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test_layout.py
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from __future__ import print_function
# Authors: Alexandre Gramfort <[email protected]>
# Denis Engemann <[email protected]>
# Martin Luessi <[email protected]>
# Eric Larson <[email protected]>
#
# License: Simplified BSD
import copy
import os.path as op
import warnings
# Set our plotters to test mode
import matplotlib
import numpy as np
from numpy.testing import (assert_array_almost_equal, assert_array_equal,
assert_allclose)
from nose.tools import assert_equal, assert_true, assert_raises
from mne.channels import (make_eeg_layout, make_grid_layout, read_layout,
find_layout)
from mne.channels.layout import (_box_size, _auto_topomap_coords,
generate_2d_layout)
from mne.utils import run_tests_if_main
from mne import pick_types, pick_info
from mne.io import read_raw_kit, _empty_info, read_info
from mne.io.constants import FIFF
from mne.bem import fit_sphere_to_headshape
from mne.utils import _TempDir
matplotlib.use('Agg') # for testing don't use X server
warnings.simplefilter('always')
io_dir = op.join(op.dirname(__file__), '..', '..', 'io')
fif_fname = op.join(io_dir, 'tests', 'data', 'test_raw.fif')
lout_path = op.join(io_dir, 'tests', 'data')
bti_dir = op.join(io_dir, 'bti', 'tests', 'data')
fname_ctf_raw = op.join(io_dir, 'tests', 'data', 'test_ctf_comp_raw.fif')
fname_kit_157 = op.join(io_dir, 'kit', 'tests', 'data', 'test.sqd')
fname_kit_umd = op.join(io_dir, 'kit', 'tests', 'data', 'test_umd-raw.sqd')
def _get_test_info():
"""Helper to make test info"""
test_info = _empty_info(1000)
loc = np.array([0., 0., 0., 1., 0., 0., 0., 1., 0., 0., 0., 1.],
dtype=np.float32)
test_info['chs'] = [
{'cal': 1, 'ch_name': 'ICA 001', 'coil_type': 0, 'coord_Frame': 0,
'kind': 502, 'loc': loc.copy(), 'logno': 1, 'range': 1.0, 'scanno': 1,
'unit': -1, 'unit_mul': 0},
{'cal': 1, 'ch_name': 'ICA 002', 'coil_type': 0, 'coord_Frame': 0,
'kind': 502, 'loc': loc.copy(), 'logno': 2, 'range': 1.0, 'scanno': 2,
'unit': -1, 'unit_mul': 0},
{'cal': 0.002142000012099743, 'ch_name': 'EOG 061', 'coil_type': 1,
'coord_frame': 0, 'kind': 202, 'loc': loc.copy(), 'logno': 61,
'range': 1.0, 'scanno': 376, 'unit': 107, 'unit_mul': 0}]
test_info._update_redundant()
test_info._check_consistency()
return test_info
def test_io_layout_lout():
"""Test IO with .lout files"""
tempdir = _TempDir()
layout = read_layout('Vectorview-all', scale=False)
layout.save(op.join(tempdir, 'foobar.lout'))
layout_read = read_layout(op.join(tempdir, 'foobar.lout'), path='./',
scale=False)
assert_array_almost_equal(layout.pos, layout_read.pos, decimal=2)
assert_true(layout.names, layout_read.names)
print(layout) # test repr
def test_io_layout_lay():
"""Test IO with .lay files"""
tempdir = _TempDir()
layout = read_layout('CTF151', scale=False)
layout.save(op.join(tempdir, 'foobar.lay'))
layout_read = read_layout(op.join(tempdir, 'foobar.lay'), path='./',
scale=False)
assert_array_almost_equal(layout.pos, layout_read.pos, decimal=2)
assert_true(layout.names, layout_read.names)
def test_auto_topomap_coords():
"""Test mapping of coordinates in 3D space to 2D"""
info = read_info(fif_fname)
picks = pick_types(info, meg=False, eeg=True, eog=False, stim=False)
# Remove extra digitization point, so EEG digitization points match up
# with the EEG channels
del info['dig'][85]
# Remove head origin from channel locations, so mapping with digitization
# points yields the same result
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL,
FIFF.FIFFV_POINT_EEG,
FIFF.FIFFV_POINT_EXTRA)
_, origin_head, _ = fit_sphere_to_headshape(info, dig_kinds, units='m')
for ch in info['chs']:
ch['loc'][:3] -= origin_head
# Use channel locations
l0 = _auto_topomap_coords(info, picks)
