Front status flags¶
Front status flags are important in scheduling manage_front calls and controlling model behavior. Some flags report on front status and can only be read, others can be changed by the user and some can be freely used. All flag methods are documented in simulator module. NeuroDevSim tries to keep the control of scheduling simple with the use of the enable(constellation) and disable(constellation) methods that directly changes status flags, but in some instances finer control is needed.
Status flags scheduling manage_front¶
manage_front is called only for Front that are active, but the order in which fronts are called depends on the growing and migrating status flags and, if either is set to True, on the position of Front in the simulation volume. Correct setting of these flags is important to reduce the likelyhood of GridCompetitionError. The active, growing and migrating flags can be set by the user or changed through the enable and disable methods:
Flag query |
Set to True |
Set to False |
Active if True |
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yes |
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yes |
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yes |
Note that active changes to True if either growing or migrating are set to True, but the reverse does not apply. All new Front created by Admin_agent.add_neurons or Front.add_child are active and growing. For fronts created by Front.add_branch only the last of the series made is active and growing unless the optional parameter enable_all is set to True. Somata created by Admin_agent.add_neurons can also be migrating if the optional parameter is set to True.
Warning
enable and disable can be called for any front. Only self or new_front created by add_child or add_branch can call set_growing(), clear_growing(), set_migrating() and clear_migrating(). Calling these methods on other fronts will change the status flags but may not affect their behavior.
As mentioned, using disable(constellation) to stop growth of self is usually sufficient to control scheduling, but sometimes more fine-grained control is required:
def manage_front(self,constellation):
...
try:
new_front = self.add_child(constellation,new_pos) # make a new front and store it
# make front stop growing but keep it active
self.clear_growing()
return # completed this call
...
In the code example above, self is kept active but is not expected to call add_child again. This could be useful if self should be able to react to some future condition as it will keep calling manage_front. If for some reason it should grow again at a later cycle, it is safer to call self.set_growing() first and wait till the next cycle to call add_child.
In the following code example a parent front is not only enabled again but set to growing after retraction of a child:
def manage_front(self,constellation):
...
parent = self.get_parent(constellation)
parent.enable(constellation,growing=True)
self.retract(constellation) # retract self
return # do not do anything else with self
...
The same effect can be obtained using self.enable_parent(constellation,growing=True).
Finally, a reminder: only keep fronts active if needed. Fronts calling manage_front without it executing any code before return can slow down simulations significantly. It is possible to disable fronts transiently using the optional parameters till_cycle, till_cycle_g or till_cycle_m:
def manage_front(self,constellation):
...
self.disable(constellation,till_cycle_g=100)
...
this will disable self till cycle 100. On cycle 100 it becomes active again with is_growing() True.
Read-only status flags¶
The following status flags are set by NeuroDevSim methods and inform on status of Front:
Flag query |
Set by method |
Meaning of True |
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shape is cylindrical, False for a sphere |
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soma migrated at previous or current cycle |
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soma migrated at some cycle |
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front has been retracted |
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a child of this front was retracted at some cycle, is reset to False after new child is made |
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front is part of an arc made by
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These status flags can be read for any Front but notice that has_moved() and has_migrated() can change value during the present cycle and for fronts other than self the timing of this change cannot be predicted.
User availabe status flags¶
The following status flags can be used as boolean variables by the user instead of making a c_bool additional attribute:
Flag query |
Set to True |
Set to False |
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These status flags can be read and set/cleared for any Front. However, if setting or clearing on a front other than self be sure that only one front can do this during a given cycle to avoid competition. See Changing attributes of Front or Substrate for more information.