def create(cls, fl_shank: FlShank) -> Shank:
validate_parameters_not_none(__name__, fl_shank.shank_id,
fl_shank.shanks_electrodes)
shank = Shank(name=str(fl_shank.shank_id))
for shanks_electrode in fl_shank.shanks_electrodes:
shank.add_shanks_electrode(shanks_electrode)
return shank
def create_data_acq_device(
cls, fl_data_acq_device: FlDataAcqDevice) -> DataAcqDevice:
validate_parameters_not_none(__name__, fl_data_acq_device.name,
fl_data_acq_device.system,
fl_data_acq_device.amplifier,
fl_data_acq_device.adc_circuit)
return DataAcqDevice(name=fl_data_acq_device.name,
system=fl_data_acq_device.system,
amplifier=fl_data_acq_device.amplifier,
adc_circuit=fl_data_acq_device.adc_circuit)
def create_camera_device(cls,
fl_camera_device: FlCameraDevice) -> CameraDevice:
validate_parameters_not_none(__name__, fl_camera_device.name,
fl_camera_device.meters_per_pixel)
return CameraDevice(name=fl_camera_device.name,
meters_per_pixel=fl_camera_device.meters_per_pixel,
manufacturer=fl_camera_device.manufacturer,
model=fl_camera_device.model,
lens=fl_camera_device.lens,
camera_name=fl_camera_device.camera_name)
def create(cls, fl_shanks_electrode: FlShanksElectrode) -> ShanksElectrode:
validate_parameters_not_none(__name__, fl_shanks_electrode.shanks_electrode_id,
fl_shanks_electrode.rel_x, fl_shanks_electrode.rel_y, fl_shanks_electrode.rel_z)
return ShanksElectrode(
name=str(fl_shanks_electrode.shanks_electrode_id),
rel_x=float(fl_shanks_electrode.rel_x),
rel_y=float(fl_shanks_electrode.rel_y),
rel_z=float(fl_shanks_electrode.rel_z),
)
def create(position: Position, series_id: int, fl_position: FlPosition):
validate_parameters_not_none(__name__, fl_position.column_labels, fl_position.position_data,
fl_position.conversion)
position.create_spatial_series(
name='series_' + str(series_id),
description=fl_position.column_labels,
data=fl_position.position_data,
conversion=fl_position.conversion,
reference_frame='Upper left corner of video frame',
timestamps=fl_position.timestamps,
)
def create(cls, nwb_content: NWBFile, fl_electrode: FlElectrode):
validate_parameters_not_none(__name__, fl_electrode.electrode_group,
fl_electrode.electrode_id)
nwb_content.add_electrode(x=0.0,
y=0.0,
z=0.0,
imp=0.0,
location='None',
filtering='None',
group=fl_electrode.electrode_group,
id=fl_electrode.electrode_id)
def create_electrode_group(cls, fl_electrode_group: FlElectrodeGroup):
validate_parameters_not_none(__name__, fl_electrode_group.name,
fl_electrode_group.description,
fl_electrode_group.location,
fl_electrode_group.device)
return ElectrodeGroup(
name=fl_electrode_group.name,
description=fl_electrode_group.description,
location=fl_electrode_group.location,
device=fl_electrode_group.device,
)
def inject_extensions(self, nwb_content: NWBFile, fl_electrode_extension: FlElectrodeExtension):
validate_parameters_not_none(
__name__,
fl_electrode_extension.rel_x,
fl_electrode_extension.rel_y,
fl_electrode_extension.rel_z,
fl_electrode_extension.hw_chan,
fl_electrode_extension.ntrode_id,
fl_electrode_extension.channel_id,
fl_electrode_extension.bad_channels,
fl_electrode_extension.probe_shank,
fl_electrode_extension.probe_electrode,
fl_electrode_extension.ref_elect_id
)
self.__join_extensions_to_electrodes(nwb_content, fl_electrode_extension)
def __build_single_camera_device(camera_metadata):
validate_parameters_not_none(
__name__, camera_metadata.get('id', None),
camera_metadata.get('meters_per_pixel', None),
camera_metadata.get('manufacturer', None),
camera_metadata.get('model', None),
camera_metadata.get('lens', None),
camera_metadata.get('camera_name', None))
return FlCameraDeviceBuilder.build(
name='camera_device ' + str(camera_metadata['id']),
meters_per_pixel=float(camera_metadata['meters_per_pixel']),
manufacturer=str(camera_metadata['manufacturer']),
model=str(camera_metadata['model']),
lens=str(camera_metadata['lens']),
camera_name=str(camera_metadata['camera_name']))
def create_probe(cls, fl_probe: FlProbe) -> Probe:
validate_parameters_not_none(__name__, fl_probe.probe_id,
fl_probe.name, fl_probe.probe_type,
fl_probe.units,
