def elastic_transform(image, kernel=(11,11), sigma=10, alpha=8):
from numpy.random import ranf
import math
displacement_field_x = np.array([[float(2*ranf(1)-1)
for x in range(image.shape[0])] for y in range(image.shape[1])]) * alpha
displacement_field_y = np.array([[float(2*ranf(1)-1)
for x in range(image.shape[0])] for y in range(image.shape[1])]) * alpha
displacement_field_x = cv2.GaussianBlur(displacement_field_x, kernel, sigma)
displacement_field_y = cv2.GaussianBlur(displacement_field_y, kernel, sigma)
result = np.zeros(image.shape)
for row in range(image.shape[1]):
for col in range(image.shape[0]):
low_ii = row + math.floor(displacement_field_x[row, col])
high_ii = row + math.ceil(displacement_field_x[row, col])
math.floor(displacement_field_x[row, col])
low_jj = col + math.floor(displacement_field_y[row, col])
high_jj = col + math.ceil(displacement_field_y[row, col])
if low_ii < 0 or low_jj < 0 or high_ii >= image.shape[1] -1 \
or high_jj >= image.shape[0] - 1:
continue
x =displacement_field_x[row, col] - math.floor(displacement_field_x[row, col])
y =displacement_field_y[row, col] - math.floor(displacement_field_y[row, col])
B =np.array([[image[low_ii, low_jj], image[low_ii, high_jj]],
[image[high_ii, low_jj], image[high_ii, high_jj]]])
A =np.array([1-x, x],dtype =float)
C =np.array([[1-y],[y]],dtype =float)
result[row, col] = np.dot(A, np.dot(B,C))
return result
def ranvec():
px = ranf()
py = ranf()
pz = ranf()
mod = (px**2 + py**2 + pz**2)**(0.5)
px /= mod
py /= mod
pz /= mod
return px, py, pz
def random_dtw(dimension, lenght_1, lenght_2, distance_for_cdist, nb_try):
distance_obtained = []
for i in range(nb_try):
x = rd.ranf((lenght_1, dimension))
y = rd.ranf((lenght_2, dimension))
x = x / x.sum(axis=1)[:, None]
y = y / y.sum(axis=1)[:, None]
d = compute_dtw(x, y, dist_for_cdist=distance_for_cdist)
distance_obtained.append(d)
return np.mean(np.asarray(distance_obtained))
def mnarHH(param, pedlist, target, tp2A, tp2B):
for ped in pedlist: #for each ped
for i in range(0,2+ped.getSibNum()): # for each person
for j in range(0, param["numMarkers"]): # for each marker
if sum(ped.getGeno(i,j)) == 1.0: # if het is in the ped
if ranf() < tp2A: # use the target specific parameter
ped.makeMissing(i,j) # one gender will have more missing data.
else:
if ranf() < tp2B:
ped.makeMissing(i,j)
return(pedlist)
def marPop(param, pedlist, target, tp2A, tp2B):
for ped in pedlist: #for each ped
for i in range(0,2+ped.getSibNum()): # for each person
for j in range(0, param["numMarkers"]): # for each marker
if ped.getPop() == target: # if they are in the target:
if ranf() < tp2A: # use the target specific parameter
ped.makeMissing(i,j) # one gender will have more missing data.
else:
if ranf() < tp2B:
ped.makeMissing(i,j)
return(pedlist)
def ranortvec(px, py, pz):
qx = ranf()
qy = ranf()
qz = ranf()
qx -= qx*px
qy -= qy*py
qz -= qz*pz
mod = (qx**2 + qy**2 + qz**2)**(0.5)
qx /= mod
qy /= mod
qz /= mod
return qx, qy, qz
def CData( N, L, scale = 1, K=-1 ):
# N = number of data vectors
# L = length of data vectors
# create a random seeds
if K==-1:
K = int( random.rand()*N/20 + N/20)
seeds = random.ranf( (K,L) )
# create random data based on deviations from seeds
data = zeros( (N,L), float )
for i in range( N ):
pick = int( random.ranf() * K )
data[i] = seeds[pick] +scale*(0.5*random.ranf(L)-0.25)
return data
def testing_walk_extractor(self,
feature_extractor,
seed_position,
iterations=100,
stepsize=4,
confined_range=None):
'''
Start random walk with seed position.
Input:
ECG signal feature extractor.
Output:
zip(pos_list, results):
walk path & predict probability at each position.
