Python replace_cell_types 예제들

예제 #1

파일: ReducedColumn.py 프로젝트: OpenSourceBrain/Thalamocortical

import opencortex.utils as oc_utils
import opencortex.build as oc_build
import opencortex
from pyneuroml import pynml


include_these_synapses=oc_utils.replace_cell_types(net_file_name="TestRunColumnSubstitution",
                                                   path_to_net="./",
                                                   new_net_id="TestRunColumnReduced",
                                                   cell_types_to_be_replaced=["L23PyrRS","L23PyrFRB_varInit"],
                                                   cell_types_replaced_by=["HH_464198958","HH_471141261"],
                                                   dir_to_new_components="../../../../OpenCortex/NeuroML2/prototypes/AllenInstituteCellTypesDB_HH",
                                                   dir_to_old_components="../../cells",
                                                   reduced_to_single_compartment=True,
                                                   validate_nml2=False,
                                                   return_synapses=True,
                                                   connection_segment_groups=None,
                                                   input_segment_groups=None,
                                                   synapse_file_tags=['.synapse.','Syn','Elect']) 
                                                   
nml_doc=pynml.read_neuroml2_file("TestRunColumnReduced.net.nml")

network=nml_doc.networks[0]

lems_file_name=oc_build.generate_lems_simulation(nml_doc, 
                                                 network, 
                                                 "TestRunColumnReduced.net.nml", 
                                                 duration =100, 
                                                 dt =0.01,
                                                 include_extra_lems_files=include_these_synapses)
     

예제 #2

파일: SubstituteCellTypes.py 프로젝트: vrhaynes/Thalamocortical

include_these_synapses = oc_utils.replace_cell_types(
    net_file_name="TestRunColumnSubstitution",
    path_to_net="./",
    new_net_id="TestRunColumnAllenInstitute",
    cell_types_to_be_replaced=["L23PyrRS", "L23PyrFRB_varInit"],
    cell_types_replaced_by=["pyr_4_sym", "bask"],
    dir_to_new_components="../../../../OpenCortex/NeuroML2/prototypes/acnet2",
    dir_to_old_components="../../cells",
    reduced_to_single_compartment=False,
    validate_nml2=False,
    return_synapses=True,
    connection_segment_groups=[{
        'Type': 'Chem',
        'PreCellType': "pyr_4_sym",
        'PreSegGroup': "soma_group",
        'PostCellType': "pyr_4_sym",
        'PostSegGroup': "dendrite_group"
    }, {
        'Type': 'Chem',
        'PreCellType': "pyr_4_sym",
        'PreSegGroup': "soma_group",
        'PostCellType': "bask",
        'PostSegGroup': "dendrite_group"
    }, {
        'Type': 'Chem',
        'PreCellType': "bask",
        'PreSegGroup': "soma_group",
        'PostCellType': "bask",
        'PostSegGroup': "dendrite_group"
    }, {
        'Type': 'Chem',
        'PreCellType': "bask",
        'PreSegGroup': "soma_group",
        'PostCellType': "pyr_4_sym",
        'PostSegGroup': "dendrite_group"
    }, {
        'Type': 'Elect',
        'PreCellType': "pyr_4_sym",
        'PreSegGroup': "apical_dends",
        'PostCellType': "pyr_4_sym",
        'PostSegGroup': "apical_dends"
    }, {
        'Type': 'Elect',
        'PreCellType': "pyr_4_sym",
        'PreSegGroup': "soma_group",
        'PostCellType': "bask",
        'PostSegGroup': "dendrite_group"
    }, {
        'Type': 'Elect',
        'PreCellType': "bask",
        'PreSegGroup': "dendrite_group",
        'PostCellType': "bask",
        'PostSegGroup': "dendrite_group"
    }, {
        'Type': 'Elect',
        'PreCellType': "bask",
        'PreSegGroup': "dendrite_group",
        'PostCellType': "pyr_4_sym",
        'PostSegGroup': "dendrite_group"
    }],
    input_segment_groups=[{
        'PostCellType': "pyr_4_sym",
        'PostSegGroup': "dendrite_group"
    }, {
        'PostCellType': "bask",
        'PostSegGroup': "dendrite_group"
    }],
    synapse_file_tags=['.synapse.', 'Syn', 'Elect'])

