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_make_flash_bem(tmpdir):
"""Test computing bem from flash images."""
tmp = str(tmpdir)
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_bem_model_topology(tmpdir):
"""Test BEM model topological checks."""
# bad topology (not enough neighboring tris)
makedirs(tmpdir.join('foo', 'bem'))
for fname in ('inner_skull', 'outer_skull', 'outer_skin'):
fname += '.surf'
copy(op.join(subjects_dir, 'sample', 'bem', fname),
str(tmpdir.join('foo', 'bem', fname)))
outer_fname = tmpdir.join('foo', 'bem', 'outer_skull.surf')
rr, tris = read_surface(outer_fname)
tris = tris[:-1]
write_surface(outer_fname, rr, tris[:-1], overwrite=True)
with pytest.raises(RuntimeError, match='Surface outer skull is not compl'):
make_bem_model('foo', None, subjects_dir=tmpdir)
# Now get past this error to reach gh-6127 (not enough neighbor tris)
rr_bad = np.concatenate([rr, np.mean(rr, axis=0, keepdims=True)], axis=0)
write_surface(outer_fname, rr_bad, tris, overwrite=True)
with pytest.raises(RuntimeError, match='Surface outer skull.*triangles'):
make_bem_model('foo', None, subjects_dir=tmpdir)
def add_volume_info(subject, surface, subjects_dir, volume='T1'):
"""Add volume info from MGZ volume
"""
import os.path as op
from mne.bem import _extract_volume_info
from mne.surface import (read_surface, write_surface)
subject_dir = op.join(subjects_dir, subject)
mri_dir = op.join(subject_dir, 'mri')
T1_mgz = op.join(mri_dir, volume + '.mgz')
new_info = _extract_volume_info(T1_mgz)
print(new_info.keys())
rr, tris, volume_info = read_surface(surface, read_metadata=True)
# volume_info.update(new_info) # replace volume info, 'head' stays
print(volume_info.keys())
import numpy as np
if 'head' not in volume_info.keys():
volume_info['head'] = np.array([2, 0, 20], dtype=np.int32)
write_surface(surface, rr, tris, volume_info=volume_info)
def test_bem_model_topology(tmpdir):
"""Test BEM model topological checks."""
# bad topology (not enough neighboring tris)
tempdir = str(tmpdir)
makedirs(op.join(tempdir, 'foo', 'bem'))
for fname in ('inner_skull', 'outer_skull', 'outer_skin'):
fname += '.surf'
copy(op.join(subjects_dir, 'sample', 'bem', fname),
op.join(tempdir, 'foo', 'bem', fname))
outer_fname = op.join(tempdir, 'foo', 'bem', 'outer_skull.surf')
rr, tris = read_surface(outer_fname)
tris = tris[:-1]
write_surface(outer_fname, rr, tris[:-1])
with pytest.raises(RuntimeError, match='Surface outer skull is not compl'):
make_bem_model('foo', None, subjects_dir=tempdir)
# Now get past this error to reach gh-6127 (not enough neighbor tris)
rr_bad = np.concatenate([rr, np.mean(rr, axis=0, keepdims=True)], axis=0)
write_surface(outer_fname, rr_bad, tris)
with pytest.raises(RuntimeError, match='Surface outer skull.*triangles'):
make_bem_model('foo', None, subjects_dir=tempdir)
def dip_depth(dip, fname_trans, subject, subjects_dir):
trans = read_trans(fname_trans)
trans = _get_trans(trans)[0]
subjects_dir = get_subjects_dir(subjects_dir=subjects_dir)
fname = os.path.join(subjects_dir, subject, 'bem', 'inner_skull.surf')
points, faces = read_surface(fname)
points = apply_trans(trans['trans'], points * 1e-3)
pos = dip.pos
ori = dip.ori
from sklearn.neighbors import NearestNeighbors
nn = NearestNeighbors()
nn.fit(points)
depth, idx = nn.kneighbors(pos, 1, return_distance=True)
idx = np.ravel(idx)
direction = pos - points[idx]
direction /= np.sqrt(np.sum(direction**2, axis=1))[:, None]
ori /= np.sqrt(np.sum(ori**2, axis=1))[:, None]
radiality = np.abs(np.sum(ori * direction, axis=1))
return np.ravel(depth), radiality
def write_labels_to_annot(labels,
subject=None,
parc=None,
overwrite=False,
subjects_dir=None,
annot_fname=None,
colormap='hsv',
hemi='both'):
"""Create a FreeSurfer annotation from a list of labels
FIX: always write both hemispheres
Parameters
----------
labels : list with instances of mne.Label
The labels to create a parcellation from.
subject : str | None
The subject for which to write the parcellation for.
parc : str | None
The parcellation name to use.
overwrite : bool
Overwrite files if they already exist.
subjects_dir : string, or None
Path to SUBJECTS_DIR if it is not set in the environment.
annot_fname : str | None
Filename of the .annot file. If not None, only this file is written
and 'parc' and 'subject' are ignored.
colormap : str
Colormap to use to generate label colors for labels that do not
have a color specified.
hemi : 'both' | 'lh' | 'rh'
The hemisphere(s) for which to write *.annot files (only applies if
annot_fname is not specified; default is 'both').
verbose : bool, str, int, or None
If not None, override default verbose level (see mne.verbose).
