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# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# Mainak Jas <mainak@neuro.hut.fi>
# Mark Wronkiewicz <wronk.mark@gmail.com>
#
# License: Simplified BSD
import os.path as op
from pathlib import Path
import numpy as np
from numpy.testing import assert_array_equal, assert_allclose
import pytest
import matplotlib.pyplot as plt
from matplotlib.colors import Colormap
from matplotlib.figure import Figure
from mne import (make_field_map, pick_channels_evoked, read_evokeds,
read_trans, read_dipole, SourceEstimate,
make_sphere_model, use_coil_def, pick_types,
setup_volume_source_space, read_forward_solution,
convert_forward_solution, MixedSourceEstimate)
from mne.source_estimate import _BaseVolSourceEstimate
from mne.io import (read_raw_ctf, read_raw_bti, read_raw_kit, read_info,
read_raw_nirx)
from mne.io._digitization import write_dig
from mne.io.pick import pick_info
from mne.io.constants import FIFF
from mne.minimum_norm import apply_inverse
from mne.viz import (plot_sparse_source_estimates, plot_source_estimates,
snapshot_brain_montage, plot_head_positions,
plot_alignment, Figure3D,
plot_brain_colorbar, link_brains, mne_analyze_colormap)
from mne.viz._3d import _process_clim, _linearize_map, _get_map_ticks
from mne.viz.utils import _fake_click, _fake_keypress, _fake_scroll, _get_cmap
from mne.utils import requires_nibabel, catch_logging, _record_warnings
from mne.datasets import testing
from mne.source_space import read_source_spaces
from mne.transforms import Transform
from mne.bem import read_bem_solution, read_bem_surfaces
data_dir = testing.data_path(download=False)
subjects_dir = op.join(data_dir, 'subjects')
trans_fname = op.join(data_dir, 'MEG', 'sample',
'sample_audvis_trunc-trans.fif')
src_fname = op.join(data_dir, 'subjects', 'sample', 'bem',
'sample-oct-6-src.fif')
dip_fname = op.join(data_dir, 'MEG', 'sample', 'sample_audvis_trunc_set1.dip')
ctf_fname = op.join(data_dir, 'CTF', 'testdata_ctf.ds')
nirx_fname = op.join(data_dir, 'NIRx', 'nirscout',
'nirx_15_2_recording_w_short')
io_dir = op.join(op.abspath(op.dirname(__file__)), '..', '..', 'io')
base_dir = op.join(io_dir, 'tests', 'data')
evoked_fname = op.join(base_dir, 'test-ave.fif')
fwd_fname = op.join(data_dir, 'MEG', 'sample',
'sample_audvis_trunc-meg-vol-7-fwd.fif')
fwd_fname2 = op.join(data_dir, 'MEG', 'sample',
'sample_audvis_trunc-meg-eeg-oct-4-fwd.fif')
base_dir = op.join(io_dir, 'bti', 'tests', 'data')
pdf_fname = op.join(base_dir, 'test_pdf_linux')
config_fname = op.join(base_dir, 'test_config_linux')
hs_fname = op.join(base_dir, 'test_hs_linux')
sqd_fname = op.join(io_dir, 'kit', 'tests', 'data', 'test.sqd')
coil_3d = """# custom cube coil def
1 9999 1 8 3e-03 0.000e+00 "QuSpin ZFOPM 3mm cube"
0.1250 -0.750e-03 -0.750e-03 -0.750e-03 0.000 0.000 1.000
0.1250 -0.750e-03 0.750e-03 -0.750e-03 0.000 0.000 1.000
0.1250 0.750e-03 -0.750e-03 -0.750e-03 0.000 0.000 1.000
0.1250 0.750e-03 0.750e-03 -0.750e-03 0.000 0.000 1.000
0.1250 -0.750e-03 -0.750e-03 0.750e-03 0.000 0.000 1.000
0.1250 -0.750e-03 0.750e-03 0.750e-03 0.000 0.000 1.000
0.1250 0.750e-03 -0.750e-03 0.750e-03 0.000 0.000 1.000
0.1250 0.750e-03 0.750e-03 0.750e-03 0.000 0.000 1.000
1 9998 1 4 3e-03 0.000e+00 "3mm square"
0.1250 -0.750e-03 -0.750e-03 0.000 0.000 0.000 1.000
0.1250 -0.750e-03 0.750e-03 0.000 0.000 0.000 1.000
0.1250 0.750e-03 -0.750e-03 0.000 0.000 0.000 1.000
0.1250 0.750e-03 0.750e-03 0.000 0.000 0.000 1.000
"""
def test_plot_head_positions():
"""Test plotting of head positions."""
info = read_info(evoked_fname)
pos = np.random.RandomState(0).randn(4, 10)
pos[:, 0] = np.arange(len(pos))
destination = (0., 0., 0.04)
with _record_warnings(): # old MPL will cause a warning
plot_head_positions(pos)
plot_head_positions(pos, mode='field', info=info,
destination=destination)
plot_head_positions([pos, pos]) # list support
pytest.raises(ValueError, plot_head_positions, ['pos'])
pytest.raises(ValueError, plot_head_positions, pos[:, :9])
pytest.raises(ValueError, plot_head_positions, pos, 'foo')
with pytest.raises(ValueError, match='shape'):
plot_head_positions(pos, axes=1.)
