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 main(args):
# 1) Install dependencies from requirements.txt (created using pipreqs)
if utils.should_run(args, 'install_reqs'):
install_reqs(args.only_verbose)
# 2) Create links
if utils.should_run(args, 'create_links'):
links_created = create_links(args.links, args.gui,
args.default_folders, args.only_verbose)
if not links_created:
print(
'Not all the links were created! Make sure all the links are created before running MMVT.'
)
# 2,5) Create fsaverage folder link
if utils.should_run(args, 'create_fsaverage_link'):
create_fsaverage_link(args.links)
# 3) Copy resources files
if utils.should_run(args, 'copy_resources_files'):
links_dir = utils.get_links_dir(args.links)
mmvt_root_dir = utils.get_link_dir(links_dir, 'mmvt')
resource_file_exist = copy_resources_files(mmvt_root_dir,
args.only_verbose)
if not resource_file_exist:
input(
'Not all the resources files were copied to the MMVT folder ({}).\n'
.format(mmvt_root_dir) +
'Please copy them manually from the mmvt_code/resources folder.\n'
+ 'Press any key to continue...')
# 4) Install the addon in Blender (depends on resources and links)
if utils.should_run(args, 'install_addon'):
from src.mmvt_addon.scripts import install_addon
install_addon.wrap_blender_call(args.only_verbose)
# 5) Install python packages in Blender
if utils.should_run(args, 'install_blender_reqs'):
install_blender_reqs()
if 'create_links_csv' in args.function:
create_empty_links_csv()
if 'create_csv' in args.function:
write_links_into_csv_file(get_all_links())
if 'find_blender' in args.function:
find_blender()
print('Finish!')
def install_blender_reqs(blender_fol='', gui=True):
# http://stackoverflow.com/questions/9956741/how-to-install-multiple-python-packages-at-once-using-pip
try:
if blender_fol == '':
blender_fol = utils.get_link_dir(utils.get_links_dir(), 'blender')
resource_fol = utils.get_resources_fol()
blender_bin_fol, python_exe = get_blender_python_exe(blender_fol, gui)
current_dir = os.getcwd()
os.chdir(blender_bin_fol)
# install blender reqs:
# todo: take this list from the reqs file
reqs = 'matplotlib zmq pizco scipy mne joblib tqdm nibabel pdfkit decorator Pillow scikit-learn gitpython decorator'
pip_cmd = '{} {}'.format(op.join('bin', python_exe),
op.join(resource_fol, 'get-pip.py'))
if not utils.is_windows():
utils.run_script(pip_cmd)
# https://github.com/pypa/pip/issues/5226
# https://stackoverflow.com/questions/49743961/cannot-upgrade-pip-9-0-1-to-9-0-3-requirement-already-satisfied/49758204#49758204
# utils.run_script('curl https://bootstrap.pypa.io/get-pip.py | python3')
install_cmd = '{} install --upgrade {} --user'.format(
op.join('bin', 'pip'), reqs)
utils.run_script(install_cmd)
else:
# https://stackoverflow.com/questions/130763/request-uac-elevation-from-within-a-python-script
install_cmd = '{} install {}'.format(op.join('Scripts', 'pip'),
reqs)
print(
'Sorry, automatically installing external python libs in python will be implemented in the future.\n'
+ 'Meanwhile, you can do the following:\n' +
'1) Open a terminal window as administrator: ' +
'Right click on the "Command Prompt" shortcut from the start menu and choose "Run as administrator"\n'
+
'2) Change the directory to "{}".\n'.format(blender_bin_fol) +
'3) Run "{}"\n'.format(pip_cmd) +
'4) Run "{}"\nGood luck!'.format(install_cmd))
# from src.mmvt_addon.scripts import install_blender_reqs
# install_blender_reqs.wrap_blender_call(args.only_verbose)
os.chdir(current_dir)
except:
print(traceback.format_exc())
print("*** Can't install pizco ***")
def ask_and_create_link(links_fol,
link_name,
message,
gui=True,
create_default_dir=False,
overwrite=True):
fol = ''
if not overwrite and utils.is_link(op.join(links_fol, link_name)):
fol = utils.get_link_dir(links_fol, link_name)
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)
utils.create_folder_link(fol, op.join(links_fol, link_name))
if create_default_dir:
utils.make_dir(op.join(fol, 'default'))
return fol
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
])
def main(args):
# If python version is < 3.5, use Blender's python
if sys.version_info[0] < 3 or sys.version_info[
0] == 3 and sys.version_info[1] < 5:
blender_fol = find_blender()
blender_bin_fol, python_exe = get_blender_python_exe(blender_fol)
blender_python_exe = op.join(blender_bin_fol, 'bin', python_exe)
if not op.isfile(blender_python_exe):
print('You must use python 3.5 or newer, or install first Blender')
else:
# rerun setup with Blender's python
args.blender_fol = blender_fol
call_args = utils.create_call_args(args)
setup_cmd = '{} -m src.setup {}'.format(blender_python_exe,
call_args)
utils.run_script(setup_cmd, print_only=False)
return
print(args)
# 1) Install dependencies from requirements.txt (created using pipreqs)
if utils.should_run(args, 'install_reqs'):
install_reqs(args.upgrade_reqs_libs, args.only_verbose)
# 2) Create links
if utils.should_run(args, 'create_links'):
links_created = create_links(args.links, args.gui,
args.default_folders, args.only_verbose,
args.links_file_name,
args.overwrite_links)
if not links_created:
print(
'Not all the links were created! Make sure all the links are created before running MMVT.'
)
# 2,5) Create fsaverage folder link
if utils.should_run(args, 'create_fsaverage_link'):
create_fsaverage_link(args.links)
# 3) Copy resources files
if utils.should_run(args, 'copy_resources_files'):
links_dir = utils.get_links_dir(args.links)
mmvt_root_dir = utils.get_link_dir(links_dir, 'mmvt')
resource_file_exist = copy_resources_files(mmvt_root_dir,
args.overwrite,
args.only_verbose)
if not resource_file_exist:
input(
'Not all the resources files were copied to the MMVT folder ({}).\n'
.format(mmvt_root_dir) +
'Please copy them manually from the mmvt_code/resources folder.\n'
+ 'Press any key to continue...')
# 4) Install the addon in Blender (depends on resources and links)
if utils.should_run(args, 'install_addon'):
from src.mmvt_addon.scripts import install_addon
install_addon.wrap_blender_call(args.only_verbose)
# 5) Install python packages in Blender
if utils.should_run(args, 'install_blender_reqs'):
install_blender_reqs(args.blender_fol)
if utils.should_run(args, 'send_email'):
send_email()
if 'create_links_csv' in args.function:
create_empty_links_csv()
if 'create_csv' in args.function:
write_links_into_csv_file(get_all_links())
if 'find_blender' in args.function:
find_blender()
if 'get_pip_update_cmd' in args.function:
get_pip_update_cmd()
if 'read_blender_link' in args.function:
read_blender_link()
def get_pip_update_cmd(package='numpy'):
blender_fol = utils.get_link_dir(utils.get_links_dir(), 'blender')
blender_bin_fol, python_exe = get_blender_python_exe(blender_fol, False)
install_cmd = '{} install --upgrade {}'.format(
op.join(blender_bin_fol, 'bin', 'pip'), package)
print(install_cmd)
def read_blender_link():
print('Blender link: {}'.format(
utils.get_link_dir(utils.get_links_dir(), 'blender')))