Notes
-----
Vertices that are not covered by any of the labels are assigned to a label
named "unknown".
"""
subjects_dir = get_subjects_dir(subjects_dir)
# get the .annot filenames and hemispheres
annot_fname, hemis = _get_annot_fname(annot_fname, subject, hemi, parc,
subjects_dir)
if not overwrite:
for fname in annot_fname:
if op.exists(fname):
raise ValueError('File %s exists. Use "overwrite=True" to '
'overwrite it' % fname)
# prepare container for data to save:
to_save = []
# keep track of issues found in the labels
duplicate_colors = []
invalid_colors = []
overlap = []
no_color = (-1, -1, -1, -1)
no_color_rgb = (-1, -1, -1)
for hemi, fname in zip(hemis, annot_fname):
hemi_labels = [label for label in labels if label.hemi == hemi]
n_hemi_labels = len(hemi_labels)
if n_hemi_labels == 0:
ctab = np.empty((0, 4), dtype=np.int32)
ctab_rgb = ctab[:, :3]
else:
hemi_labels.sort(key=lambda label: label.name)
# convert colors to 0-255 RGBA tuples
hemi_colors = [
no_color if label.color is None else tuple(
int(round(255 * i)) for i in label.color)
for label in hemi_labels
]
ctab = np.array(hemi_colors, dtype=np.int32)
ctab_rgb = ctab[:, :3]
# make color dict (for annot ID, only R, G and B count)
labels_by_color = defaultdict(list)
for label, color in zip(hemi_labels, ctab_rgb):
labels_by_color[tuple(color)].append(label.name)
# check label colors
for color, names in labels_by_color.items():
if color == no_color_rgb:
continue
if color == (0, 0, 0):
# we cannot have an all-zero color, otherw. e.g. tksurfer
# refuses to read the parcellation
msg = ('At least one label contains a color with, "r=0, '
'g=0, b=0" value. Some FreeSurfer tools may fail '
'to read the parcellation')
logger.warning(msg)
if any(i > 255 for i in color):
msg = ("%s: %s (%s)" % (color, ', '.join(names), hemi))
invalid_colors.append(msg)
if len(names) > 1:
msg = "%s: %s (%s)" % (color, ', '.join(names), hemi)
duplicate_colors.append(msg)
# replace None values (labels with unspecified color)
if labels_by_color[no_color_rgb]:
default_colors = _n_colors(n_hemi_labels,
bytes_=True,
cmap=colormap)
safe_color_i = 0 # keep track of colors known to be in hemi_colors
for i in xrange(n_hemi_labels):
if ctab[i, 0] == -1:
color = default_colors[i]
# make sure to add no duplicate color
while np.any(np.all(color[:3] == ctab_rgb, 1)):
color = default_colors[safe_color_i]
safe_color_i += 1
# assign the color
ctab[i] = color
# find number of vertices in surface
if subject is not None and subjects_dir is not None:
fpath = op.join(subjects_dir, subject, 'surf', '%s.white' % hemi)
points, _ = read_surface(fpath)
n_vertices = len(points)
else:
if len(hemi_labels) > 0:
max_vert = max(np.max(label.vertices) for label in hemi_labels)
n_vertices = max_vert + 1
else:
n_vertices = 1
msg = (' Number of vertices in the surface could not be '
'verified because the surface file could not be found; '
'specify subject and subjects_dir parameters.')
logger.warning(msg)
# Create annot and color table array to write
annot = np.empty(n_vertices, dtype=np.intp)
annot[:] = -1
# create the annotation ids from the colors
annot_id_coding = np.array((1, 2**8, 2**16))
annot_ids = list(np.sum(ctab_rgb * annot_id_coding, axis=1))
for label, annot_id in zip(hemi_labels, annot_ids):
# make sure the label is not overwriting another label
if np.any(annot[label.vertices] != -1):
other_ids = set(annot[label.vertices])
other_ids.discard(-1)
other_indices = (annot_ids.index(i) for i in other_ids)
other_names = (hemi_labels[i].name for i in other_indices)
other_repr = ', '.join(other_names)
msg = "%s: %s overlaps %s" % (hemi, label.name, other_repr)
overlap.append(msg)
annot[label.vertices] = annot_id
hemi_names = [label.name for label in hemi_labels]
# Assign unlabeled vertices to an "unknown" label
unlabeled = (annot == -1)
if np.any(unlabeled):
msg = ("Assigning %i unlabeled vertices to "
"'unknown-%s'" % (unlabeled.sum(), hemi))
logger.info(msg)
# find an unused color (try shades of gray first)
for i in range(1, 257):
if not np.any(np.all((i, i, i) == ctab_rgb, 1)):
break
if i < 256:
color = (i, i, i, 0)
else:
err = ("Need one free shade of gray for 'unknown' label. "
"Please modify your label colors, or assign the "
"unlabeled vertices to another label.")
