def render_movie(subject_fname):
args = read_args(su.get_python_argv())
if args.debug:
su.debug()
if args.rel_output_path:
mmvt_dir = op.join(su.get_links_dir(), 'mmvt')
if args.output_path == '':
args.output_path = args.play_type
args.output_path = op.join(mmvt_dir, args.subject, 'movies',
args.output_path)
su.make_dir(args.output_path)
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)
mmvt.set_light_layers_depth(args.light_layers)
mmvt.set_brain_transparency(args.brain_trans)
mmvt.filter_nodes(args.filter_nodes)
mark_electrodes(mmvt, args)
camera_fname = su.load_camera(mmvt, mmvt_dir, args)
if not op.isfile(op.join(args.output_path, 'data.pkl')):
try:
mmvt.capture_graph(args.play_type, args.output_path,
args.selection_type)
except:
print("Graph couldn't be captured!")
su.save_blend_file(subject_fname)
mmvt.render_movie(args.play_type, args.play_from, args.play_to,
camera_fname, args.play_dt, args.set_to_camera_mode)
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 render_image(subject_fname):
args = read_args(su.get_python_argv())
if args.output_path == '':
mmvt_dir = op.join(su.get_links_dir(), 'mmvt')
args.output_path = op.join(mmvt_dir, args.subject, 'figures')
su.make_dir(args.output_path)
mmvt = su.init_mmvt_addon()
mmvt.set_render_quality(args.quality)
mmvt.set_render_output_path(args.output_path)
mmvt.set_render_smooth_figure(args.smooth_figure)
if not args.hide_lh is None:
mmvt.show_hide_hemi(args.hide_lh, 'lh')
if not args.hide_rh is None:
mmvt.show_hide_hemi(args.hide_rh, 'rh')
if not args.hide_subs is None:
mmvt.show_hide_sub_corticals(args.hide_subs)
if not args.show_elecs is None:
mmvt.show_electrodes(args.show_elecs)
if not args.show_only_lead is None:
print('Showing only the current lead: {}'.format(args.show_only_lead))
mmvt.set_show_only_lead(args.show_only_lead)
if args.curr_elec not in ['', 'None']:
print('Setting current electrode to {}'.format(args.curr_elec))
mmvt.set_current_electrode(args.curr_elec)
if op.isfile(op.join(args.output_path, 'camera.pkl')):
mmvt.load_camera()
else:
cont = input('No camera file was detected in the output folder, continue?')
if not su.is_true(cont):
return
# su.save_blend_file(subject_fname)
mmvt.render_image(args.image_name, args.output_path, args.quality, args.smooth_figure, render_background=False)
su.exit_blender()
def wrap_mmvt_calls(subject_fname):
args = read_args(su.get_python_argv())
if args.debug:
su.debug()
mmvt = su.init_mmvt_addon()
mmvt_calls(mmvt, args, subject_fname)
su.exit_blender()
def run_script(subject_fname):
args = read_args(su.get_python_argv())
if args.debug:
su.debug()
mmvt = su.init_mmvt_addon()
mmvt.find_fmri_files_min_max()
clusters_names = [
f for f in mmvt.get_clusters_file_names() if args.clusters_type in f
]
print('clusters_names: {}'.format(clusters_names))
if len(args.lighting) == 1 and len(args.background_color) == 2:
args.lighting = [args.lighting] * 2
for clusters_file_name in clusters_names:
for inflated, background_color in product(args.inflated,
args.background_color):
lighting = args.lighting[
0] if background_color == 'black' else args.lighting[1]
mmvt.init_rendering(inflated, args.inflated_ratio,
args.transparency, args.light_layers_depth,
lighting, background_color,
args.rendering_in_the_background)
mmvt.load_fmri_cluster(clusters_file_name)
mmvt.plot_all_blobs()
mmvt.render_lateral_medial_split_brain(clusters_file_name,
args.quality,
args.overwrite)
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_sensors(subject_fname):
args = read_args(su.get_python_argv())
mmvt = su.init_mmvt_addon()
mmvt.import_meg_sensors()
mmvt.add_data_to_meg_sensors(args.stat)
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_connections(subject_fname):
args = read_args(su.get_python_argv())
mmvt = su.init_mmvt_addon()
mmvt.set_connection_type(args.type)
mmvt.set_connections_threshold(args.threshold)
mmvt.create_connections()
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 do_something(subject_fname):
