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 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 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 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()
osp.join(test_index_root, 'protocols', 'r1', 'subjects', subject,
'localizations', '0', 'neuroradiology'))
except OSError as ose:
if ose.errno != 17:
raise ose
return run_montage_import(inputs, force=True)
if __name__ == '__main__':
for subject in bipolar_subjects:
logger.set_subject(subject, 'R1')
sucess, _ = make_bipolar_montage(subject)
if sucess:
tal = TalReader(filename=pairs_path_template.format(
protocols_root=test_index_root, subject=subject))
new_bipolar_pairs = tal.get_bipolar_pairs()
jr = JsonIndexReader(
osp.join(reference_index_root, 'protocols', 'r1.json'))
task_event_files = list(
jr.aggregate_values('task_events', subject=subject, montage=0))
events = CMLEventReader(filename=task_event_files[0]).read()
eeg = EEGReader(events=events[:1],
channels=np.array([]),
start_time=0.0,
end_time=0.1).read()
hdf_bipolar_pairs = eeg.bipolar_pairs.values
new_bipolar_pairs = new_bipolar_pairs.astype(
hdf_bipolar_pairs.dtype)
if not np.in1d(hdf_bipolar_pairs, new_bipolar_pairs).all():
logger.info(
'\n\n%s missing from new_bipolar_pairs\n\n' %
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)
bo_recon = se.load(fname_recon)
os.symlink(osp.join(reference_index_root,'protocols','r1','subjects',subject,'localizations','0','neuroradiology'),
osp.join(test_index_root,'protocols','r1','subjects',subject,'localizations','0','neuroradiology'))
except OSError as ose:
if ose.errno != 17:
raise ose
return run_montage_import(inputs,force=True)
if __name__ == '__main__':
for subject in bipolar_subjects:
logger.set_subject(subject,'R1')
sucess, _ =make_bipolar_montage(subject)
if sucess:
tal = TalReader(filename=pairs_path_template.format(protocols_root=test_index_root,
subject= subject))
new_bipolar_pairs = tal.get_bipolar_pairs()
jr = JsonIndexReader(osp.join(reference_index_root,'protocols','r1.json'))
task_event_files = list(jr.aggregate_values('task_events',subject=subject,montage=0))
events = CMLEventReader(filename=task_event_files[0]).read()
eeg = EEGReader(events=events[:1],channels = np.array([]),start_time=0.0,end_time=0.1).read()
hdf_bipolar_pairs = eeg.bipolar_pairs.values
new_bipolar_pairs = new_bipolar_pairs.astype(hdf_bipolar_pairs.dtype)
if not np.in1d(hdf_bipolar_pairs,new_bipolar_pairs).all():
logger.info('\n\n%s missing from new_bipolar_pairs\n\n'%str(hdf_bipolar_pairs[~np.in1d(hdf_bipolar_pairs,new_bipolar_pairs)]))
if not np.in1d(new_bipolar_pairs,hdf_bipolar_pairs).all():
logger.info('\n\n%s missing from new_bipolar_pairs\n\n'%str(new_bipolar_pairs[~np.in1d(new_bipolar_pairs,hdf_bipolar_pairs)]))