Merge pull request #58 from SABS-R3-Epidemiology/spatial-weighting

Spatial weighting

pyEpiabm/docs/source/index.rst

@@ -21,6 +21,7 @@ Contents
     properties
     routines
     sweeps
+    utility
 
 
 Search

pyEpiabm/docs/source/utility.rst

@@ -0,0 +1,15 @@
+*********
+Utilities
+*********
+
+.. currentmodule:: pyEpiabm.utility
+
+Utilites provides various methods that don't act on a population directly.
+
+Overview:
+
+- :class:`DistanceFunctions`
+
+.. autoclass:: DistanceFunctions
+    :members:
+

pyEpiabm/pyEpiabm/__init__.py

@@ -15,6 +15,7 @@
 from . import property
 from . import routine
 from . import sweep
+from . import utility
 
 # Expose modules in core within pyEpiabm namespace
 

pyEpiabm/pyEpiabm/core/_compartment_counter.py

@@ -28,15 +28,6 @@ def identifier(self):
         """
         return self._identifier
 
-    def initialize(self, n_people) -> None:
-        """Initialize Compartments with n_people susceptible and 0 in all
-        of compartments (i.e. for all other InfectionStatus).
-
-        :param n_people: Number of people CompartmentCounter is tracking
-        :type n_people: int
-        """
-        self._compartments[InfectionStatus.Susceptible] = n_people
-
     def report(self, old_status: InfectionStatus,
                new_status: InfectionStatus) -> None:
         """Report Person has changed state.
@@ -47,9 +38,23 @@ def report(self, old_status: InfectionStatus,
         :param new_status: Person's new infection state
         :type new_status: InfectionStatus
         """
+        if self._compartments[old_status] <= 0:
+            raise ValueError("No people of this status in this cell.")
         self._compartments[old_status] -= 1
         self._compartments[new_status] += 1
 
+    def _increment_compartment(self, n_persons: int,
+                               infection_status: InfectionStatus) -> None:
+        """Funtion to add a block of people with the same infection status
+        to a compartment.
+
+        :param n_person: number of people being added to cell or microcell
+        :type n_person: int
+        :param infection_status: status of people being added
+        :type infection_status: InfectionStatus
+        """
+        self._compartments[infection_status] += n_persons
+
     def retrieve(self) -> typing.Dict[InfectionStatus, int]:
         """Get Compartment Counts.
         Returns dictionary of compartment counts.

pyEpiabm/pyEpiabm/core/cell.py

@@ -30,6 +30,10 @@ def __init__(self, loc: typing.Tuple[float, float] = (0, 0)):
         self.person_queue = Queue()
         self.compartment_counter = _CompartmentCounter(f"Cell {id(self)}")
 
+        if not (len(loc) == 2 and isinstance(loc[0], (float, int)) and
+                isinstance(loc[1], (float, int))):
+            raise ValueError("Location must be a tuple of float-type")
+
     def __repr__(self):
         """Returns a string representation of the Cell.
 
@@ -48,14 +52,6 @@ def add_microcells(self, n):
         for i in range(n):
             self.microcells.append(Microcell(self))
 
-    def set_location(self, loc: typing.Tuple[float, float]):
-        """Updates location of cell (used in population configuration).
-
-        :param loc: Location of the cell, as an (x,y) tuple
-        :type loc: Tuple(float, float)
-        """
-        self.location = loc
-
     def set_id(self, id: float):
         """Updates ID of cell (i.e. for input from file).
 
@@ -72,14 +68,6 @@ def enqueue_person(self, person: Person):
         """
         self.person_queue.put(person)
 
-    def _setup(self) -> None:
-        """Setup method. Should be called once Population has been setup.
-        Called by population (doesn't need to be called manually).
-        """
-        self.compartment_counter.initialize(len(self.persons))
-        for mcell in self.microcells:
-            mcell._setup()
-
     def notify_person_status_change(
             self,
             old_status: InfectionStatus,
@@ -106,3 +94,11 @@ def number_infectious(self):
                            + cell_data[InfectionStatus.InfectGP])
 
         return total_infectors
+
+    def set_location(self, loc: typing.Tuple[float, float]):
+        """Method to set or change the location of a cell.
+
+        :param loc: (x,y) coordinates of the place
+        :type loc: Tuple[float, float]
+        """
+        self.location = loc

pyEpiabm/pyEpiabm/core/household.py

@@ -29,6 +29,10 @@ def __init__(self, loc: typing.Tuple[float, float] = (1.0, 1.0),
         self.susceptibility = susceptibility
         self.infectiousness = infectiousness
 
