Python Report.data_path方法代码示例

# 需要导入模块: from mne.report import Report [as 别名]
# 或者: from mne.report.Report import data_path [as 别名]
def test_render_report():
    """Test rendering -*.fif files for mne report.
    """

    report = Report(info_fname=raw_fname)
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        report.parse_folder(data_path=base_dir)
    assert_true(len(w) == 1)

    # Check correct paths and filenames
    assert_true(raw_fname in report.fnames)
    assert_true(event_name in report.fnames)
    assert_true(report.data_path == base_dir)

    # Check if all files were rendered in the report
    fnames = glob.glob(op.join(base_dir, '*.fif'))
    bad_name = 'test_ctf_comp_raw-eve.fif'
    decrement = any(fname.endswith(bad_name) for fname in fnames)
    fnames = [fname for fname in fnames if
              fname.endswith(('-eve.fif', '-ave.fif', '-cov.fif',
                              '-sol.fif', '-fwd.fif', '-inv.fif',
                              '-src.fif', '-trans.fif', 'raw.fif',
                              'sss.fif', '-epo.fif')) and
              not fname.endswith(bad_name)]
    # last file above gets created by another test, and it shouldn't be there

    for fname in fnames:
        assert_true(''.join(report.html).find(op.basename(fname)) != -1)

    assert_equal(len(report.fnames), len(fnames))
    assert_equal(len(report.html), len(report.fnames))

    evoked1 = read_evokeds(evoked1_fname)
    evoked2 = read_evokeds(evoked2_fname)
    assert_equal(len(report.fnames) + len(evoked1) + len(evoked2) - 2,
                 report.initial_id - decrement)

    # Check saving functionality
    report.data_path = tempdir
    report.save(fname=op.join(tempdir, 'report.html'), open_browser=False)
    assert_true(op.isfile(op.join(tempdir, 'report.html')))

    # Check add_section functionality
    fig = evoked1[0].plot(show=False)
    report.add_section(figs=fig,  # test non-list input
                       captions=['evoked response'])
    assert_equal(len(report.html), len(fnames) + 1)
    assert_equal(len(report.html), len(report.fnames))
    assert_raises(ValueError, report.add_section, figs=[fig, fig],
                  captions='H')

    # Check saving same report to new filename
    report.save(fname=op.join(tempdir, 'report2.html'), open_browser=False)
    assert_true(op.isfile(op.join(tempdir, 'report2.html')))

    # Check overwriting file
    report.save(fname=op.join(tempdir, 'report.html'), open_browser=False,
                overwrite=True)
    assert_true(op.isfile(op.join(tempdir, 'report.html')))

# 需要导入模块: from mne.report import Report [as 别名]
# 或者: from mne.report.Report import data_path [as 别名]
def test_render_report():
    """Test rendering -*.fif files for mne report.
    """
    tempdir = _TempDir()
    raw_fname_new = op.join(tempdir, 'temp_raw.fif')
    event_fname_new = op.join(tempdir, 'temp_raw-eve.fif')
    cov_fname_new = op.join(tempdir, 'temp_raw-cov.fif')
    fwd_fname_new = op.join(tempdir, 'temp_raw-fwd.fif')
    inv_fname_new = op.join(tempdir, 'temp_raw-inv.fif')
    for a, b in [[raw_fname, raw_fname_new],
                 [event_fname, event_fname_new],
                 [cov_fname, cov_fname_new],
                 [fwd_fname, fwd_fname_new],
                 [inv_fname, inv_fname_new]]:
        shutil.copyfile(a, b)

    # create and add -epo.fif and -ave.fif files
    epochs_fname = op.join(tempdir, 'temp-epo.fif')
    evoked_fname = op.join(tempdir, 'temp-ave.fif')
    raw = Raw(raw_fname_new)
    picks = pick_types(raw.info, meg='mag', eeg=False)  # faster with one type
    epochs = Epochs(raw, read_events(event_fname), 1, -0.2, 0.2, picks=picks)
    epochs.save(epochs_fname)
    epochs.average().save(evoked_fname)

    report = Report(info_fname=raw_fname_new, subjects_dir=subjects_dir)
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        report.parse_folder(data_path=tempdir)
    assert_true(len(w) >= 1)