# Remove electrode position information, use digitization points from now
# on.
for ch in info['chs']:
ch['loc'].fill(0)
l1 = _auto_topomap_coords(info, picks)
assert_allclose(l1, l0, atol=1e-3)
# Test plotting mag topomap without channel locations: it should fail
mag_picks = pick_types(info, meg='mag')
assert_raises(ValueError, _auto_topomap_coords, info, mag_picks)
# Test function with too many EEG digitization points: it should fail
info['dig'].append({'r': [1, 2, 3], 'kind': FIFF.FIFFV_POINT_EEG})
assert_raises(ValueError, _auto_topomap_coords, info, picks)
# Test function with too little EEG digitization points: it should fail
info['dig'] = info['dig'][:-2]
assert_raises(ValueError, _auto_topomap_coords, info, picks)
# Electrode positions must be unique
info['dig'].append(info['dig'][-1])
assert_raises(ValueError, _auto_topomap_coords, info, picks)
# Test function without EEG digitization points: it should fail
info['dig'] = [d for d in info['dig'] if d['kind'] != FIFF.FIFFV_POINT_EEG]
assert_raises(RuntimeError, _auto_topomap_coords, info, picks)
# Test function without any digitization points, it should fail
info['dig'] = None
assert_raises(RuntimeError, _auto_topomap_coords, info, picks)
info['dig'] = []
assert_raises(RuntimeError, _auto_topomap_coords, info, picks)
def test_make_eeg_layout():
"""Test creation of EEG layout"""
tempdir = _TempDir()
tmp_name = 'foo'
lout_name = 'test_raw'
lout_orig = read_layout(kind=lout_name, path=lout_path)
info = read_info(fif_fname)
info['bads'].append(info['ch_names'][360])
layout = make_eeg_layout(info, exclude=[])
assert_array_equal(len(layout.names), len([ch for ch in info['ch_names']
if ch.startswith('EE')]))
layout.save(op.join(tempdir, tmp_name + '.lout'))
lout_new = read_layout(kind=tmp_name, path=tempdir, scale=False)
assert_array_equal(lout_new.kind, tmp_name)
assert_allclose(layout.pos, lout_new.pos, atol=0.1)
assert_array_equal(lout_orig.names, lout_new.names)
# Test input validation
assert_raises(ValueError, make_eeg_layout, info, radius=-0.1)
assert_raises(ValueError, make_eeg_layout, info, radius=0.6)
assert_raises(ValueError, make_eeg_layout, info, width=-0.1)
assert_raises(ValueError, make_eeg_layout, info, width=1.1)
assert_raises(ValueError, make_eeg_layout, info, height=-0.1)
assert_raises(ValueError, make_eeg_layout, info, height=1.1)
def test_make_grid_layout():
"""Test creation of grid layout"""
tempdir = _TempDir()
tmp_name = 'bar'
lout_name = 'test_ica'
lout_orig = read_layout(kind=lout_name, path=lout_path)
layout = make_grid_layout(_get_test_info())
layout.save(op.join(tempdir, tmp_name + '.lout'))
lout_new = read_layout(kind=tmp_name, path=tempdir)
assert_array_equal(lout_new.kind, tmp_name)
assert_array_equal(lout_orig.pos, lout_new.pos)
assert_array_equal(lout_orig.names, lout_new.names)
# Test creating grid layout with specified number of columns
layout = make_grid_layout(_get_test_info(), n_col=2)
