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Generalise 2 regions connectivity definition #28

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52 changes: 12 additions & 40 deletions NeuroML2/GenerateNeuroMLlite.py
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Original file line number Diff line number Diff line change
Expand Up @@ -207,34 +207,7 @@ def internal_connections(pops, W, pre_pop, post_pop):
[l5e_l2e, l5e_l2i, l5e_l5e, l5e_l5i],
[l5i_l2e, l5i_l2i, l5i_l5e, l5i_l5i]], dtype='U14')

elif n_areas == 2:
v1_v1_l2e_l2e = v4_v4_l2e_l2e = 'wee'; v1_v1_l5e_l5e = v4_v4_l5e_l5e = 'wee'
v1_v1_l2e_l2i = v4_v4_l2e_l2i = 'wei'; v1_v1_l5e_l5i = v4_v4_l5e_l5i = 'wei'
v1_v1_l2i_l2e = v4_v4_l2i_l2e = 'wie'; v1_v1_l5i_l5e = v4_v4_l5i_l5e = 'wie'
v1_v1_l2i_l2i = v4_v4_l2i_l2i = 'wii'; v1_v1_l5i_l5i = v4_v4_l5i_l5i = 'wii'

v1_v1_l2e_l5e = v4_v4_l2e_l5e = 'l2e_l5e'; v1_v1_l2e_l5i = v4_v4_l2e_l5i = 0;
v1_v1_l5e_l2i = v4_v4_l5e_l2i = 'l5e_l2i'; v1_v1_l5e_l2e = v4_v4_l5e_l2e = 0;
v1_v1_l2i_l5e = v4_v4_l2i_l5e = 0; v1_v1_l5i_l2i = v4_v4_l5i_l2i = 0;
v1_v1_l5i_l2e = v4_v4_l5i_l2e = 0; v1_v1_l2i_l5i = v4_v4_l2i_l5i = 0;

# interareal
v1_v4_l2e_l2e = 'FF_l2e_l2e'; v4_v1_l2e_l2e = 0; v1_v4_l2e_l2i = v4_v1_l2e_l2i = 0; v1_v4_l2e_l5e = v4_v1_l2e_l5e = 0; v1_v4_l2e_l5i = v4_v1_l2e_l5i= 0;
v1_v4_l2i_l2e = v4_v1_l2i_l2e = 0; v1_v4_l2i_l2i = v4_v1_l2i_l2i = 0; v1_v4_l2i_l5e = v4_v1_l2i_l5e = 0; v1_v4_l2i_l5i = v4_v1_l2i_l5i= 0;
v1_v4_l5e_l2e = 0; v4_v1_l5e_l2e = 'FB_l5e_l2e'; v1_v4_l5e_l2i = 0; v4_v1_l5e_l2i = 'FB_l5e_l2i'; v1_v4_l5e_l5e = 0; v4_v1_l5e_l5e = 'FB_l5e_l5e'; v1_v4_l5e_l5i = 0; v4_v1_l5e_l5i= 'FB_l5e_l2i';
v1_v4_l5i_l2e = v4_v1_l5i_l2e = 0; v1_v4_l5i_l2i = v4_v1_l5i_l2i = 0; v1_v4_l5i_l5e = v4_v1_l5i_l5e = 0; v1_v4_l5i_l5i = v4_v1_l5i_l5i= 0;

