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
