Feature

pyEpiabm/pyEpiabm/core/_compartment_counter.py

@@ -7,7 +7,7 @@
 
 from pyEpiabm.property import InfectionStatus
 
-import pyEpiabm.core
+from .parameters import Parameters
 
 
 class _CompartmentCounter:
@@ -28,9 +28,9 @@ def __init__(self, identifier: str):
         # Identifier
         self._identifier = identifier
         # Number of age groups
-        if pyEpiabm.core.Parameters.instance().use_ages:
+        if Parameters.instance().use_ages:
             self.nb_age_groups =\
-                len(pyEpiabm.core.Parameters.instance().age_proportions)
+                len(Parameters.instance().age_proportions)
         else:
             self.nb_age_groups = 1
 

pyEpiabm/pyEpiabm/core/cell.py

@@ -4,14 +4,15 @@
 
 import typing
 import numpy as np
+import re
 from queue import Queue
 from numbers import Number
 
-from pyEpiabm.core import Parameters
 from pyEpiabm.property import InfectionStatus
 from pyEpiabm.utility import DistanceFunctions
 
 from .microcell import Microcell
+from .parameters import Parameters
 from .person import Person
 from ._compartment_counter import _CompartmentCounter
 
@@ -31,7 +32,7 @@ def __init__(self, loc: typing.Tuple[float, float] = (0, 0)):
 
         """
         self.location = loc
-        self.id = hash(self)
+        self.id = str(hash(self))
         self.microcells = []
         self.persons = []
         self.places = []
@@ -70,15 +71,31 @@ def add_microcells(self, n):
         for _ in range(n):
             self.microcells.append(Microcell(self))
 
-    def set_id(self, id: float):
-        """Updates ID of cell (i.e. for input from file).
+    def set_id(self, id: str, cells: typing.List):
+        """Updates id of current cell (i.e. for input from file).
 
         Parameters
         ----------
-        id : float
+        id : str
             Identity of cell
+        cells : list
+            List of all current cells
 
         """
+        # Ensure id is a string
+        if not isinstance(id, str):
+            raise TypeError("Provided id must be a string")
+
+        # This regex will match on any string which has 1 or more digits
+        if not re.match("^\\d+$", id):
+            raise ValueError(f"Invalid id: {id}. id must be of the form 'i' "
+                             f"where i is an integer")
+
+        # Finally, check for duplicates
+        cell_ids = [cell.id for cell in cells]
+        if id in cell_ids:
+            raise ValueError(f"Duplicate id: {id}.")
+
         self.id = id
 
     def enqueue_person(self, person: Person):

pyEpiabm/pyEpiabm/core/household.py

@@ -4,6 +4,7 @@
 
 import typing
 from numbers import Number
+import re
 
 from pyEpiabm.property import InfectionStatus
 
@@ -37,6 +38,7 @@ def __init__(self, microcell, loc: typing.Tuple[float, float],
         self.cell = microcell.cell
         self.microcell = microcell
         self.isolation_location = False
+        self.id = self.microcell.id + "." + str(len(self.microcell.households))
 
         if not (len(loc) == 2 and isinstance(loc[0], Number) and
                 isinstance(loc[1], Number)):
@@ -104,3 +106,34 @@ def remove_household(self):
         """
         self.microcell.households.remove(self)
         self.cell.households.remove(self)
+
+    def set_id(self, id: str):
+        """Updates id of current household (i.e. for input from file).
+        Format of id - for example 3.1.2 represents household 2 within
+        microcell 1 within cell 3. The id will only be changed if it has the
+        correct expression.
+
+        Parameters
+        ----------
+        id : str
+            Identity of household
+
+        """
+
+        # Ensure id is a string
+        if not isinstance(id, str):
+            raise TypeError("Provided id must be a string")
+
+        # This regex will match on any string which takes the form "i.j.k"
+        # where i, j and k are integers
+        if not re.match("^\\d+\\.\\d+\\.\\d+$", id):
+            raise ValueError(f"Invalid id: {id}. id must be of the form "
+                             f"'i.j.k' where i, j, k are integers")
+
+        # Finally, check for duplicates
+        household_ids = [household.id
+                         for household in self.microcell.households]
+        if id in household_ids:
+            raise ValueError(f"Duplicate id: {id}.")
+
+        self.id = id

