def get_fl_probes(self, shanks_dict: dict, probes_valid_map: set):
fl_probes = []
for probe_type in probes_valid_map:
probe_metadata = filter_probe_by_type(self.probes_metadata,
probe_type)
fl_probes.append(
self._build_single_probe(probe_metadata=probe_metadata,
shanks=shanks_dict[probe_type]))
return fl_probes
def create_probe_electrode(cls, probes_metadata: list,
electrode_groups_metadata: list):
probe_electrode = []
for electrode_group_metadata in electrode_groups_metadata:
probe_metadata = filter_probe_by_type(
probes_metadata, electrode_group_metadata['device_type'])
for shank in probe_metadata['shanks']:
[
probe_electrode.append(electrode['id'])
for electrode in shank['electrodes']
]
return probe_electrode
def create_probe_shank(cls, probes_metadata: list,
electrode_groups_metadata: list):
probe_shank = []
for electrode_group_metadata in electrode_groups_metadata:
probe_metadata = filter_probe_by_type(
probes_metadata, electrode_group_metadata['device_type'])
[
probe_shank.extend([shank['shank_id']] *
len(shank['electrodes']))
for shank in probe_metadata['shanks']
]
return probe_shank
def get_fl_shanks_electrodes_dict(self) -> dict:
fl_shanks_electrodes_dict = {}
probes_types = []
for electrode_group_metadata in self.electrode_groups_metadata:
if electrode_group_metadata['device_type'] not in probes_types:
fl_shanks_electrodes = []
probes_types.append(electrode_group_metadata['device_type'])
probe_metadata = filter_probe_by_type(self.probes_metadata, electrode_group_metadata['device_type'])
fl_shanks_electrodes.extend(self.__build_fl_shanks_electrodes(probe_metadata))
fl_shanks_electrodes_dict[electrode_group_metadata['device_type']] = fl_shanks_electrodes
return fl_shanks_electrodes_dict
def create_rel(cls, probes_metadata: list,
electrode_groups_metadata: list) -> dict:
rel_x, rel_y, rel_z = [], [], []
for electrode_group_metadata in electrode_groups_metadata:
probe_metadata = filter_probe_by_type(
probes_metadata, electrode_group_metadata['device_type'])
for shank in probe_metadata['shanks']:
for electrode in shank['electrodes']:
rel_x.append(float(electrode['rel_x']))
rel_y.append(float(electrode['rel_y']))
rel_z.append(float(electrode['rel_z']))
return {'rel_x': rel_x, 'rel_y': rel_y, 'rel_z': rel_z}
def validate_ntrode_metadata_with_probe_metadata(metadata,
probes_metadata):
for electrode_group in metadata['electrode groups']:
probe_metadata = filter_probe_by_type(
probes_metadata, electrode_group['device_type'])
electrodes_in_probe = count_electrodes_in_probe(probe_metadata)
electrodes_in_group = count_electrodes_in_ntrode(
metadata['ntrode electrode group channel map'],
electrode_group['id'])
if electrodes_in_probe != electrodes_in_group:
raise InvalidMetadataException(
'Ntrode definition in metadata is not compatible with probe schema.'
+ 'Probe_type: ' + str(electrode_group['device_type']) +
' electrodes in this probe_type: ' +
str(electrodes_in_probe) +
'. Ntrode_metadata for electrode_group of id: ' +
str(electrode_group['id']) +
' electrodes in this electrode_group: ' +
str(electrodes_in_group))
def get_fl_electrodes(self, electrode_groups: list,
electrodes_valid_map: list,
electrode_groups_valid_map: set):
self.__validate_parameters(electrode_groups)
tmp_electrodes_valid_map = copy.deepcopy(electrodes_valid_map)
fl_electrodes = []
fl_electrode_id = -1
for electrode_group_metadata in self.electrode_groups_metadata:
probe_metadata = filter_probe_by_type(
self.probes_metadata, electrode_group_metadata['device_type'])
for shank in probe_metadata['shanks']:
for _ in shank['electrodes']:
fl_electrode_id += 1
fl_electrodes.append(
self.fl_electrodes_builder.build(
fl_electrode_id,
self.__get_electrode_group(
electrode_group_metadata, electrode_groups)))
return fl_electrodes
