From c519c825924412d870943f8d6f93b0d3e7b45a53 Mon Sep 17 00:00:00 2001
From: Dhruva Gowda Storz <dhruvastorz@gmail.com>
Date: Wed, 20 Dec 2017 17:12:56 +0530
Subject: [PATCH] Added autorun statement to Compartment_net.py.
removed pyrun1.py documentation as it is exactly the same as pyrun.py.
updated vec information in quickstart to reflect actual ouput.
---
docs/source/user/py/quickstart/demos.rst | 4 +-
.../user/py/quickstart/moose_quickstart.rst | 6 +--
moose-examples/snippets/compartment_net.py | 43 +++++++++++--------
3 files changed, 30 insertions(+), 23 deletions(-)
diff --git a/docs/source/user/py/quickstart/demos.rst b/docs/source/user/py/quickstart/demos.rst
index 390d05fb..6614ac95 100644
--- a/docs/source/user/py/quickstart/demos.rst
+++ b/docs/source/user/py/quickstart/demos.rst
@@ -45,7 +45,7 @@ Run Python from MOOSE
.. automodule:: pyrun
:members:
-.. automodule:: pyrun1
- :members:
+.. automodule: pyrun1
+.. :members:
.. _quickstart-classes:
diff --git a/docs/source/user/py/quickstart/moose_quickstart.rst b/docs/source/user/py/quickstart/moose_quickstart.rst
index 0663c443..1df78de7 100644
--- a/docs/source/user/py/quickstart/moose_quickstart.rst
+++ b/docs/source/user/py/quickstart/moose_quickstart.rst
@@ -641,9 +641,9 @@ loop through the elements in an ``vec`` like a Python list ::
shows ::
- /model/comp[0] <type 'moose.melement'>
- /model/comp[1] <type 'moose.melement'>
- /model/comp[2] <type 'moose.melement'>
+ /model[0]/comp[0] <type 'moose.Compartment'>
+ /model[0]/comp[1] <type 'moose.Compartment'>
+ /model[0]/comp[2] <type 'moose.Compartment'>
Thus elements are instances of class ``melement``. All elements in an
``vec`` share the ``id_`` of the ``vec`` which can retrieved by
diff --git a/moose-examples/snippets/compartment_net.py b/moose-examples/snippets/compartment_net.py
index 55b95f54..9bb1c5bf 100644
--- a/moose-examples/snippets/compartment_net.py
+++ b/moose-examples/snippets/compartment_net.py
@@ -65,22 +65,23 @@ 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)
- synpath = path+'/synchan'
+ comps = create_1comp_neuron('{}/neuron'.format(path), number=size) #creates population of 1comp_neurons as per ionchannel.py
+ synpath = path+'/synchan' #path under container
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')
+ m = moose.connect(comps, 'channel', synchan, 'channel', 'OneToOne') #connect neupop to channel with 1to1 connections
synhandler = moose.vec('{}/synhandler'.format(path), n=size,
dtype='SimpleSynHandler')
- moose.connect(synhandler, 'activationOut', synchan, 'activation', 'OneToOne')
- spikegen = moose.vec('{}/spikegen'.format(path), n=size, dtype='SpikeGen')
+ 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?
spikegen.threshold = 0.0
- m = moose.connect(comps, 'VmOut', spikegen, 'Vm', 'OneToOne')
+ m = moose.connect(comps, 'VmOut', spikegen, 'Vm', 'OneToOne') #connect neurons to spikegens.
return {'compartment': comps, 'spikegen': spikegen, 'synchan':
synchan, 'synhandler': synhandler}
@@ -104,12 +105,12 @@ delay: float (mean delay of synaptic transmission)
"""
for sh in synhandler:
- scount = len(spikegen)
- sh.synapse.num = scount
- sh.synapse.vec.delay = 5e-3
+ 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 #
for ii, syn in enumerate(sh.synapse):
- msg = moose.connect(spikegen[ii], 'spikeOut', syn, 'addSpike')
- print(('Connected', spikegen[ii].path, 'to', syn.path, 'on', sh.path))
+ 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
def create_network(size=2):
"""
@@ -117,10 +118,10 @@ 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)
+ pop_a = create_population(moose.Neutral('/network/pop_A'), size) #calls previously defined method to create pop a
print(pop_a)
- pop_b = create_population(moose.Neutral('/network/pop_B'), size)
- make_synapses(pop_a['spikegen'], pop_b['synhandler'])
+ 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
pulse = moose.PulseGen('pulse')
pulse.level[0] = 1e-9
pulse.delay[0] = 0.02 # disable the pulsegen
@@ -128,9 +129,10 @@ 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')
- moose.connect(vm_a, 'requestOut', pop_a['compartment'], 'getVm', 'OneToOne')
- vm_b = moose.Table('/data/Vm_B', 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(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')
@@ -141,7 +143,7 @@ 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():
"""
@@ -149,6 +151,8 @@ 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
@@ -176,6 +180,9 @@ def main():
plt.legend()
plt.show()
+if __name__ == '__main__':
+ main()
+
#
# compartment_net.py ends here
--
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