carputils.model.protocols.PEERP_subroutines Namespace Reference

Functions
def	stimulate_to_find_if_persistent (args, cmd_ref, job, mesh_name, simid, start_S2, stim)
	Stimulates starting at the start_S2 +300 timepoint until +1500 to see if the arrythmia is persistent. More...
def	get_last_act_index (vm)
	Gets the time index of the last ACT. More...
def	pacing_s1_sinus_s2_stim_point (args, cmd, job, mesh_name, simid, sinus, start_S2, start_state_file, stim_point, tsav_state)
	Pace at first from the sinus node and then from the stimulation point after start_S2 ms. More...
def	get_element_from_dat (dat_file, index_node)
	Gets float value for a single point in a dat file. More...
def	get_ring_around_stim_point (args, stim_point_index, mesh_name, stim_point, tag_str)
	Generates a ring of size 2*stim_size < x < 3*stim_size around the stimulation point. More...
def	update_refactory_window_bounds (M2, OptimizationTimePoints time_pts, simid, tsav_state)
def	update_lower_bound_when_refractory (simid, float start_S2, new_offset=60)
	Updates the lower bound which happens when the simulation is refactory (Low M2). More...
def	update_upper_bound_non_refractory (simid, float start_S2, new_offset=60)
	Updates the upper bound of the search window if the previous S2 stimuli did create a depolarizing wave (non-refractory) More...
def	compute_apd (apd_file_name, args, job, steady_state_dir)
def	store_init_arrhythmia_to_file (index_node, job, n_beat, simid, start_S2)
	Saves the current arrhythmia at the index_node to saved.txt and also stores the corresponding .igb file. More...
def	get_closest_tsav_to_act (last_ACT_i, tsav_states)
	Get the closest openCARP save state to the last ACT. More...
def	write_convergence_data (str simid, OptimizationTimePoints time_pts, int iterations, time_taken, M2, M2_mean)
def	create_debug_csv ()
def	define_save_states_for_stim (stim_start, times_array)
def	store_reentry (index_node, job, n_beat, start_S2)
def	store_non_reentry (index_node, job, n_beat, start_S2)
def	get_id_of_stimulation_point (mesh_name, simid, stim_point)

Function Documentation

compute_apd()

def carputils.model.protocols.PEERP_subroutines.compute_apd	(		apd_file_name,
			args,
			job,
			steady_state_dir
	)

create_debug_csv()

def carputils.model.protocols.PEERP_subroutines.create_debug_csv

(

)

define_save_states_for_stim()

def carputils.model.protocols.PEERP_subroutines.define_save_states_for_stim	(		stim_start,
			times_array
	)

get_closest_tsav_to_act()

def carputils.model.protocols.PEERP_subroutines.get_closest_tsav_to_act	(		last_ACT_i,
			tsav_states
	)

Get the closest openCARP save state to the last ACT.

Parameters

last_ACT_i
tsav_states	Array of tsav times :return:

get_element_from_dat()

def carputils.model.protocols.PEERP_subroutines.get_element_from_dat	(		dat_file,
			index_node
	)

Gets float value for a single point in a dat file.

Parameters

dat_file	Corresponding .dat file
index_node	The index of the node in the dat file :return:

get_id_of_stimulation_point()

def carputils.model.protocols.PEERP_subroutines.get_id_of_stimulation_point	(		mesh_name,
			simid,
			stim_point
	)

get_last_act_index()

def carputils.model.protocols.PEERP_subroutines.get_last_act_index

(

vm

)

Gets the time index of the last ACT.

Parameters

vm

:return:

get_ring_around_stim_point()

def carputils.model.protocols.PEERP_subroutines.get_ring_around_stim_point	(		args,
			stim_point_index,
			mesh_name,
			stim_point,
			tag_str
	)

Generates a ring of size 2*stim_size < x < 3*stim_size around the stimulation point.