+        if not (len(loc) == 2 and isinstance(loc[0], (float, int)) and
+                isinstance(loc[1], (float, int))):
+            raise ValueError("Location must be a tuple of float-type")
+
     def __repr__(self):
         """Returns a string representation of Household.
 

pyEpiabm/pyEpiabm/core/microcell.py

@@ -55,11 +55,13 @@ def add_people(self, n, status=InfectionStatus.Susceptible):
         :param status: Status of persons to add to cell
         :type status: InfectionStatus
         """
-        for i in range(n):
+        self.compartment_counter._increment_compartment(n, status)
+        self.cell.compartment_counter._increment_compartment(n, status)
+        for _ in range(n):
             p = Person(self)
-            p.update_status(status)
             self.cell.persons.append(p)
             self.persons.append(p)
+            p.infection_status = status
 
     def add_place(self, n: int, loc: typing.Tuple[float, float],
                   place_type):
@@ -73,12 +75,6 @@ def add_place(self, n: int, loc: typing.Tuple[float, float],
             self.cell.places.append(p)
             self.places.append(p)
 
-    def _setup(self) -> None:
-        """Setup method. Should be called once Population has been setup.
-        Called by population (doesn't need to be called manually).
-        """
-        self.compartment_counter.initialize(len(self.persons))
-
     def notify_person_status_change(
             self,
             old_status: InfectionStatus,

pyEpiabm/pyEpiabm/core/place.py

@@ -40,6 +40,10 @@ def __init__(self, loc: typing.Tuple[float, float],
         if not (self.microcell.cell == self.cell):
             raise KeyError("Microcell is not contained in cell")
 
+        if not (len(loc) == 2 and isinstance(loc[0], (float, int)) and
+                isinstance(loc[1], (float, int))):
+            raise ValueError("Location must be a tuple of float-type")
+
     def set_max_cap(self, max_capacity: int):
         """Sets the maximum capacity of a place.
 

pyEpiabm/pyEpiabm/core/population.py

@@ -31,12 +31,6 @@ def add_cells(self, n):
         for i in range(n):
             self.cells.append(Cell())
 
-    def setup(self) -> None:
-        """Setup method. Should be called once Population has been setup.
-        """
-        for cell in self.cells:
-            cell._setup()
-
     def total_people(self):
         """Returns the total number of people in the population.
         Will obviously match the configuration parameter, but useful

pyEpiabm/pyEpiabm/routine/file_population_config.py

@@ -92,7 +92,6 @@ def make_pop(input_file: str, random_seed: int = None):
                 FilePopulationFactory.add_households(new_microcell,
                                                      households)
 
-        new_pop.setup()
         return new_pop
 
     @staticmethod

pyEpiabm/pyEpiabm/routine/spatial_infection.py

@@ -2,7 +2,6 @@
 # Calculate spatial force of infection based on Covidsim code
 #
 
-import random
 from pyEpiabm.core import Person, Cell, Parameters
 
 
@@ -25,17 +24,10 @@ def cell_inf(inf_cell: Cell, timestep: int):
         R_0 = Parameters.instance().basic_reproduction_num
         total_infectors = inf_cell.number_infectious()
 
-        number_to_infect = total_infectors * R_0
-        # This gives a possible decimal for number to infect.
-        # Choose randomly for the integers either side
-        # with weights corrsponding to the distance to either
-        # integer.
-        floor = int(number_to_infect)
-
-        weights = [number_to_infect - floor, 1 - (number_to_infect - floor)]
-        number_to_infect = random.choices([floor, floor + 1],
-                                          weights=weights, k=1)[0]
-        return (number_to_infect)
+        average_number_to_infect = total_infectors * R_0
+        # This gives the expected number of infection events
+        # caused by people within this cell.
+        return (average_number_to_infect)
 
     @staticmethod
     def space_susc(susc_cell: Cell, infectee: Person,

pyEpiabm/pyEpiabm/routine/toy_population_config.py

@@ -81,7 +81,6 @@ def make_pop(pop_params: typing.Dict):
         if place_number > 0:
             ToyPopulationFactory.add_places(new_pop, place_number)
 
-        new_pop.setup()
         return new_pop
 
     @staticmethod