@testing.requires_testing_data
@pytest.mark.slowtest
def test_plot_sparse_source_estimates(renderer_interactive, brain_gc):
"""Test plotting of (sparse) source estimates."""
sample_src = read_source_spaces(src_fname)
# dense version
vertices = [s['vertno'] for s in sample_src]
n_time = 5
n_verts = sum(len(v) for v in vertices)
stc_data = np.zeros((n_verts * n_time))
stc_size = stc_data.size
stc_data[(np.random.rand(stc_size // 20) * stc_size).astype(int)] = \
np.random.RandomState(0).rand(stc_data.size // 20)
stc_data.shape = (n_verts, n_time)
stc = SourceEstimate(stc_data, vertices, 1, 1)
colormap = 'mne_analyze'
brain = plot_source_estimates(
stc, 'sample', colormap=colormap, background=(1, 1, 0),
subjects_dir=subjects_dir, colorbar=True, clim='auto')
brain.close()
del brain
with pytest.raises(TypeError, match='figure must be'):
plot_source_estimates(
stc, 'sample', figure='foo', hemi='both', clim='auto',
subjects_dir=subjects_dir)
# now do sparse version
vertices = sample_src[0]['vertno']
inds = [111, 333]
stc_data = np.zeros((len(inds), n_time))
stc_data[0, 1] = 1.
stc_data[1, 4] = 2.
vertices = [vertices[inds], np.empty(0, dtype=np.int64)]
stc = SourceEstimate(stc_data, vertices, 1, 1)
out = plot_sparse_source_estimates(
sample_src, stc, bgcolor=(1, 1, 1), opacity=0.5,
high_resolution=False)
assert isinstance(out, Figure3D)
@testing.requires_testing_data
@pytest.mark.slowtest
def test_plot_evoked_field(renderer):
"""Test plotting evoked field."""
evoked = read_evokeds(evoked_fname, condition='Left Auditory',
baseline=(-0.2, 0.0))
evoked = pick_channels_evoked(evoked, evoked.ch_names[::10]) # speed
for t, n_contours in zip(['meg', None], [21, 0]):
with pytest.warns(RuntimeWarning, match='projection'):
maps = make_field_map(evoked, trans_fname, subject='sample',
subjects_dir=subjects_dir, n_jobs=None,
ch_type=t)
evoked.plot_field(maps, time=0.1, n_contours=n_contours)
def _assert_n_actors(fig, renderer, n_actors):
__tracebackhide__ = True
assert isinstance(fig, Figure3D)
assert len(fig.plotter.renderer.actors) == n_actors
@pytest.mark.slowtest # Slow on Azure
@testing.requires_testing_data # all use trans + head surf
@pytest.mark.parametrize('system', [
'Neuromag',
'CTF',
'BTi',
'KIT',
])
def test_plot_alignment_meg(renderer, system):
"""Test plotting of MEG sensors + helmet."""
if system == 'Neuromag':
this_info = read_info(evoked_fname)
elif system == 'CTF':
this_info = read_raw_ctf(ctf_fname).info
elif system == 'BTi':
this_info = read_raw_bti(
pdf_fname, config_fname, hs_fname, convert=True,
preload=False).info
else:
assert system == 'KIT'
this_info = read_raw_kit(sqd_fname).info
meg = ['helmet', 'sensors']
if system == 'KIT':
meg.append('ref')
fig = plot_alignment(
this_info, read_trans(trans_fname), subject='sample',
subjects_dir=subjects_dir, meg=meg, eeg=False)
assert isinstance(fig, Figure3D)
# count the number of objects: should be n_meg_ch + 1 (helmet) + 1 (head)
use_info = pick_info(this_info, pick_types(
this_info, meg=True, eeg=False, ref_meg='ref' in meg, exclude=()))
n_actors = use_info['nchan'] + 2
_assert_n_actors(fig, renderer, n_actors)
@testing.requires_testing_data
def test_plot_alignment_surf(renderer):
"""Test plotting of a surface."""
info = read_info(evoked_fname)
fig = plot_alignment(
info, read_trans(trans_fname), subject='sample',
subjects_dir=subjects_dir, meg=False, eeg=False, dig=False,
surfaces=['white', 'head'])
_assert_n_actors(fig, renderer, 3) # left and right hemis plus head
@pytest.mark.slowtest # can be slow on OSX
@testing.requires_testing_data
def test_plot_alignment_basic(tmp_path, renderer, mixed_fwd_cov_evoked):
"""Test plotting of -trans.fif files and MEG sensor layouts."""