예제 #3

파일: SubstituteCellTypes.py 프로젝트: OpenSourceBrain/Thalamocortical

import opencortex.utils as oc_utils
import opencortex.build as oc_build
import opencortex
from pyneuroml import pynml


include_these_synapses=oc_utils.replace_cell_types(net_file_name="TestRunColumnSubstitution",
                           path_to_net="./",
                           new_net_id="TestRunColumnAllenInstitute",
                           cell_types_to_be_replaced=["L23PyrRS","L23PyrFRB_varInit"],
                           cell_types_replaced_by=["pyr_4_sym","bask"],
                           dir_to_new_components="../../../../OpenCortex/NeuroML2/prototypes/acnet2",
                           dir_to_old_components="../../cells",
                           reduced_to_single_compartment=False,
                           validate_nml2=False,
                           return_synapses=True,
                           connection_segment_groups=[{'Type':'Chem','PreCellType':"pyr_4_sym",'PreSegGroup':"soma_group",'PostCellType':"pyr_4_sym",'PostSegGroup':"dendrite_group"},
                                                      {'Type':'Chem','PreCellType':"pyr_4_sym",'PreSegGroup':"soma_group",'PostCellType':"bask",'PostSegGroup':"dendrite_group"},
                                                      {'Type':'Chem','PreCellType':"bask",'PreSegGroup':"soma_group",'PostCellType':"bask",'PostSegGroup':"dendrite_group"},
                                                      {'Type':'Chem','PreCellType':"bask",'PreSegGroup':"soma_group",'PostCellType':"pyr_4_sym",'PostSegGroup':"dendrite_group"},
                                                      {'Type':'Elect','PreCellType':"pyr_4_sym",'PreSegGroup':"apical_dends",'PostCellType':"pyr_4_sym",'PostSegGroup':"apical_dends"},
                                                      {'Type':'Elect','PreCellType':"pyr_4_sym",'PreSegGroup':"soma_group",'PostCellType':"bask",'PostSegGroup':"dendrite_group"},
                                                      {'Type':'Elect','PreCellType':"bask",'PreSegGroup':"dendrite_group",'PostCellType':"bask",'PostSegGroup':"dendrite_group"},
                                                      {'Type':'Elect','PreCellType':"bask",'PreSegGroup':"dendrite_group",'PostCellType':"pyr_4_sym",'PostSegGroup':"dendrite_group"}],
                            input_segment_groups=[{'PostCellType':"pyr_4_sym",'PostSegGroup':"dendrite_group"},{'PostCellType':"bask",'PostSegGroup':"dendrite_group"}],
                            synapse_file_tags=['.synapse.','Syn','Elect'])
                            
nml_doc=pynml.read_neuroml2_file("TestRunColumnAllenInstitute.net.nml")

network=nml_doc.networks[0]

lems_file_name=oc_build.generate_lems_simulation(nml_doc, 

예제 #4

import opencortex.utils as oc_utils
import opencortex.build as oc_build
import opencortex
from pyneuroml import pynml

include_these_synapses = oc_utils.replace_cell_types(
    net_file_name="TestRunColumnSubstitution",
    path_to_net="./",
    new_net_id="TestRunColumnReduced",
    cell_types_to_be_replaced=["L23PyrRS", "L23PyrFRB_varInit"],
    cell_types_replaced_by=["HH_464198958", "HH_471141261"],
    dir_to_new_components=
    "../../../../OpenCortex/NeuroML2/prototypes/AllenInstituteCellTypesDB_HH",
    dir_to_old_components="../../cells",
    reduced_to_single_compartment=True,
    validate_nml2=False,
    return_synapses=True,
    connection_segment_groups=None,
    input_segment_groups=None,
    synapse_file_tags=['.synapse.', 'Syn', 'Elect'])

nml_doc = pynml.read_neuroml2_file("TestRunColumnReduced.net.nml")

network = nml_doc.networks[0]

lems_file_name = oc_build.generate_lems_simulation(
    nml_doc,
    network,
    "TestRunColumnReduced.net.nml",
    duration=100,
    dt=0.01,