def analyse(self,cords,ns=10,absolute=True):
for (xindex,yindex) in cords:
if absolute==False:
xindex = self.center_c + xindex
yindex = self.center_r + yindex
xcoor,ycoor = self.sheet.matrixidx2sheet(xindex,yindex)
print "Starting surround analysis for cell with index coords and sheet coords: [%d,%d] [%f,%f]" % (xindex,yindex,xcoor,ycoor)
c= topo.command.pylabplot.measure_size_response.instance(sheet=self.sheet,num_phase=__main__.__dict__.get('NUM_PHASE',8),num_sizes=ns,max_size=__main__.__dict__.get('MAX_SIZE',1.5),coords=[(xcoor,ycoor)],duration=__main__.__dict__.get('duration',4.0))
c.duraton=__main__.__dict__.get('duration',4.0)
c(coords=[(xcoor,ycoor)],frequencies=[__main__.__dict__.get('FREQ',2.4)])
self.data_dict[(xindex,yindex)] = {}
self.data_dict[(xindex,yindex)]["ST"] = self.calculate_RF_sizes(xindex, yindex)
self.plot_size_tunning(xindex,yindex)
import pylab
#pylab.show()
self.data_dict[(xindex,yindex)]["OCT"] = self.perform_orientation_contrast_analysis(self.data_dict[(xindex,yindex)]["ST"],xcoor,ycoor,xindex,yindex)
self.plot_orientation_contrast_tuning(xindex,yindex)
f = open(normalize_path("dict.dat"),'wb')
import pickle
pickle.dump((self.OR,self.OS,self.MR,self.data_dict),f)
f.close()
self.plot_average_oct(independent=True)
self.plot_average_size_tuning_curve(independent=True)
if False:
self.lhi = compute_local_homogeneity_index(self.sheet.sheet_views['OrientationPreference'].view()[0]*pi,2.0)
f = open(normalize_path('lhi2.0.pickle'),'wb')
pickle.dump(self.lhi,f)
f.close()
else:
f = open(normalize_path('lhi2.0.pickle'),'rb')
self.lhi = pickle.load(f)
# determine pinwheels and domain centers
pinwheels = []
centers = []
for coords in self.data_dict.keys():
if self.lhi[coords] < 0.5:
pinwheels.append(coords)
if self.lhi[coords] > 0.5:
centers.append(coords)
self.plot_average_oct(keys=pinwheels,independent=True,string="pinwheels")
self.plot_average_oct(keys=centers,independent=True,string="domains")
pylab.figure()
pylab.imshow(self.lhi)
pylab.colorbar()
release_fig("LHI")
raster_plots_lc,raster_plots_hc = self.plot_map_feature_to_surround_modulation_feature_correlations(self.lhi,"Local Homogeneity Index")
self.correlations_figure(raster_plots_lc)
def check_RF_corrleation_vs_connection_weights_correlation():
_check_RF_corrleation_vs_connection_weights_correlation(topo.sim["V1Simple"].projections()["LGNOnAfferent"],topo.sim["V1Simple"].projections()["LGNOnAfferent"],topo.sim["V1Simple"].projections()["L4EtoE"],topo.sim["LGNOn"],topo.sim["V1Simple"],topo.sim["V1Simple"])
pylab.savefig(normalize_path('RF_connectivity_correlation_EE:' + str(topo.sim.time()) + '.png'));
_check_RF_corrleation_vs_connection_weights_correlation(topo.sim["V1Simple"].projections()["LGNOnAfferent"],topo.sim["V1SimpleInh"].projections()["LGNOnAfferentInh"],topo.sim["V1SimpleInh"].projections()["L4EtoI"],topo.sim["LGNOn"],topo.sim["V1Simple"],topo.sim["V1SimpleInh"])
pylab.savefig(normalize_path('RF_connectivity_correlation_EI:' + str(topo.sim.time()) + '.png'));
_check_RF_corrleation_vs_connection_weights_correlation(topo.sim["V1SimpleInh"].projections()["LGNOnAfferentInh"],topo.sim["V1Simple"].projections()["LGNOnAfferent"],topo.sim["V1Simple"].projections()["L4ItoE"],topo.sim["LGNOn"],topo.sim["V1SimpleInh"],topo.sim["V1Simple"])
pylab.savefig(normalize_path('RF_connectivity_correlation_IE:' + str(topo.sim.time()) + '.png'));
_check_RF_corrleation_vs_connection_weights_correlation(topo.sim["V1SimpleInh"].projections()["LGNOnAfferentInh"],topo.sim["V1SimpleInh"].projections()["LGNOnAfferentInh"],topo.sim["V1SimpleInh"].projections()["L4ItoI"],topo.sim["LGNOn"],topo.sim["V1SimpleInh"],topo.sim["V1SimpleInh"])
pylab.savefig(normalize_path('RF_connectivity_correlation_II:' + str(topo.sim.time()) + '.png'));
def measure_histogram(iterations=1000, sheet_name="V1"):
import contrib.jacommands
topo.sim["V1"].plastic = False
topo.sim.state_push()
for i in xrange(0, iterations):
topo.sim.run(1)
contrib.jacommands.collect_activity(sheet_name)
topo.sim.state_pop()
concat_activities = []
for a in contrib.jacommands.activities:
concat_activities = numpy.concatenate((concat_activities, a.flatten()), axis=1)
topo.sim["V1"].plastic = True
contrib.jacommands.activities = []
pylab.figure()
pylab.subplot(111, yscale='log')
#pylab.subplot(111)
print shape(concat_activities)
mu = sum(concat_activities) / len(concat_activities)
print mu
(bins, a, b) = pylab.hist(concat_activities, (numpy.arange(80.0) / 40.0) , visible=True)
pylab.savefig(normalize_path(str(topo.sim.time()) + 'activity_bar_histogram.png'))
bins_axis = numpy.arange(79.0) / 40.0
bins = bins * 1.0 / sum(bins)
print sum(bins)
exponential = numpy.arange(79, dtype='float32') / 40.0
# compute the mean of the actual distribution
#mu=0.024
pylab.figure()
pylab.subplot(111, yscale='log')
print len(bins_axis)
print len(bins)
print bins_axis
print bins
print numpy.exp(- (1 / mu) * (exponential+0.025))
print numpy.exp(- (1 / mu) * (exponential))
exponential = - numpy.exp(- (1 / mu) * (exponential+0.025)) + numpy.exp(- (1 / mu) * (exponential))
pylab.plot(bins_axis, bins)
pylab.plot(bins_axis, bins, 'ro')
pylab.plot(bins_axis, exponential)
pylab.plot(bins_axis, exponential, 'go')
pylab.axis(ymin=0.0000000001, ymax=100)
#pylab.axis("tight")
print mean(exponential)
print mean(bins)
#pylab.show()
pylab.savefig(normalize_path(str(topo.sim.time()) + 'activity_histogram.png'))
return bins
def specify(self, spec, tid, info):
spec_path = os.path.join(param.normalize_path(), info['root_directory'], 'specifications')
if not os.path.isdir(spec_path): os.makedirs(spec_path)
spec_file_path = os.path.join(spec_path, 'spec-%s' % tid)
prefix = [str(tid), param.normalize_path(info['root_directory'])]
if self.argorder == []: specstr = ' '.join(prefix+spec.values())
else: specstr = ' '.join(prefix + [spec[k] for k in self.argorder])
with open(spec_file_path,'w') as specfile: specfile.write(specstr)
def run_lhi_informed_analysis(self,max_curves=26,center_size=20,index=None):
if True:
self.lhi = compute_local_homogeneity_index(self.OR*pi,__main__.__dict__.get('LHI',2.0))
f = open(normalize_path('lhi'+str(__main__.__dict__.get('LHI',2.0))+'.pickle'),'wb')
pickle.dump(self.lhi,f)
f.close()
else:
f = open(normalize_path('lhi'+str(__main__.__dict__.get('LHI',2.0))+'.pickle'),'rb')
self.lhi = pickle.load(f)
lhi_center = self.lhi[self.center_r-center_size:self.center_r+center_size,self.center_c-center_size:self.center_c+center_size]
steps = []
r = RandomState(1023)
if not __main__.__dict__.get('uniform',False):
pinwheels = r.permutation(numpy.nonzero(numpy.ravel(lhi_center) < __main__.__dict__.get('cutoff',0.3))[0])
domains = r.permutation(numpy.nonzero(numpy.ravel(lhi_center) > (1-__main__.__dict__.get('cutoff',0.3)))[0])
assert len(pinwheels) > max_curves/2
#s = numpy.argsort(numpy.ravel(lhi_center))
if index == None:
for i in xrange(0,max_curves/2):
(x,y) = numpy.unravel_index(pinwheels[i],lhi_center.shape)
steps.append((x+self.center_r-center_size,y+self.center_c-center_size))
(x,y) = numpy.unravel_index(domains[i],lhi_center.shape)
steps.append((x+self.center_r-center_size,y+self.center_c-center_size))
else:
if (index % 2) == 0:
(x,y) = numpy.unravel_index(pinwheels[int(index/2)],lhi_center.shape)
steps= [(x+self.center_r-center_size,y+self.center_c-center_size)]
else:
(x,y) = numpy.unravel_index(domains[int(index/2)],lhi_center.shape)
steps= [(x+self.center_r-center_size,y+self.center_c-center_size)]
else:
bins = []
for i in xrange(0,10):
a = numpy.ravel(lhi_center) >= i*0.1
b = numpy.ravel(lhi_center) < (i+1)*0.1
bins.append(r.permutation(numpy.nonzero(numpy.multiply(a,b))[0]))
(x,y) = numpy.unravel_index(bins[index % 10][int(index/10)],lhi_center.shape)
steps= [(x+self.center_r-center_size,y+self.center_c-center_size)]
#places = r.permutation(numpy.arange(0,len(numpy.ravel(lhi_center)),1))
#(x,y) = numpy.unravel_index(places[index],lhi_center.shape)
#steps.append((x+self.center_r-center_size,y+self.center_c-center_size))
self.analyse(steps,ns=__main__.__dict__.get('number_sizes',10))
def save_snapshot(snapshot_name=None):
"""
Save a snapshot of the network's current state.
