laser_measles.demographics package#

pydantic model GADMShapefile[source]#

Bases: AdminShapefile

Show JSON schema

{
   "title": "GADMShapefile",
   "type": "object",
   "properties": {
      "shapefile": {
         "format": "path",
         "title": "Shapefile",
         "type": "string"
      },
      "admin_level": {
         "anyOf": [
            {
               "type": "integer"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Admin Level"
      },
      "dotname_fields": {
         "anyOf": [
            {
               "items": {
                  "type": "string"
               },
               "type": "array"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Dotname Fields"
      }
   },
   "required": [
      "shapefile"
   ]
}

Fields:

Validators:

check_dotname_fields » all fields

classmethod download(country_code, admin_level, directory=None, timeout=60)[source]#

Download the GADM shapefile for a given country code and return a GADMShapefile instance.

Parameters:

country_code (str) – The country code to download the shapefile for.
admin_level (int) – The admin level to download the shapefile for.
directory (str | Path | None) – The directory to download the shapefile to. If None, uses current directory.
timeout (int) – The timeout for the request.

Return type:

GADMShapefile

Returns:

A GADMShapefile instance for the downloaded shapefile.

validator check_dotname_fields » all fields[source]#

Check dotname_fields from shapefile name if not explicitly provided.

Return type:: GADMShapefile

class RasterPatchGenerator(config, verbose=True)[source]#

Bases: object

clear_cache()[source]#

Return type:: None

generate_birth_rates()[source]#

Return type:: DataFrame

generate_demographics()[source]#

Return type:: None

generate_mcv1()[source]#

MCV1 coverage, population weighted

Return type:: DataFrame

generate_mortality_rates()[source]#

Return type:: DataFrame

generate_population()[source]#

Population, counts

Return type:: DataFrame

get_cache_key(key)[source]#

Return type:: str

pydantic model RasterPatchParams[source]#

Bases: BaseModel

Show JSON schema

{
   "title": "RasterPatchParams",
   "type": "object",
   "properties": {
      "id": {
         "description": "Unique identifier for the scenario",
         "title": "Id",
         "type": "string"
      },
      "region": {
         "description": "Country identifier (ISO3 code)",
         "title": "Region",
         "type": "string"
      },
      "shapefile": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "format": "path",
               "type": "string"
            }
         ],
         "description": "Path to the shapefile",
         "title": "Shapefile"
      },
      "population_raster": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "format": "path",
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "description": "Path to the population raster",
         "title": "Population Raster"
      },
      "mcv1_raster": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "format": "path",
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "description": "Path to the MCV1 raster",
         "title": "Mcv1 Raster"
      },
      "mcv2_raster": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "format": "path",
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "description": "Path to the MCV2 raster",
         "title": "Mcv2 Raster"
      }
   },
   "required": [
      "id",
      "region",
      "shapefile"
   ]
}

Fields:

id (str)
mcv1_raster (str | pathlib.Path | None)
mcv2_raster (str | pathlib.Path | None)
population_raster (str | pathlib.Path | None)
region (str)
shapefile (str | pathlib.Path)

Validators:

shapefile_exists » shapefile

field id: str [Required]#: Unique identifier for the scenario

field mcv1_raster: str | Path | None = None#: Path to the MCV1 raster

field mcv2_raster: str | Path | None = None#: Path to the MCV2 raster

field population_raster: str | Path | None = None#: Path to the population raster

field region: str [Required]#: Country identifier (ISO3 code)

field shapefile: str | Path [Required]#

Path to the shapefile

Validated by:

shapefile_exists

validator shapefile_exists » shapefile[source]#

get_shapefile_dataframe(shapefile_path)[source]#

Get a DataFrame containing the shapefile data with DOTNAME and shape columns.

Parameters:: shapefile_path (str | Path) – The path to the shapefile.
Return type:: DataFrame
Returns:: A DataFrame with DOTNAME and shape columns.

plot_shapefile_dataframe(df, ax=None, plot_kwargs=None)[source]#

Return type:: Figure

Submodules#

laser_measles.demographics.admin_shapefile module#

Admin level shapefiles

pydantic model AdminShapefile[source]#

Bases: BaseShapefile

Shapefile of administrative units.

