def evalDir(path, i):
print(path)
frame = pd.DataFrame()
modelPaths = [os.path.join(path + '/', dir) for dir in os.listdir(path)]
onlyPickles = filter(lambda x: x.endswith('pickle'), modelPaths)
counter = 0
for modelPath in onlyPickles:
model = pickle.load(open(modelPath, 'rb'))
model = dist.Distribution(model.v, model.m, type='canonical')
dict = {'Dim': model.m.shape[0]}
dict['Sparsity'] = model.sparsity()
#print('mccc')
dict['mccc'] = timing.marginalizeCanonicalConditionCanonical(model)
#print('mccm')
dict['mccm'] = timing.marginalizeCanonicalConditionMean(model)
#print('mmcm')
dict['mmcm'] = timing.marginalizeMeanConditionMean(model)
#print('mmcc')
dict['mmcc'] = timing.marginalizeMeanConditionCanonical(model)
dict['conditionOnlyMean'] = timing.conditionOnlyMean(model)
dict['conditionOnlyCanonical'] = timing.conditionOnlyCanonical(model)
dict['mmccConvert'] = timing.marginalizeMeanConditionCanonicalConvert(
model)
dict['convertMmcc'] = timing.ConvertMarginalizeMeanConditionCanonical(
model)
frame = frame.append(dict, ignore_index=True)
frame.to_csv(path + '/' + 'inferenceOperationsSparse' + str(i) + '.csv',
index=False)
def __init__(self, width, height,
origin=(37.484101,-122.149242),
y_dir=(37.484577,-122.148812),
x_dir=(37.483828,-122.148796)):
self.player_cloud = {}
self.player_angles = {}
self.player_connections = {}
self.player_speeds = {}
self.ghost_cloud = {}
self.ghost_cloud["Ghost1"] = distribution.Distribution(emission_function=self.ghost_observation)
#rotate a geo angle CW this many degrees to get simple
self.geo_to_simp_angle = degrees(math.atan2((y_dir[1]-origin[1]),(y_dir[0]-origin[0])))
self.simp_to_geo = transform_mtx(width, height, origin, x_dir, y_dir)
self.geo_to_simp = inverse(self.simp_to_geo)
self.receiving = False
self.compass_queue = Queue()
self.snap_queue = Queue()
self.thread = Thread(target=self.run_thread)
self.thread.daemon = True # thread dies with the program
self.thread.start()
self.time_since_tick = time.time()
self.plotthread = Thread(target=self.plot_particles)
self.plotthread.daemon = True
self.plotthread.start()
def genModel(sparsity, dim):
print(str(dim) + " " + str(sparsity))
#Start with identity matrix
model = numpy.eye(dim)
#Calculate how many entries we have to set for given sparsity
numOfNNZ = ((1 - sparsity) * (dim * dim)) - dim
#Divide because the matrix is symmetric
numOfNNZsym = math.ceil(numOfNNZ / 2)
#Generate index set of elements in the upper triangle
ind = [(i, j) for i in range(1, dim) for j in range(i + 1, dim)]
#Randomly sample elements from the index set of the upper triangle
r = random.sample(list(range(0, len(ind))), numOfNNZsym)
#Retrieve the index pairs
chosenInd = [ind[i] for i in r]
#For every index pain (x,y) set m[x,y] and m[y,x] to attain symmetry
for i in chosenInd:
randomNum = random.random()
model[i[0], i[1]] = randomNum
model[i[1], i[0]] = randomNum
#Calculate information vector
inf = numpy.linalg.inv(model).dot(numpy.random.rand(dim))
#Construct compressed sparse column structure
model = scipy.sparse.csc_matrix(model)
d = dst.Distribution(inf, model, 'canonical')
with open(modelsPath + str(dim) + '/s' + str(sparsity) + '.pickle',
'wb') as f:
pickle.dump(d, f)
def evalDir(path, i):
#print(path)
frame = pd.DataFrame()
modelPaths = [os.path.join(path + '/', dir) for dir in os.listdir(path)]
onlyPickles = filter(lambda x: x.endswith('pickle'), modelPaths)
counter = 0
for modelPath in onlyPickles:
model = pickle.load(open(modelPath, 'rb'))
model = dist.Distribution(model.v, model.m, type='canonical')
dict = {'Dim': model.m.shape[0]}
dict['Sparsity'] = model.sparsity()
#print('inversionTimeSparse')
dict['inversionTimeSparse'] = timing.inversionTimeSparse(model)
#dict['inversionTimeSparseCSC'] = timing.inversionTimeSparse(model)
#print('inversionTimeSparseToDense')
#dict['inversionTimeSparseToDense'] = timing.inversionTimeSparseToDense(model)
#print('inversionTimeToDenseSplit')
#dict['inversionTimeToDenseSplit'] = timing.inversionTimeSparseToDenseSplit(model)
#print('sparseMatrixDotVectorWithScipySparse')
dict[
'sparseMatrixDotVectorWithScipySparse'] = timing.sparseMatrixDotVectorWithScipySparse(
model)
##print('sparseMatrixDotVectorWithNumpy')
#dict['sparseMatrixDotVectorWithNumpy'] = timing.sparseMatrixDotVectorWithNumpy(model)
#print('sparseSubsetFI')
dict['sparseSubsetFI'] = timing.sparseSubsetFI(model)
#print('sparseSubsetIX')
dict['sparseSubsetIX'] = timing.sparseSubsetIX(model)
#print("sparseMatrixDotMatrix")
dict['sparseMatrixDotMatrix'] = timing.sparseMatrixDotMatrix(model)
model.meanForm()
##print(model.type)
#print('inversionTimeDense')
dict['inversionTimeDense'] = timing.inversionTimeDense(model)
#print('inversionTimeDenseToSparse')
#dict['inversionTimeDenseToSparse'] = timing.inversionTimeDenseToSparse(model)
#print('denseMatrixDotVector')
dict['denseMatrixDotVector'] = timing.denseMatrixDotVector(model)
#print('denseMatrixDotVectorFlattened')
#dict['denseMatrixDotVectorFlattened'] = timing.denseMatrixDotVectorFlattened(model)
#print('denseMatrixDotMatrix')
dict['denseMatrixDotMatrix'] = timing.denseMatrixDotMatrix(model)
frame = frame.append(dict, ignore_index=True)
frame.to_csv(path + '/' + 'atomicOperations' + str(i) + '.csv',
index=False)
def histogram(distrib,
pathname,
normalised=True,
colours=None,
title=None,
xaxis_name=None,
faxis_name=None):
if isinstance(distrib, dict): # 'distrib' is a plain histogram.
