def read_session(subject, root, experiment, rhino_root):
jr = JsonIndexReader(rhino_root + '/protocols/r1.json') # Build JSON reader
pairs_path = jr.get_value('pairs', subject=subject, experiment=experiment)
tal_reader = TalReader(filename=pairs_path)
monopolar_channels = tal_reader.get_monopolar_channels()
bipolar_channels = tal_reader.get_bipolar_pairs()
jr = JsonIndexReader(rhino_root + '/protocols/r1.json') # Build JSON reader
pairs_path = jr.get_value('pairs', subject=subject, experiment=experiment)
tal_reader = TalReader(filename=pairs_path)
monopolar_channels = tal_reader.get_monopolar_channels()
p_reader = ParamsReader(dataroot=root)
params = p_reader.read()
samplerate = params['samplerate']
print samplerate
try:
raw_eeg = EEGReader(session_dataroot=root, channels = monopolar_channels)
raw_eeg = raw_eeg.read()
print raw_eeg.shape
except:
with h5py.File(root, 'r') as hfile:
raw_eeg = H5RawReader.H5RawReader.read_h5file(hfile, monopolar_channels,[0])[0]
print raw_eeg.shape
raw_eeg = TimeSeriesX.TimeSeriesX(raw_eeg,
dims=['channels', 'start_offsets', 'time'],
coords={
'channels': monopolar_channels,
'start_offsets': [0],
'time': np.arange(raw_eeg.shape[2])*1000/samplerate,
'offsets': ('time',np.arange(raw_eeg.shape[2])),
'samplerate': samplerate})
return raw_eeg
def test_talreader_on_database():
old_reader = TalReader(filename=osp.join(
utils.get_rhino_root(),
'data/eeg/R1234D/tal/R1234D_talLocs_database_bipol.mat'))
jr = JsonIndexReader(osp.join(utils.get_rhino_root(), 'protocols/r1.json'))
new_reader = TalReader(
filename=jr.get_value('pairs', subject='R1234D', experiment='FR1'))
assert (new_reader.get_bipolar_pairs() == old_reader.get_bipolar_pairs()
).all()
assert (new_reader.get_monopolar_channels() ==
old_reader.get_monopolar_channels()).all()
def test_talreader_on_database():
old_reader = TalReader(
filename=
'/Volumes/rhino_root/data/eeg/R1234D/tal/R1234D_talLocs_database_bipol.mat'
)
jr = JsonIndexReader('/Volumes/rhino_root/protocols/r1.json')
new_reader = TalReader(
filename=jr.get_value('pairs', subject='R1234D', experiment='FR1'))
assert new_reader.get_bipolar_pairs() == old_reader.get_bipolar_pairs()
assert new_reader.get_monopolar_channels(
) == old_reader.get_monopolar_channels()
def get_bp_tal_struct(sub, montage=0):
from ptsa.data.readers import TalReader
#Get electrode information -- bipolar
tal_path = '/protocols/r1/subjects/' + sub + '/localizations/0/montages/' + str(
montage) + '/neuroradiology/current_processed/pairs.json'
tal_reader = TalReader(filename=tal_path)
tal_struct = tal_reader.read()
monopolar_channels = tal_reader.get_monopolar_channels()
bipolar_pairs = tal_reader.get_bipolar_pairs()
return tal_struct, bipolar_pairs, monopolar_channels
def test_talreader_on_database():
old_reader = TalReader(filename='/Volumes/rhino_root/data/eeg/R1234D/tal/R1234D_talLocs_database_bipol.mat')
jr = JsonIndexReader('/Volumes/rhino_root/protocols/r1.json')
new_reader = TalReader(filename=jr.get_value('pairs',subject='R1234D',experiment='FR1'))
assert new_reader.get_bipolar_pairs() == old_reader.get_bipolar_pairs()
assert new_reader.get_monopolar_channels() == old_reader.get_monopolar_channels()
t = time.time()
pow_vec_orig = []
pow_vec_recon = []
print(len(recon_files))
print(len(orig_files))
assert (len(recon_files) == len(events))
experiment = 'FR1'
jr = JsonIndexReader(rhino_root +
'/protocols/r1.json') # Build JSON reader
pairs_path = jr.get_value('pairs',
subject=subject,
experiment=experiment)
tal_reader = TalReader(filename=pairs_path)
monopolar_channels = tal_reader.get_monopolar_channels()
bipolar_channels = tal_reader.get_bipolar_pairs()
recon_files = np.sort(recon_files)
orig_files = np.sort(orig_files)
data_orig_vec = []
data_recon_vec = []
for i, (recon_file,
orig_file) in enumerate(zip(recon_files, orig_files)):
if i % 100 == 0:
print(i)
fname_recon = subject_dir + recon_file
fname_orig = subject_dir + orig_file
bo_orig = se.load(fname_orig)