Adding pyb script for generating stimulations

NeuroML2/GenerateIV.py

@@ -1,5 +1,5 @@
 import sys
-import opencortex.build as oc
+import opencortex.core as oc
 import numpy as np
 
 def generate(cell_id, duration, reference, iRange):

NeuroML2/GenerateStims.py

@@ -0,0 +1,94 @@
+import sys
+
+import opencortex.core as oc
+
+import numpy as np
+
+def generate(cell_id, duration, reference, bEnsyn):
+
+    bInsyn = int(bEnsyn * 0.2)
+
+    cell_file = '%s.cell.nml'%cell_id
+
+    nml_doc, network = oc.generate_network(reference, temperature='35degC')
+
+    oc.include_neuroml2_cell_and_channels(nml_doc,cell_file,cell_id)
+
+    oc.include_neuroml2_file(nml_doc,'AMPA.synapse.nml')
+    oc.include_neuroml2_file(nml_doc,'GABA.synapse.nml')
+    oc.include_neuroml2_file(nml_doc,'NMDA.synapse.nml')
+
+    ampa1 = oc.add_poisson_firing_synapse(nml_doc,
+                                       id="ampa1",
+                                       average_rate="50 Hz",
+                                       synapse_id='AMPA')
+
+    gaba1 = oc.add_poisson_firing_synapse(nml_doc,
+                                       id="gaba1",
+                                       average_rate="50 Hz",
+                                       synapse_id='GABA')
+
+    nmda1 = oc.add_poisson_firing_synapse(nml_doc,
+                                       id="nmda1",
+                                       average_rate="50 Hz",
+                                       synapse_id='NMDA')
+
+
+    pop = oc.add_single_cell_population(network,
+                                        'L23_pop',
+                                        cell_id)
+
+
+
+
+    oc.add_targeted_inputs_to_population(network, "bEsyn_a",
+                                pop, ampa1.id, 
+                                segment_group='dendrite_group',
+                                number_per_cell = bEnsyn,
+                                all_cells=True)
+
+    oc.add_targeted_inputs_to_population(network, "bEsyn_n",
+                                pop, nmda1.id, 
+                                segment_group='dendrite_group',
+                                number_per_cell = bEnsyn,
+                                all_cells=True)
+
+    oc.add_targeted_inputs_to_population(network, "bIsyn",
+                                pop, gaba1.id, 
+                                segment_group='dendrite_group',
+                                number_per_cell = bInsyn,
+                                all_cells=True)
+
+
+    nml_file_name = '%s.net.nml'%network.id
+    oc.save_network(nml_doc, nml_file_name, validate=True)
+
+    interesting_seg_ids = [0,200,1000,2000,2500,2949]
+
+    to_plot = {'Some_voltages':[]}
+    to_save = {'%s_voltages.dat'%cell_id:[]}
+
+    for seg_id in interesting_seg_ids:
+        to_plot.values()[0].append('%s/0/%s/%s/v'%(pop.id, pop.component,seg_id))
+        to_save.values()[0].append('%s/0/%s/%s/v'%(pop.id, pop.component,seg_id))
+
+    oc.generate_lems_simulation(nml_doc, 
+                                network, 
+                                nml_file_name, 
+                                duration, 
+                                dt = 0.025,
+                               gen_plots_for_all_v = False,
+                               plot_all_segments = False,
+                               gen_plots_for_quantities = to_plot,   #  Dict with displays vs lists of quantity paths
+                               gen_saves_for_all_v = False,
+                               save_all_segments = False,
+                               gen_saves_for_quantities = to_save)   #  Dict with file names vs lists of quantity paths)
+
+
+if __name__ == "__main__":
+
+    cell_id = 'L23_NoHotSpot'
+    reference = "L23_Stim"
+    duration = 200
+
+    generate(cell_id, duration, reference, 100)

NeuroML2/L23_IV.net.nml

@@ -1,12 +1,12 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta5.xsd" id="L23_IV">
     <notes>
 
-This NeuroML 2 file was generated by OpenCortex v0.0.8 using: 
+This NeuroML 2 file was generated by OpenCortex v0.1.0 using: 
     libNeuroML v0.2.29
     pyNeuroML v0.2.10
 
     </notes>
-    <property tag="Python random seed" value="1234"/>
+    <property tag="Network seed" value="1234"/>
     <include href="L23_NoHotSpot.cell.nml"></include>
     <include href="ca.channel.nml"></include>
     <include href="it.channel.nml"></include>