diff --git a/hnn_core/viz.py b/hnn_core/viz.py index c9d7513bd..88854be36 100644 --- a/hnn_core/viz.py +++ b/hnn_core/viz.py @@ -555,53 +555,6 @@ def plot_cells(net, ax=None, show=True): for cell_name in net.cell_types: if cell_name not in cell_names: cell_names.append(cell_name) -# import hnn_core -# from hnn_core import jones_2009_model, simulate_dipole -# import matplotlib as plt - -# net = jones_2009_model(add_drives_from_params= True) -# params = hnn_core.read_params('/home/mohamed/Desktop/PhD Thesis/auditory_evoked_simulation/HNN-AEF-main/HNN_Parameters/L_Contra.param') - -# def martinotti(n_cells): -# from hnn_core.cell import Section, Cell - -# cell_name = 'martinotti' -# pos = [(5, 5, 5)] * n_cells -# # pos = net.pos_dict['L5_basket'].copy() - -# end_pts = [[0, 0, 0], [0, 0, 39.]] -# soma = Section(L=39., diam=20., cm=0.85, -# Ra=200., end_pts=end_pts) -# soma.syns = ['gabaa', 'nmda'] - -# synapses = { -# 'gabaa': { -# 'e': -80, -# 'tau1': 0.5, -# 'tau2': 5. -# }, -# 'nmda': { -# 'e': 0, -# 'tau1': 1., -# 'tau2': 20. -# } -# } -# sect_loc = ['proximal'] - -# return Cell(cell_name, pos, -# sections=soma, -# synapses=synapses, -# topology=None, -# sect_loc=sect_loc, -# gid=0) - -# net.plot_cells() -# net._add_cell_type('L5_martinotti', pos='L5_basket' ,cell_template = None) - -# simulate_dipole(net, tstop = 100, record_vsec= 'all') - -# net.add_connection(src_gids='L5_martinotti', target_gids='L5_pyramidal', loc='apical_tuft', receptor='gabaa', weight= 0.025 , delay=1.0 ,lamtha=70.0 , allow_autapses= False, probability=1) - colors= dict() markers= dict() diff --git a/test_script.py b/test_script.py new file mode 100644 index 000000000..f9d4d0f02 --- /dev/null +++ b/test_script.py @@ -0,0 +1,66 @@ +import hnn_core +from hnn_core import jones_2009_model, simulate_dipole, Network +import numpy as np +import matplotlib as plt + +params = hnn_core.read_params('/home/mohamed/Desktop/PhD Thesis/auditory_evoked_simulation/HNN-AEF-main/HNN_Parameters/L_Contra.param') +net = jones_2009_model() + + +def martinotti_template(): + from hnn_core.cell import Section, Cell + + cell_name = 'martinotti' + pos = (5, 5, 5) + # pos = net.pos_dict['L5_basket'].copy() + + end_pts = [[0, 0, 0], [0, 0, 39.]] + sections = {'soma': Section(L=39., diam=20., cm=0.85, + Ra=200., end_pts=end_pts)} + sections['soma'].syns = ['gabaa', 'nmda'] + + synapses = { + 'gabaa': { + 'e': -80, + 'tau1': 0.5, + 'tau2': 5. + }, + 'nmda': { + 'e': 0, + 'tau1': 1., + 'tau2': 20. + } + } + sect_loc = dict(proximal=['soma'], distal=['soma']) + + return Cell(cell_name, pos, + sections=sections, + synapses=synapses, + topology=None, + sect_loc=sect_loc, + gid=None) + +x1= np.linspace(0, 7, 7) +y1= np.linspace(0, 5, 5) +xv, yv = np.meshgrid(x1, y1) +pos = list() +for (x, y) in zip(xv.ravel(), yv.ravel()): + pos.append((x, y, 0.)) + +# net._add_cell_type('L5_martinotti', pos= pos, cell_template=martinotti_template()) +# net.plot_cells() + +weights_nmda_d1 = {'L2_basket': 0.019482, 'L2_pyramidal': 0.004317, + 'L5_pyramidal': 0.080074} +synaptic_delays_d1 = {'L2_basket': 0.1, 'L2_pyramidal': 0.1, + 'L5_pyramidal': 0.1} +net.add_evoked_drive( + 'evdist1', mu=63.53, sigma=3.85, numspikes=1, weights_ampa=None, + weights_nmda=weights_nmda_d1, location='distal', + synaptic_delays=synaptic_delays_d1, event_seed=4) + +simulate_dipole(net, tstop = 100, record_vsec=False) + +# net.add_connection(src_gids='L5_martinotti', target_gids='L5_pyramidal', loc='apical_tuft', receptor='gabaa', weight= 0.025 , delay=1.0 ,lamtha=70.0 , allow_autapses= False, probability=1) + + \ No newline at end of file