Python utils._TempDir函数代码示例

def test_preload_modify():
    """Test preloading and modifying data
    """
    tempdir = _TempDir()
    for preload in [False, True, 'memmap.dat']:
        raw = Raw(fif_fname, preload=preload)

        nsamp = raw.last_samp - raw.first_samp + 1
        picks = pick_types(raw.info, meg='grad', exclude='bads')

        data = rng.randn(len(picks), nsamp // 2)

        try:
            raw[picks, :nsamp // 2] = data
        except RuntimeError as err:
            if not preload:
                continue
            else:
                raise err

        tmp_fname = op.join(tempdir, 'raw.fif')
        raw.save(tmp_fname, overwrite=True)

        raw_new = Raw(tmp_fname)
        data_new, _ = raw_new[picks, :nsamp / 2]

        assert_allclose(data, data_new)

def test_volume_source_space():
    """Test setting up volume source spaces."""
    tempdir = _TempDir()
    src = read_source_spaces(fname_vol)
    temp_name = op.join(tempdir, 'temp-src.fif')
    surf = read_bem_surfaces(fname_bem, s_id=FIFF.FIFFV_BEM_SURF_ID_BRAIN)
    surf['rr'] *= 1e3  # convert to mm
    # The one in the testing dataset (uses bem as bounds)
    for bem, surf in zip((fname_bem, None), (None, surf)):
        src_new = setup_volume_source_space(
            'sample', pos=7.0, bem=bem, surface=surf, mri='T1.mgz',
            subjects_dir=subjects_dir)
        write_source_spaces(temp_name, src_new, overwrite=True)
        src[0]['subject_his_id'] = 'sample'  # XXX: to make comparison pass
        _compare_source_spaces(src, src_new, mode='approx')
        del src_new
        src_new = read_source_spaces(temp_name)
        _compare_source_spaces(src, src_new, mode='approx')
    pytest.raises(IOError, setup_volume_source_space, 'sample',
                  pos=7.0, bem=None, surface='foo',  # bad surf
                  mri=fname_mri, subjects_dir=subjects_dir)
    assert repr(src) == repr(src_new)
    assert src.kind == 'volume'
    # Spheres
    sphere = make_sphere_model(r0=(0., 0., 0.), head_radius=0.1,
                               relative_radii=(0.9, 1.0), sigmas=(0.33, 1.0))
    src = setup_volume_source_space(pos=10)
    src_new = setup_volume_source_space(pos=10, sphere=sphere)
    _compare_source_spaces(src, src_new, mode='exact')
    pytest.raises(ValueError, setup_volume_source_space, sphere='foo')
    # Need a radius
    sphere = make_sphere_model(head_radius=None)
    pytest.raises(ValueError, setup_volume_source_space, sphere=sphere)

def test_add_source_space_distances_limited():
    """Test adding distances to source space with a dist_limit."""
    tempdir = _TempDir()
    src = read_source_spaces(fname)
    src_new = read_source_spaces(fname)
    del src_new[0]['dist']
    del src_new[1]['dist']
    n_do = 200  # limit this for speed
    src_new[0]['vertno'] = src_new[0]['vertno'][:n_do].copy()
    src_new[1]['vertno'] = src_new[1]['vertno'][:n_do].copy()
    out_name = op.join(tempdir, 'temp-src.fif')
    try:
        add_source_space_distances(src_new, dist_limit=0.007)
    except RuntimeError:  # what we throw when scipy version is wrong
        raise SkipTest('dist_limit requires scipy > 0.13')
    write_source_spaces(out_name, src_new)
    src_new = read_source_spaces(out_name)

    for so, sn in zip(src, src_new):
        assert_array_equal(so['dist_limit'], np.array([-0.007], np.float32))
        assert_array_equal(sn['dist_limit'], np.array([0.007], np.float32))
        do = so['dist']
        dn = sn['dist']

