# Access postsynaptic variables in synapse equations

**URL:** <https://brian.discourse.group/t/access-postsynaptic-variables-in-synapse-equations/697>\
**Category:** Support\
**Created:** [10 May 2022 18:42 UTC](https://brian.discourse.group/t/access-postsynaptic-variables-in-synapse-equations/697 "2022-05-10T18:42:06Z")\
**Posts on this page:** 7\
**Page:** 1

<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:** [10 May 2022 18:42 UTC](https://brian.discourse.group/t/access-postsynaptic-variables-in-synapse-equations/697/1 "2022-05-10T18:42:06Z")

</div>

# Description of problem

I’m playing with voltage- and spike-time-dependent plasticity, aka Clopath et al. model. While LTD has a spike-train term with delta functions and can be moved to `on_pre` resetting, LTP has all continuous variables and should be computed in a clock-driven manner. Both LTP and LTD use linear rectificatopn for voltage and low-pass filtered voltage.

\frac{dw\_{ij}}{dt} = -A^{-}S\_j(t)\lfloor \bar{u}^-\_i - \theta\_{-}\rfloor\_{+}+ A^+\bar{x}\_j \lfloor \bar{u}^+\_i - \theta\_{-}\rfloor\_{+} \lfloor v\_i - \theta\_{+}\rfloor\_{+}

\begin{array}{rlrl} du^-\_i/dt &=\left(v-u^-\_i \right)/\tau^- & \tau^-&=10 \text{ms} \\ du^+\_i/dt &=\left(v-u^+\_i \right)/\tau^+ & \tau^+ &=7 \text{ms} \\ d\bar{x}\_i/dt &=\left(S\_i(t)-\bar{x}\_i \right)/\tau^x & \tau^x &=15 \text{ms} \\ \end{array}

where w\_{ij} is a synaptic conductance from j^{th} presynaptic neuron to i^{th} postsynaptic. v is a voltage and S(t) = \sum \delta(t-t') is a spike train.

To make code a little faster, I moved computations of low pass filtered voltages and ReLU functions to the neuron side. So, part of my neuron equations looks like that

```python
nrn_equ="""
.... neuron dynamics ....
dvlp/dt = (v-vlp)/tlpf_p : 1 # low-pass filter of the voltage for LTD
dvlm/dt = (v-vlm)/tlpf_m : 1 # low-pass filter of the voltage for LTP

vup = int(v>Tltp)*(v-Tltp) : 1
vlpup = int(vlp>Tltd)*(vlp-Tltd) : 1
vlmup = int(vlm>Tltd)*(vlm-Tltd) : 1
"""

```

Synaptic model can be implemented like this

```python
syn = Synapses(lgninput, neurons, model="""
dwsyn/dt = Altp*x*vup_post*vlpup_post/tausynscal: 1 (clock-driven) 
dx/dt = -x/tlpf_s : 1 (clock-driven) # slow presynaptic FR 
dy/dt = -y/tfrest : 1 (clock-driven) # low-pass filter for FR estimate
""",
on_pre='''
    x += 1*ms/tlpf_s
    wsyn -= Altd*(y*second/tfrest/frRef)*vlmup_post
 .... synaptic dynamics .....
''',
on_post='''
    y += 1*ms/tfrest''')

```

This code works and works well.

============================

However, to debug my model, I want to separate LTP and LTD components and record them. So I modified synaptic equations like this:

```python
syn = Synapses(lgninput, neurons, model="""
dwsyn/dt = LTP/tausynscal: 1 (clock-driven) 
dx/dt = -x/tlpf_s : 1 (clock-driven) # slow presynaptic FR 
dy/dt = -y/tfrest : 1 (clock-driven) # low-pass filter for FR estimate
LTP=Altp*x*vup_post*vlpup_post : 1
LTD : 1
""",
on_pre='''
    x += 1*ms/tlpf_s
    LTD = Altd*(y*second/tfrest/frRef)*vlmup_post
    wsyn -= LTD
 .... synaptic dynamics .....''',
on_post='''
    y += 1*ms/tfrest''')

