def getTstep(index,start,end,size):
times_answer=[]
if(index<0):
index=abs(index)
times=powerlaw.rvs(index,loc=start,scale=1,size=size)
for time in times:
times_answer.append(1/time)
else:
times_answer= powerlaw.rvs(index, loc=start, scale=end-start, size=size)
return times_answer
def generateToy():
np.random.seed(12345)
fig,ax = plt.subplots(4,sharex=True)
#fig,ax = plt.subplots(2)
powerlaw_arg = 2
triang_arg=0.7
n_samples = 500
#generate simple line with slope 1, from 0 to 1
frozen_powerlaw = powerlaw(powerlaw_arg) #powerlaw.pdf(x, a) = a * x**(a-1)
#generate triangle with peak at 0.7
frozen_triangle = triang(triang_arg) #up-sloping line from loc to (loc + c*scale) and then downsloping for (loc + c*scale) to (loc+scale).
frozen_uniform = uniform(0.2,0.5)
frozen_uniform2 = uniform(0.3,0.2)
x = np.linspace(0,1)
signal = np.random.normal(0.5, 0.1, n_samples/2)
data_frame = pd.DataFrame({'powerlaw':powerlaw.rvs(powerlaw_arg,size=n_samples),
'triangle':triang.rvs(triang_arg,size=n_samples),
'uniform':np.concatenate((uniform.rvs(0.2,0.5,size=n_samples/2),uniform.rvs(0.3,0.2,size=n_samples/2))),
'powerlaw_signal':np.concatenate((powerlaw.rvs(powerlaw_arg,size=n_samples/2),signal))})
ax[0].plot(x, frozen_powerlaw.pdf(x), 'k-', lw=2, label='powerlaw pdf')
hist(data_frame['powerlaw'],bins=100,normed=True,histtype='stepfilled',alpha=0.2,label='100 bins',ax=ax[0])
#hist(data_frame['powerlaw'],bins='blocks',fitness='poly_events',normed=True,histtype='stepfilled',alpha=0.2,label='b blocks',ax=ax[0])
ax[0].legend(loc = 'best')
ax[1].plot(x, frozen_triangle.pdf(x), 'k-', lw=2, label='triangle pdf')
hist(data_frame['triangle'],bins=100,normed=True,histtype='stepfilled',alpha=0.2,label='100 bins',ax=ax[1])
hist(data_frame['triangle'],bins='blocks',fitness='poly_events',normed=True,histtype='stepfilled',alpha=0.2,label='b blocks',ax=ax[1])
ax[1].legend(loc = 'best')
#ax[0].plot(x, frozen_powerlaw.pdf(x), 'k-', lw=2, label='powerlaw pdf')
hist(data_frame['powerlaw_signal'],bins=100,normed=True,histtype='stepfilled',alpha=0.2,label='100 bins',ax=ax[2])
#hist(data_frame['powerlaw_signal'],bins='blocks',normed=True,histtype='stepfilled',alpha=0.2,label='b blocks',ax=ax[2])
ax[2].legend(loc = 'best')
ax[3].plot(x, frozen_uniform.pdf(x)+frozen_uniform2.pdf(x), 'k-', lw=2, label='uniform pdf')
hist(data_frame['uniform'],bins=100,normed=True,histtype='stepfilled',alpha=0.2,label='100 bins',ax=ax[3])
#hist(data_frame['uniform'],bins='blocks',fitness = 'poly_events',p0=0.05,normed=True,histtype='stepfilled',alpha=0.2,label='b blocks',ax=ax[3])
ax[3].legend(loc = 'best')
plt.show()
fig.savefig('plots/toy_plots.png')
def __get_community_sizes(self):
rvs = powerlaw.rvs(
self.comm_exp,
size=self.num_comm
)
comm_sizes = [int(size) for size in (rvs * self.max_comm)]
return comm_sizes
def __get_community_degrees(self, comm_size):
rvs = powerlaw.rvs(
self.degree_exp,
size=comm_size
)
comm_degrees = [int(degree) for degree in (rvs * self.max_degree)]
return comm_degrees
def __get_community_sizes(self): rvs = powerlaw.rvs( self.comm_exp, size=self.num_comm ) comm_sizes = [int(size) for size in (rvs * self.max_comm)] return comm_sizes
def __get_community_degrees(self, comm_size): rvs = powerlaw.rvs( self.degree_exp, size=comm_size ) comm_degrees = [int(degree) for degree in (rvs * self.max_degree)] return comm_degrees
def test_rvs(self):
# a negative value in `negpowerlaw` should be the same as the `powerlaw` from `scipy.stats` when low=0 and b=1
arr1 = negpowerlaw.rvs_alt(-2.1, 0, 1, size=100000)
