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jaanalysis.py
490 lines (400 loc) · 29.4 KB
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jaanalysis.py
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import numpy
import __main__
def t_function():
"""
Basic example of an analysis command for run_batch; users are
likely to need something similar but highly customized.
"""
print 'Called complex_analysis_function'
import topo
from topo.command.analysis import save_plotgroup
from topo.base.projection import ProjectionSheet
from topo.sheet import GeneratorSheet
from topo.analysis.featureresponses import SinusoidalMeasureResponseCommand,FeatureCurveCommand
import contrib.jacommands
exec "from topo.analysis.vision import analyze_complexity" in __main__.__dict__
print 'Analysing'
import matplotlib
matplotlib.rc('xtick', labelsize=17)
matplotlib.rc('ytick', labelsize=17)
print 'Build a list of all sheets worth measuring'
f = lambda x: hasattr(x,'measure_maps') and x.measure_maps
measured_sheets = filter(f,topo.sim.objects(ProjectionSheet).values())
input_sheets = topo.sim.objects(GeneratorSheet).values()
print 'Set potentially reasonable defaults; not necessarily useful'
topo.command.analysis.coordinate=(0.0,0.0)
if input_sheets: topo.command.analysis.input_sheet_name=input_sheets[0].name
if measured_sheets: topo.command.analysis.sheet_name=measured_sheets[0].name
FeatureCurveCommand.curve_parameters=[{"contrast":30},{"contrast":50},{"contrast":70},{"contrast":90}]
import numpy
# reset treshold and desable noise before measuring maps
#m = numpy.mean(topo.sim["V1Simple"].output_fns[2].t)
#topo.sim["V1Simple"].output_fns[2].t*=0
#topo.sim["V1Simple"].output_fns[2].t+=m
#sc = topo.sim["V1Simple"].output_fns[1].generator.scale
#topo.sim["V1Simple"].output_fns[1].generator.scale=0.0
#save_plotgroup("Orientation Preference and Complexity")
save_plotgroup("Orientation Preference")
def complex_analysis_function():
"""
Basic example of an analysis command for run_batch; users are
likely to need something similar but highly customized.
"""
print 'Called complex_analysis_function'
import topo
from topo.command.analysis import save_plotgroup
from topo.base.projection import ProjectionSheet
from topo.sheet import GeneratorSheet
from topo.analysis.featureresponses import SinusoidalMeasureResponseCommand,FeatureCurveCommand
import contrib.jacommands
exec "from topo.analysis.vision import analyze_complexity" in __main__.__dict__
print 'Analysing'
import matplotlib
matplotlib.rc('xtick', labelsize=17)
matplotlib.rc('ytick', labelsize=17)
print 'Build a list of all sheets worth measuring'
f = lambda x: hasattr(x,'measure_maps') and x.measure_maps
measured_sheets = filter(f,topo.sim.objects(ProjectionSheet).values())
input_sheets = topo.sim.objects(GeneratorSheet).values()
print 'Set potentially reasonable defaults; not necessarily useful'
topo.command.analysis.coordinate=(0.0,0.0)
if input_sheets: topo.command.analysis.input_sheet_name=input_sheets[0].name
if measured_sheets: topo.command.analysis.sheet_name=measured_sheets[0].name
FeatureCurveCommand.curve_parameters=[{"contrast":30},{"contrast":50},{"contrast":70},{"contrast":90}]
import numpy
# reset treshold and desable noise before measuring maps
#m = numpy.mean(topo.sim["V1Simple"].output_fns[2].t)
#topo.sim["V1Simple"].output_fns[2].t*=0
#topo.sim["V1Simple"].output_fns[2].t+=m
#sc = topo.sim["V1Simple"].output_fns[1].generator.scale
#topo.sim["V1Simple"].output_fns[1].generator.scale=0.0
a = topo.sim["V1Complex"].in_connections[0].strength
SinusoidalMeasureResponseCommand.scale=__main__.__dict__.get("analysis_scale",0.35)
MeasureResponseCommand.scale=__main__.__dict__.get("analysis_scale",0.35)
