from __future__ import print_function import os import os.path as op from subprocess import CalledProcessError import warnings from nose.tools import assert_raises, assert_true from numpy.testing import (assert_equal, assert_allclose) from mne.datasets import sample from mne.io import Raw from mne.io import read_raw_kit from mne.io import read_raw_bti from mne import (read_forward_solution, make_forward_solution, do_forward_solution, setup_source_space, read_trans, convert_forward_solution) from mne.utils import requires_mne, _TempDir from mne.tests.test_source_space import _compare_source_spaces from mne.forward import Forward data_path = sample.data_path(download=False) fname = op.join(data_path, 'MEG', 'sample', 'sample_audvis-meg-oct-6-fwd.fif') fname_meeg = op.join(data_path, 'MEG', 'sample', 'sample_audvis-meg-eeg-oct-6-fwd.fif') fname_raw = op.join(op.dirname(__file__), '..', '..', 'io', 'tests', 'data', 'test_raw.fif') fname_evoked = op.join(op.dirname(__file__), '..', '..', 'io', 'tests', 'data', 'test-ave.fif') fname_mri = op.join(data_path, 'MEG', 'sample', 'sample_audvis_raw-trans.fif') subjects_dir = os.path.join(data_path, 'subjects') temp_dir = _TempDir() # make a file that exists with some data in it existing_file = op.join(temp_dir, 'test.fif') with open(existing_file, 'w') as fid: fid.write('aoeu') def _compare_forwards(fwd, fwd_py, n_sensors, n_src, meg_rtol=1e-4, meg_atol=1e-9): """Helper to test forwards""" # check source spaces assert_equal(len(fwd['src']), len(fwd_py['src'])) _compare_source_spaces(fwd['src'], fwd_py['src'], mode='approx') for surf_ori in [False, True]: if surf_ori: # use copy here to leave our originals unmodified fwd = convert_forward_solution(fwd, surf_ori, copy=True) fwd_py = convert_forward_solution(fwd, surf_ori, copy=True) for key in ['nchan', 'source_nn', 'source_rr', 'source_ori', 'surf_ori', 'coord_frame', 'nsource']: print(key) assert_allclose(fwd_py[key], fwd[key], rtol=1e-4, atol=1e-7) assert_allclose(fwd_py['mri_head_t']['trans'], fwd['mri_head_t']['trans'], rtol=1e-5, atol=1e-8) assert_equal(fwd_py['sol']['data'].shape, (n_sensors, n_src)) assert_equal(len(fwd['sol']['row_names']), n_sensors) assert_equal(len(fwd_py['sol']['row_names']), n_sensors) # check MEG print('check MEG') assert_allclose(fwd['sol']['data'][:306], fwd_py['sol']['data'][:306], rtol=meg_rtol, atol=meg_atol) # check EEG if fwd['sol']['data'].shape[0] > 306: print('check EEG') assert_allclose(fwd['sol']['data'][306:], fwd_py['sol']['data'][306:], rtol=1e-3, atol=1e-3) @sample.requires_sample_data @requires_mne def test_make_forward_solution_kit(): """Test making fwd using KIT, BTI, and CTF (compensated) files """ fname_bem = op.join(subjects_dir, 'sample', 'bem', 'sample-5120-bem-sol.fif') kit_dir = op.join(op.dirname(__file__), '..', '..', 'io', 'kit', 'tests', 'data') sqd_path = op.join(kit_dir, 'test.sqd') mrk_path = op.join(kit_dir, 'test_mrk.sqd') elp_path = op.join(kit_dir, 'test_elp.txt') hsp_path = op.join(kit_dir, 'test_hsp.txt') mri_path = op.join(kit_dir, 'trans-sample.fif') fname_kit_raw = op.join(kit_dir, 'test_bin_raw.fif') bti_dir = op.join(op.dirname(__file__), '..', '..', 'io', 'bti', 'tests', 'data') bti_pdf = op.join(bti_dir, 'test_pdf_linux') bti_config = op.join(bti_dir, 'test_config_linux') bti_hs = op.join(bti_dir, 'test_hs_linux') fname_bti_raw = op.join(bti_dir, 'exported4D_linux_raw.fif') fname_ctf_raw = op.join(op.dirname(__file__), '..', '..', 'io', 'tests', 'data', 'test_ctf_comp_raw.fif') # first set up a testing source space fname_src = op.join(temp_dir, 'oct2-src.fif') src = setup_source_space('sample', fname_src, 'oct2', subjects_dir=subjects_dir) # first use mne-C: convert file, make forward solution fwd = do_forward_solution('sample', fname_kit_raw, src=fname_src, mindist=0.0, bem=fname_bem, mri=mri_path, eeg=False, meg=True, subjects_dir=subjects_dir) assert_true(isinstance(fwd, Forward)) # now let's use python with the same raw file fwd_py = make_forward_solution(fname_kit_raw, mindist=0.0, src=src, eeg=False, meg=True, bem=fname_bem, mri=mri_path) _compare_forwards(fwd, fwd_py, 157, 108) assert_true(isinstance(fwd_py, Forward)) # now let's use mne-python all the way raw_py = read_raw_kit(sqd_path, mrk_path, elp_path, hsp_path) # without ignore_ref=True, this should throw an error: assert_raises(NotImplementedError, make_forward_solution, raw_py.info, mindist=0.0, src=src, eeg=False, meg=True, bem=fname_bem, mri=mri_path) fwd_py = make_forward_solution(raw_py.info, mindist=0.0, src=src, eeg=False, meg=True, bem=fname_bem, mri=mri_path, ignore_ref=True) _compare_forwards(fwd, fwd_py, 