distrib = distribution.Distribution(distrib)
assert isinstance(distrib, distribution.Distribution)
if title is None:
title = get_title_placeholder()
if normalised:
title_addon = "[normalised] "
else:
title_addon = ""
title_addon += (
"#bars=" + str(len(distrib.get_histogram())) + ", "
"sum bars=" +
format(sum([value
for _, value in distrib.get_histogram().items()]), ".3f") +
", "
"sum x*bar=" + format(
sum([x * value
for x, value in distrib.get_histogram().items()]), ".3f") +
", "
"median=" + format(distrib.get_median(), ".3f") + ", "
"mean=" + format(distrib.get_mean(), ".3f") + ", "
"mean freq.=" + format(
1.0 / (distrib.get_mean() if abs(distrib.get_mean()) > 0.00001 else
0.00001), ".3f") + ", "
"variance=" + format(distrib.get_variance(), ".3f") + ", "
"std. deviation=" + format(distrib.get_standard_deviation(), ".3f") +
", "
"CV=" + format(distrib.get_coefficient_of_variation(), ".3f"))
title = title.replace(get_title_placeholder(), title_addon)
if normalised:
points = distrib.get_probability_points()
else:
points = distrib.get_points()
if len(distrib.get_events()) < 2:
bar_width = 0.8
else:
bar_width = min(
map(lambda x: abs(x[1] - x[0]),
zip(distrib.get_events()[:-1],
distrib.get_events()[1:])))
__write_xplot(
lambda ax, x, y: ax.bar(x, y, bar_width, color=colours, align="center"
), points, pathname, title, xaxis_name,
faxis_name)
def test_copy():
sigma = hlp.randomPositiveSemidefinite(dims)
mu = np.random.rand(dims)
d = dst.Distribution(mu, sigma, 'moment')
c = d.copy()
# Check if different objects
assert c is not d
# Check if entities hold equal values
assert c.equalsVerbose(d)
# Check if deep-copy succeeded
assert c.v is not d.v
# Check if deep-copy succeeded
assert c.m is not d.m
def test_Conversion():
sigma = hlp.randomPositiveSemidefinite(dims)
mu = np.random.rand(dims).T
d = dst.Distribution(mu, sigma, 'mean')
dd = ddst.DistributionDense(mu, sigma, 'mean')
print(type(dd))
a = d.copy()
b = dd.copy()
# Check if multiple conversions don't change equality
for i in range(1, 100):
#print(i)
a.canonicalForm()
a.meanForm()
b.canonicalForm()
b.meanForm()
assert a.isCloseVerbose(d)
assert b.isCloseVerbose(dd)
def doit(hist, n, ofile):
xhist = hist.copy()
for k in xhist.keys():
xhist[k] = 0
isi = distribution.Distribution(hist)
print(isi)
ofile.write(str(isi) + "\n")
for _ in range(n):
e = isi.next_event()
assert e in hist.keys()
xhist[e] += 1
osum = 0.0
xsum = 0.0
for k in hist.keys():
osum += hist[k]
xsum += xhist[k]
if xsum > 0:
for k in xhist.keys():
xhist[k] *= osum / xsum
return xhist
def histogram(self, distrib, colours=None, normalised=None, legend=None):
if isinstance(distrib, dict): # 'distrib' is a plain histogram.