pyEpiabm/pyEpiabm/core/microcell.py

@@ -5,6 +5,7 @@
 import typing
 from numbers import Number
 import logging
+import re
 
 from pyEpiabm.property import InfectionStatus
 
@@ -24,6 +25,7 @@ class Microcell:
         An instance of :class:`Cell`
 
     """
+
     def __init__(self, cell):
         """Constructor Method.
 
@@ -33,12 +35,12 @@ def __init__(self, cell):
             Microcell's parent :class:`Cell` instance
 
         """
-        self.id = hash(self)
         self.persons = []
         self.places = []
         self.households = []
         self.cell = cell
         self.location = cell.location
+        self.id = self.cell.id + "." + str(len(self.cell.microcells))
         self.compartment_counter = _CompartmentCounter(
             f"Microcell {id(self)}")
 
@@ -52,17 +54,33 @@ def __repr__(self):
 
         """
         return f"Microcell with {len(self.persons)} people" + \
-            f" at location {self.location}."
+               f" at location {self.location}."
 
     def set_id(self, id):
-        """Updates ID of microcell (i.e. for input from file).
+        """Updates id of current microcell (i.e. for input from file).
 
         Parameters
         ----------
-        id : float
+        id : str
             Identity of microcell
 
         """
+
+        # Ensure id is a string
+        if not isinstance(id, str):
+            raise TypeError("Provided id must be a string")
+
+        # This regex will match on any string which takes the form "i.j" where
+        # i and j are integers
+        if not re.match("^\\d+\\.\\d+$", id):
+            raise ValueError(f"Invalid id: {id}. id must be of the form 'i.j' "
+                             f"where i, j are integers")
+
+        # Finally, check for duplicates
+        microcell_ids = [microcell.id for microcell in self.cell.microcells]
+        if id in microcell_ids:
+            raise ValueError(f"Duplicate id: {id}.")
+
         self.id = id
 
     def add_person(self, person):
@@ -123,27 +141,40 @@ def add_place(self, n: int, loc: typing.Tuple[float, float],
             self.cell.places.append(p)
             self.places.append(p)
 
-    def add_household(self, people: list):
+    def add_household(self, people: list, update_person_id: bool = True):
         """Adds a default :class:`Household` to Microcell and fills it with
         a number of :class:`Person` s.
 
         Parameters
         ----------
         people : list
             List of :class:`People` to add to household
+        update_person_id : bool
+            Boolean representing whether we wish to update the id of the
+            people of the household when the function is called or not
 
         """
         if len(people) != 0:
             household = Household(self, loc=self.location)
-            for person in people:
+            for i, person in enumerate(people):
                 household.add_person(person)
+
+                if update_person_id:
+                    person.set_id(household.id + "." + str(i))
+                else:
+                    # If the person already has a household, then do not change
+                    # their id
+                    logging.info(f"Person {person.id} has moved to "
+                                 f"household {household.id} but has "
+                                 f"not changed id")
+
         else:
             logging.info("Cannot create an empty household")
 
     def notify_person_status_change(
-            self,
-            old_status: InfectionStatus,
-            new_status: InfectionStatus,
+        self,
+        old_status: InfectionStatus,
+        new_status: InfectionStatus,
             age_group) -> None:
         """Notify Microcell that a person's status has changed.
 
