_infections

Operations for zeroing or modifying infections in humans and vectors.

zero_human_infections(humans, *, keep_ids=None)

Reset infection state of individuals to uninfected.

Parameters:

Name	Type	Description	Default
humans	Any	Iterable of individual dicts (e.g., node.individualHumans).	required
keep_ids	list[int]	SUID IDs of individuals to skip.	None

Returns:

Type	Description
int	Number of individuals whose infections were zeroed.

Raises:

Type	Description
KeyError	If an individual is missing expected infection fields.

Source code in emodpy_malaria/serialization/_infections.py

def zero_human_infections(
    humans: Any,
    *,
    keep_ids: list[int] | None = None,
) -> int:
    """Reset infection state of individuals to uninfected.

    Args:
        humans (Any): Iterable of individual dicts (e.g., ``node.individualHumans``).
        keep_ids (list[int] ): SUID IDs of individuals to skip.

    Returns:
        Number of individuals whose infections were zeroed.

    Raises:
        KeyError: If an individual is missing expected infection fields.
    """
    if keep_ids is None:
        keep_ids = []

    count = 0
    for person in humans:
        if person.suid.id in keep_ids:
            continue

        missing_keys = set(UNINFECTED_HUMAN_TEMPLATE) - set(person)
        if missing_keys:
            raise KeyError(
                f"Individual is missing expected infection fields: {missing_keys}"
            )
        person.update(UNINFECTED_HUMAN_TEMPLATE)
        count += 1

    return count

zero_infections(ser_pop, *, ignore_node_ids=None, keep_individual_ids=None, remove_vectors=False)

Zero all infections in the loaded population (in-place).

Resets human infection fields to uninfected state and either resets or removes infected vectors.

Parameters:

Name	Type	Description	Default
ser_pop	SerializedPopulation	A loaded SerializedPopulation.	required
ignore_node_ids	list[int]	Node external IDs to skip entirely.	None
keep_individual_ids	list[int]	Individual SUID IDs whose infections are preserved.	None
remove_vectors	bool	If True, remove infected/infectious vector cohorts. If False (default), reset their state to STATE_ADULT.	False

Source code in emodpy_malaria/serialization/_infections.py

def zero_infections(
    ser_pop: SerializedPopulation,
    *,
    ignore_node_ids: list[int] | None = None,
    keep_individual_ids: list[int] | None = None,
    remove_vectors: bool = False,
) -> None:
    """Zero all infections in the loaded population (in-place).

    Resets human infection fields to uninfected state and either resets
    or removes infected vectors.

    Args:
        ser_pop (SerializedPopulation): A loaded SerializedPopulation.
        ignore_node_ids (list[int] ): Node external IDs to skip entirely.
        keep_individual_ids (list[int] ): Individual SUID IDs whose infections are preserved.
        remove_vectors (bool): If True, remove infected/infectious vector cohorts.
            If False (default), reset their state to STATE_ADULT.
    """
    if ignore_node_ids is None:
        ignore_node_ids = []
    if keep_individual_ids is None:
        keep_individual_ids = []

    for node in ser_pop.nodes:
        if node.externalId in ignore_node_ids:
            logger.info("Skipping node %s", node.externalId)
            continue

        logger.info("Zeroing infections in node %s", node.externalId)
        zero_vector_infections(node.m_vectorpopulations, remove=remove_vectors)
        zero_human_infections(node.individualHumans, keep_ids=keep_individual_ids)

zero_vector_infections(vector_pop_list, *, remove=False)

Reset or remove infections from vector populations.

Parameters:

Name	Type	Description	Default
vector_pop_list	Any	List of vector populations (node.m_vectorpopulations).	required
remove	bool	If True, remove infected/infectious cohorts entirely. If False (default), reset to STATE_ADULT.	False

Returns:

Type	Description
int	Number of vector cohorts affected.

Source code in emodpy_malaria/serialization/_infections.py

def zero_vector_infections(
    vector_pop_list: Any,
    *,
    remove: bool = False,
) -> int:
    """Reset or remove infections from vector populations.

    Args:
        vector_pop_list (Any): List of vector populations
            (``node.m_vectorpopulations``).
        remove (bool): If True, remove infected/infectious cohorts entirely.
            If False (default), reset to STATE_ADULT.

    Returns:
        Number of vector cohorts affected.
    """
    count = 0
    for idx, vector_population in enumerate(vector_pop_list):
        for queue in INFECTION_QUEUES:
            cohorts = vector_population[queue]["collection"]

            if remove:
                kept = [
                    c for c in cohorts
                    if c.state != STATE_INFECTED and c.state != STATE_INFECTIOUS
                ]
                removed = len(cohorts) - len(kept)
                vector_pop_list[idx][queue]["collection"] = kept
                count += removed
            else:
                for cohort in cohorts:
                    if cohort.state in (STATE_INFECTED, STATE_INFECTIOUS):
                        cohort.state = STATE_ADULT
                        cohort.progress = 0.0
                        cohort.m_pStrain = NullPtr()
                        count += 1

    return count