amici.amici¶
Core C++ bindings¶
This module encompasses the complete public C++ API of AMICI, which was
exposed via swig. All functions listed here are directly accessible in the
main amici package, i.e., amici.amici.ExpData
is available as
amici.ExpData
.
Usage of functions and classes from the base amici
package is
generally recommended as they often include convenience wrappers that avoid
common pitfalls when accessing C++ types from python and implement some
nonstandard type conversions.
Classes
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Swig-Generated class templating common python types including |
Generic implementation for a context manager, explicitly deletes copy and move operators for derived classes |
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Swig-Generated class templating common python types including |
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ExpData carries all information about experimental or condition-specific data |
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Swig-Generated class that implements smart pointers to ExpData as objects. |
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Swig-Generated class templating common python types including |
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An enumeration. |
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Swig-Generated class templating common python types including |
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An enumeration. |
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An enumeration. |
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An enumeration. |
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An enumeration. |
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The Model class represents an AMICI ODE/DAE model. |
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The ModelContext temporarily stores amici::Model::state and restores it when going out of scope |
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Swig-Generated class that implements smart pointers to Model as objects. |
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An enumeration. |
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An enumeration. |
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An enumeration. |
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Swig-Generated class, which, in contrast to other Vector classes, does not allow for simple interoperability with common python types, but must be created using |
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An enumeration. |
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Stores all data to be returned by |
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Swig-Generated class that implements smart pointers to ReturnData as objects. |
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An enumeration. |
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An enumeration. |
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An enumeration. |
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The Solver class provides a generic interface to CVODES and IDAS solvers, individual realizations are realized in the CVodeSolver and the IDASolver class. |
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Swig-Generated class that implements smart pointers to Solver as objects. |
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An enumeration. |
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An enumeration. |
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Swig-Generated class templating |
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Swig-Generated class templating common python types including |
Functions Summary
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Returns the current backtrace as std::string |
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Apply parameter scaling according to scaling |
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Remove parameter scaling according to scaling |
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Core integration routine. |
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Same as runAmiciSimulation, but for multiple ExpData instances. |
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Apply parameter scaling according to scaling |
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Remove parameter scaling according to the parameter scaling in pscale |
Functions
-
amici.amici.
backtraceString
(maxFrames: int) → str[source]¶ Returns the current backtrace as std::string
- Parameters
maxFrames (
int
) – Number of frames to include- Return type
string
- Returns
Backtrace
-
amici.amici.
getScaledParameter
(unscaledParameter: float, scaling: amici.amici.ParameterScaling) → float[source]¶ Apply parameter scaling according to scaling
- Parameters
unscaledParameter (
float
) –scaling (
amici.amici.ParameterScaling
) – parameter scaling
- Return type
- Returns
Scaled parameter
-
amici.amici.
getUnscaledParameter
(scaledParameter: float, scaling: amici.amici.ParameterScaling) → float[source]¶ Remove parameter scaling according to scaling
- Parameters
scaledParameter (
float
) – scaled parameterscaling (
amici.amici.ParameterScaling
) – parameter scaling
- Return type
- Returns
Unscaled parameter
-
amici.amici.
parameterScalingFromIntVector
(intVec: amici.amici.IntVector) → amici.amici.ParameterScalingVector[source]¶ - Return type
-
amici.amici.
runAmiciSimulation
(solver: amici.amici.Solver, edata: amici.amici.ExpData, model: amici.amici.Model, rethrow: bool = False) → amici.amici.ReturnData[source]¶ Core integration routine. Initializes the solver and runs the forward and backward problem.
- Parameters
solver (
amici.amici.Solver
) – Solver instanceedata (
amici.amici.ExpData
) – pointer to experimental data objectmodel (
amici.amici.Model
) – model specification objectrethrow (
bool
) – rethrow integration exceptions?
- Return type
- Returns
rdata pointer to return data object
-
amici.amici.
runAmiciSimulations
(solver: amici.amici.Solver, edatas: amici.amici.ExpDataPtrVector, model: amici.amici.Model, failfast: bool, num_threads: int) → Iterable[amici.amici.ReturnData][source]¶ Same as runAmiciSimulation, but for multiple ExpData instances. When compiled with OpenMP support, this function runs multi-threaded.
- Parameters
solver (
amici.amici.Solver
) – Solver instanceedatas (
amici.amici.ExpDataPtrVector
) – experimental data objectsmodel (
amici.amici.Model
) – model specification objectfailfast (
bool
) – flag to allow early terminationnum_threads (
int
) – number of threads for parallel execution
- Return type
Iterable[ReturnData]
- Returns
vector of pointers to return data objects
-
amici.amici.
scaleParameters
(bufferUnscaled: Iterable[float], pscale: Iterable[amici.amici.ParameterScaling], bufferScaled: Iterable[float]) → None[source]¶ Apply parameter scaling according to scaling
- Parameters
bufferUnscaled (
typing.Iterable
[float
]) –pscale (
typing.Iterable
[amici.amici.ParameterScaling
]) – parameter scalingbufferScaled (
typing.Iterable
[float
]) – destination
- Return type
-
amici.amici.
unscaleParameters
(bufferScaled: Iterable[float], pscale: Iterable[amici.amici.ParameterScaling], bufferUnscaled: Iterable[float]) → None[source]¶ Remove parameter scaling according to the parameter scaling in pscale
All vectors must be of same length.
- Parameters
bufferScaled (
typing.Iterable
[float
]) – scaled parameterspscale (
typing.Iterable
[amici.amici.ParameterScaling
]) – parameter scalingbufferUnscaled (
typing.Iterable
[float
]) – unscaled parameters are written to the array
- Return type