def read_args(argv=None):
parser = su.add_default_args()
parser.add_argument('-t', '--type', help='connection type', required=False, default='')
parser.add_argument('--threshold', help='connection threshold', required=False, default=0, type=int)
args = su.parse_args(parser, argv)
rois_file_exist = op.isfile(op.join(su.get_mmvt_dir(), args.subject, 'rois_con.npz'))
electrodes_file_exist = op.isfile(op.join(su.get_mmvt_dir(), args.subject, 'electrodes_con.npz'))
if args.type == '':
if rois_file_exist and electrodes_file_exist:
raise Exception('More than one connection file exist, please select one using the -t flag')
elif rois_file_exist:
args.type = 'rois'
elif electrodes_file_exist:
args.type = 'electrodes'
else:
raise Exception('No connection file was found!\n'+
'ROIs connection file: rois_con.npz\n' +
'Electrodes connection file: electrodes_con.npz')
elif args.type == 'rois':
if not rois_file_exist:
raise Exception('You chose ROIs connection, but the file rois_con.npz does not exist!')
elif args.type == 'electrodes':
if not electrodes_file_exist:
raise Exception('You chose electrodes connection, but the file electrodes_con.npz does not exist!')
return args
def read_args(argv=None):
parser = su.add_default_args()
parser.add_argument('-r', '--radius', help='radius', required=False, default=0.15, type=float)
parser.add_argument('-p', '--pos_file', help='position file', required=False, default='', type=su.str_arr_type)
args = su.parse_args(parser, argv)
if len(args.subjects) == 0:
args.subjects = [args.subject]
if len(args.pos_file) == 0:
args.pos_file = [''] * len(args.subjects)
pos_files = []
for subject, pos_file in zip(args.subjects, args.pos_file):
args.subject = subject
pos_files_fol = op.join(su.get_mmvt_dir(), args.subject, 'electrodes')
if pos_file == '':
pos_file_options = glob.glob(op.join(pos_files_fol, 'electrodes*positions*.npz'))
if args.bipolar:
pos_file_options = [fname for fname in pos_file_options if 'bipolar' in fname]
else:
pos_file_options = [fname for fname in pos_file_options if 'bipolar' not in fname]
if len(pos_file_options) == 0:
raise Exception('No electrodes position files in {}!'.format(pos_files_fol))
elif len(pos_file_options) == 1:
pos_file = pos_file_options[0]
print('electrodes file: {}'.format(pos_file))
else:
raise Exception('More than one electrodes positions files in {}'.format(pos_files_fol) +
'please indicate which one using the -p flag')
pos_files.append(pos_file)
args.pos_file = pos_files
if len(args.pos_file) == 1:
args.pos_file = args.pos_file[0]
return args
def create_new_subject_file(args):
# Create a file for the new subject
if len(args.subjects) == 0:
args.subjects = [args.subject]
for subject in args.subjects:
args.subject = subject
new_fname = su.get_subject_fname(args)
empty_subject_fname = op.join(su.get_mmvt_dir(), "empty_subject.blend")
if not op.isfile(empty_subject_fname):
shutil.copy(op.join(su.get_resources_dir(), "empty_subject.blend"), empty_subject_fname)
if op.isfile(new_fname):
overwrite = input("The file {} already exist, do you want to overwrite? ".format(new_fname))
if su.is_true(overwrite):
os.remove(new_fname)
shutil.copy(op.join(su.get_mmvt_dir(), "empty_subject.blend"), new_fname)
else:
shutil.copy(op.join(su.get_mmvt_dir(), "empty_subject.blend"), new_fname)
def render_electrodes_probs(subject_fname):
args = read_args(su.get_python_argv())
figures_dir = su.get_figures_dir(args)
if args.rel_output_path:
args.output_path = op.join(figures_dir, args.output_path)
su.make_dir(args.output_path)
# Set the labeling file
labeling_fname = '{}_{}_electrodes_cigar_r_*_l_*{}*.pkl'.format(args.subject, args.real_atlas,