'''
results = list()
pos_list = list()
pos_dict = dict()
# Benchmarking
feature_collecting_time_cost = 0
predict_time_cost = 0
pos = seed_position
for pi in xrange(0, iterations):
# Boundary
if pos < 0:
pos = 0
elif pos >= len(feature_extractor.signal_in):
pos = len(feature_extractor.signal_in) - 1
pos_list.append(pos)
if pos not in pos_dict:
start_time = time.time()
feature_vector = np.array(feature_extractor.frompos(pos))
feature_vector = feature_vector.reshape(1, -1)
feature_collecting_time_cost += time.time() - start_time
start_time = time.time()
value = self.regressor.predict(feature_vector)
predict_time_cost += time.time() - start_time
pos_dict[pos] = value
else:
value = pos_dict[pos]
results.append(value)
# Update next position
threshold = (value + 1.0) / 2.0
# threshold = self.sigmod_function(threshold)
direction = -1.0 if random.ranf() >= threshold else 1.0
pos += int(direction * stepsize)
# Next position confined range
if confined_range is not None:
if pos > confined_range[1]:
pos = confined_range[1]
elif pos < confined_range[0]:
pos = confined_range[0]
# print 'Feature collecting time cost: %f secs.' % feature_collecting_time_cost
# print 'Prediction time cost %f seconds.' % predict_time_cost
return zip(pos_list, results)
def generate_matrix(size=10): mat = [] for i in range(size): line = random.ranf(size) line = line/sum(line) mat.append(line) return mat
def uniform_motion(map_width, map_height, posX=None, posY=None, velX=None, velY=None):
if posX == None or posY == None:
posX = map_width / 2 + 0.5
posY = map_height / 2 + 0.5
if velX == None or velY == None:
start_velocity = 1.0
angle = RNG.ranf() * 2 * NP.pi
velX = start_velocity * NP.cos(angle)
velY = start_velocity * NP.sin(angle)
X = posX
Y = posY
while True:
a = yield (X, Y)
if a != None:
raise StopIteration
X += velX
Y += velY
while (X < 0) or (X > map_width):
if X < 0:
X = -X
velX = -velX
if X > map_width:
X = 2 * map_width - X
velX = -velX
while (Y < 0) or (Y > map_width):
if Y < 0:
Y = -Y
velY = -velY
if Y > map_width:
Y = 2 * map_width - Y
velY = -velY
def skip_test_bma(self):
storage = StorageFactory().get_storage('dict_storage')
storage.write_table(table_name='dataset',
table_data={
"id":
arange(100) + 1,
"attr1":
concatenate((random.randint(0, 10, 50),
random.randint(20, 40, 50))),
"attr2":
random.ranf(100),
"outcome":
array(50 * [0] + 50 * [1])
})
ds = Dataset(in_storage=storage, in_table_name='dataset', id_name="id")
specification = EquationSpecification(
variables=array(["constant", "attr2", "attr1"]),
coefficients=array(["constant", "ba2", "ba1"]))
filename = 'bma_output.pdf'
model = RegressionModel(
estimate_config={'bma_imageplot_filename': filename})
model.estimate(specification,
ds,
"outcome",
procedure="opus_core.bma_for_linear_regression_r")
def create_samples(m3dprefix, argv): # debug print "create samples ..." # retrieve mass mass = float(sys.argv[1]) # debug print "using mass ...", mass, "mmol P m^(-3)" # retrieve tracers tracers = sys.argv[2:] ntracer = len(tracers) # debug print "using tracer(s) ...", tracers # read data lsm, vol = create_samples_read_data() # normalize volumes volnorm = vol / sum(vol) # divide mass by no of tracers masstracer = mass / ntracer # loop over tracers for itracer in range(ntracer): # get random values val = 0.5 + 0.25 * npr.ranf(vol.shape) # scale val = masstracer * val / sum(val * volnorm) # debug # print val # print min(val), max(val) # print sum(val * volnorm) # save vector filepath = "init.%s.petsc" % tracers[itracer] write_PETSc_vec(val, filepath)
def shootPosAngle(self, n):
angleList = []
val = random.ranf(n)
deltaX, x, y = 0., 0., 0.
j = 1
for v in val : # цикл по множеству необходимых значений косинуса
#print "in first for v = " , v
for i in range(0, FirstOrder.cosTeta.size) :
# print "in second for"
if(self.p_probability[i] >= v) :
deltaX = v - self.p_probability[i]
y = self.p_energyBin[i] - self.p_energyBin[i-1]
x = self.p_probability[i] - self.p_probability[i-1]
angleList.append(deltaX*y/x + self.p_energyBin[i])
if(deltaX*y/x + self.p_energyBin[i] < -0.999995):
print 'Yes, you got it!'
if(deltaX*y/x + self.p_energyBin[i] > 0.999995):
print 'Ups, you got it!'
break
# angleList.append(3.) # vot tuta xerznaet
return asarray(angleList)
def choosePop(param):
n = range(0,param["numPopulations"])
x = ranf()
if x < param["popProportions"]:
return(0)
else:
return(1)
def GenerateRandom(cls,
nodes_nmb,
edges_nmb,
capacity_min=0,
capacity_max=0):
"""
Create graph with specified number of nodes and arcs, where random nodes are connected to random nodes.
Does not contain self loop.
Set to every arc in the graph random value of the capacity from min to max.
"""
network_graph = nx.gnm_random_graph(nodes_nmb,
edges_nmb,
directed=True)
nx.set_edge_attributes(network_graph, {
edge: np.around(
(capacity_max - capacity_min) * nrnd.ranf() + capacity_min, 3)
for edge in nx.edges(network_graph)
},
name='capacity')
self = cls(network_graph)
self.capacity_min = capacity_min
self.capacity_max = capacity_max
return self
def GenerateRandomSrcDst(self, pair_nmb):
"""Create specified number of the random tuples: (source, destination). """
nodes_nmb = nx.number_of_nodes(self.network_graph)
nodes_array = np.arange(0, nodes_nmb)
#path number cant be greater than number of arc excluding self loops
pair_nmb = np.amin([pair_nmb, nodes_nmb * nodes_nmb - nodes_nmb])
src_dst_list = pair_nmb * [None]
#iterate shuffle nodes array and select pair of nodes from it
for i in range(len(src_dst_list)):
src_dest_cand = None
src_dst_list[i] = src_dest_cand
while src_dest_cand in src_dst_list:
nrnd.shuffle(nodes_array)
src_node = nodes_array[0]
dst_node = nodes_array[1]
src_dest_cand = (src_node, dst_node)
src_dst_list[i] = src_dest_cand
#add arc to the graph if it doesn't exist
if not nx.has_path(self.network_graph, src_node, dst_node):
nx.add_path(
self.network_graph,
src_dst_list[i],
capacity=np.around(
(self.capacity_max - self.capacity_min) * nrnd.ranf() +
self.capacity_min, 3))
self.SetSrcDst(*src_dst_list)
def realization(vs,H_XXZ,basis,real):
"""
This function computes the entropies for a single disorder realisation.
