def initialise(self):
"""Initialisation method for EpithelialSystem, run only once when first created. Sets up the world's epithelial """
initialInfected = int(
(Worldspace.GRID_WIDTH * Worldspace.GRID_HEIGHT) *
self.INFECT_INIT) if int(
(Worldspace.GRID_WIDTH * Worldspace.GRID_HEIGHT) *
self.INFECT_INIT) > 1 else 1
self.initialInfected = initialInfected
self.containingCount = initialInfected
self.healthyCount = (Worldspace.GRID_WIDTH *
Worldspace.GRID_HEIGHT) - initialInfected
# Create epithelial cell at every site, add to system's cell list
for i in xrange(Worldspace.GRID_WIDTH):
for j in xrange(Worldspace.GRID_HEIGHT):
tempECell = EpithelialCell(Vector2d(i, j))
if EpithelialSystem.RANDOM_AGE:
tempECell.age = RNG.randint(0,
EpithelialCell.CELL_LIFESPAN)
self.world[i][j].eCell = tempECell
self.cells.append(tempECell)
# Set random epithelial cells to containing for initial infected count
while initialInfected > 0:
randomx = RNG.randint(0, Worldspace.GRID_WIDTH - 1)
randomy = RNG.randint(0, Worldspace.GRID_HEIGHT - 1)
tempECell = self.world[randomx][randomy].getECell()
if tempECell.State == EpithelialStates.HEALTHY:
tempECell.State = EpithelialStates.CONTAINING
if FocusSystem.ENABLED:
self.fSys.addNewFocus(tempECell)
initialInfected -= 1
def initialise(self):
"""Create the initial density of virgin cells in the worldspace, and add them to the system's cell list."""
for i in range(ImmuneSystem.INIT_CELLS):
x = RNG.randint(0, Worldspace.GRID_WIDTH - 1)
y = RNG.randint(0, Worldspace.GRID_HEIGHT - 1)
cell = ImmuneCell(Vector2d(x, y))
cell.age = RNG.randint(0, ImmuneCell.IMM_LIFESPAN)
self.cells.append(cell)
self.world[x][y].getImmCells().append(cell)
self.virginCount += 1
def __updateMaintenance(self):
"""Private method, should only be called from public update() method. Creates new virgin immune cells to maintain minimum density as required."""
cell = None
while self.virginCount < self.INIT_CELLS:
x = RNG.randint(0, Worldspace.GRID_WIDTH - 1)
y = RNG.randint(0, Worldspace.GRID_HEIGHT - 1)
cell = ImmuneCell(Vector2d(x, y))
self.world[x][y].getImmCells().append(cell)
self.cells.append(cell)
self.virginCount += 1
def setUp(self):
Systems.ImmuneSystem.BASE_IMM_CELL = 0.00015
Systems.EpithelialSystem.INFECT_INIT = 0.01
Worldspace.GRID_WIDTH = 3
Worldspace.GRID_HEIGHT = 3
Cells.ImmuneCell.IMM_LIFESPAN = 1008
self.world = []
for x in xrange(Worldspace.GRID_WIDTH):
self.world.append([])
for y in xrange(Worldspace.GRID_HEIGHT):
self.world[x].append(Worldsite(Vector2d(x, y)))
self.eSys = Systems.EpithelialSystem(self.world)
self.iSys = Systems.ImmuneSystem(self.world)
def __updateRecruitment(self):
"""Private method, should only be called from public update() method. Creates new immune cells randomly about the Worldspace as required."""
cell = None
for i in xrange(len(self.recruitmentTimes) - 1, -1, -1):
self.recruitmentTimes[i] += 1
if self.recruitmentTimes[i] >= ImmuneSystem.RECRUITMENT_DELAY:
del self.recruitmentTimes[i]
self.currentRecruitment += ImmuneSystem.RECRUITMENT
if self.currentRecruitment >= 1:
self.currentRecruitment -= 1
x = RNG.randint(0, Worldspace.GRID_WIDTH - 1)
y = RNG.randint(0, Worldspace.GRID_HEIGHT - 1)
cell = ImmuneCell(Vector2d(x, y))
ImmuneSystem.setNextState(cell, ImmuneStates.MATURE)
self.matureCount += 1
self.world[x][y].getImmCells().append(cell)
self.cells.append(cell)
def run(self, settings):
"""Main loop."""
