def test_read_channel_index(self):
'''
test that when filtering on channels, the returned channel order
is the requested one.
'''
filename = test_file('gdf2', 'read')
f = XFile(filename, 'r', 'gdf2')
self.assertGreater(len(f.channels), 2)
ch0 = f.channels[0]
ch1 = f.channels[1]
data_01 = f.read([ch0['name'], ch1['name']])
data_10 = f.read([ch1['name'], ch0['name']])
# test that data_01 and data_10 are the same data
# with swapped channels
# same dimensions
self.assertEqual(len(data_01.shape), 2)
self.assertEqual(len(data_10.shape), 2)
self.assertEqual(data_01.shape, data_10.shape)
# same data
self.assertTrue((data_01[:, 0] == data_10[:, 1]).all())
self.assertTrue((data_01[:, 1] == data_10[:, 0]).all())
def test_read_filter(self):
f = XFile(test_file('gdf2', 'read'), 'r')
data = f.read(['EEG0'])
# only test that we have a 2D array of floats
self.assertIs(type(data), numpy.ndarray)
self.assertIs(type(data[0][0]), numpy.float64)
self.assertEqual(len(data.shape), 2)
ns, nch = data.shape
self.assertEqual(nch, 1)
def test_readonly_fields(self):
'ensure read-only fields cannot be written'
f = XFile(test_file('gdf2', 'write'), 'w', 'gdf2')
with self.assertRaises(AttributeError):
f.len = 42
with self.assertRaises(AttributeError):
f.filename = 'dummy'
with self.assertRaises(AttributeError):
f.filetype = 'dummy'
def test_read_simple(self):
'read smoke test'
for filetype in TEST_FILES:
f = XFile(test_file(filetype, 'read'), 'r', filetype)
data = f.read()
# only test that we have a 2D array of floats
self.assertIs(type(data), numpy.ndarray)
self.assertGreater(len(data), 1)
self.assertGreater(len(data[0]), 1)
self.assertIs(type(data[0][0]), numpy.float64)
def test_read_channels_invalid_chunk(self):
'''
test that when the chunk is invalid (the endding time is smaller
than the starting time), the filtering is done on the required
channels for the whole laps of time of the recording.
'''
filename = test_file('gdf2', 'read')
f = XFile(filename, 'r', 'gdf2')
start = 124
end = 16
with self.assertRaises(IndexError):
f.read(chunk=(start, end))
def test_read_channels_index_chunk(self):
'''
test that when filtering on channels and a certain laps of time,
the returned channel order and chunk of time are the requested one.
'''
filename = test_file('gdf2', 'read')
f = XFile(filename, 'r', 'gdf2')
self.assertGreater(len(f.channels), 2)
ch0 = f.channels[0]
ch1 = f.channels[1]
start = 18
end = 128
data_01 = f.read([ch0['name'], ch1['name']], (start, end))
data_10 = f.read([ch1['name'], ch0['name']], (start, end))
fulldata_01 = f.read([ch0['name'], ch1['name']
]) # assumption: the function read with
# channels argument is correct
fulldata_10 = f.read([ch1['name'], ch0['name']
]) # assumption: the function read with
# channels argument is correct
# test that each channel read contains end - start samples
self.assertEqual(data_01.shape[0], end - start + 1)
self.assertEqual(data_10.shape[0], end - start + 1)
self.assertEqual(data_01.shape[1], 2)
self.assertEqual(data_10.shape[1], 2)
# test that data_01 and data_10 are the same data
# with swapped channels between the chunck of time
# same dimensions
self.assertEqual(len(data_01.shape), 2)
self.assertEqual(len(data_10.shape), 2)
self.assertEqual(data_01.shape, data_10.shape)
# same data
self.assertTrue((data_01[:, 0] == data_10[:, 1]).all())
self.assertTrue((data_01[:, 1] == data_10[:, 0]).all())
# test that the data read in the chunk correspond to the
# required data
for chan in range(2):
for i in range(start, end + 1):
self.assertEqual(data_01[i - start][chan],
fulldata_01[i][chan])
self.assertEqual(data_10[i - start][chan],
fulldata_10[i][chan])
def test_read_channels_index_invalid_chunk(self):
'''
test that when the chunk is invalid (the endding time is smaller
than the starting time), the filtering is done on the required
channels for the whole laps of time of the recording.