args = read_args(su.get_python_argv())
if args.debug:
su.debug()
mmvt = su.init_mmvt_addon()
# Call mmvt functions
su.save_blend_file(subject_fname)
su.exit_blender()
def import_connections(subject_fname):
args = read_args(su.get_python_argv())
mmvt = su.init_mmvt_addon()
mmvt.set_connection_type(args.type)
mmvt.set_connections_threshold(args.threshold)
mmvt.create_connections()
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 install_blender_reqs():
import pip
pip.main(['install', '--upgrade', 'pip'])
libs = ['zmq', 'pizco', 'scipy', 'mne', 'joblib']
for lib in libs:
try:
pip.main(['install', lib])
except:
print('Error in installing {}!'.format(lib))
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 wrap_mmvt_calls(subject_fname):
args = read_args(su.get_python_argv())
if args.debug:
su.debug()
mmvt = su.init_mmvt_addon()
if args.modality == 'meg':
mmvt.import_meg_sensors(args.overwrite_sensors)
if args.load_data:
mmvt.add_data_to_meg_sensors(args.stat)
elif args.modality == 'eeg':
mmvt.import_eeg_sensors(args.overwrite_sensors)
if args.load_data:
mmvt.add_data_to_eeg_sensors()
else:
print('args.modality should be eeg or meg!')
su.save_blend_file(subject_fname)
su.exit_blender()
def run_script(subject_fname):
args = read_args(su.get_python_argv())
if args.debug:
su.debug()
mmvt = su.init_mmvt_addon()
mmvt.find_fmri_files_min_max()
clusters_names = [f for f in mmvt.get_clusters_file_names() if args.clusters_type in f]
print('clusters_names: {}'.format(clusters_names))
if len(args.lighting) == 1 and len(args.background_color) == 2:
args.lighting = [args.lighting] * 2
for clusters_file_name in clusters_names:
for inflated, background_color in product(args.inflated, args.background_color):
lighting = args.lighting[0] if background_color == 'black' else args.lighting[1]
mmvt.init_rendering(inflated, args.inflated_ratio, args.transparency, args.light_layers_depth,
lighting, background_color, args.rendering_in_the_background)
mmvt.load_fmri_cluster(clusters_file_name)
mmvt.plot_all_blobs()
mmvt.render_lateral_medial_split_brain(clusters_file_name, args.quality, args.overwrite)
su.save_blend_file(subject_fname)
su.exit_blender()
def do_something(subject_fname):
args = read_args(su.get_python_argv())
if args.debug:
su.debug()
mmvt = su.init_mmvt_addon()
mu = mmvt.utils
# Call mmvt functions
script_check_ret = mmvt.scripts.check_script(mu.namebase(args.script_name),
return_all=True)
if script_check_ret is None:
print('Can\'t call the script {}!'.format(args.script_name))
return
lib, (run_func, init_func, draw_func, params) = script_check_ret
for param_tup in args.script_params:
if len(param_tup.split(':')) != 2:
continue
param_name, param_val = param_tup.split(':')
mu.set_prop(param_name, param_val)
run_func(mmvt)
su.exit_blender()
def render_image(subject_fname):
args = read_args(su.get_python_argv())
if args.output_path == '':
mmvt_dir = op.join(su.get_links_dir(), 'mmvt')
args.output_path = op.join(mmvt_dir, args.subject, 'figures')
su.make_dir(args.output_path)
mmvt = su.init_mmvt_addon()
mmvt.set_render_quality(args.quality)
mmvt.set_render_output_path(args.output_path)
mmvt.set_render_smooth_figure(args.smooth_figure)
if not args.hide_lh is None:
mmvt.show_hide_hemi(args.hide_lh, 'lh')
if not args.hide_rh is None:
mmvt.show_hide_hemi(args.hide_rh, 'rh')
if not args.hide_subs is None:
mmvt.show_hide_sub_corticals(args.hide_subs)
if not args.show_elecs is None:
mmvt.show_electrodes(args.show_elecs)
if not args.show_only_lead is None:
print('Showing only the current lead: {}'.format(args.show_only_lead))
mmvt.set_show_only_lead(args.show_only_lead)
if args.curr_elec not in ['', 'None']:
print('Setting current electrode to {}'.format(args.curr_elec))
mmvt.set_current_electrode(args.curr_elec)
if not args.show_connections is None:
mmvt.show_hide_connections(args.show_connections)
if op.isfile(op.join(args.output_path, 'camera.pkl')):
mmvt.load_camera()
else:
cont = input(
'No camera file was detected in the output folder, continue?')