'_bipolar' if args.bipolar else '')
labels_fol = op.join(su.get_mmvt_dir(), args.subject, 'electrodes')
labeling_files = glob.glob(op.join(labels_fol, labeling_fname))
if len(labeling_files) == 0:
print('No labeling files in {}!'.format(labels_fol))
return
if len(labeling_files) > 1:
print('More than one labeling files in {}, please choose one using the --labeling flag'.format(labels_fol))
return
else:
labeling_file = labeling_files[0]
mmvt = su.init_mmvt_addon()
mmvt.show_hide_hemi(args.hide_lh, 'lh')
mmvt.show_hide_hemi(args.hide_rh, 'rh')
mmvt.show_hide_sub_corticals(args.hide_subs)
mmvt.set_render_quality(args.quality)
mmvt.set_render_output_path(args.output_path)
mmvt.set_render_smooth_figure(args.smooth_figure)
if op.isfile(op.join(args.output_path, 'camera.pkl')):
mmvt.load_camera()
else:
# Try to find the camera in the figures folder
if op.isfile(op.join(figures_dir, 'camera.pkl')):
mmvt.set_render_output_path(figures_dir)
mmvt.load_camera()
mmvt.set_render_output_path(args.output_path)
else:
cont = input('No camera file was detected in the output folder, continue?')
if not su.is_true(cont):
return
mmvt.set_electrodes_labeling_file(labeling_file)
mmvt.show_electrodes()
mmvt.color_the_relevant_lables(True)
leads = mmvt.get_leads()
for lead in leads:
electrodes = mmvt.get_lead_electrodes(lead)
for electrode in electrodes:
print(electrode)
mmvt.clear_cortex()
mmvt.set_current_electrode(electrode, lead)
mmvt.render_image(electrode)
su.save_blend_file(subject_fname)
su.exit_blender()
def check_if_all_figures_were_rendered(args):
from src.utils import figures_utils as fu
from src.mmvt_addon import fMRI_panel as fmri
subject_fol = op.join(su.get_mmvt_dir(), args.subject)
figures_fol = op.join(subject_fol, 'figures')
clusters_file_names, _ = fmri.get_clusters_files(subject_fol)
clusters_names = [f for f in clusters_file_names if args.clusters_type in f]
render_figures = False
all_figures = []
for clusters_name, inflated, background_color in product(clusters_names, args.inflated, args.background_color):
figures_fnames = fu.get_brain_perspectives_figures(
figures_fol, inflated, background_color, clusters_name, args.inflated_ratio)
all_figures.extend(figures_fnames)
if any(not op.isfile(f) for f in figures_fnames):
render_figures = True
break
return render_figures
def post_script(args):
from src.utils import figures_utils as fu
from src.mmvt_addon import fMRI_panel as fmri
from src.utils import utils
subject_fol = op.join(su.get_mmvt_dir(), args.subject)
figures_fol = op.join(subject_fol, 'figures')
clusters_file_names, _ = fmri.get_clusters_files(subject_fol)
clusters_names = [f for f in clusters_file_names if args.clusters_type in f]
print('clusters_names: {}'.format(clusters_names))
fmri_files_minmax_fname = op.join(subject_fol, 'fmri', 'fmri_files_minmax_cm.pkl')
data_min, data_max, colors_map_name = utils.load(fmri_files_minmax_fname)
for clusters_name, inflated, background_color in product(clusters_names, args.inflated, args.background_color):
print('Combing figures for {}, inflated: {}, background color: {}'.format(
clusters_name, inflated, background_color))
perspectives_image_fname = fu.combine_four_brain_perspectives(
figures_fol, inflated, args.dpi, background_color,
clusters_name, args.inflated_ratio, True, args.overwrite)
fu.combine_brain_with_color_bar(
data_max, data_min, perspectives_image_fname, colors_map_name, args.overwrite, args.dpi,
args.x_left_crop, args.x_right_crop, args.y_top_crop, args.y_buttom_crop,
args.w_fac, args.h_fac, background_color)