```

This code returns an error, which I don’t understand

```auto
ERROR Brian 2 encountered an unexpected error. If you think this is a bug in Brian 2, please report this issue either to the discourse forum at <http://brian.discourse.group/>, or to the issue tracker at <https://github.com/brian-team/brian2/issues>. Please include this file with debug information in your report: /tmp/brian_debug_8n4izity.log Additionally, you can also include a copy of the script that was run, available at: /tmp/brian_script_35ik7dpv.py Thanks! [brian2]
Traceback (most recent call last):
  File "PLS-cortex.py", line 448, in <module>
    onenrnpres_srec = StateMonitor(syn,"wsyn x y LTP LTD".split(),record=synids,dt=mth["/rec/cont/dt"]*ms)
  File "/home/rth/.local/lib/python3.8/site-packages/brian2/monitors/statemonitor.py", line 248, in __init__
    self.variables.add_reference(f'_source_{varname}',
  File "/home/rth/.local/lib/python3.8/site-packages/brian2/core/variables.py", line 1829, in add_reference
    self.add_referred_subexpression(name, group, var, index)
  File "/home/rth/.local/lib/python3.8/site-packages/brian2/core/variables.py", line 1768, in add_referred_subexpression
    self.add_referred_subexpression(new_name,
  File "/home/rth/.local/lib/python3.8/site-packages/brian2/core/variables.py", line 1773, in add_referred_subexpression
    self.add_reference(new_name,
  File "/home/rth/.local/lib/python3.8/site-packages/brian2/core/variables.py", line 1821, in add_reference
    raise TypeError(f"Cannot link variable '{name}' to '{varname}' in "
TypeError: Cannot link variable ' ___source_LTP_synapses_vup_post_synapses__ vup_post_neurongroup_v' to '_vup_post_neurongroup_v' in group 'synapses' -- need to precalculate direct indices but index _postsynaptic_idx can change

```

It may be related to standalone OpenMP mode, I used to load all cores of my processor.

```python
set_device('cpp_standalone')
prefs.devices.cpp_standalone.openmp_threads = npth

```

---

<div class="post-metadata">

**Author:** ![schmitts](https://yyz2.discourse-cdn.com/free1/user_avatar/brian.discourse.group/schmitts/32/191_2.png) [@schmitts](https://brian.discourse.group/u/schmitts)\
**Post date:** [11 May 2022 06:50 UTC](https://brian.discourse.group/t/access-postsynaptic-variables-in-synapse-equations/697/2 "2022-05-11T06:50:47Z")

</div>

Hi!

I guess the culprit is setting only some synapses to be recorded in conjunction with standalone mode:

```auto
record=synids

```

Can you try to record all synapses (only as a check)?

Cheers,

Sebastian

---

<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:** [11 May 2022 12:21 UTC](https://brian.discourse.group/t/access-postsynaptic-variables-in-synapse-equations/697/3 "2022-05-11T12:21:08Z")

</div>

Hi Sebastian, thank you for looking into it!  
It doesn’t seem that the problem in recording, but in caches somewhere.  
I add this line of code:

```auto
os.system("rm -fR tmp __pycache__ /home/rth/.cython/brian_extensions/_cython_magic_* "+standalone_dir)

```

and the problem is gone.  
However, it’s a bit odd, so maybe something else is going on here.

---

<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:** [11 May 2022 12:55 UTC](https://brian.discourse.group/t/access-postsynaptic-variables-in-synapse-equations/697/4 "2022-05-11T12:55:30Z")

</div>

Hi Sebastian,  
After 1/2 hour investigation I should admit that you were right, and I overlooked a bug in my script 🪲.

It is related to synaptic recording.