arr2 = powerlaw.rvs(2.1, 0, 1, size=100000)
# test same distribution by mean and variance (within 2 decimal places)
self.assertAlmostEqual(np.mean(arr1), np.mean(arr2), 2)
self.assertAlmostEqual(np.var(arr1), np.var(arr2), 2)
def gen_random(db, cur, pedge, min_cycle, max_cycle, min_bytes, max_bytes):
pedge = float(pedge)
min_cycle = int(min_cycle)
max_cycle = int(max_cycle)
min_bytes = int(min_bytes)
max_bytes = int(max_bytes)
peers = [peer_number for peer_number, in cur.execute(u"SELECT peer_number FROM predefined_identities ORDER BY peer_number")]
numargs = powerlaw.numargs
[a] = [0.9,] * numargs
for first_peer_number, second_peer_number in itertools.combinations(peers, 2):
assert first_peer_number < second_peer_number, [first_peer_number, second_peer_number]
if random.random() < pedge:
cycle = random.randint(min_cycle, max_cycle)
upload_first_to_second = powerlaw.rvs(a)*max_bytes #random.randint(min_bytes, max_bytes)
upload_second_to_first = powerlaw.rvs(a)*max_bytes #random.randint(min_bytes, max_bytes)
cur.execute(u"INSERT INTO predefined_books (first_peer_number, second_peer_number, cycle, upload_first_to_second, upload_second_to_first) VALUES (?, ?, ?, ?, ?)",
(first_peer_number, second_peer_number, cycle, upload_first_to_second, upload_second_to_first))
def get_one2many_mm(bs,
h,
w,
mean_match_query_term=None,
mean_match_doc_term=None,
dist='binomial'):
'''
Get match matrix with one query term matching many doc terms.
@param bs: batch size
@param h: height of the matrix (number of query terms)
@param w: width of the matrix (number of document terms)
@return: a numpy array of size (bs, h, w)
'''
if dist not in {'binomial', 'power_law', 'custom'}:
raise Exception('not supported distribution.')
mms = []
for i in range(bs):
data = [1] * w
col = range(w)
row = np.random.choice(h, w)
mms.append(csr_matrix((data, (row, col)), shape=(h, w)).toarray())
q_match_prob = min(1, mean_match_query_term /
h) if mean_match_query_term != None else 0.5
d_match_prob = min(1, mean_match_doc_term /
w) if mean_match_doc_term != None else 0.5
if dist == 'custom':
# select rows (query terms) and columns (doc terms) independently
mask = np.random.choice(2, size=(bs, h, 1), p=[1-q_match_prob, q_match_prob]) * \
np.random.choice(2, size=(bs, 1, w), p=[1-d_match_prob, d_match_prob])
elif dist == 'binomial':
# the number of columns (doc terms) with match obeys binomial distribution
# the probability of a column to be reserved (have match) is q_match_prob*d_match_prob
mask = np.random.choice(
2,
size=(bs, h, w),
p=[1 - q_match_prob * d_match_prob, q_match_prob * d_match_prob])
elif dist == 'power_law':
# the number of columns (doc terms) with match obeys power law distribution
d_match_nums = []
while len(d_match_nums) < bs:
n = math.floor(powerlaw.rvs(POWER_LOW_A) * (POWER_LOW_MAX + 1))
if n <= w:
d_match_nums.append(n)
#print(np.histogram(d_match_nums, bins=range(w + 1)))
#plt.hist(d_match_nums, bins=range(w + 1))
#plt.show()
def ind_to_arr(inds, len):
arr = np.zeros((len), dtype=np.float32)
arr[inds] = 1
return arr
mask = np.stack([
ind_to_arr(np.random.choice(w, size=(n), replace=False), w)
for n in d_match_nums
])
mask = np.expand_dims(mask, axis=1)
return get_eval_mm(mask * np.stack(mms))
def __init__(self, num_of_worker, a, alpha, beta, seed=2020):
self.alpha = alpha
self.beta = beta
self.num_of_workers = num_of_worker
np.random.seed(seed)
self.num_of_samples = [
math.ceil(i)
for i in powerlaw.rvs(a, size=self.num_of_workers) * 2000