    # Check correct paths and filenames
    fnames = glob.glob(op.join(tempdir, '*.fif'))
    for fname in fnames:
        assert_true(op.basename(fname) in
                    [op.basename(x) for x in report.fnames])
        assert_true(''.join(report.html).find(op.basename(fname)) != -1)

    assert_equal(len(report.fnames), len(fnames))
    assert_equal(len(report.html), len(report.fnames))

    # Check saving functionality
    report.data_path = tempdir
    report.save(fname=op.join(tempdir, 'report.html'), open_browser=False)
    assert_true(op.isfile(op.join(tempdir, 'report.html')))

    assert_equal(len(report.html), len(fnames))
    assert_equal(len(report.html), len(report.fnames))

    # Check saving same report to new filename
    report.save(fname=op.join(tempdir, 'report2.html'), open_browser=False)
    assert_true(op.isfile(op.join(tempdir, 'report2.html')))

    # Check overwriting file
    report.save(fname=op.join(tempdir, 'report.html'), open_browser=False,
                overwrite=True)
    assert_true(op.isfile(op.join(tempdir, 'report.html')))

# 需要导入模块: from mne.report import Report [as 别名]
# 或者: from mne.report.Report import data_path [as 别名]

#.........这里部分代码省略.........

    Returns
    -------
    report : mne.report.Report
        The mne report.

    Side-effects
    ------------
    - make results dir if it does not exists
    - sets log file for sterr output
    - writes log file with runtime information
    """
    if use_agg is True:
        import matplotlib
        matplotlib.use('Agg')

    if not callable(script):
        if not op.isfile(script):
            raise ValueError('sorry, this is not a script!')
    if not op.isdir(results_dir) and not callable(script):
        results_dir = op.join(op.dirname(op.dirname(script)), results_dir)
    else:
        results_dir = op.join(op.curdir, results_dir)

    if not callable(script):
        step = op.splitext(op.split(script)[1])[0]
    else:
        step = script.__name__

    if not op.isabs(results_dir):
        results_dir = op.abspath(results_dir)

    start_path = op.dirname(results_dir)
    results_dir = op.join(results_dir, step)
    if not op.exists(results_dir):
        logger.info('generating results dir')
        _forec_create_dir(results_dir, start=start_path)

    if run_id is None:
        run_id = create_run_id()
        logger.info('generated run id: %s' % run_id)
    else:
        logger.info('using existing run id: %s' % run_id)

    logger.info('preparing logging:')
    logging_dir = op.join(results_dir, run_id)
    if not op.exists(logging_dir):
        logger.info('... making logging directory: %s' % logging_dir)
        os.mkdir(logging_dir)
    else:
        logger.info('... using logging directory: %s' % logging_dir)
    modules = get_versions(sys)
    runtime_log = op.join(logging_dir, 'run_time.json')
    with open(runtime_log, 'w') as fid:
        json.dump(modules, fid)
    logger.info('... writing runtime info to: %s' % runtime_log)

    script_code_out = op.join(logging_dir, 'script.py')
    if callable(script):
        script_code_in = inspect.getsourcefile(script)
    else:
        script_code_in = script

    if not op.isfile(script_code_out):
        with open(script_code_out, 'w') as fid:
            with open(script_code_in) as script_fid:
                source_code = script_fid.read()
            fid.write(source_code)
    logger.info('... logging source code of calling script')

    if config is None:
        config = 'config.py'

    if op.isabs(config):
        config_fname = config
    else:
        config_fname = ''

    config_code = op.join(  # weird behavior of join if last arg is path
        results_dir, run_id, op.split(config_fname)[-1])
    if not op.isfile(config_fname):
        logger.info('... No config found. Logging nothing.')
    elif op.isfile(config_code):
        logger.info('... Config already written. I assume that you are using'
                    ' the same run_id for different runs of your script.')
    else:
        with open(config_code, 'w') as fid:
            with open(config_fname) as config_fid:
                source_code = config_fid.read()
            fid.write(source_code)
        logger.info('... logging source code of "%s".' % config_fname)

