def extract_coordinates_from_talstructs(subject_localization, rootdir="/"):
talstruct_base_path = os.path.join(rootdir,
"data10/RAM/subjects/{}/tal/{}_talLocs_database_{}.mat")
# TODO: Use PathFinder once the matlab talstructs are available
bipol_reader = TalReader(filename=talstruct_base_path.format(subject_localization,
subject_localization,
'bipol'),
struct_type='bi')
bipol_structs = bipol_reader.read()
mono_reader = TalReader(filename=talstruct_base_path.format(subject_localization,
subject_localization,
'monopol'),
struct_type='mono')
mono_structs = mono_reader.read()
mono_start_df = get_coords(mono_structs, 'monopolar')
mono_start_df["contact_name"] = "o" + mono_start_df["contact_name"]
mono_adj_df = get_coords(mono_structs, 'monopolar', atlas='Dykstra')
bipo_adj_df = get_coords(bipol_structs, 'bipolar', atlas='Dykstra')
all_coord_df = pd.concat([mono_start_df, mono_adj_df, bipo_adj_df])
return all_coord_df
def get_tal_structs_row(subject,anode_tag,cathode_tag):
# '/Users/m/data/eeg/R1111M/tal/R1111M_talLocs_database_bipol.mat'
# tal_path = join(mount_point,'data/eeg/',subject,'tal',subject+'_talLocs_database_bipol.mat')
tal_path = str(join(mount_point,'data/eeg/',subject,'tal',subject+'_talLocs_database_monopol.mat'))
tal_reader = TalReader(filename=tal_path,struct_name='talStruct')
tal_structs = tal_reader.read()
# sel = tal_structs[np.where(tal_structs.tagName == anode_tag+'-'+cathode_tag)]
sel = tal_structs[np.where((tal_structs.tagName == anode_tag)|(tal_structs.tagName == cathode_tag))]
if not len(sel):
sel = tal_structs[np.where((tal_structs.tagName == anode_tag)|(tal_structs.tagName == cathode_tag))]
if not len(sel):
tal_path = str(join(mount_point,'data/eeg/',subject,'tal',subject+'_talLocs_database_stimOnly.mat'))
tal_reader = TalStimOnlyReader(filename=tal_path)
tal_structs = tal_reader.read()
sel = tal_structs[np.where((tal_structs.tagName == anode_tag)|(tal_structs.tagName == cathode_tag))]
if not len(sel):
sel = tal_structs[np.where((tal_structs.tagName == anode_tag)|(tal_structs.tagName == cathode_tag))]
return sel
def get_tal_structs_row(subject, anode_tag, cathode_tag):
# '/Users/m/data/eeg/R1111M/tal/R1111M_talLocs_database_bipol.mat'
# tal_path = join(mount_point,'data/eeg/',subject,'tal',subject+'_talLocs_database_bipol.mat')
tal_path = str(
join(mount_point, 'data/eeg/', subject, 'tal',
subject + '_talLocs_database_monopol.mat'))
tal_reader = TalReader(filename=tal_path, struct_name='talStruct')
tal_structs = tal_reader.read()
# sel = tal_structs[np.where(tal_structs.tagName == anode_tag+'-'+cathode_tag)]
sel = tal_structs[np.where((tal_structs.tagName == anode_tag)
| (tal_structs.tagName == cathode_tag))]
if not len(sel):
sel = tal_structs[np.where((tal_structs.tagName == anode_tag)
| (tal_structs.tagName == cathode_tag))]
if not len(sel):
tal_path = str(
join(mount_point, 'data/eeg/', subject, 'tal',
subject + '_talLocs_database_stimOnly.mat'))
tal_reader = TalStimOnlyReader(filename=tal_path)
tal_structs = tal_reader.read()
sel = tal_structs[np.where((tal_structs.tagName == anode_tag)
| (tal_structs.tagName == cathode_tag))]
if not len(sel):
sel = tal_structs[np.where((tal_structs.tagName == anode_tag)
| (tal_structs.tagName == cathode_tag))]
return sel
def extract_electrode_positions(tal_path):
from ptsa.data.readers import TalReader
tal_reader = TalReader(filename=tal_path)
tal_structs = tal_reader.read()
lh_selector = np.array(map( lambda loc : loc.startswith('Left'), tal_structs.Loc1))
rh_selector = np.array(map( lambda loc : loc.startswith('Right'), tal_structs.Loc1))
lh_avg_surf = tal_structs.avgSurf[lh_selector]