        # clean out distances > 0.007 in C code
        do.data[do.data > 0.007] = 0
        do.eliminate_zeros()

        # make sure we have some comparable distances
        assert np.sum(do.data < 0.007) > 400

        # do comparison over the region computed
        d = (do - dn)[:sn['vertno'][n_do - 1]][:, :sn['vertno'][n_do - 1]]
        assert_allclose(np.zeros_like(d.data), d.data, rtol=0, atol=1e-6)

def test_flash_bem():
    """Test mne flash_bem."""
    check_usage(mne_flash_bem, force_help=True)
    # Using the sample dataset
    subjects_dir = op.join(sample.data_path(download=False), 'subjects')
    # Copy necessary files to tempdir
    tempdir = _TempDir()
    mridata_path = op.join(subjects_dir, 'sample', 'mri')
    subject_path_new = op.join(tempdir, 'sample')
    mridata_path_new = op.join(subject_path_new, 'mri')
    os.makedirs(op.join(mridata_path_new, 'flash'))
    os.makedirs(op.join(subject_path_new, 'bem'))
    shutil.copyfile(op.join(mridata_path, 'T1.mgz'),
                    op.join(mridata_path_new, 'T1.mgz'))
    shutil.copyfile(op.join(mridata_path, 'brain.mgz'),
                    op.join(mridata_path_new, 'brain.mgz'))
    # Copy the available mri/flash/mef*.mgz files from the dataset
    flash_path = op.join(mridata_path_new, 'flash')
    for kind in (5, 30):
        in_fname = op.join(mridata_path, 'flash', 'mef%02d.mgz' % kind)
        shutil.copyfile(in_fname, op.join(flash_path, op.basename(in_fname)))
    # Test mne flash_bem with --noconvert option
    # (since there are no DICOM Flash images in dataset)
    out_fnames = list()
    for kind in ('outer_skin', 'outer_skull', 'inner_skull'):
        out_fnames.append(op.join(subject_path_new, 'bem', 'outer_skin.surf'))
    assert not any(op.isfile(out_fname) for out_fname in out_fnames)
    with ArgvSetter(('-d', tempdir, '-s', 'sample', '-n'),
                    disable_stdout=False, disable_stderr=False):
        mne_flash_bem.run()
    # do they exist and are expected size
    for out_fname in out_fnames:
        _, tris = read_surface(out_fname)
        assert len(tris) == 5120

def test_read_write_info():
    """Test IO of info
    """
    tempdir = _TempDir()
    info = read_info(raw_fname)
    temp_file = op.join(tempdir, 'info.fif')
    # check for bug `#1198`
    info['dev_head_t']['trans'] = np.eye(4)
    t1 = info['dev_head_t']['trans']
    write_info(temp_file, info)
    info2 = read_info(temp_file)
    t2 = info2['dev_head_t']['trans']
    assert_true(len(info['chs']) == len(info2['chs']))
    assert_array_equal(t1, t2)
    # proc_history (e.g., GH#1875)
    creator = u'é'
    info = read_info(chpi_fname)
    info['proc_history'][0]['creator'] = creator
    info['hpi_meas'][0]['creator'] = creator
    info['subject_info']['his_id'] = creator
    write_info(temp_file, info)
    info = read_info(temp_file)
    assert_equal(info['proc_history'][0]['creator'], creator)
    assert_equal(info['hpi_meas'][0]['creator'], creator)
    assert_equal(info['subject_info']['his_id'], creator)

def test_make_morph_maps():
    """Test reading and creating morph maps."""
    # make a new fake subjects_dir
    tempdir = _TempDir()
    for subject in ('sample', 'sample_ds', 'fsaverage_ds'):
        os.mkdir(op.join(tempdir, subject))
        os.mkdir(op.join(tempdir, subject, 'surf'))
        regs = ('reg', 'left_right') if subject == 'fsaverage_ds' else ('reg',)
        for hemi in ['lh', 'rh']:
            for reg in regs:
                args = [subject, 'surf', hemi + '.sphere.' + reg]
                copyfile(op.join(subjects_dir, *args),
                         op.join(tempdir, *args))