'''
filename = test_file('gdf2', 'read')
f = XFile(filename, 'r', 'gdf2')
self.assertGreater(len(f.channels), 2)
ch0 = f.channels[0]
ch1 = f.channels[1]
start = 36
end = 18
with self.assertRaises(IndexError):
f.read([ch0['name'], ch1['name']], (start, end))
def test_with_keyword(self):
'test that enter/exit functions work as expected'
with XFile(test_file('gdf2', 'read'), 'r') as f:
data = f.read(['EEG0'])
self.assertIs(type(data), numpy.ndarray)
self.assertIs(type(data[0][0]), numpy.float64)
self.assertEqual(len(data.shape), 2)
ns, nch = data.shape
self.assertEqual(nch, 1)
def test_read_channels_chunk(self):
'''
test that when filtering on a required laps of time,
the returned chunk of time is the requested one.
'''
filename = test_file('gdf2', 'read')
f = XFile(filename, 'r', 'gdf2')
start = 16
end = 624
data = f.read(chunk=(start, end))
fulldata = f.read() # assumption: the function read without
# argument is correct
# test that each channel read contains end - start samples
self.assertEqual(data.shape[0], end - start + 1)
self.assertEqual(data.shape[1], len(f.channels))
# test that the data read in the chunk correspond to the
# required data
for i in range(start, end + 1):
for chan in range(len(f.channels)):
self.assertEqual(data[i - start][chan], fulldata[i][chan])
def test_write_many_channels_transposed(self):
'read/write more realistic test with transposed array'
filetype = 'gdf2'
filename = test_file(filetype, 'write')
ns = 5 * 1000
nch = 23
test_array = numpy.random.rand(nch, ns).T
f = XFile(filename, 'w', filetype)
f.fs = 500
for i in range(nch):
ch_name = 'test_channel_{:d}'.format(i)
f.channels.append(Channel(ch_name, -2., 2., 'dummy'))
f.write(test_array)
# open back for reading
f = XFile(filename, 'r', filetype)
# test metadatas
# self.assertEqual(f.fs, 42)
self.assertEqual(len(f.channels), nch)
for i in range(nch):
ch_name = 'test_channel_{:d}'.format(i)
self.assertEqual(
f.channels[i], {
'name': ch_name,
'physical_min': -2.,
'physical_max': 2.,
'unit': 'dummy'
})
# test data
data = f.read()
# test the first few data only: xdf formats do not support writing
# less than a record. Record length is not configurable.
self.assertGreaterEqual(len(data), ns)
self.assertEqual(len(data[0]), nch)
for i in range(ns):
for j in range(nch):
self.assertAlmostEqual(data[i][j],
test_array[i][j],
places=precision(filetype))
def test_write_simple(self):
'read/write smoke test'
for filetype in ['edf', 'bdf', 'gdf2']:
filename = test_file(filetype, 'write')
test_array = numpy.random.rand(7, 1) # ns = 7, nch = 1
f = XFile(filename, 'w', filetype)
f.fs = 42
f.channels.append(Channel('test_channel', -2., 2., 'dummy'))
f.write(test_array)
# open back for reading
f = XFile(filename, 'r', filetype)
# test metadatas
# self.assertEqual(f.fs, 42)
self.assertEqual(len(f.channels), 1)
self.assertEqual(
f.channels[0], {
'name': 'test_channel',
'physical_min': -2.,
'physical_max': 2.,
'unit': 'dummy'
})
# test data
data = f.read()
# test the first few data only: xdf formats do not support writing
# less than a record. Record length is not configurable.
self.assertGreater(len(data), len(test_array))
self.assertEqual(len(data[0]), 1)
for i in range(len(test_array)):
# TODO: be less permissive
# The rounding error depends on the closest stored data type
# eg. edf only supported 16-bits data types, and that comes with
# severe changes during rounding ...
self.assertAlmostEqual(data[i][0],
test_array[i][0],
places=precision(filetype))
def test_readwrite_fields(self):
'ensure that we can write on writable fields'
f = XFile(test_file('gdf2', 'write'), 'w', 'gdf2')
f.channels.append(Channel('test_channel', -2., 2., 'dummy'))
self.assertEqual(len(f.channels), 1)
self.assertEqual(
f.channels[0], {
'name': 'test_channel',
'physical_min': -2.,
'physical_max': 2.,
'unit': 'dummy'
})
f.fs = 42.
self.assertEqual(f.fs, 42.)
f.record_time = 42.
self.assertEqual(f.record_time, 42.)
f.subject_desc = "dummy subject desc"
self.assertEqual(f.subject_desc, "dummy subject desc")
f.session_desc = "dummy session desc"
self.assertEqual(f.session_desc, "dummy session desc")
def test_read_any(self):
'''ensure filetype is optional when reading
read -> read from file
'''
f = XFile(test_file('gdf2', 'read'), 'r')
self.assertEqual(f.filetype, 'gdf')
def test_write_gdf1(self):
'writing gdf1 files raise an error'
# remove and merge into test_write_simple() once fixed
filename = test_file('gdf1', 'write')
with self.assertRaises(NotImplementedError):
f = XFile(filename, 'w', 'gdf1')