def __init__(self,_simulator,_frequency=1):
SteppableBasePy.__init__(self,_simulator,_frequency)
if save_flag:
if template_flag:
trackers['start_tracker'] = Tracker2( file_name = save_dir+'/start_cells_'+time_info+'.csv' , template = TEMPLATES['start_tracker'] )
print 'loaded start template'
else:
trackers['start_tracker'] = Tracker2( file_name = save_dir+'/start_cells_'+time_info+'.csv')
def __init__(self,_simulator,_frequency=1):
MitosisSteppableBase.__init__(self,_simulator, _frequency)
if save_flag:
if template_flag:
preprocessor = TrackerPreprocessor( generate_divison_preprocessor(start_time=49999, remove_roots=True) )
trackers['mitosis_tracker'] = Tracker2( file_name=save_dir+'/division_events_'+time_info+'.csv' , template=TEMPLATES['mitosis_tracker'] , preprocessor=preprocessor )
print 'loaded mitosis_tracker'
else:
trackers['mitosis_tracker'] = Tracker2( file_name=save_dir+'/division_events_'+time_info+'.csv' )
def __init__(self,_simulator,_frequency=100):
SteppableBasePy.__init__(self,_simulator,_frequency)
if save_flag:
if template_flag:
trackers['cell_tracker'] = Tracker2( file_name = save_dir+'/cell_count_'+time_info+'.csv' , template = TEMPLATES['cell_tracker'] )
trackers['volume_tracker'] = Tracker2( file_name = save_dir+'/volume_'+time_info+'.csv' , template = TEMPLATES['volume_tracker'] )
print 'cell and volume trackers'
else:
trackers['cell_tracker'] = Tracker2( file_name = save_dir+'/cell_count_'+time_info+'.csv' )
trackers['volume_tracker'] = Tracker2( file_name = save_dir+'/volume_'+time_info+'.csv' )
def __init__(self,_simulator,_frequency=100):
SteppableBasePy.__init__(self,_simulator,_frequency)
if save_flag:
if template_flag:
preprocessor = TrackerPreprocessor( generate_logger_preprocessor( start_time = 49999 ) )
trackers['cell_tracker'] = Tracker2( file_name = save_dir+'/cell_count_'+time_info+'.csv' , template = TEMPLATES['cell_tracker'] , preprocessor=preprocessor)
trackers['volume_tracker'] = Tracker2( file_name = save_dir+'/volume_'+time_info+'.csv' , template = TEMPLATES['volume_tracker'] , preprocessor=preprocessor)
print 'cell and volume trackers'
else:
trackers['cell_tracker'] = Tracker2( file_name = save_dir+'/cell_count_'+time_info+'.csv' )
trackers['volume_tracker'] = Tracker2( file_name = save_dir+'/volume_'+time_info+'.csv' )
def finish(self):
if save_flag:
tracker = Tracker2( file_name = save_dir+'/finish_cells_'+time_info+'.csv' )
for cell in self.cellList:
z = cell.zCOM
y = cell.yCOM
x = cell.xCOM
tracker.stash( [ cell.id , cell.type , x , y , z ] )
tracker.save_stash() # save final cell data
trackers['start_tracker'].save_stash() # save initial cell data
save_genomes2( [ genome[1] for genome in genomes.items() ] , file_name = save_dir+'/genomes_'+time_info+'.csv' ) #save genomes
def step(self, mcs):
print "INSIDE DEATH CHECK STEPPABLE"
for cell in self.cellList:
z = cell.zCOM
y = cell.yCOM
x = cell.xCOM
if cell.type == self.DEAD: continue
if not ((x >= LATTICE['x_min'] and x <= LATTICE['x_max']) and
(y >= LATTICE['y_min'] and y <= LATTICE['y_max'])):
if cell.type == self.CANCER1 or cell.type == self.CANCER2:
if save_flag:
# save the final positions of all cells.
tracker = Tracker2(file_name=save_dir +
'/finish_cells_' + time_info +
'.csv')
for cell in self.cellList:
z = cell.zCOM
y = cell.yCOM
x = cell.xCOM
tracker.stash([cell.id, cell.type, x, y, z])
tracker.save_stash() # save final cell data
# save all the genomes
save_genomes2(
[genome[1] for genome in genomes.items()],
file_name=save_dir + '/genomes_' + time_info +
'.csv') #save genomes
#save all the trackers
for tracker_name, tracker in trackers.items():
tracker.save_stash()
# stop the simulation
self.stopSimulation()
#endif save flag
#endif celltype check
# cell.lambdaVolume = 5
cell.type = self.DEAD
self.lambdaVolume = 1
del genomes[cell.id]
def __init__(self, _simulator, _frequency=1):
SteppableBasePy.__init__(self, _simulator, _frequency)
if save_flag:
self.start_tracker = Tracker2(file_name=save_dir +
'/start_cells_' + time_info + '.csv')
def __init__(self, _simulator, _frequency=10):
SteppableBasePy.__init__(self, _simulator, _frequency)
self.cell_tracker = Tracker2(file_name=save_dir + '/cell_count_' +
time_info + '.csv')
self.volume_tracker = Tracker2(file_name=save_dir + '/volume_' +
time_info + '.csv')
def __init__(self, _simulator, _frequency=1):
MitosisSteppableBase.__init__(self, _simulator, _frequency)
if save_flag:
self.mitosis_tracker = Tracker2(
file_name=save_dir + '/division_events_' + time_info + '.csv')