The snapshot is saved as a gzip-compressed Python binary pickle.
As this function uses Python's 'pickle' module, it is subject to
the same limitations (see the pickle module's documentation) -
with the notable exception of class attributes. Python does not
pickle class attributes, but this function stores class attributes
of any Parameterized class that is declared within the topo
package. See the param.parameterized.PicklableClassAttributes
class for more information.
"""
if not snapshot_name:
snapshot_name = topo.sim.basename() + ".typ"
# For now we just search topo, but could do same for other packages.
# CEBALERT: shouldn't it be topo and param? I guess we already get
# many classes defined in param because they are imported into
# topo at some point anyway.
topoPOclassattrs = PicklableClassAttributes(topo,exclusions=('plotting','tests','tkgui'),
startup_commands=topo.sim.startup_commands)
paramPOclassattrs = PicklableClassAttributes(param)
imagenPOclassattrs = PicklableClassAttributes(imagen)
numbergenPOclassattrs = PicklableClassAttributes(numbergen)
from topo.misc.commandline import global_params
topo.sim.RELEASE=topo.release
topo.sim.VERSION=topo.version
to_save = (UnpickleEnvironmentCreator(topo.release,topo.version),
PickleMain(),
global_params,
topoPOclassattrs,
paramPOclassattrs,
imagenPOclassattrs,
numbergenPOclassattrs,
topo.sim)
try:
snapshot_file=gzip.open(normalize_path(snapshot_name),'wb',compresslevel=5)
except NameError:
snapshot_file=open(normalize_path(snapshot_name),'wb')
pickle.dump(to_save,snapshot_file,2)
snapshot_file.close()
def save_snapshot(snapshot_name=None):
"""
Save a snapshot of the network's current state.
The snapshot is saved as a gzip-compressed Python binary pickle.
As this function uses Python's 'pickle' module, it is subject to
the same limitations (see the pickle module's documentation) -
with the notable exception of class attributes. Python does not
pickle class attributes, but this function stores class attributes
of any Parameterized class that is declared within the topo
package. See the param.parameterized.PicklableClassAttributes
class for more information.
"""
if not snapshot_name:
snapshot_name = topo.sim.basename() + ".typ"
# For now we just search topo, but could do same for other packages.
# CEBALERT: shouldn't it be topo and param? I guess we already get
# many classes defined in param because they are imported into
# topo at some point anyway.
topoPOclassattrs = PicklableClassAttributes(topo,exclusions=('plotting','tests','tkgui'),
startup_commands=topo.sim.startup_commands)
paramPOclassattrs = PicklableClassAttributes(param)
imagenPOclassattrs = PicklableClassAttributes(imagen)
numbergenPOclassattrs = PicklableClassAttributes(numbergen)
from topo.misc.commandline import global_params
topo.sim.RELEASE=topo.release
topo.sim.VERSION=topo.version
to_save = (UnpickleEnvironmentCreator(topo.release,topo.version),
PickleMain(),
global_params,
topoPOclassattrs,
paramPOclassattrs,
imagenPOclassattrs,
numbergenPOclassattrs,
topo.sim)
try:
snapshot_file=gzip.open(normalize_path(snapshot_name),'wb',compresslevel=5)
except NameError:
snapshot_file=open(normalize_path(snapshot_name),'wb')
pickle.dump(to_save,snapshot_file,2)
snapshot_file.close()
def configure_launch(self, dval):
"""
Determine the root directory from the launcher to configure the analysis
object appropriately, save the final state and set up the launcher's exit
callable.
"""
(task_launcher, batch_analysis) = dval
command_template = task_launcher.command_template
if self.reduce_timestamp is not None:
return self.reduce_directory(task_launcher)
arg_specifier = task_launcher.arg_specifier
analysis_arguments = batch_analysis.analysis_arguments
specifier_keys = set(arg_specifier.varying_keys() + arg_specifier.constant_keys())
if not (analysis_arguments <= specifier_keys):
clashes = analysis_arguments - specifier_keys
raise Exception("Analysis keys %s not set in the specifier" % list(clashes))
command_template.analysis_arguments = list(analysis_arguments)
root_directory = param.normalize_path(task_launcher.root_directory_name())
batch_analysis.root_directory = root_directory
task_launcher.script_path = batch_analysis.script_path
batch_analysis.save()
if self.skip_reduce or batch_analysis.map_reduces != []:
task_launcher.reduction_fn = RunBatchAnalysis.reduce_batch(root_directory)
return True
def generate(plotgroup_names):
assert topo.sim.name==sim_name
assert topo.sim['V1'].nominal_density==8
assert topo.sim.time()==100
for name in plotgroup_names:
print "* Generating data for plotgroups['%s']"%name
views = {}
sheet = topo.sim['V1']
_reset_views(sheet)
plotgroups[name]._exec_pre_plot_hooks()
sheets_views = views[sheet.name] = {}
if hasattr(sheet,'sheet_views'):
sheets_views['sheet_views'] = sheet.sheet_views
if hasattr(sheet,'curve_dict'):
sheets_views['curve_dict'] = sheet.curve_dict
filename = normalize_path('tests/%s_t%s_%s.data'%(sim_name,topo.sim.timestr(),
name.replace(' ','_')))
print "Saving results to %s" % (filename)
f = open(filename,'wb')
pickle.dump((topo.version,views),f)
f.close()
def initialize_clissom_data(name, **kw):
out_dir = normalize_path("topo/tests/reference/%s_BaseN%s_BaseRN%s/" %
(name, kw['BaseN'], kw['BaseRN']))
global filename_base
filename_base = out_dir + "/%s." % name
if not os.path.exists(out_dir):
os.mkdir(out_dir)
clissom_support_files = glob.glob(
"topo/tests/reference/support_clissom/*")
for f in clissom_support_files:
os.system("cp %s %s" % (f, out_dir))
os.system("cp topo/tests/reference/%s.param %s" % (name, out_dir))
cwd = os.getcwd()
os.chdir(out_dir)
os.system("gzip -dc lissom5.gz > lissom5")
os.system("chmod +x %s" % "lissom5")
_set_clissom_params(name, out_dir, **kw)
print "------------------------------------------------------------"
print "Generating c++ lissom results in %s" % out_dir
c = _clissomcmd(name)
print c
os.system(c)
print "------------------------------------------------------------"
os.chdir(cwd)
else:
print "Skipping c++ lissom data generation: results already exist in %s" % out_dir
def _setup_launch(self):
"""
Method to be used by all launchers that prepares the root directory and
generate basic launch information for command templates to use. Prepends
some information to the description, registers a timestamp and return a
dictionary of useful launch information constant across all tasks.