    logger.info('... preparing Report')
    report = Report(title=step)
    report.data_path = logging_dir
    std_logfile = op.join(logging_dir, 'run_output.log')
    logger.info('... setting logfile: %s' % std_logfile)
    set_log_file(std_logfile)

    return report, run_id, results_dir, logger

# 需要导入模块: from mne.report import Report [as 别名]
# 或者: from mne.report.Report import data_path [as 别名]
def test_render_report():
    """Test rendering -*.fif files for mne report."""
    tempdir = _TempDir()
    raw_fname_new = op.join(tempdir, 'temp_raw.fif')
    event_fname_new = op.join(tempdir, 'temp_raw-eve.fif')
    cov_fname_new = op.join(tempdir, 'temp_raw-cov.fif')
    fwd_fname_new = op.join(tempdir, 'temp_raw-fwd.fif')
    inv_fname_new = op.join(tempdir, 'temp_raw-inv.fif')
    for a, b in [[raw_fname, raw_fname_new],
                 [event_fname, event_fname_new],
                 [cov_fname, cov_fname_new],
                 [fwd_fname, fwd_fname_new],
                 [inv_fname, inv_fname_new]]:
        shutil.copyfile(a, b)

    # create and add -epo.fif and -ave.fif files
    epochs_fname = op.join(tempdir, 'temp-epo.fif')
    evoked_fname = op.join(tempdir, 'temp-ave.fif')
    # Speed it up by picking channels
    raw = read_raw_fif(raw_fname_new, preload=True)
    raw.pick_channels(['MEG 0111', 'MEG 0121'])
    epochs = Epochs(raw, read_events(event_fname), 1, -0.2, 0.2)
    epochs.save(epochs_fname)
    # This can take forever (stall Travis), so let's make it fast
    # Also, make sure crop range is wide enough to avoid rendering bug
    epochs.average().crop(0.1, 0.2).save(evoked_fname)

    report = Report(info_fname=raw_fname_new, subjects_dir=subjects_dir)
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        report.parse_folder(data_path=tempdir, on_error='raise')
    assert_true(len(w) >= 1)
    assert_true(repr(report))

    # Check correct paths and filenames
    fnames = glob.glob(op.join(tempdir, '*.fif'))
    for fname in fnames:
        assert_true(op.basename(fname) in
                    [op.basename(x) for x in report.fnames])
        assert_true(''.join(report.html).find(op.basename(fname)) != -1)

    assert_equal(len(report.fnames), len(fnames))
    assert_equal(len(report.html), len(report.fnames))
    assert_equal(len(report.fnames), len(report))

    # Check saving functionality
    report.data_path = tempdir
    report.save(fname=op.join(tempdir, 'report.html'), open_browser=False)
    assert_true(op.isfile(op.join(tempdir, 'report.html')))

    assert_equal(len(report.html), len(fnames))
    assert_equal(len(report.html), len(report.fnames))

    # Check saving same report to new filename
    report.save(fname=op.join(tempdir, 'report2.html'), open_browser=False)
    assert_true(op.isfile(op.join(tempdir, 'report2.html')))

    # Check overwriting file
    report.save(fname=op.join(tempdir, 'report.html'), open_browser=False,
                overwrite=True)
    assert_true(op.isfile(op.join(tempdir, 'report.html')))

    # Check pattern matching with multiple patterns
    pattern = ['*raw.fif', '*eve.fif']
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        report.parse_folder(data_path=tempdir, pattern=pattern)
    assert_true(len(w) >= 1)
    assert_true(repr(report))

    fnames = glob.glob(op.join(tempdir, '*.raw')) + \
        glob.glob(op.join(tempdir, '*.raw'))
    for fname in fnames:
        assert_true(op.basename(fname) in
                    [op.basename(x) for x in report.fnames])
        assert_true(''.join(report.html).find(op.basename(fname)) != -1)

    assert_raises(ValueError, Report, image_format='foo')
    assert_raises(ValueError, Report, image_format=None)