    for subject_from, subject_to, xhemi in (
            ('fsaverage_ds', 'sample_ds', False),
            ('fsaverage_ds', 'fsaverage_ds', True)):
        # trigger the creation of morph-maps dir and create the map
        with warnings.catch_warnings(record=True):
            mmap = read_morph_map(subject_from, subject_to, tempdir,
                                  xhemi=xhemi)
        mmap2 = read_morph_map(subject_from, subject_to, subjects_dir,
                               xhemi=xhemi)
        assert_equal(len(mmap), len(mmap2))
        for m1, m2 in zip(mmap, mmap2):
            # deal with sparse matrix stuff
            diff = (m1 - m2).data
            assert_allclose(diff, np.zeros_like(diff), atol=1e-3, rtol=0)

    # This will also trigger creation, but it's trivial
    with warnings.catch_warnings(record=True):
        mmap = read_morph_map('sample', 'sample', subjects_dir=tempdir)
    for mm in mmap:
        assert_true((mm - sparse.eye(mm.shape[0], mm.shape[0])).sum() == 0)

def test_make_flash_bem():
    """Test computing bem from flash images."""
    tmp = _TempDir()
    bemdir = op.join(subjects_dir, 'sample', 'bem')
    flash_path = op.join(subjects_dir, 'sample', 'mri', 'flash')

    for surf in ('inner_skull', 'outer_skull', 'outer_skin'):
        copy(op.join(bemdir, surf + '.surf'), tmp)
        copy(op.join(bemdir, surf + '.tri'), tmp)
    copy(op.join(bemdir, 'inner_skull_tmp.tri'), tmp)
    copy(op.join(bemdir, 'outer_skin_from_testing.surf'), tmp)

    # This function deletes the tri files at the end.
    try:
        make_flash_bem('sample', overwrite=True, subjects_dir=subjects_dir,
                       flash_path=flash_path)
        for surf in ('inner_skull', 'outer_skull', 'outer_skin'):
            coords, faces = read_surface(op.join(bemdir, surf + '.surf'))
            surf = 'outer_skin_from_testing' if surf == 'outer_skin' else surf
            coords_c, faces_c = read_surface(op.join(tmp, surf + '.surf'))
            assert_equal(0, faces.min())
            assert_equal(coords.shape[0], faces.max() + 1)
            assert_allclose(coords, coords_c)
            assert_allclose(faces, faces_c)
    finally:
        for surf in ('inner_skull', 'outer_skull', 'outer_skin'):
            remove(op.join(bemdir, surf + '.surf'))  # delete symlinks
            copy(op.join(tmp, surf + '.tri'), bemdir)  # return deleted tri
            copy(op.join(tmp, surf + '.surf'), bemdir)  # return moved surf
        copy(op.join(tmp, 'inner_skull_tmp.tri'), bemdir)
        copy(op.join(tmp, 'outer_skin_from_testing.surf'), bemdir)
    plt.close('all')

def test_flash_bem():
    """Test mne flash_bem."""
    check_usage(mne_flash_bem, force_help=True)
    # Using the sample dataset
    subjects_dir = op.join(sample.data_path(download=False), 'subjects')
    # Copy necessary files to tempdir
    tempdir = _TempDir()
    mridata_path = op.join(subjects_dir, 'sample', 'mri')
    mridata_path_new = op.join(tempdir, 'sample', 'mri')
    os.makedirs(op.join(mridata_path_new, 'flash'))
    os.makedirs(op.join(tempdir, 'sample', 'bem'))
    shutil.copyfile(op.join(mridata_path, 'T1.mgz'),
                    op.join(mridata_path_new, 'T1.mgz'))
    shutil.copyfile(op.join(mridata_path, 'brain.mgz'),
                    op.join(mridata_path_new, 'brain.mgz'))
    # Copy the available mri/flash/mef*.mgz files from the dataset
    files = glob.glob(op.join(mridata_path, 'flash', 'mef*.mgz'))
    for infile in files:
        shutil.copyfile(infile, op.join(mridata_path_new, 'flash',
                                        op.basename(infile)))
    # Test mne flash_bem with --noconvert option
    # (since there are no DICOM Flash images in dataset)
    currdir = os.getcwd()
    with ArgvSetter(('-d', tempdir, '-s', 'sample', '-n'),
                    disable_stdout=False, disable_stderr=False):
        mne_flash_bem.run()
    os.chdir(currdir)

