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 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()