# generate fiducials file for testing
tempdir = str(tmp_path)
fiducials_path = op.join(tempdir, 'fiducials.fif')
fid = [{'coord_frame': 5, 'ident': 1, 'kind': 1,
'r': [-0.08061612, -0.02908875, -0.04131077]},
{'coord_frame': 5, 'ident': 2, 'kind': 1,
'r': [0.00146763, 0.08506715, -0.03483611]},
{'coord_frame': 5, 'ident': 3, 'kind': 1,
'r': [0.08436285, -0.02850276, -0.04127743]}]
write_dig(fiducials_path, fid, 5)
evoked = read_evokeds(evoked_fname)[0]
info = evoked.info
sample_src = read_source_spaces(src_fname)
pytest.raises(TypeError, plot_alignment, 'foo', trans_fname,
subject='sample', subjects_dir=subjects_dir)
pytest.raises(OSError, plot_alignment, info, trans_fname,
subject='sample', subjects_dir=subjects_dir, src='foo')
pytest.raises(ValueError, plot_alignment, info, trans_fname,
subject='fsaverage', subjects_dir=subjects_dir,
src=sample_src)
sample_src.plot(subjects_dir=subjects_dir, head=True, skull=True,
brain='white')
# mixed source space
mixed_src = mixed_fwd_cov_evoked[0]['src']
assert mixed_src.kind == 'mixed'
fig = plot_alignment(
info, meg=['helmet', 'sensors'], dig=True,
coord_frame='head', trans=Path(trans_fname),
subject='sample', mri_fiducials=fiducials_path,
subjects_dir=subjects_dir, src=mixed_src)
assert isinstance(fig, Figure3D)
renderer.backend._close_all()
# no-head version
renderer.backend._close_all()
# trans required
with pytest.raises(ValueError, match='transformation matrix.*in head'):
plot_alignment(info, trans=None, src=src_fname)
with pytest.raises(ValueError, match='transformation matrix.*in head'):
plot_alignment(info, trans=None, mri_fiducials=True)
with pytest.raises(ValueError, match='transformation matrix.*in head'):
plot_alignment(info, trans=None, surfaces=['brain'])
assert mixed_src[0]['coord_frame'] == FIFF.FIFFV_COORD_HEAD
with pytest.raises(ValueError, match='head-coordinate source space in mr'):
plot_alignment(trans=None, src=mixed_src, coord_frame='mri')
# all coord frames
plot_alignment(info) # works: surfaces='auto' default
for coord_frame in ('meg', 'head', 'mri'):
plot_alignment(
info, meg=['helmet', 'sensors'], dig=True, coord_frame=coord_frame,
trans=Path(trans_fname), subject='sample', src=src_fname,
mri_fiducials=fiducials_path, subjects_dir=subjects_dir)
renderer.backend._close_all()
# EEG only with strange options
evoked_eeg_ecog_seeg = evoked.copy().pick_types(meg=False, eeg=True)
with evoked_eeg_ecog_seeg.info._unlock():
evoked_eeg_ecog_seeg.info['projs'] = [] # "remove" avg proj
evoked_eeg_ecog_seeg.set_channel_types({'EEG 001': 'ecog',
'EEG 002': 'seeg'})
with catch_logging() as log:
plot_alignment(evoked_eeg_ecog_seeg.info, subject='sample',
trans=trans_fname, subjects_dir=subjects_dir,
surfaces=['white', 'outer_skin', 'outer_skull'],
meg=['helmet', 'sensors'],
eeg=['original', 'projected'], ecog=True, seeg=True,
verbose=True)
log = log.getvalue()
assert 'ecog: 1' in log
assert 'seeg: 1' in log
renderer.backend._close_all()
sphere = make_sphere_model(info=info, r0='auto', head_radius='auto')
bem_sol = read_bem_solution(op.join(subjects_dir, 'sample', 'bem',
'sample-1280-1280-1280-bem-sol.fif'))
bem_surfs = read_bem_surfaces(op.join(subjects_dir, 'sample', 'bem',
'sample-1280-1280-1280-bem.fif'))
sample_src[0]['coord_frame'] = 4 # hack for coverage
plot_alignment(info, trans_fname, subject='sample',
eeg='projected', meg='helmet', bem=sphere, dig=True,
surfaces=['brain', 'inner_skull', 'outer_skull',
'outer_skin'])
plot_alignment(info, trans_fname, subject='sample', meg='helmet',
subjects_dir=subjects_dir, eeg='projected', bem=sphere,
surfaces=['head', 'brain'], src=sample_src)
# no trans okay, no mri surfaces
plot_alignment(info, bem=sphere, surfaces=['brain'])
with pytest.raises(ValueError, match='A head surface is required'):
plot_alignment(info, trans=trans_fname, subject='sample',
subjects_dir=subjects_dir, eeg='projected',
surfaces=[])
with pytest.raises(RuntimeError, match='No brain surface found'):
plot_alignment(info, trans=trans_fname, subject='foo',