raise ValueError(err)
# find the id
annot_id = np.sum(annot_id_coding * color[:3])
# update data to write
annot[unlabeled] = annot_id
ctab = np.vstack((ctab, color))
hemi_names.append("unknown")
# convert to FreeSurfer alpha values
ctab[:, 3] = 255 - ctab[:, 3]
# remove hemi ending in names
hemi_names = [
name[:-3] if name.endswith(hemi) else name for name in hemi_names
]
to_save.append((fname, annot, ctab, hemi_names))
issues = []
if duplicate_colors:
msg = ("Some labels have the same color values (all labels in one "
"hemisphere must have a unique color):")
duplicate_colors.insert(0, msg)
issues.append('\n'.join(duplicate_colors))
if invalid_colors:
msg = ("Some labels have invalid color values (all colors should be "
"RGBA tuples with values between 0 and 1)")
invalid_colors.insert(0, msg)
issues.append('\n'.join(invalid_colors))
if overlap:
msg = ("Some labels occupy vertices that are also occupied by one or "
"more other labels. Each vertex can only be occupied by a "
"single label in *.annot files.")
overlap.insert(0, msg)
issues.append('\n'.join(overlap))
if issues:
raise ValueError('\n\n'.join(issues))
# write it
for fname, annot, ctab, hemi_names in to_save:
logger.info(' writing %d labels to %s' % (len(hemi_names), fname))
_write_annot(fname, annot, ctab, hemi_names)
logger.info('[done]')
def write_labels_to_annot(labels, subject=None, parc=None, overwrite=False,
subjects_dir=None, annot_fname=None,
colormap='hsv', hemi='both'):
"""Create a FreeSurfer annotation from a list of labels
FIX: always write both hemispheres
Parameters
----------
labels : list with instances of mne.Label
The labels to create a parcellation from.
subject : str | None
The subject for which to write the parcellation for.
parc : str | None
The parcellation name to use.
overwrite : bool
Overwrite files if they already exist.
subjects_dir : string, or None
Path to SUBJECTS_DIR if it is not set in the environment.
annot_fname : str | None
Filename of the .annot file. If not None, only this file is written
and 'parc' and 'subject' are ignored.
colormap : str
Colormap to use to generate label colors for labels that do not
have a color specified.
hemi : 'both' | 'lh' | 'rh'
The hemisphere(s) for which to write *.annot files (only applies if
annot_fname is not specified; default is 'both').
verbose : bool, str, int, or None
If not None, override default verbose level (see mne.verbose).
Notes
-----
Vertices that are not covered by any of the labels are assigned to a label
named "unknown".
"""
subjects_dir = get_subjects_dir(subjects_dir)
# get the .annot filenames and hemispheres
annot_fname, hemis = _get_annot_fname(annot_fname, subject, hemi, parc,
subjects_dir)
if not overwrite:
for fname in annot_fname:
if op.exists(fname):
raise ValueError('File %s exists. Use "overwrite=True" to '
'overwrite it' % fname)
# prepare container for data to save:
to_save = []
# keep track of issues found in the labels
duplicate_colors = []
invalid_colors = []
overlap = []
no_color = (-1, -1, -1, -1)
no_color_rgb = (-1, -1, -1)
for hemi, fname in zip(hemis, annot_fname):
hemi_labels = [label for label in labels if label.hemi == hemi]
n_hemi_labels = len(hemi_labels)
if n_hemi_labels == 0:
ctab = np.empty((0, 4), dtype=np.int32)
ctab_rgb = ctab[:, :3]
else:
hemi_labels.sort(key=lambda label: label.name)
# convert colors to 0-255 RGBA tuples
hemi_colors = [no_color if label.color is None else
tuple(int(round(255 * i)) for i in label.color)
for label in hemi_labels]
ctab = np.array(hemi_colors, dtype=np.int32)
ctab_rgb = ctab[:, :3]
# make color dict (for annot ID, only R, G and B count)
labels_by_color = defaultdict(list)
for label, color in zip(hemi_labels, ctab_rgb):
labels_by_color[tuple(color)].append(label.name)
# check label colors
for color, names in labels_by_color.items():
if color == no_color_rgb:
continue
if color == (0, 0, 0):
# we cannot have an all-zero color, otherw. e.g. tksurfer
# refuses to read the parcellation
msg = ('At least one label contains a color with, "r=0, '
