void IndividualHumanVector::ApplyTotalBitingExposure()
{
// Make random draw whether to acquire new infection
// dt incorporated already in ExposeIndividual function arguments
float acquisition_probability = float(EXPCDF(-m_total_exposure));
if ( randgen->e() >= acquisition_probability ) return;
// Choose a strain based on a weighted draw over values from all vector-to-human pools
float strain_cdf_draw = randgen->e() * m_total_exposure;
std::vector<strain_exposure_t>::iterator it = std::lower_bound( m_strain_exposure.begin(), m_strain_exposure.end(), strain_cdf_draw, compare_strain_exposure_float_less());
AcquireNewInfection(&(it->first));
}
void IndividualHumanMalaria::ApplyTotalBitingExposure()
{
// Unlike for vector sims, don't do the draw on probability of *any* infectious bites, i.e. EXPCDF(-m_total_exposure)
// We will instead do a Poisson draw on how many infectious bites, with the equivalent behavior for zero bites.
// Downstream (in createInfection), we will use the number of infected hepatocytes to initialize new infections.
// First calculate number of infectious bites
int n_infectious_bites = CalculateInfectiousBites();
if ( n_infectious_bites == 0 ) return;
// Then do sporozoite challenge (caching inital infected hepatocyte count for createInfection)
if ( ChallengeWithBites( n_infectious_bites ) )
{
// If there is a non-zero number of initial infected hepatocytes,
// choose a strain based on a weighted draw over values from all vector-to-human pools and acquire infection
float strain_cdf_draw = randgen->e() * m_total_exposure;
std::vector<strain_exposure_t>::iterator it = std::lower_bound( m_strain_exposure.begin(), m_strain_exposure.end(), strain_cdf_draw, compare_strain_exposure_float_less());
AcquireNewInfection(&(it->first));
}
}
void IndividualHumanPy::Expose( const IContagionPopulation* cp, float dt, TransmissionRoute::Enum transmission_route )
{
#ifdef ENABLE_PYTHON_FEVER
if( cp->GetTotalContagion() == 0 )
{
return;
}
LOG_DEBUG_F( "Calling py:expose with contagion pop %f\n", cp->GetTotalContagion() );
static auto pFunc = PythonSupportPtr->IdmPyInit( PythonSupport::SCRIPT_PYTHON_FEVER.c_str(), "expose" );
if( pFunc )
{
// pass individual id AND dt
static PyObject * vars = PyTuple_New(4);
vars = Py_BuildValue( "llls", GetSuid().data, int(cp->GetTotalContagion()), int(dt), PyLong_FromLong( transmission_route == TransmissionRoute::TRANSMISSIONROUTE_ENVIRONMENTAL ? 0 : 1 ) );
PyObject * retVal = PyObject_CallObject( pFunc, vars );
if( retVal == nullptr )
{
PyErr_Print();
std::stringstream msg;
msg << "Embedded python code failed: PyObject_CallObject failed in call to 'expose'.";
throw Kernel::IllegalOperationException( __FILE__, __LINE__, __FUNCTION__, msg.str().c_str() );
}
bool val = false;
PyArg_Parse( retVal, "b", &val );
if( val )
{
StrainIdentity strainId;
AcquireNewInfection(&strainId);
}
#if !defined(_WIN32) || !defined(_DEBUG)
Py_DECREF( retVal );
#endif
}
return;
#endif
}