subjects_dir=subjects_dir, surfaces=['brain'])
assert all(surf['coord_frame'] == FIFF.FIFFV_COORD_MRI
for surf in bem_sol['surfs'])
plot_alignment(info, trans_fname, subject='sample', meg=[],
subjects_dir=subjects_dir, bem=bem_sol, eeg=True,
surfaces=['head', 'inflated', 'outer_skull', 'inner_skull'])
assert all(surf['coord_frame'] == FIFF.FIFFV_COORD_MRI
for surf in bem_sol['surfs'])
plot_alignment(info, trans_fname, subject='sample',
meg=True, subjects_dir=subjects_dir,
surfaces=['head', 'inner_skull'], bem=bem_surfs)
# single-layer BEM can still plot head surface
assert bem_surfs[-1]['id'] == FIFF.FIFFV_BEM_SURF_ID_BRAIN
bem_sol_homog = read_bem_solution(op.join(subjects_dir, 'sample', 'bem',
'sample-1280-bem-sol.fif'))
for use_bem in (bem_surfs[-1:], bem_sol_homog):
with catch_logging() as log:
plot_alignment(info, trans_fname, subject='sample',
meg=True, subjects_dir=subjects_dir,
surfaces=['head', 'inner_skull'], bem=use_bem,
verbose=True)
log = log.getvalue()
assert 'not find the surface for head in the provided BEM model' in log
# sphere model
sphere = make_sphere_model('auto', 'auto', info)
src = setup_volume_source_space(sphere=sphere)
plot_alignment(
info, trans=Transform('head', 'mri'), eeg='projected',
meg='helmet', bem=sphere, src=src, dig=True,
surfaces=['brain', 'inner_skull', 'outer_skull', 'outer_skin'])
sphere = make_sphere_model('auto', None, info) # one layer
# if you ask for a brain surface with a 1-layer sphere model it's an error
with pytest.raises(RuntimeError, match='Sphere model does not have'):
plot_alignment(
trans=trans_fname, subject='sample', subjects_dir=subjects_dir,
surfaces=['brain'], bem=sphere)
# but you can ask for a specific brain surface, and
# no info is permitted
plot_alignment(
trans=trans_fname, subject='sample', meg=False, coord_frame='mri',
subjects_dir=subjects_dir, surfaces=['white'], bem=sphere,
show_axes=True)
renderer.backend._close_all()
# TODO: We need to make this class public and document it properly
# assert isinstance(fig, some_public_class)
# 3D coil with no defined draw (ConvexHull)
info_cube = pick_info(info, np.arange(6))
with info._unlock():
info['dig'] = None
info_cube['chs'][0]['coil_type'] = 9999
info_cube['chs'][1]['coil_type'] = 9998
with pytest.raises(RuntimeError, match='coil definition not found'):
plot_alignment(info_cube, meg='sensors', surfaces=())
coil_def_fname = op.join(tempdir, 'temp')
with open(coil_def_fname, 'w') as fid:
fid.write(coil_3d)
# make sure our other OPMs can be plotted, too
for ii, kind in enumerate(('QUSPIN_ZFOPM_MAG', 'QUSPIN_ZFOPM_MAG2',
'FIELDLINE_OPM_MAG_GEN1',
'KERNEL_OPM_MAG_GEN1'), 2):
info_cube['chs'][ii]['coil_type'] = getattr(
FIFF, f'FIFFV_COIL_{kind}')
with use_coil_def(coil_def_fname):
with catch_logging() as log:
plot_alignment(info_cube, meg='sensors', surfaces=(), dig=True,
verbose='debug')
log = log.getvalue()
assert 'planar geometry' in log
# one layer bem with skull surfaces:
with pytest.raises(RuntimeError, match='Sphere model does not.*boundary'):
plot_alignment(info=info, trans=trans_fname,
subject='sample', subjects_dir=subjects_dir,
surfaces=['brain', 'head', 'inner_skull'], bem=sphere)
# wrong eeg value:
with pytest.raises(ValueError, match='Invalid value for the .eeg'):
plot_alignment(info=info, trans=trans_fname,
subject='sample', subjects_dir=subjects_dir, eeg='foo')
# wrong meg value:
with pytest.raises(ValueError, match='Invalid value for the .meg'):
plot_alignment(info=info, trans=trans_fname,
subject='sample', subjects_dir=subjects_dir, meg='bar')
# multiple brain surfaces:
with pytest.raises(ValueError, match='Only one brain surface can be plot'):
plot_alignment(info=info, trans=trans_fname,
subject='sample', subjects_dir=subjects_dir,
surfaces=['white', 'pial'])
with pytest.raises(TypeError, match='surfaces.*must be'):
plot_alignment(info=info, trans=trans_fname,
subject='sample', subjects_dir=subjects_dir,
surfaces=[1])
with pytest.raises(ValueError, match='Unknown surface type'):
plot_alignment(info=info, trans=trans_fname,
