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, Stimulus sinus_elecs, 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 the ring of nodes on which PEERP checks whether the S2 stimulus captured and whether an arrhythmia persists. More...
def	get_surface_ring (mesh_name, ring_base, stim_point_index, stim_point, size, geom_type, tag_str)
	Writes the PEERP ring measured along the mesh (RING_DISTANCE 'surface', see get_ring_around_stim_point). More...
def	read_mesh_elements (mesh_name)
	Reads an openCARP mesh ({mesh_name}.pts, {mesh_name}.elem). More...
def	get_stimulated_nodes (pts, stim_point, stim_size, geom_type)
	Selects the nodes inside the S2 electrode the same way openCARP does (point_in_shape, nodal selection). More...
def	distance_along_mesh (pts, elements, sources)
	Shortest distance from each node to the nearest source node along straight segments between nodes of a common element (the mesh edges; for elements with more than three nodes also their diagonals, which lie inside the element). 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
	)

distance_along_mesh()

def carputils.model.protocols.PEERP_subroutines.distance_along_mesh	(		pts,
			elements,
			sources
	)

Shortest distance from each node to the nearest source node along straight segments between nodes of a common element (the mesh edges; for elements with more than three nodes also their diagonals, which lie inside the element).

Parameters

pts	Node coordinates (n, 3)
elements	List of (element type, connectivity, tags) as returned by read_mesh_elements
sources	Indices of the source nodes

Returns

distance per node (n,), inf for nodes not connected to any source

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 the ring of nodes on which PEERP checks whether the S2 stimulus captured and whether an arrhythmia persists.

The distance is chosen by get_config().RING_DISTANCE: 'euclidean': surface nodes at a straight-line distance 2*stim_size < x < 3*stim_size from the stimulation point (meshtool extract surface). 'surface': surface nodes whose distance to the nearest stimulated node, measured along the mesh, lies in (2*stim_size - r, 3*stim_size - r), where r is the electrode extent from the stimulation point (stim_size for a sphere, stim_size/2 for a box), and whose straight-line distance to every stimulated node exceeds 2*stim_size - r. In a flat sheet this is the same band as 'euclidean'. On curved or folded surfaces the straight-line ring lies further away along the surface than intended, so the wave needs longer to reach it; the along-mesh ring keeps the intended distance. The ring file is named by node and stim size, so runs with different stim sizes can share a mesh directory.

Parameters

args	Has to contain args.stim_size and optionally args.stim_geom_type (1 sphere, 2 box; default 2)
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, comma separated; empty for all elements

Returns

Path of the .vtx file holding the ring nodes

get_stimulated_nodes()

def carputils.model.protocols.PEERP_subroutines.get_stimulated_nodes	(		pts,
			stim_point,
			stim_size,
			geom_type
	)

Selects the nodes inside the S2 electrode the same way openCARP does (point_in_shape, nodal selection).

Parameters

pts	Node coordinates (n, 3)
stim_point	Centre of the electrode
stim_size	Sphere radius (geom_type 1) or box edge length (geom_type 2)
geom_type	1 sphere, 2 box

Returns

indices of the stimulated nodes and the electrode extent from the centre

get_surface_ring()

def carputils.model.protocols.PEERP_subroutines.get_surface_ring	(		mesh_name,
			ring_base,
			stim_point_index,
			stim_point,
			size,
			geom_type,
			tag_str
	)

Writes the PEERP ring measured along the mesh (RING_DISTANCE 'surface', see get_ring_around_stim_point).

Parameters

mesh_name	The name of the main mesh
ring_base	Path prefix of the ring file
stim_point_index	The index of the stimulation point
stim_point	The coordinates of the stimulation point
size	Stimulus size (sphere radius or box edge length)
geom_type	Electrode shape, 1 sphere, 2 box
tag_str	Element tags of the atrial surface, comma separated; empty for all elements

Returns

Path of the .vtx file holding the ring nodes

pacing_s1_sinus_s2_stim_point()

def carputils.model.protocols.PEERP_subroutines.pacing_s1_sinus_s2_stim_point	(		args,
			cmd,
			job,
			mesh_name,
			simid,
		Stimulus	sinus_elecs,
			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_elecs	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:

read_mesh_elements()

def carputils.model.protocols.PEERP_subroutines.read_mesh_elements

(

mesh_name

)

Reads an openCARP mesh ({mesh_name}.pts, {mesh_name}.elem).

Parameters

mesh_name

The name of the mesh without extension

Returns

node coordinates (n, 3) and a list of (element type, connectivity (m, k), tags (m,)) per element type

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
	)