# Vertical positions should be equal
assert_true(layout.pos[0, 1] == layout.pos[1, 1])
# Horizontal positions should be unequal
assert_true(layout.pos[0, 0] != layout.pos[1, 0])
# Box sizes should be equal
assert_array_equal(layout.pos[0, 3:], layout.pos[1, 3:])
def test_find_layout():
"""Test finding layout"""
import matplotlib.pyplot as plt
assert_raises(ValueError, find_layout, _get_test_info(), ch_type='meep')
sample_info = read_info(fif_fname)
grads = pick_types(sample_info, meg='grad')
sample_info2 = pick_info(sample_info, grads)
mags = pick_types(sample_info, meg='mag')
sample_info3 = pick_info(sample_info, mags)
# mock new convention
sample_info4 = copy.deepcopy(sample_info)
for ii, name in enumerate(sample_info4['ch_names']):
new = name.replace(' ', '')
sample_info4['chs'][ii]['ch_name'] = new
eegs = pick_types(sample_info, meg=False, eeg=True)
sample_info5 = pick_info(sample_info, eegs)
lout = find_layout(sample_info, ch_type=None)
assert_equal(lout.kind, 'Vectorview-all')
assert_true(all(' ' in k for k in lout.names))
lout = find_layout(sample_info2, ch_type='meg')
assert_equal(lout.kind, 'Vectorview-all')
# test new vector-view
lout = find_layout(sample_info4, ch_type=None)
assert_equal(lout.kind, 'Vectorview-all')
assert_true(all(' ' not in k for k in lout.names))
lout = find_layout(sample_info, ch_type='grad')
assert_equal(lout.kind, 'Vectorview-grad')
lout = find_layout(sample_info2)
assert_equal(lout.kind, 'Vectorview-grad')
lout = find_layout(sample_info2, ch_type='grad')
assert_equal(lout.kind, 'Vectorview-grad')
lout = find_layout(sample_info2, ch_type='meg')
assert_equal(lout.kind, 'Vectorview-all')
lout = find_layout(sample_info, ch_type='mag')
assert_equal(lout.kind, 'Vectorview-mag')
lout = find_layout(sample_info3)
assert_equal(lout.kind, 'Vectorview-mag')
lout = find_layout(sample_info3, ch_type='mag')
assert_equal(lout.kind, 'Vectorview-mag')
lout = find_layout(sample_info3, ch_type='meg')
assert_equal(lout.kind, 'Vectorview-all')
lout = find_layout(sample_info, ch_type='eeg')
assert_equal(lout.kind, 'EEG')
lout = find_layout(sample_info5)
assert_equal(lout.kind, 'EEG')
lout = find_layout(sample_info5, ch_type='eeg')
assert_equal(lout.kind, 'EEG')
# no common layout, 'meg' option not supported
lout = find_layout(read_info(fname_ctf_raw))
assert_equal(lout.kind, 'CTF-275')
fname_bti_raw = op.join(bti_dir, 'exported4D_linux_raw.fif')
lout = find_layout(read_info(fname_bti_raw))
assert_equal(lout.kind, 'magnesWH3600')
raw_kit = read_raw_kit(fname_kit_157)
lout = find_layout(raw_kit.info)
assert_equal(lout.kind, 'KIT-157')
raw_kit.info['bads'] = ['MEG 13', 'MEG 14', 'MEG 15', 'MEG 16']
lout = find_layout(raw_kit.info)
assert_equal(lout.kind, 'KIT-157')
raw_umd = read_raw_kit(fname_kit_umd)
lout = find_layout(raw_umd.info)
assert_equal(lout.kind, 'KIT-UMD-3')
# Test plotting
lout.plot()
lout.plot(picks=np.arange(10))
plt.close('all')
def test_box_size():
"""Test calculation of box sizes."""
