Example #1
0
def setup(parameter_set,
          generate=False,
          duration=1080, #Match time run in Figure 1C of Kato et. al, Cell 2015 http://dx.doi.org/10.1016/j.cell.2015.09.034
          dt=0.1,
          target_directory='examples',
          include_muscles = True):

    exec('from parameters_%s import ParameterisedModel'%parameter_set)
    params = ParameterisedModel()

    # Match the labelled cells in Figure 1C of Kato et. al, Cell 2015 http://dx.doi.org/10.1016/j.cell.2015.09.034
    cells_to_stimulate = ["AVAR", "AVAL", "RIMR", "RIML", "AVER", "VA01", "SABVL", "OLQVL", "DB01", "VB01", "DB02", "RMER", "RMEL", "RID", "AVBR", "RIBL", "VB02", "RMED", "RMEV", "AVBL", "SMDVL", "SMDVR", "RIVL", "RIVR", "OLQVR", "OLQDL", "AIBL", "AIBR", "OLQDR", "RIFR", "SMBDR"]


    # Plot some directly stimulated & some not stimulated
    cells_to_plot = ["AVAR", "AVAL", "RIMR", "RIML", "AVER", "VA01", "SABVL", "OLQVL", "DB01", "VB01", "DB02", "RMER", "RMEL", "RID", "AVBR", "RIBL", "VB02", "RMED", "RMEV", "AVBL", "SMDVL", "SMDVR", "RIVL", "RIVR", "OLQVR", "OLQDL", "AIBL", "AIBR", "OLQDR", "RIFR", "SMBDR"]

    reference = "c302_%s_Kato"%parameter_set

    cell_names, conns = c302.get_cell_names_and_connection()

    if generate:
        c302.generate(reference,
             params,
             cells_to_plot=cells_to_plot,
             cells_to_stimulate=cells_to_stimulate,
             include_muscles = include_muscles,
             duration=duration,
             dt=dt,
             vmin=-72 if parameter_set=='A' else -52,
             vmax=-48 if parameter_set=='A' else -28,
             validate=(parameter_set!='B'),
             target_directory=target_directory)

    return cell_names, cells_to_stimulate, params, include_muscles
def setup(parameter_set, 
          generate=False,
          duration=500, 
          dt=0.1,
          target_directory='examples',
          include_muscles = True):
    
    exec('from parameters_%s import ParameterisedModel'%parameter_set)
    params = ParameterisedModel()
    
    # Some random set of neurons
    cells_to_stimulate = ["ADAL", "ADAR", "M1","M2L","M3L","M3R","M4","I1R","I2L","I5","I6","MI","NSMR","MCL","ASEL", "AVEL", "AWAR", "DB1", "DVC", "RIAR", "RMDDL"]
    
    # Plot some directly stimulated & some not stimulated
    cells_to_plot      = ["ADAL", "ADAR", "PVDR", "BDUR","I1R","I2L"]
    
    reference = "c302_%s_Full"%parameter_set
    
    cell_names, conns = c302.get_cell_names_and_connection()
    
    if generate:
        c302.generate(reference, 
             params, 
             cells_to_plot=cells_to_plot, 
             cells_to_stimulate=cells_to_stimulate, 
             include_muscles = include_muscles,
             duration=duration, 
             dt=dt, 
             vmin=-72 if parameter_set=='A' else -52, 
             vmax=-48 if parameter_set=='A' else -28,
             validate=(parameter_set!='B'),
             target_directory=target_directory) 
             
    return cell_names, cells_to_stimulate, params, include_muscles
Example #3
0
def setup(
        parameter_set,
        generate=False,
        duration=1000,
        dt=0.05,
        target_directory='examples',
        muscles_to_include=None,  # None => All!
        data_reader="SpreadsheetDataReader",
        param_overrides={},
        config_param_overrides={},
        verbose=True):

    exec('from parameters_%s import ParameterisedModel' % parameter_set,
         globals())
    params = ParameterisedModel()

