def import_electrodes(subject_fname):
args = read_args(su.get_python_argv())
mmvt = su.init_mmvt_addon()
mmvt.import_electrodes(args.pos_file, args.bipolar, args.radius)
mmvt.set_render_output_path = su.get_figures_dir(args)
su.save_blend_file(subject_fname)
su.exit_blender()
def create_new_subject(subject_fname):
args = read_args(su.get_python_argv())
mmvt = su.init_mmvt_addon()
mmvt.import_brain()
mmvt.set_render_output_path = su.get_figures_dir(args)
su.save_blend_file(subject_fname)
su.exit_blender()
def create_new_subject(subject_fname):
args = read_args(su.get_python_argv())
mmvt = su.init_mmvt_addon()
mmvt.import_brain()
mmvt.set_render_output_path = su.get_figures_dir(args)
su.save_blend_file(subject_fname)
su.exit_blender()
def import_electrodes(subject_fname):
args = read_args(su.get_python_argv())
mmvt = su.init_mmvt_addon()
mmvt.import_electrodes(args.pos_file, args.bipolar, args.radius)
mmvt.set_render_output_path = su.get_figures_dir(args)
su.save_blend_file(subject_fname)
su.exit_blender()
def import_meg(subject_fname):
args = read_args(su.get_python_argv())
mmvt = su.init_mmvt_addon()
mmvt.add_data_to_parent_brain_obj(args.stat)
mmvt.add_data_to_brain()
mmvt.set_render_output_path = su.get_figures_dir(args)
su.save_blend_file(subject_fname)
su.exit_blender()
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 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 wrap_mmvt_calls(subject_fname):
args = read_args(su.get_python_argv())
mmvt = su.init_mmvt_addon()
mmvt.import_brain()
mmvt.set_render_output_path = su.get_figures_dir(args)
su.save_blend_file(subject_fname)
with open(args.log_fname, 'w') as text_file:
print(args, file=text_file)
try:
su.exit_blender()
except:
pass
def wrap_mmvt_calls(subject_fname):
args = read_args(su.get_python_argv())
if args.debug:
su.debug()
mmvt = su.init_mmvt_addon()
mmvt.utils.write_to_stderr('{} Importing electrodes...'.format(
args.subject))
if args.overwrite:
mmvt.utils.delete_hierarchy('Deep_electrodes')
mmvt.import_electrodes(args.pos_file, mmvt.ELECTRODES_LAYER, args.bipolar,
args.radius)
mmvt.set_render_output_path = su.get_figures_dir(args)
su.save_blend_file(subject_fname)
mmvt.utils.write_to_stderr('{} Done!'.format(args.subject))
su.exit_blender()
def import_meg(subject_fname):
args = read_args(su.get_python_argv())
mmvt = su.init_mmvt_addon()
try:
mmvt.add_data_to_parent_brain_obj(args.stat)
except:
logging.error('Error in add_data_to_parent_brain_obj!')
logging.error(traceback.format_exc())
try:
mmvt.add_data_to_brain()
except:
logging.error('Error in add_data_to_brain!')
logging.error(traceback.format_exc())
try:
mmvt.set_render_output_path = su.get_figures_dir(args)
except:
logging.error('Error in set_render_output_path!')
logging.error(traceback.format_exc())
try:
su.save_blend_file(subject_fname)
except:
logging.error('Error in save_blend_file!')
logging.error(traceback.format_exc())
su.exit_blender()
def import_meg(subject_fname):
args = read_args(su.get_python_argv())
mmvt = su.init_mmvt_addon()
try:
mmvt.add_data_to_parent_brain_obj(args.stat)
except:
logging.error('Error in add_data_to_parent_brain_obj!')
logging.error(traceback.format_exc())
try:
mmvt.add_data_to_brain()
except:
logging.error('Error in add_data_to_brain!')
logging.error(traceback.format_exc())
try:
mmvt.set_render_output_path = su.get_figures_dir(args)
except:
logging.error('Error in set_render_output_path!')
logging.error(traceback.format_exc())
try:
su.save_blend_file(subject_fname)
except:
logging.error('Error in save_blend_file!')
logging.error(traceback.format_exc())
su.exit_blender()