def test_mne_c_design():
    """Test MNE-C filter design."""
    tempdir = _TempDir()
    temp_fname = op.join(tempdir, 'test_raw.fif')
    out_fname = op.join(tempdir, 'test_c_raw.fif')
    x = np.zeros((1, 10001))
    x[0, 5000] = 1.
    time_sl = slice(5000 - 4096, 5000 + 4097)
    sfreq = 1000.
    RawArray(x, create_info(1, sfreq, 'eeg')).save(temp_fname)

    tols = dict(rtol=1e-4, atol=1e-4)
    cmd = ('mne_process_raw', '--projoff', '--raw', temp_fname,
           '--save', out_fname)
    run_subprocess(cmd)
    h = design_mne_c_filter(sfreq, None, 40)
    h_c = read_raw_fif(out_fname)[0][0][0][time_sl]
    assert_allclose(h, h_c, **tols)

    run_subprocess(cmd + ('--highpass', '5', '--highpassw', '2.5'))
    h = design_mne_c_filter(sfreq, 5, 40, 2.5)
    h_c = read_raw_fif(out_fname)[0][0][0][time_sl]
    assert_allclose(h, h_c, **tols)

    run_subprocess(cmd + ('--lowpass', '1000', '--highpass', '10'))
    h = design_mne_c_filter(sfreq, 10, None, verbose=True)
    h_c = read_raw_fif(out_fname)[0][0][0][time_sl]
    assert_allclose(h, h_c, **tols)

def test_cov_estimation_on_raw_segment():
    """Test estimation from raw on continuous recordings (typically empty room)
    """
    tempdir = _TempDir()
    raw = Raw(raw_fname, preload=False)
    cov = compute_raw_data_covariance(raw)
    cov_mne = read_cov(erm_cov_fname)
    assert_true(cov_mne.ch_names == cov.ch_names)
    assert_true(linalg.norm(cov.data - cov_mne.data, ord='fro')
                / linalg.norm(cov.data, ord='fro') < 1e-4)

    # test IO when computation done in Python
    cov.save(op.join(tempdir, 'test-cov.fif'))  # test saving
    cov_read = read_cov(op.join(tempdir, 'test-cov.fif'))
    assert_true(cov_read.ch_names == cov.ch_names)
    assert_true(cov_read.nfree == cov.nfree)
    assert_array_almost_equal(cov.data, cov_read.data)

    # test with a subset of channels
    picks = pick_channels(raw.ch_names, include=raw.ch_names[:5])
    cov = compute_raw_data_covariance(raw, picks=picks)
    assert_true(cov_mne.ch_names[:5] == cov.ch_names)
    assert_true(linalg.norm(cov.data - cov_mne.data[picks][:, picks],
                ord='fro') / linalg.norm(cov.data, ord='fro') < 1e-4)
    # make sure we get a warning with too short a segment
    raw_2 = raw.crop(0, 1)
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        cov = compute_raw_data_covariance(raw_2)
    assert_true(len(w) == 1)