fl_probe.probe_description,
fl_probe.contact_side_numbering,
fl_probe.contact_size, fl_probe.shanks)
probe = Probe(id=fl_probe.probe_id,
name=fl_probe.name,
probe_type=fl_probe.probe_type,
units=fl_probe.units,
probe_description=fl_probe.probe_description,
contact_side_numbering=fl_probe.contact_side_numbering,
contact_size=fl_probe.contact_size)
for shank in fl_probe.shanks:
probe.add_shank(shank)
return probe
def get_fl_tasks(self):
validate_parameters_not_none(__name__, self.metadata['tasks'])
task_list = []
for task in self.metadata["tasks"]: # for each task
# Set task_environment to "none" if not in metadata
if "task_environment" not in task.keys():
task_environment = "none"
else:
task_environment = task["task_environment"]
# Append task to list
task_list.append(
self.__get_single_fl_task(
task_name=task['task_name'],
task_description=task['task_description'],
camera_id=[
int(camera_id) for camera_id in task['camera_id']
],
task_epochs=[int(epoch) for epoch in task['task_epochs']],
task_environment=task_environment))
return task_list
def create_header_device(cls,
fl_header_device: FlHeaderDevice) -> HeaderDevice:
validate_parameters_not_none(__name__, fl_header_device.name,
fl_header_device.global_configuration)
return HeaderDevice(
name=fl_header_device.name,
headstage_serial=fl_header_device.
global_configuration['headstage_serial'],
headstage_smart_ref_on=fl_header_device.
global_configuration['headstage_smart_ref_on'],
realtime_mode=fl_header_device.
global_configuration['realtime_mode'],
headstage_auto_settle_on=fl_header_device.
global_configuration['headstage_auto_settle_on'],
timestamp_at_creation=fl_header_device.
global_configuration['timestamp_at_creation'],
controller_firmware_version=fl_header_device.
global_configuration['controller_firmware_version'],
controller_serial=fl_header_device.
global_configuration['controller_serial'],
save_displayed_chan_only=fl_header_device.
global_configuration['save_displayed_chan_only'],
headstage_firmware_version=fl_header_device.
global_configuration['headstage_firmware_version'],
qt_version=fl_header_device.global_configuration['qt_version'],
compile_date=fl_header_device.global_configuration['compile_date'],
compile_time=fl_header_device.global_configuration['compile_time'],
file_prefix=fl_header_device.global_configuration['file_prefix'],
headstage_gyro_sensor_on=fl_header_device.
global_configuration['headstage_gyro_sensor_on'],
headstage_mag_sensor_on=fl_header_device.
global_configuration['headstage_mag_sensor_on'],
trodes_version=fl_header_device.
global_configuration['trodes_version'],
headstage_accel_sensor_on=fl_header_device.
global_configuration['headstage_accel_sensor_on'],
commit_head=fl_header_device.global_configuration['commit_head'],
system_time_at_creation=fl_header_device.
global_configuration['system_time_at_creation'],
file_path=fl_header_device.global_configuration['file_path'])
def create_nwb_electrode_group(
cls, fl_nwb_electrode_group: FlNwbElectrodeGroup):
validate_parameters_not_none(__name__, fl_nwb_electrode_group.name,
fl_nwb_electrode_group.description,
fl_nwb_electrode_group.location,
fl_nwb_electrode_group.device,
fl_nwb_electrode_group.targeted_location,
fl_nwb_electrode_group.targeted_x,
fl_nwb_electrode_group.targeted_y,
fl_nwb_electrode_group.targeted_z,
fl_nwb_electrode_group.units)
return NwbElectrodeGroup(
name=fl_nwb_electrode_group.name,
description=fl_nwb_electrode_group.description,
location=fl_nwb_electrode_group.location,
device=fl_nwb_electrode_group.device,
targeted_location=fl_nwb_electrode_group.targeted_location,
targeted_x=fl_nwb_electrode_group.targeted_x,
targeted_y=fl_nwb_electrode_group.targeted_y,
targeted_z=fl_nwb_electrode_group.targeted_z,
units=fl_nwb_electrode_group.units,
)
def create_device(cls, fl_device: FlDevice) -> Device:
validate_parameters_not_none(__name__, fl_device.name)
return Device(name=str(fl_device.name))
def __validate_parameters(electrode_groups: list):
[
validate_parameters_not_none(__name__, electrode_group.name)
for electrode_group in electrode_groups
]