#if((float(topo.sim.time()) >= 5003.0) and (float(topo.sim.time()) < 5004.0)):
# topo.sim["V1Complex"].in_connections[0].strength=0
# SinusoidalMeasureResponseCommand.frequencies=[3.0]
# if((float(topo.sim.time()) >= 5005.0) and (float(topo.sim.time()) < 5006.0)):
# SinusoidalMeasureResponseCommand.frequencies=[3.0]
# if((float(topo.sim.time()) >= 5006.0) and (float(topo.sim.time()) < 5007.0)):
# topo.sim["V1Complex"].in_connections[0].strength=0
# SinusoidalMeasureResponseCommand.frequencies=[2.4]
# if((float(topo.sim.time()) >= 5007.0) and (float(topo.sim.time()) < 5008.0)):
# SinusoidalMeasureResponseCommand.frequencies=[2.4]
# if((float(topo.sim.time()) >= 10002.0) and (float(topo.sim.time()) < 10003.0)):
# topo.sim["V1Complex"].in_connections[0].strength=0
# SinusoidalMeasureResponseCommand.frequencies=[2.4]
# if((float(topo.sim.time()) >= 10003.0) and (float(topo.sim.time()) < 10004.0)):
# topo.sim["V1Complex"].in_connections[0].strength=0
# SinusoidalMeasureResponseCommand.frequencies=[3.0]
# if((float(topo.sim.time()) >= 10004.0) and (float(topo.sim.time()) < 10005.0)):
# SinusoidalMeasureResponseCommand.frequencies=[2.4]
# if((float(topo.sim.time()) >= 10005.0) and (float(topo.sim.time()) < 10006.0)):
# SinusoidalMeasureResponseCommand.frequencies=[3.0]
save_plotgroup("Orientation Preference and Complexity")
save_plotgroup("Activity")
# Plot all projections for all measured_sheets
for s in measured_sheets:
for p in s.projections().values():
save_plotgroup("Projection",projection=p)
if(float(topo.sim.time()) >= 10005.0):
print 'Measuring orientations'
SinusoidalMeasureResponseCommand.frequencies=[2.4]
topo.command.pylabplot.measure_or_tuning_fullfield.instance(sheet=topo.sim["V1Complex"])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0,0]",sheet=topo.sim["V1Complex"],coords=[(0,0)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.1,0.1]",sheet=topo.sim["V1Complex"],coords=[(0.1,0.1)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.1,-0.1]",sheet=topo.sim["V1Complex"],coords=[(0.1,-0.1)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[-0.1,0.1]",sheet=topo.sim["V1Complex"],coords=[(-0.1,0.1)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[-0.1,-0.1]",sheet=topo.sim["V1Complex"],coords=[(-0.1,-0.1)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.2,0.2]",sheet=topo.sim["V1Complex"],coords=[(0.2,0.2)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.2,-0.2]",sheet=topo.sim["V1Complex"],coords=[(0.2,-0.2)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[-0.2,0.2]",sheet=topo.sim["V1Complex"],coords=[(-0.2,0.2)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[-0.2,-0.2]",sheet=topo.sim["V1Complex"],coords=[(-0.2,-0.2)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0,0.1]",sheet=topo.sim["V1Complex"],coords=[(0.0,0.1)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0,-0.1]",sheet=topo.sim["V1Complex"],coords=[(0.0,-0.1)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[-0.1,0]",sheet=topo.sim["V1Complex"],coords=[(-0.1,0.0)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.1,0]",sheet=topo.sim["V1Complex"],coords=[(0.1,-0.0)])()
topo.command.pylabplot.measure_or_tuning_fullfield.instance(sheet=topo.sim["V1Simple"])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="SimpleORTC[0,0]",sheet=topo.sim["V1Simple"],coords=[(0,0)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="SimpleORTC[0.1,0.1]",sheet=topo.sim["V1Simple"],coords=[(0.1,0.1)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="SimpleORTC[0.1,-0.1]",sheet=topo.sim["V1Simple"],coords=[(0.1,-0.1)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="SimpleORTC[-0.1,0.1]",sheet=topo.sim["V1Simple"],coords=[(-0.1,0.1)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="SimpleORTC[-0.1,-0.1]