def test_read_segment():
    """Test writing raw kit files when preload is False
    """
    tempdir = _TempDir()
    raw1 = read_raw_kit(sqd_path, mrk_path, elp_path, hsp_path, stim='<',
                        preload=False)
    raw1_file = op.join(tempdir, 'test1-raw.fif')
    raw1.save(raw1_file, buffer_size_sec=.1, overwrite=True)
    raw2 = read_raw_kit(sqd_path, mrk_path, elp_path, hsp_path, stim='<',
                        preload=True)
    raw2_file = op.join(tempdir, 'test2-raw.fif')
    raw2.save(raw2_file, buffer_size_sec=.1, overwrite=True)
    data1, times1 = raw1[0, 0:1]

    raw1 = Raw(raw1_file, preload=True)
    raw2 = Raw(raw2_file, preload=True)
    assert_array_equal(raw1._data, raw2._data)
    data2, times2 = raw2[0, 0:1]
    assert_array_almost_equal(data1, data2)
    assert_array_almost_equal(times1, times2)
    raw3 = read_raw_kit(sqd_path, mrk_path, elp_path, hsp_path, stim='<',
                        preload=True)
    assert_array_almost_equal(raw1._data, raw3._data)
    raw4 = read_raw_kit(sqd_path, mrk_path, elp_path, hsp_path, stim='<',
                        preload=False)
    raw4.load_data()
    buffer_fname = op.join(tempdir, 'buffer')
    assert_array_almost_equal(raw1._data, raw4._data)
    raw5 = read_raw_kit(sqd_path, mrk_path, elp_path, hsp_path, stim='<',
                        preload=buffer_fname)
    assert_array_almost_equal(raw1._data, raw5._data)

def test_io_cov():
    """Test IO for noise covariance matrices
    """
    tempdir = _TempDir()
    cov = read_cov(cov_fname)
    cov.save(op.join(tempdir, 'test-cov.fif'))
    cov2 = read_cov(op.join(tempdir, 'test-cov.fif'))
    assert_array_almost_equal(cov.data, cov2.data)

    cov2 = read_cov(cov_gz_fname)
    assert_array_almost_equal(cov.data, cov2.data)
    cov2.save(op.join(tempdir, 'test-cov.fif.gz'))
    cov2 = read_cov(op.join(tempdir, 'test-cov.fif.gz'))
    assert_array_almost_equal(cov.data, cov2.data)

    cov['bads'] = ['EEG 039']
    cov_sel = pick_channels_cov(cov, exclude=cov['bads'])
    assert_true(cov_sel['dim'] == (len(cov['data']) - len(cov['bads'])))
    assert_true(cov_sel['data'].shape == (cov_sel['dim'], cov_sel['dim']))
    cov_sel.save(op.join(tempdir, 'test-cov.fif'))

    cov2 = read_cov(cov_gz_fname)
    assert_array_almost_equal(cov.data, cov2.data)
    cov2.save(op.join(tempdir, 'test-cov.fif.gz'))
    cov2 = read_cov(op.join(tempdir, 'test-cov.fif.gz'))
    assert_array_almost_equal(cov.data, cov2.data)

    # test warnings on bad filenames
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        cov_badname = op.join(tempdir, 'test-bad-name.fif.gz')
        write_cov(cov_badname, cov)
        read_cov(cov_badname)
    assert_true(len(w) == 2)

def test_make_scalp_surfaces():
    """Test mne make_scalp_surfaces"""
    check_usage(mne_make_scalp_surfaces)
    # Copy necessary files to avoid FreeSurfer call
    tempdir = _TempDir()
    surf_path = op.join(subjects_dir, 'sample', 'surf')
    surf_path_new = op.join(tempdir, 'sample', 'surf')
    os.mkdir(op.join(tempdir, 'sample'))
    os.mkdir(surf_path_new)
    os.mkdir(op.join(tempdir, 'sample', 'bem'))
    shutil.copy(op.join(surf_path, 'lh.seghead'), surf_path_new)