@@ -177,8 +208,8 @@ def set_location(self, loc: typing.Tuple[float, float]):
 
     def count_icu(self):
         return sum(map(lambda person: person.infection_status ==
-                   InfectionStatus.InfectICU, self.persons))
+                       InfectionStatus.InfectICU, self.persons))
 
     def count_infectious(self):
         return sum(map(lambda person: person.is_infectious() is
-                   True, self.persons))
+                       True, self.persons))

pyEpiabm/pyEpiabm/core/person.py

@@ -3,6 +3,7 @@
 #
 
 import random
+import re
 
 from pyEpiabm.property import InfectionStatus
 
@@ -54,6 +55,8 @@ def __init__(self, microcell, age_group=None):
         self.key_worker = False
         self.date_positive = None
         self.is_vaccinated = False
+        self.id = self.microcell.id + "." + "." + \
+            str(len(self.microcell.persons))
 
         self.set_random_age(age_group)
 
@@ -110,7 +113,7 @@ def is_susceptible(self):
             Whether person is currently susceptible
 
         """
-        return self.infection_status == InfectionStatus.\
+        return self.infection_status == InfectionStatus. \
             Susceptible
 
     def __repr__(self):
@@ -214,12 +217,43 @@ def remove_person(self):
         Used to remove travellers from the population.
 
         """
-        self.microcell.cell.compartment_counter.\
+        self.microcell.cell.compartment_counter. \
             _increment_compartment(-1, self.infection_status,
                                    self.age_group)
-        self.microcell.compartment_counter.\
+        self.microcell.compartment_counter. \
             _increment_compartment(-1, self.infection_status,
                                    self.age_group)
         self.microcell.cell.persons.remove(self)
         self.microcell.persons.remove(self)
         self.household.persons.remove(self)
+
+    def set_id(self, id: str):
+        """Updates id of current person (i.e. for input from file).
+        id format: 4.3.2.1 represents cell 4, microcell 3 within this cell,
+        household 2 within this microcell, and person 1 within this
+        household. The id will only be changed if it is of the correct format.
+
+        Parameters
+        ----------
+        id : str
+            Identity of person
+
+        """
+
+        # Ensure id is a string
+        if not isinstance(id, str):
+            raise TypeError("Provided id must be a string")
+
+        # This regex will match on any string which takes the form "i.j.k.l"
+        # where i, j, k and l are integers (k can be empty)
+        if not re.match("^\\d+\\.\\d+\\.\\d*\\.\\d+$", id):
+            raise ValueError(f"Invalid id: {id}. id must be of the form "
+                             f"'i.j.k.l' where i, j, k, l are integers (k"
+                             f"can be empty)")
+
+        # Finally, check for duplicates
+        person_ids = [person.id for person in self.microcell.persons]
+        if id in person_ids:
+            raise ValueError(f"Duplicate id: {id}.")
+
+        self.id = id

pyEpiabm/pyEpiabm/core/population.py

@@ -42,9 +42,10 @@ def add_cells(self, n):
             Number of empty :class:`Cell` s to add
 
         """
+        base_num = len(self.cells)
         for i in range(n):
             self.cells.append(Cell())
-            self.cells[i].set_id(i)
+            self.cells[i + base_num].set_id(str(i + base_num), self.cells)
 
     def total_people(self):
         """Returns the total number of people in the population.

pyEpiabm/pyEpiabm/intervention/travel_isolation.py

@@ -1,7 +1,7 @@
 #
 # Travel isolation Class
 #
-
+import logging
 import random
 
 from pyEpiabm.core import Parameters
@@ -75,6 +75,11 @@ def __call__(self, time):
                                     selected_household = random.choice(
                                         existing_households)
                                     selected_household.add_person(person)
+                                    logging.info(f"Person {person.id} has "
+                                                 f"finished isolating and "
+                                                 f"has moved to household "
+                                                 f"{selected_household.id}")
+
                                 else:
                                     person.household.isolation_location = \
                                         False
@@ -91,9 +96,10 @@ def __call__(self, time):
                                 if len(person.household.persons) > 1:
                                     # Remove from old household
                                     person.household.persons.remove(person)
-                                    # Put in new household
+                                    # Move to temporary household
+                                    # N.B Person ID is not changed
                                     person.microcell.add_household([
-                                        person])
+                                        person], update_person_id=False)
                                     person.household.isolation_location = \
                                         True
                                 else: