def ask_and_create_link(links_fol,
link_name,
message,
gui=True,
create_default_dir=False,
overwrite=True):
fol = ''
ret = False
if not overwrite and utils.is_link(op.join(links_fol, link_name)):
fol = utils.get_link_dir(links_fol, link_name)
ret = True
else:
choose_folder = mmvt_input(message, gui) == 'Ok'
if choose_folder:
root_fol = utils.get_parent_fol(links_fol)
fol = utils.choose_folder_gui(root_fol,
message) if gui else input()
if fol != '':
create_real_folder(fol)
ret = utils.create_folder_link(fol,
op.join(links_fol, link_name),
overwrite=overwrite)
if create_default_dir:
utils.make_dir(op.join(fol, 'default'))
return fol, ret
def create_real_folder(real_fol):
try:
if real_fol == '':
real_fol = utils.get_resources_fol()
utils.make_dir(real_fol)
except:
print('Error with creating the folder "{}"'.format(real_fol))
print(traceback.format_exc())
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 create_default_link(links_fol,
link_name,
default_fol_name,
create_default_dir=False,
overwrite=True):
root_fol = utils.get_parent_fol(levels=3)
fol = op.join(root_fol, default_fol_name)
create_real_folder(fol)
ret = utils.create_folder_link(fol,
op.join(links_fol, link_name),
overwrite=overwrite)
if create_default_dir:
utils.make_dir(op.join(fol, 'default'))
return fol, ret
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])
def create_links(links_fol_name='links',
gui=True,
default_folders=False,
only_verbose=False,
links_file_name='links.csv',
overwrite=True):
links_fol = utils.get_links_dir(links_fol_name)
if only_verbose:
print('making links dir {}'.format(links_fol))
else:
utils.make_dir(links_fol)
links_names = [
'blender', 'mmvt', 'subjects', 'eeg', 'meg', 'fMRI', 'electrodes'
]
# if not utils.is_windows():
# links_names.insert(1, 'subjects')
if not overwrite:
all_links_exist = utils.all([
utils.is_link(op.join(links_fol, link_name))
for link_name in links_names
])
if all_links_exist:
print('All links exist!')
links = {
link_name: utils.get_link_dir(links_fol, link_name)
for link_name in links_names
}
write_links_into_csv_file(links, links_fol, links_file_name)
return True
if not utils.is_windows() and not utils.is_link(
op.join(links_fol, 'freesurfer')):
if os.environ.get('FREESURFER_HOME', '') == '':
print(
'If you are going to use FreeSurfer locally, please source it and rerun'
)
# If you choose to continue, you'll need to create a link to FreeSurfer manually")
cont = input("Do you want to continue (y/n)?")
if cont.lower() != 'y':
return
else:
freesurfer_fol = os.environ['FREESURFER_HOME']
if not only_verbose:
create_real_folder(freesurfer_fol)
mmvt_message = 'Please select where do you want to put the blend files '
subjects_message = \
'Please select where do you want to store the FreeSurfer recon-all files neccessary for MMVT.\n' + \
'(It is prefered to create a local folder, because MMVT is going to save files to this directory) '
blender_message = 'Please select where did you install Blender '
meg_message = 'Please select where do you want to put the MEG files (Cancel if you are not going to use MEG data) '
eeg_message = 'Please select where do you want to put the EEG files (Cancel if you are not going to use EEG data) '
fmri_message = 'Please select where do you want to put the fMRI files (Cancel if you are not going to use fMRI data) '
electrodes_message = 'Please select where do you want to put the electrodes files (Cancel if you are not going to use electrodes data) '
blender_fol = find_blender()
if blender_fol != '':
utils.create_folder_link(blender_fol, op.join(links_fol, 'blender'),
overwrite)
else:
ask_and_create_link(links_fol, 'blender', blender_message, gui,
overwrite)
default_message = "Would you like to set default links to the MMVT's folders?\n" + \
"You can always change that later by running\n" + \
"python -m src.setup -f create_links"
create_default_folders = default_folders or mmvt_input(
default_message, gui, 4) == 'Yes'
messages = [
mmvt_message, subjects_message, eeg_message, meg_message, fmri_message,
electrodes_message
]
deafault_fol_names = [
'mmvt_blend', 'subjects', 'eeg', 'meg', 'fMRI', 'electrodes'
]
# if not utils.is_windows():
# messages.insert(0, subjects_message)
create_default_dirs = [False] * 3 + [True] * 2 + [False] * 2
links = {}
if not only_verbose:
for link_name, default_fol_name, message, create_default_dir in zip(
links_names[1:], deafault_fol_names, messages,
create_default_dirs):
fol = ''
if not create_default_folders:
fol, ret = ask_and_create_link(links_fol,
link_name,
message,
gui,
create_default_dir,
overwrite=overwrite)
if fol == '' or create_default_folders:
fol, ret = create_default_link(links_fol,
link_name,
default_fol_name,
create_default_dir,
overwrite=overwrite)
if ret:
print('The "{}" link was created to {}'.format(link_name, fol))
links[link_name] = fol
links = get_all_links(links, links_fol)
write_links_into_csv_file(links, links_fol, links_file_name)
return utils.all([
utils.is_link(op.join(links_fol, link_name))
for link_name in links_names
])