---

<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:** [11 May 2022 13:04 UTC](https://brian.discourse.group/t/access-postsynaptic-variables-in-synapse-equations/697/5 "2022-05-11T13:04:22Z")

</div>

Hi everyone,

> [@rth](#):
>
> It doesn’t seem that the problem in recording, but in caches somewhere.

huh, I don’t quite see how the cache plays a role here… The problem is a very technical one, and one that we could certainly handle better, but it is entangled deeply with the code generation machinery. Here’s a (minimal ?) example that generates the same error:

```python
G = NeuronGroup(2, '''v : 1
                      x = 2*v : 1''')
S = Synapses(G, G, '''w : 1
                      y = w + x_post : 1''')
S.connect()
mon = StateMonitor(S, 'y', record=[0])

```

This fails with:

```pytb
TypeError: Cannot link variable ' ___source_y_synapses_x_post_synapses__ x_post_neurongroup_v' to '_x_post_neurongroup_v' in group 'synapses' -- need to precalculate direct indices but index _postsynaptic_idx can change

```

The problem is due to the use of the subexpression `x` from the postsynaptic cell as part of a subexpression in the synapse. Brian can handle these things, and its approach is using indices. E.g. here, we need the value of `v[postsynaptic_idcs[record_idx]]` when we loop over `record_idx` to record all the values we ask for. To make our code machinery not too complex, we try to limit this a bit, and pre-calculate the direct indices that we need. However, this errors out since it is worried about `postysnaptic_idcs` being “dynamic” – the `StateMonitor` wants to calculate these indices when it is initialized, but in particular in standalone mode this might not be possible since the postsynaptic indices have not been determined yet. Again, just to be clear, this is not handled well here and there are many situations (including yours, I think) where we could actually make this work. It is just not supported by the way things are done currently.

All that said, there are at least two workarounds (I’ll demonstrate them with my simple example, but hopefully they are easy to transfer).

1. Do not use subexpressions, but record things individually and reconstruct them afterwards:

```python
# ...group definitions
S_mon = StateMonitor(S, 'w', record=[0])
G_mon = StateMonitor(S, 'x', record=S.j[0])
# Result is `S_mon.w + G_mon.x`

```

1. Use `(constant over dt)` for the subexpressions

```python
G = NeuronGroup(2, '''v : 1
                      x = 2*v : 1 (constant over dt)''')
S = Synapses(G, G, '''w : 1
                      y = w + x_post : 1 (constant over dt)''')

```

Using `constant over dt` means that these are no longer subexpressions, but e.g. `x = 2*v` is replaced by `x: 1` together with a `run_regularly` operation that sets `x = 2*v` at the beginning of the time step. When such a variable is referred in a differential equation, this is not exactly equivalent (e.g. `rk4` will only use one value instead of several slightly different values), but in practice this shouldn’t be an issue if the variable changes slowly with respect to the simulation time step.

> [@schmitts](#):
>
> Can you try to record all synapses (only as a check)?

Actually, using `record=True` is not possible in standalone mode. The reason is similar to what I described above: `StateMonitor` wants to determine the indices of the synapses to record from, but in standalone mode the synapses do not exist yet.

---

<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:** [11 May 2022 13:17 UTC](https://brian.discourse.group/t/access-postsynaptic-variables-in-synapse-equations/697/6 "2022-05-11T13:17:02Z")

</div>

> [@mstimberg](#):
>
> huh, I don’t quite see how the cache plays a role here…

@mstimberg, yes, it was my fault. I tried to debug and overlooked some flags in my script.

> [@mstimberg](#):
>
> 1. Do not use subexpressions, but record things individually and reconstruct them afterwards:

I see how it may work. Do you mean

```auto
G_mon = StateMonitor(G, 'x', record=S.j[0])

```

---

<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:** [11 May 2022 13:21 UTC](https://brian.discourse.group/t/access-postsynaptic-variables-in-synapse-equations/697/7 "2022-05-11T13:21:46Z")

</div>

> [@rth](#):
>
> I see how it may work. Do you mean
> 
> ```auto
> G_mon = StateMonitor(G, 'x', record=S.j[0])
> 
> ```

Sorry, yes. Alternatively (and more reasonable if you would otherwise record the same values several times), you could use

```auto
G_mon = StateMonitor(G, 'x', record=True)

```

and use the indices when you reconstruct the values, i.e. something like

```auto
y_values = S_mon.w + G_mon.x[S.j[:], :]

```