def create_electrodes_points(
subject, args
): # bipolar=False, create_points_files=True, create_volume_file=False,
# way_points=False, electrodes_pos_fname=''):
if args.elecs_names is None:
return
groups = set(
[utils.elec_group(name, args.bipolar) for name in args.elecs_names])
freeview_command = 'freeview -v T1.mgz:opacity=0.3 aparc+aseg.mgz:opacity=0.05:colormap=lut ' + \
('-w ' if args.way_points else '-c ')
for group in groups:
postfix = 'label' if args.way_points else 'dat'
freeview_command = freeview_command + group + postfix + ' '
group_pos = np.array([
pos for name, pos in zip(args.elecs_names, args.elecs_pos)
if utils.elec_group(name, args.bipolar) == group
])
file_name = '{}.{}'.format(group, postfix)
with open(op.join(BLENDER_ROOT_DIR, subject, 'freeview', file_name),
'w') as fp:
writer = csv.writer(fp, delimiter=' ')
if args.way_points:
writer.writerow(
['#!ascii label , from subject vox2ras=Scanner'])
writer.writerow([len(group_pos)])
points = np.hstack((np.ones(
(len(group_pos), 1)) * -1, group_pos,
np.ones((len(group_pos), 1))))
writer.writerows(points)
else:
writer.writerows(group_pos)
writer.writerow(['info'])
writer.writerow(['numpoints', len(group_pos)])
writer.writerow(['useRealRAS', '0'])
if args.create_volume_file:
import nibabel as nib
from itertools import product
sig = nib.load(op.join(BLENDER_ROOT_DIR, subject, 'freeview',
'T1.mgz'))
sig_header = sig.get_header()
data = np.zeros((256, 256, 256), dtype=np.int16)
# positions_ras = np.array(utils.to_ras(electrodes_positions, round_coo=True))
elecs_pos = np.array(args.elecs_pos, dtype=np.int16)
for pos_ras in elecs_pos:
for x, y, z in product(*([[d + i for i in range(-5, 6)]
for d in pos_ras])):
data[z, y, z] = 1
img = nib.Nifti1Image(data, sig_header.get_affine(), sig_header)
nib.save(
img,
op.join(BLENDER_ROOT_DIR, subject, 'freeview',
'electrodes.nii.gz'))
def read_csv_file(csv_fname, save_as_bipolar):
csv_lines = np.genfromtxt(csv_fname,
dtype=str,
delimiter=',',
skip_header=1)
electrodes = defaultdict(list)
for line in csv_lines:
subject = line[0].lower()
elecs_names = [e.strip() for e in line[1:3].tolist()]
elecs_groups = [utils.elec_group(e) for e in elecs_names]
if elecs_groups[0] == elecs_groups[1]:
elec_name = '{}-{}'.format(elecs_names[1], elecs_names[0])
else:
print('The electrodes has different groups! {}, {}'.format(
elecs_groups[0], elecs_groups[1]))
continue
coords1 = line[3:6].astype(np.float)
coords2 = line[6:9].astype(np.float)
if save_as_bipolar:
coords = (coords1 + (coords2 - coords1) / 2)
electrodes[subject].append((elec_name, coords))
else:
electrodes[subject].append((elecs_names[0], coords1))
electrodes[subject].append((elecs_names[1], coords2))
return electrodes
def load_stim_file(subject, args):
stim_fname = op.join(
MMVT_DIR, subject, 'electrodes',
'{}{}.npz'.format(args.file_frefix, args.stim_channel))
stim = np.load(stim_fname)
labels, psd, time, freqs = (stim[k]
for k in ['labels', 'psd', 'time', 'freqs'])
bipolar = '-' in labels[0]
data = None
freqs_dim = psd.shape.index(len(freqs))
labels_dim = psd.shape.index(len(labels))
if time.ndim > 0:
time_dim = psd.shape.index(len(time))
else:
time_dim = next(iter(set(range(3)) - set([freqs_dim, labels_dim])))
T, L, F = psd.shape[time_dim], psd.shape[labels_dim], psd.shape[freqs_dim]
if args.downsample > 1:
time = utils.downsample(time, args.downsample)
colors = None
conditions = []
for freq_ind, (freq_from, freq_to) in enumerate(freqs):
if data is None:
