def process_distributed_sm_measurement(directory):
from topo.command.basic import load_snapshot
import cPickle as pickle
data_dict = {}
load_snapshot('snapshot.typ')
for a in os.listdir(directory):
b = os.path.join(directory,a);
b = os.path.join(b,'dict.dat');
f = open(b,'r')
d = pickle.load(f)
data_dict.update(d)
sa = surround_analysis()
for (x,y) in data_dict.keys():
sa.plot_size_tunning(x,y)
sa.plot_orientation_contrast_tuning_abs(x,y)
self.plot_histograms_of_measures()
#lhi = compute_local_homogeneity_index(self.sheet.sheet_views['OrientationPreference'].view()[0]*pi,0.5)
#self.plot_map_feature_to_surround_modulation_feature_correlations(lhi,"Local Homogeneity Index")
#self.plot_map_feature_to_surround_modulation_feature_correlations(self.sheet.sheet_views['OrientationSelectivity'].view()[0],"OrientationSelectivity")
#self.plot_map_feature_to_surround_modulation_feature_correlations(self.sheet.sheet_views['OrientationPreference'].view()[0]*numpy.pi,"OrientationPreference")
def compare_with_and_without_snapshot_LoadSnapshot(script="examples/lissom.ty"):
data_filename=os.path.split(script)[1]+"_PICKLETEST"
snapshot_filename=os.path.split(script)[1]+"_PICKLETEST.typ_"
locn = resolve_path(os.path.join('tests',data_filename))
print "Loading pickle from %s"%locn
try:
data = pickle.load(open(locn,"rb"))
except IOError:
print "\nData file '"+data_filename+"' could not be opened; run _A() first"
raise
# retrieve parameters used when script was run
run_for=data['run_for']
break_at=data['break_at']
look_at=data['look_at']
# # CEBALERT: shouldn't need to re-list - should be able to read from data!
# cortex_density=data['cortex_density']
# lgn_density=data['lgn_density']
# retina_density=data['retina_density']
# dims=data['dims']
# dataset=data['dataset']
from topo.command.basic import load_snapshot
locn = resolve_path(os.path.join('tests',snapshot_filename))
print "Loading snapshot at %s"%locn
try:
load_snapshot(locn)
except IOError:
print "\nPickle file '"+snapshot_filename+"' could not be opened; run _B() first."
raise
assert topo.sim.time()==break_at
assert_array_equal(data[topo.sim.time()],topo.sim[look_at].activity,
err_msg="\nAt topo.sim.time()=%d"%topo.sim.time())
print "Match at %s after loading snapshot"%topo.sim.time()
topo.sim.run(run_for-break_at)
assert_array_equal(data[topo.sim.time()],topo.sim[look_at].activity,
err_msg="\nAt topo.sim.time()=%d"%topo.sim.time())
print "Match at %s after running loaded snapshot"%topo.sim.time()
def loadModelSnapshot(saveSnapshotTime,
LGNRingNo=5, V1RingNo=5, basename='snapshot'):
# LGNRingNo and V1RingNo are paramters that change the model structure
typPath = '../models/snapshots/'
loadSnapshot = "%s-LGN%s-V1%s-T%s.typ" % (basename, str(LGNRingNo), str(V1RingNo), str(saveSnapshotTime))
if saveSnapshotTime is not None:
fullTypPath = typPath+loadSnapshot
snapshotExists = os.path.exists(fullTypPath)
# Load snapshot and return
if snapshotExists:
print "Loading snapshot %s" % loadSnapshot
load_snapshot(typPath+loadSnapshot)
print ("Snapshot %s loaded." % loadSnapshot)
return False
else:
# saveSnapshotFlag. True indicates a snapshot is needed as it is desired but doesn't exist.
return True
else:
return False
def process_distributed_sm_measurement(directory):
from topo.command.basic import load_snapshot
import cPickle as pickle
data_dict = {}
load_snapshot('snapshot.typ')
for a in os.listdir(directory):
b = os.path.join(directory,a);
b = os.path.join(b,'dict.dat');
f = open(b,'r')
d = pickle.load(f)
data_dict.update(d)
sa = surround_analysis()
for (x,y) in data_dict.keys():
sa.plot_size_tunning(x,y)
sa.plot_orientation_contrast_tuning_abs(x,y)
self.plot_histograms_of_measures()
def GCALTemporal(stimulus = None,
timestep=0.5,
ringParams = ('MAX','MAX'),
saveSnapshotTime = None,
plastic=True,
LGN_TC = None,
LGNFFStrength = 2.33,
GCStrength=0.6,
GCDelay=0.01,
LGNDistanceDelay=None,
# V1 Settings
V1_TC = None,
V1FFStrength=1.5,
ExcStrength=1.7,
InhStrength=-1.4,
LateralDelay=0.01,
V1DistanceDelay=None,
HomeoFactor=1.0,
HomeoPlastic = False ):
VSDSheetFlag = True; saveSnapshotFlag = False; LOAD = None
###################################################
# Modifying sheets #
####################
modelName = 'fit-LGN-V1.py'
(LGNRingNo,V1RingNo) = ringParams
if LOAD is not None:
typPath = '../models/snapshots/'
load_snapshot(typPath+LOAD)
else:
print "Modifying model loaded in memory"
########################
# Sheets Modifications #
########################
p = gcal_vanilla.makeParams()
gcal_vanilla.makeSheets(p)
# Switch out the LISSOM sheets for continuous ones
switchAllSheets(VSDSheetFlag)
# Setup the input generator
setupRetina(stimulus, timestep)
# Connecting with original GCAL connections
gcal_vanilla.connectGCAL(p,LGNRingNo,V1RingNo)
############################
# Connection Modifications #
############################
'Alternatively, could use topo.sheet[<name>].projection(<name>)'
conns = dict([(el.name,el) for el in topo.sim.connections()])
''' AfferentToLGNOn, AfferentToLGNOff, LGNOnAfferent, LGNOffAfferent,
GCLGNOn-*, GCLGNOff-*, LateralInhibitory-*, LateralExcitatory-*
'''
