_trial, np.array([0., 2., 1.]), t_event) self.assertRaises(ValueError, ephys_fpga._assign_events_to_trial, t_trial_start, np.array([0., 2., 1.]))
[docs] class TestWheelExtraction(unittest.TestCase):
[docs] def setUp(self) -> None: self.ta = np.array([2, 4, 6, 8, 12, 14, 16, 18]) self.pa = np.array([1, -1, 1, -1, 1, -1, 1, -1]) self.tb = np.array([3, 5, 7, 9, 11, 13, 15, 17]) self.pb = np.array([1, -1, 1, -1, 1, -1, 1, -1])
[docs] def test_x1_decoding(self): p_ = np.array([1, 2, 1, 0]) t_ = np.array([2, 6, 11, 15]) t, p = ephys_fpga._rotary_encoder_positions_from_fronts(self.ta, self.pa, self.tb, self.pb, ticks=np.pi * 2, coding='x1') self.assertTrue(np.all(t == t_)) self.assertTrue(np.all(p == p_))
[docs] def test_x4_decoding(self): p_ = np.array([1, 2, 3, 4, 5, 6, 7, 8, 7, 6, 5, 4, 3, 2, 1, 0]) / 4 t_ = np.array([2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18]) t, p = ephys_fpga._rotary_encoder_positions_from_fronts(self.ta, self.pa, self.tb, self.pb, ticks=np.pi * 2, coding='x4') self.assertTrue(np.all(t == t_)) self.assertTrue(np.all(np.isclose(p, p_)))
[docs] def test_x2_decoding(self): p_ = np.array([1, 2, 3, 4, 3, 2, 1, 0]) / 2 t_ = np.array([2, 4, 6, 8, 12, 14, 16, 18]) t, p = ephys_fpga._rotary_encoder_positions_from_fronts(self.ta, self.pa, self.tb, self.pb, ticks=np.pi * 2, coding='x2') self.assertTrue(np.all(t == t_)) self.assertTrue(np.all(p == p_))
[docs] def test_wheel_trace_from_sync(self): """Test ephys_fpga._rotary_encoder_positions_from_fronts function.""" pos_ = - np.array([-1, 0, -1, -2, -1, -2]) * (np.pi / ephys_fpga.WHEEL_TICKS) ta = np.array([1, 2, 3, 4, 5, 6]) tb = np.array([0.5, 3.2, 3.3, 3.4, 5.25, 5.5]) pa = (np.mod(np.arange(6), 2) - 0.5) * 2 pb = (np.mod(np.arange(6) + 1, 2) - .5) * 2 t, pos = ephys_fpga._rotary_encoder_positions_from_fronts(ta, pa, tb, pb, coding='x2') self.assertTrue(np.all(np.isclose(pos_, pos))) pos_ = - np.array([-1, 0, -1, 0, -1, -2]) * (np.pi / ephys_fpga.WHEEL_TICKS) tb = np.array([0.5, 3.2, 3.4, 5.25]) pb = (np.mod(np.arange(4) + 1, 2) - .5) * 2 t, pos = ephys_fpga._rotary_encoder_positions_from_fronts(ta, pa, tb, pb, coding='x2') self.assertTrue(np.all(np.isclose(pos_, pos)))
[docs] class TestExtractedWheelUnits(unittest.TestCase): """Tests the infer_wheel_units function.""" wheel_radius_cm = 3.1
[docs] def setUp(self) -> None: """ Create the wheel position data for testing: the positions attribute holds a dictionary of units, each holding a dictionary of encoding types to test, e.g. positions = { 'rad': { 'X1': ..., 'X2': ..., 'X4': ... }, 'cm': { 'X1': ..., 'X2': ..., 'X4': ... } } :return: """ def x(unit, enc=int(1), wheel_radius=self.wheel_radius_cm): radius = 1 if unit == 'rad' else wheel_radius return 1 / ephys_fpga.WHEEL_TICKS * np.pi * 2 * radius / enc # A pseudo-random sequence of integrated fronts seq = np.array([-1, 0, 1, 2, 1, 2, 3, 4, 3, 2, 1, 0, -1, -2, 1, -2]) encs = (1, 2, 4) # Encoding types to test units = ('rad', 'cm') # Units to test self.positions = {unit: {f'X{e}': x(unit, e) * seq for e in encs} for unit in units}
[docs] def test_extract_wheel_moves(self): for unit in self.positions.keys(): for encoding, pos in self.positions[unit].items(): result = infer_wheel_units(pos) self.assertEqual(unit, result[0], f'failed to determine units for {encoding}') expected = int(ephys_fpga.WHEEL_TICKS * int(encoding[1])) self.assertEqual(expected, result[1], f'failed to determine number of ticks for {encoding} in {unit}') self.assertEqual(encoding, result[2], f'failed to determine encoding in {unit}')
[docs] class TestWheelMovesExtraction(unittest.TestCase):
[docs] def setUp(self) -> None: """ Test data is in the form ((inputs), (outputs)) where inputs is a tuple containing a numpy array of timestamps and one of positions; outputs is a tuple of outputs from the functions. For details, see help on TestWheel.setUp method in module brainbox.tests.test_behavior """ pickle_file = Path(__file__).parents[3].joinpath('brainbox', 'tests', 'fixtures', 'wheel_test.p') if not pickle_file.exists(): self.test_data = None else: with open(pickle_file, 'rb') as f: self.test_data = pickle.load(f) # Some trial times for trial_data[1] self.trials = {'goCue_times': np.array([162.5, 105.6, 55]), 'feedback_times': np.array([164.3, 108.3, 56])}
