def __updateCollisions(self):
"""This is a private method, and should only be called from the public update() method. Discovers collisions and determines merges."""
for focus in self.foci.values():
if focus.isEnabled:
collisions = {}
for i in xrange(len(focus.perimeter)):
perimeterCell = focus.perimeter[i]
perimeterNeighbours = Worldspace.getMooreNeighbours(
self.world, perimeterCell.location,
EpithelialStates.INFECTION_DEATH)
for neighbour in perimeterNeighbours:
if neighbour.focusId != perimeterCell.focusId:
if collisions.has_key(neighbour.focusId):
if not (neighbour.location
in collisions[neighbour.focusId]):
collisions[neighbour.focusId].append(
neighbour.location)
else:
continue
else:
collisions[neighbour.focusId] = [
neighbour.location
]
for collisionList in collisions.values():
collisionCount = len(collisionList)
if collisionCount > (
len(focus.perimeter) *
(FocusSystem.COLLISION_MERGE_PERCENTAGE / 100.0)
if len(focus.perimeter) *
(FocusSystem.COLLISION_MERGE_PERCENTAGE / 100.0) > 1
else 1):
focus.isEnabled = False
if FocusSystem.DEBUG_TEXT_ENABLED:
Log.out("Merge detected on Focus #%s" % focus.id)
self.mergeDetected.append(focus)
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 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 __debugPrint(self):
"""Debug method, to be removed. Prints the focus by id and it's area."""
for focus in self.foci.values():
if focus.isEnabled:
Log.out("Focus #%s: %s" % (focus.id, focus.cellCount))