--- arguments ---
vs: vector of ramp speeds
H_XXZ: time-dep. Heisenberg Hamiltonian with driven zz-interactions
basis: spin_basis_1d object containing the spin basis
n_real: number of disorder realisations; used only for timing
"""
ti = time() # get start time
#
global v # declare ramp speed v a global variable
#
seed() # the random number needs to be seeded for each parallel process
#
# draw random field uniformly from [-1.0,1.0] for each lattice site
unscaled_fields=-1+2*ranf((basis.L,))
# define z-field operator site-coupling list
h_z=[[unscaled_fields[i],i] for i in range(basis.L)]
# static list
disorder_field = [["z",h_z]]
# compute disordered z-field Hamiltonian
no_checks={"check_herm":False,"check_pcon":False,"check_symm":False}
Hz=hamiltonian(disorder_field,[],basis=basis,dtype=np.float64,**no_checks)
# compute the MBL and ETH Hamiltonians for the same disorder realisation
H_MBL=H_XXZ+h_MBL*Hz
H_ETH=H_XXZ+h_ETH*Hz
#
### ramp in MBL phase ###
v=1.0 # reset ramp speed to unity
# calculate the energy at infinite temperature for initial MBL Hamiltonian
eigsh_args={"k":2,"which":"BE","maxiter":1E4,"return_eigenvectors":False}
Emin,Emax=H_MBL.eigsh(time=0.0,**eigsh_args)
E_inf_temp=(Emax+Emin)/2.0
# calculate nearest eigenstate to energy at infinite temperature
E,psi_0=H_MBL.eigsh(time=0.0,k=1,sigma=E_inf_temp,maxiter=1E4)
psi_0=psi_0.reshape((-1,))
# calculate the eigensystem of the final MBL hamiltonian
E_final,V_final=H_MBL.eigh(time=(0.5/vs[-1]))
# evolve states and calculate entropies in MBL phase
run_MBL=[_do_ramp(psi_0,H_MBL,basis,v,E_final,V_final) for v in vs]
run_MBL=np.vstack(run_MBL).T
#
### ramp in ETH phase ###
v=1.0 # reset ramp speed to unity
# calculate the energy at infinite temperature for initial ETH hamiltonian
Emin,Emax=H_ETH.eigsh(time=0.0,**eigsh_args)
E_inf_temp=(Emax+Emin)/2.0
# calculate nearest eigenstate to energy at infinite temperature
E,psi_0=H_ETH.eigsh(time=0.0,k=1,sigma=E_inf_temp,maxiter=1E4)
psi_0=psi_0.reshape((-1,))
# calculate the eigensystem of the final ETH hamiltonian
E_final,V_final=H_ETH.eigh(time=(0.5/vs[-1]))
# evolve states and calculate entropies in ETH phase
run_ETH=[_do_ramp(psi_0,H_ETH,basis,v,E_final,V_final) for v in vs]
run_ETH=np.vstack(run_ETH).T # stack vertically elements of list run_ETH
# show time taken
print "realization {0}/{1} took {2:.2f} sec".format(real+1,n_real,time()-ti)
#
return run_MBL,run_ETH
def randomHalf(self, n):
leftCount = 0
# Loops through each ball in the current position
for i in range(int(n)):
if rand.ranf() < 0.5: # 50% chance of running
leftCount += 1 # Adds 1 ball to the total balls bouncing left
return leftCount
def genmonster(level):
if ranf() <= 0.25:
rang = 3
kind = "ranged"
else:
rang = 1
kind = "melee"
return Monster(level = level,r = rang,kind = kind)
def generate_initial_estimates(self):
# deltas is S-by-K matrix
k = self.count_data.num_categories
non_zero_means = (self.count_data.arr > 0).sum(axis=0).astype('float64') / self.count_data.N_all
deltas = non_zero_means.repeat(self.num_segments).reshape([self.num_segments, k], order='F')
deltas += (random.ranf(size=deltas.size)*0.05).reshape(deltas.shape)
deltas[deltas >= 1] = 0.95
return deltas
def genmonster(level):
if ranf() <= 0.25:
rang = 3
kind = "ranged"
else:
rang = 1
kind = "melee"
return Monster(level=level, r=rang, kind=kind)
def map_base_kernel(s, dim, init_hyper_fixed):
if init_hyper_fixed:
# TODO: ARD
# if dim == 1:
if s == 's':
k = RBF(dim, lengthscales=1, variance=0.5)
elif s == 'r':
k = RQ(dim, lengthscales=1, variance=0.5, alpha=0.5)
elif s == 'p':
k = Per(dim, period=1, lengthscales=0.1, variance=0.5)
else:
k = Lin(dim, variance=0.5)
# else:
# if s == 's':
# k = RBF(dim, lengthscales=1 * np.ones(dim), variance=0.5)
# elif s == 'r':
# k = RQ(dim, lengthscales=1 * np.ones(dim), variance=0.5, alpha=0.5)
# elif s == 'p':
# k = Per(dim, period=1, lengthscales=0.1, variance=0.5)
# else:
# k = Lin(dim, variance=0.5 * np.ones(dim))
else:
if dim == 1:
# this is for reusing hypers of trained models
if s == 's':
k = RBF(dim, lengthscales=rnd.ranf() * 5)
elif s == 'r':
k = RQ(dim, lengthscales=rnd.ranf() * 5)
elif s == 'p':
k = Per(dim,
period=rnd.ranf() * 5,
lengthscales=rnd.ranf() * 5)
else:
k = Lin(dim, variance=rnd.ranf() * 10)
else:
if s == 's':
k = RBF(dim, lengthscales=rnd.ranf(dim) * 5)
elif s == 'r':
k = RQ(dim, lengthscales=rnd.ranf(dim) * 5)
elif s == 'p':
k = Per(dim,
period=rnd.ranf() * 5,
lengthscales=rnd.ranf() * 5)
else:
k = Lin(dim, variance=rnd.ranf(dim) * 10)
return k
def mcar(param, pedlist):
percMissing = float(param["missingParam1"])
for ped in pedlist:
for i in range(0,2+ped.getSibNum()):
for j in range(0, param["numMarkers"]):