W = np.array([ [v1_v1_l2e_l2e, v1_v1_l2e_l2i, v1_v1_l2e_l5e, v1_v1_l2e_l5i, v1_v4_l2e_l2e, v1_v4_l2e_l2i, v1_v4_l2e_l5e, v1_v4_l2e_l5i],
[v1_v1_l2i_l2e, v1_v1_l2i_l2i, v1_v1_l2i_l5e, v1_v1_l2i_l5i, v1_v4_l2i_l2e, v1_v4_l2i_l2i, v1_v4_l2i_l5e, v1_v4_l2i_l5i],
[v1_v1_l5e_l2e, v1_v1_l5e_l2i, v1_v1_l5e_l5e, v1_v1_l5e_l5i, v1_v4_l5e_l2e, v1_v4_l5e_l2i, v1_v4_l5e_l5e, v1_v4_l5e_l5i],
[v1_v1_l5i_l2e, v1_v1_l5i_l2i, v1_v1_l5i_l5e, v1_v1_l5i_l5i, v1_v4_l5i_l2e, v1_v4_l5i_l2i, v1_v4_l5i_l5e, v1_v4_l5i_l5i],
[v4_v1_l2e_l2e, v4_v1_l2e_l2i, v4_v1_l2e_l5e, v4_v1_l2e_l5i, v4_v4_l2e_l2e, v4_v4_l2e_l2i, v4_v4_l2e_l5e, v4_v4_l2e_l5i],
[v4_v1_l2i_l2e, v4_v1_l2i_l2i, v4_v1_l2i_l5e, v4_v1_l2i_l5i, v4_v4_l2i_l2e, v4_v4_l2i_l2i, v4_v4_l2i_l5e, v4_v4_l2i_l5i],
[v4_v1_l5e_l2e, v4_v1_l5e_l2i, v4_v1_l5e_l5e, v4_v1_l5e_l5i, v4_v4_l5e_l2e, v4_v4_l5e_l2i, v4_v4_l5e_l5e, v4_v4_l5e_l5i],
[v4_v1_l5i_l2e, v4_v1_l5i_l2i, v4_v1_l5i_l5e, v4_v1_l5i_l5i, v4_v4_l5i_l2e, v4_v4_l5i_l2i, v4_v4_l5i_l5e, v4_v4_l5i_l5i]],
dtype='U14')

elif n_areas > 2:
elif n_areas >= 2:

nlayers = 4 #(L2/3E, L5/6, L2/3I, L5/6I)

Expand Down Expand Up @@ -948,6 +921,13 @@ def internal_connections(pops, W, pre_pop, post_pop):

elif '-interareal' in sys.argv:
from interareal import interareal_analysis, interareal_plt
from itertools import product
import pandas as pd

ranking = pd.read_csv('../Python/interareal/areas_ranking.txt')
with open('../Python/interareal/connectivity.pickle', 'rb') as handle:
conn = pickle.load(handle)


# Set model settings
wee = JEE; wei = JIE; wie = JEI; wii = JII; l5e_l2i = .75; l2e_l5e = 1
Expand All @@ -957,7 +937,6 @@ def internal_connections(pops, W, pre_pop, post_pop):
minfreq_l23 = 30. # Hz
minfreq_l56 = 3. # Hz

net_id='Interareal'


if '-3rois' not in sys.argv and \
Expand All @@ -967,7 +946,8 @@ def internal_connections(pops, W, pre_pop, post_pop):
# Note: For testing porpose, only the rest simulation is performed if the flag '-analysis' is not
# passed
areas = ['V1', 'V4']
nareas = len(areas)
conn = get_connectivity(conn, areas, ranking, conn_bin=None)
net_id='Interareal_%d' %(len(areas))

# for testing purpose generate one single simulation
if '-analysis' in sys.argv:
Expand Down Expand Up @@ -1003,7 +983,7 @@ def internal_connections(pops, W, pre_pop, post_pop):
i_l5e_l2i=l5e_l2i, i_l2e_l5e=l2e_l5e,
areas=areas,
dt=dt, duration=duration, Iext=Iext_rest, count=stat,
net_id=net_id)
net_id=net_id, conn=conn)
# Run in some simulators
check_to_generate_or_run(sys.argv, sim_rest)
simulator = 'jNeuroML'
Expand All @@ -1018,7 +998,7 @@ def internal_connections(pops, W, pre_pop, post_pop):
i_l5e_l2i=l5e_l2i, i_l2e_l5e=l2e_l5e,
areas=areas,
dt=dt, duration=duration, Iext=Iext_stim, count=stat,
net_id=net_id)
net_id=net_id, conn=conn)
# Run in some simulators
check_to_generate_or_run(sys.argv, sim_stim)
simulator = 'jNeuroML'
Expand Down Expand Up @@ -1071,14 +1051,6 @@ def internal_connections(pops, W, pre_pop, post_pop):

else:
#Load the array with the ordered rank
from itertools import product
import pandas as pd

ranking = pd.read_csv('../Python/interareal/areas_ranking.txt')
with open('../Python/interareal/connectivity.pickle', 'rb') as handle:
conn = pickle.load(handle)



if '-3rois' in sys.argv:
areas = ['V1', 'V4', 'MT']
Expand Down
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