# initialize the data matrix (electrodes_num x T x freqs_num)
data = np.zeros((L, T, F))
psd_slice = get_psd_freq_slice(psd, freq_ind, freqs_dim, time_dim)
if args.downsample > 1:
psd_slice = utils.downsample(psd_slice, args.downsample)
data[:, :, freq_ind] = psd_slice
data_min, data_max = utils.calc_min_max(psd_slice,
norm_percs=args.norm_percs)
if colors is None:
colors = np.zeros((*data.shape, 3))
for elec_ind, elec_name in enumerate(labels):
elec_group = utils.elec_group(elec_name, bipolar)
# if elec_group in ['LVF', 'RMT']:
# colors[elec_ind, :, freq_ind] = utils.mat_to_colors(psd_slice[elec_ind], data_min, data_max, colorsMap='BuGn')
# else:
colors[elec_ind, :,
freq_ind] = utils.mat_to_colors(psd_slice[elec_ind],
data_min,
data_max,
colorsMap=args.colors_map)
conditions.append('{}-{}Hz'.format(freq_from, freq_to))
output_fname = op.join(
MMVT_DIR, subject, 'electrodes',
'stim_electrodes_{}{}_{}.npz'.format(args.file_frefix,
'bipolar' if bipolar else '',
args.stim_channel))
print('Saving {}'.format(output_fname))
np.savez(output_fname,
data=data,
names=labels,
conditions=conditions,
colors=colors)
return dict(data=data, labels=labels, conditions=conditions, colors=colors)
def create_electrodes_points(subject, args): # bipolar=False, create_points_files=True, create_volume_file=False,
# way_points=False, electrodes_pos_fname=''):
if args.elecs_names is None:
return
groups = set([utils.elec_group(name, args.bipolar) for name in args.elecs_names])
freeview_command = 'freeview -v T1.mgz:opacity=0.3 aparc+aseg.mgz:opacity=0.05:colormap=lut ' + \
('-w ' if args.way_points else '-c ')
for group in groups:
postfix = 'label' if args.way_points else 'dat'
freeview_command = freeview_command + group + postfix + ' '
group_pos = np.array([pos for name, pos in zip(args.elecs_names, args.elecs_pos) if
utils.elec_group(name, args.bipolar) == group])
file_name = '{}.{}'.format(group, postfix)
with open(op.join(MMVT_DIR, subject, 'freeview', file_name), 'w') as fp:
writer = csv.writer(fp, delimiter=' ')
if args.way_points:
writer.writerow(['#!ascii label , from subject vox2ras=Scanner'])
writer.writerow([len(group_pos)])
points = np.hstack((np.ones((len(group_pos), 1)) * -1, group_pos, np.ones((len(group_pos), 1))))
writer.writerows(points)
else:
writer.writerows(group_pos)
writer.writerow(['info'])
writer.writerow(['numpoints', len(group_pos)])
writer.writerow(['useRealRAS', '0'])
if args.create_volume_file:
import nibabel as nib
from itertools import product
sig = nib.load(op.join(MMVT_DIR, subject, 'freeview', 'T1.mgz'))
sig_header = sig.get_header()
data = np.zeros((256, 256, 256), dtype=np.int16)
# positions_ras = np.array(utils.to_ras(electrodes_positions, round_coo=True))
elecs_pos = np.array(args.elecs_pos, dtype=np.int16)
for pos_ras in elecs_pos:
for x, y, z in product(*([[d+i for i in range(-5,6)] for d in pos_ras])):
data[z,y,z] = 1
img = nib.Nifti1Image(data, sig_header.get_affine(), sig_header)
nib.save(img, op.join(MMVT_DIR, subject, 'freeview', 'electrodes.nii.gz'))
def sort_groups(first_electrodes, transformed_first_pos, groups_hemi, bipolar):
sorted_groups = {}
for hemi in ['rh', 'lh']:
# groups_pos = sorted([(pos[0], group) for (group, elc), pos in zip(
# first_electrodes.items(), transformed_first_pos) if groups_hemi[utils.elec_group(elc, bipolar)] == hemi])
groups_pos = []
for (group, elc), pos in zip(first_electrodes.items(), transformed_first_pos):
group_hemi = groups_hemi[utils.elec_group(elc, bipolar)]
if group_hemi == hemi:
groups_pos.append((pos[0], group))