"""
root_name = self.root_directory_name()
self.root_directory = param.normalize_path(root_name)
if not os.path.isdir(self.root_directory):
os.makedirs(self.root_directory)
metrics_dir = os.path.join(self.root_directory, 'metrics')
if not os.path.isdir(metrics_dir) and self.arg_specifier.dynamic:
os.makedirs(metrics_dir)
return {
'root_directory': self.root_directory,
'timestamp': self.timestamp,
'varying_keys': self.arg_specifier.varying_keys(),
'constant_keys': self.arg_specifier.constant_keys(),
'constant_items': self.arg_specifier.constant_items(),
'batch_name': self.batch_name,
'batch_tag': self.tag,
'batch_description': self.description
}
def __call__(self):
"""
Calls the collector specified by the user in the run_batch
context. Invoked as an analysis function by RunBatchCommand.
"""
self.collector.interval_hook = topo.sim.run
topo_time = topo.sim.time()
filename = '%s%s_%s' % (self._info.batch_name,
('[%s]' % self._info.batch_tag
if self._info.batch_tag else ''),
topo_time)
viewtree = Layout()
viewtree = self.collector(viewtree, times=[topo_time])
spec_metadata = [(key, self._info.specs[key])
for key in self.metadata if '.' not in key]
path_metadata = [(key, viewtree.items.get(tuple(key.split('.')), float('nan')))
for key in self.metadata if '.' in key]
Pickler.save(viewtree,
param.normalize_path(filename),
key=dict(spec_metadata + path_metadata + [('time',topo_time)]))
def configure_launch(self, dval):
"""
Determine the root directory from the launcher to configure the analysis
object appropriately, save the final state and set up the launcher's exit
callable.
"""
(task_launcher, batch_analysis) = dval
command_template = task_launcher.command_template
if self.reduce_timestamp is not None:
return self.reduce_directory(task_launcher)
arg_specifier = task_launcher.arg_specifier
analysis_arguments = batch_analysis.analysis_arguments
specifier_keys = set(arg_specifier.varying_keys() + arg_specifier.constant_keys())
if not (analysis_arguments <= specifier_keys):
clashes = analysis_arguments - specifier_keys
raise Exception("Analysis keys %s not set in the specifier" % list(clashes))
command_template.analysis_arguments = list(analysis_arguments)
root_directory = param.normalize_path(task_launcher.root_directory_name())
batch_analysis.root_directory = root_directory
task_launcher.script_path = batch_analysis.script_path
batch_analysis.save()
if self.skip_reduce or batch_analysis.map_reduces != []:
task_launcher.reduction_fn = RunBatchAnalysis.reduce_batch(root_directory)
return True
def compare_with_and_without_snapshot_NoSnapshot(script="models/lissom.ty",look_at='V1',cortex_density=8,lgn_density=4,retina_density=4,dims=['or','od','dr','cr','dy','sf'],dataset="Gaussian",run_for=10,break_at=5):
data_filename=os.path.split(script)[1]+"_PICKLETEST"
# we must execute in main because e.g. scheduled events are run in __main__
# CEBALERT: should set global params
__main__.__dict__['cortex_density']=cortex_density
__main__.__dict__['lgn_density']=lgn_density
__main__.__dict__['retina_density']=retina_density
__main__.__dict__['dims']=dims
__main__.__dict__['dataset']=dataset
execfile(script,__main__.__dict__)
data = {}
topo.sim.run(break_at)
data[topo.sim.time()]= copy.deepcopy(topo.sim[look_at].activity)
topo.sim.run(run_for-break_at)
data[topo.sim.time()]= copy.deepcopy(topo.sim[look_at].activity)
data['run_for']=run_for
data['break_at']=break_at
data['look_at']=look_at
data['cortex_density']=cortex_density
data['lgn_density']=lgn_density
data['retina_density']=retina_density
data['dims']=dims
data['dataset']=dataset
locn = normalize_path(os.path.join("tests",data_filename))
print "Writing pickle to %s"%locn
pickle.dump(data,open(locn,'wb'),2)
def generate(plotgroup_names):
assert topo.sim.name == sim_name
assert topo.sim['V1'].nominal_density == 8
assert topo.sim.time() == 100
for name in plotgroup_names:
print "* Generating data for plotgroups['%s']" % name
views = {}
sheet = topo.sim['V1']
_reset_views(sheet)
plotgroups[name]._exec_pre_plot_hooks()
sheets_views = views[sheet.name] = {}
if hasattr(sheet, 'sheet_views'):
sheets_views['sheet_views'] = sheet.sheet_views
if hasattr(sheet, 'curve_dict'):
sheets_views['curve_dict'] = sheet.curve_dict
filename = normalize_path(
'tests/%s_t%s_%s.data' %
(sim_name, topo.sim.timestr(), name.replace(' ', '_')))
print "Saving results to %s" % (filename)
f = open(filename, 'wb')
pickle.dump((topo.version, views), f)
f.close()
def __call__(self,times=None,**kwargs):
if topo.sim.time() != times[-1]:
return None
for coidx,coord in enumerate(self.unit_list):
prefix = str(coord) + "_"
unit = topo.sim[self.sheet].sheet2matrixidx(coord[0],coord[1])
topo.command.pylabplot.measure_orientation_contrast(preference_fn=DSF_MaxValue,curve_parameters=self.c_dict,
num_phase=self.num_phases,sheet=self.sheet,coords=[coord],
contrastcenter=self.center_contrast,num_orientation=self.num_orientation,
sizecenter=self.sizecenter,sizesurround=self.sizesurround,thickness=self.thickness,
measurement_prefix=prefix)
for cidx,contrast in enumerate(self.surround_contrasts):
or_keys = sorted(topo.sim[self.sheet].curve_dict[prefix+'orientationsurround']['Contrastsurround = {c}%'.format(c=int(contrast))].keys(),key=lambda x: float(x))
for oidx,orientation in enumerate(or_keys):
unit = topo.sim[self.sheet].sheet2matrixidx(coord[0],coord[1])
units = [(unit[0]+x_offset,unit[1]+y_offset) for x_offset in xrange(-1,2) for y_offset in xrange(-1,2)]
activity = topo.sim[self.sheet].curve_dict[prefix+'orientationsurround']['Contrastsurround = {c}%'.format(c=int(contrast))][orientation].view()[0]
for uidx,unit in enumerate(units):
self.CSTC[oidx,uidx,cidx,coidx] = activity[unit[0]][unit[1]]
if self.pickle:
pkl_file = open(param.normalize_path('CSTC.pkl'), 'wb')
pickle.dump((self.CSTC,(or_keys,self.unit_list,self.surround_contrasts,self.sheet,self.unit_list)), pkl_file)
pkl_file.close()
def save_script_repr(script_name=None):
"""
Save the current simulation as a Topographica script.
Generates a script that, if run, would generate a simulation with
the same architecture as the one currently in memory. This can be
useful when defining networks in place, so that the same general
configuration can be recreated later. It also helps when
comparing two similar networks generated with different scripts,
so that the corresponding items can be matched rigorously.
Note that the result of this operation is usually just a starting
point for further editing, because it will not usually be runnable
as-is (for instance, some parameters may not have runnable
representations). Even so, this is usually a good start.
