carputils
Doxygen code documentation for the python framework controlling openCARP
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Functions | |
def | converge_to_EB (args, job, meshname, cmd_ref, stim_index, simid, nodes_to_check_str, startstatef, start_S2, upper_bound, lower_bound) |
def | PEERP (args, job, cmd_ref, meshname, sinus, stim_points, steady_state_dir) |
Pacing at the End of the Effective Refractory Period: More... | |
def | stimulation (args, start, start_bcl, end_bcl, step, n_beats, stim_index) |
def | RP_E (args, job, cmd_ref, meshname, stim_points, steady_state_dir) |
Rapid Pacing with reentry check at the End: More... | |
def | check_propagation (args, job, meshname, cmd_ref, stim_index, simid, nodes_to_check_str, startstatef, start_S2) |
def | RP_B (args, job, cmd_ref, meshname, stim_points, steady_state_dir) |
Rapid Pacing with reentry check after every Beat: More... | |
def | assignRandomCoord (points, sing_points) |
def | assignDirection (coordinates) |
def | makeCircle3D (startCoord, radius, seedNum, normV, point1, point2, nodes) |
def | assignPhaseValues (seeds, originalCoord, directions, normV, point1, point2, nodes) |
def | planeInfo (coordinate, nodes, triangles) |
def | deflate (x) |
def | csr_row_set_nz_to_val (csr, row, value=0) |
Set all nonzero elements (elements currently in the sparsity pattern) to the given value. More... | |
def | eikonal_solver (nodes, triangles, knownNodes, phi0) |
def | assignWallValues (surfacePoints, allPoints, surfaceValues) |
def | PSD (args, job, cmd, meshname, xyz, triangles, centre) |
Phase Singularity Distribution: More... | |
def carputils.model.induceReentry.assignDirection | ( | coordinates | ) |
def carputils.model.induceReentry.assignPhaseValues | ( | seeds, | |
originalCoord, | |||
directions, | |||
normV, | |||
point1, | |||
point2, | |||
nodes | |||
) |
def carputils.model.induceReentry.assignRandomCoord | ( | points, | |
sing_points | |||
) |
def carputils.model.induceReentry.assignWallValues | ( | surfacePoints, | |
allPoints, | |||
surfaceValues | |||
) |
def carputils.model.induceReentry.check_propagation | ( | args, | |
job, | |||
meshname, | |||
cmd_ref, | |||
stim_index, | |||
simid, | |||
nodes_to_check_str, | |||
startstatef, | |||
start_S2 | |||
) |
def carputils.model.induceReentry.converge_to_EB | ( | args, | |
job, | |||
meshname, | |||
cmd_ref, | |||
stim_index, | |||
simid, | |||
nodes_to_check_str, | |||
startstatef, | |||
start_S2, | |||
upper_bound, | |||
lower_bound | |||
) |
def carputils.model.induceReentry.csr_row_set_nz_to_val | ( | csr, | |
row, | |||
value = 0 |
|||
) |
Set all nonzero elements (elements currently in the sparsity pattern) to the given value.
Useful to set to 0 mostly.
def carputils.model.induceReentry.deflate | ( | x | ) |
def carputils.model.induceReentry.eikonal_solver | ( | nodes, | |
triangles, | |||
knownNodes, | |||
phi0 | |||
) |
def carputils.model.induceReentry.makeCircle3D | ( | startCoord, | |
radius, | |||
seedNum, | |||
normV, | |||
point1, | |||
point2, | |||
nodes | |||
) |
def carputils.model.induceReentry.PEERP | ( | args, | |
job, | |||
cmd_ref, | |||
meshname, | |||
sinus, | |||
stim_points, | |||
steady_state_dir | |||
) |
Pacing at the End of the Effective Refractory Period:
It triggers ectopic beats at the end of the effective refractory period, computed as the minimum coupling interval at which the action potential could propagate in the tissue.
Input parser arguments (args), output directory (job.ID), struct containing imp_regions and gregions (cmd_ref), meshname, sinus node location (sinus), stimulation point location (x,y,z) and prepacing directory (steady_state_dir)
def carputils.model.induceReentry.planeInfo | ( | coordinate, | |
nodes, | |||
triangles | |||
) |
def carputils.model.induceReentry.PSD | ( | args, | |
job, | |||
cmd, | |||
meshname, | |||
xyz, | |||
triangles, | |||
centre | |||
) |
Phase Singularity Distribution:
It consists of manually placing phase singularities on the geometrical model and then solving the Eikonal equation to estimate the activation time map. Based on this initial state, you can simulate electrical wave propagation by solving the monodomain equation.
Input parser arguments (args), output directory (job.ID), struct containing imp_regions and gregions (cmd_ref), meshname, stimulation point location (x,y,z) and prepacing directory (steady_state_dir)
def carputils.model.induceReentry.RP_B | ( | args, | |
job, | |||
cmd_ref, | |||
meshname, | |||
stim_points, | |||
steady_state_dir | |||
) |
Rapid Pacing with reentry check after every Beat:
It consists of a train of electrical stimulations with decreasing coupling interval (args.step) between args.start_bcl and args.end_bcl. It can give multiple beats with the same cycle length (args.max_n_beats_RP) and it checks for arrhythmia induction after every beat.
Input parser arguments (args), output directory (job.ID), struct containing imp_regions and gregions (cmd_ref), meshname, stimulation point location (x,y,z) and prepacing directory (steady_state_dir)
def carputils.model.induceReentry.RP_E | ( | args, | |
job, | |||
cmd_ref, | |||
meshname, | |||
stim_points, | |||
steady_state_dir | |||
) |
Rapid Pacing with reentry check at the End:
It consists of a train of electrical stimulations with decreasing coupling interval (args.step) between args.start_bcl and args.end_bcl. It can give multiple beats with the same cycle length (args.max_n_beats_RP) and it checks for arrhythmia induction at the end of the protocol
Input parser arguments (args), output directory (job.ID), struct containing imp_regions and gregions (cmd_ref), meshname, stimulation point location (x,y,z) and prepacing directory (steady_state_dir)
def carputils.model.induceReentry.stimulation | ( | args, | |
start, | |||
start_bcl, | |||
end_bcl, | |||
step, | |||
n_beats, | |||
stim_index | |||
) |