# if we roll the dice and it comes up missing, choose a missing var.
if ranf() < percMissing:
ped.makeMissing(i,j)
return(pedlist)
def _trial(self, person_transition_func, n_days, transition_cdf, transition_cdf_kwargs={}):
'''Generic trial function of event to create a state transition'''
transition_performed = False
if rnd.ranf() < transition_cdf(n_days, **transition_cdf_kwargs):
person_transition_func()
transition_performed = True
return transition_performed
def Test3():
'''Test case 3: random walk.'''
qt = QTloader()
record_name = 'sel46'
sig = qt.load(record_name)
raw_sig = sig['sig']
random_forest_config = dict(max_depth=10)
walker = RandomWalker(target_label='P',
random_forest_config=random_forest_config)
print 'training...'
start_time = time.time()
walker.do_training_on_qt(record_name='sel103')
print 'trianing used %.3f seconds' % (time.time() - start_time)
seed_position = 100000
import matplotlib.pyplot as plt
plt.figure(1)
plt.plot(sig['sig'], label=record_name)
for ti in xrange(0, 20):
seed_position += int(200.0 * random.ranf())
print 'testing...(%d)' % seed_position
start_time = time.time()
results = walker.testing_walk(sig['sig'],
seed_position,
iterations=100,
stepsize=10)
print 'testing used %.3f seconds' % (time.time() - start_time)
pos_list, values = zip(*results)
predict_pos = np.mean(pos_list[len(pos_list) / 2:])
# amp_list = [raw_sig[int(x)] for x in pos_list]
amp_list = []
bias = raw_sig[pos_list[0]]
for pos in pos_list:
amp_list.append(bias)
bias -= 0.01
plt.plot(predict_pos,
raw_sig[int(predict_pos)],
'ro',
markersize=14,
label='predict position')
plt.plot(pos_list,
amp_list,
'r',
label='walk path',
markersize=3,
linewidth=8,
alpha=0.3)
plt.grid(True)
plt.xlim(min(pos_list) - 100, max(pos_list) + 100)
plt.legend()
plt.show(block=False)
pdb.set_trace()
def rand_unit_complex(shape, ftype='double'):
"""Return random complex values in the [0, 1) interval.
Parameters
----------
shape : int or sequence of ints
Output shape. For instance, if the shape is ``(m, n)``, then ``m * n``
samples are drawn.
ftype : str or dtype, optional
Output float type. Choose between 'single', 'double', or 'longdouble'.
Default is 'double', in which case the output array will be composed of
128-bit complex floats.
Returns
-------
out : ndarray of complex floats
"""
from numpy.random import ranf
return ranf(shape).astype(ftype) + 1j * ranf(shape).astype(ftype)
def findFlows(flowModel, flowMeasurements):
flowGuess = 0.1 + 5.0 * ranf(
flowModel.nFlows + flowModel.nsched) # includes timeoffsets
result = lsq(optFunc,
flowGuess,
bounds=(flowModel.lowerBounds, flowModel.upperBounds),
loss='huber',
args=(flowMeasurements, flowModel))
plotResids = formatResids(flowMeasurements, result.fun)
return result
def model_PO(self, graph: Graph) -> Union[Graph, GraphView]:
graph_copy = graph
if self.save:
self.graph.save("graph.xml.gz")
print("stored graph and modeled graph")
return graph
if self.parameters["Observable"]["Problem"] == "Total":
return graph_copy
elif self.parameters["Observable"]["Problem"] == "Partial":
# Different methods of partial observability
if "Sample" in self.parameters["Observable"]:
# "NProbability" = 0.4 means that each node has a 40% chance to be pruned
if self.parameters["Observable"]["Sample"]["Nodes"] == "Random":
graph_copy = GraphView(graph_copy, vfilt=lambda v: ranf() <= self.parameters["Observable"]["Sample"]["NProbability"])
# elif self.parameters["Observable"]["Sample"]["Nodes"] == "MaxDeg":
# graph_copy = GraphView()
if self.parameters["Observable"]["Sample"]["Edges"] == "Random":
graph_copy = GraphView(graph_copy, efilt=lambda v: ranf() <= self.parameters["Observable"]["Sample"]["EProbability"])
return graph_copy
def generate_initial_estimates(self):
N, K = self.data.arr.shape
# mus is S-by-K matrix
mus = self.data.arr.mean(axis=0)
mus = mus.repeat(self.num_segments).reshape([self.num_segments, K], order='F')
mus += random.ranf(size=mus.size).reshape(mus.shape)
# sigmas is S-by-K-by-K array
sigmas = np.eye(K).repeat(self.num_segments).reshape([self.num_segments, K, K], order='F')
return mus, sigmas
def Test1():
'''Test case 1'''
qt = QTloader()
record_name = 'sel103'
sig = qt.load(record_name)
raw_sig = sig['sig']
walker = RandomWalker()
print 'training...'
