""" Tests of neo.io.hdf5io_new """ import unittest import sys import numpy as np from numpy.testing import assert_array_equal from quantities import kHz, mV, ms, second, nA try: import h5py HAVE_H5PY = True except ImportError: HAVE_H5PY = False from neo.io.hdf5io import NeoHdf5IO from neo.test.iotest.common_io_test import BaseTestIO from neo.test.iotest.tools import get_test_file_full_path @unittest.skipUnless(HAVE_H5PY, "requires h5py") class ReadOldNeoHdf5IOTest(BaseTestIO, unittest.TestCase): """ Test that data generated by NeoHdf5IO in Neo versions 0.3, 0.4 are read correctly. """ ioclass = NeoHdf5IO files_to_test = ["neo_hdf5_example.h5"] files_to_download = files_to_test def test_read_with_merge(self): test_file = get_test_file_full_path(self.ioclass, filename=self.files_to_test[0], directory=self.local_test_dir, clean=False) io = NeoHdf5IO(test_file) blocks = io.read_all_blocks(merge_singles=True) # general tests, true for both blocks for block in blocks: for segment in block.segments: self.assertEqual(segment.block, block) # tests of Block #1, which is constructed from "array" (multi-channel) # objects, so should be straightforward to convert to the version 0.5 API block0 = blocks[0] self.assertEqual(block0.name, "block1") self.assertEqual(block0.index, 1234) self.assertEqual(block0.annotations["foo"], "bar") self.assertEqual(len(block0.segments), 3) for segment in block0.segments: self.assertEqual(len(segment.analogsignals), 2) as0 = segment.analogsignals[0] self.assertEqual(as0.shape, (1000, 4)) self.assertEqual(as0.sampling_rate, 1 * kHz) self.assertEqual(as0.units, mV) self.assertEqual(as0.segment, segment) self.assertEqual(len(segment.spiketrains), 4) st = segment.spiketrains[-1] self.assertEqual(st.units, ms) self.assertEqual(st.t_stop, 1000 * ms) self.assertEqual(st.t_start, 0 * ms) self.assertEqual(st.segment, segment) self.assertEqual(len(segment.events), 1) ev = segment.events[0] assert_array_equal(ev.labels, np.array(['trig0', 'trig1', 'trig2'], dtype=(sys.byteorder == 'little' and '<' or '>') + 'U5')) self.assertEqual(ev.units, second) assert_array_equal(ev.magnitude, np.arange(0, 30, 10)) self.assertEqual(ev.segment, segment) self.assertEqual(len(segment.epochs), 1) ep = segment.epochs[0] assert_array_equal(ep.labels, np.array(['btn0', 'btn1', 'btn2'], dtype=(sys.byteorder == 'little' and '<' or '>') + 'U4')) assert_array_equal(ep.durations.magnitude, np.array([10, 5, 7])) self.assertEqual(ep.units, second) assert_array_equal(ep.magnitude, np.arange(0, 30, 10)) self.assertEqual(ep.segment, segment) self.assertEqual(len(segment.irregularlysampledsignals), 2) iss0 = segment.irregularlysampledsignals[0] self.assertEqual(iss0.shape, (3, 2)) assert_array_equal(iss0.times, [0.01, 0.03, 0.12] * second) assert_array_equal(iss0.magnitude, np.array([[4, 3], [5, 4], [6, 3]])) self.assertEqual(iss0.units, nA) self.assertEqual(iss0.segment, segment) iss1 = segment.irregularlysampledsignals[1] self.assertEqual(iss1.shape, (3, 1)) assert_array_equal(iss1.times, [0.02, 0.05, 0.15] * second) self.assertEqual(iss1.units, nA) assert_array_equal(iss1.magnitude, np.array([[3], [4], [3]])) # tests of Block #2, which is constructed from "singleton" # (single-channel) objects, so is potentially tricky to convert to the # version 0.5 API block1 = blocks[1] self.assertEqual(block1.name, "block2") for segment in block1.segments: self.assertEqual(len(segment.analogsignals), 2) as0 = segment.analogsignals[0] self.assertEqual(as0.shape, (1000, 4)) self.assertEqual(as0.sampling_rate, 1 * kHz) self.assertEqual(as0.units, mV) self.assertEqual(as0.segment, segment) self.assertEqual(len(segment.spiketrains), 7) st = segment.spiketrains[-1] self.assertEqual(st.units, ms) self.assertEqual(st.t_stop, 1000 * ms) self.assertEqual(st.t_start, 0 * ms) self.assertEqual(st.segment, segment) self.assertEqual(len(segment.events), 0) self.assertEqual(len(segment.epochs), 0) self.assertEqual(len(block1.channel_indexes), 3) ci0 = block1.channel_indexes[0] self.assertEqual(ci0.name, "electrode1") self.assertEqual(len(ci0.analogsignals), 1) as00 = ci0.analogsignals[0] self.assertEqual(as00.segment, segment) self.assertEqual(as00.shape, (1000, 4)) self.assertEqual(id(as00), id(segment.analogsignals[0])) self.assertEqual(as00.mean(), segment.analogsignals[0].mean()) self.assertEqual(as00.channel_index, ci0) assert_array_equal(ci0.index, np.array([0, 1, 2, 3])) assert_array_equal(ci0.channel_ids, np.array([0, 1, 2, 3])) self.assertEqual(len(ci0.units), 2) self.assertEqual(len(ci0.units[0].spiketrains), 2) self.assertEqual(id(ci0.units[0].spiketrains[0]), id(block1.segments[0].spiketrains[0])) self.assertEqual(id(ci0.units[0].spiketrains[1]), id(block1.segments[1].spiketrains[0])) self.assertEqual(id(ci0.units[1].spiketrains[0]), id(block1.segments[0].spiketrains[1])) ci1 = block1.channel_indexes[1] self.assertEqual(ci1.name, "electrode2") self.assertEqual(len(ci1.analogsignals), 1) as10 = ci1.analogsignals[0] self.assertEqual(as10.segment, segment) self.assertEqual(as10.shape, (1000, 4)) self.assertEqual(id(as10), id(segment.analogsignals[1])) self.assertEqual(as10.mean(), segment.analogsignals[1].mean()) self.assertEqual(as10.channel_index, ci1) assert_array_equal(ci1.index, np.array([0, 1, 2, 3])) assert_array_equal(ci1.channel_ids, np.array([4, 5, 6, 7])) self.assertEqual(len(ci1.units), 5) self.assertEqual(id(ci1.units[0].spiketrains[0]), id(block1.segments[0].spiketrains[2])) self.assertEqual(id(ci1.units[3].spiketrains[1]), id(block1.segments[1].spiketrains[5])) ci2 = block1.channel_indexes[2] self.assertEqual(ci2.name, "my_favourite_channels") self.assertEqual(len(ci2.analogsignals), 1) self.assertEqual(id(ci2.analogsignals[0]), id(as00)) assert_array_equal(ci2.index, np.array([1, 3])) assert_array_equal(ci2.channel_ids, np.array([1, 3]))