def __init__(self,_simulator,_frequency=1): MitosisSteppableBase.__init__(self,_simulator, _frequency) # 0 - parent child position will be randomized between mitosis event # negative integer - parent appears on the 'left' of the child # positive integer - parent appears on the 'right' of the child self.setParentChildPositionFlag(0)
def __init__(self,_simulator,_frequency, _params_container ): self.statsReporter = StatsReporter() self.params_container = _params_container MitosisSteppableBase.__init__(self,_simulator, _frequency) self.y_GZ_mitosis_border_percent = 0.5 ## The position, in fraction of the GZ (from posteriormost EN stripe to posterior of GZ, ## of the border between mitosis regions in the GZ (measured from the posterior) r_mitosis_R0 = self.params_container.getNumberParam('r_mitosis_R0') r_mitosis_R1 = self.params_container.getNumberParam('r_mitosis_R1') r_mitosis_R2 = self.params_container.getNumberParam('r_mitosis_R2') r_mitosis_R3 = self.params_container.getNumberParam('r_mitosis_R3') self.r_mitosis_list=[r_mitosis_R0,r_mitosis_R1,r_mitosis_R2,r_mitosis_R3] self.window = 500 # length of window in MCS (see above) self.Vmin_divide = 60 # minimum volume, in pixels, at which cells can divide self.Vmax = 90 # maximum volume to which cells can grow self.mitosisVisualizationFlag = 1 # if nonzero, turns on mitosis visualization self.mitosisVisualizationWindow = 100 # number of MCS that cells stay labeled as having divided # Set r_grow for each region: pixels per MCS added to cell's volume r_grow_R0=0 r_grow_R1=0 r_grow_R2=0 r_grow_R3=0.05 self.r_grow_list=[r_grow_R0,r_grow_R1,r_grow_R2,r_grow_R3] # t_grow_R0=self.calculate_t_grow(r_mitosis_R0) # t_grow_R1=self.calculate_t_grow(r_mitosis_R1) # t_grow_R2=self.calculate_t_grow(r_mitosis_R2) # t_grow_R3=self.calculate_t_grow(r_mitosis_R3) # self.t_grow_list=[t_grow_R0,t_grow_R1,t_grow_R2,t_grow_R3] self.fraction_AP_oriented=0.5 self.statsReporter.displayStats(['rg_RO', r_grow_R0, 'rg_R1', r_grow_R1, 'rg_R2', r_grow_R2, 'rg_R3', r_grow_R3])
def __init__(self,_simulator,_frequency=1): MitosisSteppableBase.__init__(self,_simulator, _frequency) self.y_GZ_mitosis_border_percent = 0.5 ## The position, in fraction of the GZ (from posteriormost EN stripe to posterior of GZ, ## of the border between mitosis regions in the GZ (measured from the posterior) r_mitosis_R0 = 0.0 # approximate fraction of cells dividing in a given window in region 0 (anterior to EN) r_mitosis_R1 = 0.0 # approximate fraction of cells dividing in a given window in region 1 (EN striped region) r_mitosis_R2 = 0.0 # approximate fraction of cells dividing in a given window in region 2 (anterior GZ) r_mitosis_R3 = 0.5 # approximate fraction of cells dividing in a given window in region 3 (posterior GZ) self.r_mitosis_list=[r_mitosis_R0,r_mitosis_R1,r_mitosis_R2,r_mitosis_R3] self.window = 500 # length of window in MCS (see above) self.Vmin_divide = 60 # minimum volume, in pixels, at which cells can divide self.Vmax = 90 # maximum volume to which cells can grow self.mitosisVisualizationFlag = 1 # if nonzero, turns on mitosis visualization self.mitosisVisualizationWindow = 100 # number of MCS that cells stay labeled as having divided # Set r_grow for each region: pixels per MCS added to cell's volume r_grow_R0=0 r_grow_R1=0 r_grow_R2=0 r_grow_R3=0.05 self.r_grow_list=[r_grow_R0,r_grow_R1,r_grow_R2,r_grow_R3] # t_grow_R0=self.calculate_t_grow(r_mitosis_R0) # t_grow_R1=self.calculate_t_grow(r_mitosis_R1) # t_grow_R2=self.calculate_t_grow(r_mitosis_R2) # t_grow_R3=self.calculate_t_grow(r_mitosis_R3) # self.t_grow_list=[t_grow_R0,t_grow_R1,t_grow_R2,t_grow_R3] self.fraction_AP_oriented=0.5
def __init__(self, _simulator, _frequency=1): MitosisSteppableBase.__init__(self, _simulator, _frequency) # 0 - parent child position will be randomized between mitosis event # negative integer - parent appears on the 'left' of the child # positive integer - parent appears on the 'right' of the child self.setParentChildPositionFlag(-1)
