Pynest microcircuit #451

hendrikrth · 2016-08-05T13:09:33Z

The example files of NEST are lacking a PyNEST version of the microcircuit #450. To compensate this I would like you to include my branch. As reviewers I suggest @jhnnsnk and @mschmidt87.

jhnnsnk · 2016-09-09T09:58:31Z

pynest/examples/pynest-microcircuit/readme.md

+May 2016
+
+## Description ##
+This is a PyNEST implementation of the SLI cortical microcircuit from the microcircuit model by Potjans and Diesmann (2014): The cell-type specific


This is a PyNEST implementation of the microcircuit model ...
(no need to mention SLI)

mschmidt87 · 2016-11-06T22:45:02Z

👍 from me.

jhnnsnk · 2016-11-08T16:07:17Z

pynest/examples/Potjans_2014/network.py

+            'Seeds for random number generators of virtual processes: %r'
+            % rng_seeds
+            )
+        print('Global random number generator seed:%i' % grng_seed)


Add a space in front of %i for being consistent.

jhnnsnk · 2016-11-08T16:12:52Z

pynest/examples/Potjans_2014/network.py

+
+    def connect_devices(self):
+        """ Connects the recording devices to the microcircuit."""
+        print('%s of 2 Devices connected' % (len(self.net_dict['rec_dev'])))


It prints "1 of 2 Devices connected" if only a spike detector is used which sounds as if something was missing. I suggest to be specific and print "Spike Detector connected" or/and "Voltmeter connected".

jhnnsnk · 2016-11-08T16:16:58Z

pynest/examples/Potjans_2014/example.py

+
+
+# Initialize the network and pass parameters to it.
+net = network.Network(sim_dict, net_dict, stim_dict)


It would be nice to time also the network initialization.

jhnnsnk · 2016-11-08T16:21:32Z

pynest/examples/Potjans_2014/example.py

+t1 = time.time()
+net.setup()
+time_con = time.time()-t1
+print("Time to create the connections: %.2f seconds" % time_con)


Since the units ms and Hz are printed as well, why not just writing s instead of seconds?

jhnnsnk · 2016-11-08T16:30:03Z

pynest/examples/Potjans_2014/readme.md

+
+How to use the example:
+
+To run the microcircuit on a local machine, adjust the variables `N_scaling` and `K_scaling` in `network_params.py` to 0.1 and create an output directory called `data`. `N_scaling` adjusts the number of neurons and `K_scaling` the number of connections to be simulated. The full network can be run by adjusting these values to 1. If this is done, the option to print the time progress should be set to False in the file `sim_params.py`. For running, use `python example.py`. The output will be saved in the directory `data`.


Remove

and create an output directory called data.

since this is now done automatically.

jhnnsnk · 2016-11-08T16:32:02Z

pynest/examples/Potjans_2014/network.py

+        """ This function simulates the microcircuit."""
+        nest.Simulate(self.sim_dict['t_sim'])
+
+    def evaluate(self, raster_plot_time_idx, fire_rate_time_idx):


You could save the generated plots directly in the output directory together with the raw data.

jhnnsnk · 2016-11-08T16:51:08Z

pynest/examples/Potjans_2014/stimulus_params.py

+    # Standard deviation of the postsynaptic potential (in relative units).
+    'PSP_sd': 0.1,
+    # Start of the thalamic input (in ms).
+    'th_start': 700.0,


It would be nice to set the default stimulus intervals somewhere into the default plotting interval so that their effect is directly visible by eye.

I kept the thalamus stimulus interval, since this is the stimulus interval of the sli version. I therefore changed the interval of the spike raster plot.