    # Some random set of neurons
    cells_to_stimulate = [
        "ADAL", "ADAR", "M1", "M2L", "M3L", "M3R", "M4", "I1R", "I2L", "I5",
        "I6", "MI", "NSMR", "MCL", "ASEL", "AVEL", "AWAR", "DB1", "DVC",
        "RIAR", "RMDDL"
    ]
    cells_to_stimulate = ['PVCL', 'PVCR']
    cells_to_stimulate = ['PLML', 'PLMR']
    #cells_to_stimulate = ['AVBL','AVBR']

    # Plot some directly stimulated & some not stimulated
    cells_to_plot = ["ADAL", "ADAR", "PVDR", "BDUR", "I1R", "I2L"]
    cells_to_plot = [
        'AVBL', 'AVBR', 'PVCL', 'PVCR', 'DB1', 'DB2', 'VB1', 'VB2', 'DD1',
        'DD2', 'VD1', 'VD2'
    ]

    reference = "c302_%s_Full" % parameter_set

    cell_names, conns = c302.get_cell_names_and_connection()

    nml_doc = None

    if generate:
        nml_doc = c302.generate(reference,
                                params,
                                cells_to_plot=cells_to_plot,
                                cells_to_stimulate=cells_to_stimulate,
                                muscles_to_include=muscles_to_include,
                                duration=duration,
                                dt=dt,
                                vmin=-72 if parameter_set == 'A' else -52,
                                vmax=-48 if parameter_set == 'A' else -28,
                                target_directory=target_directory,
                                param_overrides=param_overrides,
                                verbose=verbose,
                                data_reader=data_reader)

    return cell_names, cells_to_stimulate, params, muscles_to_include, nml_doc
Example #4
0
def setup(
        parameter_set,
        generate=False,
        duration=1080,  #Match time run in Figure 1C of Kato et. al, Cell 2015 http://dx.doi.org/10.1016/j.cell.2015.09.034
        dt=0.1,
        target_directory='examples',
        muscles_to_include=None,
        data_reader="SpreadsheetDataReader",
        param_overrides={},
        config_param_overrides={},
        verbose=True):

    exec('from parameters_%s import ParameterisedModel' % parameter_set)
    params = ParameterisedModel()

    # Match the labelled cells in Figure 1C of Kato et. al, Cell 2015 http://dx.doi.org/10.1016/j.cell.2015.09.034
    cells_to_stimulate = [
        "AVAR", "AVAL", "RIMR", "RIML", "AVER", "VA01", "SABVL", "OLQVL",
        "DB01", "VB01", "DB02", "RMER", "RMEL", "RID", "AVBR", "RIBL", "VB02",
        "RMED", "RMEV", "AVBL", "SMDVL", "SMDVR", "RIVL", "RIVR", "OLQVR",
        "OLQDL", "AIBL", "AIBR", "OLQDR", "RIFR", "SMBDR"
    ]

    # Plot some directly stimulated & some not stimulated
    cells_to_plot = [
        "AVAR", "AVAL", "RIMR", "RIML", "AVER", "VA01", "SABVL", "OLQVL",
        "DB01", "VB01", "DB02", "RMER", "RMEL", "RID", "AVBR", "RIBL", "VB02",
        "RMED", "RMEV", "AVBL", "SMDVL", "SMDVR", "RIVL", "RIVR", "OLQVR",
        "OLQDL", "AIBL", "AIBR", "OLQDR", "RIFR", "SMBDR"
    ]

    reference = "c302_%s_Kato" % parameter_set

    cell_names, conns = c302.get_cell_names_and_connection()

    if generate:
        c302.generate(reference,
                      params,
                      cells_to_plot=cells_to_plot,
                      cells_to_stimulate=cells_to_stimulate,
                      muscles_to_include=muscles_to_include,
                      duration=duration,
                      dt=dt,
                      vmin=-72 if parameter_set == 'A' else -52,
                      vmax=-48 if parameter_set == 'A' else -28,
                      target_directory=target_directory,
                      param_overrides=param_overrides,
                      verbose=verbose,
                      data_reader=data_reader)