distrib = distribution.Distribution(distrib)
assert isinstance(distrib, distribution.Distribution)
if normalised:
points = distrib.get_probability_points()
else:
points = distrib.get_points()
if len(distrib.get_events()) < 2:
bar_width = 0.8
else:
bar_width = min(
map(lambda x: abs(x[1] - x[0]),
zip(distrib.get_events()[:-1],
distrib.get_events()[1:])))
self.make_plot(
lambda ax, x, y: ax.bar(x,
y,
bar_width,
color=self._choose_colours(colours),
align="center",
label=legend), points, legend is not None)
def main(massfunction = 0, starformationhistory = 0, A_v = 10.0, sfr = .01, apera = 24000,\
maxage = 2000000., distance = 8.0, appendix='default', quiet=0, precise=0):
"""main(massfunction = 0, starformationhistory = 0, A_v = 10.0, sfr = .01, apera = 24000,\
maxage = 2000000., distance = 8.0, appendix='default', quiet=0, precise=0)
Creates a sample of stars
Parameters
----------
massfunction distribution:
relatively in mass, with lower and upper restriction, see also what the distribution must provide
starformation history distribution:
relatively in age, with lower and upper restriction, see also what the distribution must provide
A_v float:
value for the visual extinction
sfr float:
average star formation rate in M_sun/year (only if precise = True)
apera float:
used aperture size for selecting the fluxes of the protostars
maxage float:
age of the star formation site, sfr is assumed to be constant
distance float:
distance to the simulated starformation site
appendix String:
sets the outputfilename, default is the starting time (via time.time())
quiet boolean:
if true (=1) suppresses all standard output
precise boolean:
if true (=1) sample single star till expected mass reached based on the
integrated starformationhistory times the starformationrate
else sfr is the number of expected stars and the starformationrate is
calculated by the cumulated mass divided by the formation time
The distributions must provide an object which has the following members:
float cdf(float x) returns the integrated distribution up to x, is used to calculate
the expected mass
float _upperbound returns the upper limit of the distribution, is used to calculate
the expected mass
float[] sample(int n) returns an array of n floats, sampled from the distribution
float mean() returns the mean value of the distribution
Returns
----------
returns a fits file in the out-folder, either using the appendix as filename or the time of the
starting of the script in order to prevent overwriting existing files
In the header of the fits-file are the values: A_v, sfr, apera, maxage and distance recorded
In the data part are the age, mass, modelnumber and the uncorrected and corrected fluxes
"""
if quiet:
output_stream = StringIO()
else:
output_stream = sys.stdout
t0 = time()
if appendix == 'default': # making sure not to overwrite former output
appendix = t0 # by using the starting time as an unique id
#parameter settings
k_v = 211.4 # opacity in v_band in cm^2/g
# wavelength of the corresponding filterband in microns
wavelength = [
1.235, 1.662, 2.159, 3.550, 4.493, 5.731, 7.872, 23.68, 71.42, 155.9
]
models = ['2H', '2J', '2K', 'I1', 'I2', 'I3', 'I4', 'M1', 'M2', 'M3']
if massfunction == 0 and starformationhistory == 0:
# star mass function
kroupa = np.vectorize(functions.kroupa)
massfunction = dist.Distribution(kroupa, .1, 50.)
#star formation history
constant_sfr = np.vectorize(functions.constant_sfr)
starformationhistory = dist.Distribution(constant_sfr, 1000., maxage)
cumass = 0. #sampled mass
stars = [] #storing for the sample
sfh = starformationhistory
t1 = time() #startup completed
if precise:
n = 0
exmass = sfh.cdf()(sfh._upperbound) * sfr #expected mass formed
while cumass < exmass:
mass, age = massfunction.sample(), sfh.sample()
cumass = cumass + mass
stars.append([n, age, mass])
if n % 10000 == 0:
print(n, cumass, file=output_stream) #reporting progress
n = n + 1
else:
n = sfr
mass, age = massfunction.sample(n), sfh.sample(n)
cumass = np.sum(mass)
exmass = n * massfunction.mean()
stars = [[i, age[i], mass[i]] for i in range(n)]
sfr = cumass / (sfh._upperbound - sfh._lowerbound
) #average star formation rate
print('number of sampled stars: %s' % n, file=output_stream)
print('mass of sampled stars: %s' % cumass, file=output_stream)
print('mean mass: %s' % (cumass / n), file=output_stream)
print('expected mass of stars: %s' % exmass, file=output_stream)
t2 = time() # sampleing completed
# python code for model contact
#initial parameters
model = [fits.open('models/%s.fits' % mod)
for mod in models] # fits-data for the model
param = fits.open('models/parameters.fits.gz') # modelparameter
app_num = [
np.interp(apera, model[i][2].data.field(0),
range(model[i][2].data.field(0).size))
for i in range(len(models))
]
# sampling viewing angle
angle = np.random.random_integers(0, 9, len(stars))
#reading model grid
mass = param[1].data['MASSC'][::10]
age = param[1].data['TIME'][::10]
grid = np.vstack([age, mass]).transpose()
#converting to logspace
stars = np.asarray(stars)
grid = np.log10(grid)
stars[:, 1:] = np.log10(stars[:, 1:])
output = stars.tolist() #creating output
#normalizing for nearest neighbor search
grid[0, :] = grid[0, :] / (grid[0, :].max() - grid[0, :].min())
grid[1, :] = grid[1, :] / (grid[1, :].max() - grid[1, :].min())
stars[1, :] = stars[1, :] / (grid[0, :].max() - grid[0, :].min())
stars[2, :] = stars[2, :] / (grid[1, :].max() - grid[1, :].min())
t3 = time() #model data load complete
tree = scipy.spatial.cKDTree(grid, leafsize=10) #search tree
matches = [tree.query(star[1:], k=1)[1]
for star in stars] #saves matches with (dist, index)
t4 = time() #matching sample to data complete
# extracting fluxes
fluxes = [0 for j in range(len(models))]
indices = 10 * np.asarray(matches) + angle
for j in range(len(models)):
fluxes[j] = model[j][1].data[indices]['TOTAL_FLUX'][:, app_num[j]]
# applying extinction
extinction = np.loadtxt('models/extinction_law.ascii')
k_lambda = np.interp(wavelength, extinction[:, 0], extinction[:, 1])
correctionfactor = 10.**(-.4 * A_v * k_lambda / k_v)
newfluxes = [0 for j in range(len(models))]
for j in range(len(models)):
newfluxes[j] = np.asarray(
fluxes[j]) * correctionfactor[j] * (1. / distance)**2
t5 = time() #extracting fluxes complete
# saving data
fluxes = np.asarray(fluxes)
newfluxes = np.asarray(newfluxes)
output = np.vstack(
[np.asarray(output).transpose(), matches, fluxes,
newfluxes]).transpose()
# create table
# data table
t = Table()
t.add_column(Column(name='age', data=output[:, 1]))
t.add_column(Column(name='mass', data=output[:, 2]))
t.add_column(Column(name='model', data=output[:, 3]))
for i in range(len(models)):
t.add_column(Column(name='%s' % models[i], data=output[:, 4 + i]))
for i in range(len(models)):
t.add_column(
Column(name='c%s' % models[i], data=output[:,
4 + len(models) + i]))
# head table
header = Table()
header.add_column(Column(name='AV', data=[A_v]))
header.add_column(Column(name='SFR', data=[sfr]))
header.add_column(Column(name='APPERA', data=[apera]))
header.add_column(Column(name='MAXAGE', data=[maxage]))
header.add_column(Column(name='DIST', data=[distance]))
fits.writeto('out/%s' % appendix, np.array(t), clobber=True)
fits.append('out/%s' % appendix, np.array(header), clobber=True)
t6 = time() #saving complete
# timing possibility for optimization efforts
print('starting script at %f' % (t0), file=output_stream)
print('initializing %f' % (t1 - t0), file=output_stream)
print("sampleing %f" % (t2 - t1), file=output_stream)
print("model data load %f" % (t3 - t2), file=output_stream)
print("matching model %f" % (t4 - t3), file=output_stream)
print("extracting fluxes %f" % (t5 - t4), file=output_stream)
print("saving %f" % (t6 - t5), file=output_stream)
print("________________________", file=output_stream)
print("total runtime %f" % (t6 - t0), file=output_stream)
print("finishing script %f" % t6, file=output_stream)
#main(sfr = .08) # for testing purposes and directly called from bash
def _test_alignment_of_aligned_spike_trains(info):
"""
Checks alignment of spike trains all aligned to a pivot
spike train. Test is conducted for several alignment
coefficients.
