/usr/lib/python2.7/dist-packages/neo/test/iotest/test_pynnio.py is in python-neo 0.3.3-2.
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"""
Tests of the neo.io.pynnio.PyNNNumpyIO and neo.io.pynnio.PyNNTextIO classes
"""
# needed for python 3 compatibility
from __future__ import absolute_import, division
import os
try:
import unittest2 as unittest
except ImportError:
import unittest
import numpy as np
import quantities as pq
from neo.core import Segment, AnalogSignal, SpikeTrain
from neo.io import PyNNNumpyIO, PyNNTextIO
from neo.test.tools import assert_arrays_equal, assert_file_contents_equal
#TODO: common test fails.
from neo.test.iotest.common_io_test import BaseTestIO
#class CommonTestPyNNNumpyIO(BaseTestIO, unittest.TestCase):
# ioclass = PyNNNumpyIO
NCELLS = 5
class CommonTestPyNNTextIO(BaseTestIO, unittest.TestCase):
ioclass = PyNNTextIO
read_and_write_is_bijective = False
def read_test_file(filename):
contents = np.load(filename)
data = contents["data"]
metadata = {}
for name, value in contents['metadata']:
try:
metadata[name] = eval(value)
except Exception:
metadata[name] = value
return data, metadata
read_test_file.__test__ = False
class BaseTestPyNNIO(object):
__test__ = False
def tearDown(self):
if os.path.exists(self.test_file):
os.remove(self.test_file)
def test_write_segment(self):
in_ = self.io_cls(self.test_file)
write_test_file = "write_test.%s" % self.file_extension
out = self.io_cls(write_test_file)
out.write_segment(in_.read_segment(lazy=False, cascade=True))
assert_file_contents_equal(self.test_file, write_test_file)
if os.path.exists(write_test_file):
os.remove(write_test_file)
def build_test_data(self, variable='v'):
metadata = {
'size': NCELLS,
'first_index': 0,
'first_id': 0,
'n': 505,
'variable': variable,
'last_id': 4,
'last_index': 5,
'dt': 0.1,
'label': "population0",
}
if variable == 'v':
metadata['units'] = 'mV'
elif variable == 'spikes':
metadata['units'] = 'ms'
data = np.empty((505, 2))
for i in range(NCELLS):
# signal
data[i*101:(i+1)*101, 0] = np.arange(i, i+101, dtype=float)
# index
data[i*101:(i+1)*101, 1] = i*np.ones((101,), dtype=float)
return data, metadata
build_test_data.__test__ = False
class BaseTestPyNNIO_Signals(BaseTestPyNNIO):
def setUp(self):
self.test_file = "test_file_v.%s" % self.file_extension
self.write_test_file("v")
def test_read_segment_containing_analogsignals_using_eager_cascade(self):
# eager == not lazy
io = self.io_cls(self.test_file)
segment = io.read_segment(lazy=False, cascade=True)
self.assertIsInstance(segment, Segment)
self.assertEqual(len(segment.analogsignals), NCELLS)
as0 = segment.analogsignals[0]
self.assertIsInstance(as0, AnalogSignal)
assert_arrays_equal(as0,
AnalogSignal(np.arange(0, 101, dtype=float),
sampling_period=0.1*pq.ms,
t_start=0*pq.s,
units=pq.mV))
as4 = segment.analogsignals[4]
self.assertIsInstance(as4, AnalogSignal)
assert_arrays_equal(as4,
AnalogSignal(np.arange(4, 105, dtype=float),
sampling_period=0.1*pq.ms,
t_start=0*pq.s,
units=pq.mV))
# test annotations (stuff from file metadata)
def test_read_analogsignal_using_eager(self):
io = self.io_cls(self.test_file)
as3 = io.read_analogsignal(lazy=False, channel_index=3)
self.assertIsInstance(as3, AnalogSignal)
assert_arrays_equal(as3,
AnalogSignal(np.arange(3, 104, dtype=float),
sampling_period=0.1*pq.ms,
t_start=0*pq.s,
units=pq.mV))