    return cell_names, cells_to_stimulate, params, muscles_to_include
Example #5
0
def setup(parameter_set, 
          generate=False,
          duration=1000, 
          dt=0.05,
          target_directory='examples',
          muscles_to_include = None, # None => All!
          data_reader="SpreadsheetDataReader",
          param_overrides={},
          config_param_overrides={},
          verbose=True):
    
    exec('from parameters_%s import ParameterisedModel'%parameter_set, globals())
    params = ParameterisedModel()
    
    # Some random set of neurons
    cells_to_stimulate = ["ADAL", "ADAR", "M1","M2L","M3L","M3R","M4","I1R","I2L","I5","I6","MI","NSMR","MCL","ASEL", "AVEL", "AWAR", "DB1", "DVC", "RIAR", "RMDDL"]
    cells_to_stimulate = ['PVCL','PVCR']
    cells_to_stimulate = ['PLML','PLMR']
    #cells_to_stimulate = ['AVBL','AVBR']
    
    # Plot some directly stimulated & some not stimulated
    cells_to_plot      = ["ADAL", "ADAR", "PVDR", "BDUR","I1R","I2L"]
    cells_to_plot      = ['AVBL','AVBR','PVCL', 'PVCR', 'DB1','DB2','VB1','VB2','DD1','DD2','VD1','VD2']
    
    reference = "c302_%s_Full"%parameter_set
    
    cell_names, conns = c302.get_cell_names_and_connection()
    
    nml_doc = None
    
    if generate:
        nml_doc = c302.generate(reference, 
             params, 
             cells_to_plot=cells_to_plot, 
             cells_to_stimulate=cells_to_stimulate, 
             muscles_to_include = muscles_to_include,
             duration=duration, 
             dt=dt, 
             vmin=-72 if parameter_set=='A' else -52, 
             vmax=-48 if parameter_set=='A' else -28,
             target_directory=target_directory,
             param_overrides=param_overrides,
             verbose=verbose,
             data_reader=data_reader)
             
    return cell_names, cells_to_stimulate, params, muscles_to_include, nml_doc
Example #6
0
def setup(parameter_set,
          generate=False,
          duration=1000,
          dt=0.05,
          target_directory='examples',
          include_muscles=True):

    exec('from parameters_%s import ParameterisedModel' % parameter_set)
    params = ParameterisedModel()

    # Some random set of neurons
    cells_to_stimulate = [
        "ADAL", "ADAR", "M1", "M2L", "M3L", "M3R", "M4", "I1R", "I2L", "I5",
        "I6", "MI", "NSMR", "MCL", "ASEL", "AVEL", "AWAR", "DB1", "DVC",
        "RIAR", "RMDDL"
    ]
    cells_to_stimulate = ['PVCL', 'PVCR']

    # Plot some directly stimulated & some not stimulated
    cells_to_plot = ["ADAL", "ADAR", "PVDR", "BDUR", "I1R", "I2L"]
    cells_to_plot = [
        'AVBL', 'AVBR', 'PVCL', 'PVCR', 'DB1', 'DB2', 'VB1', 'VB2', 'DD1',
        'DD2', 'VD1', 'VD2'
    ]

    reference = "c302_%s_Full" % parameter_set

    cell_names, conns = c302.get_cell_names_and_connection()

    if generate:
        c302.generate(reference,
                      params,
                      cells_to_plot=cells_to_plot,
                      cells_to_stimulate=cells_to_stimulate,
                      include_muscles=include_muscles,
                      duration=duration,
                      dt=dt,
                      vmin=-72 if parameter_set == 'A' else -52,
                      vmax=-48 if parameter_set == 'A' else -28,
                      validate=(parameter_set != 'B'),
                      target_directory=target_directory)

    return cell_names, cells_to_stimulate, params, include_muscles