def create_merged_bayesian_network_for_event(
event,
prefix,
bayesian_network,
assert_merge_definitions=False,
logger=StdOutLogger(verbose=False)):
merge_def_list = BayesianNetworkMergeUtils.create_merge_definition_list(
event, prefix, merge_singleton_events=False)
logger.log('Merging...', includeTimestamp=True)
logger.set_carriage_reset(True)
count = len(merge_def_list)
for index, merge_def in enumerate(merge_def_list):
logger.log("\rMerging '%s' (%i of %i)" %
(merge_def.get_merged_event(), index + 1, count),
includeTimestamp=True)
merge_defs = DistributionEventMergeDefinitions(
event.name,
bayesian_network,
allow_unspecified_events=True,
assert_merge_definitions=assert_merge_definitions)
merge_defs.set_merge_definitions([merge_def])
bn_wrapper = BayesianNetworkWrapper(bayesian_network)
bayesian_network = bn_wrapper.create_network_with_merged_events(
merge_defs, bake=True)
logger.set_carriage_reset(False)
logger.log('Merging done!', includeTimestamp=True)
return bayesian_network
def instantiate(foldername, logger=StdOutLogger(verbose=False)):
broker = DefaultPersistenceHandler._get_filenames_broker(foldername)
out = DefaultPersistenceHandler._load_cells_from_filename_broker(
broker, logger)
logger.log('Donors loaded from folder ' + foldername,
includeTimestamp=True,
onlyIfVerbose=False)
return out
def checkFloatValBounds(self,
dictKey,
valueString,
lowerBound=None,
upperBound=None):
val = self.configParser.getfloat(dictKey, valueString)
if lowerBound != None:
if val < lowerBound:
val = self.getFloatDefault(dictKey, valueString)
Log.err("value of " + valueString + " must be >= " +
str(lowerBound) + ", using default instead = " +
str(val))
if upperBound != None:
if val > upperBound:
val = self.getFloatDefault(dictKey, valueString)
Log.err("value of " + valueString + " must be <= " +
str(upperBound) + ", using default instead = " +
str(val))
return val
def create_merged_bayesian_network_for_events(
events,
prefixes,
bayesian_network,
assert_merge_definitions=False,
logger=StdOutLogger(verbose=False)):
for event, prefix in zip(events, prefixes):
bayesian_network = BayesianNetworkMergeUtils.create_merged_bayesian_network_for_event(
event, prefix, bayesian_network, assert_merge_definitions,
logger)
return bayesian_network
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 __init__(self, params_fn, marginals_fn, name='', logger=StdOutLogger(verbose=False)):
self._logger = logger
self._params_fn = params_fn
self._marginal_fn = marginals_fn
self._name = name
self._genmodel = GenModel(params_fn, marginals_fn)
self._logger.log('GenModelWrapper.GenModel class loaded (%s, %s)' % (params_fn, marginals_fn),
onlyIfVerbose=True)
self._init_names_and_nicknames()
self._insertion_compositions = self._init_insertion_compositions()
self._insertion_lengths = self._init_insertion_lengths()
self._network_wrapper = self._init_network_wrapper()
self._logger.log('GenModelWrapper loaded', onlyIfVerbose=True)
def __init__(self, logger=StdOutLogger(False)):
self._items = {}
self._models = GenModelWrappers(logger)
self._logger = logger
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 __init__(self, logger=StdOutLogger(verbose=False)):
self._logger = logger
self._gen_model_wrapper = None
self._gen_model = None
def __init__(self, logger=StdOutLogger(verbose=False)):
super(DefaultPersistenceHandler, self).__init__(logger)
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))
def __init__(self, logger=StdOutLogger(verbose=False)):
super(VChoiceContentValidator, self).__init__(logger)
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
merge_defs.set_merge_definitions([merge_def1])
return merge_defs
data_folder = get_testdata_folder()
fn_ced = os.path.join(data_folder, 'models_imgt_ref_dir_sep2019', 'HC')
fn_1363 = os.path.join(fn_ced, '1363_TRB')
out_marginals = os.path.join(fn_1363, '1363_TRB_marginals.txt')
out_params = os.path.join(fn_1363, '1363_TRB_params.txt')
print out_marginals
print out_params
out_marginals = 'C:/CiR/pTCR/IGOR_models/Unproductive_models/models_imgt_ref_dir_sep2019/HC/1365_TRB/1365_TRB_marginals.txt'
out_params = 'C:/CiR/pTCR/IGOR_models/Unproductive_models/models_imgt_ref_dir_sep2019/HC/1365_TRB/1365_TRB_params.txt'
gmw = GenModelWrapper(out_params, out_marginals, '1363_TRB_', StdOutLogger())
gmw.merge_alleles(assert_merge_definitions=True)
bn = gmw.get_bayesian_network_wrapper().get_network()
# truncate_bn = create_truncated_network(bn)
# truncate_bn_wrapper = BayesianNetworkWrapper(truncate_bn)
merge_defs = create_merg_defs(bn)
merged_bayesian_network = gmw.get_bayesian_network_wrapper(
).create_network_with_merged_events(merge_defs, bake=False)
merged_bayesian_network.bake()
bnwrapper = BayesianNetworkWrapper(merged_bayesian_network)
states = {}
n = gmw.get_eventname_for_nickname('v_choice')
state = bnwrapper.get_state(n)
states[n] = state
def __init__(self, logger=StdOutLogger(verbose=False)):
super(DefaultValidator, self).__init__(logger)
self._v_choice_content_validator = VChoiceContentValidator()
self._out = None
self._template = None
def SetConfiguration(self):
"""Reads the values from the config.ini file into a dictionary and returns it.
