mitral_responses.append(array(mitral._vmTableSoma))
return (mitral_responses, mitral_responses_binned)
#----------------------------------------------------------------
if __name__ == "__main__":
sim = constOdorResponse()
includeProjections = []
tweaks = build_tweaks(CLUB_MITRALS, NO_SPINE_INH, NO_SINGLES,\
NO_JOINTS, NO_MULTIS, NO_PGS, ONLY_TWO_MITS, includeProjections)
BINNED = True
## if not BINNED, save the full mitral Vm-s
## and not just their spiketimes by setting spiketable = False below.
network = OBNetwork(OBNet_file, synchan_activation_correction, tweaks,\
mpirank=mpirank, invivo=IN_VIVO, spiketable=BINNED)
#printNetTree() # from moose_utils.py
## monitor those interneurons that are connected to mitral indices 0 and 1
## save only spiketimes by setting extras_spikes_only=True
sim.setupStim(network, avgnum=0)
mitral_responses, mitral_responses_binned = sim.run(network, BINNED)
figure()
title('Glomerulus 0')
if BINNED:
deltabin = RESPIRATION / NUMBINS
# Take only the last respiration cycle
timevec = arange(
SETTLETIME + (NUM_RESPS - 1) * RESPIRATION + deltabin / 2, RUNTIME,
deltabin)
mitral_responses = mitral_responses_binned
#### if only one process is called, plot one odor directly
if mpisize == 1:
sim = odorResponse()
## includeProjections gets used only if ONLY_TWO_MITS is True:
## Keep below projections to 'second order cells'
## i.e. to cells (granules) connected to mits0&1.
## The connections between second order cell
## and mits0&1 are automatically retained of course.
## 'PG' includes 'ORN_PG', 'PG_mitral', 'mitral_PG' and 'SA_PG'
includeProjections = ['PG','granule_baseline']
tweaks = build_tweaks(CLUB_MITRALS, NO_SPINE_INH, NO_SINGLES, NO_JOINTS,\
NO_MULTIS, NO_PGS, ONLY_TWO_MITS, includeProjections, mitralsidekickidx)
BINNED = False
## if not BINNED, save the full mitral Vm-s
## and not just their spiketimes by setting spiketable = False below.
network = OBNetwork(OBNet_file, synchan_activation_correction, tweaks,\
mpirank, granfilebase, spiketable=BINNED)
#printNetTree() # from moose_utils.py
## monitor those interneurons that are connected to mitral indices 0 and 1
## save only spiketimes by setting extras_spikes_only=True
#extras_spikes_only = True
#tables = setupTables(network, NO_PGS, NO_SINGLES, NO_JOINTS,\
# {'mitrals':[0,1]}, spikes=extras_spikes_only)
avgnum = 0
inhnum = 5
sim.setupStim(network, inhnum, avgnum)
mitral_responses,mitral_responses_binned = sim.run(network,binned=BINNED)
#if not extras_spikes_only:
# timevec = arange(0.0,RUNTIME+1e-12,PLOTDT)
# plot_extras(timevec, tables, NO_PGS, NO_SINGLES, NO_JOINTS)
if len(sys.argv)>2: uniquestr = sys.argv[2]+'_' # _ necessary, else say 'morphs2'+mpirank is screwed
else: uniquestr = 'pulseinresp_'
#### if only one process is called, plot one odor directly
if mpisize == 1:
sim = odorResponse()
## 'PG' includes 'ORN_PG', 'PG_mitral', 'mitral_PG' and 'SA_PG'
if ONLY_TWO_MITS and not NO_PGS: includeProjections = ['PG']
else: includeProjections = []
tweaks = build_tweaks(CLUB_MITRALS, NO_SPINE_INH, NO_SINGLES,\
NO_JOINTS, NO_MULTIS, NO_PGS, ONLY_TWO_MITS,\
includeProjections=includeProjections, nolateral=NO_LATERAL)