walker.do_training_on_qt(record_name=record_name)
print 'testing...'
results = walker.testing_n(sig['sig'], 100)
left_pos_list = [x[0] for x in results if x[1] <= 0]
left_value_list = [x[1] for x in results if x[1] <= 0]
right_pos_list = [x[0] for x in results if x[1] > 0]
right_value_list = [x[1] for x in results if x[1] > 0]
import matplotlib.pyplot as plt
plt.figure(1)
plt.plot(sig['sig'], label=record_name)
amp_list = [raw_sig[x] for x in left_pos_list]
plt.plot(left_pos_list, amp_list, 'r<', label='left', markersize=15)
# Annotate
for x, y, score in zip(left_pos_list, amp_list, left_value_list):
plt.annotate('%.3f' % score,
xy=(x, y),
xytext=(x + random.ranf() * 2.0 - 1, y + random.ranf()),
arrowprops=dict(arrowstyle='->', ))
amp_list = [raw_sig[x] for x in right_pos_list]
plt.plot(right_pos_list, amp_list, 'b>', label='right', markersize=15)
# Annotate
for x, y, score in zip(right_pos_list, amp_list, right_value_list):
plt.annotate('%.3f' % score,
xy=(x, y),
xytext=(x + random.ranf() * 2.0 - 1, y - random.ranf()),
arrowprops=dict(arrowstyle='->', ))
plt.grid(True)
plt.xlim(100000, 110000)
plt.show()
def TransformTrace (links, fail_links, mttf, mttr, stable, end_time, bootstrap):
new_trace = []
ctime = 0.0
for link in links:
new_trace.append("%f %s up"%(ctime, link))
if bootstrap:
new_trace.append("1.0 compute_and_update")
ctime += stable
up_links = set(links)
down_links = set()
set_up_at = defaultdict(list)
while ctime < end_time:
ctime = ctime + mttf * random.ranf()
set_up = list()
for t in sorted(set_up_at.keys()):
if t < ctime:
for l in set_up_at[t]:
new_trace.append("%f %s up"%(t, l))
set_up.append(l)
del(set_up_at[t])
to_fail = None
failable_links = set(fail_links) - set(down_links)
if len(failable_links) == 0:
# Nothing to fail
min_time = sorted(set_up_at.keys())[0]
ctime = min_time
else:
to_fail = random.choice(list(failable_links))
up_links.remove(to_fail)
down_links.add(to_fail)
new_trace.append("%f %s down"%(ctime, to_fail))
recovery_time = random.exponential(mttr)
assert(recovery_time) > 0
set_up_at[ctime + recovery_time].append(to_fail)
for l in set_up:
new_trace.append("%f %s up"%(t, l))
up_links.add(l)
down_links.remove(l)
for t in sorted(set_up_at.keys()):
for l in set_up_at[t]:
new_trace.append("%f %s up"%(t, l))
up_links.add(l)
down_links.remove(l)
ctime = t
# Otherwise end instantly
new_trace.append("%f end"%end_time)
return (end_time, new_trace)
def ScaleMutation(individual, magnitude = 0.1): mutated = np.copy(individual) valid_layers = np.argmax(mutated == 0) or len(mutated) sign = 1 if ranf() > 0.5 else -1 mutated[:valid_layers] += sign * int((np.sum(mutated) * magnitude) // valid_layers) # If there are invalid layer sizes (<= 0), avoid a crash by # making them the mean of the valid elements. if len(mutated[:valid_layers][mutated[:valid_layers] <= 0]) > 0: mean = np.mean(mutated[:valid_layers][mutated[:valid_layers] > 0]) mutated[:valid_layers][mutated[:valid_layers] <= 0] = int(mean) return mutated
def InitializePopulation(pop_size, input_size, max_hidden): # Matrix of individuals pop = np.zeros((pop_size,max_hidden),dtype=np.int32) # Initialize their first layer (used as a base for subsequent ones). pop[:,0] = randint(input_size,int(input_size*1.75), size=pop.shape[0],dtype=np.int32) # Choose how many layers each individual will have. active_layers = choice(np.arange(1,max_hidden+1),size=pop_size) for i in range(pop_size): if active_layers[i] > 1: middle = int(active_layers[i]/2.0)+1 # Middle layer is the biggest. for j in range(1,middle): # Go from smaller to bigger layers. pop[i,j] = pop[i,j-1] + pop[i,j-1] * ranf() for j in range(middle,active_layers[i]): # From bigger to smaller. pop[i,j] = max(int(pop[i,0]/2.0), int(pop[i,j-1] - pop[i,j-1] * ranf())) return pop
def process(self):
u = self.data_handler.get_node(self.inputs).get_value()
for i, val in enumerate(u):
if val > 0:
self.active[i] = True
u[i] = 0 if self.active[i] else val
out = np.zeros([self.n_extruders, self.n_sensors])
for e in range(self.n_extruders):
for s in range(self.n_sensors):
out[e,
s] = self.x1[e] + self.ambient_temp + (ranf() - 0.5) * 0.5
self.x3[e] = (self.alpha *
(u[e] - self.ambient_temp - self.x1[e]) -
self.beta * self.x2[e]) * self.dt
self.x2[e] += self.x3[e]