self.avgFociAreaMM2 = None
if Graph.SHOW:
data = SimulationData()
graph = OverallSimulationDataGraph()
graph.setXMeasurement('hours')
graph.setTimestepsInXMeasurement(6)
fociAreaGraph = FociAreaGraph()
#fociAreaGraph = FociAreaGraph(True, Worldspace.GRID_WIDTH, Worldspace.GRID_HEIGHT)
fociAreaGraph.setXMeasurement('hours')
fociAreaGraph.setTimestepsInXMeasurement(6)
if SimVis.ENABLED:
q.put((simVis.display, (), {}))
self.numberOfRuns = settings["iNumberOfRuns"]
self.runTime = settings["iRunTime"]
self.debugTextEnabled = settings["bDebugTextEnabled"]
#initialise runs
run = 0
while run < self.numberOfRuns:
if self.debugTextEnabled:
startTime = time.clock()
Log.out("Start time: %s" % startTime)
#re-initialize world and systems if not on the initial run
world = []
for x in xrange(Worldspace.GRID_WIDTH):
world.append([])
for y in xrange(Worldspace.GRID_HEIGHT):
world[x].append(Worldsite(Vector2d(x, y)))
eSys = Systems.EpithelialSystem(world)
immSys = Systems.ImmuneSystem(world)
eSys.initialise()
if (Systems.ImmuneSystem.ISENABLED):
immSys.initialise()
if Graph.SHOW:
graph.setTotalEpithelialCells(Worldspace.GRID_WIDTH *
Worldspace.GRID_HEIGHT)
graph.setBaseImmuneCells(immSys.INIT_CELLS)
graph.initRun()
fociAreaGraph.initRun()
if SimVis.ENABLED:
simVis.init(world, run + 1)
# Run simulation for a given number of timesteps
# 10 days = 1440 timesteps
timesteps = 0
while timesteps <= self.runTime:
eSys.update()
if (Systems.ImmuneSystem.ISENABLED):
immSys.update()
eSys.synchronise()
if (Systems.ImmuneSystem.ISENABLED):
immSys.synchronise()
if Graph.SHOW:
data.time = timesteps
data.eCellsHealthy = eSys.healthyCount
data.eCellsContaining = eSys.containingCount
data.eCellsExpressing = eSys.expressingCount
data.eCellsInfectious = eSys.infectiousCount
data.eCellsDead = eSys.naturalDeathCount + eSys.infectionDeathCount
data.immCellsTotal = immSys.virginCount + immSys.matureCount
graph.addSimulationData(data)
if (Systems.FocusSystem.ENABLED):
area = 0.0
c = 0
for foci in eSys.fSys.foci.values():
if foci.isEnabled:
if foci.cellCount != 0:
area += foci.cellCount
c += 1
if c == 0:
area = 0
else:
area = area / c
self.avgFociAreaMM2 = fociAreaGraph.addAverageFociAreaData(
area, timesteps)
if self.debugTextEnabled:
Log.out('%d: %d' % (run + 1, timesteps))
Log.out("Infected cells: %s" %
(eSys.containingCount + eSys.expressingCount +
eSys.infectiousCount))
Log.out("Healthy: %s" % (eSys.healthyCount))
Log.out("Containing: %s" % (eSys.containingCount))
Log.out("Expressing: %s" % (eSys.expressingCount))
Log.out("Infectious: %s" % (eSys.infectiousCount))
Log.out(
"Dead: %s" %
(eSys.naturalDeathCount + eSys.infectionDeathCount))
Log.out("Virgin: %s" % (immSys.virginCount))
Log.out("Mature: %s" % (immSys.matureCount))
if Systems.FocusSystem.ENABLED and self.avgFociAreaMM2 != None:
#Log.out("Average focus area: %s" % (eSys.avgFociArea))
Log.out("Average focus area (mm2): %s" %
(self.avgFociAreaMM2))
Log.out("\n")
if SimVis.ENABLED:
if timesteps == 0 or timesteps % 72 == 0:
simVis.drawSimWorld(True, timesteps)
else:
simVis.drawSimWorld(False, timesteps)
if Systems.FocusSystem.ENABLED:
if len(eSys.fSys.mergeDetected) > 0:
for i in xrange(
len(eSys.fSys.mergeDetected) - 1, -1, -1):
if SimVis.HIGHLIGHT_COLLISIONS:
focus = eSys.fSys.mergeDetected[i]
for perimeterCell in focus.perimeter:
simVis.drawCollision(perimeterCell)
del eSys.fSys.mergeDetected[i]
# HACK: For debugging/testing purposes. Will be removed/refactored soon.
if SimVis.HIGHLIGHT_COLLISIONS and SimVis.ENABLED:
simVis._SimVis__savePILImageToFile(False)
simVis._SimVis__updateCanvas(False)
#if Systems.FocusSystem.DEBUG_TEXT_ENABLED:
#raw_input()
timesteps += 1
if (Systems.FocusSystem.ENABLED):
if self.debugTextEnabled:
out = "remaining usable foci: "
c = 0
for focus in eSys.fSys.foci.values():
if focus.isEnabled and focus.cellCount > 0:
c += 1
out += str(focus.id) + ", "
Log.out(out + " count = " + str(c) + "\n")
if self.debugTextEnabled:
endTime = time.clock()
Log.out("End time: %s" % endTime)
Log.out("Elapsed time: %s" % (endTime - startTime))
#increment run
run += 1
# All runs finished: display results graph
if Graph.SHOW:
if (Systems.FocusSystem.ENABLED):
q.put((fociAreaGraph.showGraph, ([True]), {}))
q.put((graph.showGraph, ([True]), {}))
running = False
def setUp(self):
self.testsite = Worldsite(Vector2d(2,2))
self.testsite.eCell = EpithelialCell(Vector2d(2,2))
self.testsite.immCells = [ImmuneCell(Vector2d(2,2))]