# No points. Box size should be 1,1.
assert_allclose(_box_size([]), (1.0, 1.0))
# Create one point. Box size should be 1,1.
point = [(0, 0)]
assert_allclose(_box_size(point), (1.0, 1.0))
# Create two points. Box size should be 0.5,1.
points = [(0.25, 0.5), (0.75, 0.5)]
assert_allclose(_box_size(points), (0.5, 1.0))
# Create three points. Box size should be (0.5, 0.5).
points = [(0.25, 0.25), (0.75, 0.25), (0.5, 0.75)]
assert_allclose(_box_size(points), (0.5, 0.5))
# Create a grid of points. Box size should be (0.1, 0.1).
x, y = np.meshgrid(np.linspace(-0.5, 0.5, 11), np.linspace(-0.5, 0.5, 11))
x, y = x.ravel(), y.ravel()
assert_allclose(_box_size(np.c_[x, y]), (0.1, 0.1))
# Create a random set of points. This should never break the function.
rng = np.random.RandomState(42)
points = rng.rand(100, 2)
width, height = _box_size(points)
assert_true(width is not None)
assert_true(height is not None)
# Test specifying an existing width.
points = [(0.25, 0.25), (0.75, 0.25), (0.5, 0.75)]
assert_allclose(_box_size(points, width=0.4), (0.4, 0.5))
# Test specifying an existing width that has influence on the calculated
# height.
points = [(0.25, 0.25), (0.75, 0.25), (0.5, 0.75)]
assert_allclose(_box_size(points, width=0.2), (0.2, 1.0))
# Test specifying an existing height.
points = [(0.25, 0.25), (0.75, 0.25), (0.5, 0.75)]
assert_allclose(_box_size(points, height=0.4), (0.5, 0.4))
# Test specifying an existing height that has influence on the calculated
# width.
points = [(0.25, 0.25), (0.75, 0.45), (0.5, 0.75)]
assert_allclose(_box_size(points, height=0.1), (1.0, 0.1))
# Test specifying both width and height. The function should simply return
# these.
points = [(0.25, 0.25), (0.75, 0.45), (0.5, 0.75)]
assert_array_equal(_box_size(points, width=0.1, height=0.1), (0.1, 0.1))
# Test specifying a width that will cause unfixable horizontal overlap and
# essentially breaks the function (height will be 0).
points = [(0.25, 0.25), (0.75, 0.25), (0.5, 0.75)]
assert_array_equal(_box_size(points, width=1), (1, 0))
# Test adding some padding.
# Create three points. Box size should be a little less than (0.5, 0.5).
points = [(0.25, 0.25), (0.75, 0.25), (0.5, 0.75)]
assert_allclose(_box_size(points, padding=0.1), (0.9 * 0.5, 0.9 * 0.5))
def test_generate_2d_layout():
"""Test creation of a layout from 2d points."""
snobg = 10
sbg = 15
side = range(snobg)
bg_image = np.random.RandomState(42).randn(sbg, sbg)
w, h = [.2, .5]
# Generate fake data
xy = np.array([(i, j) for i in side for j in side])
lt = generate_2d_layout(xy, w=w, h=h)
# Correct points ordering / minmaxing
comp_1, comp_2 = [(5, 0), (7, 0)]
assert_true(lt.pos[:, :2].max() == 1)
assert_true(lt.pos[:, :2].min() == 0)
with np.errstate(invalid='ignore'): # divide by zero
assert_allclose(xy[comp_2] / float(xy[comp_1]),
lt.pos[comp_2] / float(lt.pos[comp_1]))
assert_allclose(lt.pos[0, [2, 3]], [w, h])
# Correct number elements
assert_true(lt.pos.shape[1] == 4)
assert_true(len(lt.box) == 4)
# Make sure background image normalizing is correct
lt_bg = generate_2d_layout(xy, bg_image=bg_image)
assert_allclose(lt_bg.pos[:, :2].max(), xy.max() / float(sbg))
run_tests_if_main()