self.x1[e] += self.x2[e] + (ranf() - 0.5)
self.data_handler.get_node(self.outputs).set_value(out.tolist())
def set_up(g, params) -> None:
weight = g.new_edge_property("double")
weight.set_value(1.0)
g.edge_properties["weight"] = weight
threshold = g.new_vertex_property("double", vals=ranf(len(g.get_vertices())))
g.vertex_properties["threshold"] = threshold
for v in g.vertices():
for e in v.out_edges():
g.edge_properties["weight"][e] = 1 / v.out_degree() if 1 / v.out_degree() < g.edge_properties["weight"][e] else g.edge_properties["weight"][e]
return g
def callPheno(peds, params):
for ped in peds:
for j in range(0, ped.getSibNum()):
thisPheno = ped.getSibPheno(j)
prob = min(1.0,exp(thisPheno)) # cap the probability
if params['modelType'] == 'random':
ped.setSibPhenoCall(j, float(random.randint(1,3,1)[0]))
else:
if ranf() < prob:
ped.setSibPhenoCall(j, 2.0)
else:
ped.setSibPhenoCall(j, 1.0)
return()
def genOneMarker(self, param, i):
probs = param["markerFreqs"]
popProbs = probs[self.popStr]
y = ranf(2)
if y[0] < popProbs[i]:
a = 1
else:
a = 0
if y[1] < popProbs[i]:
b = 1
else:
b = 0
return(a,b)
def main(msg):
print 'Probability:', PROBABILITY
print
while True:
for addr in RECIPIENTS:
A = random.ranf()
if A < PROBABILITY:
print
print '%s : Sending to "%s"' % (time.strftime(DATE_FORMAT), addr),
sendStopTo((addr,))
sys.stdout.write('.')
sys.stdout.flush()
time.sleep(TIMESTEP)
def attack(self,atk,defend):
""""""
if ranf() <= atk.accuracy:
hit = atk.attack - defend.defense
if type(atk) == Player and self.player.equipped["Weapon"].stat.get("backstab",0) == 1:
hit = atk.attack*3
if ranf < 0.05:
hit = hit*2
if hit < 0:
hit = 0
defend.hp -= hit
self.outputfunc(" A Hit! {} has {} hp remaining".format(defend.name,defend.hp))
else:
self.outputfunc("{} missed!".format(atk.name))
def create_fake_posterior_gram(same, randomi, long, mult_compare_to_noise,
lenght_1, lenght_2, dimension):
if lenght_1 > lenght_2:
lenght_1, lenght_2 = lenght_2, lenght_1
if same:
to_activate = np.random.randint(dimension, size=lenght_1)
x = rd.ranf((lenght_1, dimension))
y = rd.ranf((lenght_1, dimension))
for i in range(lenght_1):
x[i, to_activate[i]] = mult_compare_to_noise
y[i, to_activate[i]] = mult_compare_to_noise
x = x / x.sum(axis=1)[:, None]
y = y / y.sum(axis=1)[:, None]
return x, y
if randomi:
to_activate_1 = np.random.randint(dimension, size=lenght_1)
to_activate_2 = np.random.randint(dimension, size=lenght_2)
x = rd.ranf((lenght_1, dimension))
y = rd.ranf((lenght_2, dimension))
for i in range(lenght_1):
x[i, to_activate_1[i]] = mult_compare_to_noise
for i in range(lenght_2):
y[i, to_activate_2[i]] = mult_compare_to_noise
x = x / x.sum(axis=1)[:, None]
y = y / y.sum(axis=1)[:, None]
return x, y
if long:
to_activate = np.random.randint(dimension, size=lenght_1)
x = rd.ranf((lenght_1, dimension))
y = rd.ranf((lenght_2, dimension))
for i in range(lenght_1):
x[i, to_activate[i]] = mult_compare_to_noise
iter = 0
to_copy = 0
to_double = [
random.randint(0, lenght_1 - 1) for i in range(lenght_2 - lenght_1)
]
to_double = sorted(to_double)
begin = 0
while iter < lenght_2:
if to_copy in to_double[begin:]:
y[iter, :] = x[to_copy, :]
begin += 1
iter += 1
else:
y[iter, :] = x[to_copy, :]
to_copy += 1
iter += 1
x = x / x.sum(axis=1)[:, None]
y = y / y.sum(axis=1)[:, None]
return x, y
def simul_gauss(x_sample, y_sample, GN=20):
# simulate the gaussians:
gaussians = deque()
for i in xrange(GN):
x = rd.randint(1, M-1)
y = rd.randint(1, M-1)
dx = sqrt(M) * rd.ranf()
dy = sqrt(M) * rd.ranf()
align = 0e0 #pi * rd.ranf()
gaussians.append([[x, y], [dx, dy], align])
theta_zero = ones(N)
for m, d, theta in gaussians:
print(m, d, theta)
x = rd.normal(m[0], d[0], N)
y = rd.normal(m[1], d[1], N)
if theta != 0e0:
print(theta_zero[x < m[0]].shape, theta_zero[x >= m[0]].shape)
vecl = sqrt((x - m[0])**2 + (y - m[1])**2)
theta_zero[x < m[0]] = 2e0*pi - arccos((x - m[0])/vecl)[x < m[0]]
theta_zero[x >= m[0]] = arccos((x - m[0])/vecl)[x >= m[0]]
theta = theta + theta_zero
x_sample.append( vecl * cos(theta) + m[0])
y_sample.append( vecl * sin(theta) + m[1])
else:
x_sample.append(x)
y_sample.append(y)
return x_sample, y_sample
def realization(H_Heis, psi_0, basis, diag_op, times, real):
"""
This function computes the entropies for a single disorder realisation.
--- arguments ---
vs: vector of ramp speeds
H_Heis: static Heisenberg Hamiltonian
basis: spin_basis_1d object containing the spin basis
n_real: number of disorder realisations; used only for timing
"""
ti = time() # get start time
#
seed() # the random number needs to be seeded for each parallel process
#
# draw random field uniformly from [-1.0,1.0] for each lattice site
unscaled_fields = -1 + 2 * ranf((basis.L, ))
# define z-field operator site-coupling list
h_z = [[unscaled_fields[i], i] for i in range(basis.L)]
# static list
disorder_field = [["z", h_z]]
# compute disordered z-field Hamiltonian
no_checks = {"check_herm": False, "check_pcon": False, "check_symm": False}
Hz = hamiltonian(disorder_field, [],
basis=basis,
dtype=np.float64,
**no_checks)
# compute the MBL and ETH Hamiltonians for the same disorder realisation
H_MBL = H_Heis + h_MBL * Hz
#
expO = exp_op(H_MBL)
psi_t = psi_0
time_old = 0
imb = []
# Sent=[]
# sub_sizes=[1,2,3]
for a_time in times:
expO.set_a(-1j * (a_time - time_old))
time_old = a_time
psi_t = expO.dot(psi_t)
imb.append(np.einsum('i,i,i', np.conj(psi_t), diag_op, psi_t))
# Sent.append([map(lambda x: ent_entropy(psi_t,basis,chain_subsys=range(x,x+size))["Sent"],range(basis.L-size+1)) for size in sub_sizes])
# imb_at_t = lambda time: diag_op_exp(expO,psi_0,diag_op,time)
# imb = list(map(imb_at_t,times))
# imb = list(map(imb_at_t,times))
# show time taken
print("realization {0}/{1} took {2:.2f} sec".format(
real + 1, n_real,
time() - ti))
#
return np.real(imb)
def TransformTrace (trace, mean, stable):
new_trace = []
ctime = stable
for t in trace:
parts = t.strip().split()
if parts[-1] == 'up' or parts[-1] == 'down':
if len(parts) == 3:
new_trace.append(t.strip())
else:
ctime = ctime + mean * random.ranf()
new_trace.append("%f %s"%(ctime, t.strip()))
elif parts[-1] == 'end':
ctime = ctime + float(parts[0])
new_trace.append("%f end"%ctime)
return (ctime, new_trace)
def hyperbolic_motion(map_width, map_height, posX=None, posY=None, velX=None, velY=None, accX=None, accY=None):
if posX == None or posY == None:
posX = map_width / 2 + 0.5
posY = map_height / 2 + 0.5
if velX == None or velY == None:
start_velocity = 1.0
angle = RNG.ranf() * 2 * NP.pi
velX = start_velocity * NP.cos(angle)
velY = start_velocity * NP.sin(angle)
if accX == None or accY == None:
accX = (NP.floor(RNG.ranf() * 5) - 2.0) / 10.0
accY = 0
X = posX
Y = posY
while True:
a = yield (X, Y)
if a != None:
raise StopIteration
X += velX
Y += velY
velX += accX
velY += accY
while (X < 0) or (X > map_width):
if X < 0:
X = -X
velX = -velX
if X > map_width:
X = 2 * map_width - X
velX = -velX
while (Y < 0) or (Y > map_width):
if Y < 0:
Y = -Y
velY = -velY
if Y > map_width:
Y = 2 * map_width - Y
velY = -velY
def UniformCrossover(parent1, parent2, max_features, prob=0.5):
offspring = np.copy(parent1)
for i in range(len(parent1)):
if parent1[i] != parent2[i]:
offspring[i] = parent1[i] if ranf() <= prob else parent2[i]
offspring_ones = offspring[offspring > 0]
if len(offspring_ones) > max_features:
offspring_ones[choice(len(offspring_ones),
replace=False,
size=len(offspring_ones) - max_features)] = 0
offspring[offspring > 0] = offspring_ones
elif len(offspring_ones) < 1: # For this rather unlikely situation,
offspring = np.copy(parent2) # just avoid increasing the running time.
