Skip to content

_population

MalariaSerializedPopulation: malaria-aware wrapper around SerializedPopulation.

MalariaSerializedPopulation

Malaria-aware wrapper around emod_api's SerializedPopulation.

Provides malaria-specific convenience methods for inspection, modification, and export of .dtk serialized population files. Delegates to the underlying SerializedPopulation for all low-level file I/O.

Parameters:

Name Type Description Default
file_path str | Path

Path to a .dtk serialized population file.

 required
Source code in emodpy_malaria/serialization/_population.py 
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
class MalariaSerializedPopulation:
    """Malaria-aware wrapper around emod_api's SerializedPopulation.

    Provides malaria-specific convenience methods for inspection,
    modification, and export of ``.dtk`` serialized population files.
    Delegates to the underlying SerializedPopulation for all low-level
    file I/O.

    Args:
        file_path (str | Path): Path to a ``.dtk`` serialized population file.
    """

    def __init__(self, file_path: str | Path) -> None:
        self._file_path = Path(file_path)
        self._ser_pop = SerializedPopulation(str(self._file_path))

    @property
    def ser_pop(self) -> SerializedPopulation:
        """The underlying emod_api SerializedPopulation object."""
        return self._ser_pop

    @property
    def file_path(self) -> Path:
        """Original file path."""
        return self._file_path

    @property
    def nodes(self):
        """All nodes (delegated to SerializedPopulation.nodes)."""
        return self._ser_pop.nodes

    @property
    def simulation(self):
        """Simulation-level data dict."""
        return self._ser_pop.dtk.simulation

    @property
    def header(self):
        """File header metadata."""
        return self._ser_pop.dtk.header

    @property
    def version(self) -> int:
        """DTK file format version."""
        return self._ser_pop.dtk.header.version

    @property
    def num_nodes(self) -> int:
        """Number of nodes in the file."""
        return len(self._ser_pop.nodes)

    def get_next_infection_suid(self) -> dict:
        """Get a unique SUID for a new infection."""
        return self._ser_pop.get_next_infection_suid()

    def get_next_individual_suid(self, node_id: int) -> dict:
        """Get a unique SUID for a new individual in the given node."""
        return self._ser_pop.get_next_individual_suid(node_id)

    def write(self, output_file: str | Path = "my_sp_file.dtk") -> None:
        """Write the (possibly modified) population to a file.

        Args:
            output_file (str | Path): Destination file path. Parent directories are
                created if they do not exist.
        """
        output_path = Path(output_file)
        output_path.parent.mkdir(parents=True, exist_ok=True)
        self._ser_pop.write(str(output_path))

    # -- Inspection --

    def summary(self) -> dict:
        """Return a summary dict with node counts, human counts, etc."""
        from emodpy_malaria.serialization._inspect import summarize
        return summarize(self._ser_pop)

    def find_parameter(self, name: str) -> list[str]:
        """Search for a parameter by name (fuzzy) and return matching paths."""
        from emodpy_malaria.serialization._inspect import find_parameter
        return find_parameter(self._ser_pop, name)

    def __repr__(self) -> str:
        return (
            f"MalariaSerializedPopulation("
            f"file='{self._file_path.name}', "
            f"version={self.version}, "
            f"nodes={self.num_nodes})"
        )

file_path property

Original file path.

header property

File header metadata.

nodes property

All nodes (delegated to SerializedPopulation.nodes).

num_nodes property

Number of nodes in the file.

ser_pop property

The underlying emod_api SerializedPopulation object.

simulation property

Simulation-level data dict.

version property

DTK file format version.

find_parameter(name)

Search for a parameter by name (fuzzy) and return matching paths.

Source code in emodpy_malaria/serialization/_population.py 
89
90
91
92
def find_parameter(self, name: str) -> list[str]:
    """Search for a parameter by name (fuzzy) and return matching paths."""
    from emodpy_malaria.serialization._inspect import find_parameter
    return find_parameter(self._ser_pop, name)

get_next_individual_suid(node_id)

Get a unique SUID for a new individual in the given node.

Source code in emodpy_malaria/serialization/_population.py 
67
68
69
def get_next_individual_suid(self, node_id: int) -> dict:
    """Get a unique SUID for a new individual in the given node."""
    return self._ser_pop.get_next_individual_suid(node_id)

get_next_infection_suid()

Get a unique SUID for a new infection.

Source code in emodpy_malaria/serialization/_population.py 
63
64
65
def get_next_infection_suid(self) -> dict:
    """Get a unique SUID for a new infection."""
    return self._ser_pop.get_next_infection_suid()

summary()

Return a summary dict with node counts, human counts, etc.

Source code in emodpy_malaria/serialization/_population.py 
84
85
86
87
def summary(self) -> dict:
    """Return a summary dict with node counts, human counts, etc."""
    from emodpy_malaria.serialization._inspect import summarize
    return summarize(self._ser_pop)

write(output_file='my_sp_file.dtk')

Write the (possibly modified) population to a file.

Parameters:

Name Type Description Default
output_file str | Path

Destination file path. Parent directories are created if they do not exist.

 'my_sp_file.dtk'
Source code in emodpy_malaria/serialization/_population.py 
71
72
73
74
75
76
77
78
79
80
def write(self, output_file: str | Path = "my_sp_file.dtk") -> None:
    """Write the (possibly modified) population to a file.

    Args:
        output_file (str | Path): Destination file path. Parent directories are
            created if they do not exist.
    """
    output_path = Path(output_file)
    output_path.parent.mkdir(parents=True, exist_ok=True)
    self._ser_pop.write(str(output_path))