BINNED = False
## if not BINNED, save the full mitral Vm-s
## and not just their spiketimes by setting spiketable = False below.
network = OBNetwork(OBNet_file, synchan_activation_correction, tweaks,\
mpirank, 'pulseinresp', granfilebase, spiketable=BINNED)
#printNetTree() # from moose_utils.py
## monitor those interneurons that are connected to mitral indices 0 and 1
## save only spiketimes by setting extras_spikes_only=True
extras_spikes_only = True
tables = setupTables(network, NO_PGS, NO_SINGLES, NO_JOINTS, NO_MULTIS,\
{'mitrals':[0,1]}, spikes=extras_spikes_only)
## To watch the pre compartment of mit2 that inhibits soma of mit 1
#mit2 = moose.Cell('/mitrals_2')
#mit2.precomp = moose.Compartment(get_matching_children(mit2, ['Seg0_sec_dendd4_4_278'])[0])
#mit2._vmTablePrecomp = setupTable("vmTablePrecomp",mit2.precomp,'Vm')
sim.setupStim(network, ('A',), avgnum=0)
## widely different resting potentials of mit0 and mit1
if VARY_MITS_RMP:
tweak_field('/mitrals_0/##[TYPE=Compartment]', 'Em', '-58e-3')
tweak_field('/mitrals_1/##[TYPE=Compartment]', 'Em', '-70e-3')
uniquestr = 'adi_'
## includeProjections gets used only if ONLY_TWO_MITS is True:
## Keep below projections to 'second order cells'
## i.e. to cells (granules) connected to mits0&1.
## The connections between second order cell
## and mits0&1 are automatically retained of course.
## no need for 'PG' below as 'ORN_PG' and 'SA_PG' are not needed,
## and 'PG_mitral', 'mitral_PG' connections to/from mits0&1 are kept automatically.
includeProjections = ['granule_baseline']
tweaks = build_tweaks( CLUB_MITRALS, NO_SPINE_INH,\
NO_SINGLES, NO_JOINTS, NO_MULTIS, NO_PGS, ONLY_TWO_MITS,\
includeProjections, (mitralmainidx,mitralsidekickidx) )
## send mpirank to put in ORN filenames / gran baseline temp files
## so they do not clash between mpi processes
## also, unique str, so that temp files of morphs, pulses, etc do not overlap
network = OBNetwork(OBNet_file, synchan_activation_correction,\
tweaks, mpirank, uniquestr, granfilebase, spiketable=SPIKETABLE)
#printNetTree() # from moose_utils.py
setup_stim(network)
## if SPIKETABLE: record the Vm-s of a few interneurons
## else: record spiketimes of all interneurons
tables = setupTables(network,
NO_PGS,
NO_SINGLES,
NO_JOINTS,
NO_MULTIS,
args={'mitrals': (mitralmainidx, )},
spikes=SPIKETABLE)
run_inhibition(network, tables)
if __name__ == "__main__":
#### if only one process is called, plot one sim directly
if mpisize == 1:
#### run the slave processes
sim = odorResponse()