"""
if not script_name:
script_name = topo.sim.basename() + "_script_repr.ty"
header = ("# Generated by Topographica %s on %s\n\n" %
(topo.release,time.strftime("%a, %d %b %Y %H:%M:%S +0000", time.gmtime())))
script = header+topo.sim.script_repr()
script_file = open(normalize_path(script_name),'w')
script_file.write(script)
def initialize_clissom_data(name, **kw):
out_dir = normalize_path("topo/tests/reference/%s_BaseN%s_BaseRN%s/" % (name, kw["BaseN"], kw["BaseRN"]))
global filename_base
filename_base = out_dir + "/%s." % name
if not os.path.exists(out_dir):
os.mkdir(out_dir)
clissom_support_files = glob.glob("topo/tests/reference/support_clissom/*")
for f in clissom_support_files:
os.system("cp %s %s" % (f, out_dir))
os.system("cp topo/tests/reference/%s.param %s" % (name, out_dir))
cwd = os.getcwd()
os.chdir(out_dir)
os.system("gzip -dc lissom5.gz > lissom5")
os.system("chmod +x %s" % "lissom5")
_set_clissom_params(name, out_dir, **kw)
print "------------------------------------------------------------"
print "Generating c++ lissom results in %s" % out_dir
c = _clissomcmd(name)
print c
os.system(c)
print "------------------------------------------------------------"
os.chdir(cwd)
else:
print "Skipping c++ lissom data generation: results already exist in %s" % out_dir
def __call__(self,times=None,**kwargs):
# if analysis_group('b'):
# return None
if self.pickle:
or_pkl = open(param.normalize_path('ormap_{time}.pkl'.format(time=topo.sim.time())),'wb')
pkl_data = {}
for f in self.frequencies:
save_plotgroup("Orientation Preference",use_cached_results=False,saver_params={'filename_suffix':'_{0}'.format(f)},
pre_plot_hooks=[measure_sine_pref.instance(frequencies=[f],num_phase=self.num_phase,num_orientation=self.num_orientation,
preference_fn=DSF_WeightedAverage(value_scale=(0., 1./math.pi)))])
if self.pickle:
for sheet in self.sheets:
im = topo.sim[sheet].sheet_views['OrientationPreference'].view()[0][0:-1,0:-1]
try:
polar_or = image.hue_to_polar(im)
pwdata = analysisJL.polarmap_contours(polar_or)
pws = analysisJL.identify_pinwheels(*pwdata)
pwbitsofinformation = type('pwdata', (), dict(zip(['recontours', 'imcontours', 'intersections', 'pinwheels'] , pwdata+(pws,) )))
pw_results = analysisJL.pinwheel_analysis(im, len(pws), ignore_DC=False)
pkl_data['OR_Analysis_{freq}_{sheet}'.format(freq = f,sheet=sheet)] = pw_results
except:
print "OR Pinwheel Analysis failed"
or_sel = topo.sim[sheet].sheet_views['OrientationSelectivity'].view()[0]
pkl_data['OrientationPreference_{freq}_{sheet}'.format(freq = f,sheet=sheet)] = im
pkl_data['OrientationSelectivity_{freq}_{sheet}'.format(freq = f,sheet=sheet)] = or_sel
if self.pickle:
pickle.dump(pkl_data,or_pkl)
def _print_vc_info(filename):
"""Save the version control status of the current code to the specified file."""
try:
import subprocess
f = open(normalize_path(filename),'w')
f.write("Information about working copy used for batch run\n\n")
f.write("topo.version=%s\n"% topo.version)
f.flush()
vctype,commands = _get_vc_commands()
for cmd in commands:
fullcmd = [vctype,cmd] if isinstance(cmd,str) else [vctype]+cmd
# Note that we do not wait for the process below to finish
# (by calling e.g. wait() on the Popen object). Although
# this was probably done unintentionally, for a slow svn
# connection, it's an advantage. But it does mean the
# output of each command can appear in the file at any
# time (i.e. the command outputs appear in the order of
# finishing, rather than in the order of starting, making
# it impossible to label the commands).
subprocess.Popen(fullcmd,stdout=f,stderr=subprocess.STDOUT)
except:
print "Unable to retrieve version control information."
finally:
f.close()
def save_script_repr(script_name=None):
"""
Save the current simulation as a Topographica script.
Generates a script that, if run, would generate a simulation with
the same architecture as the one currently in memory. This can be
useful when defining networks in place, so that the same general
configuration can be recreated later. It also helps when
comparing two similar networks generated with different scripts,
so that the corresponding items can be matched rigorously.
Note that the result of this operation is usually just a starting
point for further editing, because it will not usually be runnable
as-is (for instance, some parameters may not have runnable
representations). Even so, this is usually a good start.
"""
if not script_name:
script_name = topo.sim.basename() + "_script_repr.ty"
header = ("# Generated by Topographica %s on %s\n\n" %
(topo.release,
time.strftime("%a, %d %b %Y %H:%M:%S +0000", time.gmtime())))
script = header + topo.sim.script_repr()
script_file = open(normalize_path(script_name), 'w')
script_file.write(script)
def _print_vc_info(filename):
"""Save the version control status of the current code to the specified file."""
try:
import subprocess
f = open(normalize_path(filename), 'w')
f.write("Information about working copy used for batch run\n\n")
f.write("topo.version=%s\n" % topo.version)
f.flush()
vctype, commands = _get_vc_commands()
for cmd in commands:
fullcmd = [vctype, cmd] if isinstance(cmd, str) else [vctype] + cmd
# Note that we do not wait for the process below to finish
# (by calling e.g. wait() on the Popen object). Although
# this was probably done unintentionally, for a slow svn
# connection, it's an advantage. But it does mean the
# output of each command can appear in the file at any
# time (i.e. the command outputs appear in the order of
# finishing, rather than in the order of starting, making
# it impossible to label the commands).
subprocess.Popen(fullcmd, stdout=f, stderr=subprocess.STDOUT)
except:
print "Unable to retrieve version control information."
finally:
f.close()
def __call__(self,output_fn,init_time=0,final_time=None,**params):
p=ParamOverrides(self,params)
if final_time is None:
final_time=topo.sim.time()
attrs = p.attrib_names if len(p.attrib_names)>0 else output_fn.attrib_names
for a in attrs:
pylab.figure(figsize=(6,4))
isint=pylab.isinteractive()
pylab.ioff()
pylab.grid(True)
ylabel=p.ylabel
pylab.ylabel(a+" "+ylabel)
pylab.xlabel('Iteration Number')
coords = p.units if len(p.units)>0 else output_fn.units
for coord in coords:
y_data=[y for (x,y) in output_fn.values[a][coord]]
x_data=[x for (x,y) in output_fn.values[a][coord]]
if p.raw==True:
plot_data=zip(x_data,y_data)
pylab.save(normalize_path(p.filename+a+'(%.2f, %.2f)' %(coord[0], coord[1])),plot_data,fmt='%.6f', delimiter=',')
pylab.plot(x_data,y_data, label='Unit (%.2f, %.2f)' %(coord[0], coord[1]))
(ymin,ymax)=p.ybounds
pylab.axis(xmin=init_time,xmax=final_time,ymin=ymin,ymax=ymax)
if isint: pylab.ion()
pylab.legend(loc=0)
p.title=topo.sim.name+': '+a
p.filename_suffix=a
self._generate_figure(p)
def __call__(self):
"""
Calls the collector specified by the user in the run_batch
context. Invoked as an analysis function by RunBatchCommand.
"""
self.collector.interval_hook = topo.sim.run
topo_time = topo.sim.time()
filename = '%s%s_%s' % (self._info.batch_name,
('[%s]' % self._info.batch_tag
if self._info.batch_tag else ''), topo_time)
viewtree = Layout()
viewtree = self.collector(viewtree, times=[topo_time])
spec_metadata = [(key, self._info.specs[key]) for key in self.metadata
if '.' not in key]
path_metadata = [(key,
viewtree.items.get(tuple(key.split('.')),
float('nan')))
for key in self.metadata if '.' in key]
Pickler.save(viewtree,
param.normalize_path(filename),
key=dict(spec_metadata + path_metadata +
[('time', topo_time)]))
def _analyse_push_pull_connectivity1(sheet_name,proj_name):
"""
It assumes orientation preference was already measured.
