def get_all_links(links={}, links_fol=None, links_fol_name='links'):
if links_fol is None:
links_fol = utils.get_links_dir(links_fol_name)
all_links = [
utils.namebase(f) for f in glob.glob(op.join(links_fol, '*'))
if utils.is_link(f)
]
all_links = {
link_name: utils.get_link_dir(links_fol, link_name)
for link_name in all_links if link_name not in links
}
links = utils.merge_two_dics(links, all_links)
return links
def copy_resources_files(mmvt_root_dir, overwrite=True, only_verbose=False):
resource_dir = utils.get_resources_fol()
utils.make_dir(op.join(op.join(mmvt_root_dir, 'color_maps')))
files = [
'aparc.DKTatlas40_groups.csv', 'atlas.csv', 'sub_cortical_codes.txt',
'FreeSurferColorLUT.txt', 'empty_subject.blend', 'high_level_atlas.csv'
]
cm_files = glob.glob(op.join(resource_dir, 'color_maps', '*.npy'))
all_files_exist = utils.all(
[op.isfile(op.join(mmvt_root_dir, file_name)) for file_name in files])
all_cm_files_exist = utils.all([
op.isfile(
op.join(mmvt_root_dir, 'color_maps',
'{}.npy'.format(utils.namebase(fname))))
for fname in cm_files
])
if all_files_exist and all_cm_files_exist and not overwrite:
if only_verbose:
print('All files exist!')
return True
if not all_cm_files_exist or overwrite:
for color_map_file in glob.glob(
op.join(resource_dir, 'color_maps', '*.npy')):
new_file_name = op.join(mmvt_root_dir, 'color_maps',
color_map_file.split(op.sep)[-1])
# print('Copy {} to {}'.format(color_map_file, new_file_name))
print('Coping {} to {}'.format(color_map_file, new_file_name))
if not only_verbose:
try:
shutil.copy(color_map_file, new_file_name)
except:
print('Can\'t copy {} to {}!'.format(
color_map_file, new_file_name))
if not all_files_exist or overwrite:
for file_name in files:
print('Copying {} to {}'.format(op.join(resource_dir, file_name),
op.join(mmvt_root_dir, file_name)))
if not only_verbose:
local_fname = op.join(resource_dir, file_name)
if op.isfile(op.join(resource_dir, file_name)):
try:
shutil.copy(local_fname,
op.join(mmvt_root_dir, file_name))
except:
print('Can\'t copy {}'.format(file_name))
else:
print(
'{} is missing, please update your code from github (git pull)'
.format(op.join(resource_dir, file_name)))
return utils.all(
[op.isfile(op.join(mmvt_root_dir, file_name)) for file_name in files])
def copy_resources_files(mmvt_root_dir, only_verbose=False):
resource_dir = utils.get_resources_fol()
utils.make_dir(op.join(op.join(mmvt_root_dir, 'color_maps')))
files = [
'aparc.DKTatlas40_groups.csv', 'atlas.csv', 'sub_cortical_codes.txt',
'FreeSurferColorLUT.txt', 'empty_subject.blend', 'high_level_atlas.csv'
]
cm_files = glob.glob(op.join(resource_dir, 'color_maps', '*.npy'))
all_files_exist = utils.all(
[op.isfile(op.join(mmvt_root_dir, file_name)) for file_name in files])
all_cm_files_exist = utils.all([
op.isfile(
op.join(mmvt_root_dir, 'color_maps',
'{}.npy'.format(utils.namebase(fname))))
for fname in cm_files
])
if all_files_exist and all_cm_files_exist:
if only_verbose:
print('All files exist!')
return True
if not all_cm_files_exist:
for color_map_file in glob.glob(
op.join(resource_dir, 'color_maps', '*.npy')):
new_file_name = op.join(mmvt_root_dir, 'color_maps',
color_map_file.split(op.sep)[-1])
# print('Copy {} to {}'.format(color_map_file, new_file_name))
if only_verbose:
print('Coping {} to {}'.format(color_map_file, new_file_name))
else:
shutil.copy(color_map_file, new_file_name)
if not all_files_exist:
for file_name in files:
if only_verbose:
print('Copying {} to {}'.format(
op.join(resource_dir, file_name),
op.join(mmvt_root_dir, file_name)))
else:
shutil.copy(op.join(resource_dir, file_name),
op.join(mmvt_root_dir, file_name))
return utils.all(
[op.isfile(op.join(mmvt_root_dir, file_name)) for file_name in files])