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config.py
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config.py
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import mne
import os
import pandas as pd
exclude_subjects = dict(camcan=["CC220352"],
ds117=["sub001", "sub005", "sub016"])
def get_subjects_dir(dataset_name="camcan"):
if dataset_name == "camcan":
subjects_dir = "/storage/store/data/camcan-mne/freesurfer/"
elif dataset_name == "ds117":
subjects_dir = "/storage/store/work/agramfort/mne-biomag-group-demo/"
subjects_dir += "subjects/"
elif dataset_name == "sample":
data_path = "/storage/store/data/mne_data/MNE-sample-data"
subjects_dir = os.path.join(data_path, 'subjects')
else:
raise ValueError("Unknown dataset %s." % dataset_name)
return subjects_dir
def get_subjects_dir_subj(subject="sample"):
if subject.startswith('CC'):
dataset_name = "camcan"
else:
dataset_name = subject
return get_subjects_dir(dataset_name)
def get_data_path():
username = os.environ.get('USER')
if "hjana" in username:
data_path = "/storage/store/data/mne_data/MNE-sample-data"
else:
data_path = mne.datasets.sample.data_path()
return data_path
def get_trans_fname(subject, dataset_name="camcan"):
if dataset_name == "camcan":
path = "/storage/store/data/camcan-mne/trans/"
path += "sub-%s-trans.fif" % subject
elif dataset_name == "ds117":
path = "/storage/store/work/agramfort/mne-biomag-group-demo/"
path += "ds117/%s/MEG/%s-trans.fif" % (subject, subject)
else:
raise ValueError("Unknown dataset %s." % dataset_name)
return path
def get_bem_fname(subject, dataset_name="camcan"):
if dataset_name == "camcan":
path = "/storage/store/data/camcan-mne/freesurfer/"
path += "%s/bem/%s-meg-bem.fif" % (subject, subject)
elif dataset_name == "ds117":
path = "/storage/store/work/agramfort/mne-biomag-group-demo/"
path += "subjects/%s/bem/%s-5120-bem-sol.fif" % (subject, subject)
else:
raise ValueError("Unknown dataset %s." % dataset_name)
return path
def get_raw_fname(subject, dataset_name="camcan", task_type="passive"):
if dataset_name == "camcan":
path = "/storage/store/data/camcan/camcan47/cc700/meg/pipeline/"
path += "release004/data/aamod_meg_get_fif_00001/%s/%s/" % (subject,
task_type)
path += "%s_raw.fif" % task_type
elif dataset_name == "ds117":
path = "/storage/store/work/agramfort/mne-biomag-group-demo/"
path += "ds117/%s/MEG/run_01_raw.fif" % subject
else:
raise ValueError("Unknown dataset %s." % dataset_name)
return path
def get_ave_fname(subject, dataset_name="camcan", task_type="passive"):
if dataset_name == "camcan":
path = "/storage/store/work/hjanati/datasets/data/camcan/meg/"
path += "%s/%s_stim_sensors-ave.fif" % (subject, task_type)
elif dataset_name == "ds117":
path = "/storage/store/work/agramfort/mne-biomag-group-demo/"
path += "MEG/%s/%s_highpass-NoneHz-ave.fif" % (subject, subject)
else:
raise ValueError("Unknown dataset %s." % dataset_name)
return path
def get_cov_fname(subject, dataset_name="camcan", task_type="passive"):
if dataset_name == "camcan":
path = "/storage/store/work/hjanati/datasets/data/camcan/meg/"
path += "%s/%s_stim_sensors-cov.fif" % (subject, task_type)
elif dataset_name == "ds117":
path = "/storage/store/work/agramfort/mne-biomag-group-demo/"
path += "MEG/%s/%s_highpass-NoneHz-cov.fif" % (subject, subject)
else:
raise ValueError("Unknown dataset %s." % dataset_name)
return path
def get_epo_fname(subject, dataset_name="camcan", task_type="passive"):
if dataset_name == "camcan":
path = "/storage/store/work/hjanati/datasets/data/camcan/meg/"
path += "%s/%s_stim_sensors-epo.fif" % (subject, task_type)
elif dataset_name == "ds117":
path = "/storage/store/work/agramfort/mne-biomag-group-demo/"
path += "MEG/%s/%s_highpass-NoneHz-epo.fif" % (subject, subject)
else:
raise ValueError("Unknown dataset %s." % dataset_name)
return path
def get_fwd_fname(subject, dataset_name="camcan"):
path = "/storage/store/work/hjanati/datasets/camcan/leadfields"
path += "/%s-fwd.fif" % subject
return path
def get_leadfield_fname(subject, dataset_name="camcan"):
path = "/storage/store/work/hjanati/datasets/camcan/leadfields"
path += "/%s-lfd.fif" % subject
return path
def get_subjects_list(dataset_name="camcan", age_min=0, age_max=100,
raw_only=False, ave_only=False):
if dataset_name == "camcan":
df = pd.read_csv("/storage/store/work/hjanati/datasets/data"
"/camcan/age.csv")
path = "/storage/store/data/camcan-mne/trans/"
df = df[(df.age < age_max) & (df.age > age_min)]
all_subjects = list(df.Observations)
subjects = []
for subject in all_subjects:
fname0 = get_raw_fname(dataset_name, subject)
check0 = os.path.exists(fname0)
if raw_only and check0:
subjects.append(subject)
continue
fname4 = get_ave_fname(dataset_name, subject)
check4 = os.path.exists(fname4)
if ave_only and check4:
subjects.append(subject)
continue
fname1 = get_bem_fname(dataset_name, subject)
fname2 = path + "../freesurfer/%s/surf/lh.white" % subject
fname3 = get_trans_fname(dataset_name, subject)
check1 = os.path.exists(fname1)
check2 = os.path.exists(fname2)
check3 = os.path.exists(fname3)
check5 = subject not in exclude_subjects[dataset_name]
if check1 * check2 * check3 * check0 * check4 * check5:
subjects.append(subject)
elif dataset_name == "ds117":
subjects = ["sub%03d" % i for i in range(1, 20)
if "sub%03d" % i not in exclude_subjects[dataset_name]]
else:
raise ValueError("Unknown dataset %s." % dataset_name)
return subjects