subject='sample', subjects_dir=subjects_dir,
surfaces=['foo'])
with pytest.raises(TypeError, match="must be an instance of "):
plot_alignment(info=info, trans=trans_fname,
subject='sample', subjects_dir=subjects_dir,
surfaces=dict(brain='super clear'))
with pytest.raises(ValueError, match="must be between 0 and 1"):
plot_alignment(info=info, trans=trans_fname,
subject='sample', subjects_dir=subjects_dir,
surfaces=dict(brain=42))
fwd_fname = op.join(data_dir, 'MEG', 'sample',
'sample_audvis_trunc-meg-eeg-oct-4-fwd.fif')
fwd = read_forward_solution(fwd_fname)
plot_alignment(subject='sample', subjects_dir=subjects_dir,
trans=trans_fname, fwd=fwd,
surfaces='white', coord_frame='head')
fwd = convert_forward_solution(fwd, force_fixed=True)
plot_alignment(subject='sample', subjects_dir=subjects_dir,
trans=trans_fname, fwd=fwd,
surfaces='white', coord_frame='head')
fwd['coord_frame'] = FIFF.FIFFV_COORD_MRI # check required to get to MRI
with pytest.raises(ValueError, match='transformation matrix.*in head coo'):
plot_alignment(info, trans=None, fwd=fwd)
# surfaces as dict
plot_alignment(subject='sample', coord_frame='head',
trans=trans_fname, subjects_dir=subjects_dir,
surfaces={'white': 0.4, 'outer_skull': 0.6, 'head': None})
@testing.requires_testing_data
def test_plot_alignment_fnirs(renderer, tmp_path):
"""Test fNIRS plotting."""
# Here we use subjects_dir=tmp_path, since no surfaces should actually
# be loaded!
# fNIRS (default is pairs)
info = read_raw_nirx(nirx_fname).info
assert info['nchan'] == 26
kwargs = dict(trans='fsaverage', subject='fsaverage', surfaces=(),
verbose=True, subjects_dir=tmp_path)
with catch_logging() as log:
fig = plot_alignment(info, **kwargs)
log = log.getvalue()
assert f'fnirs_cw_amplitude: {info["nchan"]}' in log
_assert_n_actors(fig, renderer, info['nchan'])
fig = plot_alignment(
info, fnirs=['channels', 'sources', 'detectors'], **kwargs)
_assert_n_actors(fig, renderer, 3)
@pytest.mark.slowtest # can be slow on OSX
@testing.requires_testing_data
def test_process_clim_plot(renderer_interactive, brain_gc):
"""Test functionality for determining control points with stc.plot."""
sample_src = read_source_spaces(src_fname)
kwargs = dict(subjects_dir=subjects_dir, smoothing_steps=1,
time_viewer=False, show_traces=False)
vertices = [s['vertno'] for s in sample_src]
n_time = 5
n_verts = sum(len(v) for v in vertices)
stc_data = np.random.RandomState(0).rand((n_verts * n_time))
stc_data.shape = (n_verts, n_time)
stc = SourceEstimate(stc_data, vertices, 1, 1, 'sample')
# Test for simple use cases
brain = stc.plot(**kwargs)
assert brain.data['center'] is None
brain.close()
brain = stc.plot(clim=dict(pos_lims=(10, 50, 90)), **kwargs)
assert brain.data['center'] == 0.
brain.close()
brain = stc.plot(colormap='hot', clim='auto', **kwargs)
brain.close()
brain = stc.plot(colormap='mne', clim='auto', **kwargs)
brain.close()
brain = stc.plot(clim=dict(kind='value', lims=(10, 50, 90)), figure=99,
**kwargs)
brain.close()
with pytest.raises(TypeError, match='must be a'):
stc.plot(clim='auto', figure=[0], **kwargs)
# Test for correct clim values
with pytest.raises(ValueError, match='monotonically'):
stc.plot(clim=dict(kind='value', pos_lims=[0, 1, 0]), **kwargs)
with pytest.raises(ValueError, match=r'.*must be \(3,\)'):
stc.plot(colormap='mne', clim=dict(pos_lims=(5, 10, 15, 20)), **kwargs)
with pytest.raises(ValueError, match="'value', 'values', and 'percent'"):
stc.plot(clim=dict(pos_lims=(5, 10, 15), kind='foo'), **kwargs)
with pytest.raises(ValueError, match='must be "auto" or dict'):
stc.plot(colormap='mne', clim='foo', **kwargs)
with pytest.raises(TypeError, match='must be an instance of'):
plot_source_estimates('foo', clim='auto', **kwargs)
with pytest.raises(ValueError, match='hemi'):
stc.plot(hemi='foo', clim='auto', **kwargs)
with pytest.raises(ValueError, match='Exactly one'):
stc.plot(clim=dict(lims=[0, 1, 2], pos_lims=[0, 1, 2], kind='value'),
**kwargs)
# Test handling of degenerate data: thresholded maps
stc._data.fill(0.)
