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Simulator.py
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Simulator.py
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from CellState import CellState
import copy
import pyopencl as cl
import sys
import os
import cPickle
class Simulator:
"""
This class is in charge of running the simulation, creating the various models
and stepping them forward in time. It is the control interface for the gui
or script that is running the simulation.
Stores a map from cell_id to CellState, which stores the current simulation
state of each cell.
Constructed on a user-defined python file. This file implements a
function setup(Simulator, Gui) that constructs the required modules
(Regulator, Signalling, Integrator), and calls Simulator.init(). It
can also create Renderers and add them by calling
Simulator.addRenderer(renderer) so that the simulation can be
visualised.
"""
def __init__(self, moduleName, dt, pickleSteps=50, pickleFileRoot=False):
self.dt = dt
self._next_id = 1
self._next_idx = 0
self.idToIdx = {}
# Map from id to cell state
self.cellStates = {}
self.reg = None
self.phys = None
self.sig = None
self.integ = None
self.renderers = []
self.stepNum = 0
self.savePickle =False
self.pickleSteps = pickleSteps
self.lineage = {}
self.init_cl()
if moduleName:
self.moduleName = moduleName
self.module = __import__(self.moduleName, globals(), locals(), [], -1)
self.module.setup(self)
import time
self.startTime = time.localtime()
self.pickleFileRoot = pickleFileRoot if pickleFileRoot else self.moduleName + '-' + time.strftime('%H-%M-%d-%m-%y', self.startTime)
self.pickleDir = os.path.join('data', self.pickleFileRoot)
os.mkdir(self.pickleDir) # raises OSError if dir already exists
# write a copy of the model into the dir (for reference)
self.moduleStr = open(self.module.__file__, 'rU').read()
open(os.path.join(self.pickleDir, self.moduleName), 'w').write(self.moduleStr)
def next_id(self):
id = self._next_id
self._next_id += 1
return id
def next_idx(self):
idx = self._next_idx
self._next_idx += 1
return idx
# Currently, the user-defined regulation module creates the
# biophysics, regulation, and signalling objects in a function
# setup().
#
# We pass in the empty simulator object, ie. setup(sim)
# and have the user-defined func initialise the 3 modules
def init(self, phys, reg, sig, integ):
self.phys = phys
self.reg = reg
self.sig = sig
self.phys.setRegulator(reg)
if self.reg:
self.reg.setBiophysics(phys)
if integ:
self.integ = integ
self.integ.setRegulator(reg)
if self.sig:
self.sig.setBiophysics(phys)
self.sig.setRegulator(reg)
self.integ.setSignalling(sig)
self.reg.setSignalling(sig)
def init_cl(self):
"""Set up the OpenCL context."""
platform = cl.get_platforms()[0]
if sys.platform == 'darwin':
self.CLContext = cl.Context(devices=[platform.get_devices()[0]])
else:
self.CLContext = cl.Context(properties=[(cl.context_properties.PLATFORM, platform)],
devices=[platform.get_devices()[0]])
self.CLQueue = cl.CommandQueue(self.CLContext)
print (platform.get_devices()[0]).get_info(cl.device_info.DRIVER_VERSION)
def getOpenCL(self):
return (self.CLContext, self.CLQueue)
def setCellStates(self, cellStates):
# Set cell states, e.g. from pickle file
self.cellStates = cellStates
def addRenderer(self, renderer):
self.renderers.append(renderer)
def reset(self):
# Delete the models, they might be holding up memory/GPU resources?
if self.phys:
del self.phys
if self.sig:
del self.sig
if self.integ:
del self.integ
if self.reg:
del self.reg
# Lose old cell states
self.cellStates = {}
# Recreate models via module setup
self.module.setup(self)
#self.phys.reset()
#if self.sig:
# self.sig.reset()
#self.integ.reset()
def divide(self, pState):
pState.divideFlag = False
pid = pState.id
d1id = self.next_id()
d2id = self.next_id()
d1State = copy.copy(pState)
d2State = copy.copy(pState)
d1State.id = d1id
d2State.id = d2id
self.lineage[d1id] = pid
self.lineage[d2id] = pid
# Update CellState map
self.cellStates[d1id] = d1State
self.cellStates[d2id] = d2State
del self.cellStates[pid]
# Update indexing, reuse parent index for d1
d1State.idx = pState.idx
self.idToIdx[d1id] = pState.idx
d2State.idx = self.next_idx()
self.idToIdx[d2id] = d2State.idx
del self.idToIdx[pid]
# Divide the cell in each model
asymm = getattr(pState, 'asymm', [1, 1])
self.phys.divide(pState, d1State, d2State, f1=asymm[0], f2=asymm[1])
if self.integ:
self.integ.divide(pState, d1State, d2State)
self.reg.divide(pState, d1State, d2State)
def addCell(self, cellType=0, **kwargs):
cid = self.next_id()
cs = CellState(cid)
cs.idx = self.next_idx()
cs.cellType = cellType
self.idToIdx[cid] = cs.idx
self.cellStates[cid] = cs
if self.integ:
self.integ.addCell(cs)
if self.reg:
self.reg.addCell(cs)
if self.sig:
self.sig.addCell(cs)
self.phys.addCell(cs, **kwargs)
def step(self):
if self.reg:
self.reg.step(self.dt)
if self.sig:
self.sig.step(self.dt)
self.phys.step(self.dt)
if self.integ:
self.integ.step(self.dt)
states = dict(self.cellStates)
for (cid,state) in states.items():
if state.divideFlag:
self.divide(state)
if self.savePickle and self.stepNum%self.pickleSteps==0:
self.writePickle()
self.stepNum += 1
def writePickle(self):
filename = os.path.join(self.pickleDir, 'step-%05i.pickle' % self.stepNum)
outfile = open(filename, 'wb')
if self.integ:
sigData = (self.sig.gridSize, self.sig.gridOrig, self.integ.gridDim, self.integ.signalLevel.reshape(self.integ.gridDim))
data = (self.cellStates, sigData, self.lineage)
else:
data = (self.cellStates, self.lineage)
cPickle.dump(data, outfile, protocol=-1)