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Merge pull request #11 from OpenSourceBrain/experimental
 Check for source_ids/channel_ids
2 parents 367dddd + 116f06d commit 129d6c2

13 files changed

Lines changed: 47 additions & 41 deletions

‎.github/workflows/omv-ci.yml‎

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@@ -13,7 +13,7 @@ jobs:
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strategy:
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fail-fast: false
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matrix:
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python-version: [ "3.9", "3.10", "3.11" ] # Brian no longer supported on py3.8
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python-version: [ "3.10", "3.12", "3.13" ] # Brian no longer supported on py3.9!
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engine: [ jNeuroML, jNeuroML_NEURON, jNeuroML_PyNN_NEURON, jNeuroML_validate, PyNN_NEURON, PyNN_Nest, PyNN_NeuroML, PyNN_Brian2]
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steps:
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- name: Install additional packages
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run: |
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pip install scipy sympy matplotlib cython tables
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# pip install 'numpy<=1.23.0' # see https://github.com/OpenSourceBrain/osb-model-validation/issues/91
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pip install matplotlib "cython<3.1.0" # let omv handle other deps...
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- name: Run OMV tests on engine ${{ matrix.engine }}

‎NeuroML2/ConnectionsTest.net.nml‎

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@@ -2,8 +2,8 @@
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<notes>
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This NeuroML 2 file has been generated from:
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PyNN v0.11.0
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libNeuroML v0.6.3
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pyNeuroML v1.3.7
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libNeuroML v0.6.8
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pyNeuroML v1.3.19
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</notes>
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<IF_cond_alpha id="IF_cond_alpha_pop_pre" cm="1.0" i_offset="0.9" tau_syn_E="2.0" tau_syn_I="5.0" v_init="-65.0" tau_m="20.0" tau_refrac="5.0" v_reset="-65.0" v_rest="-65.0" v_thresh="-50.0" e_rev_E="0.0" e_rev_I="-70.0"/>
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<IF_cond_alpha id="IF_cond_alpha_pop_post" cm="1.0" i_offset="0.9" tau_syn_E="2.0" tau_syn_I="5.0" v_init="-65.0" tau_m="20.0" tau_refrac="5.0" v_reset="-65.0" v_rest="-65.0" v_thresh="-50.0" e_rev_E="0.0" e_rev_I="-70.0"/>
@@ -17,38 +17,38 @@
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<property tag="radius" value="5"/>
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<property tag="color" value="0 0.6 0"/>
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<instance id="0">
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<location x="-9.771402205615921" y="41.107735197887862" z="8.380479496098125"/>
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<location x="67.968888080621582" y="-70.657158602734654" z="-18.315070185150397"/>
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</instance>
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<instance id="1">
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<location x="11.787241779479075" y="-22.917415323944468" z="-69.969358778846896"/>
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<location x="60.184476562654041" y="60.493279624680454" z="-4.759239011557659"/>
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</instance>
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<instance id="2">
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<location x="24.148166862976762" y="-10.126267539995236" z="-6.507356698049249"/>
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<location x="27.189024038368114" y="-73.036270319949594" z="-25.447207420452678"/>
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</instance>
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<instance id="3">
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<location x="-14.878199498615952" y="49.650874267039804" z="18.835272881150388"/>
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<location x="-24.852298939173203" y="-12.272599182378062" z="3.750079672379081"/>
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</instance>
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<instance id="4">
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<location x="37.92567221050809" y="-22.437678624311431" z="-38.190180651135641"/>
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<location x="24.133497816283622" y="10.517195276874403" z="-29.329915036014633"/>
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</instance>
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</population>
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<population id="pop_post" component="IF_cond_alpha_pop_post" size="5" type="populationList">
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<property tag="radius" value="5"/>
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<property tag="color" value="0 0.2 0.6"/>
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<instance id="0">
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<location x="-30.357177121657621" y="148.821597074248928" z="41.550393258456353"/>
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<location x="24.765200337632276" y="242.663676551724933" z="75.097696646567741"/>
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</instance>
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<instance id="1">
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<location x="-75.487951984450333" y="241.449664932469261" z="4.06371645195327"/>
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<location x="45.028559466580795" y="226.140823198868731" z="48.181218144946691"/>
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</instance>
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<instance id="2">
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<location x="53.196249421914075" y="144.47758109254687" z="46.851975572138628"/>
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<location x="52.54517028397283" y="161.954657204140887" z="-5.258407353297101"/>
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</instance>
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<instance id="3">
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<location x="-20.844985362062317" y="188.239068673352108" z="-57.809991974759043"/>
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<location x="-33.575509675391338" y="195.289896982416423" z="-19.682584593824927"/>
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</instance>
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<instance id="4">
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<location x="41.000859853632619" y="279.306766456403295" z="35.048479751214437"/>
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<location x="-14.798277951638838" y="173.216535964582647" z="93.772913738872958"/>
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</instance>
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</population>
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<projection id="pop_pre__TO__pop_post" presynapticPopulation="pop_pre" postsynapticPopulation="pop_post" synapse="syn__pop_pre__TO__pop_post">