"""
assert isinstance(info, TestInfo)
seed = 0
def get_next_seed():
nonlocal seed
seed += 1
return seed
numpy.random.seed(get_next_seed())
def make_spike_train(is_excitatory=True,
mean_frequency=None,
percentage_of_regularity_phases=None,
seed=None):
if mean_frequency is None:
mean_frequency = 15.0 if is_excitatory else 60.0
if percentage_of_regularity_phases is None:
percentage_of_regularity_phases = 0.0
return spike_train.create(
distribution.hermit_distribution_with_desired_mean(
1.0 / mean_frequency, 0.003, 0.3, 0.0001, pow_y=2, seed=seed)
if is_excitatory else
distribution.hermit_distribution_with_desired_mean(1.0 /
mean_frequency,
0.001,
0.08,
0.0001,
bin_size=0.0002,
pow_y=2,
seed=seed),
percentage_of_regularity_phases)
pivot_trains = [
(make_spike_train(True, seed=get_next_seed()), "epivot"),
(make_spike_train(False, seed=get_next_seed()), "ipivot"),
]
nsteps = 1000000
dt = 0.0001
start_time = 0.0
def simulate_trains(trains):
t = start_time
for step in range(nsteps):
utility.print_progress_string(step, nsteps)
for train, _ in trains:
train.on_time_step(t, dt)
t += dt
print("Simulating pivot trains")
simulate_trains(pivot_trains)
def make_aligned_train(pivot,
alignment_coefficient,
dispersion_fn,
is_excitatory=True,
mean_frequency=None,
seed=None):
assert isinstance(pivot, spike_train.SpikeTrain)
train = make_spike_train(is_excitatory, mean_frequency, 0.0, seed)
train.set_spike_history_alignment(pivot.get_spikes_history(),
alignment_coefficient, dispersion_fn)
return train
dispersion_fn = datalgo.AlignmentDispersionToSpikesHistory(2.0)
other_trains = [[
(make_aligned_train(pivot,
coef,
dispersion_fn,
kind,
seed=get_next_seed()),
kname + str(idx) + "_" + format(coef, ".2f"))
for kind, kname in [(True, "e"), (False, "i")] for idx in range(2)
for coef in [-1.0, -0.75, -0.5, -0.25, 0.0, 0.25, 0.5, 0.75, 1.0]
] for pivot, _ in pivot_trains]
print("Simulating other trains")
simulate_trains(
[train for pivot_trains in other_trains for train in pivot_trains])
print("Saving results:")
for pivot_desc_pair, pivot_trains in zip(pivot_trains, other_trains):
pivot = pivot_desc_pair[0]
pivot_desc = pivot_desc_pair[1]
outdir = os.path.join(info.output_dir, pivot_desc)
os.makedirs(outdir, exist_ok=True)
print(" Saving statistics of spike train: " + pivot_desc)
with open(os.path.join(outdir, "stats_" + pivot_desc + ".json"),
"w") as ofile:
ofile.write(
json.dumps(
{
"configuration": pivot.get_configuration(),
"statistics": pivot.get_statistics()
},
sort_keys=True,
indent=4))
print(" Saving spike event distributions of spike train: " +
pivot_desc)
plot.histogram(datalgo.make_histogram(
datalgo.make_difference_events(pivot.get_spikes_history()), dt,
start_time),
os.path.join(outdir, "distrib_" + pivot_desc + ".png"),
normalised=False)
for i in range(len(pivot_trains)):
train_i, desc_i = pivot_trains[i]
print(" Saving statistics of spike train: " + desc_i)
with open(os.path.join(outdir, "stats_" + desc_i + ".json"),
"w") as ofile:
ofile.write(
json.dumps(
{
"configuration": train_i.get_configuration(),
"statistics": train_i.get_statistics()
},
sort_keys=True,
indent=4))
print(" Saving spike event distributions of spike train: " +
desc_i)
plot.histogram(datalgo.make_histogram(
datalgo.make_difference_events(train_i.get_spikes_history()),
dt, start_time),
os.path.join(outdir, "distrib_" + desc_i + ".png"),
normalised=False)
print(" Saving alignment histogram: " + desc_i + " VS " +
pivot_desc)
hist_pair = datalgo.make_alignment_histograms_of_spike_histories(
train_i.get_spikes_history(), pivot.get_spikes_history(),
0.005, dt / 2.0)
plot.histogram(
hist_pair[0],
os.path.join(outdir,
"hist_" + desc_i + "_vs_" + pivot_desc + ".png"),
normalised=False)
for j in range(i + 1, len(pivot_trains)):
train_j, desc_j = pivot_trains[j]
print(" Saving alignment histogram: " + desc_i + " VS " +
desc_j)
hist_pair = datalgo.make_alignment_histograms_of_spike_histories(
train_i.get_spikes_history(), train_j.get_spikes_history(),
0.005, dt / 2.0)
# plot.histogram(
# hist_pair[0],
# os.path.join(outdir, "hist_" + desc_i + "_vs_" + desc_j + ".png"),
# normalised=False
# )
# plot.histogram(
# hist_pair[1],
# os.path.join(outdir, "hist_" + desc_j + "_vs_" + desc_i + ".png")
# )
print(" Saving alignment curve: " + desc_i + " VS " +
desc_j)
with plot.Plot(
os.path.join(
outdir, "curve_" + desc_i + "_vs_" + desc_j +
".png")) as plt:
plt.curve(datalgo.interpolate_discrete_function(