'g=0, b=0" value. Some FreeSurfer tools may fail '
'to read the parcellation')
logger.warning(msg)
if any(i > 255 for i in color):
msg = ("%s: %s (%s)" % (color, ', '.join(names), hemi))
invalid_colors.append(msg)
if len(names) > 1:
msg = "%s: %s (%s)" % (color, ', '.join(names), hemi)
duplicate_colors.append(msg)
# replace None values (labels with unspecified color)
if labels_by_color[no_color_rgb]:
default_colors = _n_colors(n_hemi_labels, bytes_=True,
cmap=colormap)
safe_color_i = 0 # keep track of colors known to be in hemi_colors
for i in xrange(n_hemi_labels):
if ctab[i, 0] == -1:
color = default_colors[i]
# make sure to add no duplicate color
while np.any(np.all(color[:3] == ctab_rgb, 1)):
color = default_colors[safe_color_i]
safe_color_i += 1
# assign the color
ctab[i] = color
# find number of vertices in surface
if subject is not None and subjects_dir is not None:
fpath = os.path.join(subjects_dir, subject, 'surf',
'%s.white' % hemi)
points, _ = read_surface(fpath)
n_vertices = len(points)
else:
if len(hemi_labels) > 0:
max_vert = max(np.max(label.vertices) for label in hemi_labels)
n_vertices = max_vert + 1
else:
n_vertices = 1
msg = (' Number of vertices in the surface could not be '
'verified because the surface file could not be found; '
'specify subject and subjects_dir parameters.')
logger.warning(msg)
# Create annot and color table array to write
annot = np.empty(n_vertices, dtype=np.int)
annot[:] = -1
# create the annotation ids from the colors
annot_id_coding = np.array((1, 2 ** 8, 2 ** 16))
annot_ids = list(np.sum(ctab_rgb * annot_id_coding, axis=1))
for label, annot_id in zip(hemi_labels, annot_ids):
# make sure the label is not overwriting another label
if np.any(annot[label.vertices] != -1):
other_ids = set(annot[label.vertices])
other_ids.discard(-1)
other_indices = (annot_ids.index(i) for i in other_ids)
other_names = (hemi_labels[i].name for i in other_indices)
other_repr = ', '.join(other_names)
msg = "%s: %s overlaps %s" % (hemi, label.name, other_repr)
overlap.append(msg)
annot[label.vertices] = annot_id
hemi_names = [label.name for label in hemi_labels]
# Assign unlabeled vertices to an "unknown" label
unlabeled = (annot == -1)
if np.any(unlabeled):
msg = ("Assigning %i unlabeled vertices to "
"'unknown-%s'" % (unlabeled.sum(), hemi))
logger.info(msg)
# find an unused color (try shades of gray first)
for i in range(1, 257):
if not np.any(np.all((i, i, i) == ctab_rgb, 1)):
break
if i < 256:
color = (i, i, i, 0)
else:
err = ("Need one free shade of gray for 'unknown' label. "
"Please modify your label colors, or assign the "
"unlabeled vertices to another label.")
raise ValueError(err)
# find the id
annot_id = np.sum(annot_id_coding * color[:3])
# update data to write
annot[unlabeled] = annot_id
ctab = np.vstack((ctab, color))
hemi_names.append("unknown")
# convert to FreeSurfer alpha values
ctab[:, 3] = 255 - ctab[:, 3]
# remove hemi ending in names
hemi_names = [name[:-3] if name.endswith(hemi) else name
for name in hemi_names]
to_save.append((fname, annot, ctab, hemi_names))
issues = []
if duplicate_colors:
msg = ("Some labels have the same color values (all labels in one "
"hemisphere must have a unique color):")
duplicate_colors.insert(0, msg)
issues.append(os.linesep.join(duplicate_colors))
if invalid_colors:
msg = ("Some labels have invalid color values (all colors should be "
"RGBA tuples with values between 0 and 1)")
invalid_colors.insert(0, msg)
issues.append(os.linesep.join(invalid_colors))
if overlap:
msg = ("Some labels occupy vertices that are also occupied by one or "
"more other labels. Each vertex can only be occupied by a "
"single label in *.annot files.")
overlap.insert(0, msg)
issues.append(os.linesep.join(overlap))
if issues:
raise ValueError('\n\n'.join(issues))
# write it
for fname, annot, ctab, hemi_names in to_save:
logger.info(' writing %d labels to %s' % (len(hemi_names), fname))
_write_annot(fname, annot, ctab, hemi_names)
logger.info('[done]')
