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Arritmic3D Python API

enum identifiers for SystemEventType

NODE_EVENT : Activation or deactivation in a node

EXT_ACTIVATION : External activation of the tissue

FILE_WRITE : Event for writing output to a file

OTHER : Other events not defined

NO_EVENT : There are no more events. Simulation has finished.

arritmic3d.CardiacTissue(ncells_x, ncells_y, ncells_z, x_spacing, y_spacing, z_spacing)

Constructor of the CardiacTissue class.

Parameters:

ncells_x, ncells_y, ncells_z: int

x_spacing, y_spacing, z_spacing: float

InitPy(cell_types_, parameters_, fiber_orientation_)

Initialize the tissue from Python. Calls Init with a vector of parameters. It can be called again to initialize the data for a new simulation.

Parameters:

cell_types_ : Vector of cell types.

parameters_ : Dictionary with the parameters.

fiber_orientation_ : Vector of fiber orientations.

InitModels(fileAPD, fileCV)

Initialize the models for the APD and CV update. ** Should be called before InitPy **

fileAPD : CSV file definition for APD models

fileCV : CSV file definition for CV models

SetInitialAPD(APD_)

Set the initial APD for the nodes. The DI is automatically set based on the APD. The first activation should be near time 0.

ChangeParameters(parameters_)

Change the parameters of the tissue nodes. Simulation can continue normally.

SaveState(binaryFile)

Save the state of simulation. It stores the state of all nodes and the event queue, so simulation can continue at this exact moment in a different program.

binaryFile : Name of the binary file where the state will be stored

LoadState(binaryFile)

Load the state of a simulation. Size and spacing of the grid should be exactly the same as the stored simulation. InitModels should be called before calling LoadState. InitPy should ** not ** be called.

binaryFile : Name of the binary file

size()

Get the number of nodes in the tissue

GetNumLiveNodes()

Get the number of nodes not VOID in the tissue

GetSizeX()

Get the number of nodes in the X direction

GetSizeY()

Get the number of nodes in the Y direction

GetSizeZ()

Get the number of nodes in the Z direction

GetIndex (int x, int y, int z)

Get the id (index) of node with coordinates (x, y, z)

SetTimer (float t)

Set a timer for the simulation

Parameters:

t : Period (time between events) in milliseconds.

GetTime()

Get the current time of the tissue

GetStates()

Get the states of the tissue nodes.

Returns:

Vector of states (int) of the tissue nodes.

GetAPD()

Get the APD of the tissue nodes.

Returns:

Vector of APD of the tissue nodes.

GetCV()

Get the conduction velocity of the tissue nodes.

Returns:

Vector of conduction velocity of the tissue nodes.

GetDI()

Get the DI (diastolic interval) of the tissue nodes.

Returns:

Vector of DI of the tissue nodes.

GetLastDI()

Get the DI (diastolic interval) of the last activation of the tissue nodes.

Returns:

Vector of DI of the tissue nodes.

GetLAT()

Get the LAT (Last Activation Time) of the tissue nodes.

Returns:

Vector of LAT of the tissue nodes.

GetBeat()

Get the beat id of the tissue nodes.

Returns:

Vector of beat id (int) of the tissue nodes.

GetAPDVariation()

Get the variation in the APD from last activation to actual activation of the tissue nodes.

Returns:

Vector of APD variation of the tissue nodes.

GetAPDMeanVariation()

Get the mean variation in the APD from last activation to actual activation of the tissue nodes.

Returns:

Mean of APD variation (float)

ResetVariations()

Reset the accumulator of the mean variation in the APD before the beginning of a new activation in the tissue.

GetSensorInfo()

Get the information of all sensors.

Returns:

A map where the key is the node ID and the value is a vector of sensor data.

GetSensorDataNames()

Get the names of the data stored in the sensors.

Returns:

A vector of strings containing the names of the data.

GetDefaultParameters()

Return a dictionary with the default parameters for the nodes. int values are converted to float.

Returns:

Dictionary with the parameters.

arritmic3d(case_dir, config={}, save_run_config=True)

Run the Arritmic3D simulation in the given case directory with the provided configuration dictionary.

Parameters:

case_dir : Output directory where results will be saved.

config : Configuration dictionary with simulation parameters. Fields provided here override those in any configuration file found in case_dir.

save_run_config : If True (default), saves the actual run configuration to arr3D_config_run.json.

test_case(output_dir)

Generate and run a built-in S1-S2 test case in the given output directory.

Parameters:

output_dir : Output directory where results will be saved. Must not exist or be empty.

build_slab(args, save=True)

Build the slab grid based on parsed arguments and optionally save to file.

Parameters:

args : Parsed arguments for grid generation.

save : If True, saves the generated slab to the specified output file.

Returns:

The generated rectilinear grid.

load_case_config(case_dir)

Check for a config file in the case directory and load it if present.

Parameters:

case_dir : Directory to check for a configuration file.

Returns:

Dictionary with the parameters if a config file is found, None otherwise.