datalgo.approximate_discrete_function(
distribution.Distribution(
hist_pair[0]).get_probability_points())),
legend=desc_i + " -> " + desc_j)
plt.curve(datalgo.interpolate_discrete_function(
datalgo.approximate_discrete_function(
distribution.Distribution(
hist_pair[1]).get_probability_points())),
legend=desc_j + " -> " + desc_i)
plot.event_board_per_partes(
[pivot.get_spikes_history()] +
[train.get_spikes_history() for train, _ in pivot_trains],
os.path.join(outdir, "spikes_board.png"), start_time,
start_time + nsteps * dt, 1.0, 5, lambda p: print(
" Saving spikes board part: " + os.path.basename(p)),
[[plot.get_random_rgb_colour()] * len(pivot.get_spikes_history())]
+ [[plot.get_random_rgb_colour()] * len(train.get_spikes_history())
for train, _ in pivot_trains],
" " + plot.get_title_placeholder() + " SPIKES BOARD")
return 0 # No failures
def _test_aligned_spike_trains(info):
"""
Checks alignment of spike trains for different alignment coefficients.
"""
assert isinstance(info, TestInfo)
# def make_alignment_histogram(name, lo_event, hi_event, dt, num_events=None):
# if num_events is None:
# num_events = int((hi_event - lo_event) / dt) + 1
# raw_events = [lo_event + (i / float(num_events - 1)) * (hi_event - lo_event) for i in range(0, num_events)]
# events = []
# for e in raw_events:
# t = 0.0
# while e > t + 1.5 * dt:
# t += dt
# events.append(t)
# half_epsilon = 0.5 * (dt / 10)
# coefs = []
# for i in range(len(events)):
# for j in range(i + 1, len(events)):
# dist = events[j] - events[i]
# shift = dt
# while shift < dist:
# if not (shift < half_epsilon or shift > dist - half_epsilon):
# # print(format(shift, ".3f") + " / " + format(dist, ".3f") + " = " + format(shift/dist, ".3f") +
# # " ---> " +
# # format(shift/dt, ".3f") + " / " + format(dist / dt, ".3f") + " = " + format((shift/dt)/(dist/dt), ".3f"))
# coef = max(-1.0, min(2.0 * shift / dist - 1.0, 1.0))
# coefs.append(coef)
# shift += dt
# coefs = sorted(coefs)
# hist = datalgo.make_histogram(coefs, 0.005, 0.0, 1)
# plot.histogram(
# hist,
# os.path.join(info.output_dir, name + ".png"),
# normalised=False
# )
# return 0
# make_alignment_histogram("xhist", 0.003, 0.030, 0.0001)
# make_alignment_histogram("yhist", 0.003, 0.130, 0.0001)
# return 0
seed = 0
def get_next_seed():
nonlocal seed
seed += 1
return seed
numpy.random.seed(get_next_seed())
def make_spike_train(is_excitatory=True,
mean_frequency=None,
percentage_of_regularity_phases=None,
seed=None):
# min_event = 0.003
# max_event = 0.030
# num_events = 28
# return spike_train.create(
# distribution.Distribution(
# {(min_event + (i / float(num_events - 1)) * (max_event - min_event)): 1.0 / float(num_events)
# for i in range(0, num_events)},
# seed
# ),
# 0.0
# )
if mean_frequency is None:
mean_frequency = 15.0 if is_excitatory else 60.0
if percentage_of_regularity_phases is None:
percentage_of_regularity_phases = 0.0
return spike_train.create(
distribution.hermit_distribution_with_desired_mean(
1.0 / mean_frequency, 0.003, 0.3, 0.0001, pow_y=2, seed=seed)
if is_excitatory else
distribution.hermit_distribution_with_desired_mean(1.0 /
mean_frequency,
0.001,
0.08,
0.0001,
bin_size=0.0002,
pow_y=2,
seed=seed),
percentage_of_regularity_phases)
pivot_trains = [
(make_spike_train(True, seed=get_next_seed()), "epivot"),
(make_spike_train(False, seed=get_next_seed()), "ipivot"),
]
nsteps = 1000000
dt = 0.0001
start_time = 0.0
def simulate_trains(trains):
t = start_time
for step in range(nsteps):
utility.print_progress_string(step, nsteps)
for train, _ in trains:
train.on_time_step(t, dt)
t += dt
print("Simulating pivot trains")
simulate_trains(pivot_trains)
def make_aligned_train(pivot,
alignment_coefficient,
dispersion_fn,
is_excitatory=True,
mean_frequency=None,
seed=None):
assert isinstance(pivot, spike_train.SpikeTrain)
train = make_spike_train(is_excitatory, mean_frequency, 0.0, seed)
train.set_spike_history_alignment(pivot.get_spikes_history(),
alignment_coefficient, dispersion_fn)
return train
dispersion_fn = datalgo.AlignmentDispersionToSpikesHistory(2.0)
other_trains = [
(make_spike_train(True, seed=get_next_seed()), "eunaligned"),
(make_spike_train(False, seed=get_next_seed()), "iunaligned"),
] + [(make_aligned_train(
pivot, coef, dispersion_fn, kind, seed=get_next_seed()),
kname + "aligned(" + desc + "," + format(coef, ".2f") + ")")
for pivot, desc in pivot_trains
for kind, kname in [(True, "e"), (False, "i")]
