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 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 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 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_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()
su.call_script(__file__, args, run_in_background=run_in_background)
def read_args(argv=None):
parser = su.add_default_args()
# Add more args here
return su.parse_args(parser, argv)
def init_mmvt_addon(subject_fname):
# args = read_args(su.get_python_argv())
# if args.debug:
# su.debug()
su.init_mmvt_addon()
print('Finish init MMVT!')
if __name__ == '__main__':
import sys
if len(sys.argv) > 2 and sys.argv[2] in ['--python', '--background']:
subject_fname = sys.argv[1]
init_mmvt_addon(subject_fname)
elif len(sys.argv) >= 2:
subject = sys.argv[1]
atlas = sys.argv[2]
run_in_background = su.is_true(
sys.argv[3]) if len(sys.argv) >= 4 else False
run(subject, atlas, run_in_background)
else:
print('Not enough parameters were sent!')