    # SVG rendering
    report = Report(info_fname=raw_fname_new, subjects_dir=subjects_dir,
                    image_format='svg')
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        report.parse_folder(data_path=tempdir, on_error='raise')

# 需要导入模块: from mne.report import Report [as 别名]
# 或者: from mne.report.Report import data_path [as 别名]
def test_render_report():
    """Test rendering -*.fif files for mne report."""
    tempdir = _TempDir()
    raw_fname_new = op.join(tempdir, 'temp_raw.fif')
    event_fname_new = op.join(tempdir, 'temp_raw-eve.fif')
    cov_fname_new = op.join(tempdir, 'temp_raw-cov.fif')
    fwd_fname_new = op.join(tempdir, 'temp_raw-fwd.fif')
    inv_fname_new = op.join(tempdir, 'temp_raw-inv.fif')
    for a, b in [[raw_fname, raw_fname_new],
                 [event_fname, event_fname_new],
                 [cov_fname, cov_fname_new],
                 [fwd_fname, fwd_fname_new],
                 [inv_fname, inv_fname_new]]:
        shutil.copyfile(a, b)

    # create and add -epo.fif and -ave.fif files
    epochs_fname = op.join(tempdir, 'temp-epo.fif')
    evoked_fname = op.join(tempdir, 'temp-ave.fif')
    raw = read_raw_fif(raw_fname_new)
    picks = pick_types(raw.info, meg='mag', eeg=False)  # faster with one type
    epochs = Epochs(raw, read_events(event_fname), 1, -0.2, 0.2, picks=picks)
    epochs.save(epochs_fname)
    epochs.average().save(evoked_fname)

    report = Report(info_fname=raw_fname_new, subjects_dir=subjects_dir)
    if sys.version.startswith('3.5'):  # XXX Some strange MPL/3.5 error...
        raise SkipTest('Python 3.5 and mpl have unresolved issues')
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        report.parse_folder(data_path=tempdir, on_error='raise')
    assert_true(len(w) >= 1)
    assert_true(repr(report))

    # Check correct paths and filenames
    fnames = glob.glob(op.join(tempdir, '*.fif'))
    for fname in fnames:
        assert_true(op.basename(fname) in
                    [op.basename(x) for x in report.fnames])
        assert_true(''.join(report.html).find(op.basename(fname)) != -1)

    assert_equal(len(report.fnames), len(fnames))
    assert_equal(len(report.html), len(report.fnames))
    assert_equal(len(report.fnames), len(report))

    # Check saving functionality
    report.data_path = tempdir
    report.save(fname=op.join(tempdir, 'report.html'), open_browser=False)
    assert_true(op.isfile(op.join(tempdir, 'report.html')))

    assert_equal(len(report.html), len(fnames))
    assert_equal(len(report.html), len(report.fnames))

    # Check saving same report to new filename
    report.save(fname=op.join(tempdir, 'report2.html'), open_browser=False)
    assert_true(op.isfile(op.join(tempdir, 'report2.html')))

    # Check overwriting file
    report.save(fname=op.join(tempdir, 'report.html'), open_browser=False,
                overwrite=True)
    assert_true(op.isfile(op.join(tempdir, 'report.html')))

    # Check pattern matching with multiple patterns
    pattern = ['*raw.fif', '*eve.fif']
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        report.parse_folder(data_path=tempdir, pattern=pattern)
    assert_true(len(w) >= 1)
    assert_true(repr(report))

    fnames = glob.glob(op.join(tempdir, '*.raw')) + \
        glob.glob(op.join(tempdir, '*.raw'))
    for fname in fnames:
        assert_true(op.basename(fname) in
                    [op.basename(x) for x in report.fnames])
        assert_true(''.join(report.html).find(op.basename(fname)) != -1)