Ok. Please update the comment on the plotting interval accordingly.

jhnnsnk · 2016-11-08T16:59:12Z

pynest/examples/Potjans_2014/network.py

+            else:
+                os.mkdir(self.sim_dict['data_path'])
+                print('data directory created')
+        print('Data will be written to %s' % self.data_path)


If used with MPI such statements are currently printed once per process. Please print them only on Rank 0 unless you want to print something specific to a process.

jhnnsnk · 2016-11-08T17:15:22Z

pynest/examples/Potjans_2014/network.py

+            '0 << /model /%s >> GetLocalNodes' % self.net_dict['neuron_model']
+            )
+        local_nodes = nest.sli_pop()
+        vp = nest.GetStatus(local_nodes)[0]['vp']


If run with both MPI and threads, taking the vp of the first local node is not correct. For example, with 2 MPI processes and 2 threads, one gets the MPI ranks 0 and 1, but the vps 0,1,2 and 3. For accessing the right pyrngs, I think we cannot avoid to extract all vps correponding to the local nodes. I will give a suggestion soon.

This might be a possible solution to the problem:

for thread in np.arange(nest.GetKernelStatus('local_num_threads')): local_nodes = nest.GetNodes([0], {'model': self.net_dict['neuron_model'], 'thread': thread}, local_only=True)[0] vp = nest.GetStatus(local_nodes)[0]['vp'] # same thread on MPI proc -> same vp nest.SetStatus( local_nodes, 'V_m', self.pyrngs[vp].normal( self.net_dict['neuron_params']['V0_mean'], self.net_dict['neuron_params']['V0_sd'], len(local_nodes)))

I fixed this, using your solution.

jhnnsnk · 2016-11-09T09:48:08Z

pynest/examples/Potjans_2014/network.py

+            self.DC_amp_e = compute_DC(self.net_dict, self.w_ext)
+
+        print(
+            'The Number of neurons is scaled by a factor of: %.2f'


Number -> number

jhnnsnk · 2016-11-09T11:24:05Z

Hi, during testing with both MPI and threads, I noticed that the initialization of membrane voltages did not work correctly. I made a suggestion inline how this could be solved. Apart from this, I made some other minor comments for improvement.

fixed initialization of membrane potentials, with provided solution

mschmidt87

Hi, thanks to @albada , I took another look at the code and discovered some typos. Please fix them.

mschmidt87 · 2016-11-24T10:56:46Z

pynest/examples/Potjans_2014/example.py

+# along with NEST.  If not, see <http://www.gnu.org/licenses/>.
+
+'''
+pynest microcicuit example


Please correct to microcircuit. Also in All other files that have this typo.

fixed this and all other typos

mschmidt87 · 2016-11-24T10:57:58Z

pynest/examples/Potjans_2014/helpers.py

+
+
+def get_weight(PSP_val, net_dict):
+    """ Function computes weight to elicit a change in the membrane potential.


Please change to "Computes" in accordance to the documentation of other functions.

Changes this and adapted this style in all other functions

mschmidt87 · 2016-11-24T10:58:44Z

pynest/examples/Potjans_2014/helpers.py

+        )
+    # If the network is scaled the indegrees are calculated in the same
+    # fashion as in the original version of the circuit, which is
+    # written in sli


insert '.' at the end.

mschmidt87 · 2016-11-24T10:59:17Z

pynest/examples/Potjans_2014/helpers.py

+def adj_w_ext_to_K(K_full, K_scaling, w, w_from_PSP, DC, net_dict, stim_dict):
+    """ Adjustment of weights to scaling is dine in this function.
+
+    With this funtion the recurrent and external weights are adjusted


mschmidt87 · 2016-11-24T11:00:02Z

pynest/examples/Potjans_2014/helpers.py

+
+
+def load_spike_times(path, name, begin, end):
+    """ This function loads spike times of each spike detector.


Change to "Loads..."

mschmidt87 · 2016-11-24T12:12:42Z

pynest/examples/Potjans_2014/sim_params.py

+# along with NEST.  If not, see <http://www.gnu.org/licenses/>.
+
+'''
+microcicuit simulation parameters


microcircuit

mschmidt87 · 2016-11-24T12:12:51Z

pynest/examples/Potjans_2014/sim_params.py

+microcicuit simulation parameters
+---------------------------------
+
+Simulation Parameters for the microcircuit.


