amici.numpy

C++ object views

This module provides views on C++ objects for efficient access.

Functions

evaluate(expr, rdata)

Evaluate a symbolic expression based on the given simulation outputs.

Classes

ExpDataView(edata)	Interface class for C++ Exp Data objects that avoids possibly costly copies of member data.
ReturnDataView(rdata)	Interface class for C++ amici.ReturnData objects that avoids possibly costly copies of member data.
SwigPtrView(swigptr)	Interface class to expose std::vector<double> and scalar members of swig wrapped C++ objects as numpy array attributes and fields.

class amici.numpy.ExpDataView(edata)

Interface class for C++ Exp Data objects that avoids possibly costly copies of member data.

NOTE: This currently assumes that the underlying ExpData does not change after instantiating an ExpDataView.

__init__(edata)

Constructor

Parameters:

edata (amici.amici.ExpDataPtr | amici.amici.ExpData) – pointer to the ExpData instance

get(k[, d]) → D[k] if k in D, else d.  d defaults to None.

items() → a set-like object providing a view on D's items

keys() → a set-like object providing a view on D's keys

values() → an object providing a view on D's values

class amici.numpy.ReturnDataView(rdata)

Interface class for C++ amici.ReturnData objects that avoids possibly costly copies of member data.

__init__(rdata)

Constructor

Parameters:

rdata (amici.amici.ReturnDataPtr | amici.amici.ReturnData) – pointer to the ReturnData instance

by_id(entity_id, field=None, model=None)

Get the value of a given field for a named entity.

Parameters:

• entity_id (str) – The ID of the model entity that is to be extracted from field (e.g. a state ID).

• field (str) – The requested field, e.g. ‘x’ for model states. This is optional if field would be one of {'x', 'y', 'w'}

• model (amici.amici.Model) – The model from which this ReturnDataView was generated. This is optional if this ReturnData was generated with solver.getReturnDataReportingMode() == amici.RDataReporting.full.

Return type:

numpy.array

get(k[, d]) → D[k] if k in D, else d.  d defaults to None.

items() → a set-like object providing a view on D's items

keys() → a set-like object providing a view on D's keys

values() → an object providing a view on D's values

class amici.numpy.SwigPtrView(swigptr)

Interface class to expose std::vector<double> and scalar members of swig wrapped C++ objects as numpy array attributes and fields. This class is memory efficient as copies of the underlying C++ objects is only created when respective fields are accessed for the first time. Cached copies are used for all subsequent calls.

Variables:

• _swigptr – pointer to the C++ object

• _field_names – names of members that will be exposed as numpy arrays

• _field_dimensions – dimensions of numpy arrays

• _cache – dictionary with cached values

__init__(swigptr)

Constructor

Parameters:

swigptr – pointer to the C++ object

get(k[, d]) → D[k] if k in D, else d.  d defaults to None.

items() → a set-like object providing a view on D's items

keys() → a set-like object providing a view on D's keys

values() → an object providing a view on D's values

amici.numpy.evaluate(expr, rdata)

Evaluate a symbolic expression based on the given simulation outputs.

Parameters:

• expr (str | sympy.core.expr.Expr) – A symbolic expression, e.g. a sympy expression or a string that can be sympified. Can include state variable, expression, and observable IDs, depending on whether the respective data is available in the simulation results. Parameters are not yet supported.

• rdata (amici.numpy.ReturnDataView) – The simulation results.

Return type:

numpy.array

Returns:

The evaluated expression for the simulation output timepoints.