"""
projection = topo.sim[sheet_name].projections()[proj_name]
or_pref = topo.sim[projection.src.name].sheet_views['OrientationPreference'].view()[0]*numpy.pi
phase_pref = topo.sim[projection.src.name].sheet_views['PhasePreference'].view()[0]*numpy.pi*2
or_pref_target = topo.sim[projection.dest.name].sheet_views['OrientationPreference'].view()[0]*numpy.pi
phase_pref_target = topo.sim[projection.dest.name].sheet_views['PhasePreference'].view()[0]*2*numpy.pi
app = []
app_or = []
av1 = []
av2 = []
for (i,cf) in enumerate(projection.cfs.flatten()):
this_or = or_pref.flatten()[i]
this_phase = phase_pref.flatten()[i]
ors = cf.input_sheet_slice.submatrix(or_pref).flatten()
phases = cf.input_sheet_slice.submatrix(phase_pref).flatten()
weights = numpy.multiply(cf.weights,cf.mask)
#Let's compute the mean orientation preference of connecting neurons
z = circ_mean(numpy.array([ors]),weights=numpy.array([weights.flatten()]),axis=1,low=0.0,high=numpy.pi,normalize=False)
app_or.append(z[0])
#First lets compute the average phase of neurons which are within 30 degrees of the given neuron
within_30_degrees = numpy.nonzero((circular_dist(ors,this_or,numpy.pi) < (numpy.pi/6.0))*1.0)[0]
#if len(within_30_degrees) != 0:
z = circ_mean(numpy.array([phases]),weights=numpy.array([weights.flatten()]),axis=1,low=0.0,high=numpy.pi*2,normalize=False)
app.append(z[0])
#else:
# app.append(0.0)
#Now lets compare the average connection strength to neurons oriented within 30 degrees and having the same phase (within 60 degrees), with the average connections strength to neurons more than 30 degrees off in orientation
outside_30_degrees = numpy.nonzero(circular_dist(ors,this_or,numpy.pi) > numpy.pi/6.0)[0]
within_30_degrees_and_same_phase = numpy.nonzero(numpy.multiply(circular_dist(ors,this_or,numpy.pi) < numpy.pi/6.0,circular_dist(phases,this_phase,2*numpy.pi) < numpy.pi/3.0))[0]
if len(outside_30_degrees) != 0:
av1.append(numpy.mean(weights.flatten()[outside_30_degrees])/max(len(outside_30_degrees),1.0))
else:
av1.append(0.0)
if len(within_30_degrees_and_same_phase) != 0:
av2.append(numpy.mean(weights.flatten()[within_30_degrees_and_same_phase])/max(len(within_30_degrees_and_same_phase),1.0))
else:
av2.append(0.0)
import pylab
pylab.figure()
pylab.subplot(3,1,1)
pylab.plot(numpy.array(app_or),or_pref_target.flatten(),'ro')
pylab.title(proj_name)
pylab.subplot(3,1,2)
pylab.plot(numpy.array(app),phase_pref_target.flatten(),'ro')
pylab.subplot(3,1,3)
pylab.bar(numpy.arange(2), (numpy.mean(av1),numpy.mean(av2)), 0.35, color='b')
pylab.savefig(normalize_path('PPconnectivity: ' + proj_name + str(topo.sim.time()) + '.png'));
def save_to_disk(self, **params):
imgs = numpy.array([p.bitmap.image for p in self.plotgroup.plots], dtype=object).reshape(
self.plotgroup.proj_plotting_shape
)
img = make_contact_sheet(imgs, (3, 3, 3, 3), 3)
img.save(
normalize_path(self.filename(self.plotgroup.sheet.name + "_" + self.plotgroup.projection.name, **params))
)
def __init__(self,sheet_name="V1Complex",prefix=None):
if prefix:
f = open(prefix+'data_dict.pickle','rb')
(self.OR,self.OS,self.MR,self.data_dict) = pickle.load(f)
f.close()
if True:
self.lhi = compute_local_homogeneity_index(self.OR*pi,__main__.__dict__.get('LHI',2.0))
f = open(normalize_path('lhi'+str(__main__.__dict__.get('LHI',2.0))+'.pickle'),'wb')
pickle.dump(self.lhi,f)
f.close()
else:
f = open(normalize_path('lhi'+str(__main__.__dict__.get('LHI',2.0))+'.pickle'),'rb')
self.lhi = pickle.load(f)
else:
import topo
self.sheet_name=sheet_name
self.sheet=topo.sim[sheet_name]
# Center mask to matrixidx center
self.center_r,self.center_c = self.sheet.sheet2matrixidx(0,0)
self.center_x,self.center_y = self.sheet.matrixidx2sheet(self.center_r,self.center_c)
from topo.analysis.featureresponses import PatternPresenter
PatternPresenter.duration=__main__.__dict__.get('duration',4.0) #!
import topo.command.pylabplot
reload(topo.command.pylabplot)
FeatureCurveCommand.curve_parameters=[{"contrast":self.low_contrast},{"contrast":self.high_contrast}]
FeatureCurveCommand.display=True
FeatureCurveCommand.sheet=topo.sim[sheet_name]
SinusoidalMeasureResponseCommand.num_phase=8
SinusoidalMeasureResponseCommand.frequencies=[__main__.__dict__.get('FREQ',2.4)]
SinusoidalMeasureResponseCommand.scale=self.high_contrast/100.0
MeasureResponseCommand.scale=self.high_contrast/100.0
FeatureCurveCommand.num_orientation=12
FeatureResponses.repetitions = __main__.__dict__.get('repetitions',1)
#topo.command.pylabplot.measure_or_tuning_fullfield.instance(sheet=topo.sim["V1Complex"])()
FeatureCurveCommand.curve_parameters=[{"contrast":self.low_contrast},{"contrast":self.high_contrast}]
self.OR = topo.sim["V1Complex"].sheet_views['OrientationPreference'].view()[0]
self.OS = topo.sim["V1Complex"].sheet_views['OrientationSelectivity'].view()[0]
self.MR = topo.sim["V1Complex"].sheet_views['ComplexSelectivity'].view()[0]
def release_fig(filename=None):
import pylab
pylab.show._needmain=False
if filename is not None:
fullname=filename+str(topo.sim.time())+".png"
pylab.savefig(normalize_path(fullname))
else:
pylab.show()
def plot_ASTC(self):
f = open(param.normalize_path('iDoG_Fit_%s.txt' % self.sheet), 'w')
for uidx,unit in enumerate(self.unit_list):
for cidx,contrast in enumerate(self.contrasts):
fig = plt.figure()
plt.title('{sheet}{unit} Contrast:{contrast}% Time:{time} Area Summation Curve'.format(sheet=self.sheet,unit=topo.sim[self.sheet].sheet2matrixidx(unit[0],unit[1]),contrast=contrast,time=str(float(topo.sim.time()))))
plt.plot(self.sizes,self.ASTC[:,cidx,uidx],label='Measured Response')
if self.size_fitted_curve != None:
plt.plot(self.sizes,self.size_fitted_curve[:,cidx,uidx],label='Fitted Response - SI: {0:.3f} o_e: {1:.3f} vdeg, o_i: {2:.3f} vdeg'.format(self.size_fitv[2,cidx,uidx],self.size_fitv[0,cidx,uidx],self.size_fitv[1,cidx,uidx]))
plt.xlabel('Stimulus Diameter (in deg of visual angle)')
plt.ylabel('Activity')
lgd = plt.legend(loc = 'upper center', bbox_to_anchor = (0.5, -0.1))
path = param.normalize_path('{sheet}{unit}{contrast}__{time:09.2f}_Size_TC.pdf'.format(sheet=self.sheet,unit=str(unit),time=float(topo.sim.time()),contrast=contrast))
plt.savefig(path,bbox_extra_artists=[lgd],bbox_inches='tight',format='pdf')
plt.close(fig)
f.write('{unit},{contrast}: {fit};{estim}\n'.format(sheet=self.sheet,unit=str(unit),contrast=contrast,fit=str(self.size_fitv[:,cidx,uidx]),estim=self.size_est[:,cidx,uidx]))
f.close()
def save_script_repr(self):
script_name = asksaveasfilename(filetypes=SCRIPT_FILETYPES,
initialdir=normalize_path(),
initialfile=topo.sim.basename()+"_script_repr.ty")
if script_name:
topo.command.save_script_repr(script_name)
self.messageBar.response('Script saved to ' + script_name)
def __call__(self,times=None,**kwargs):
if topo.sim.time() != times[-1]:
return None
measure_rfs(sampling_area=self.unit_slice,input_sheet=topo.sim[self.input_sheet],
sampling_interval=self.sampling_rate,pattern_presenter=CoordinatedPatternGenerator(RawRectangle()))
# Get Retina Information
retina = topo.sim[self.input_sheet]
sheet = topo.sim[self.measurement_sheet]
left, bottom, right, top = sheet.nominal_bounds.lbrt()
sheet_density = float(sheet.nominal_density)
x_units,y_units = sheet.shape
unit_size = 1.0 / sheet_density
half_unit_size = (unit_size / 2.0) # saves repeated calculation.
