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 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 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]