[docs] def test_extract_wheel_moves(self): test_data = self.test_data[1] # Wrangle data into expected form re_ts = test_data[0][0] re_pos = test_data[0][1] logname = 'ibllib.io.extractors.training_wheel' with self.assertLogs(logname, level='INFO') as cm: wheel_moves = extract_wheel_moves(re_ts, re_pos) self.assertEqual([f'INFO:{logname}:Wheel in cm units using X2 encoding'], cm.output) n = 56 # expected number of movements self.assertTupleEqual(wheel_moves['intervals'].shape, (n, 2), 'failed to return the correct number of intervals') self.assertEqual(wheel_moves['peakAmplitude'].size, n) self.assertEqual(wheel_moves['peakVelocity_times'].size, n) # Check the first 3 intervals ints = np.array([[24.78462599, 25.22562599], [29.58762599, 31.15062599], [31.64262599, 31.81662599]]) actual = wheel_moves['intervals'][:3, ] self.assertIsNone(np.testing.assert_allclose(actual, ints), 'unexpected intervals') # Check amplitudes actual = wheel_moves['peakAmplitude'][-3:] expected = [0.50255486, -1.70103154, 1.00740789] self.assertIsNone(np.testing.assert_allclose(actual, expected), 'unexpected amplitudes') # Check peak velocities actual = wheel_moves['peakVelocity_times'][-3:] expected = [175.13662599, 176.65762599, 178.57262599] self.assertIsNone(np.testing.assert_allclose(actual, expected), 'peak times') # Test extraction in rad re_pos = wh.cm_to_rad(re_pos) with self.assertLogs(logname, level='INFO') as cm: wheel_moves = ephys_fpga.extract_wheel_moves(re_ts, re_pos) self.assertEqual([f'INFO:{logname}:Wheel in rad units using X2 encoding'], cm.output) # Check the first 3 intervals. As position thresholds are adjusted by units and # encoding, we should expect the intervals to be identical to above actual = wheel_moves['intervals'][:3, ] self.assertIsNone(np.testing.assert_allclose(actual, ints), 'unexpected intervals')
[docs] def test_movement_log(self): """ Integration test for inferring the units and decoding type for wheel data input for extract_wheel_moves. Only expected to work for the default wheel diameter. """ ta = np.array([2, 4, 6, 8, 12, 14, 16, 18]) pa = np.array([1, -1, 1, -1, 1, -1, 1, -1]) tb = np.array([3, 5, 7, 9, 11, 13, 15, 17]) pb = np.array([1, -1, 1, -1, 1, -1, 1, -1]) logname = 'ibllib.io.extractors.training_wheel' for unit in ['cm', 'rad']: for i in (1, 2, 4): encoding = 'X' + str(i) r = 3.1 if unit == 'cm' else 1 # print(encoding, unit) t, p = ephys_fpga._rotary_encoder_positions_from_fronts( ta, pa, tb, pb, ticks=1024, coding=encoding.lower(), radius=r) expected = f'INFO:{logname}:Wheel in {unit} units using {encoding} encoding' with self.assertLogs(logname, level='INFO') as cm: ephys_fpga.extract_wheel_moves(t, p) self.assertEqual([expected], cm.output)
[docs] def test_extract_first_movement_times(self): test_data = self.test_data[1] wheel_moves = ephys_fpga.extract_wheel_moves(test_data[0][0], test_data[0][1]) first, is_final, ind = extract_first_movement_times(wheel_moves, self.trials) np.testing.assert_allclose(first, [162.48462599, 105.62562599, np.nan]) np.testing.assert_array_equal(is_final, [False, True, False]) np.testing.assert_array_equal(ind, [46, 18])
[docs] class TestFpgaTrials(unittest.TestCase): """Test FpgaTrials class."""
[docs] def test_time_fields(self): """Test for FpgaTrials._time_fields static method.""" expected = ('intervals', 'fooBar_times_bpod', 'spike_times', 'baz_timestamps') fields = ephys_fpga.FpgaTrials._time_fields(expected + ('position', 'timebase', 'fooBaz')) self.assertCountEqual(expected, fields)
[docs] def test_is_trials_object_attribute(self): """Test for FpgaTrials._is_trials_object_attribute method.""" extractor = ephys_fpga.FpgaTrials('subject/2020-01-01/001') # Should assume this is a trials attribute if no save name defined self.assertTrue(extractor._is_trials_object_attribute('stimOnTrigger_times')) # Save name not trials attribute self.assertFalse(extractor._is_trials_object_attribute('wheel_position')) # Save name is trials attribute self.assertTrue(extractor._is_trials_object_attribute('table')) # Check with toy variables extractor.var_names += ('foo_bar',) extractor.save_names += (None,) self.assertTrue(extractor._is_trials_object_attribute('foo_bar')) self.assertFalse(extractor._is_trials_object_attribute('foo_bar', variable_length_vars='foo_bar')) extractor.save_names = extractor.save_names[:-1] + ('_ibl_foo.bar_times.csv',) self.assertFalse(extractor._is_trials_object_attribute('foo_bar'))
if __name__ == '__main__': unittest.main(exit=False, verbosity=2)