# Sample V1
v1_units = 4
sampling_range = (top - half_unit_size - (unit_size * np.floor((y_units-v1_units)/2)) , bottom + half_unit_size + (unit_size * np.ceil(y_units-v1_units)/2))
# Create Samplign Grid
spacing = np.linspace(sampling_range[0],sampling_range[1], sheet.density)
X, Y = np.meshgrid(spacing, spacing)
sheet_coords = zip(X.flatten(),Y.flatten())
coords = list(set([sheet.sheet2matrixidx(x,y) for (x,y) in sheet_coords]))
# Filter and sort RFs
keys = [key for key in retina.sheet_views.keys() if key[0] == 'RFs']
filtered_keys = sorted(list(set([key for key in keys if sheet.sheet2matrixidx(key[2],key[3]) in coords])),key=operator.itemgetter(2,3))
rfs = np.dstack([topo.sim[self.input_sheet].sheet_views[key].view()[0] for key in filtered_keys])
coords = np.vstack([(key[2],key[3]) for key in filtered_keys])
plt.imsave(param.normalize_path('central_rf.png'),rfs[:,:,int(len(rfs[0,0,:])/2)])
# Pickle and save
if self.pickle:
pkl_file = open(param.normalize_path('RFs.pkl'), 'wb')
pickle.dump((coords,rfs), pkl_file)
pkl_file.close()
try:
img = rf_image(rfs,coords,norm='All')
img.save(param.normalize_path('V1_RFs_{time}.png'.format(time=topo.sim.time())))
except:
pass
def save_to_disk(self,**params):
imgs = numpy.array([p.bitmap.image
for p in self.plotgroup.plots],
dtype=object).reshape(
self.plotgroup.proj_plotting_shape)
img = make_contact_sheet(imgs, (3,3,3,3), 3)
img.save(normalize_path(self.filename(
self.plotgroup.sheet.name+"_"+
self.plotgroup.projection.name,**params)))
def __save_to_png(self):
plot = self._right_click_info['plot']
filename = self.plotgroup.filesaver.filename(plot.label(),file_format="png")
PNG_FILETYPES = [('PNG images','*.png'),('All files','*')]
snapshot_name = asksaveasfilename(filetypes=PNG_FILETYPES,
initialdir=normalize_path(),
initialfile=filename)
if snapshot_name:
plot.bitmap.image.save(snapshot_name)
def __save_to_png(self):
plot = self._right_click_info['plot']
filename = self.plotgroup.filesaver.filename(plot.label(),file_format="png")
PNG_FILETYPES = [('PNG images','*.png'),('All files','*')]
snapshot_name = asksaveasfilename(filetypes=PNG_FILETYPES,
initialdir=normalize_path(),
initialfile=filename)
if snapshot_name:
plot.bitmap.image.save(snapshot_name)
def plot_SFTC(self):
"""
Plot SFTC and Fitted DoG Curve
"""
f = open(param.normalize_path('DoG_Fit_%s.txt' % self.sheet), 'w')
for uidx,unit in enumerate(self.unit_list):
for cidx,contrast in enumerate(self.contrasts):
fig = plt.figure()
plt.title('{sheet}{unit} Contrast:{contrast}% Time:{time} SF Tuning Curve'.format(sheet=self.sheet,unit=topo.sim[self.sheet].sheet2matrixidx(unit[0],unit[1]),contrast=contrast,time=topo.sim.time()))
plt.plot(self.frequencies,self.SFTC[:,cidx,uidx],label='Measured Response')
plt.plot(self.frequencies,self.sf_fitted_curve[:,cidx,uidx],label='Fitted Response - SI: {0:.3f} o_e: {1:.3f} vdeg, o_i: {2:.3f} vdeg'.format(self.sf_fitv[2,cidx,uidx],self.sf_fitv[0,cidx,uidx],self.sf_fitv[1,cidx,uidx]))
plt.xlabel('Spatial Frequency (cyc/deg)')
plt.ylabel('Activity')
lgd = plt.legend(loc = 'upper center', bbox_to_anchor = (0.5, -0.1))
path = param.normalize_path('{sheet}{unit}{contrast}__{time:09.2f}_SFTC.pdf'.format(sheet=self.sheet,unit=str(unit),time=float(topo.sim.time()),contrast=contrast))
plt.savefig(path,bbox_extra_artists=[lgd],bbox_inches='tight',format='pdf')
plt.close(fig)
f.write('{sheet}{unit}{contrast}: {fit}\n'.format(sheet=self.sheet,unit=str(unit),contrast=contrast,fit=str(self.sf_fitv[:,cidx,uidx])))
f.close()
def __call__(self,times=None):
if topo.sim.time() != times[-1]:
return None
if self.sf_measure:
self.frequencies = np.linspace(0.0,self.sf_max,self.sf_steps)
self.measure_SFTC()
try:
self.fit_DoG()
except:
pass
#self.plot_SFTC()
if self.pickle:
pkl_file = open(param.normalize_path('SFTC_%s.pkl' % self.sheet), 'wb')
pickle.dump((self.SFTC,self.frequencies,self.contrasts,self.unit_list), pkl_file)
pkl_file.close()
if self.size_measure:
self.sizes = np.linspace(0.0,self.size_max,self.size_steps)
self.frequency = [0]*len(self.unit_list)
for uidx,unit in enumerate(self.unit_list):
if self.sf_measure:
self.frequency[uidx] = self.frequencies[self.SFTC[:,-1,uidx].argmax()]
else:
self.frequency[uidx] = self.sf_fallback
self.measure_ASTC()
if self.pickle:
pkl_file = open(param.normalize_path('ASTC_%s.pkl' % self.sheet), 'wb')
pickle.dump((self.ASTC,(self.sizes,self.contrasts,self.unit_list)), pkl_file)
pkl_file.close()
try:
self.fit_iDoG()
except:
pass
def __save_to_postscript(self):
plot = self._right_click_info['plot']
canvas = self._right_click_info['event'].widget
filename = self.plotgroup.filesaver.filename(plot.label(),file_format="eps")
POSTSCRIPT_FILETYPES = [('Encapsulated PostScript images','*.eps'),
('PostScript images','*.ps'),('All files','*')]
snapshot_name = asksaveasfilename(filetypes=POSTSCRIPT_FILETYPES,
initialdir=normalize_path(),
initialfile=filename)
if snapshot_name:
canvas.postscript(file=snapshot_name)
def __save_to_postscript(self):
plot = self._right_click_info['plot']
canvas = self._right_click_info['event'].widget
filename = self.plotgroup.filesaver.filename(plot.label(),file_format="eps")
POSTSCRIPT_FILETYPES = [('Encapsulated PostScript images','*.eps'),
('PostScript images','*.ps'),('All files','*')]
snapshot_name = asksaveasfilename(filetypes=POSTSCRIPT_FILETYPES,
initialdir=normalize_path(),
initialfile=filename)
if snapshot_name:
canvas.postscript(file=snapshot_name)
def activity_stats(times=None, **kwargs):
if analysis_group('a'):
return None
sheets = ['LGNOff','LGNOn','V1Exc','V1Inh']
f = open(param.normalize_path('mean_activity.txt'), 'a')
for sheet in sheets:
mean_activity = np.mean(topo.sim[sheet].activity)
max_activity = np.max(topo.sim[sheet].activity)
f.write('{sheet},{time}: Mean {act:.3f} Max {max_act:.3f}\n'.format(sheet=sheet,time=topo.sim.time(),act=mean_activity,max_act=max_activity))
f.close()
def _setup_streams_path(self):
streams_path = os.path.join(param.normalize_path(),
self.root_directory, "streams")
try:
os.makedirs(streams_path)
except:
pass