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=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, _params_container): self.statsReporter = StatsReporter() self.params_container = _params_container MitosisSteppableBase.__init__(self, _simulator, _frequency) self.y_GZ_mitosis_border_percent = 0.5 ## The position, in fraction of the GZ (from posteriormost EN stripe to posterior of GZ, ## of the border between mitosis regions in the GZ (measured from the posterior) r_mitosis_R0 = self.params_container.getNumberParam('r_mitosis_R0') r_mitosis_R1 = self.params_container.getNumberParam('r_mitosis_R1') r_mitosis_R2 = self.params_container.getNumberParam('r_mitosis_R2') r_mitosis_R3 = self.params_container.getNumberParam('r_mitosis_R3') self.r_mitosis_list = [ r_mitosis_R0, r_mitosis_R1, r_mitosis_R2, r_mitosis_R3 ] self.window = 500 # length of window in MCS (see above) self.Vmin_divide = 60 # minimum volume, in pixels, at which cells can divide self.Vmax = 90 # maximum volume to which cells can grow self.mitosisVisualizationFlag = 1 # if nonzero, turns on mitosis visualization self.mitosisVisualizationWindow = 100 # number of MCS that cells stay labeled as having divided # Set r_grow for each region: pixels per MCS added to cell's volume r_grow_R0 = 0 r_grow_R1 = 0 r_grow_R2 = 0 r_grow_R3 = 0.05 self.r_grow_list = [r_grow_R0, r_grow_R1, r_grow_R2, r_grow_R3] # t_grow_R0=self.calculate_t_grow(r_mitosis_R0) # t_grow_R1=self.calculate_t_grow(r_mitosis_R1) # t_grow_R2=self.calculate_t_grow(r_mitosis_R2) # t_grow_R3=self.calculate_t_grow(r_mitosis_R3) # self.t_grow_list=[t_grow_R0,t_grow_R1,t_grow_R2,t_grow_R3] self.fraction_AP_oriented = 0.5 self.statsReporter.displayStats([ 'rg_RO', r_grow_R0, 'rg_R1', r_grow_R1, 'rg_R2', r_grow_R2, 'rg_R3', r_grow_R3 ])
def __init__(self, _simulator, _frequency, _params_container, _stats_reporter): MitosisSteppableBase.__init__(self, _simulator, _frequency) self.reporter = _stats_reporter self.params_container = _params_container self.y_GZ_mitosis_border_percent = self.params_container.getNumberParam('y_GZ_mitosis_border_percent') self.transition_times = self.params_container.getListParam('mitosis_transition_times') self.transition_counter = 0 ## current simulation time window self.r_mitosis_R0 = self.params_container.getListParam('r_mitosis_R0') # e.g. [0.0, 0.0, 0.0] self.r_mitosis_R1 = self.params_container.getListParam('r_mitosis_R1') # e.g. [0.0, 0.0, 0.0] self.r_mitosis_R2 = self.params_container.getListParam('r_mitosis_R2') # e.g. [0.0, 0.5, 0.0] self.r_mitosis_R3 = self.params_container.getListParam('r_mitosis_R3') # e.g. [0.5, 0.5, 0.5] self.r_grow_R0 = self.params_container.getListParam('r_grow_R0') # e.g. [0.0,0.0,0.0] self.r_grow_R1 = self.params_container.getListParam('r_grow_R1') # e.g. [0.0,0.0,0.0] self.r_grow_R2 = self.params_container.getListParam('r_grow_R2') # e.g [0.0,0.0,0.0] self.r_grow_R3 = self.params_container.getListParam('r_grow_R3') # e.g. [0.05,0.05,0.05] self.r_grow_list = [self.r_grow_R0[0], self.r_grow_R1[0], self.r_grow_R2[0], self.r_grow_R3[0]] self.fraction_AP_oriented = self.params_container.getNumberParam('mitosis_fraction_AP_oriented') self.window = self.params_container.getNumberParam('mitosis_window') self.Vmin_divide = self.params_container.getNumberParam('mitosis_Vmin_divide') self.Vmax = self.params_container.getNumberParam('mitosis_Vmax') self.mitosisVisualizationFlag = self.params_container.getNumberParam('mitosis_visualization_flag') self.mitosisVisualizationWindow = self.params_container.getNumberParam('mitosis_visualization_window')
def __init__(self,_simulator,_frequency=1,_V_div=180,_divType="Random"): MitosisSteppableBase.__init__(self,_simulator, _frequency) self.V_div=_V_div; self.divType=_divType
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')
def __init__(self, _simulator, _frequency=1): MitosisSteppableBase.__init__(self, _simulator, _frequency) self.scalarCycBField = self.createScalarFieldCellLevelPy("CycB")
def __init__(self,_simulator,_frequency=1): MitosisSteppableBase.__init__(self,_simulator, _frequency) if save_flag: self.mitosis_tracker = Tracker2(file_name='../division_events_' + time_info + '.csv')
def __init__(self,_simulator,_frequency=1): MitosisSteppableBase.__init__(self,_simulator, _frequency) self.fieldNameExternalVEGF = 'VEGF_ext' self.fieldNameSolubleVEGF = 'VEGF_sol'
def __init__(self,_simulator,_frequency=1, trackerInstance=None, genomes=[Genome(mutation_rate=0),Genome(mutation_rate=5)]): MitosisSteppableBase.__init__(self,_simulator, _frequency) self.trackerInstance = trackerInstance self.genomes = genomes
def __init__(self,_simulator,_frequency=10): MitosisSteppableBase.__init__(self,_simulator, _frequency)
def __init__(self,_simulator,_frequency=1): MitosisSteppableBase.__init__(self,_simulator, _frequency)
def __init__(self, simulator, model, _frequency=1): MitosisSteppableBase.__init__(self, simulator, _frequency) self.model = model self.execConfig = model.execConfig self.timeMCS = 0