groups_pos = sorted(groups_pos)
sorted_groups[hemi] = [group_pos[1] for group_pos in groups_pos]
return sorted_groups
def create_freeview_cmd(subject, args):#, atlas, bipolar, create_points_files=True, way_points=False):
blender_freeview_fol = op.join(MMVT_DIR, subject, 'freeview')
freeview_command = 'freeview -v T1.mgz:opacity=0.3 ' + \
'{0}+aseg.mgz:opacity=0.05:colormap=lut:lut={0}ColorLUT.txt '.format(args.atlas)
if args.elecs_names:
groups = set([utils.elec_group(name, args.bipolar) for name in args.elecs_names])
freeview_command += '-w ' if args.way_points else '-c '
postfix = '.label' if args.way_points else '.dat'
for group in groups:
freeview_command += group + postfix + ' '
utils.make_dir(blender_freeview_fol)
with open(op.join(blender_freeview_fol, 'run_freeview.sh'), 'w') as sh_file:
sh_file.write(freeview_command)
print(freeview_command)
def find_first_electrode_per_group(electrodes, positions, bipolar=False):
groups = OrderedDict() # defaultdict(list)
first_electrodes = OrderedDict()
for elc, pos in zip(electrodes, positions):
elc_group = utils.elec_group(elc, bipolar)
if elc_group not in groups:
groups[elc_group] = []
groups[elc_group].append((elc, pos))
first_pos = np.empty((len(groups), 3))
for ind, (group, group_electrodes) in enumerate(groups.items()):
first_electrode = sorted(group_electrodes)[0]
first_pos[ind, :] = first_electrode[1]
first_electrodes[group] = first_electrode[0]
return first_electrodes, first_pos, groups
def create_freeview_cmd(subject, args):#, atlas, bipolar, create_points_files=True, way_points=False):
blender_freeview_fol = op.join(MMVT_DIR, subject, 'freeview')
freeview_command = 'freeview -v T1.mgz:opacity=0.3 ' + \
'{0}+aseg.mgz:opacity=0.05:colormap=lut:lut={0}ColorLUT.txt '.format(args.atlas)
if args.elecs_names:
groups = set([utils.elec_group(name, args.bipolar) for name in args.elecs_names])
freeview_command += '-w ' if args.way_points else '-c '
postfix = '.label' if args.way_points else '.dat'
for group in groups:
freeview_command += group + postfix + ' '
utils.make_dir(blender_freeview_fol)
freeview_cmd_fname = op.join(blender_freeview_fol, 'run_freeview.sh')
with open(freeview_cmd_fname, 'w') as sh_file:
sh_file.write(freeview_command)
print(freeview_command)
return op.isfile(freeview_cmd_fname)
def create_electrodes_groups_coloring(subject, bipolar, coloring_fname='electrodes_groups_coloring.csv'):
electrodes, groups = get_electrodes_groups(subject, bipolar)
colors_rgb_and_names = cu.get_distinct_colors_and_names(len(groups) - 1, boynton=True)
group_colors = dict()
coloring_fname = op.join(MMVT_DIR, subject, 'coloring', coloring_fname)
coloring_names_fname = op.join(MMVT_DIR, subject, 'coloring', 'electrodes_groups_coloring_names.csv')
with open(coloring_names_fname, 'w') as colors_names_file:
for group, (color_rgb, color_name) in zip(groups, colors_rgb_and_names):
if 'ref' in group.lower():
continue
group_colors[group] = color_rgb
colors_names_file.write('{},{}\n'.format(group, color_name))
with open(coloring_fname, 'w') as colors_file:
for elc in electrodes:
if 'ref' in elc.lower():
continue
elc_group = utils.elec_group(elc, bipolar)
colors_file.write('{},{},{},{}\n'.format(elc, *group_colors[elc_group]))
def load_stim_file(subject, args):
stim_fname = op.join(MMVT_DIR, subject, 'electrodes', '{}{}.npz'.format(
args.file_frefix, args.stim_channel))
stim = np.load(stim_fname)
labels, psd, time, freqs = (stim[k] for k in ['labels', 'psd', 'time', 'freqs'])
