Todo

Improve autoapi module

circadapt

@package CircAdapt.

CircAdapt is a modelling framework of the cardiovascular system. The framework is written in C++ and this package is a wrapper to use CircAdapt in python. The default CircAdapt is empty. The other class descriptions automatically build the corresponding model.

Package Contents

Classes

CircAdapt

Wrapper to communicate with c++ code.

Functions

load_plugin_components(filename)

Load a plugin from a library.

Attributes

DEFAULT_PATH_TO_CIRCADAPT

Default path to CircAdapt.dll.

Subpackages

• circadapt.adapt
• circadapt.components
  • circadapt.components.cavity
  • circadapt.components.connector
  • circadapt.components.global_functions
  • circadapt.components.node
  • circadapt.components.patch
  • circadapt.components.solver
  • circadapt.components.wall
• circadapt.error
• circadapt.matlab
• circadapt.model
  • circadapt.model.benchmark
  • circadapt.model.vanosta2023
• circadapt.plot

Submodules

• circadapt.settings
• circadapt.smart_components
• circadapt.smart_components_circulation
• circadapt.smart_components_heart

Objects

circadapt.DEFAULT_PATH_TO_CIRCADAPT = 'CircAdapt.'

Default path to CircAdapt.dll.

Do not change this unless you develop the c++ code. By default, it points to the compiled dll file in the package.

circadapt.load_plugin_components(filename: str)

Load a plugin from a library.

These plugins will be loaded every time a new model is loaded.

Parameters

filenamestr

path to library.

class circadapt.CircAdapt(solver: str = None, model: str = 'Custom', path_to_circadapt: str = None, model_state: dict = None)

Wrapper to communicate with c++ code.

Parameters

solver: str (optional)

Name of solver to be build. If not given, the default models solver is used.

model: str

Name of the model to be build.

path_to_circadapt: str (optional)

Path to CircAdapt library. If not given, the default_path_to_circadapt is used.

model_state: (multi)

Model state to be loaded. (default) -> load model reference from package False -> do nothing str -> load filename dict -> load given model state

build()

Build model.

Add and link components in the model. By default, the model is empty. This function will be used in derived model builts.

get_model_reference(model_state: any = None) → dict

Return reference model state as a dictionary.

If model_state is string, it is assumed to be a file location. This file will be loaded and returned. If is none, the default reference will be loaded. If no default reference available, it will be created and stored in the current active directory.

Parameters

model_statestr or None, optional

Location of model state. The default is None.

Raises

ValueError

DESCRIPTION.

Returns

dict

Dictonary with model state.

load_reference()

Load reference of current model from the package.

load_plugin_components(path_to_library: str)

Load a plugin

Parameters

path_to_librarystr

Path to library.

run(n_beats: int = 1, stable: bool = False, export: bool = True) → None

Run the model by solving the ODEs for n_beats.

The currently loaded model, model state, and parameterization will be used to run n_beats. Optional, more beats are performed until the model is hemodynamically stable (stable=True). By default, all data will be exported (export=True). By disabling this (export=False), the model runs faster by only solving the state variables in case a backward ODE solver is used.

Parameters

n_beats: int, optional (default: True)

Number of beats

stable: bool, optional (default: False)

Run beats until simulation is hemodynamically stable

export: bool, optional (default: False)

Future

is_stable() → bool

Check if simulation is hemodynamically stable.

get(par: str, dtype: any = None) → any

Get parameter from the model.

Parameters

par: str

Parameter name to get. This string value contains the parameter that will be obtained and the component from which it will be obtained. Components, its subcomponents, and the parameter name at the and are separated with a dot.

dtype: string or type, optional (default = None)

The type of parameter that will be obtained. If not specified, it will be detairmined automatically. If computational cost is important, it is better to specify the dtype.

Returns

Get value: type depending on dtype.

Returns the value stored in the c++ object

set(par: str, val: any, dtype=None) → bool

Set parameter from dtype with value val.

Parameters

par: str

Parameter name to get. This string value contains the parameter that will be obtained and the component from which it will be obtained. Components, its subcomponents, and the parameter name at the and are separated with a dot.

val: any

Value to be set. The value must be the same as the parameter used.

dtype: string or type, optional (default = None)

The type of parameter that will be obtained. If not specified, it will be detairmined automatically. If computational cost is important, it is better to specify the dtype.

Returns

bool: success or not

trigger(par) → bool

Trigger a function.

Objects in the model may have a function that can be triggered. This can be done by triggering the function using the ‘par’ parameter similar to the set function, only without a parameter.

Parameters

parstr

Function in object that will be triggered. It has a similar form to the set/get par, i.e. ‘Component.subcomponent.function_name’

Returns

is_success (bool)

add_component(comp_type: str, comp_name: str, base: str = '') → bool

Add component to CircAdapt object.

Parameters

comp_type: str

Type of object to create in the ComponentFactory

comp_name: str

Name of the new object to create

base: char, optional (default=’’)

Parent object of new component

Returns

is_success (bool)

set_component(par, obj) → bool

Set component to the parameter of a CircAdapt object.

Parameters

par: str

Parameter of object to link object obj to

obj: str

Object to set

model_import(model_state, check_model_state=False) → None

Load model_state into CircAdapt object.

Style and model_state version is automatically recognized.

Parameters

model_state: dict

model_state with data to set

obj: str

Object to set

model_export(style: str = None) → dict

Return the stored model state.

Parameters

style: str (optional)

Style to follow. If not given, the default style from the model is used.

Returns

dict

save(filename: str, ext: str = None) → None

Save model to filename with extention.

Parameters

filename: str

Filename to save file to. Filename must have extention .npy or .mat

ext: str (optional)

Extention of the file. If not given, the last 3 letters of the filename is used to determine the save method.

load(filename: str) → None

Load a model dataset from a filename.

Parameters

filename: str

Path to file that will be loaded. The extension must be .npy or .mat.

is_success() → bool

Return false if vectors contain nan.

Returns

bool

abstract copy()

Return a copy of itself.