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')