Parameters:

admin_level (int) – Admin level of the shapefile.
dotname_fields (list[str]) – List of fields to use for dotname. e.g., [“ADMIN0”, “ADMIN1”, “ADMIN2”]

Show JSON schema

{
   "title": "AdminShapefile",
   "description": "Shapefile of administrative units.\n\nArgs:\n    admin_level (int): Admin level of the shapefile.\n    dotname_fields (list[str]): List of fields to use for dotname. e.g., [\"ADMIN0\", \"ADMIN1\", \"ADMIN2\"]",
   "type": "object",
   "properties": {
      "shapefile": {
         "format": "path",
         "title": "Shapefile",
         "type": "string"
      },
      "admin_level": {
         "anyOf": [
            {
               "type": "integer"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Admin Level"
      },
      "dotname_fields": {
         "anyOf": [
            {
               "items": {
                  "type": "string"
               },
               "type": "array"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Dotname Fields"
      }
   },
   "required": [
      "shapefile"
   ]
}

Fields:

admin_level (int | None)
dotname_fields (list[str] | None)

field admin_level: int | None = None#

field dotname_fields: list[str] | None = None#

add_dotname()[source]#

Add a DOTNAME to the shapefil (e.g., ADMIN0:ADMIN1:ADMIN2)

Return type:: None

get_shapefile_parent()[source]#

Get the parent directory of the shapefile.

Return type:: Path

shape_subdivide(patch_size_km)[source]#

Subdivide the shapefile for a given administrative level into patches of approximately equal area.

Parameters:: patch_size_km (int) – Size of the patch in square kilometers.
Return type:: None

laser_measles.demographics.base module#

class DemographicsGeneratorProtocol(*args, **kwargs)[source]#

Bases: Protocol

generate_population()[source]#

Return type:: DataFrame

generate_birth_rates()[source]#

Return type:: DataFrame

generate_mortality_rates()[source]#

Return type:: DataFrame

class ShapefileProtocol(*args, **kwargs)[source]#

Bases: Protocol

add_dotname()[source]#

Return type:: None

get_dataframe()[source]#

Return type:: DataFrame

pydantic model BaseShapefile[source]#

Bases: BaseModel

Show JSON schema

{
   "title": "BaseShapefile",
   "type": "object",
   "properties": {
      "shapefile": {
         "format": "path",
         "title": "Shapefile",
         "type": "string"
      }
   },
   "required": [
      "shapefile"
   ]
}

Fields:

shapefile (pathlib.Path)

field shapefile: Path [Required]#

classmethod convert_to_path(v)[source]#

Wrap a classmethod, staticmethod, property or unbound function and act as a descriptor that allows us to detect decorated items from the class’ attributes.

This class’ __get__ returns the wrapped item’s __get__ result, which makes it transparent for classmethods and staticmethods.

wrapped#: The decorator that has to be wrapped.

decorator_info#: The decorator info.

shim#: A wrapper function to wrap V1 style function.

add_dotname()[source]#

Return type:: None

get_dataframe()[source]#

Get a Polars DataFrame containing the shapefile data and fields.

Return type:: DataFrame
Returns:: A Polars DataFrame.

laser_measles.demographics.cache module#

load_cache(cache_dir=None)[source]#

Load the cache for the application.

Parameters:: cache_dir (str | None) – The cache directory to use. If None, the default cache directory will be used.
Return type:: Cache
Returns:: The cache object.

get_cache_dir()[source]#

Get the cache directory for the application.

Return type:: str

clear_cache(cache_dir=None)[source]#

Clear diskcache data from the application cache.

Return type:: None

clear_all_cache()[source]#

Clear all cached data from the application cache.

Return type:: None

clear_cache_dir(dir)[source]#

Clear all cached data from a specific directory.

Return type:: None

get_all_cache_keys()[source]#

Get all the cache keys for the application.