",sheet=topo.sim["V1Simple"],coords=[(-0.1,-0.1)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="SimpleORTC[0.2,0.2]",sheet=topo.sim["V1Simple"],coords=[(0.2,0.2)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="SimpleORTC[0.2,-0.2]",sheet=topo.sim["V1Simple"],coords=[(0.2,-0.2)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="SimpleORTC[-0.2,0.2]",sheet=topo.sim["V1Simple"],coords=[(-0.2,0.2)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="SimpleORTC[-0.2,-0.2]",sheet=topo.sim["V1Simple"],coords=[(-0.2,-0.2)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="SimpleORTC[0,0.1]",sheet=topo.sim["V1Simple"],coords=[(0.0,0.1)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="SimpleORTC[0,-0.1]",sheet=topo.sim["V1Simple"],coords=[(0.0,-0.1)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="SimpleORTC[-0.1,0]",sheet=topo.sim["V1Simple"],coords=[(-0.1,0.0)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="SimpleORTC[0.1,0]",sheet=topo.sim["V1Simple"],coords=[(0.1,-0.0)])()
#topo.sim["V1Simple"].output_fns[1].generator.scale=sc
topo.sim["V1Complex"].in_connections[0].strength = a
#topo.sim["V1Complex"].in_connections[0].strength=st
def push_pull_analysis_function():
print 'Push pull complex_analysis_function'
import topo
import numpy
from topo.command.analysis import save_plotgroup
from topo.base.projection import ProjectionSheet
from topo.sheet import GeneratorSheet
from topo.analysis.featureresponses import SinusoidalMeasureResponseCommand,FeatureCurveCommand
import contrib.jacommands
from contrib.push_pull.CCLISSOM_push_pull_extra import check_RF_corrleation_vs_connection_weights_correlation
from param import normalize_path
exec "from topo.analysis.vision import analyze_complexity" in __main__.__dict__
SinusoidalMeasureResponseCommand.frequencies=[2.4]
SinusoidalMeasureResponseCommand.scale=__main__.__dict__.get("analysis_scale",1.0)
print 'Analysing'
import matplotlib
matplotlib.rc('xtick', labelsize=17)
matplotlib.rc('ytick', labelsize=17)
print 'Build a list of all sheets worth measuring'
f = lambda x: hasattr(x,'measure_maps') and x.measure_maps
measured_sheets = filter(f,topo.sim.objects(ProjectionSheet).values())
input_sheets = topo.sim.objects(GeneratorSheet).values()
print 'Set potentially reasonable defaults; not necessarily useful'
topo.command.analysis.coordinate=(0.0,0.0)
if input_sheets: topo.command.analysis.input_sheet_name=input_sheets[0].name
if measured_sheets: topo.command.analysis.sheet_name=measured_sheets[0].name
FeatureCurveCommand.curve_parameters=[{"contrast":30},{"contrast":50},{"contrast":70},{"contrast":90}]
save_plotgroup("Orientation Preference and Complexity")
save_plotgroup("Activity",normalize="Individually")
# Plot all projections for all measured_sheets
for s in measured_sheets:
for p in s.projections().values():
save_plotgroup("Projection",projection=p,density=3.0)
print 'Starting push pull analysis'
#analyse_push_pull_connectivity()
check_RF_corrleation_vs_connection_weights_correlation()
print 'Finished push pull analysis'
return
if(float(topo.sim.time()) >= 10005.0):
print 'Measuring orientations'
SinusoidalMeasureResponseCommand.frequencies=[2.4]
topo.command.pylabplot.measure_or_tuning_fullfield.instance(sheet=topo.sim["V1Simple"])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0,0]",sheet=topo.sim["V1Simple"],coords=[(0,0)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.1,0.1]",sheet=topo.sim["V1Simple"],coords=[(0.1,0.1)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.1,-0.1]",sheet=topo.sim["V1Simple"],coords=[(0.1,-0.1)])()
def complex_surround_analysis_function():
"""
Basic example of an analysis command for run_batch; users are
likely to need something similar but highly customized.