]
self.X = []
self.Y = []
def get_powerlaw_random_role_assignment(num_nodes, num_roles, alpha=3.0, seed=1000):
random_role_assignment = np.zeros((num_nodes, num_roles))
np.random.seed(seed=seed)
simulated_data = pl.rvs(alpha, size=num_nodes)
hist, bins = np.histogram(simulated_data, bins=num_roles-1)
default_value = 1.0
test = []
roles = np.digitize(simulated_data, bins)
for node, role in zip(xrange(num_nodes), roles):
test.append(role)
random_role_assignment[node][role - 1] = default_value
return random_role_assignment
def generate_weights(nr_signals,
sumTo=1,
distribution="uniform",
powerlaw_param=0.5):
if distribution == "normal":
r = [normal(0, 3) for i in range(0, nr_signals)]
elif distribution == "uniform":
r = np.zeros(nr_signals) + 1 / nr_signals
elif distribution == "powerlaw":
r = powerlaw.rvs(powerlaw_param, size=nr_signals)
r = [round(i / sum(r), 3) * sumTo for i in r]
s = sum(r)
return [i / s * sumTo for i in r]
def distribute_files(file_list, dht, m, n_f, node_number):
''' distribute the files at the nodes of the ring based on theirs key (id) after hasing their names
popularity= the value that calculated from powerlaw.rvs, take the first 5 digits. As popularity at that point
is a float number, it willl be multiplied by 100.
At the end we roundup the value. Popularity=round(power_law*(100))'''
files = {}
r = powerlaw.rvs(0.75, size=n_f)
popularity = [float(str(x)[:5]) for x in r]
for ind, i in enumerate(file_list):
pop = popularity[ind] * (100)
pop = round(pop)
files[generate_hash_name(i)] = [i, int(pop)]
return files
def sample_ecc(x, planet, P_orb):
"""
Samples eccentricities using a Beta distribution
for planets (see Kipping 2013) and a power law
distirbution for binaries (see Moe & Di Stefano 2017).
Args:
x (numpy array): Random numbers between 0 and 1.
planet (bool): True if planet and False if binary.
P_orb (float): Orbital period.
Returns:
x (numpy array): Sampled eccentricities.
"""
size = len(x)
if planet == True:
x = beta.rvs(0.867, 3.030, size=size)
else:
if P_orb <= 10:
# note the variable is nu+1, not nu
x = powerlaw.rvs(0.2, size=size)
else:
x = powerlaw.rvs(0.6, size=size)
return x
def main(a):
#arg = raw_input("Zipf & Pareto belongs to power law. Please select: 1: Pareto\'s Law, 2: Zipf\'s law") )
fig, ax = plt.subplots(1, 1)
mean, var, skew, kurt = powerlaw.stats(a, moments='mvsk')
x = power_law_dist(a)
ax.plot(x, powerlaw.pdf(x, a), 'r-', lw=5, alpha=0.6, label='powerlaw pdf')
rv = powerlaw(a)
ax.plot(x, rv.pdf(x), 'k-', lw=2, label='frozen pdf')
r = powerlaw.rvs(a, size=1000)
ax.legend(loc='best', frameon=False)
#plt.plt(x,y)
plt.show()
def hashing(requests, nodes):
"""Function that read the given file line by line and hash each string using SHA-1.
The function returns a list of tuples. Each tuple has the requested item, the file's name and a random start"""
hash_list = []
with open('filenames.txt') as f:
count = 0
lines = random.sample(f.readlines(), requests)
popularity = powerlaw.rvs(1.65,
size=len(lines),
discrete=True,
scale=10)
for line in lines:
hash_object = hashlib.sha1(line)
hash_key = int(hash_object.hexdigest(), 16) % (2**15)
hash_tuple = (hash_key, line.rstrip('\n'), popularity[count])
hash_list.append(hash_tuple)
count += 1
return hash_list
def generate_time_stamps(hyper_params={}):
"""
Generates time stamps for using power law to sample the average number of points per day,
and using a poisson distribution to sample the the number of points per day.