# should test annotations: 'channel_index', etc.
def test_read_spiketrain_should_fail_with_analogsignal_file(self):
io = self.io_cls(self.test_file)
self.assertRaises(TypeError, io.read_spiketrain, channel_index=0)
class BaseTestPyNNIO_Spikes(BaseTestPyNNIO):
def setUp(self):
self.test_file = "test_file_spikes.%s" % self.file_extension
self.write_test_file("spikes")
def test_read_segment_containing_spiketrains_using_eager_cascade(self):
io = self.io_cls(self.test_file)
segment = io.read_segment(lazy=False, cascade=True)
self.assertIsInstance(segment, Segment)
self.assertEqual(len(segment.spiketrains), NCELLS)
st0 = segment.spiketrains[0]
self.assertIsInstance(st0, SpikeTrain)
assert_arrays_equal(st0,
SpikeTrain(np.arange(0, 101, dtype=float),
t_start=0*pq.s,
t_stop=101*pq.ms,
units=pq.ms))
st4 = segment.spiketrains[4]
self.assertIsInstance(st4, SpikeTrain)
assert_arrays_equal(st4,
SpikeTrain(np.arange(4, 105, dtype=float),
t_start=0*pq.s,
t_stop=105*pq.ms,
units=pq.ms))
# test annotations (stuff from file metadata)
def test_read_spiketrain_using_eager(self):
io = self.io_cls(self.test_file)
st3 = io.read_spiketrain(lazy=False, channel_index=3)
self.assertIsInstance(st3, SpikeTrain)
assert_arrays_equal(st3,
SpikeTrain(np.arange(3, 104, dtype=float),
t_start=0*pq.s,
t_stop=104*pq.s,
units=pq.ms))
# should test annotations: 'channel_index', etc.
def test_read_analogsignal_should_fail_with_spiketrain_file(self):
io = self.io_cls(self.test_file)
self.assertRaises(TypeError, io.read_analogsignal, channel_index=2)
class BaseTestPyNNNumpyIO(object):
io_cls = PyNNNumpyIO
file_extension = "npz"
def write_test_file(self, variable='v', check=False):
data, metadata = self.build_test_data(variable)
metadata_array = np.array(sorted(metadata.items()))
np.savez(self.test_file, data=data, metadata=metadata_array)
if check:
data1, metadata1 = read_test_file(self.test_file)
assert metadata == metadata1, "%s != %s" % (metadata, metadata1)
assert data.shape == data1.shape == (505, 2), \
"%s, %s, (505, 2)" % (data.shape, data1.shape)
assert (data == data1).all()
assert metadata["n"] == 505
write_test_file.__test__ = False
class BaseTestPyNNTextIO(object):
io_cls = PyNNTextIO
file_extension = "txt"
def write_test_file(self, variable='v', check=False):
data, metadata = self.build_test_data(variable)
with open(self.test_file, 'wb') as f:
for item in sorted(metadata.items()):
f.write(("# %s = %s\n" % item).encode('utf8'))
np.savetxt(f, data)
if check:
raise NotImplementedError
write_test_file.__test__ = False
class TestPyNNNumpyIO_Signals(BaseTestPyNNNumpyIO, BaseTestPyNNIO_Signals,
unittest.TestCase):
__test__ = True
class TestPyNNNumpyIO_Spikes(BaseTestPyNNNumpyIO, BaseTestPyNNIO_Spikes,
unittest.TestCase):
__test__ = True
class TestPyNNTextIO_Signals(BaseTestPyNNTextIO, BaseTestPyNNIO_Signals,
unittest.TestCase):
__test__ = True
class TestPyNNTextIO_Spikes(BaseTestPyNNTextIO, BaseTestPyNNIO_Spikes,
unittest.TestCase):
__test__ = True
if __name__ == '__main__':
unittest.main()
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