Source code for emod_api.demographics.Node

import json
import math
from emod_api.demographics.Updateable import Updateable
from emod_api.demographics.PropertiesAndAttributes import IndividualAttributes, IndividualProperty, IndividualProperties, NodeAttributes


[docs]class Node(Updateable): # TODO: clean this up, without being all caps it looks like a modifiable attribute of a Node, not a class const default_population = 1000 # ability to resolve between Nodes res_in_degrees = 2.5 / 60 def __init__(self, lat, lon, pop, name: str = None, area: float = None, forced_id: int = None, individual_attributes: IndividualAttributes = None, individual_properties: IndividualProperties = None, node_attributes: NodeAttributes = None, meta: dict = None): """ Represent a Node (the metapopulation unit) Args: lat (float): Latitude in degrees lon (float): Longitude in degrees pop (float): Population name (str, optional): Facility name area (float, optional): Area forced_id (int, optional): A custom id instead of the default ID based on lat/lon individual_attributes (:py:class:`emod_api.demographics.PropertiesAndAttributes.IndividualAttributes`, optional): individual_properties (:py:class:`emod_api.demographics.PropertiesAndAttributes.IndividualProperty`, optional): node_attributes (:py:class:`emod_api.demographics.PropertiesAndAttributes.NodeAttributes`, optional): """ super().__init__() self.forced_id = forced_id self.meta = meta if meta else {} self.individual_attributes = individual_attributes if individual_attributes else IndividualAttributes() self.individual_properties = individual_properties if individual_properties else IndividualProperties() self.node_attributes = NodeAttributes(latitude=lat, longitude=lon, initial_population=pop, name=name, area=area) if node_attributes is not None: self.node_attributes.update(node_attributes) # TODO/NOTE: the name attribute here does not exist in EMOD and will not appear in any reports. At best it is # for user convenience during the emodpy/api phase of building inputs. # https://github.com/InstituteforDiseaseModeling/emod-api/issues/693 if name is not None: self.name = name @property def name(self): return self.node_attributes.name @name.setter def name(self, value): self.node_attributes.name = value def __repr__(self): return f"{self.node_attributes.name} - ({self.node_attributes.latitude},{self.node_attributes.longitude})"
[docs] def has_individual_property(self, property_key: str) -> bool: return self.individual_properties.has_individual_property(property_key=property_key)
[docs] def get_individual_property(self, property_key: str) -> IndividualProperty: if not self.has_individual_property(property_key=property_key): raise Exception(f"No such individual property {property_key} exists in node: {self.id}") ip_by_name = {ip.property: ip for ip in self.individual_properties} return ip_by_name[property_key]
# TODO: refactor this to report self.meta (metadata) as code using this is forced to workaround the oversight # https://github.com/InstituteforDiseaseModeling/emod-api/issues/702
[docs] def to_dict(self) -> dict: """ Translate node structure to a dictionary for EMOD """ d = {"NodeID": self.id, "NodeAttributes": self.node_attributes.to_dict()} if self.individual_attributes: d["IndividualAttributes"] = self.individual_attributes.to_dict() if self.individual_properties: ip_dict = {"IndividualProperties": []} for ip in self.individual_properties: ip_dict["IndividualProperties"].append(ip.to_dict()) d.update(ip_dict) return d
[docs] def to_tuple(self): """ Returns a tuple of (latitude, longitude, and initial population) """ return self.node_attributes.latitude, self.node_attributes.longitude, self.node_attributes.initial_population
@property def id(self): """ Returns the node ID""" return ( self.forced_id if self.forced_id is not None else nodeid_from_lat_lon(self.node_attributes.latitude, self.node_attributes.longitude, self.res_in_degrees) )
[docs] @classmethod def init_resolution_from_file(cls, fn): if "30arcsec" in fn: cls.res_in_degrees = 30 / 3600.0 elif "2_5arcmin" in fn: cls.res_in_degrees = 2.5 / 30 else: raise Exception("Don't recognize resolution from demographics filename")
[docs] @classmethod def from_data(cls, data: dict): """ Function used to create the node object from data (most likely coming from a demographics file) Args: data (dict): Contains the node definitions Returns: A :py:class:`emod_api.Demographics.Node.Node` """ nodeid = data["NodeID"] node_attributes_dict = dict(data.get("NodeAttributes")) attributes = data["NodeAttributes"] latitude = attributes.pop("Latitude") longitude = attributes.pop("Longitude") population = attributes.pop("InitialPopulation", Node.default_population) name = attributes.pop("FacilityName", nodeid) individual_attributes_dict = data.get("IndividualAttributes") individual_properties_dict = data.get("IndividualProperties") individual_properties = IndividualProperties() if individual_properties_dict: if type(individual_properties_dict) is