"""
params = {
'period': 30,
'a': 0.2,
'max_average': 15,
# 'start_date': np.datetime64('2020-07-18'),
'start_date': datetime.datetime(2020, 7, 18, 0, 0, 0, 0),
'random_state': 1234
}
params.update(hyper_params)
np.random.seed(params['random_state'])
max_avg = params['max_average']
period = params['period']
start_date = params['start_date']
avg_num_per_day = int(
np.ceil(powerlaw.rvs(params['a'], size=1)[0] * max_avg))
num_per_day_lst = np.random.poisson(avg_num_per_day, period)
# time_stamps = []
# for idx, num in enumerate(num_per_day_lst):
# time_stamps += num*[start_date + idx]
time_stamps = []
for idx, num in enumerate(num_per_day_lst):
new_times = []
extra_seconds = (np.random.random(num) * 3600 * 24).astype(int)
extra_microseconds = (np.random.random(num) * 1000000).astype(int)
for i in range(num):
diff_time = datetime.timedelta(idx, int(extra_seconds[i]),
int(extra_microseconds[i]))
new_time = start_date + diff_time
unix_time = new_time.timestamp()
new_times.append(unix_time)
time_stamps += sorted(new_times)
return time_stamps
def generate_distribution(p, min_holdings, num_of_banks, num_of_assets, fit=False, fixed_mean=False, average=16+2.0/3):
if fixed_mean:
min_holdings = calc_min_holdings(average,p)
# np.random.seed(1)
while True:
rvss = 1/powerlaw.rvs(p, scale=1/min_holdings, size=num_of_banks)
if max(rvss) < num_of_assets:
break
fixed_rvs = rvss.copy()
round_rvs = map(round, fixed_rvs)
if fit:
hist, bins = np.histogram(rvss, bins=np.logspace(np.log10(min(rvss)), np.log10(max(rvss))))
fitfunc = lambda p, x: p[0]*x**p[1]
errfunc = lambda p, x, y: fitfunc(p, x) - y
p0theo = (p-1)*(min_holdings**(p-1))
p0 = [0.5, -3]
p1, success = optimize.leastsq(errfunc,p0[:], args=(bins[:-1], hist))
# plt.plot(bins[:-1],hist,'.',hold=True)
# plt.hold()
# plt.plot(bins[:-1], fitfunc(p1,bins[:-1]), hold=True)
print p1, p0theo, np.mean(rvss)
return round_rvs
# Display the probability density function (``pdf``): x = np.linspace(powerlaw.ppf(0.01, a), powerlaw.ppf(0.99, a), 100) ax.plot(x, powerlaw.pdf(x, a), 'r-', lw=5, alpha=0.6, label='powerlaw pdf') # Alternatively, the distribution object can be called (as a function) # to fix the shape, location and scale parameters. This returns a "frozen" # RV object holding the given parameters fixed. # Freeze the distribution and display the frozen ``pdf``: rv = powerlaw(a) ax.plot(x, rv.pdf(x), 'k-', lw=2, label='frozen pdf') # Check accuracy of ``cdf`` and ``ppf``: vals = powerlaw.ppf([0.001, 0.5, 0.999], a) np.allclose([0.001, 0.5, 0.999], powerlaw.cdf(vals, a)) # True # Generate random numbers: r = powerlaw.rvs(a, size=1000) # And compare the histogram: ax.hist(r, normed=True, histtype='stepfilled', alpha=0.2) ax.legend(loc='best', frameon=False) plt.show()
parser.add_argument("--R",
"--r",
type=int,
help="Number of requests. (default 1000)",
default=1000)
args = parser.parse_args()
#print "Given N: ", args.N
#print "Number of requests: ",args.R
chord = Chord(args.N - 1, args.R)
chord.assignFilesToNodes()
chord.updateTables()
requestList = powerlaw.rvs(1.65,
size=args.R,
discrete=True,
scale=chord.getMaxNodes())
lst = [choice(chord.getNodeList()) for i in range(0, args.R)]
#print chord.getAliveNodes()
for (node, request) in zip(lst, requestList):
node.writeToQueue([request, node.getNodeId()])
while True:
c = 0
for node in chord.getNodeList():
request = node.readFromQueue()
if request == None: #no pending Requests in the i-nodes Queue
c += 1
else:
def generate_snapshot(lit_venue_count = 3, dark_venue_count = 3):
orderbook = {}
#lit venues first
for lv in range(lit_venue_count):
orderbook[lit_venues[lv]] = {}
# buy first
side = 1
limit = 0
price = 100
while (limit < 5):
nb_orders = int(round(10*powerlaw.rvs(0.6)))
if nb_orders > 0:
orderbook[lit_venues[lv]][price] = []
for i in range(nb_orders):
size = int(round(normal(100, 30))) # total qty
iceberg = powerlaw.rvs(0.8) # ratio of visible qty
decay = random()
o = Order()
o.side = side
o.price = price
o.size = size
o.shown = int(iceberg * size)
o.decay = decay
o.id = "Order_%f_%d" %(price, i)
o.symbol = lit_venues[lv]
orderbook[lit_venues[lv]][price].append(o)
limit += 1
price -= 1
side = -1
limit = 0
price = 101
while (limit < 5):
nb_orders = int(round(10*powerlaw.rvs(0.6)))
if nb_orders > 0:
orderbook[lit_venues[lv]][price] = []
for i in range(nb_orders):
size = int(round(normal(100, 30))) # total qty
iceberg = powerlaw.rvs(0.8) # ratio of visible qty
decay = random()
o = Order()
o.side = side
o.price = price
o.size = size
o.shown = int(iceberg * size)
o.decay = decay
o.id = "Order_%f_%d" %(price, i)
o.symbol = lit_venues[lv]
orderbook[lit_venues[lv]][price].append(o)
limit += 1
price += 1
return orderbook
import time
#import pdb
###########################################################
random.seed()
output = open("syndata.txt", "w+")
S = range(4) # list of stages
S_label = ['breeding', 'fattening', 'trader',
'slaughter'] # or whatever 'piglet production',
#ns = [45426, 34518, 15631, 2333] # number of barns of every stage
ns = [4500, 3400, 1500, 600]
theta = [
expon.rvs(scale=1 / 0.013), #lambda=0.013
lognorm.rvs(s=1.27, scale=math.exp(3.62)),
lognorm.rvs(s=1.06, scale=math.exp(4.3079)),
100 * powerlaw.rvs(a=1.42)
] #alpha=1.42
birth_rate = [1.81, 0.09, 0.0, 0.0]
mortal_rate = [0.00042, 0.08, 0.01, 1]
# T is a set of possible transactions
T = {(0, 1, 60, 1, 0.6), (1, 2, 120, 1, 0.6), (2, 3, 1, 1, 0.7)}
barnlist = []
barn_index = {
} # dict of pairs (start_index, end_index) giving the index ranges of barns of each type
breeding_no = 47894
fattening_no = 31628
trader_no = 15631
slaughterh_no = 2755
import numpy as np, pandas as pd, matplotlib.pyplot as plt
from scipy.stats import beta, powerlaw
n_draws = int(1e4)
a, b = 1.12, 3.09
ecc_pl = beta.rvs(a, b, size=n_draws)
eta = 0.5 # roughly
# f(x,a) = ax^{a-1} for scipy's built-in powerlaw distribution.
ecc_stellar = powerlaw.rvs(eta + 1, size=n_draws)
plt.hist(ecc_pl, color='C0', label='beta (1.12,3.09)', alpha=0.5)
plt.hist(ecc_stellar, color='C1', label='powerlaw (e^{0.5})', alpha=0.5)
plt.xlabel('ecc')
plt.legend()
outpath = '../results/beta_vs_powerlaw.png'
plt.savefig(outpath, dpi=350)
print('made {}'.format(outpath))
def _isotropic_spinmag(samples):
a1 = powerlaw.rvs(3, size=len(samples))
a2 = powerlaw.rvs(3, size=len(samples))
return a1, a2
def derive_mass_semimaj_constraints(setupfn,
rvfitdir,
chainpath,
verbose=False,
multiprocess=True):
np.random.seed(42)
chaindf = pd.read_csv(chainpath)
(rvtimes, rvs, rverrs, resid, telvec, dvdt, curv, dvdt_merr, dvdt_perr,
time_base) = _get_fit_results(setupfn, rvfitdir)
# #NOTE: debugging
# n_mass_grid_edges = 31 # a 4x4 grid has 5 edges. want: 64+1, 128+1...
# n_sma_grid_edges = 31 # a 4x4 grid has 5 edges.
# n_injections_per_cell = 16 # 500 # want: 500
# NOTE: production
n_mass_grid_edges = 129 # a 4x4 grid has 5 edges. want: 64+1, 128+1...
n_sma_grid_edges = 129 # a 4x4 grid has 5 edges.
n_injections_per_cell = 512 # 500 # want: 500
mass_grid = (
np.logspace(np.log10(1), np.log10(900), num=n_mass_grid_edges) *
u.Mjup)
sma_grid = (np.logspace(np.log10(3), np.log10(500), num=n_sma_grid_edges) *
u.AU)
log_like_arr = np.zeros(
(n_mass_grid_edges - 1, n_sma_grid_edges - 1, n_injections_per_cell))
ao_detected_arr = np.zeros_like(log_like_arr)
sizestr = '{}x{}x{}'.format(n_mass_grid_edges - 1, n_sma_grid_edges - 1,
n_injections_per_cell)
outpath = ('../data/rv_simulations/mass_semimaj_loglikearr_{}.pickle'.
format(sizestr))
if not os.path.exists(outpath):
for mass_upper, sma_upper in product(mass_grid[1:], sma_grid[1:]):
mass_left_ind = np.argwhere(mass_grid == mass_upper) - 1
sma_left_ind = np.argwhere(sma_grid == sma_upper) - 1
mass_lower = mass_grid[mass_left_ind].squeeze()
sma_lower = sma_grid[sma_left_ind].squeeze()
pstr = ('{:s} {:.2f}, {:.2f}, {:.2f}, {:.2f}'.format(
datetime.now().isoformat(), mass_lower, mass_upper, sma_lower,
sma_upper))
print(pstr)
# sample the models from the chain
rv_model_single_planet_and_linear_trend, chain_sample_params = (
draw_models(setupfn,
rvfitdir,
chaindf,
rvtimes,
n_samples=n_injections_per_cell))
# n_sample x n_rvs array of the "RV - 1 planet" model (leaving in the
# linear trend).
# note: if there were a curvature term, it wuld go in here too.
full_resid = (rvs - rv_model_single_planet_and_linear_trend +
(nparr(chain_sample_params.dvdt)[:, None] *
(rvtimes[None, :] - time_base)))
# draw (a_c, M_c, e_c) for each simulated companion
mass_c = loguniform(low=np.log10(mass_lower.value),
high=np.log10(mass_upper.value),
size=n_injections_per_cell)
sma_c = loguniform(low=np.log10(sma_lower.value),
high=np.log10(sma_upper.value),
size=n_injections_per_cell)
cos_incl_c = np.random.uniform(0, 1, size=n_injections_per_cell)
incl_c = np.rad2deg(np.arccos(cos_incl_c))
ecc_c = np.zeros(n_injections_per_cell)
# case: companion is a planet. use Kipping (2013).
a, b = 1.12, 3.09
_ecc_c_planetary = beta.rvs(a, b, size=n_injections_per_cell)
# case: companion is a star. go for Moe & Di Stefano (2017), Eq 17.
period_c = (((sma_c * u.AU)**(3) * 4 * np.pi**2 /
(const.G * (MSTAR + mass_c * u.Mjup)))**(1 / 2)).to(
u.day)
# Moe & Di Stefano (2017), Eq 17.
eta = 0.6 - 0.7 / (np.log10(period_c.to(u.day).value) - 0.5)
# f(x,a) = ax^{a-1} for scipy's built-in powerlaw distribution.
_ecc_c_stellar = powerlaw.rvs(eta + 1, size=n_injections_per_cell)
# assign the eccentricties piece-wise at 10 Mjup.
cutoff = 10 # Mjup
ecc_c[mass_c <= cutoff] = _ecc_c_planetary[mass_c <= cutoff]
ecc_c[mass_c > cutoff] = _ecc_c_stellar[mass_c > cutoff]