Simulation parameters

mschmidt87 · 2016-11-24T12:13:11Z

pynest/examples/Potjans_2014/sim_params.py

+    'local_num_threads': 1,
+    # Recording interval of the membrane potential (in ms).
+    'rec_V_int': 1.0,
+    # If True data will be overwritten,


If True, data...

mschmidt87 · 2016-11-24T12:13:18Z

pynest/examples/Potjans_2014/sim_params.py

+    # Recording interval of the membrane potential (in ms).
+    'rec_V_int': 1.0,
+    # If True data will be overwritten,
+    # if False a NESTError is raised if the files already exist.


If False, ...

mschmidt87 · 2016-11-24T12:13:32Z

pynest/examples/Potjans_2014/stimulus_params.py

+# along with NEST.  If not, see <http://www.gnu.org/licenses/>.
+
+'''
+microcicuit stimulus parameters


microcircuit

some typos were fixed and a comment about the initialization of the membrane potentials was changed

jhnnsnk · 2016-12-14T10:10:56Z

👍

heplesser · 2016-12-14T10:34:07Z

@hendrikrth Thank you for porting this important model to PyNEST! @jhnnsnk @mschmidt87 Thank you for your thorough review!

hendrikrth added 4 commits August 4, 2016 19:32

Initial commit of pynest microcircuit

fa38fdd

Fixed most pep8 complaints

fec06fe

Fixed pep8 errors

b87bbfd

Pep8 errors removed

f4b8a2e

heplesser assigned mschmidt87 and jhnnsnk Aug 8, 2016

jhnnsnk reviewed Sep 9, 2016
View reviewed changes

jhnnsnk reviewed Nov 8, 2016

View reviewed changes

jhnnsnk reviewed Nov 9, 2016

View reviewed changes

hendrikrth added 2 commits November 17, 2016 10:33

included comments by jhnnsnk

e0a43d8

fixed initialization of membrane potentials, with provided solution

switched thalamus input to false and fixed pep8

0d5504c

heplesser added ZC: Documentation DO NOT USE THIS LABEL and removed ZC: PyNEST DO NOT USE THIS LABEL labels Nov 17, 2016

Adapted documentation about spike raster plot

d8257db

mschmidt87 suggested changes Nov 24, 2016

View reviewed changes

fixed typos and changed a comment

c673032

some typos were fixed and a comment about the initialization of the membrane potentials was changed

mschmidt87 approved these changes Dec 14, 2016

View reviewed changes

jhnnsnk approved these changes Dec 14, 2016

View reviewed changes

heplesser merged commit 102e338 into nest:master Dec 14, 2016

jougs mentioned this pull request Feb 7, 2018

PyNEST version of the microcircuit #450

Closed



		# Initialize the network and pass parameters to it.
		net = network.Network(sim_dict, net_dict, stim_dict)


		How to use the example:

		To run the microcircuit on a local machine, adjust the variables `N_scaling` and `K_scaling` in `network_params.py` to 0.1 and create an output directory called `data`. `N_scaling` adjusts the number of neurons and `K_scaling` the number of connections to be simulated. The full network can be run by adjusting these values to 1. If this is done, the option to print the time progress should be set to False in the file `sim_params.py`. For running, use `python example.py`. The output will be saved in the directory `data`.



		def get_weight(PSP_val, net_dict):
		""" Function computes weight to elicit a change in the membrane potential.



		def load_spike_times(path, name, begin, end):
		""" This function loads spike times of each spike detector.

Pynest microcircuit #451

Pynest microcircuit #451

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hendrikrth commented Aug 5, 2016

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mschmidt87 commented Nov 6, 2016

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jhnnsnk Nov 8, 2016 • edited Loading

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jhnnsnk commented Nov 9, 2016

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jhnnsnk commented Dec 14, 2016

heplesser commented Dec 14, 2016

jhnnsnk Nov 8, 2016 •

edited

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