bipolar = '-' in labels[0]
data = None
freqs_dim = psd.shape.index(len(freqs))
labels_dim = psd.shape.index(len(labels))
if time.ndim > 0:
time_dim = psd.shape.index(len(time))
else:
time_dim = next(iter(set(range(3)) - set([freqs_dim, labels_dim])))
T, L, F = psd.shape[time_dim], psd.shape[labels_dim], psd.shape[freqs_dim]
if args.downsample > 1:
time = utils.downsample(time, args.downsample)
colors = None
conditions = []
for freq_ind, (freq_from, freq_to) in enumerate(freqs):
if data is None:
# initialize the data matrix (electrodes_num x T x freqs_num)
data = np.zeros((L, T, F))
psd_slice = get_psd_freq_slice(psd, freq_ind, freqs_dim, time_dim)
if args.downsample > 1:
psd_slice = utils.downsample(psd_slice, args.downsample)
data[:, :, freq_ind] = psd_slice
data_min, data_max = utils.calc_min_max(psd_slice, norm_percs=args.norm_percs)
if colors is None:
colors = np.zeros((*data.shape, 3))
for elec_ind, elec_name in enumerate(labels):
elec_group = utils.elec_group(elec_name, bipolar)
# if elec_group in ['LVF', 'RMT']:
# colors[elec_ind, :, freq_ind] = utils.mat_to_colors(psd_slice[elec_ind], data_min, data_max, colorsMap='BuGn')
# else:
colors[elec_ind, :, freq_ind] = utils.mat_to_colors(psd_slice[elec_ind], data_min, data_max, colorsMap=args.colors_map)
conditions.append('{}-{}Hz'.format(freq_from, freq_to))
output_fname = op.join(MMVT_DIR, subject, 'electrodes', 'stim_electrodes_{}{}_{}.npz'.format(
args.file_frefix, 'bipolar' if bipolar else '', args.stim_channel))
print('Saving {}'.format(output_fname))
np.savez(output_fname, data=data, names=labels, conditions=conditions, colors=colors)
return dict(data=data, labels=labels, conditions=conditions, colors=colors)
def create_volume_with_electrodes(electrodes,
subjects_dir,
merge_to_pairs=True,
overwrite=False):
for subject in electrodes.keys():
if not op.isfile(op.join(SUBJECTS_DIR, subject, 'mri', 'T1.mgz')):
print(f'No T1 file for {subject}')
continue
t1_header = nib.load(op.join(SUBJECTS_DIR, subject, 'mri',
'T1.mgz')).header
fol = utils.make_dir(op.join(subjects_dir, subject, 'electrodes'))
output_fname = op.join(fol, 'stim_electrodes.nii.gz')
data = np.zeros((256, 256, 256), dtype=np.int16)
if merge_to_pairs:
groups = defaultdict(list)
for elc_name, coords in electrodes[subject]:
groups[utils.elec_group(elc_name)].append(elc_name, coords)
for group in groups.keys():
pair_data = np.zeros((256, 256, 256), dtype=np.int16)
for elc_name, coords in groups[group]:
vox = tkreg_to_vox(t1_header, coords)
pair_data[tuple(vox)] = 1000
pair_output_fname = op.join(fol, f'stim_{elc_name}.nii.gz')
if not op.isfile(elc_output_fname) or overwrite:
pass
else:
for elc_name, coords in electrodes[subject]:
vox = tkreg_to_vox(t1_header, coords)
# data[tuple(vox)] = 1000
elc_output_fname = op.join(fol, f'stim_{elc_name}.nii.gz')
if not op.isfile(elc_output_fname) or overwrite:
elc_data = np.zeros((256, 256, 256), dtype=np.int16)
elc_data[tuple(vox)] = 1000
elc_img = nib.Nifti1Image(elc_data, t1_header.get_affine(),
t1_header)
print(f'Saving {elc_output_fname}')
nib.save(elc_img, elc_output_fname)
def get_electrodes_groups(subject, bipolar):
electrodes, _ = read_electrodes_file(subject, bipolar)
groups = set()
for elc in electrodes:
groups.add(utils.elec_group(elc, bipolar))
return electrodes, groups
def get_groups_pos(electrodes, positions, bipolar):
groups = defaultdict(list)
for elc, pos in zip(electrodes, positions):
elc_group = utils.elec_group(elc, bipolar)
groups[elc_group].append(pos)
return groups
