Storing additional attributes

It may be useful or necessary to store attributes that are not automatically stored by NeuroDevSim either because they need to be analyzed or plotted, or to prepare for Importing a simulation. These may either be user defined Additional attributes or attributes like Neuron firing_rate for which only the initial value is stored by default.

The admin.attrib_to_db method supports such storing. attrib_to_db is called in the main part of the code, anytime after at least one instance of the Front subclass has been made, for example by add_neurons. This code sample causes Front.num_children to be stored for all instances of SimpleNeuronFront:

if __name__ == '__main__':
    ...
    neuron_types = [SimpleNeuronFront,AxonFront]
    admin = Admin_agent(...)

    admin.add_neurons(SimpleNeuronFront,"simple_neuron",1,[[...],[...]],30.)

    admin.attrib_to_db(SimpleNeuronFront,"num_children","int")

attrib_to_db requires minimally 3 parameters: the subclass of ``Front`` for which the attribute should be stored, the name of the attribute to be stored and a sql_type. The latter defines the format that should be used to store the parameter in the database and should be one of the following:

sql_type	ctypes or class	columns in the data table
int	c_bool, c_short, c_int, c_long	1 int column containing the value
real	c_double	1 real column containing the value
text	c_char	1 text column containing the text
id	id	2 int columns containing both parts
point	Point	3 real columns containing x, y, z

An example of storing an additional attribute:

class SimpleNeuronFront(SynFront):
    _fields_ = SynFront._fields_ + [('signal', c_double)]
...

if __name__ == '__main__':
    ...
    neuron_types = [SimpleNeuronFront,AxonFront]
    admin = Admin_agent(...)

    admin.add_neurons(SimpleNeuronFront,"integrate_neuron",1,[[...],[...]],30.)

    admin.attrib_to_db(SimpleNeuronFront,"signal","real")

attrib_to_db will only store attributes that are not stored yet or that are not being updated. Trying to store an unchanging attribute that is always stored, like for example Front.radius or Neuron.neuron_name will cause an error.

By default attrib_to_db assumes that the attribute to store belongs to Front, but for Neuron firing_rate and CV_ISI and for Synapse weight can be stored but the class needs to be specified in the object optional parameter:

admin.attrib_to_db(AxonFront,"firing_rate","real",object=Neuron)
admin.attrib_to_db(SimpleNeuronFront,"weight","real",object=Synapse)

If multiple attributes from the same Front subclass or object are to be stored they can be specified as a list:

admin.attrib_to_db(AxonFront,["firing_rate","CV_ISI"],["real","real"],object=Neuron)

Note that sql_type then also becomes a list, because not all attributes may have the same type. It is not possible to combine attributes from different object types in a list.

Another optional parameter controls how often the attribute is saved. By default it is saved for every cycle after the attrib_to_db call, but this may not be necessary. If the attribute is stored to prepare for Importing a simulation then only its final value is needed. This can be achieved by setting the last_only optional parameter to True:

if __name__ == '__main__':
    ...
    neuron_types = [SimpleNeuronFront,AxonFront]
    admin = Admin_agent(...)
    admin.importable_db = True

    admin.add_neurons(AxonFront,"axon",10,[[...],[...]],1.,axon=[...])

    admin.attrib_to_db(AxonFront,"goalID","id",last_only=True)

goaldID will now only be stored for the last cycle of the simulation.

The last optional parameter of attrib_to_db controls for which neurons data will be stored. The neuron_name optional parameter will limit storage to data belonging to neurons with this name (neuron_name is a wildcard).

Several use cases of attrib_to_db are shown in the Database notebook, this also includes analysis and plotting of stored data. An Importing a simulation use case is shown in the Import notebook.