"""
import topo
from topo.command.analysis import save_plotgroup
from topo.analysis.featureresponses import SinusoidalMeasureResponseCommand,FeatureCurveCommand
from topo.base.projection import ProjectionSheet
from topo.sheet import GeneratorSheet
from topo.command import save_snapshot
from param import normalize_path
import contrib.jacommands
import contrib.surround_analysis_new_cleaned
exec "from topo.analysis.vision import analyze_complexity" in __main__.__dict__
import matplotlib
matplotlib.rc('xtick', labelsize=17)
matplotlib.rc('ytick', labelsize=17)
SinusoidalMeasureResponseCommand.frequencies=[2.4]
SinusoidalMeasureResponseCommand.scale=__main__.__dict__.get("analysis_scale",0.3)
from topo.analysis.featureresponses import PatternPresenter
PatternPresenter.duration=4.0
import topo.command.pylabplot
reload(topo.command.pylabplot)
# Build a list of all sheets worth measuring
f = lambda x: hasattr(x,'measure_maps') and x.measure_maps
measured_sheets = filter(f,topo.sim.objects(ProjectionSheet).values())
input_sheets = topo.sim.objects(GeneratorSheet).values()
# Set potentially reasonable defaults; not necessarily useful
topo.command.analysis.coordinate=(0.0,0.0)
if input_sheets: topo.command.analysis.input_sheet_name=input_sheets[0].name
if measured_sheets: topo.command.analysis.sheet_name=measured_sheets[0].name
save_plotgroup("Orientation Preference and Complexity")
save_plotgroup("Activity",normalize='Individually')
# Plot all projections for all measured_sheets
for s in measured_sheets:
for p in s.projections().values():
save_plotgroup("Projection",projection=p)
if(float(topo.sim.time()) > 6020.0):
if __main__.__dict__.get("save",False):
save_snapshot(normalize_path('snapshot.typ'))
#contrib.surround_analysis.run_dynamics_analysis(0.0,0.0,0.7,__main__.__dict__.get("analysis_scale",0.3))
#topo.command.pylabplot.measure_or_tuning_fullfield.instance(sheet=topo.sim["V1Complex"])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0,0]",sheet=topo.sim["V1Complex"],coords=[(0,0)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.1,0.1]",sheet=topo.sim["V1Complex"],coords=[(0.1,0.1)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.1,-0.1]",sheet=topo.sim["V1Complex"],coords=[(0.1,-0.1)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[-0.1,0.1]",sheet=topo.sim["V1Complex"],coords=[(-0.1,0.1)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[-0.1,-0.1]",sheet=topo.sim["V1Complex"],coords=[(-0.1,-0.1)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.2,0.2]",sheet=topo.sim["V1Complex"],coords=[(0.2,0.2)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.2,-0.2]",sheet=topo.sim["V1Complex"],coords=[(0.2,-0.2)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[-0.2,0.2]",sheet=topo.sim["V1Complex"],coords=[(-0.2,0.2)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[-0.2,-0.2]",sheet=topo.sim["V1Complex"],coords=[(-0.2,-0.2)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0,0.1]",sheet=topo.sim["V1Complex"],coords=[(0.0,0.1)