for coef in [-1.0, -0.75, -0.5, -0.25, 0.0, 0.25, 0.5, 0.75, 1.0]]
print("Simulating other trains")
simulate_trains(other_trains)
print("Saving results:")
for pivot, pivot_desc in pivot_trains:
print(" Saving statistics of spike train: " + pivot_desc)
with open(
os.path.join(info.output_dir, "stats_" + pivot_desc + ".json"),
"w") as ofile:
ofile.write(
json.dumps(
{
"configuration": pivot.get_configuration(),
"statistics": pivot.get_statistics()
},
sort_keys=True,
indent=4))
print(" Saving spike event distributions of spike train: " +
pivot_desc)
plot.histogram(datalgo.make_histogram(
datalgo.make_difference_events(pivot.get_spikes_history()), dt,
start_time),
os.path.join(info.output_dir,
"distrib_" + pivot_desc + ".png"),
normalised=False)
for other, other_desc in other_trains:
print(" Saving statistics of spike train: " + other_desc)
with open(
os.path.join(info.output_dir, "stats_" + other_desc + ".json"),
"w") as ofile:
ofile.write(
json.dumps(
{
"configuration": other.get_configuration(),
"statistics": other.get_statistics()
},
sort_keys=True,
indent=4))
print(" Saving spike event distributions of spike train: " +
other_desc)
plot.histogram(datalgo.make_histogram(
datalgo.make_difference_events(other.get_spikes_history()), dt,
start_time),
os.path.join(info.output_dir,
"distrib_" + other_desc + ".png"),
normalised=False)
for pivot, pivot_desc in pivot_trains:
for other, other_desc in other_trains:
print(" Saving alignment histograms: " + pivot_desc + " VS " +
other_desc)
hist_pair = datalgo.make_alignment_histograms_of_spike_histories(
pivot.get_spikes_history(), other.get_spikes_history(), 0.005,
dt / 2.0)
plot.histogram(hist_pair[0],
os.path.join(
info.output_dir, "hist_" + pivot_desc + "_vs_" +
other_desc + ".png"),
normalised=False)
plot.histogram(
hist_pair[1],
os.path.join(
info.output_dir,
"hist_" + pivot_desc + "_vs_" + other_desc + "_inv.png"))
print(" Saving alignment curve: " + pivot_desc + " VS " +
other_desc)
with plot.Plot(
os.path.join(
info.output_dir, "curve_" + pivot_desc + "_vs_" +
other_desc + ".png")) as plt:
plt.curve(datalgo.interpolate_discrete_function(
datalgo.approximate_discrete_function(
distribution.Distribution(
hist_pair[0]).get_probability_points())),
legend=pivot_desc + " -> " + other_desc)
plt.curve(datalgo.interpolate_discrete_function(
datalgo.approximate_discrete_function(
distribution.Distribution(
hist_pair[1]).get_probability_points())),
legend=other_desc + " -> " + pivot_desc)
plot.event_board_per_partes(
[pivot.get_spikes_history()] +
[other.get_spikes_history() for other, _ in other_trains],
os.path.join(info.output_dir,
"spikes_board_" + pivot_desc + ".png"), start_time,
start_time + nsteps * dt, 1.0, 5, lambda p: print(
" Saving spikes board part: " + os.path.basename(p)),
[[plot.get_random_rgb_colour()] * len(pivot.get_spikes_history())]
+ [[plot.get_random_rgb_colour()] * len(other.get_spikes_history())
for other, _ in other_trains],
" " + plot.get_title_placeholder() + " SPIKES BOARD")
return 0 # No failures
Verify that ciphertext = Encrypt(plaintext, key) and delete those which fail this test (due to comms error)
"""
count = 0
# Generate hypotheticals
for i in range(self.acq.numTraces):
ptStr = self.ptNumpyArray2String(self.acq.inputtext[i])
ctStr1 = (des_block.des_block(ptStr, 64)).encipher(self.key)
ctStr2 = self.ptNumpyArray2String(self.acq.outputtext[i])
if (ctStr1 != ctStr2):
acq.traces = np.delete(acq.traces, i, axis=0)
acq.inputtext = np.delete(acq.inputtext, i, axis=0)
acq.outputtext = np.delete(acq.outputtext, i, axis=0)
count += 1
print "Deleted %d traces" % count
def ptNumpyArray2String(self, inputtext):
ptStr = ""
for i in range(self.acq.blockSize):
ptStr += hex2str(inputtext[i])
return ptStr
if __name__ == "__main__":
#acq = LoadTraces.LoadTraces('cw_tc6+trim.trs')
acq = LoadTraces.LoadTraces('traces/0005.trs', 100000)
v = Verify(acq)
v.verify2()
d = distribution.Distribution(acq)
print "sbox 1 of 0005"
d.sboxInputs(0x1f, 1)
def add_player(self, name, connection):
self.player_cloud[name] = distribution.Distribution(num_particles=200, emission_function=self.player_observation, transition_function=lambda x: self.player_transition(name, x))
self.player_angles[name] = 0.0
self.player_connections[name] = connection
self.player_speeds[name] = 0.0
def test_operationsSparse():
marginalizeTo = [1, 2, 4, 5]
condition = [0, 1]
condVal = [0.5, 0.5]
cov = np.matrix([[3, 0, 0, 2, 0, 2], [0, 1, 0.5, 0, 0, 0],
[0, 0.5, 1, 0, 0, 0], [2, 0, 0, 2, 0, 1],
[0, 0, 0, 0, 1, 0], [2, 0, 0, 1, 0, 2]])
mean = [0.5, 0.5, 0.5, 0.5, 0.5, 0.5]
# Invert matrix and compute information vector
prec = np.linalg.inv(cov)
inf = prec.dot(mean)
# Construct Distribution objects
sparse_dist = dst.Distribution(mean, cov, 'mean')
sparse_dist_canonical = dst.Distribution(inf, sp.csc_matrix(prec),
'canonical')
# Marginalize "by hand"
cov_marginalized = np.take(np.take(cov, marginalizeTo, axis=0),
marginalizeTo,
axis=1)
mean_marginalized = np.take(mean, marginalizeTo)
# Marginalize both distributions with methods
sparse_dist_marginalized = sparse_dist.marginalize(marginalizeTo)
sparse_dist_canonical_marginalized = sparse_dist_canonical.marginalize(
marginalizeTo)
# models are close
assert (np.allclose(sparse_dist_marginalized.m, cov_marginalized))
assert (np.allclose(sparse_dist_marginalized.v, mean_marginalized))
#Covert canonical to mean and check if close
temp = sparse_dist_canonical_marginalized.copy()
temp.meanForm()
assert (np.allclose(temp.m, sparse_dist_marginalized.m))
assert (np.allclose(temp.v, sparse_dist_marginalized.v))
#Compute canonical 'by hand', a little bit redundant^^
prec_marginalized = np.linalg.inv(cov_marginalized)
inf_marginalized = prec_marginalized.dot(mean_marginalized)
assert (np.allclose(prec_marginalized,
sparse_dist_canonical_marginalized.m.todense()))
assert (np.allclose(inf_marginalized,
sparse_dist_canonical_marginalized.v))
# Compute conditioned distribution by hand
complementary_conditioning_set = list(
set(range(0, prec_marginalized.shape[0])) - set(condition))
prec_final = np.take(np.take(prec_marginalized,
complementary_conditioning_set,
axis=0),
complementary_conditioning_set,
axis=1)
l_ji = np.take(np.take(prec_marginalized,
complementary_conditioning_set,
axis=0),
condition,
axis=1)
l_jj_i = np.linalg.inv(
np.take(np.take(prec_marginalized,
complementary_conditioning_set,
axis=0),
complementary_conditioning_set,
axis=1))
inf_final = np.squeeze(
np.asarray(
np.subtract(
np.take(inf_marginalized, complementary_conditioning_set),
l_ji.dot(l_jj_i).dot(condVal))))
cov_final = np.linalg.inv(prec_final)
mean_final = cov_final.dot(inf_final.T)
# Check conditioning on canonical form
canonicalMarginalizedConditioned = sparse_dist_canonical_marginalized.condition(
condition, condVal)
assert (np.allclose(prec_final,
canonicalMarginalizedConditioned.m.todense()))
assert (np.allclose(inf_final, canonicalMarginalizedConditioned.v))
# Check conditioning on mean form
sparse_dist_marginalized_conditioned = sparse_dist_marginalized.condition(
condition, condVal)
print('--------------------------------------')
print(cov_final)
print('--------------------------------------')
print(sparse_dist_marginalized_conditioned.m)
print('--------------------------------------')
print(mean_final)
print('--------------------------------------')
print(sparse_dist_marginalized_conditioned.v)
assert (np.allclose(cov_final, sparse_dist_marginalized_conditioned.m))
assert (np.allclose(mean_final, sparse_dist_marginalized_conditioned.v))
#Convert to canonical Form and check again
sparse_dist_marginalized_conditioned.canonicalForm()
assert (np.allclose(prec_final,
sparse_dist_marginalized_conditioned.m.todense()))
assert (np.allclose(inf_final, sparse_dist_marginalized_conditioned.v))
def main(n = 150000, quiet = False):
"""main(n = 150000, quiet = False)
This script produces a grid of expected numbers of stars according to the selection
criteria of Yusef-Zedah et al. 2009, 702,178-225 The Astrophysical Journal.
The grid is in av for visual extinction, apera for aperature size and age for the maxage
of the starformation size
Parameters
----------
n integer:
number of stars to be sampled per parameter set
quiet boolean:
if true suppresses all standard output
Returns
----------
A number of fits-files with the sampled stars for different parameters to be specified in
this file.
Standard output is used to report progress, it will print out the parameter set to be
progressed next and the completeness of the script as
AV aperaturesize maxage completeness ETA
ETA is the time to complete in seconds based on the single last operation
"""
t0 = time() #timing possibility
if quiet:
output_stream = StringIO()
else:
output_stream = sys.stdout
print(t0,file=output_stream)
sfr = .01
# star mass function
kroupa = np.vectorize(functions.kroupa)
mf = dist.Distribution(kroupa, .1, 50.)
#star formation history
constant_sfr = np.vectorize(functions.constant_sfr)
ages = np.logspace(5,7,7)
sf = [dist.Distribution(constant_sfr, 1000., ages[i]) for i in range(len(ages))]
#sfr = [150000*mf.mean()/(ages[i]-1000.) for i in range(len(ages))]
t1 = time() # finished reading the distributions
print(t1,file=output_stream)
# setting up model data
aperas = np.logspace(2, 5, 4)
avs = np.linspace(10.0, 50.0, 5)
l = 1
mpold, tmpnew = 0., time()
parameters = []
for i in range(len(avs)):
for j in range(len(aperas)):
for k in range(len(ages)):
tmpold, tmpnew = tmpnew, time()
starformation.main(massfunction = mf, starformationhistory = sf[k], \
A_v = avs[i], sfr = n, apera = aperas[j], maxage = ages[k], \
appendix = "%s_%03d_%06d_%09d" % ('sim',avs[i],aperas[j],ages[k]), quiet=True, precise=False)
print(avs[i],aperas[j],ages[k], l/len(avs)/len(aperas)/len(ages), (len(avs)*len(aperas)*len(ages)-l)*(tmpnew-tmpold),file=output_stream)
l = l+1
parameters.append([avs[i],aperas[j],ages[k]])
t2 = time() # end of simulation
print(t2, t1, t2-t1)
print ('number of simulations run: %s' %l , file=output_stream)
head = ['#','AV', 'Aperature_size', 'Age']
f = open('out/__head', 'w')
f.write( ','.join(head)+'\n' )
np.savetxt(f, parameters)
f.close()
t3 = time() # end of saving data
analysis.main('out')
print ('analysis complete' , file=output_stream)
t4 = time() # end of analysing data
print( 'starting script at %f' %(t0), file=output_stream)
print( 'initializing %f' %(t1-t0), file=output_stream)
print( "running simulation %f" %(t2-t1), file=output_stream)
print( "writing data %f" %(t3-t2), file=output_stream)
print( "analysing data %f" %(t4-t3), file=output_stream)
print( "________________________", file=output_stream)
print( "total runtime %f" %(t4-t0), file=output_stream)
print( "finishing script %f" %t4, file=output_stream)
def __init__(self, spiking_distribution, percentage_of_regularity_phases,
noise_length_distribution, regularity_length_distribution,
max_spikes_buffer_size, regularity_chunk_size,
recording_controller, seed):
"""
:param spiking_distribution:
The distribution used for generation of spike events.
:param percentage_of_regularity_phases:
Specifies a percentage (in range 0..100) of whole simulation time, when algorithm enforcing
correlations of inter-spike-intervals will be active. In the remaining time the algorithm will
be inactive.
:param noise_length_distribution:
A distribution specifying durations of phases when the spikes-correlation algorithm is inactive.
:param regularity_length_distribution:
A distribution specifying durations of phases when the spikes-correlation algorithm is active.
:param max_spikes_buffer_size:
Spikes generated by `spiking_distribution' are stored a buffer, before they proceed to the
spike train algorithms. Size of the buffer affects correlation degree of spikes in the spikes
train. Greater value gives greater degree of correlation. Values in range 75..150 give good
results. The value 100 can be considered as default value. However, we recommend to do
same experimentation to tune the values to get correlation degree you need.
:param regularity_chunk_size:
:param recording_controller:
It is a function taking two arguments `last_recording_time' and `current_time' returning a bool.
It tells the train whether recording of a spike event should be performed at `current_time' or not.
The first parameter `last_recording_time' represents the last time when this function returned True
to the train. Note that initial time of the simulation is considered as a time when the function
returned True. Here are two basic examples of the function:
lambda last_recording_time, current_time: True # Record all generated spikes
lambda last_recording_time, current_time: False # Disable recording of spikes
Look also to assertions below to see requirements (preconditions) of the parameters described above.
"""
assert isinstance(spiking_distribution, distribution.Distribution)
assert type(percentage_of_regularity_phases) in [int, float]
assert 0 <= percentage_of_regularity_phases and percentage_of_regularity_phases <= 100
assert isinstance(noise_length_distribution, distribution.Distribution)
assert isinstance(regularity_length_distribution,
distribution.Distribution)
assert regularity_length_distribution.get_mean() > 0.0001
assert isinstance(max_spikes_buffer_size,
int) and max_spikes_buffer_size >= 1
assert isinstance(regularity_chunk_size,
int) and regularity_chunk_size in range(
1, max_spikes_buffer_size)
self._spiking_distribution = spiking_distribution
self._phases_distribution = distribution.Distribution(
{
"regularity": percentage_of_regularity_phases,
"noise": 100 - percentage_of_regularity_phases
}, seed)
self._noise_length_distribution = noise_length_distribution
self._regularity_length_distribution = regularity_length_distribution
self._regularity_chunk_index_low = -1
self._regularity_chunk_index_high = -1
self._regularity_chunk_size = regularity_chunk_size
self._spikes_buffer = []
self._spikes_buffer_creation_times = []
self._max_spikes_buffer_size = max_spikes_buffer_size
self._is_noise_phase_active = True
self._next_spike_time = None
self._phase_start_time = None
self._phase_end_time = None
self._last_recording_time = None
self._spikes_history = []
self._recording_controller = recording_controller
self._statistics = SpikeTrain.get_initial_statistics()
self._rnd_generator = random.Random(seed)
self._alignment_spike_history = None
self._alignment_coefficient = None
self._alignment_dispersion_fn = None