## includeProjections gets used only if ONLY_TWO_MITS is True:
## Keep below projections to 'second order cells'
## i.e. to cells (granules) connected to mits0&1.
## The connections between second order cell
## and mits0&1 are automatically retained of course.
# 'PG' includes 'ORN_PG', 'PG_mitral', 'mitral_PG' and 'SA_PG'
includeProjections = ['PG','granule_baseline']
tweaks = build_tweaks(CLUB_MITRALS, NO_SPINE_INH, NO_SINGLES, NO_JOINTS,\
NO_MULTIS, NO_PGS, ONLY_TWO_MITS, includeProjections, mitralsidekickidx)
network = OBNetwork(OBNet_file, synchan_activation_correction, tweaks,\
mpirank, granfilebase+'_noresp', spiketable=False)
#printNetTree() # from moose_utils.py
trialnum = 0
sinnum = 0
sim.setupStim(network, sinnum, trialnum)
mitral_responses = sim.run(network, binned=False)
timevec = arange(SETTLETIME,SETTLETIME+SIN_RUNTIME+3*PLOTDT/2.0,PLOTDT)
plot(timevec, mitral_responses[0])
show()
#### multiple processes
else:
if mpirank == boss:
#### collate at boss process
## mitral_responses_list[avgnum][sinnum][mitnum][spikenum]
sim = PGvsGranule()
includeProjections = []
# the post_segment on the mitral must be ~ this distance from the soma
args = [100e-6, 'IPSP'] # meters
elif sim_option == 'PGvsGranuleIPSC':
sim = PGvsGranule()
includeProjections = []
# the post_segment on the mitral must be ~ this distance from the soma
args = [100e-6, 'IPSC'] # meters
else:
print "Sorry wrong option.", err_string
sys.exit(1)
tweaks = build_tweaks( CLUB_MITRALS, NO_SPINE_INH, NO_SINGLES, NO_JOINTS,\
NO_MULTIS, NO_PGS, ONLY_TWO_MITS, includeProjections, (mitralidx,mitralsidekickidx) )
network = OBNetwork(OBNet_file, synchan_activation_correction,\
tweaks, mpirank, granfilebase, spiketable=False)
#printNetTree() # from moose_utils.py
sim.setup_stim(network, args)
spikes = True
tables = setupTables(network, NO_PGS, NO_SINGLES, NO_JOINTS, spikes=spikes)
sim.run_inhibition(
network,
args) # tests simset_inhibition i.e. inhibition between two mitrals
if spikes:
bins = 20
timevec = arange(0.0, REALRUNTIME, REALRUNTIME / float(bins))
plot_extras_spikes(timevec, tables, NO_PGS, NO_SINGLES, NO_JOINTS,
bins, RUNTIME, SETTLETIME)
else:
timevec = arange(0.0, RUNTIME + 1e-12, PLOTDT)
if __name__ == "__main__":
if mpisize == 1:
## if only one process is called, plot one odor directly
sim = odorResponse()
## 'PG' includes 'ORN_PG', 'PG_mitral', 'mitral_PG' and 'SA_PG'
if ONLY_TWO_MITS and not NO_PGS: includeProjections = ['PG']
else: includeProjections = []
tweaks = build_tweaks(CLUB_MITRALS, NO_SPINE_INH, NO_SINGLES,\
NO_JOINTS, NO_MULTIS, NO_PGS, ONLY_TWO_MITS,\
includeProjections=includeProjections, nolateral=NO_LATERAL)
BINNED = True #False
## if not BINNED, save the full mitral Vm-s and
## not just their spiketimes by setting spiketable = False below.
uniquestr = 'pulses_'
network = OBNetwork(OBNet_file, synchan_activation_correction, tweaks,\
mpirank, uniquestr, granfilebase+'_noresp_extra', spiketable=BINNED)
#printNetTree() # from moose_utils.py
## monitor those interneurons that are connected to mitral indices 0 and 1
## save only spiketimes by setting spikes=True
extras_spikes_only = False #True
tables = setupTables(network, NO_PGS, NO_SINGLES, NO_JOINTS, NO_MULTIS,\
{'mitrals':[0,1]}, spikes=extras_spikes_only)
## pulse 0 is random air pulse, pulse 1 is odor A,
## pulse 2 is odor B, so on alternately, last pulse is A&B.
pulse_i = 1
sim.setupStim(network, pulse_i, avgnum=0)
## widely different resting potentials of mit0 and mit1
if VARY_MITS_RMP:
tweak_field('/mitrals_0/##[TYPE=Compartment]', 'Em', '-58e-3')
tweak_field('/mitrals_1/##[TYPE=Compartment]', 'Em', '-70e-3')
mit0soma_Im = setupTable('mit0somaIm', network.mitralTable[0].soma,