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0,-0.1]",sheet=topo.sim["V1Complex"],coords=[(0.0,-0.1)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[-0.1,0]",sheet=topo.sim["V1Complex"],coords=[(-0.1,0.0)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.1,0]",sheet=topo.sim["V1Complex"],coords=[(0.1,-0.0)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.3,0.3]",sheet=topo.sim["V1Complex"],coords=[(0.3,0.3)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.3,-0.3]",sheet=topo.sim["V1Complex"],coords=[(0.3,-0.3)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[-0.3,0.3]",sheet=topo.sim["V1Complex"],coords=[(-0.3,0.3)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[-0.3,-0.3]",sheet=topo.sim["V1Complex"],coords=[(-0.3,-0.3)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.24,0.24]",sheet=topo.sim["V1Complex"],coords=[(0.24,0.24)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.24,-0.24]",sheet=topo.sim["V1Complex"],coords=[(0.24,-0.24)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[-0.24,0.24]",sheet=topo.sim["V1Complex"],coords=[(-0.24,0.42)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[-0.24,-0.24]",sheet=topo.sim["V1Complex"],coords=[(-0.24,-0.24)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0,0.24]",sheet=topo.sim["V1Complex"],coords=[(0.0,0.24)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0,-0.24]",sheet=topo.sim["V1Complex"],coords=[(0.0,-0.42)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[-0.24,0]",sheet=topo.sim["V1Complex"],coords=[(-0.24,0.0)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.24,0]",sheet=topo.sim["V1Complex"],coords=[(0.24,-0.0)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0,0.3]",sheet=topo.sim["V1Complex"],coords=[(0.0,0.3)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0,-0.3]",sheet=topo.sim["V1Complex"],coords=[(0.0,-0.3)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[-0.3,0]",sheet=topo.sim["V1Complex"],coords=[(-0.3,0.0)])()
#topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.3,0]",sheet=topo.sim["V1Complex"],coords=[(0.3,-0.0)])()
#contrib.surround_analysis_new_cleaned.surround_analysis("V1Complex").run_analysis_with_step_grid(4,4,max_curves=__main__.__dict__.get("max_curves",20))
contrib.surround_analysis_new_cleaned.surround_analysis("V1Complex").run_lhi_informed_analysis(max_curves=__main__.__dict__.get("max_curves",20),center_size=__main__.__dict__.get("center_size",20))
#contrib.surround_analysis_new.surround_analysis("V1Complex").analyse([(0,0),(3,0),(-3,0),(0,3),(0,-3),(3,3),(3,-3),(-3,3),(-3,-3),(6,0),(-6,0),(0,6),(0,-6),(6,6),(6,-6),(-6,6),(-6,-6)],__main__.__dict__.get("number_sizes",10))
#contrib.surround_analysis_new.surround_analysis("V1Complex").analyse([(57,57),(53,67),(57,59),(61,63),(53,49),(67,65),(51,67),(67,61),(55,49),(47,59),(63,51)],__main__.__dict__.get("number_sizes",10))
def v2_analysis_function():
"""
Basic example of an analysis command for run_batch; users are
likely to need something similar but highly customized.