Returns dict() <str, dyanmic>
"""
try:
self.configParser.read(os.getcwd() + "\\config.ini")
sections = self.configParser.sections()
if len(sections) == 0:
self.__reconstruct()
return self.SetConfiguration()
for section in xrange(len(sections)):
configSettings = dict()
str = sections[section]
if str == "World":
configSettings[
"bIsToroidal"] = self.configParser.getboolean(
str, "bIsToroidal")
configSettings["iGridWidth"] = self.checkIntValBounds(
str, "iGridWidth", 1)
configSettings["iGridHeight"] = self.checkIntValBounds(
str, "iGridHeight", 1)
Worldspace.Configure(configSettings)
elif str == "General":
self.configSettings[
"iNumberOfRuns"] = self.checkIntValBounds(
str, "iNumberOfRuns", 1)
self.configSettings["iRunTime"] = self.checkIntValBounds(
str, "iRunTime", 0)
self.configSettings[
"bDebugTextEnabled"] = self.configParser.getboolean(
str, "bDebugTextEnabled")
elif str == "Interface":
pass
elif str == "ImmuneSystem":
configSettings["fBaseImmCell"] = self.checkFloatValBounds(
str, "fBaseImmCell", 0)
configSettings[
"bIsEnabled"] = self.configParser.getboolean(
str, "bIsEnabled")
configSettings["fRecruitment"] = self.checkFloatValBounds(
str, "fRecruitment", 0)
configSettings["iRecruitDelay"] = self.checkIntValBounds(
str, "iRecruitDelay", 0)
Systems.ImmuneSystem.Configure(configSettings)
elif str == "EpithelialSystem":
configSettings["fInfectInit"] = self.checkFloatValBounds(
str, "fInfectInit", 0)
configSettings[
"bRegenEnabled"] = self.configParser.getboolean(
str, "bRegenEnabled")
configSettings[
"bRandomAge"] = self.configParser.getboolean(
str, "bRandomAge")
Systems.EpithelialSystem.Configure(configSettings)
elif str == "FocusSystem":
configSettings[
"bIsEnabled"] = self.configParser.getboolean(
str, "bIsEnabled")
configSettings[
"iCollisionsForMergePercentage"] = self.checkIntValBounds(
str, "iCollisionsForMergePercentage", 0, 100)
configSettings[
"bDebugTextEnabled"] = self.configParser.getboolean(
str, "bDebugTextEnabled")
Systems.FocusSystem.Configure(configSettings)
elif str == "ImmuneCell":
configSettings["iImmuneLifespan"] = self.checkIntValBounds(
str, "iImmuneLifespan", 0)
Cells.ImmuneCell.Configure(configSettings)
elif str == "EpithelialCell":
configSettings[
"iEpithelialLifespan"] = self.checkIntValBounds(
str, "iEpithelialLifespan", 0)
configSettings["iDivisionTime"] = self.checkIntValBounds(
str, "iDivisionTime", 0)
configSettings["iExpressDelay"] = self.checkIntValBounds(
str, "iExpressDelay", 0)
configSettings["iInfectDelay"] = self.checkIntValBounds(
str, "iInfectDelay", 0)
configSettings["iInfectLifespan"] = self.checkIntValBounds(
str, "iInfectLifespan", 0)
configSettings["fInfectRate"] = self.checkFloatValBounds(
str, "iInfectRate", 0)
Cells.EpithelialCell.Configure(configSettings)
elif str == "SimulationVisualisation":
configSettings[
"bIsEnabled"] = self.configParser.getboolean(
str, "bIsEnabled")
configSettings[
"bSnapshotEnabled"] = self.configParser.getboolean(
str, "bSnapshotEnabled")
configSettings["iSnapshotHeight"] = self.checkIntValBounds(
str, "iSnapshotHeight", 0)
configSettings["iSnapshotWidth"] = self.checkIntValBounds(
str, "iSnapshotWidth", 0)
configSettings["iSquareSize"] = self.checkIntValBounds(
str, "iSquareSize", 1)
configSettings[
"bDebugFocusIdEnabled"] = self.configParser.getboolean(
str, "bDebugFocusIdEnabled")
configSettings[
"bHighlightCollisions"] = self.configParser.getboolean(
str, "bHighlightCollisions")
SimulationVisualization.SimVis.Configure(configSettings)
elif str == "Graph":
configSettings[
"bShowGraphOnFinish"] = self.configParser.getboolean(
str, "bShowGraphOnFinish")
Graph.Graph.Configure(configSettings)
except Exception as e:
if self.reconstruct == False:
Log.err("Error in config file: " + e.message)
Log.err("Restoring to defaults...")
self.__reconstruct()
return self.SetConfiguration()
else:
raise Exception("Failed to reconstruct config.ini file")
return self.configSettings
def __init__(self, logger=StdOutLogger(verbose=False)):
self._logger = logger
self._items = {}
