emodpy_malaria.serialization.zero_infections module

emodpy_malaria.serialization.zero_infections.zero_vector_infections(vector_pop_list: list, remove=False)

Resets infections in vectors or removes infections from vectors.

Parameters:

• vector_pop_list – list of vector population in a node.

• remove – If True all infected vectors are removed from serialized population. If set to False (default) all vectors in the simulation are reset to state STATE_ADULT.

Returns:

None

emodpy_malaria.serialization.zero_infections.zero_human_infections(humans: List[dict], keep_ids: list | None = None)

Sets the infection state of individuals to uninfected.

Parameters:

• humans – All humans in a node

• keep_ids – ids of individuals that will be skipped, i.e. infection state is not changed

Returns:

None

emodpy_malaria.serialization.zero_infections.zero_infections(source_filename: str, dest_filename: str, ignore_nodes: List[int], keep_individuals: List[int], remove=False) → None

Removes/resets infections from humans and vectors.

Parameters:

• source_filename – input file

• dest_filename – output file

• ignore_nodes – list of node ids. These nodes are skipped.

• keep_individuals – Ids of individuals. These individuals are skipped.

• remove – If true infections are removed from vectors, if false infections are reset.

Returns:

None

emodpy_malaria.serialization.zero_infections.zero_infection_path(in_out_paths: list, ser_date: list, ignore_nodeids: list | None = None, keep_humanids: list | None = None)

Loop over all .dtk files in ser_paths that have ser_date in the file name but not ‘zero’ and remove human and

vector infections. ‘_zero’ is appended to the output files.

Parameters:

• in_out_paths – a list of lists of paths for directories to look into for .dtk files

• ser_date – List of timestamps

• ignore_nodeids – list of nodes that are ignored

• keep_humanids – infections are not removed from these humans