if not su.is_true(cont):
return
# su.save_blend_file(subject_fname)
mmvt.render_image(args.image_name,
args.output_path,
args.quality,
args.smooth_figure,
render_background=False)
su.exit_blender()
def render_movie(subject_fname):
args = read_args(su.get_python_argv())
if args.rel_output_path:
mmvt_dir = op.join(su.get_links_dir(), 'mmvt')
args.output_path = op.join(mmvt_dir, args.subject, 'movies', args.output_path)
su.make_dir(args.output_path)
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:
cont = input('No camera file was detected in the output folder, continue?')
if not su.is_true(cont):
return
if not op.isfile(op.join(args.output_path, 'data.pkl')):
mmvt.capture_graph(args.play_type, args.output_path, args.selection_type)
su.save_blend_file(subject_fname)
mmvt.render_movie(args.play_type, args.play_from, args.play_to, args.play_dt)
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()
def add_fmri_dynamics_to_parent_obj(subject_fname):
mmvt = su.init_mmvt_addon()
mmvt.add_fmri_dynamics_to_parent_obj(add_fmri_subcorticals_data=True)
su.save_blend_file(subject_fname)
su.exit_blender()
def render_image_blender(subject_fname):
args = read_args(su.get_python_argv())
if args.debug:
su.debug()
mmvt_dir = su.get_link_dir(su.get_links_dir(), 'mmvt')
subject = su.get_subject_name(subject_fname)
if args.output_path == '':
args.output_path = op.join(mmvt_dir, args.subject, 'figures')
su.make_dir(args.output_path)
mmvt = su.init_mmvt_addon()
mmvt.set_render_quality(args.quality)
mmvt.set_render_output_path(args.output_path)
mmvt.set_render_smooth_figure(args.smooth_figure)
if not args.hide_lh is None:
mmvt.show_hide_hemi(args.hide_lh, 'lh')
if not args.hide_rh is None:
mmvt.show_hide_hemi(args.hide_rh, 'rh')
if not args.hide_subs is None:
mmvt.show_hide_sub_corticals(args.hide_subs)
if not args.show_elecs is None:
mmvt.show_electrodes(args.show_elecs)
if not args.show_only_lead is None:
print('Showing only the current lead: {}'.format(args.show_only_lead))
mmvt.set_show_only_lead(args.show_only_lead)
if args.curr_elec not in ['', 'None']:
print('Setting current electrode to {}'.format(args.curr_elec))
mmvt.set_current_electrode(args.curr_elec)
if not args.show_connections is None:
mmvt.show_hide_connections(args.show_connections)
mmvt.filter_nodes(args.filter_nodes)
if args.inflated:
mmvt.show_inflated()
mmvt.set_inflated_ratio = args.inflated_ratio
mmvt.set_background_color(args.background_color)
mmvt.set_lighting(args.lighting)
for image_name, camera in zip(args.image_name, args.camera):
if camera == '':
camera = op.join(mmvt_dir, subject, 'camera', 'camera.pkl')
print('Camera fname: {}'.format(camera))
if op.isfile(camera):
mmvt.load_camera(camera)
else:
camera = op.join(mmvt_dir, subject, 'camera', 'camera.pkl')
print('Camera was not found, loading default camera')
mmvt.load_camera(camera)
# if args.interactive:
# cont = input('No camera file was detected in the output folder, continue?')
# if not su.is_true(cont):
# continue
# else:
# su.stdout_print('No camera file was detected in the output folder!!!')
# continue
# su.save_blend_file(subject_fname)
print('Rendering {}->{}'.format(image_name, args.output_path))
mmvt.render_image(image_name,
args.output_path,
args.quality,
args.smooth_figure,
render_background=False,
overwrite=args.overwrite)
su.stdout_print('*** finish rendering! ***')
su.exit_blender()
def do_something(subject_fname):
args = read_args(su.get_python_argv())
mmvt = su.init_mmvt_addon()
# Call mmvt functions
su.save_blend_file(subject_fname)
su.exit_blender()