‎NeuroML2/Inputs.net.nml‎

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<notes>
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This NeuroML 2 file has been generated from:
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PyNN v0.11.0
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libNeuroML v0.6.3
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pyNeuroML v1.3.7
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libNeuroML v0.6.8
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pyNeuroML v1.3.19
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</notes>
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<pulseGenerator id="DCSource_DCSource_0" delay="50.0ms" duration="350.0ms" amplitude="0.9nA"/>
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<compoundInput id="ACSource_ACSource_1">

‎NeuroML2/LEMS_Sim_Inputs.xml‎

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<!--
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This LEMS file has been generated from:
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PyNN v0.11.0
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libNeuroML v0.6.3
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pyNeuroML v1.3.7
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libNeuroML v0.6.8
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pyNeuroML v1.3.19
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-->
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<!-- Specify which component to run -->

‎NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml‎

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<!--
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This LEMS file has been generated from:
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PyNN v0.11.0
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libNeuroML v0.6.3
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pyNeuroML v1.3.7
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libNeuroML v0.6.8
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pyNeuroML v1.3.19
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-->
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<!-- Specify which component to run -->

‎NeuroML2/Positions.net.nml.h5‎

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‎NeuroML2/PyNN_NeuroML2_Export.net.nml‎

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<notes>
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This NeuroML 2 file has been generated from:
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PyNN v0.11.0
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libNeuroML v0.6.3
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pyNeuroML v1.3.7
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libNeuroML v0.6.8
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pyNeuroML v1.3.19
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</notes>
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<IF_curr_alpha id="IF_curr_alpha_pop_IF_curr_alpha" cm="1.0" i_offset="0.9" tau_syn_E="2.0" tau_syn_I="5.0" v_init="-65.0" tau_m="20.0" tau_refrac="10.0" v_reset="-62.0" v_rest="-65.0" v_thresh="-52.0"/>
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<IF_curr_exp id="IF_curr_exp_pop_IF_curr_exp" cm="1.0" i_offset="1.0" tau_syn_E="2.0" tau_syn_I="5.0" v_init="-65.0" tau_m="20.0" tau_refrac="8.0" v_reset="-70.0" v_rest="-65.0" v_thresh="-50.0"/>

‎PyNN/InputsTest.py‎

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data = pop.get_data('v', gather=False)
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analogsignal = data.segments[0].analogsignals[0]
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name = analogsignal.name
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source_ids = analogsignal.annotations['source_ids']
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def get_source_ids_as(analogsignal):
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if 'source_ids' in analogsignal.annotations:
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return analogsignal.annotations['source_ids']
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elif 'channel_ids' in analogsignal.annotations: # See https://github.com/NeuralEnsemble/PyNN/pull/762
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return analogsignal.annotations['channel_ids']
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source_ids = get_source_ids_as(analogsignal)
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filename = "%s_%s.dat"%(pop.label,name)
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print('Saving data recorded for %s in pop %s, global ids: %s to %s'%(name, pop.label, source_ids, filename))
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times_vm_a = []
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sim.end()
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if '-gui' in sys.argv:
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if simulator_name in ['neuron', 'nest', 'brian']:
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if simulator_name in ['neuron', 'nest', 'brian2']:
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import matplotlib.pyplot as plt
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print("Plotting results of simulation in %s"%simulator_name)

‎PyNN/LEMS_2007One_pynn.py‎

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This PyNN file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
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org.neuroml.export v1.10.1
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org.neuroml.model v1.10.1
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jLEMS v0.11.1
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org.neuroml.export v1.11.0
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org.neuroml.model v1.11.0
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jLEMS v0.12.0
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'''
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# Main PyNN script for: net1

‎PyNN/RS.mod‎

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COMMENT
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This NEURON file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
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org.neuroml.export v1.10.1
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org.neuroml.model v1.10.1
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jLEMS v0.11.1
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org.neuroml.export v1.11.0
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org.neuroml.model v1.11.0
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jLEMS v0.12.0
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ENDCOMMENT
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