def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, max_cells=max_cells, max_contacts=32, max_sqs=128**2, jitter_z=False, reg_param=2, gamma=10)
biophys.addPlane((0,0,-0.5), (0,0,1), 0.2)
biophys.addPlane((0,0,0.5), (0,0,-1), 1e-4)
regul = ModuleRegulator(sim, __file__) # use this file for reg too
# Only biophys and regulation
sim.init(biophys, regul, None, None)
#sim.addCell(cellType=0, pos=(0,0,0))
#load data from pickle file
import cPickle
data = cPickle.load(open('data/BiofilmWallLessCrash_no_alternation_9-12-56-25-09-12/step-00700.pickle','r'))
cellStates = data[0]
print "Loading %i cells"%len(cellStates)
sim.cellStates = cellStates
regul.cellStates = cellStates
biophys.load_from_cellstates(cellStates)
idx_map = {}
for id,state in sim.cellStates.iteritems():
idx_map[state.id] = state.idx
sim.idToIdx = idx_map
# parents = data[1]
# for id,state in sim.cellStates.iteritems():
# p = lineage(parents, [1,2], id)
# if p == 1: state.color = [0, 1, 0]
# elif p == 2: state.color = [0, 0, 1]
#import numpy.random
#cellcols = numpy.random.uniform(0,1,81*3)
#cellcols.shape = (81,3)
#for id,state in sim.cellStates.iteritems():
# state.color = list(cellcols[state.cellType,:])
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, max_cells=max_cells, max_contacts=32, max_sqs=64**2, jitter_z=False, reg_param=2)
regul = ModuleRegulator(sim, __file__) # use this file for reg too
sim.init(biophys, regul, None, None)
# load from pickle file
import pickle
(cs, lineage) = pickle.load(open('data/biophysCL-01-03-13-04-12/step-02450.pickle','r'))
print "Loading %i cells..."%len(cs)
sim.setCellStates(cs)
biophys.load_from_cellstates(cs)
#for (i,cell) in sim.cellStates.items():
# cell.color = [0.1, 0.1+1000.0*cell.species[3],
# 0.1+200.0*cell.species[4]]
# for (i,cell) in sim.cellStates.items():
# cell.color = [0.1, cell.species[3]*0.1, cell.species[4]*0.1]
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
