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Updates recording of currents provided by stimulating devices #720

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appukuttan-shailesh opened this Issue May 15, 2017 · 2 comments

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appukuttan-shailesh commented May 15, 2017

This is a continuation of the discussion towards the end of #663.

The following needs to be updated:

  • Setting the recordables: GetDefaults('..._generator')['recordables']
  • Appropriate updates to unit test to include above
  • For noise generator, set current = 0, when no target neuron connected
  • For noise generator, keep the current value constant for the duration of noise_generator's dt
    (solutions for above discussed in #663)

One outstanding issue is possibly regarding the current generated by AC source. Consider the following:
ac = nest.Create('ac_generator', 1, params = {'amplitude': 550.0, 'offset': 1000.0, 'frequency': 100.0, 'phase' : 0.0, 'origin' : 2.5, 'start' : 2.5, 'stop' : 40.0})

The values that are computed are:

t (ms) <-> I (pA)
4.9    <-> 0.0
5.0    <-> 1034.53478574
5.1    <-> 1068.93327846
5.2    <-> 1103.05972302

min_delay = 1.0

t (ms) <-> V (mV)
5.9    <-> -70.0
6.0    <-> -70.0
6.1    <-> -69.58756241
6.2    <-> -69.16415163

Shouldn't the value at t = 5.0, be I = 1000.00.... i.e. offset + sin(t=0).
ac_jump_v2
For Brian and NEURON, the current and voltage values are as follows:
(ignoring timestamps owing to differences in simulator execution)

Current:
0.0
1000.0
1034.53479
1068.93328
1103.05972

Voltage:
-70.0
-70.0
-69.90049751
-69.79805377
-69.69269695
-69.58446864

The absence of this value (1000.0) in NEST, I believe, causes a more abrupt change in both the current and voltage at the start of current injection as seen below, which is absent in the next cycle (starting at 15 ms). The change in Vm is more gradual in case of Brian and NEURON (as seen in the values above).

@heplesser , @gtrensch : Any thoughts on this? My current workaround for this is to compensate for the jump by adjusting the phase appropriately. But I believe there should be a more elegant fix, if this is infact considered an issue with the AC source.

@appukuttan-shailesh appukuttan-shailesh changed the title from Updates recording of signals provided by stimulating devices to Updates recording of currents provided by stimulating devices May 15, 2017

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appukuttan-shailesh May 15, 2017

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@gtrensch : I have pulled the changes from your repository and updated L348 here:
https://github.com/appukuttan-shailesh/nest-simulator/blob/bugfix_get_recordables/models/noise_generator.cpp#L348

Once we decide on the AC source, I shall create a pull request.

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appukuttan-shailesh commented May 15, 2017

@gtrensch : I have pulled the changes from your repository and updated L348 here:
https://github.com/appukuttan-shailesh/nest-simulator/blob/bugfix_get_recordables/models/noise_generator.cpp#L348

Once we decide on the AC source, I shall create a pull request.

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heplesser May 19, 2017

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@appukuttan-shailesh @gtrensch I will try to work on this early next week.

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heplesser commented May 19, 2017

@appukuttan-shailesh @gtrensch I will try to work on this early next week.

appukuttan-shailesh added a commit to appukuttan-shailesh/nest-simulator that referenced this issue May 24, 2017

appukuttan-shailesh added a commit to appukuttan-shailesh/nest-simulator that referenced this issue May 25, 2017

@heplesser heplesser closed this in 9b0c0b4 May 26, 2017

heplesser added a commit that referenced this issue May 29, 2017

Merge pull request #733 from appukuttan-shailesh/bugfix_get_recordables
Fixes #720 Issues related to current recording from devices
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