with pytest.warns(RuntimeWarning, match='All data were zero'):
brain = plot_source_estimates(stc, **kwargs)
brain.close()
def _assert_mapdata_equal(a, b):
__tracebackhide__ = True
assert set(a.keys()) == {'clim', 'colormap', 'transparent'}
assert a.keys() == b.keys()
assert a['transparent'] == b['transparent'], 'transparent'
aa, bb = a['clim'], b['clim']
assert aa.keys() == bb.keys(), 'clim keys'
assert aa['kind'] == bb['kind'] == 'value'
key = 'pos_lims' if 'pos_lims' in aa else 'lims'
assert_array_equal(aa[key], bb[key], err_msg=key)
assert isinstance(a['colormap'], Colormap), 'Colormap'
assert isinstance(b['colormap'], Colormap), 'Colormap'
assert a['colormap'].name == b['colormap'].name
def test_process_clim_round_trip():
"""Test basic input-output support."""
# With some negative data
out = _process_clim('auto', 'auto', True, -1.)
want = dict(
colormap=mne_analyze_colormap([0, 0.5, 1], 'matplotlib'),
clim=dict(kind='value', pos_lims=[1, 1, 1]),
transparent=True,)
_assert_mapdata_equal(out, want)
out2 = _process_clim(**out)
_assert_mapdata_equal(out, out2)
_linearize_map(out) # smoke test
ticks = _get_map_ticks(out)
assert_allclose(ticks, [-1, 0, 1])
# With some positive data
out = _process_clim('auto', 'auto', True, 1.)
want = dict(
colormap=_get_cmap('hot'),
clim=dict(kind='value', lims=[1, 1, 1]),
transparent=True,)
_assert_mapdata_equal(out, want)
out2 = _process_clim(**out)
_assert_mapdata_equal(out, out2)
_linearize_map(out)
ticks = _get_map_ticks(out)
assert_allclose(ticks, [1])
# With some actual inputs
clim = dict(kind='value', pos_lims=[0, 0.5, 1])
out = _process_clim(clim, 'auto', True)
want = dict(
colormap=mne_analyze_colormap([0, 0.5, 1], 'matplotlib'),
clim=clim, transparent=True)
_assert_mapdata_equal(out, want)
_linearize_map(out)
ticks = _get_map_ticks(out)
assert_allclose(ticks, [-1, -0.5, 0, 0.5, 1])
clim = dict(kind='value', pos_lims=[0.25, 0.5, 1])
out = _process_clim(clim, 'auto', True)
want = dict(
colormap=mne_analyze_colormap([0, 0.5, 1], 'matplotlib'),
clim=clim, transparent=True)
_assert_mapdata_equal(out, want)
_linearize_map(out)
ticks = _get_map_ticks(out)
assert_allclose(ticks, [-1, -0.5, -0.25, 0, 0.25, 0.5, 1])
@testing.requires_testing_data
@requires_nibabel()
def test_stc_mpl():
"""Test plotting source estimates with matplotlib."""
sample_src = read_source_spaces(src_fname)
vertices = [s['vertno'] for s in sample_src]
n_time = 5
n_verts = sum(len(v) for v in vertices)
stc_data = np.ones((n_verts * n_time))
stc_data.shape = (n_verts, n_time)
stc = SourceEstimate(stc_data, vertices, 1, 1, 'sample')
stc.plot(subjects_dir=subjects_dir, time_unit='s', views='ven',
hemi='rh', smoothing_steps=7, subject='sample',
backend='matplotlib', spacing='oct1', initial_time=0.001,
colormap='Reds')
fig = stc.plot(subjects_dir=subjects_dir, time_unit='ms', views='dor',
hemi='lh', smoothing_steps=7, subject='sample',
backend='matplotlib', spacing='ico2', time_viewer=True,
colormap='mne')
time_viewer = fig.time_viewer
_fake_click(time_viewer, time_viewer.axes[0], (0.5, 0.5)) # change t
_fake_keypress(time_viewer, 'ctrl+right')
_fake_keypress(time_viewer, 'left')
pytest.raises(ValueError, stc.plot, subjects_dir=subjects_dir,
hemi='both', subject='sample', backend='matplotlib')
pytest.raises(ValueError, stc.plot, subjects_dir=subjects_dir,
time_unit='ss', subject='sample', backend='matplotlib')
@pytest.mark.slowtest
@pytest.mark.timeout(60) # can sometimes take > 60 sec
@testing.requires_testing_data
@requires_nibabel()
@pytest.mark.parametrize('coord_frame, idx, show_all, title',
[('head', 'gof', True, 'Test'),
('mri', 'amplitude', False, None)])
def test_plot_dipole_mri_orthoview(coord_frame, idx, show_all, title):
"""Test mpl dipole plotting."""