157, 108, meg_rtol=1e-3, meg_atol=1e-7) # BTI python end-to-end versus C fwd = do_forward_solution('sample', fname_bti_raw, src=fname_src, mindist=0.0, bem=fname_bem, mri=mri_path, eeg=False, meg=True, subjects_dir=subjects_dir) raw_py = read_raw_bti(bti_pdf, bti_config, bti_hs) fwd_py = make_forward_solution(raw_py.info, mindist=0.0, src=src, eeg=False, meg=True, bem=fname_bem, mri=mri_path) _compare_forwards(fwd, fwd_py, 248, 108) # now let's test CTF w/compensation fwd_py = make_forward_solution(fname_ctf_raw, mindist=0.0, src=src, eeg=False, meg=True, bem=fname_bem, mri=fname_mri) fwd = do_forward_solution('sample', fname_ctf_raw, src=fname_src, mindist=0.0, bem=fname_bem, mri=fname_mri, eeg=False, meg=True, subjects_dir=subjects_dir) _compare_forwards(fwd, fwd_py, 274, 108) # CTF with compensation changed in python ctf_raw = Raw(fname_ctf_raw, compensation=2) fwd_py = make_forward_solution(ctf_raw.info, mindist=0.0, src=src, eeg=False, meg=True, bem=fname_bem, mri=fname_mri) with warnings.catch_warnings(record=True): fwd = do_forward_solution('sample', ctf_raw, src=fname_src, mindist=0.0, bem=fname_bem, mri=fname_mri, eeg=False, meg=True, subjects_dir=subjects_dir) _compare_forwards(fwd, fwd_py, 274, 108) @sample.requires_sample_data def test_make_forward_solution(): """Test making M-EEG forward solution from python """ fname_src = op.join(subjects_dir, 'sample', 'bem', 'sample-oct-6-src.fif') fname_bem = op.join(subjects_dir, 'sample', 'bem', 'sample-5120-5120-5120-bem-sol.fif') fwd_py = make_forward_solution(fname_raw, mindist=5.0, src=fname_src, eeg=True, meg=True, bem=fname_bem, mri=fname_mri) assert_true(isinstance(fwd_py, Forward)) fwd = read_forward_solution(fname_meeg) assert_true(isinstance(fwd, Forward)) _compare_forwards(fwd, fwd_py, 366, 22494) @sample.requires_sample_data @requires_mne def test_do_forward_solution(): """Test wrapping forward solution from python """ mri = read_trans(fname_mri) fname_fake = op.join(temp_dir, 'no_have.fif') # ## Error checks # bad subject assert_raises(ValueError, do_forward_solution, 1, fname_raw, subjects_dir=subjects_dir) # bad meas assert_raises(ValueError, do_forward_solution, 'sample', 1, subjects_dir=subjects_dir) # meas doesn't exist assert_raises(IOError, do_forward_solution, 'sample', fname_fake, subjects_dir=subjects_dir) # don't specify trans and meas assert_raises(ValueError, do_forward_solution, 'sample', fname_raw, subjects_dir=subjects_dir) # specify both trans and meas assert_raises(ValueError, do_forward_solution, 'sample', fname_raw, trans='me', mri='you', subjects_dir=subjects_dir) # specify non-existent trans assert_raises(IOError, do_forward_solution, 'sample', fname_raw, trans=fname_fake, subjects_dir=subjects_dir) # specify non-existent mri assert_raises(IOError, do_forward_solution, 'sample', fname_raw, mri=fname_fake, subjects_dir=subjects_dir) # specify non-string mri assert_raises(ValueError, do_forward_solution, 'sample', fname_raw, mri=1, subjects_dir=subjects_dir) # specify non-string trans assert_raises(ValueError, do_forward_solution, 'sample', fname_raw, trans=1, subjects_dir=subjects_dir) # test specifying an actual trans in python space -- this should work but # the transform I/O reduces our accuracy -- so we'll just hack a test here # by making it bomb with eeg=False and meg=False assert_raises(ValueError, do_forward_solution, 'sample', fname_raw, mri=mri, eeg=False, meg=False, subjects_dir=subjects_dir) # mindist as non-integer assert_raises(TypeError, do_forward_solution, 'sample', fname_raw, mri=fname_mri, mindist=dict(), subjects_dir=subjects_dir) # mindist as string but not 'all' assert_raises(ValueError, do_forward_solution, 'sample', fname_raw, mri=fname_mri, eeg=False, mindist='yall', subjects_dir=subjects_dir) # src, spacing, and bem as non-str assert_raises(ValueError, do_forward_solution, 'sample', fname_raw, mri=fname_mri, src=1, subjects_dir=subjects_dir) assert_raises(ValueError, do_forward_solution, 'sample', fname_raw, mri=fname_mri, spacing=1, subjects_dir=subjects_dir) assert_raises(ValueError, do_forward_solution, 'sample', fname_raw, mri=fname_mri, bem=1, subjects_dir=subjects_dir) # no overwrite flag assert_raises(IOError, do_forward_solution, 'sample', fname_raw, existing_file, mri=fname_mri, subjects_dir=subjects_dir) # let's catch an MNE error, this time about trans being wrong assert_raises(CalledProcessError, do_forward_solution, 'sample', fname_raw, existing_file, trans=fname_mri, overwrite=True, spacing='oct6', subjects_dir=subjects_dir) # No need to actually calculate and check here, since it's effectively # done in previous tests.