#
# do a max-likelihood fit for time and argument of periastron.
#
if multiprocess:
tasks = [(pd.DataFrame({
'time': rvtimes,
'tel': telvec,
'mnvel': full_resid[ix, :],
'errvel': rverrs
}), {
k: chain_sample_params.iloc[ix][k]
for k in chain_sample_params.columns
if 'gamma' in k or 'jit' in k
}, mass_c[ix], sma_c[ix], incl_c[ix], ecc_c[ix])
for ix in range(n_injections_per_cell)]
nworkers = mp.cpu_count()
maxworkertasks = 1000
pool = mp.Pool(nworkers, maxtasksperchild=maxworkertasks)
result = pool.map(maxlike_worker, tasks)
pool.close()
pool.join()
loglike_vals, ao_detected_vals = (nparr(result)[:, 0],
nparr(result)[:, 1])
if not multiprocess:
# serial approach
loglike_vals, ao_detected_vals = [], []
for ix in range(n_injections_per_cell):
data = pd.DataFrame({
'time': rvtimes,
'tel': telvec,
'mnvel': full_resid[ix, :],
'errvel': rverrs
})
gammajit_dict = {
k: chain_sample_params.iloc[ix][k]
for k in chain_sample_params.columns
if 'gamma' in k or 'jit' in k
}
post = initialize_sim_posterior(data, mass_c[ix] * u.Mjup,
sma_c[ix] * u.AU,
incl_c[ix], ecc_c[ix],
gammajit_dict)
post = radvel.fitting.maxlike_fitting(post, verbose=False)
ao_detected = get_AO_detectability(mass_c[ix], sma_c[ix],
incl_c[ix], ecc_c[ix],
post)
if verbose:
print(post.logprob())
loglike_vals.append(post.logprob())
ao_detected_vals.append(ao_detected)
log_like_arr[mass_left_ind,
sma_left_ind, :] = (nparr(loglike_vals))
ao_detected_arr[mass_left_ind,
sma_left_ind, :] = (nparr(ao_detected_vals))
ostr = ('\t loglike: {:.1f}. ao_detected_frac: {:.2f}'.format(
np.nanmean(nparr(loglike_vals)),
np.nanmean(nparr(ao_detected_vals))))
print(ostr)
with open(outpath, 'wb') as outf:
pickle.dump(log_like_arr, outf, protocol=pickle.HIGHEST_PROTOCOL)
print('saved {}'.format(outpath))
outpath = outpath.replace('loglikearr', 'aodetectedarr')
with open(outpath, 'wb') as outf:
pickle.dump(ao_detected_arr,
outf,
protocol=pickle.HIGHEST_PROTOCOL)
print('saved {}'.format(outpath))
else:
log_like_arr = pickle.load(open(outpath, 'rb'))
ao_detected_arr = pickle.load(
open(outpath.replace('loglikearr', 'aodetectedarr'), 'rb'))
#
# Convert log-likelihood values to relative probability by taking the exp.
# Then average out the "sample" dimension (mass, sma, eccentricity, etc).
#
rv_log_like = np.log(np.exp(log_like_arr).mean(axis=2))
rv_and_ao_log_like = np.log(
nparr(np.exp(log_like_arr) * (1 - ao_detected_arr)).mean(axis=2))
# -2*logprob == chi^2
# Convert likelihood values to a normalized probability via
# P ~ -exp(-chi^2/2)
rv_prob_arr = np.exp(rv_log_like) / np.exp(rv_log_like).sum().sum()
rv_and_ao_prob_arr = np.exp(rv_and_ao_log_like) / np.exp(
rv_and_ao_log_like).sum().sum()
return rv_prob_arr, rv_and_ao_prob_arr, mass_grid, sma_grid
def quad(size=1, lb=0., ub=1.):
return powerlaw.rvs(3., loc=lb, scale=ub - lb, size=int(size))
def _power_law_dist(self):
return powerlaw.rvs(1.66, random_state=2)
def qdist(nsamples):
#From Allen 2007
gamma = 1.8
randomq = powerlaw.rvs(gamma+1,size=nsamples)
return randomq
def generateToy():
np.random.seed(12345)
fig, ax = plt.subplots(4, sharex=True)
#fig,ax = plt.subplots(2)
powerlaw_arg = 2
triang_arg = 0.7
n_samples = 500
#generate simple line with slope 1, from 0 to 1
frozen_powerlaw = powerlaw(
powerlaw_arg) #powerlaw.pdf(x, a) = a * x**(a-1)
#generate triangle with peak at 0.7
frozen_triangle = triang(
triang_arg
) #up-sloping line from loc to (loc + c*scale) and then downsloping for (loc + c*scale) to (loc+scale).