dict: individual_properties.append(individual_properties_dict) if type(individual_properties_dict) is list: for ip in individual_properties_dict: individual_properties.add(IndividualProperty(property=ip["Property"], values=ip["Values"], transitions=ip["Transitions"], initial_distribution=ip["Initial_Distribution"])) individual_attributes = None if individual_attributes_dict: individual_attributes = IndividualAttributes().from_dict(individual_attributes_dict) node_attributes = None if node_attributes_dict: node_attributes = NodeAttributes().from_dict(node_attributes_dict) # Create the node cls.node = Node(node_attributes.latitude, node_attributes.longitude, node_attributes.initial_population, name=name, forced_id=nodeid, individual_attributes=individual_attributes, individual_properties=individual_properties, node_attributes=node_attributes) return cls.node
@property def pop(self): """ initial population """ return self.node_attributes.initial_population @pop.setter def pop(self, value): self.node_attributes.initial_population = value @property def lon(self): """ longitude """ return self.node_attributes.longitude @lon.setter def lon(self, value): self.node_attributes.longitude = value @property def lat(self): """ latitude """ return self.node_attributes.latitude @lat.setter def lat(self, value): self.node_attributes.latitude = value @property def birth_rate(self): """ birth rate in births per person per day""" return self.node_attributes.birth_rate @birth_rate.setter def birth_rate(self, value): self.node_attributes.birth_rate = value def _set_individual_attributes(self, ind_attribute: IndividualAttributes): self.individual_attributes = ind_attribute def _set_individual_properties(self, ind_properties: IndividualProperties): self.individual_properties = ind_properties def _add_individual_property(self, ind_property: IndividualProperty): self.individual_properties.add(ind_property) def _set_node_attributes(self, node_attributes: NodeAttributes): self.node_attributes = node_attributes def _set_mortality_distribution(self, distribution: IndividualAttributes.MortalityDistribution = None): self.individual_attributes.mortality_distribution = distribution def _set_mortality_distribution_female(self, distribution: IndividualAttributes.MortalityDistribution = None): self.individual_attributes.mortality_distribution_female = distribution def _set_mortality_distribution_male(self, distribution: IndividualAttributes.MortalityDistribution = None): self.individual_attributes.mortality_distribution_male = distribution def _set_fertility_distribution(self, distribution: IndividualAttributes.FertilityDistribution = None): self.individual_attributes.fertility_distribution = distribution # TODO: if an age distribution is set, we are using a complex distribution (always?). # Should disable self.individual_attributesage_distribution_flag (None). # https://github.com/InstituteforDiseaseModeling/emod-api/issues/705 def _set_age_distribution(self, distribution: IndividualAttributes.AgeDistribution = None): self.individual_attributes.age_distribution = distribution
[docs]class OverlayNode(Node): """ Node that only requires an ID. Use to overlay a Node. """ def __init__(self, node_id, latitude=None, longitude=None, initial_population=None, **kwargs ): super(OverlayNode, self).__init__(latitude, longitude, initial_population, forced_id=node_id, **kwargs )
[docs]def get_xpix_ypix(nodeid): """ Get pixel position from nodid. Inverse of :py:func:`nodeid_from_lat_lon` """ ypix = (nodeid - 1) & 2 ** 16 - 1 xpix = (nodeid - 1) >> 16 # shift bits to the right return (xpix, ypix)
[docs]def lat_lon_from_nodeid(nodeid, res_in_deg=Node.res_in_degrees): """ Inverse of :py:func:`nodeid_from_lat_lon` """ xpix, ypix = get_xpix_ypix(nodeid) lat = (0.5 + ypix) * res_in_deg - 90.0 lon = (0.5 + xpix) * res_in_deg - 180.0 return (lat, lon)
[docs]def xpix_ypix_from_lat_lon(lat, lon, res_in_deg=Node.res_in_degrees): """ Pixel position (origin is -90°N and -180°E). No modular arithmentic is done.""" xpix = int(math.floor((lon + 180.0) / res_in_deg)) ypix = int(math.floor((lat + 90.0) / res_in_deg)) return xpix, ypix
[docs]def nodeid_from_lat_lon(lat, lon, res_in_deg=Node.res_in_degrees): """ Generate unique identifier from lat, lon. Inverse of :py:func:`lat_lon_from_nodeid` """ xpix, ypix = xpix_ypix_from_lat_lon(lat, lon, res_in_deg) nodeid = (xpix << 16) + ypix + 1 return nodeid
[docs]def nodes_for_DTK(filename, nodes): """ Write nodes to a file in JSON format for EMOD Args: filename (str): Name of output file nodes (list): List of :py:class:`emod_api.Demographics.Node.Node` """ with open(filename, "w") as f: json.dump( {"Nodes": [{"NodeID": n.id, "NodeAttributes": n.to_dict()} for n in nodes]}, f, indent=4, )
[docs]def basicNode(lat: float = 0, lon: float = 0, pop: int = int(1e6), name: str = "node_name", forced_id: int = 1): """ A single node with population 1 million """ return Node(lat, lon, pop, name=name, forced_id=forced_id)