dipoles = read_dipole(dip_fname)
trans = read_trans(trans_fname)
fig = dipoles.plot_locations(trans=trans, subject='sample',
subjects_dir=subjects_dir,
coord_frame=coord_frame, idx=idx,
show_all=show_all, title=title,
mode='orthoview')
_fake_scroll(fig, 0.5, 0.5, 1) # scroll up
_fake_scroll(fig, 0.5, 0.5, -1) # scroll down
_fake_keypress(fig, 'up')
_fake_keypress(fig, 'down')
_fake_keypress(fig, 'a') # some other key
ax = fig.add_subplot(211)
with pytest.raises(TypeError, match='instance of Axes3D'):
dipoles.plot_locations(trans, 'sample', subjects_dir, ax=ax)
@testing.requires_testing_data
@pytest.mark.parametrize('surf, coord_frame, ax, title', [
pytest.param('white', 'mri', None, None, marks=pytest.mark.slowtest),
pytest.param(None, 'head', None, None, marks=pytest.mark.slowtest),
(None, 'mri_rotated', 'mpl', 'check'),
])
def test_plot_dipole_mri_outlines(surf, coord_frame, ax, title):
"""Test mpl dipole plotting."""
dipoles = read_dipole(dip_fname)
trans = read_trans(trans_fname)
if ax is not None:
assert isinstance(ax, str) and ax == 'mpl', ax
_, ax = plt.subplots(3, 1)
ax = list(ax)
with pytest.raises(ValueError, match='but the length is 2'):
dipoles.plot_locations(
trans, 'sample', subjects_dir, ax=ax[:2], mode='outlines')
fig = dipoles.plot_locations(
trans=trans, subject='sample', subjects_dir=subjects_dir,
mode='outlines', coord_frame=coord_frame, surf=surf, ax=ax,
title=title)
assert isinstance(fig, Figure)
@testing.requires_testing_data
def test_plot_dipole_orientations(renderer):
"""Test dipole plotting in 3d."""
dipoles = read_dipole(dip_fname)
trans = read_trans(trans_fname)
for coord_frame, mode in zip(['head', 'mri'],
['arrow', 'sphere']):
fig = dipoles.plot_locations(
trans=trans, subject='sample', subjects_dir=subjects_dir,
mode=mode, coord_frame=coord_frame)
assert isinstance(fig, Figure3D)
renderer.backend._close_all()
@pytest.mark.slowtest # slow on Azure
@testing.requires_testing_data
def test_snapshot_brain_montage(renderer):
"""Test snapshot brain montage."""
info = read_info(evoked_fname)
fig = plot_alignment(
info, trans=Transform('head', 'mri'), subject='sample',
subjects_dir=subjects_dir)
xyz = np.vstack([ich['loc'][:3] for ich in info['chs']])
ch_names = [ich['ch_name'] for ich in info['chs']]
xyz_dict = dict(zip(ch_names, xyz))
xyz_dict[info['chs'][0]['ch_name']] = [1, 2] # Set one ch to only 2 vals
# Make sure wrong types are checked
pytest.raises(TypeError, snapshot_brain_montage, fig, xyz)
# All chs must have 3 position values
pytest.raises(ValueError, snapshot_brain_montage, fig, xyz_dict)
# Make sure we raise error if the figure has no scene
pytest.raises(ValueError, snapshot_brain_montage, None, info)
@pytest.mark.slowtest # can be slow on OSX
@testing.requires_testing_data
@pytest.mark.parametrize('pick_ori', ('vector', None))
@pytest.mark.parametrize('kind', ('surface', 'volume', 'mixed'))
def test_plot_source_estimates(renderer_interactive, all_src_types_inv_evoked,
pick_ori, kind, brain_gc):
"""Test plotting of scalar and vector source estimates."""
backend = renderer_interactive._get_3d_backend()
invs, evoked = all_src_types_inv_evoked
inv = invs[kind]
with _record_warnings(): # PCA mag
stc = apply_inverse(evoked, inv, pick_ori=pick_ori)
stc.data[1] *= -1 # make it signed
meth_key = 'plot_3d' if isinstance(stc, _BaseVolSourceEstimate) else 'plot'
stc.subject = 'sample'
meth = getattr(stc, meth_key)
kwargs = dict(subjects_dir=subjects_dir,
time_viewer=False, show_traces=False, # for speed
smoothing_steps=1, verbose='error', src=inv['src'],
volume_options=dict(resolution=None), # for speed
)
if pick_ori != 'vector':
kwargs['surface'] = 'white'
kwargs['backend'] = backend
brain = meth(**kwargs)
brain.close()
del brain
these_kwargs = kwargs.copy()
these_kwargs['show_traces'] = 'foo'
with pytest.raises(ValueError, match='show_traces'):
meth(**these_kwargs)
del these_kwargs
if pick_ori == 'vector':
with pytest.raises(ValueError, match='use "pos_lims"'):
meth(**kwargs, clim=dict(pos_lims=[1, 2, 3]))
if kind in ('volume', 'mixed'):
with pytest.raises(TypeError, match='when stc is a mixed or vol'):
these_kwargs = kwargs.copy()
these_kwargs.pop('src')
meth(**these_kwargs)
with pytest.raises(ValueError, match='cannot be used'):