"""
import topo
from topo.command.analysis import save_plotgroup
from topo.base.projection import ProjectionSheet
from topo.sheet import GeneratorSheet
exec "from topo.analysis.vision import analyze_complexity" in __main__.__dict__
from param import normalize_path
topo.sim["V1Simple"].measure_maps = True
topo.sim["V1Complex"].measure_maps = True
topo.sim["V2"].measure_maps = True
topo.sim["V2"].in_connections[0].strength=4
save_plotgroup("Orientation Preference and Complexity")
# Plot all projections for all measured_sheets
measured_sheets = [s for s in topo.sim.objects(ProjectionSheet).values()
if hasattr(s,'measure_maps') and s.measure_maps]
for s in measured_sheets:
for p in s.projections().values():
save_plotgroup("Projection",projection=p)
save_plotgroup("Activity")
# topo.sim["V1Simple"].measure_maps = False
# topo.sim["V1Complex"].measure_maps = False
save_plotgroup("Corner OR Preference")
from topo.command import save_snapshot
# save_snapshot(normalize_path('snapshot.typ'))
activity_history=numpy.array([])
def rf_analysis():
import topo
import pylab
import topo.analysis.vision
import contrib.jacommands
from topo.command.analysis import save_plotgroup
from topo.base.projection import ProjectionSheet
from topo.sheet import GeneratorSheet
from topo.command.analysis import measure_or_tuning_fullfield, measure_or_pref
from topo.command.pylabplot import cyclic_tuning_curve
from param import normalize_path
if(float(topo.sim.time()) <=20010):
save_plotgroup("Orientation Preference")
save_plotgroup("Activity")
# Plot all projections for all measured_sheets
measured_sheets = [s for s in topo.sim.objects(ProjectionSheet).values()
if hasattr(s,'measure_maps') and s.measure_maps]
for s in measured_sheets:
for p in s.projections().values():
save_plotgroup("Projection",projection=p)
prefix="WithGC"
measure_or_tuning_fullfield()
s=topo.sim["V1"]
cyclic_tuning_curve(filename_suffix=prefix,filename="OrientationTC:V1:[0,0]",sheet=s,coords=[(0,0)],x_axis="orientation")
cyclic_tuning_curve(filename_suffix=prefix,filename="OrientationTC:V1:[0.1,0.1]",sheet=s,coords=[(0.1,0.1)],x_axis="orientation")
cyclic_tuning_curve(filename_suffix=prefix,filename="OrientationTC:V1:[-0.1,-0.1]",sheet=s,coords=[(-0.1,-0.1)],x_axis="orientation")
cyclic_tuning_curve(filename_suffix=prefix,filename="OrientationTC:V1:[0.1,-0.1]",sheet=s,coords=[(0.1,-0.1)],x_axis="orientation")
cyclic_tuning_curve(filename_suffix=prefix,filename="OrientationTC:V1:[-0.1,0.1]",sheet=s,coords=[(-0.1,0.1)],x_axis="orientation")
else:
topo.command.activity_history = numpy.concatenate((contrib.jacommands.activity_history,topo.sim["V1"].activity.flatten()),axis=1)
if(float(topo.sim.time()) == 20000):
topo.sim["V1"].plastic=False
contrib.jacommands.homeostatic_analysis_function()
if(float(topo.sim.time()) == 20001):
pylab.figure()
def gc_homeo_af():
import contrib.jsldefs
import topo.command.pylabplot
import contrib.jacommands
from topo.command.analysis import save_plotgroup
from topo.analysis.featureresponses import FeatureResponses , PatternPresenter, FeatureMaps
#FeatureResponses.repetitions=10
FeatureMaps.selectivity_multiplier=20
PatternPresenter.duration=0.2
PatternPresenter.apply_output_fns=False
import topo.command.pylabplot
reload(topo.command.pylabplot)
on = topo.sim["LGNOn"].in_connections[0].strength
off = topo.sim["LGNOff"].in_connections[0].strength
if __main__.__dict__.get("GC",False):
topo.sim["LGNOn"].in_connections[0].strength=0
topo.sim["LGNOff"].in_connections[0].strength=0
contrib.jsldefs.homeostatic_analysis_function()
topo.command.pylabplot.fftplot(topo.sim["V1"].sheet_views["OrientationPreference"].view()[0],filename="V1ORMAPFFT")
from topo.misc.filepath import normalize_path, application_path
from scipy.io import write_array
import numpy
write_array(normalize_path(str(topo.sim.time())+"orprefmap.txt"), topo.sim["V1"].sheet_views["OrientationPreference"].view()[0])