rh_avg_surf = tal_structs.avgSurf[rh_selector]
return lh_avg_surf, rh_avg_surf
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 extract_electrode_positions(tal_path):
from ptsa.data.readers import TalReader
tal_reader = TalReader(filename=tal_path)
tal_structs = tal_reader.read()
lh_selector = np.array(
map(lambda loc: loc.startswith('Left'), tal_structs.Loc1))
rh_selector = np.array(
map(lambda loc: loc.startswith('Right'), tal_structs.Loc1))
lh_avg_surf = tal_structs.avgSurf[lh_selector]
rh_avg_surf = tal_structs.avgSurf[rh_selector]
return lh_avg_surf, rh_avg_surf
def extract_electrode_positions(tal_path,
electrode_types=['D', 'G', 'S'],
hemi=['R', 'L']):
from ptsa.data.readers import TalReader
tal_reader = TalReader(filename=tal_path)
tal_structs = tal_reader.read()
electrode_types_lower = map(lambda t: t.lower(), electrode_types)
electrode_type_selector = np.array(
map(lambda eType: eType.lower() in electrode_types_lower,
tal_structs.eType))
h_data = tal_structs[['avgSurf', 'eType']]
h_data = h_data[electrode_type_selector]
return h_data
def extract_electrode_positions(tal_path, electrode_types=['D', 'G', 'S'], hemi=['R','L']):
from ptsa.data.readers import TalReader
tal_reader = TalReader(filename=tal_path)
tal_structs = tal_reader.read()
electrode_types_lower = map(lambda t: t.lower(), electrode_types)
electrode_type_selector = np.array(map(lambda eType: eType.lower() in electrode_types_lower, tal_structs.eType))
h_data = tal_structs[['avgSurf','eType']]
h_data = h_data[electrode_type_selector]
return h_data
def extract_electrode_positions(tal_path, electrode_types=['D', 'G', 'S']):
from ptsa.data.readers import TalReader
tal_reader = TalReader(filename=tal_path)
tal_structs = tal_reader.read()
lh_selector = np.array(map(lambda loc: loc.upper().startswith('L'), tal_structs.tagName))
rh_selector = np.array(map(lambda loc: loc.upper().startswith('R'), tal_structs.tagName))
electrode_types_lower = map(lambda t: t.lower(), electrode_types)
electrode_type_selector = np.array(map(lambda eType: eType.lower() in electrode_types_lower, tal_structs.eType))
lh_data = tal_structs[['avgSurf','eType']]
rh_data = tal_structs[['avgSurf','eType']]
lh_data = lh_data[lh_selector & electrode_type_selector]
rh_data = rh_data[rh_selector & electrode_type_selector]
return lh_data,rh_data
def extract_electrode_positions(tal_path, electrode_types=['D', 'G', 'S']):
from ptsa.data.readers import TalReader
tal_reader = TalReader(filename=tal_path)
tal_structs = tal_reader.read()
lh_selector = np.array(map(lambda loc: loc.upper().startswith('L'), tal_structs.tagName))
rh_selector = np.array(map(lambda loc: loc.upper().startswith('R'), tal_structs.tagName))
electrode_types_lower = map(lambda t: t.lower(), electrode_types)
electrode_type_selector = np.array(map(lambda eType: eType.lower() in electrode_types_lower, tal_structs.eType))
lh_data = tal_structs[['avgSurf','eType']]
rh_data = tal_structs[['avgSurf','eType']]
lh_data = lh_data[lh_selector & electrode_type_selector]
rh_data = rh_data[rh_selector & electrode_type_selector]
return lh_data,rh_data
def construct_significant_elec_info(df):
tal_structs = None
subject = ''
lh_selector = None
rh_selector = None
lh_data_combined = None
rh_data_combined = None
for index, row in df.iterrows():
if subject != row['Subject']:
subject = row['Subject']
# '/Users/m/data/eeg/R1111M/tal/R1111M_talLocs_database_bipol.mat'
tal_path = join(mount_point,'data/eeg/',subject,'tal',subject+'_talLocs_database_bipol.mat')
tal_reader = TalReader(filename=tal_path)
tal_structs = tal_reader.read()
lh_selector = np.array(map(lambda loc: loc.upper().startswith('L'), tal_structs.tagName))