these_kwargs = kwargs.copy()
these_kwargs.update(show_traces=True, time_viewer=False)
meth(**these_kwargs)
# flatmaps (mostly a lot of error checking)
these_kwargs = kwargs.copy()
these_kwargs.update(surface='flat', views='auto', hemi='both',
verbose='debug')
if kind == 'surface' and pick_ori != 'vector':
with catch_logging() as log:
with pytest.raises(FileNotFoundError, match='flatmap'):
meth(**these_kwargs) # sample does not have them
log = log.getvalue()
assert 'offset: 0' in log
fs_stc = stc.copy()
fs_stc.subject = 'fsaverage' # this is wrong, but don't have to care
flat_meth = getattr(fs_stc, meth_key)
these_kwargs.pop('src')
if pick_ori == 'vector':
pass # can't even pass "surface" variable
elif kind != 'surface':
with pytest.raises(TypeError, match='SourceEstimate when a flatmap'):
flat_meth(**these_kwargs)
else:
brain = flat_meth(**these_kwargs)
brain.close()
del brain
these_kwargs.update(surface='inflated', views='flat')
with pytest.raises(ValueError, match='surface="flat".*views="flat"'):
flat_meth(**these_kwargs)
# just test one for speed
if kind != 'mixed':
return
brain = meth(
views=['lat', 'med', 'ven'], hemi='lh',
view_layout='horizontal', **kwargs)
brain.close()
assert brain._subplot_shape == (1, 3)
del brain
these_kwargs = kwargs.copy()
these_kwargs['volume_options'] = dict(blending='foo')
with pytest.raises(ValueError, match='mip'):
meth(**these_kwargs)
these_kwargs['volume_options'] = dict(badkey='foo')
with pytest.raises(ValueError, match='unknown'):
meth(**these_kwargs)
# with resampling (actually downsampling but it's okay)
these_kwargs['volume_options'] = dict(resolution=20., surface_alpha=0.)
brain = meth(**these_kwargs)
brain.close()
del brain
@pytest.mark.parametrize('orientation', ('horizontal', 'vertical'))
@pytest.mark.parametrize('diverging', (True, False))
@pytest.mark.parametrize('lims', ([0.5, 1, 10], [0, 1, 10]))
def test_brain_colorbar(orientation, diverging, lims):
"""Test brain colorbar plotting."""
_, ax = plt.subplots()
clim = dict(kind='value')
if diverging:
clim['pos_lims'] = lims
else:
clim['lims'] = lims
cbar = plot_brain_colorbar(ax, clim, orientation=orientation)
ax = cbar.ax # in newer mpl this can be inset axes relative to the orig
if orientation == 'vertical':
have, empty = ax.get_yticklabels, ax.get_xticklabels
else:
have, empty = ax.get_xticklabels, ax.get_yticklabels
if diverging:
if lims[0] == 0:
ticks = list(-np.array(lims[1:][::-1])) + lims
else:
ticks = list(-np.array(lims[::-1])) + [0] + lims
else:
ticks = lims
ax.figure.canvas.draw_idle()
assert_array_equal(
[float(h.get_text().replace('−', '-')) for h in have()], ticks)
assert_array_equal(empty(), [])
@pytest.mark.slowtest # slow-ish on Travis OSX
@testing.requires_testing_data
def test_mixed_sources_plot_surface(renderer_interactive):
"""Test plot_surface() for mixed source space."""
src = read_source_spaces(fwd_fname2)
N = np.sum([s['nuse'] for s in src]) # number of sources
T = 2 # number of time points
S = 3 # number of source spaces
rng = np.random.RandomState(0)
data = rng.randn(N, T)
vertno = S * [np.arange(N // S)]
stc = MixedSourceEstimate(data, vertno, 0, 1)
brain = stc.surface().plot(views='lat', hemi='split',
subject='fsaverage', subjects_dir=subjects_dir,
colorbar=False)
brain.close()
del brain
@testing.requires_testing_data
@pytest.mark.slowtest
def test_link_brains(renderer_interactive):
"""Test plotting linked brains."""
sample_src = read_source_spaces(src_fname)
vertices = [s['vertno'] for s in sample_src]
n_time = 5
n_verts = sum(len(v) for v in vertices)
stc_data = np.zeros((n_verts * n_time))
stc_size = stc_data.size
stc_data[(np.random.rand(stc_size // 20) * stc_size).astype(int)] = \
np.random.RandomState(0).rand(stc_data.size // 20)
stc_data.shape = (n_verts, n_time)
stc = SourceEstimate(stc_data, vertices, 1, 1)
colormap = 'mne_analyze'
brain = plot_source_estimates(
stc, 'sample', colormap=colormap,
background=(1, 1, 0),
subjects_dir=subjects_dir, colorbar=True,
clim='auto'
)
with pytest.raises(ValueError, match='is empty'):
link_brains([])
with pytest.raises(TypeError, match='type is Brain'):
link_brains('foo')
link_brains(brain, time=True, camera=True)
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