amici.ode_export.ODEExporter

class amici.ode_export.ODEExporter(ode_model, outdir=None, verbose=False, assume_pow_positivity=False, compiler=None, allow_reinit_fixpar_initcond=True, generate_sensitivity_code=True)[source]

The ODEExporter class generates AMICI C++ files for ODE model as defined in symbolic expressions.

Variables
  • model – ODE definition

  • outdir – see amici.ode_export.ODEExporter.set_paths()

  • verbose – more verbose output if True

  • assume_pow_positivity

    if set to true, a special pow function is used to avoid problems with state variables that may become negative due to numerical errors

    compiler: distutils/setuptools compiler selection to build the python extension

  • functions – carries C++ function signatures and other specifications

  • model_name – name of the model that will be used for compilation

  • model_path – path to the generated model specific files

  • model_swig_path – path to the generated swig files

  • allow_reinit_fixpar_initcond – indicates whether reinitialization of initial states depending on fixedParameters is allowed for this model

  • _build_hints – If the given model uses special functions, this set contains hints for model building.

  • generate_sensitivity_code – Specifies whether code for sensitivity computation is to be generated

__init__(ode_model, outdir=None, verbose=False, assume_pow_positivity=False, compiler=None, allow_reinit_fixpar_initcond=True, generate_sensitivity_code=True)[source]

Generate AMICI C++ files for the ODE provided to the constructor.

Parameters
:param generate_sensitivity_code specifies whether code required for

sensitivity computation will be generated

Methods Summary

__init__(ode_model[, outdir, verbose, …])

Generate AMICI C++ files for the ODE provided to the constructor.

compile_model()

Compiles the generated code it into a simulatable module

generate_model_code()

Generates the native C++ code for the loaded model and a Matlab script that can be run to compile a mex file from the C++ code

set_name(model_name)

Sets the model name

set_paths(output_dir)

Set output paths for the model and create if necessary

Methods

__init__(ode_model, outdir=None, verbose=False, assume_pow_positivity=False, compiler=None, allow_reinit_fixpar_initcond=True, generate_sensitivity_code=True)[source]

Generate AMICI C++ files for the ODE provided to the constructor.

Parameters
:param generate_sensitivity_code specifies whether code required for

sensitivity computation will be generated

compile_model()[source]

Compiles the generated code it into a simulatable module

Return type

None

generate_model_code()[source]

Generates the native C++ code for the loaded model and a Matlab script that can be run to compile a mex file from the C++ code

Return type

None

set_name(model_name)[source]

Sets the model name

Parameters

model_name (str) – name of the model (may only contain upper and lower case letters, digits and underscores, and must not start with a digit)

Return type

None

set_paths(output_dir)[source]

Set output paths for the model and create if necessary

Parameters

output_dir (str) – relative or absolute path where the generated model code is to be placed. will be created if does not exists.

Return type

None