Return type:: list[str]

laser_measles.demographics.gadm module#

GADM shapefiles

pydantic model GADMShapefile[source]#

Bases: AdminShapefile

Show JSON schema

{
   "title": "GADMShapefile",
   "type": "object",
   "properties": {
      "shapefile": {
         "format": "path",
         "title": "Shapefile",
         "type": "string"
      },
      "admin_level": {
         "anyOf": [
            {
               "type": "integer"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Admin Level"
      },
      "dotname_fields": {
         "anyOf": [
            {
               "items": {
                  "type": "string"
               },
               "type": "array"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Dotname Fields"
      }
   },
   "required": [
      "shapefile"
   ]
}

Fields:

Validators:

check_dotname_fields » all fields

classmethod download(country_code, admin_level, directory=None, timeout=60)[source]#

Download the GADM shapefile for a given country code and return a GADMShapefile instance.

Parameters:

country_code (str) – The country code to download the shapefile for.
admin_level (int) – The admin level to download the shapefile for.
directory (str | Path | None) – The directory to download the shapefile to. If None, uses current directory.
timeout (int) – The timeout for the request.

Return type:

GADMShapefile

Returns:

A GADMShapefile instance for the downloaded shapefile.

validator check_dotname_fields » all fields[source]#

Check dotname_fields from shapefile name if not explicitly provided.

Return type:: GADMShapefile

laser_measles.demographics.raster_patch module#

Raster patch generator for demographic data. You can use this to generate initial conditions (e.g, population, MCV1 coverage) for a laser-measles scenario.

pydantic model RasterPatchParams[source]#

Bases: BaseModel

Show JSON schema

{
   "title": "RasterPatchParams",
   "type": "object",
   "properties": {
      "id": {
         "description": "Unique identifier for the scenario",
         "title": "Id",
         "type": "string"
      },
      "region": {
         "description": "Country identifier (ISO3 code)",
         "title": "Region",
         "type": "string"
      },
      "shapefile": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "format": "path",
               "type": "string"
            }
         ],
         "description": "Path to the shapefile",
         "title": "Shapefile"
      },
      "population_raster": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "format": "path",
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "description": "Path to the population raster",
         "title": "Population Raster"
      },
      "mcv1_raster": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "format": "path",
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "description": "Path to the MCV1 raster",
         "title": "Mcv1 Raster"
      },
      "mcv2_raster": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "format": "path",
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "description": "Path to the MCV2 raster",
         "title": "Mcv2 Raster"
      }
   },
   "required": [
      "id",
      "region",
      "shapefile"
   ]
}

Fields:

id (str)
mcv1_raster (str | pathlib.Path | None)
mcv2_raster (str | pathlib.Path | None)
population_raster (str | pathlib.Path | None)
region (str)
shapefile (str | pathlib.Path)

Validators:

shapefile_exists » shapefile

field id: str [Required]#: Unique identifier for the scenario

field mcv1_raster: str | Path | None = None#: Path to the MCV1 raster

field mcv2_raster: str | Path | None = None#: Path to the MCV2 raster

field population_raster: str | Path | None = None#: Path to the population raster

field region: str [Required]#: Country identifier (ISO3 code)

field shapefile: str | Path [Required]#

Path to the shapefile

Validated by:

shapefile_exists

validator shapefile_exists » shapefile[source]#

class RasterPatchGenerator(config, verbose=True)[source]#

Bases: object

generate_demographics()[source]#

Return type:: None

get_cache_key(key)[source]#

Return type:: str

generate_population()[source]#

Population, counts

Return type:: DataFrame

generate_mcv1()[source]#

MCV1 coverage, population weighted

Return type:: DataFrame

clear_cache()[source]#

Return type:: None

generate_birth_rates()[source]#

Return type:: DataFrame

generate_mortality_rates()[source]#

Return type:: DataFrame

laser_measles.demographics.shapefiles module#

check_field(path, field_name)[source]#

Return type:: bool

add_dotname(path, dot_name_fields, dotname_symbol=':', append_suffix='dotname', inplace=False, field_name='DOTNAME')[source]#

Add a DOTNAME to the shapefile.

Return type:: None

get_shapefile_dataframe(shapefile_path)[source]#

Get a DataFrame containing the shapefile data with DOTNAME and shape columns.

Parameters:: shapefile_path (str | Path) – The path to the shapefile.
Return type:: DataFrame
Returns:: A DataFrame with DOTNAME and shape columns.

plot_shapefile_dataframe(df, ax=None, plot_kwargs=None)[source]#

Return type:: Figure