#######
# LGN #
#######
# FEEDFORWARD DELAY IS ABOUT 15MS FOR BOTH STAGES
# Afferent from Retina to LGNOn/Off. Delay and strength.
setConnDelay('AfferentToLGNOn',15.0,conns)
setConnDelay('AfferentToLGNOff',15.0,conns)
setConnStrength('AfferentToLGNOn', LGNFFStrength,conns)
setConnStrength('AfferentToLGNOff', LGNFFStrength,conns)
assert GCStrength > 0
modifyLateralConnections(conns, 'GCLGNOn', GCStrength, GCDelay, LGNDistanceDelay)
modifyLateralConnections(conns, 'GCLGNOff', GCStrength, GCDelay, LGNDistanceDelay)
######
# V1 #
######
setConnDelay('LGNOnAfferent',15.0,conns)
setConnDelay('LGNOffAfferent',15.0,conns)
setConnStrength('LGNOnAfferent', V1FFStrength,conns)
setConnStrength('LGNOffAfferent' ,V1FFStrength,conns)
assert ExcStrength > 0; assert InhStrength < 0
modifyLateralConnections(conns, 'LateralExcitatory', ExcStrength, LateralDelay, V1DistanceDelay)
modifyLateralConnections(conns, 'LateralInhibitory', InhStrength, LateralDelay, V1DistanceDelay)
##########################
# Sheet output functions #
##########################
setLGNOutputFns(LGN_TC)
setV1OutputFns(V1_TC, HomeoFactor, HomeoPlastic)
###############################
# Plasticity and snapshotting #
###############################
if saveSnapshotFlag:
setSheetPlasticity(plastic=True) # No point making snapshot if plasticity if off
saveSnapShot(saveSnapshotTime)
setSheetPlasticity(plastic) # Set as desired
import numpy
from contrib.jacommands import LateralOrientationAnnisotropy
from topo.analysis.featureresponses import MeasureResponseCommand, FeatureMaps, SinusoidalMeasureResponseCommand, FeatureCurveCommand
FeatureMaps.num_orientation=16
MeasureResponseCommand.scale=1.0
MeasureResponseCommand.duration=4.0
SinusoidalMeasureResponseCommand.frequencies=[2.4]
FeatureCurveCommand.num_orientation=16
FeatureCurveCommand.curve_parameters=[{"contrast":15},{"contrast":50},{"contrast":90}]
from topo.command.basic import load_snapshot
#load_snapshot('./DATA/LESI/LESI-NEW-SMALL/CCSimple_010000.00_ormap.typ')
load_snapshot('./DATA/LESI/LESI-NEW-LARGE-LargeRegion/CCSimple_010000.00_with_map.typ')
from topo.command.basic import wipe_out_activity, clear_event_queue
wipe_out_activity()
clear_event_queue()
from topo.pattern.basic import SineGrating, Disk
class SineGratingDiskTemp(SineGrating):
mask_shape = param.Parameter(default=Disk(smoothing=0,size=1.0))
def set_parameters(a,b,c,d,e,f,g,h,i,j,k,l,m):
print a,b,c,d,e,f,g,h,i,j,k,l,m
topo.sim["V1Simple"].projections()["V1SimpleFeedbackExc1"].strength=b
topo.sim["V1Simple"].projections()["V1SimpleFeedbackInh"].strength=c
topo.sim["V1Complex"].projections()["LongEE"].strength=d
from topo.numbergen import UniformRandom, BoundedNumber, ExponentialDecay
from topo.command.basic import pattern_present
from param import normalize_path
import numpy
from topo.analysis.featureresponses import MeasureResponseCommand, FeatureMaps, SinusoidalMeasureResponseCommand, FeatureCurveCommand
FeatureMaps.num_orientation=16
MeasureResponseCommand.scale=1.0
MeasureResponseCommand.duration=4.0
SinusoidalMeasureResponseCommand.frequencies=[2.4]
FeatureCurveCommand.num_orientation=16
FeatureCurveCommand.curve_parameters=[{"contrast":15},{"contrast":50},{"contrast":90}]
from topo.command.basic import load_snapshot
load_snapshot('CCSimple_010005_new_or_map.00.typ')
from topo.command.basic import wipe_out_activity, clear_event_queue
wipe_out_activity()
clear_event_queue()
from topo.pattern.basic import SineGrating, Disk
class SineGratingDiskTemp(SineGrating):
mask_shape = param.Parameter(default=Disk(smoothing=0,size=1.0))
def set_parameters(a,b,c,d,e,f,g,h,i,j,k,l):
print a,b,c,d,e,f,g,h,i,j,k,l
topo.sim["V1Simple"].projections()["V1SimpleFeedbackExc1"].strength=b
topo.sim["V1Simple"].projections()["V1SimpleFeedbackInh"].strength=c
topo.sim["V1Complex"].projections()["LongEE"].strength=d