frozen_uniform = uniform(0.2, 0.5)
frozen_uniform2 = uniform(0.3, 0.2)
x = np.linspace(0, 1)
signal = np.random.normal(0.5, 0.1, n_samples / 2)
data_frame = pd.DataFrame({
'powerlaw':
powerlaw.rvs(powerlaw_arg, size=n_samples),
'triangle':
triang.rvs(triang_arg, size=n_samples),
'uniform':
np.concatenate((uniform.rvs(0.2, 0.5, size=n_samples / 2),
uniform.rvs(0.3, 0.2, size=n_samples / 2))),
'powerlaw_signal':
np.concatenate((powerlaw.rvs(powerlaw_arg,
size=n_samples / 2), signal))
})
ax[0].plot(x, frozen_powerlaw.pdf(x), 'k-', lw=2, label='powerlaw pdf')
hist(data_frame['powerlaw'],
bins=100,
normed=True,
histtype='stepfilled',
alpha=0.2,
label='100 bins',
ax=ax[0])
#hist(data_frame['powerlaw'],bins='blocks',fitness='poly_events',normed=True,histtype='stepfilled',alpha=0.2,label='b blocks',ax=ax[0])
ax[0].legend(loc='best')
ax[1].plot(x, frozen_triangle.pdf(x), 'k-', lw=2, label='triangle pdf')
hist(data_frame['triangle'],
bins=100,
normed=True,
histtype='stepfilled',
alpha=0.2,
label='100 bins',
ax=ax[1])
hist(data_frame['triangle'],
bins='blocks',
fitness='poly_events',
normed=True,
histtype='stepfilled',
alpha=0.2,
label='b blocks',
ax=ax[1])
ax[1].legend(loc='best')
#ax[0].plot(x, frozen_powerlaw.pdf(x), 'k-', lw=2, label='powerlaw pdf')
hist(data_frame['powerlaw_signal'],
bins=100,
normed=True,
histtype='stepfilled',
alpha=0.2,
label='100 bins',
ax=ax[2])
#hist(data_frame['powerlaw_signal'],bins='blocks',normed=True,histtype='stepfilled',alpha=0.2,label='b blocks',ax=ax[2])
ax[2].legend(loc='best')
ax[3].plot(x,
frozen_uniform.pdf(x) + frozen_uniform2.pdf(x),
'k-',
lw=2,
label='uniform pdf')
hist(data_frame['uniform'],
bins=100,
normed=True,
histtype='stepfilled',
alpha=0.2,
label='100 bins',
ax=ax[3])
#hist(data_frame['uniform'],bins='blocks',fitness = 'poly_events',p0=0.05,normed=True,histtype='stepfilled',alpha=0.2,label='b blocks',ax=ax[3])
ax[3].legend(loc='best')
plt.show()
fig.savefig('plots/toy_plots.png')
#100*powerlaw.rvs(a = 1.42)
#lognorm.rvs( s = 1.06 , scale = math.exp(4.3079 )
theta = [lambda: expon.rvs(scale = 1 / 0.013), #lambda=0.013
lambda: 2 * lognorm.rvs(s = 1.27, scale = math.exp(3.62)),
lambda: 3.1 * lognorm.rvs(scale = 23.97,s = 1.83,loc = 1),
lambda: 10 * lognorm.rvs(s = 1.32, scale = math.exp(4.54))] #alpha=1.42
birth_rate = [1.81,0.2,0.0,0.0]
mortal_rate = [0.0042,0.0008,0.0001,1]
min_bch_size = [lambda: lognorm.rvs(s=1.44,scale=math.exp(3.23)),
lambda: lognorm.rvs(s=0.89,scale=math.exp(4.07)),
lambda: expon.rvs(scale =1/0.0078 ) ]
loyalty = [lambda: beta.rvs(0.83, 0.7),
lambda: beta.rvs(1.54, 0.67),
lambda: powerlaw.rvs(0.54)]
# T is a set of possible transactions
T = {(0,1,60),(1,2,120),(2,3,0)}
barnlist = []
barn_index = {} # dict of pairs (start_index, end_index) giving the index ranges of barns of each type
breeding_no=47894
fattening_no=31628
trader_no=15631
slaughterh_no=2755
class Barn:
"""
describe the attributes and methods for each barn
"""
def __init__(self, Barn_id, stage_type, capacity, destination, gis, Dlist):
def graph_gen(self_con, other_con, nodes=100, groups=10):
corr = lambda x, y: self_con if x == y else other_con
g, bm = random_graph(nodes, lambda: (powerlaw.rvs(2.4, size=1) * -1 + 1) * 20, directed=False, model="blockmodel-traditional", block_membership=lambda: np.random.randint(int(groups)), vertex_corr=corr)
# poisson(10).rvs(1)
return g, bm