write_array(normalize_path(str(topo.sim.time())+"orselmap.txt"), topo.sim["V1"].sheet_views["OrientationSelectivity"].view()[0])
topo.sim["LGNOn"].in_connections[0].strength = on
topo.sim["LGNOff"].in_connections[0].strength = off
print float(topo.sim.time())
if(float(topo.sim.time()) > 19002.0):
#topo.sim["V1"].output_fns[2].scale=0.0
save_plotgroup("Position Preference")
PatternPresenter.duration=1.0
PatternPresenter.apply_output_fns=True
import topo.command.pylabplot
reload(topo.command.pylabplot)
topo.command.pylabplot.measure_or_tuning_fullfield.instance(sheet=topo.sim["V1"],repetitions=10)(repetitions=10)
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0,0]",sheet=topo.sim["V1"],coords=[(0,0)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0,0]",sheet=topo.sim["V1"],coords=[(0.1,0)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0,0]",sheet=topo.sim["V1"],coords=[(0.1,0.1)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0,0]",sheet=topo.sim["V1"],coords=[(0,0.1)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.1,0.1]",sheet=topo.sim["V1"],coords=[(0.1,0.1)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.1,-0.1]",sheet=topo.sim["V1"],coords=[(0.1,-0.1)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[-0.1,0.1]",sheet=topo.sim["V1"],coords=[(-0.1,0.1)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[-0.1,-0.1]",sheet=topo.sim["V1"],coords=[(-0.1,-0.1)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.2,0.2]",sheet=topo.sim["V1"],coords=[(0.2,0.2)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.2,-0.2]",sheet=topo.sim["V1"],coords=[(0.2,-0.2)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[-0.2,0.2]",sheet=topo.sim["V1"],coords=[(-0.2,0.2)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[-0.2,-0.2]",sheet=topo.sim["V1"],coords=[(-0.2,-0.2)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0,0.1]",sheet=topo.sim["V1"],coords=[(0.0,0.1)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0,-0.1]",sheet=topo.sim["V1"],coords=[(0.0,-0.1)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[-0.1,0]",sheet=topo.sim["V1"],coords=[(-0.1,0.0)])()
topo.command.pylabplot.cyclic_tuning_curve.instance(x_axis="orientation",filename="ORTC[0.1,0]",sheet=topo.sim["V1"],coords=[(0.1,-0.0)])()
if(float(topo.sim.time()) > 20000.0):
topo.sim["V1"].output_fns[1].plastic=False
contrib.jacommands.measure_histogram(iterations=1000)
def saver_function():
from topo.command import save_snapshot
save_snapshot(normalize_path('snapshot.typ'))
def empty():
a = 1
def sa():
import topo
from topo.command.analysis import save_plotgroup
from param import normalize_path
import contrib.jacommands
import contrib.surround_analysis_new_cleaned
from topo.analysis.featureresponses import SinusoidalMeasureResponseCommand,FeatureCurveCommand
reload(contrib.surround_analysis_new_cleaned)
s = normalize_path.prefix
exec "from topo.analysis.vision import analyze_complexity" in __main__.__dict__
from topo.analysis.featureresponses import FeatureResponses , PatternPresenter, FeatureMaps
PatternPresenter.duration=4.0
normalize_path.prefix = s
SinusoidalMeasureResponseCommand.scale=__main__.__dict__.get("analysis_scale",1.0)
SinusoidalMeasureResponseCommand.frequencies=[2.4]
if __main__.__dict__.get("Max",False):
from topo.misc.distribution import DSF_MaxValue
preference_fn=DSF_MaxValue(value_scale=(0., 1./numpy.pi),selectivity_scale=(0.,17.0))
topo.command.pylabplot.measure_or_tuning_fullfield.instance(sheet=topo.sim["V1Complex"],preference_fn=preference_fn)()
else:
save_plotgroup("Orientation Preference and Complexity")
contrib.surround_analysis_new_cleaned.surround_analysis("V1Complex").run_lhi_informed_analysis(max_curves=__main__.__dict__.get("max_curves",20),center_size=__main__.__dict__.get("center_size",20),index=__main__.__dict__.get("index",0))
#contrib.surround_analysis_new_cleaned.surround_analysis("V1Complex").analyse([__main__.__dict__.get("coords",(0,0))],__main__.__dict__.get("number_sizes",15),absolute=False)