# Waiting till these directories exist (otherwise potential qstat error)
while not os.path.isdir(streams_path):
pass
return streams_path
def analyse_connectivity(sheet_name,proj_name,lhi):
or_bins = numpy.linspace(0,numpy.pi/2,30)
projection = topo.sim[sheet_name].projections()[proj_name]
or_pref = topo.sim[projection.src.name].sheet_views['OrientationPreference'].view()[0]*numpy.pi
or_pref_target = topo.sim[projection.dest.name].sheet_views['OrientationPreference'].view()[0]*numpy.pi
domain_orientation_connection_strength = numpy.zeros((30,1))
pinwheel_orientation_connection_strength = numpy.zeros((30,1))
pinwheels = numpy.where(lhi.flatten()<0.1)[0]
domains = numpy.where(lhi.flatten()>0.9)[0]
for i in pinwheels:
cf = projection.cfs.flatten()[i]
this_or = or_pref_target.flatten()[i]
ors = cf.input_sheet_slice.submatrix(or_pref).flatten()
weights = numpy.multiply(cf.weights,cf.mask).flatten()
for j,k in enumerate(numpy.digitize(circular_dist(ors,this_or,numpy.pi),or_bins)):
print k
pinwheel_orientation_connection_strength[k-1] += weights[j]
for i in domains:
cf = projection.cfs.flatten()[i]
this_or = or_pref_target.flatten()[i]
ors = cf.input_sheet_slice.submatrix(or_pref).flatten()
weights = numpy.multiply(cf.weights,cf.mask).flatten()
for j,k in enumerate(numpy.digitize(circular_dist(ors,this_or,numpy.pi),or_bins)):
domain_orientation_connection_strength[k-1] += weights[j]
import pylab
pylab.figure()
pylab.subplot(2,1,1)
pylab.hold('on')
pylab.plot(numpy.linspace(0,numpy.pi/2,30,endpoint=False)+numpy.pi/2/60,pinwheel_orientation_connection_strength,'k',linewidth=2.0)
pylab.plot(numpy.linspace(0,numpy.pi/2,30,endpoint=False)+numpy.pi/2/60,pinwheel_orientation_connection_strength,'ko')
pylab.title(proj_name,fontsize=20)
pylab.autoscale(tight=True)
pylab.title('pinwheels')
pylab.subplot(2,1,2)
pylab.hold('on')
pylab.plot(numpy.linspace(0,numpy.pi/2,30,endpoint=False)+numpy.pi/2/60,domain_orientation_connection_strength,'k',linewidth=2.0)
pylab.plot(numpy.linspace(0,numpy.pi/2,30,endpoint=False)+numpy.pi/2/60,domain_orientation_connection_strength,'ko')
pylab.title(proj_name,fontsize=20)
pylab.autoscale(tight=True)
pylab.title('domains')
from param import normalize_path
pylab.savefig(normalize_path('PPconnectivity: ' + proj_name + str(topo.sim.time()) + '.png'));
def _save_parameters(p,filename):
from topo.misc.commandline import global_params
g = {'global_params_specified':p,
'global_params_all':dict(global_params.get_param_values())}
for d in g.values():
if 'name' in d:
del d['name']
if 'print_level' in d:
del d['print_level']
pickle.dump(g,open(normalize_path(filename),'w'))
def _save_parameters(p,filename):
from topo.misc.commandline import global_params
g = {'global_params_specified':p,
'global_params_all':dict(global_params.get_param_values())}
for d in g.values():
if 'name' in d:
del d['name']
if 'print_level' in d:
del d['print_level']
pickle.dump(g,open(normalize_path(filename),'w'))
def run_script(self):
"""
Dialog to run a user-selected script
The script is exec'd in __main__.__dict__ (i.e. as if it were specified on the commandline.)
"""
script = askopenfilename(initialdir=normalize_path(),filetypes=SCRIPT_FILETYPES)
if script in ('',(),None): # (representing the various ways no script was selected in the dialog)
self.messageBar.response('Run canceled')
else:
execfile(script,__main__.__dict__)
self.messageBar.response('Ran ' + script)
sim_name_from_filename(script)
self.title(topo.sim.name)
def reduce_directory(self, task_launcher):
task_launcher.timestamp = self.reduce_timestamp
root_directory = param.normalize_path(task_launcher.root_directory_name())
print "Running reduce in directory %s" % os.path.basename(root_directory)
log_name = "%s.log" % task_launcher.batch_name
log_path = os.path.join(root_directory, log_name)
assert os.path.exists(log_path), 'Cannot find log file %s' % log_name
with open(log_path,'r') as log:
splits = (line.split() for line in log)
spec_log = [(int(split[0]), json.loads(" ".join(split[1:]))) for split in splits]
task_launcher.reduction_fn(spec_log, root_directory)
return False
def unit_bitpattern(times=None,**kwargs):
if analysis_group('b'):
return None
sheets = [('V1Exc','LGNOff','LGNOffAfferent'),('V1Exc','LGNOn','LGNOnAfferent')]
units = [(0,0)]
f = open(param.normalize_path('mean_bitpattern.txt'), 'a')
for sidx, sheet in enumerate(sheets):
for uidx,unit in enumerate(units):
coords = topo.sim[sheet[0]].sheet2matrixidx(unit[0],unit[1])
shape = topo.sim[sheet[0]].projections()[sheet[2]].cfs[coords[0]][coords[1]].weights.shape
coords = topo.sim[sheet[1]].sheet2matrixidx(unit[0],unit[1])
if shape[0] % 2:
activity = topo.sim[sheet[1]].activity[coords[0]-np.ceil(shape[0]/2):coords[0]+np.floor(shape[0]/2),coords[1]-np.ceil(shape[1]/2):coords[1]+np.floor(shape[1]/2)]
else:
activity = topo.sim[sheet[1]].activity[coords[0]-np.floor(shape[0]/2):coords[0]+np.floor(shape[0]/2),coords[1]-np.floor(shape[1]/2):coords[1]+np.floor(shape[1]/2)]
path = param.normalize_path('{unit}__{time:09.2f}_{sheet}BitPattern.png'.format(sheet=sheet[2],unit=str(unit),time=float(topo.sim.time())))
plt.imsave(path, activity, cmap=plt.cm.gray)
mean_activity = np.mean(activity)
f.write('{sheet},{unit},{time}: {act:.3f}\n'.format(sheet=sheet[2],unit=unit,time=topo.sim.time(),act=mean_activity))
f.close()
def reduce_directory(self, task_launcher):
task_launcher.timestamp = self.reduce_timestamp
root_directory = param.normalize_path(task_launcher.root_directory_name())
print "Running reduce in directory %s" % os.path.basename(root_directory)
log_name = "%s.log" % task_launcher.batch_name
log_path = os.path.join(root_directory, log_name)
assert os.path.exists(log_path), "Cannot find log file %s" % log_name
with open(log_path, "r") as log:
splits = (line.split() for line in log)
spec_log = [(int(split[0]), json.loads(" ".join(split[1:]))) for split in splits]
task_launcher.reduction_fn(spec_log, root_directory)
return False
def extract_log(log_path, dict_type=dict):
"""
Parses the log file generated by a launcher and returns dictionary with
tid keys and specification values.
