multielectrode_grasp/code/python-neo/neo/test/iotest/test_klustakwikio.py

# -*- coding: utf-8 -*-
"""
Tests of neo.io.klustakwikio
"""

# needed for python 3 compatibility
from __future__ import absolute_import

import glob
import os.path
import sys
import tempfile

import unittest

import numpy as np
import quantities as pq

import neo
from neo.test.iotest.common_io_test import BaseTestIO
from neo.test.tools import assert_arrays_almost_equal
from neo.io.klustakwikio import KlustaKwikIO, HAVE_MLAB


@unittest.skipUnless(HAVE_MLAB, "requires matplotlib")
@unittest.skipIf(sys.version_info[0] > 2, "not Python 3 compatible")
class testFilenameParser(unittest.TestCase):
    """Tests that filenames can be loaded with or without basename.

    The test directory contains two basenames and some decoy files with
    malformed group numbers."""
    def setUp(self):
        self.dirname = os.path.join(tempfile.gettempdir(),
                                    'files_for_testing_neo',
                                    'klustakwik/test1')
        if not os.path.exists(self.dirname):
            raise unittest.SkipTest('data directory does not exist: ' +
                                    self.dirname)

    def test1(self):
        """Tests that files can be loaded by basename"""
        kio = KlustaKwikIO(filename=os.path.join(self.dirname, 'basename'))
        if not BaseTestIO.use_network:
            raise unittest.SkipTest("Requires download of data from the web")
        fetfiles = kio._fp.read_filenames('fet')

        self.assertEqual(len(fetfiles), 2)
        self.assertEqual(os.path.abspath(fetfiles[0]),
                         os.path.abspath(os.path.join(self.dirname,
                                                      'basename.fet.0')))
        self.assertEqual(os.path.abspath(fetfiles[1]),
                         os.path.abspath(os.path.join(self.dirname,
                                                      'basename.fet.1')))

    def test2(self):
        """Tests that files are loaded even without basename"""
        pass

        # this test is in flux, should probably have it default to
        # basename = os.path.split(dirname)[1] when dirname is a directory
        #~ dirname = os.path.normpath('./files_for_tests/klustakwik/test1')
        #~ kio = KlustaKwikIO(filename=dirname)
        #~ fetfiles = kio._fp.read_filenames('fet')

        #~ # It will just choose one of the two basenames, depending on which
        #~ # is first, so just assert that it did something without error.
        #~ self.assertNotEqual(len(fetfiles), 0)

    def test3(self):
        """Tests that files can be loaded by basename2"""
        kio = KlustaKwikIO(filename=os.path.join(self.dirname, 'basename2'))
        if not BaseTestIO.use_network:
            raise unittest.SkipTest("Requires download of data from the web")
        clufiles = kio._fp.read_filenames('clu')

        self.assertEqual(len(clufiles), 1)
        self.assertEqual(os.path.abspath(clufiles[1]),
                         os.path.abspath(os.path.join(self.dirname,
                                                      'basename2.clu.1')))


@unittest.skipUnless(HAVE_MLAB, "requires matplotlib")
@unittest.skipIf(sys.version_info[0] > 2, "not Python 3 compatible")
class testRead(unittest.TestCase):
    """Tests that data can be read from KlustaKwik files"""
    def setUp(self):
        self.dirname = os.path.join(tempfile.gettempdir(),
                                    'files_for_testing_neo',
                                    'klustakwik/test2')
        if not os.path.exists(self.dirname):
            raise unittest.SkipTest('data directory does not exist: ' +
                                    self.dirname)

    def test1(self):
        """Tests that data and metadata are read correctly"""
        kio = KlustaKwikIO(filename=os.path.join(self.dirname, 'base'),
                           sampling_rate=1000.)
        block = kio.read()[0]
        seg = block.segments[0]
        self.assertEqual(len(seg.spiketrains), 4)

        for st in seg.spiketrains:
            self.assertEqual(st.units, np.array(1.0) * pq.s)
            self.assertEqual(st.t_start, 0.0)

        self.assertEqual(seg.spiketrains[0].name, 'unit 1 from group 0')
        self.assertEqual(seg.spiketrains[0].annotations['cluster'], 1)
        self.assertEqual(seg.spiketrains[0].annotations['group'], 0)
        self.assertTrue(np.all(seg.spiketrains[0].times == np.array([.100,
                                                                     .200])))

        self.assertEqual(seg.spiketrains[1].name, 'unit 2 from group 0')
        self.assertEqual(seg.spiketrains[1].annotations['cluster'], 2)
        self.assertEqual(seg.spiketrains[1].annotations['group'], 0)
        self.assertEqual(seg.spiketrains[1].t_start, 0.0)
        self.assertTrue(np.all(seg.spiketrains[1].times == np.array([.305])))

        self.assertEqual(seg.spiketrains[2].name, 'unit -1 from group 1')
        self.assertEqual(seg.spiketrains[2].annotations['cluster'], -1)
        self.assertEqual(seg.spiketrains[2].annotations['group'], 1)
        self.assertEqual(seg.spiketrains[2].t_start, 0.0)
        self.assertTrue(np.all(seg.spiketrains[2].times == np.array([.253])))

