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 find_blender_in_linux(fol, look_for_dirs=True):
blender_fol = ''
if look_for_dirs:
output = utils.get_command_output(
"find {} -name '*blender*' -type d".format(fol))
blender_fols = output.split('\n')
blender_fols = [
fol for fol in blender_fols
if op.isfile(op.join(fol, 'blender.svg')) or 'blender.app' in fol
]
if len(blender_fols) >= 1:
# todo: let the user select which one
blender_fol = blender_fols[0]
else:
output = utils.get_command_output(
"find {} -name '*blender*'".format(fol))
blender_fols = output.split('\n')
blender_fols = [
fol for fol in blender_fols
if utils.is_link(fol) and op.isfile(op.join(fol, 'blender.svg'))
]
if len(blender_fols) >= 1:
# todo: let the user select which one
blender_fol = blender_fols[0]
return blender_fol
def create_fsaverage_link(links_fol_name='links'):
freesurfer_home = os.environ.get('FREESURFER_HOME', '')
if freesurfer_home != '':
links_fol = utils.get_links_dir(links_fol_name)
subjects_dir = utils.get_link_dir(links_fol, 'subjects',
'SUBJECTS_DIR')
fsaverage_link = op.join(subjects_dir, 'fsaverage')
if not utils.is_link(fsaverage_link):
fsveareg_fol = op.join(freesurfer_home, 'subjects', 'fsaverage')
utils.create_folder_link(fsveareg_fol, fsaverage_link)
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 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
])
