Get Spike Properties

GetSpikeProperties.py

def get_percent_error( value , target ):
	return ( ( abs( value - target ) / target ) * 100.0 )

def get_spike_properties( voltages , times ):
	threshold = -70.2 # mV

	voltage_recordings_np = voltages.as_numpy()
	time_recordings_np = times.as_numpy()

	peak_voltage = np.max( voltage_recordings_np )
	peak_voltage_index = np.argmax( voltage_recordings_np )
	# print( f"Peak Voltage Index === {peak_voltage_index}" )
	# print( f"Peak Voltage Time === {time_recordings_np[ peak_voltage_index ]}" )
	time_of_ahp_start = time_recordings_np[ peak_voltage_index ]
	time_of_ahp_start_index = 0
	for i in range( ( peak_voltage_index + 10 ) , len( voltage_recordings_np ) ):
		if voltage_recordings_np[ i ] < threshold:
			time_of_ahp_start = time_recordings_np[ i ]
			time_of_ahp_start_index = i
			break

	time_of_ahp_end = -1
	time_of_ahp_end_index = -1
	for i in range( time_of_ahp_start_index , len( voltage_recordings_np ) ):
		if voltage_recordings_np[ i ] >= threshold:
			time_of_ahp_end = time_recordings_np[ i ]
			time_of_ahp_end_index = i
			break

	ahp_duration = ( time_of_ahp_end - time_of_ahp_start )

	minimum_voltage = np.min( voltage_recordings_np )
	minimum_voltage_index = np.argmin( voltage_recordings_np )
	time_of_minimum_voltage = time_recordings_np[ minimum_voltage_index ]
	threshold_halfway_point = ( minimum_voltage + ( ( ( abs( threshold ) - abs( minimum_voltage ) ) / 2 ) * -1 ) )
	# print( f"AHP Half-Decay === {threshold_halfway_point} mV" )
	time_of_ahp_half_decay = -1
	time_of_ahp_half_decay_index = -1

	for i in range( minimum_voltage_index , len( voltage_recordings_np ) ):
		if voltage_recordings_np[ i ] >= threshold_halfway_point:
			time_of_ahp_half_decay = time_recordings_np[ i ]
			time_of_ahp_half_decay_index = i
			break
	ahp_half_decay_duration = ( time_of_ahp_half_decay - time_of_minimum_voltage )

	ap_height = ( peak_voltage - threshold )
	ahp_depth = ( abs( minimum_voltage ) - abs( threshold ) )

	return {
		"action_potential": {
			"height": {
				"value": ap_height ,
				"error": get_percent_error( ap_height , 82.7 ) ,
			} ,
		} ,
		"after_hyper_polarization": {
			"depth": {
				"value": ahp_depth ,
				"error": get_percent_error( ahp_depth , 4.8 ) ,
			} ,
			"duration": {
				"value": ahp_duration ,
				"error": get_percent_error( ahp_duration , 163.1 ) ,
			} ,
			"half-decay": {
				"value": ahp_half_decay_duration ,
				"error": get_percent_error( ahp_half_decay_duration , 41.5 )
			}
		} ,
	}

# Set up a voltage recording at the soma
voltage_recording = h.Vector()
voltage_recording.record( cell.soma( 0.5 )._ref_v )

# Setup time vector
time_recording = h.Vector()
time_recording.record( h._ref_t )

h.run()

spike_properties = get_spike_properties( voltage_recording , time_recording )
pprint( spike_properties )