From 7b389f6f22531db956daf6b46b530c4b860aee13 Mon Sep 17 00:00:00 2001
From: Dhruva Gowda Storz <dhruvastorz@gmail.com>
Date: Wed, 20 Dec 2017 17:23:59 +0530
Subject: [PATCH] uploaded fixed compartment_net.py without all my comments
---
moose-examples/snippets/compartment_net.py | 42 +++++++++++-----------
1 file changed, 20 insertions(+), 22 deletions(-)
diff --git a/moose-examples/snippets/compartment_net.py b/moose-examples/snippets/compartment_net.py
index 9bb1c5bf..b77b25db 100644
--- a/moose-examples/snippets/compartment_net.py
+++ b/moose-examples/snippets/compartment_net.py
@@ -65,23 +65,22 @@ def create_population(container, size):
This uses **ionchannel.create_1comp_neuron**.
"""
- #I imagine that layers in a network will consist of such populations
path = container.path
print((path, size, type(path)))
- comps = create_1comp_neuron('{}/neuron'.format(path), number=size) #creates population of 1comp_neurons as per ionchannel.py
- synpath = path+'/synchan' #path under container
+ comps = create_1comp_neuron('{}/neuron'.format(path), number=size)
+ synpath = path+'/synchan'
print((synpath, size, type(size)))
synchan = moose.vec(synpath, n=size, dtype='SynChan')
synchan.Gbar = 1e-8
synchan.tau1 = 2e-3
synchan.tau2 = 2e-3
- m = moose.connect(comps, 'channel', synchan, 'channel', 'OneToOne') #connect neupop to channel with 1to1 connections
+ m = moose.connect(comps, 'channel', synchan, 'channel', 'OneToOne')
synhandler = moose.vec('{}/synhandler'.format(path), n=size,
dtype='SimpleSynHandler')
- moose.connect(synhandler, 'activationOut', synchan, 'activation', 'OneToOne') #connect handler - channel
- spikegen = moose.vec('{}/spikegen'.format(path), n=size, dtype='SpikeGen') #create spikegen through vec. Bu why?
+ moose.connect(synhandler, 'activationOut', synchan, 'activation', 'OneToOne')
+ spikegen = moose.vec('{}/spikegen'.format(path), n=size, dtype='SpikeGen')
spikegen.threshold = 0.0
- m = moose.connect(comps, 'VmOut', spikegen, 'Vm', 'OneToOne') #connect neurons to spikegens.
+ m = moose.connect(comps, 'VmOut', spikegen, 'Vm', 'OneToOne')
return {'compartment': comps, 'spikegen': spikegen, 'synchan':
synchan, 'synhandler': synhandler}
@@ -105,12 +104,12 @@ delay: float (mean delay of synaptic transmission)
"""
for sh in synhandler:
- scount = len(spikegen)#len(spikegen) = number of spikegens? AKA no. of vecs?
- sh.synapse.num = scount #sets number of synapses equal to number of spikegens. Only need one synhandler then?
- sh.synapse.vec.delay = 5e-3 #
+ scount = len(spikegen)
+ sh.synapse.num = scount
+ sh.synapse.vec.delay = 5e-3
for ii, syn in enumerate(sh.synapse):
- msg = moose.connect(spikegen[ii], 'spikeOut', syn, 'addSpike') #for each synapse, connect each spikegen to each synapse one to one
- print(('Connected', spikegen[ii].path, 'to', syn.path, 'on', sh.path)) #flavour text
+ msg = moose.connect(spikegen[ii], 'spikeOut', syn, 'addSpike')
+ print(('Connected', spikegen[ii].path, 'to', syn.path, 'on', sh.path))
def create_network(size=2):
"""
@@ -118,10 +117,10 @@ def create_network(size=2):
pop_B and connect them up.
"""
net = moose.Neutral('network')
- pop_a = create_population(moose.Neutral('/network/pop_A'), size) #calls previously defined method to create pop a
+ pop_a = create_population(moose.Neutral('/network/pop_A'), size)
print(pop_a)
- pop_b = create_population(moose.Neutral('/network/pop_B'), size) #create second population (like a layer I guess?)
- make_synapses(pop_a['spikegen'], pop_b['synhandler']) #connects spikegens of population a to new synapses connected to synhandler of population b
+ pop_b = create_population(moose.Neutral('/network/pop_B'), size)
+ make_synapses(pop_a['spikegen'], pop_b['synhandler'])
pulse = moose.PulseGen('pulse')
pulse.level[0] = 1e-9
pulse.delay[0] = 0.02 # disable the pulsegen
@@ -129,10 +128,9 @@ def create_network(size=2):
pulse.delay[1] = 1e9
data = moose.Neutral('/data')
vm_a = moose.Table('/data/Vm_A', n=size)
- moose.connect(pulse, 'output', pop_a['compartment'], 'injectMsg', 'OneToAll') #connects pulsegen to pop a) #1 to all here means it connect
- # s the single pulsegen to all neurons in pop a
- moose.connect(vm_a, 'requestOut', pop_a['compartment'], 'getVm', 'OneToOne') #connects table to pop a
- vm_b = moose.Table('/data/Vm_B', size) #
+ moose.connect(pulse, 'output', pop_a['compartment'], 'injectMsg', 'OneToAll')
+ moose.connect(vm_a, 'requestOut', pop_a['compartment'], 'getVm', 'OneToOne')
+ vm_b = moose.Table('/data/Vm_B', size)
moose.connect(vm_b, 'requestOut', pop_b['compartment'], 'getVm', 'OneToOne')
gksyn_b = moose.Table('/data/Gk_syn_b', n=size)
moose.connect(gksyn_b, 'requestOut', pop_b['synchan'], 'getGk', 'OneToOne')
@@ -143,7 +141,7 @@ def create_network(size=2):
'Vm_A': vm_a,
'Vm_B': vm_b,
'Gsyn_B': gksyn_b
- } #return dict object with all the created objects within.
+ }
def main():
"""
@@ -151,8 +149,6 @@ def main():
connected via alpha synapses. It also shows the use of SynChan class to create a
network of single-compartment neurons connected by synapse.
"""
-
- ##main is mostly clocksetting, method calling and plotting
simtime = 0.1
simdt = 0.25e-5
plotdt = 0.25e-3
@@ -180,6 +176,8 @@ def main():
plt.legend()
plt.show()
+
+
if __name__ == '__main__':
main()
--
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