# Using equations encapsulated in class objects

**URL:** <https://brian.discourse.group/t/using-equations-encapsulated-in-class-objects/830>\
**Category:** Support\
**Tags:** equations\
**Created:** [6 November 2022 19:44 UTC](https://brian.discourse.group/t/using-equations-encapsulated-in-class-objects/830 "2022-11-06T19:44:21Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![orbitalhybrid](https://avatars.discourse-cdn.com/v4/letter/o/48db29/32.png) [@orbitalhybrid](https://brian.discourse.group/u/orbitalhybrid)\
**Post date:** [6 November 2022 19:44 UTC](https://brian.discourse.group/t/using-equations-encapsulated-in-class-objects/830/1 "2022-11-06T19:44:22Z")

</div>

# Description of problem

Hi Brian folk,

I’m working on a class project that utilizes Izhikevich neurons connected by alpha synapses in Brian2. The package works great, but I have a separate script that generates groups of these neurons in a class initializer (e.g. a Bug class that has attributes in the form of neuron groups known as LeftLeg and RightLeg).

I’ve been trying to run a simulation with this design but am running into issues with the Network running in the background. I tried passing in the objects containing the equations to the Network (e.g. Animal1.LeftEye) but this didn’t work. The Network simply can’t see the equations defined.

Is there a way I can get the scope to see these equations?

# Minimal code to reproduce problem

My code can be found [here](https://github.com/orbitalhybridization/BasicNeuralModeling/blob/main/social_bug.py), and I am simply trying to create instances of bugs in another script.

# What you have aready tried

Above code, and creating the objects in the same script in which the classes are defined

# Expected output (if relevant)

# Actual output (if relevant)

# Full traceback of error (if relevant)

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<div class="post-metadata">

**Author:** ![mstimberg](https://yyz2.discourse-cdn.com/free1/user_avatar/brian.discourse.group/mstimberg/32/11_2.png) [@mstimberg](https://brian.discourse.group/u/mstimberg)\
**Post date:** [7 November 2022 09:35 UTC](https://brian.discourse.group/t/using-equations-encapsulated-in-class-objects/830/2 "2022-11-07T09:35:50Z")

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Hi @orbitalhybrid When you go away from the “flat script” structure, you need to manually add all objects to a `Network` object (see e.g. [Running a simulation — Brian 2 2.5.1 documentation](https://brian2.readthedocs.io/en/stable/user/running.html#networks)). In general, this object is the only thing that you’d need to store, since you can access all objects stored in the `Network` object like in a dictionary, using their name. Note that this is much more convenient, if you set explicit names for the objects, since otherwise they have default names such as `neurongroup`, `neurongroup_1`, etc.:

```python
    group = NeuronGroup(..., name='my_name')
    group2 = NeuronGroup(..., name='other_name')
    self.network = Network(group, group2)
    self.network['my_name'].v = ... # same effect as group.v = ...

```

If you prefer, you can of course also keep storing the `NeuronGroup` objects as attributes of the class in addition to adding them to the `Network` object. The only thing that is important is that all objects that are part of your simulation (neurons, synapses, monitors, …) have been added to the `Network` at some point.  
You’ll then need to call `run` on the network object (e.g. `self.network.run`).

Note that there is a second change that is most likely necessary: the `run`/`Network.run` command needs to “see” the external constants that are used in the equations. E.g. the following works:

```python
tau = 10*ms
group = NeuronGroup(1, 'dv/dt = -v/tau : 1')
net = Network(group)
net.run(100*ms) # ← can "see" tau

```

but the following will fail, complaining that it does not know “tau”:

```python
class MySim:
    def __init__ (self):
        self.tau = 10*ms
        group = NeuronGroup(1, 'dv/dt = -v/tau : 1')
        self.net = Network(group)

sim = MySim()
sim.net.run(100*ms) # ← does not "see" tau

```

One solution is to use the `namespace` argument, that can be used to explicitly pass a dictionary with the external parameters ([Namespaces — Brian 2 2.5.1 documentation](https://brian2.readthedocs.io/en/stable/advanced/namespaces.html)). If you already store all constants in attributes of your object, the easiest would be to use it like this:

```python
sim = MySim()
sim.net.run(100*ms, namespace=vars(sim))

```

Hope that helps!

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<div class="post-metadata">

**Author:** ![rth](https://yyz2.discourse-cdn.com/free1/user_avatar/brian.discourse.group/rth/32/16_2.png) [@rth](https://brian.discourse.group/u/rth)\
**Post date:** [8 November 2022 13:32 UTC](https://brian.discourse.group/t/using-equations-encapsulated-in-class-objects/830/3 "2022-11-08T13:32:08Z")

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@mstimberg just out of curiosity, can @orbitalhybrid’s class be a derived class from the `Network`? For example,

```python
class Bug(Network):
   .....
   def add_brain(self):
        self.neurons = NeuronGroup( .... )
        self.synapses = .....
        self.add(self.neurons, self.synapses)

bug_population = [Bug() for _ in range(1000)]
net = Network(bug_population)

```

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<div class="post-metadata">

**Author:** ![mstimberg](https://yyz2.discourse-cdn.com/free1/user_avatar/brian.discourse.group/mstimberg/32/11_2.png) [@mstimberg](https://brian.discourse.group/u/mstimberg)\
**Post date:** [8 November 2022 13:40 UTC](https://brian.discourse.group/t/using-equations-encapsulated-in-class-objects/830/4 "2022-11-08T13:40:10Z")

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Hi @rth. Yes and no: you can derive a class from `Network` and use this class instead of the original network (even though I would rather store the network in an attribute: [Composition over inheritance - Wikipedia](https://en.wikipedia.org/wiki/Composition_over_inheritance)), but you cannot combine several networks into a single network. Also, having thousands of `NeuronGroup`/`Synapses` objects to represent a population would be rather inefficient. If possible, you should instead use groups of neurons that represent several individuals at once.