        self.assertEqual(seg.spiketrains[3].name, 'unit 2 from group 1')
        self.assertEqual(seg.spiketrains[3].annotations['cluster'], 2)
        self.assertEqual(seg.spiketrains[3].annotations['group'], 1)
        self.assertEqual(seg.spiketrains[3].t_start, 0.0)
        self.assertTrue(np.all(seg.spiketrains[3].times == np.array([.050,
                                                                     .152])))

    def test2(self):
        """Checks that cluster id autosets to 0 without clu file"""
        kio = KlustaKwikIO(filename=os.path.join(self.dirname, 'base2'),
                           sampling_rate=1000.)
        block = kio.read()[0]
        seg = block.segments[0]
        self.assertEqual(len(seg.spiketrains), 1)
        self.assertEqual(seg.spiketrains[0].name, 'unit 0 from group 5')
        self.assertEqual(seg.spiketrains[0].annotations['cluster'], 0)
        self.assertEqual(seg.spiketrains[0].annotations['group'], 5)
        self.assertEqual(seg.spiketrains[0].t_start, 0.0)
        self.assertTrue(np.all(seg.spiketrains[0].times == np.array([0.026,
                                                                     0.122,
                                                                     0.228])))


@unittest.skipUnless(HAVE_MLAB, "requires matplotlib")
@unittest.skipIf(sys.version_info[0] > 2, "not Python 3 compatible")
class testWrite(unittest.TestCase):
    def setUp(self):
        self.dirname = os.path.join(tempfile.gettempdir(),
                                    'files_for_testing_neo',
                                    'klustakwik/test3')
        if not os.path.exists(self.dirname):
            raise unittest.SkipTest('data directory does not exist: ' +
                                    self.dirname)

    def test1(self):
        """Create clu and fet files based on spiketrains in a block.

        Checks that
            Files are created
            Converted to samples correctly
            Missing sampling rate are taken from IO reader default
            Spiketrains without cluster info are assigned to cluster 0
            Spiketrains across segments are concatenated
        """
        block = neo.Block()
        segment = neo.Segment()
        segment2 = neo.Segment()
        block.segments.append(segment)
        block.segments.append(segment2)

        # Fake spiketrain 1, will be sorted
        st1 = neo.SpikeTrain(times=[.002, .004, .006], units='s', t_stop=1.)
        st1.annotations['cluster'] = 0
        st1.annotations['group'] = 0
        segment.spiketrains.append(st1)

        # Fake spiketrain 1B, on another segment. No group specified,
        # default is 0.
        st1B = neo.SpikeTrain(times=[.106], units='s', t_stop=1.)
        st1B.annotations['cluster'] = 0
        segment2.spiketrains.append(st1B)

        # Fake spiketrain 2 on same group, no sampling rate specified
        st2 = neo.SpikeTrain(times=[.001, .003, .011], units='s', t_stop=1.)
        st2.annotations['cluster'] = 1
        st2.annotations['group'] = 0
        segment.spiketrains.append(st2)

        # Fake spiketrain 3 on new group, with different sampling rate
        st3 = neo.SpikeTrain(times=[.05, .09, .10], units='s', t_stop=1.)
        st3.annotations['cluster'] = -1
        st3.annotations['group'] = 1
        segment.spiketrains.append(st3)

        # Fake spiketrain 4 on new group, without cluster info
        st4 = neo.SpikeTrain(times=[.005, .009], units='s', t_stop=1.)
        st4.annotations['group'] = 2
        segment.spiketrains.append(st4)

        # Create empty directory for writing
        delete_test_session()

        # Create writer with default sampling rate
        kio = KlustaKwikIO(filename=os.path.join(self.dirname, 'base1'),
                           sampling_rate=1000.)
        kio.write_block(block)

        # Check files were created
        for fn in ['.fet.0', '.fet.1', '.clu.0', '.clu.1']:
            self.assertTrue(os.path.exists(os.path.join(self.dirname,
                                                        'base1' + fn)))

        # Check files contain correct content
        # Spike times on group 0
        data = file(os.path.join(self.dirname, 'base1.fet.0')).readlines()
        data = [int(d) for d in data]
        self.assertEqual(data, [0, 2, 4, 6, 1, 3, 11, 106])

        # Clusters on group 0
        data = file(os.path.join(self.dirname, 'base1.clu.0')).readlines()
        data = [int(d) for d in data]
        self.assertEqual(data, [2, 0, 0, 0, 1, 1, 1, 0])

        # Spike times on group 1
        data = file(os.path.join(self.dirname, 'base1.fet.1')).readlines()
        data = [int(d) for d in data]
        self.assertEqual(data, [0, 50, 90, 100])

        # Clusters on group 1
        data = file(os.path.join(self.dirname, 'base1.clu.1')).readlines()
        data = [int(d) for d in data]
        self.assertEqual(data, [1, -1, -1, -1])