Whole connecting tissue is stored in {mesh_name}_tag_{stim_point_index}.surf.vtx. Ring around the stim point is stored in {mesh_name}_node_{stim_point_index}.vtx

Parameters

args	Has to contain args.stim_size
stim_point_index	The index of the stimulation point
mesh_name	The name of the main mesh
stim_point	The coordinates of the stimulation point
tag_str	Element tags of the atrial surface :return:

pacing_s1_sinus_s2_stim_point()

def carputils.model.protocols.PEERP_subroutines.pacing_s1_sinus_s2_stim_point	(		args,
			cmd,
			job,
			mesh_name,
			simid,
			sinus,
			start_S2,
			start_state_file,
			stim_point,
			tsav_state
	)

Pace at first from the sinus node and then from the stimulation point after start_S2 ms.

Parameters

args
cmd
job
mesh_name
simid
sinus	The sinus region defined as -stimulius[0].geometry, >sinus node id<
start_S2	Start time of the S2 stimulus
start_state_file
stim_point	The stimulation point for the S2 stimulus
tsav_state	First save point. Also start_S2-1 and start_S2+60 are saved :return:

stimulate_to_find_if_persistent()

def carputils.model.protocols.PEERP_subroutines.stimulate_to_find_if_persistent	(		args,
			cmd_ref,
			job,
			mesh_name,
			simid,
			start_S2,
			stim
	)

Stimulates starting at the start_S2 +300 timepoint until +1500 to see if the arrythmia is persistent.

Parameters

args	Has to include args.M_lump for mass lumping option
cmd_ref
job	Job object for executing on cmd
mesh_name
simid	Simulation ID for openCARP
start_S2
stim	Stimulation parameters. Should be a stimulus without a current, to just see the result of the previous S2 stimuli :return:

store_init_arrhythmia_to_file()

def carputils.model.protocols.PEERP_subroutines.store_init_arrhythmia_to_file	(		index_node,
			job,
			n_beat,
			simid,
			start_S2
	)

Saves the current arrhythmia at the index_node to saved.txt and also stores the corresponding .igb file.

Parameters

index_node
job
n_beat
simid
start_S2	:return:

store_non_reentry()

def carputils.model.protocols.PEERP_subroutines.store_non_reentry	(		index_node,
			job,
			n_beat,
			start_S2
	)

store_reentry()

def carputils.model.protocols.PEERP_subroutines.store_reentry	(		index_node,
			job,
			n_beat,
			start_S2
	)

update_lower_bound_when_refractory()

def carputils.model.protocols.PEERP_subroutines.update_lower_bound_when_refractory	(		simid,
		float	start_S2,
			new_offset = 60
	)

Updates the lower bound which happens when the simulation is refactory (Low M2).

Parameters

simid	Main working directoryold_file = os.path.join(str(simid), 'vm.igb')
start_S2	Start of the S2 stimulus in ms
new_offset	Offset of the S2 stimulus in ms which will be stored in state_upper_bound.roe :return:

update_refactory_window_bounds()

def carputils.model.protocols.PEERP_subroutines.update_refactory_window_bounds	(		M2,
		OptimizationTimePoints	time_pts,
			simid,
			tsav_state
	)

update_upper_bound_non_refractory()

def carputils.model.protocols.PEERP_subroutines.update_upper_bound_non_refractory	(		simid,
		float	start_S2,
			new_offset = 60
	)

Updates the upper bound of the search window if the previous S2 stimuli did create a depolarizing wave (non-refractory)

Parameters

simid	Main working directoryold_file = os.path.join(str(simid), 'vm.igb')
start_S2	Start of the S2 stimulus in ms
new_offset	Offset of the S2 stimulus in ms which will be stored in state_upper_bound.roe :return:

write_convergence_data()

def carputils.model.protocols.PEERP_subroutines.write_convergence_data	(	str	simid,
		OptimizationTimePoints	time_pts,
		int	iterations,
			time_taken,
			M2,
			M2_mean
	)