rh_selector = np.array(map(lambda loc: loc.upper().startswith('R'), tal_structs.tagName))
lh_data = tal_structs[['avgSurf','eType','tagName']]
rh_data = tal_structs[['avgSurf','eType','tagName']]
lh_data = lh_data[lh_selector]
rh_data = rh_data[rh_selector]
lh_sel = get_elec_data_coords_array(lh_data[np.where(lh_data.tagName == row['stimAnodeTag']+'-'+row['stimCathodeTag'])])
lh_sel_flip = get_elec_data_coords_array(lh_data[np.where(lh_data.tagName == row['stimCathodeTag']+'-'+row['stimAnodeTag'])])
rh_sel = get_elec_data_coords_array(rh_data[np.where(rh_data.tagName == row['stimAnodeTag']+'-'+row['stimCathodeTag'])])
rh_sel_flip = get_elec_data_coords_array(rh_data[np.where(rh_data.tagName == row['stimCathodeTag']+'-'+row['stimAnodeTag'])])
lh_data_combined = append_to_combined(lh_data_combined,lh_sel,lh_sel_flip)
rh_data_combined = append_to_combined(rh_data_combined,rh_sel,rh_sel_flip)
# lh_sel_stack = vstack_arrays(lh_sel,lh_sel_flip)
# rh_sel_stack = vstack_arrays(rh_sel,rh_sel_flip)
#
#
# lh_tmp = np.vstack((lh_sel,lh_sel_flip))
# rh_tmp = np.vstack((rh_sel,rh_sel_flip))
#
# if not lh_data_combined:
# lh_data_combined = lh_tmp
# else:
# lh_data_combined = np.vstack((lh_data_combined,lh_tmp))
#
# if not rh_data_combined:
# rh_data_combined = rh_tmp
# else:
# rh_data_combined = np.vstack((rh_data_combined,rh_tmp))
print rh_data_combined
print lh_data_combined
return lh_data_combined, rh_data_combined
def test_with_version_no():
fname = osp.join(osp.dirname(__file__), 'data', 'pairs.json')
tal_reader = TalReader(filename=fname)
tal_reader.read()
def construct_significant_elec_info(df):
tal_structs = None
subject = ''
lh_selector = None
rh_selector = None
lh_data_combined = None
rh_data_combined = None
for index, row in df.iterrows():
if subject != row['Subject']:
subject = row['Subject']
# '/Users/m/data/eeg/R1111M/tal/R1111M_talLocs_database_bipol.mat'
tal_path = join(mount_point, 'data/eeg/', subject, 'tal',
subject + '_talLocs_database_bipol.mat')
tal_reader = TalReader(filename=tal_path)
tal_structs = tal_reader.read()
lh_selector = np.array(
map(lambda loc: loc.upper().startswith('L'),
tal_structs.tagName))
rh_selector = np.array(
map(lambda loc: loc.upper().startswith('R'),
tal_structs.tagName))
lh_data = tal_structs[['avgSurf', 'eType', 'tagName']]
rh_data = tal_structs[['avgSurf', 'eType', 'tagName']]
lh_data = lh_data[lh_selector]
rh_data = rh_data[rh_selector]
lh_sel = get_elec_data_coords_array(
lh_data[np.where(lh_data.tagName == row['stimAnodeTag'] + '-' +
row['stimCathodeTag'])])
lh_sel_flip = get_elec_data_coords_array(
lh_data[np.where(lh_data.tagName == row['stimCathodeTag'] + '-' +
row['stimAnodeTag'])])
rh_sel = get_elec_data_coords_array(
rh_data[np.where(rh_data.tagName == row['stimAnodeTag'] + '-' +
row['stimCathodeTag'])])
rh_sel_flip = get_elec_data_coords_array(
rh_data[np.where(rh_data.tagName == row['stimCathodeTag'] + '-' +
row['stimAnodeTag'])])
lh_data_combined = append_to_combined(lh_data_combined, lh_sel,
lh_sel_flip)
rh_data_combined = append_to_combined(rh_data_combined, rh_sel,
rh_sel_flip)
# lh_sel_stack = vstack_arrays(lh_sel,lh_sel_flip)
# rh_sel_stack = vstack_arrays(rh_sel,rh_sel_flip)
#
#
# lh_tmp = np.vstack((lh_sel,lh_sel_flip))
# rh_tmp = np.vstack((rh_sel,rh_sel_flip))
#
# if not lh_data_combined:
# lh_data_combined = lh_tmp
# else:
# lh_data_combined = np.vstack((lh_data_combined,lh_tmp))
#
# if not rh_data_combined:
# rh_data_combined = rh_tmp
# else:
# rh_data_combined = np.vstack((rh_data_combined,rh_tmp))
print rh_data_combined
print lh_data_combined
return lh_data_combined, rh_data_combined