        # Spike times on group 2
        data = file(os.path.join(self.dirname, 'base1.fet.2')).readlines()
        data = [int(d) for d in data]
        self.assertEqual(data, [0, 5, 9])

        # Clusters on group 2
        data = file(os.path.join(self.dirname, 'base1.clu.2')).readlines()
        data = [int(d) for d in data]
        self.assertEqual(data, [1, 0, 0])

        # Empty out test session again
        delete_test_session()


@unittest.skipUnless(HAVE_MLAB, "requires matplotlib")
@unittest.skipIf(sys.version_info[0] > 2, "not Python 3 compatible")
class testWriteWithFeatures(unittest.TestCase):
    def setUp(self):
        self.dirname = os.path.join(tempfile.gettempdir(),
                                    'files_for_testing_neo',
                                    'klustakwik/test4')
        if not os.path.exists(self.dirname):
            raise unittest.SkipTest('data directory does not exist: ' +
                                    self.dirname)

    def test1(self):
        """Create clu and fet files based on spiketrains in a block.

        Checks that
            Files are created
            Converted to samples correctly
            Missing sampling rate are taken from IO reader default
            Spiketrains without cluster info are assigned to cluster 0
            Spiketrains across segments are concatenated
        """
        block = neo.Block()
        segment = neo.Segment()
        segment2 = neo.Segment()
        block.segments.append(segment)
        block.segments.append(segment2)

        # Fake spiketrain 1
        st1 = neo.SpikeTrain(times=[.002, .004, .006], units='s', t_stop=1.)
        st1.annotations['cluster'] = 0
        st1.annotations['group'] = 0
        wff = np.array([
            [11.3, 0.2],
            [-0.3, 12.3],
            [3.0, -2.5]])
        st1.annotations['waveform_features'] = wff
        segment.spiketrains.append(st1)

        # Create empty directory for writing
        if not os.path.exists(self.dirname):
            os.mkdir(self.dirname)
        delete_test_session(self.dirname)

        # Create writer
        kio = KlustaKwikIO(filename=os.path.join(self.dirname, 'base2'),
                           sampling_rate=1000.)
        kio.write_block(block)

        # Check files were created
        for fn in ['.fet.0', '.clu.0']:
            self.assertTrue(os.path.exists(os.path.join(self.dirname,
                                                        'base2' + fn)))

        # Check files contain correct content
        fi = file(os.path.join(self.dirname, 'base2.fet.0'))

        # first line is nbFeatures
        self.assertEqual(fi.readline(), '2\n')

        # Now check waveforms and times are same
        data = fi.readlines()
        new_wff = []
        new_times = []
        for line in data:
            line_split = line.split()
            new_wff.append([float(val) for val in line_split[:-1]])
            new_times.append(int(line_split[-1]))
        self.assertEqual(new_times, [2, 4, 6])
        assert_arrays_almost_equal(wff, np.array(new_wff), .00001)

        # Clusters on group 0
        data = file(os.path.join(self.dirname, 'base2.clu.0')).readlines()
        data = [int(d) for d in data]
        self.assertEqual(data, [1, 0, 0, 0])

        # Now read the features and test same
        block = kio.read_block()
        train = block.segments[0].spiketrains[0]
        assert_arrays_almost_equal(wff, train.annotations['waveform_features'],
                                   .00001)

        # Empty out test session again
        delete_test_session(self.dirname)


@unittest.skipUnless(HAVE_MLAB, "requires matplotlib")
@unittest.skipIf(sys.version_info[0] > 2, "not Python 3 compatible")
class CommonTests(BaseTestIO, unittest.TestCase):
    ioclass = KlustaKwikIO

    # These are the files it tries to read and test for compliance
    files_to_test = [
        'test2/base',
        'test2/base2',
        ]

    # Will fetch from g-node if they don't already exist locally
    # How does it know to do this before any of the other tests?
    files_to_download = [
        'test1/basename.clu.0',
        'test1/basename.fet.-1',
        'test1/basename.fet.0',
        'test1/basename.fet.1',
        'test1/basename.fet.1a',
        'test1/basename.fet.a1',
        'test1/basename2.clu.1',
        'test1/basename2.fet.1',
        'test1/basename2.fet.1a',
        'test2/base2.fet.5',
        'test2/base.clu.0',
        'test2/base.clu.1',
        'test2/base.fet.0',
        'test2/base.fet.1',
        'test3/base1.clu.0',
        'test3/base1.clu.1',
        'test3/base1.clu.2',
        'test3/base1.fet.0',
        'test3/base1.fet.1',
        'test3/base1.fet.2'
        ]


def delete_test_session(dirname=None):
    """Removes all file in directory so we can test writing to it"""
    if dirname is None:
        dirname = os.path.join(os.path.dirname(__file__),
                               'files_for_tests/klustakwik/test3')
    for fi in glob.glob(os.path.join(dirname, '*')):
        os.remove(fi)


if __name__ == '__main__':
    unittest.main()