    orig_fs = os.getenv('FREESURFER_HOME', None)
    orig_mne = os.getenv('MNE_ROOT')
    if orig_fs is not None:
        del os.environ['FREESURFER_HOME']
    cmd = ('-s', 'sample', '--subjects-dir', tempdir)
    os.environ['_MNE_TESTING_SCALP'] = 'true'
    try:
        with ArgvSetter(cmd, disable_stdout=False, disable_stderr=False):
            assert_raises(RuntimeError, mne_make_scalp_surfaces.run)
            os.environ['FREESURFER_HOME'] = tempdir  # don't need it
            del os.environ['MNE_ROOT']
            assert_raises(RuntimeError, mne_make_scalp_surfaces.run)
            os.environ['MNE_ROOT'] = orig_mne
            mne_make_scalp_surfaces.run()
            assert_raises(IOError, mne_make_scalp_surfaces.run)  # no overwrite
    finally:
        if orig_fs is not None:
            os.environ['FREESURFER_HOME'] = orig_fs
        os.environ['MNE_ROOT'] = orig_mne
        del os.environ['_MNE_TESTING_SCALP']

def test_make_forward_solution_sphere():
    """Test making a forward solution with a sphere model."""
    temp_dir = _TempDir()
    fname_src_small = op.join(temp_dir, 'sample-oct-2-src.fif')
    src = setup_source_space('sample', 'oct2', subjects_dir=subjects_dir,
                             add_dist=False)
    write_source_spaces(fname_src_small, src)  # to enable working with MNE-C
    out_name = op.join(temp_dir, 'tmp-fwd.fif')
    run_subprocess(['mne_forward_solution', '--meg', '--eeg',
                    '--meas', fname_raw, '--src', fname_src_small,
                    '--mri', fname_trans, '--fwd', out_name])
    fwd = read_forward_solution(out_name)
    sphere = make_sphere_model(verbose=True)
    fwd_py = make_forward_solution(fname_raw, fname_trans, src, sphere,
                                   meg=True, eeg=True, verbose=True)
    _compare_forwards(fwd, fwd_py, 366, 108,
                      meg_rtol=5e-1, meg_atol=1e-6,
                      eeg_rtol=5e-1, eeg_atol=5e-1)
    # Since the above is pretty lax, let's check a different way
    for meg, eeg in zip([True, False], [False, True]):
        fwd_ = pick_types_forward(fwd, meg=meg, eeg=eeg)
        fwd_py_ = pick_types_forward(fwd, meg=meg, eeg=eeg)
        assert_allclose(np.corrcoef(fwd_['sol']['data'].ravel(),
                                    fwd_py_['sol']['data'].ravel())[0, 1],
                        1.0, rtol=1e-3)

def test_read_segment():
    """Test writing raw eeg files when preload is False
    """
    tempdir = _TempDir()
    raw1 = read_raw_brainvision(vhdr_path, eog=eog, preload=False)
    raw1_file = op.join(tempdir, 'test1-raw.fif')
    raw1.save(raw1_file, overwrite=True)
    raw11 = Raw(raw1_file, preload=True)
    data1, times1 = raw1[:, :]
    data11, times11 = raw11[:, :]
    assert_array_almost_equal(data1, data11, 8)
    assert_array_almost_equal(times1, times11)
    assert_equal(sorted(raw1.info.keys()), sorted(raw11.info.keys()))

    raw2 = read_raw_brainvision(vhdr_path, eog=eog, preload=True)
    raw2_file = op.join(tempdir, 'test2-raw.fif')
    raw2.save(raw2_file, overwrite=True)
    data2, times2 = raw2[:, :]
    assert_array_equal(data1, data2)
    assert_array_equal(times1, times2)

    raw1 = Raw(raw1_file, preload=True)
    raw2 = Raw(raw2_file, preload=True)
    assert_array_equal(raw1._data, raw2._data)

    # save with buffer size smaller than file
    raw3_file = op.join(tempdir, 'test3-raw.fif')
    raw3 = read_raw_brainvision(vhdr_path, eog=eog)
    raw3.save(raw3_file, buffer_size_sec=2)
    raw3 = Raw(raw3_file, preload=True)
    assert_array_equal(raw3._data, raw1._data)