Ordering can be maintained by setting dict_type to the appropriate
constructor. Keys are converted from unicode to strings for kwarg use.
"""
with open(param.normalize_path(log_path), 'r') as log:
splits = (line.split() for line in log)
uzipped = ((int(split[0]), json.loads(" ".join(split[1:])))
for split in splits)
szipped = [(i, dict((str(k), v) for (k, v) in d.items()))
for (i, d) in uzipped]
return dict_type(szipped)
def resume_launch(cls):
"""
Resumes the execution of the launcher if environment contains
LANCET_ANALYSIS_DIR. This information allows the
launcher.pickle file to be unpickled to resume the launch.
"""
if "LANCET_ANALYSIS_DIR" not in os.environ: return False
root_path = param.normalize_path(os.environ["LANCET_ANALYSIS_DIR"])
del os.environ["LANCET_ANALYSIS_DIR"]
pickle_path = os.path.join(root_path, 'launcher.pickle')
launcher = pickle.load(open(pickle_path, 'rb'))
launcher.collate_and_launch()
return True
def load_snapshot(self):
"""
Dialog to load a user-selected snapshot (see topo.command.load_snapshot() ).
"""
snapshot_name = askopenfilename(initialdir=normalize_path(),filetypes=SAVED_FILETYPES)
if snapshot_name in ('',(),None):
self.messageBar.response('No snapshot loaded.')
else:
self.messageBar.dynamicinfo('Loading snapshot (may take some time)...')
self.update_idletasks()
topo.command.load_snapshot(snapshot_name)
self.messageBar.response('Loaded snapshot ' + snapshot_name)
self.title(topo.sim.name)
self.auto_refresh()
def _generate_figure(self,p):
"""
Helper function to display a figure on screen or save to a file.
p should be a ParamOverrides instance containing the current
set of parameters.
"""
pylab.show._needmain=False
if p.filename is not None:
# JABALERT: need to reformat this as for other plots
fullname=p.filename+p.filename_suffix+str(topo.sim.time())+"."+p.file_format
pylab.savefig(normalize_path(fullname), dpi=p.file_dpi)
else:
self._set_windowtitle(p.title)
pylab.show()
def save(self):
"""Save the movie frames."""
filename_pat = self.name.join(self.filename_fmt.split('%n'))
filename_pat = self.filename_time_fmt.join(filename_pat.split('%t'))
filename_pat = self.filetype.join(filename_pat.split('%T'))
filename_pat = normalize_path(filename_pat,prefix=self.filename_prefix)
dirname = os.path.dirname(filename_pat)
if not os.access(dirname,os.F_OK):
os.makedirs(dirname)
self.verbose('Writing',len(self.frames),'to files like "%s"'%filename_pat)
for t,f in zip(self.frame_times,self.frames):
filename = filename_pat% t
self.debug("Writing frame",repr(filename))
f.image.save(filename)
def analyse(self,steps=[],ns=10,offset_x=0,offset_y=0):
print self.low_contrast
print self.high_contrast
#save_plotgroup("Orientation Preference and Complexity")
#save_plotgroup("Position Preference")
for (x,y) in steps:
xindex = self.center_r+offset_x+x
yindex = self.center_c+offset_y+y
xcoor,ycoor = self.sheet.matrixidx2sheet(xindex,yindex)
c= topo.command.pylabplot.measure_size_response.instance(sheet=self.sheet,num_phase=__main__.__dict__.get('NUM_PHASE',8),num_sizes=ns,max_size=__main__.__dict__.get('MAX_SIZE',1.5),coords=[(xcoor,ycoor)])
c.duraton=4.0 #!
c(coords=[(xcoor,ycoor)],frequencies=[__main__.__dict__.get('FREQ',2.4)])
self.data_dict[(xindex,yindex)] = {}
self.data_dict[(xindex,yindex)]["ST"] = self.calculate_RF_sizes(xindex, yindex)
self.plot_size_tunning(xindex,yindex)
self.data_dict[(xindex,yindex)]["OCT"] = self.perform_orientation_contrast_analysis(self.data_dict[(xindex,yindex)]["ST"],xcoor,ycoor,xindex,yindex)
self.plot_orientation_contrast_tuning(xindex,yindex)
self.plot_orientation_contrast_tuning_abs(xindex,yindex)
f = open(normalize_path("dict.dat"),'wb')
import pickle
pickle.dump(self.data_dict,f)
f.close()
if True:
self.lhi = compute_local_homogeneity_index(self.sheet.sheet_views['OrientationPreference'].view()[0]*pi,2.0)
f = open(prefix+'lhi2.0.pickle','wb')
pickle.dump(self.lhi,f)
f.close()
else:
f = open(prefix+'lhi2.0.pickle','rb')
self.lhi = pickle.load(f)
pylab.figure()
pylab.imshow(self.lhi)
pylab.colorbar()
release_fig("LHI")
self.plot_map_feature_to_surround_modulation_feature_correlations(self.lhi,"Local Homogeneity Index")
def save_snapshot(self):
"""
Dialog to save a snapshot (see topo.command.save_snapshot() ).
Adds the file extension .typ if not already present.
"""
snapshot_name = asksaveasfilename(filetypes=SAVED_FILETYPES,
initialdir=normalize_path(),
initialfile=topo.sim.basename()+".typ")
if snapshot_name in ('',(),None):
self.messageBar.response('No snapshot saved.')
else:
if not snapshot_name.endswith('.typ'):
snapshot_name = snapshot_name + SAVED_FILE_EXTENSION
self.messageBar.dynamicinfo('Saving snapshot (may take some time)...')
self.update_idletasks()
topo.command.save_snapshot(snapshot_name)
self.messageBar.response('Snapshot saved to ' + snapshot_name)
def phase_preference_scatter_plot(sheet_name,diameter=0.39):
r = numbergen.UniformRandom(seed=1023)
preference_map = topo.sim[sheet_name].sheet_views['PhasePreference']
offset_magnitude = 0.03
datax = []
datay = []
(v,bb) = preference_map.view()
for z in zeros(66):
x = (r() - 0.5)*2*diameter
y = (r() - 0.5)*2*diameter
rand = r()
xoff = sin(rand*2*pi)*offset_magnitude
yoff = cos(rand*2*pi)*offset_magnitude
xx = max(min(x+xoff,diameter),-diameter)
yy = max(min(y+yoff,diameter),-diameter)
x = max(min(x,diameter),-diameter)
y = max(min(y,diameter),-diameter)
[xc1,yc1] = topo.sim[sheet_name].sheet2matrixidx(xx,yy)
[xc2,yc2] = topo.sim[sheet_name].sheet2matrixidx(x,y)
if((xc1==xc2) & (yc1==yc2)): continue
datax = datax + [v[xc1,yc1]]
datay = datay + [v[xc2,yc2]]
for i in range(0,len(datax)):
datax[i] = datax[i] * 360
datay[i] = datay[i] * 360
if(datay[i] > datax[i] + 180): datay[i]= datay[i]- 360
if((datax[i] > 180) & (datay[i]> 180)): datax[i] = datax[i] - 360; datay[i] = datay[i] - 360
if((datax[i] > 180) & (datay[i] < (datax[i]-180))): datax[i] = datax[i] - 360; #datay[i] = datay[i] - 360
f = pylab.figure()
ax = f.add_subplot(111, aspect='equal')
pylab.plot(datax,datay,'ro')
pylab.plot([0,360],[-180,180])
pylab.plot([-180,180],[0,360])
pylab.plot([-180,-180],[360,360])
ax.axis([-180,360,-180,360])
pylab.xticks([-180,0,180,360], [-180,0,180,360])
pylab.yticks([-180,0,180,360], [-180,0,180,360])
pylab.grid()
pylab.savefig(normalize_path(str(topo.sim.timestr()) + sheet_name + "_scatter.png"))