# 需要导入模块: from mne.report import Report [as 别名]
# 或者: from mne.report.Report import data_path [as 别名]
def test_render_report():
    """Test rendering -*.fif files for mne report."""
    tempdir = _TempDir()
    raw_fname_new = op.join(tempdir, 'temp_raw.fif')
    ms_fname_new = op.join(tempdir, 'temp_ms_raw.fif')
    event_fname_new = op.join(tempdir, 'temp_raw-eve.fif')
    cov_fname_new = op.join(tempdir, 'temp_raw-cov.fif')
    fwd_fname_new = op.join(tempdir, 'temp_raw-fwd.fif')
    inv_fname_new = op.join(tempdir, 'temp_raw-inv.fif')
    for a, b in [[raw_fname, raw_fname_new],
                 [ms_fname, ms_fname_new],
                 [event_fname, event_fname_new],
                 [cov_fname, cov_fname_new],
                 [fwd_fname, fwd_fname_new],
                 [inv_fname, inv_fname_new]]:
        shutil.copyfile(a, b)

    # create and add -epo.fif and -ave.fif files
    epochs_fname = op.join(tempdir, 'temp-epo.fif')
    evoked_fname = op.join(tempdir, 'temp-ave.fif')
    # Speed it up by picking channels
    raw = read_raw_fif(raw_fname_new, preload=True)
    raw.pick_channels(['MEG 0111', 'MEG 0121'])
    raw.del_proj()
    epochs = Epochs(raw, read_events(event_fname), 1, -0.2, 0.2)
    epochs.save(epochs_fname)
    # This can take forever (stall Travis), so let's make it fast
    # Also, make sure crop range is wide enough to avoid rendering bug
    epochs.average().crop(0.1, 0.2).save(evoked_fname)

    report = Report(info_fname=raw_fname_new, subjects_dir=subjects_dir)
    with pytest.warns(RuntimeWarning, match='Cannot render MRI'):
        report.parse_folder(data_path=tempdir, on_error='raise')
    assert repr(report)

    # Check correct paths and filenames
    fnames = glob.glob(op.join(tempdir, '*.fif'))
    for fname in fnames:
        assert (op.basename(fname) in
                [op.basename(x) for x in report.fnames])
        assert (''.join(report.html).find(op.basename(fname)) != -1)

    assert_equal(len(report.fnames), len(fnames))
    assert_equal(len(report.html), len(report.fnames))
    assert_equal(len(report.fnames), len(report))

    # Check saving functionality
    report.data_path = tempdir
    fname = op.join(tempdir, 'report.html')
    report.save(fname=fname, open_browser=False)
    assert (op.isfile(fname))
    with open(fname, 'rb') as fid:
        html = fid.read().decode('utf-8')
    assert '(MaxShield on)' in html

    assert_equal(len(report.html), len(fnames))
    assert_equal(len(report.html), len(report.fnames))

    # Check saving same report to new filename
    report.save(fname=op.join(tempdir, 'report2.html'), open_browser=False)
    assert (op.isfile(op.join(tempdir, 'report2.html')))

    # Check overwriting file
    report.save(fname=op.join(tempdir, 'report.html'), open_browser=False,
                overwrite=True)
    assert (op.isfile(op.join(tempdir, 'report.html')))

    # Check pattern matching with multiple patterns
    pattern = ['*raw.fif', '*eve.fif']
    with pytest.warns(RuntimeWarning, match='Cannot render MRI'):
        report.parse_folder(data_path=tempdir, pattern=pattern)
    assert (repr(report))

    fnames = glob.glob(op.join(tempdir, '*.raw')) + \
        glob.glob(op.join(tempdir, '*.raw'))
    for fname in fnames:
        assert (op.basename(fname) in
                [op.basename(x) for x in report.fnames])
        assert (''.join(report.html).find(op.basename(fname)) != -1)

    pytest.raises(ValueError, Report, image_format='foo')
    pytest.raises(ValueError, Report, image_format=None)

    # SVG rendering
    report = Report(info_fname=raw_fname_new, subjects_dir=subjects_dir,
                    image_format='svg')
    with pytest.warns(RuntimeWarning, match='Cannot render MRI'):
        report.parse_folder(data_path=tempdir, on_error='raise')

    # ndarray support smoke test
    report.add_figs_to_section(np.zeros((2, 3, 3)), 'caption', 'section')