return offspring
def attack(self, atk, defend):
""""""
if ranf() <= atk.accuracy:
hit = atk.attack - defend.defense
if type(atk) == Player and self.player.equipped["Weapon"].stat.get(
"backstab", 0) == 1:
hit = atk.attack * 3
if ranf < 0.05:
hit = hit * 2
if hit < 0:
hit = 0
defend.hp -= hit
self.outputfunc(" A Hit! {} has {} hp remaining".format(
defend.name, defend.hp))
else:
self.outputfunc("{} missed!".format(atk.name))
def CreateOffspring(parents,
crossover,
mutation,
max_features,
crossover_prob=0.9,
mutation_prob=0.1):
n_crossovers = round(parents.shape[0] * crossover_prob)
offspring = np.empty((n_crossovers, parents.shape[1]), dtype=bool)
for n in range(n_crossovers):
p1, p2 = choice(parents.shape[0], replace=False, size=2)
offspring[n] = crossover(parents[p1], parents[p2], max_features)
if ranf() <= mutation_prob:
offspring[n] = mutation(offspring[n], max_features)
return offspring
def float_generator_func(min_val=0,max_val=100,shape=None):
"""Generate random float numbers
Generate a random float number in the range of min_val and max_val.
Args:
min_val (float): lower bound for random numbers
max_val (float): upper bound for random numbers
Return:
float: random number
"""
delta = max_val-min_val
while True:
yield min_val+delta*random.ranf(size=shape)
def _simulate(self, t) -> Graph:
g = self.graph
g_ = GraphView(g,
vfilt=lambda v: g.vertex_properties["active"][v] == t)
while g_.num_vertices() != 0:
for n in g_.vertices():
# Go through the neighboors
v = g.vertex(n)
for e_neighbour, n_neighbour in zip(v.out_edges(),
v.out_neighbors()):
# Check if the node is activated and make sure not to give it a second life
if g.edge_properties["weight"][e_neighbour] >= ranf(1) \
and g.vertex_properties["active"][n_neighbour] == 0:
g.vertex_properties["active"][n_neighbour] = t + 1
t += 1
g_ = GraphView(
g, vfilt=lambda v: g.vertex_properties["active"][v] == t)
return g
def __init__(self, x_start, y_start, generation_number=-1, behavior_graph=None, name=None):
super().__init__(x_start, y_start)
# TODO: Create some kind of individual-level memory
# TODO: Create bot fields that can control signal movement, size, and investment
self.behavior = behavior_graph
self.speed = 1
self.child_investment = 600
self.max_age = 5000
self.peak_energy = 0
self.generation_number = generation_number
self.target_point = x_start, y_start
self.signal = None
self.signal_direction = ranf()*2*math.pi
self.message_signal_type = 0
Bot.counter += 1
if name is None:
self.name = "Bot_" + str(Bot.counter)
else:
self.name = name
def TransformTrace (links, fail_links, mttf, mttr, stable, end_time, bootstrap):
new_trace = []
ctime = 0.0
for link in links:
new_trace.append("%f %s up"%(ctime, link))
if bootstrap:
new_trace.append("1.0 compute_and_update")
ctime += stable
up_links = set(links)
down_links = set()
set_up_at = defaultdict(list)
while ctime < end_time:
ctime = ctime + mttf * random.ranf()
recovery_time = random.exponential(mttr)
new_trace.append("%f down_active %f"%(ctime, recovery_time))
# Otherwise end instantly
new_trace.append("%f end"%end_time)
return (end_time, new_trace)
def estimate(test,pars,X,Y,N):
''' Estimate covariance of region allowed by test(z,*pars)
draw points from box defined by X and Y till N points pass
test
'''
N = int(N)
Z = np.empty((N,2))
i = 0
while i<N:
# Next line draws N trails
z = nr.ranf(2*N).reshape((N,2))*[X[1]-X[0],Y[1]-Y[0]] + [X[0],Y[0]]
t = test(z,*pars) # t is a vector of N Boolean values
for j in xrange(N):
if t[j]:
Z[i,:] = z[j,:]
i += 1
if i >= N:
break
return np.dot(Z.T,Z)/N
def noise_padding(x,dt,Tpad,amp=1e-8):
"""
Adds random noise at the beginning of a timeseries
to avoid 0 division in rmean.
"""
# Create the random noise padding
Npad=int(Tpad/dt)
padding=zeros(Npad)
for i in range(Npad):
padding[i]=(ranf() - 0.5) * amp
# insert the padding before the timeseries
Nxx=len(x) + Npad
xx=empty(Nxx)
xx[0:Npad]=padding
xx[Npad:]=x
return(xx)
def TransformTrace (links, fail_links, nfailures, mttf, mttr, stable, end_time):
new_trace = []
ctime = 0.0
for link in links:
new_trace.append("%f %s up"%(ctime, link))
ctime += stable
up_links = set(links)
set_up_at = defaultdict(list)
for fail in xrange(nfailures):
ctime = ctime + mttf * random.ranf()
set_up = list()
for t in sorted(set_up_at.keys()):
if t < ctime:
for l in set_up_at[t]:
new_trace.append("%f %s up"%(t, l))
set_up.append(l)
del(set_up_at[t])
if len(up_links) == 0:
# Nothing to fail
continue
while True:
to_fail = random.choice(list(fail_links))
if to_fail in up_links:
up_links.remove(to_fail)
break
new_trace.append("%f %s down"%(ctime, to_fail))
recovery_time = random.exponential(mttr)
assert(recovery_time) > 0
set_up_at[ctime + recovery_time].append(to_fail)
for l in set_up:
up_links.add(l)
for t in sorted(set_up_at.keys()):
for l in set_up_at[t]:
new_trace.append("%f %s up"%(t, l))
up_links.add(l)
ctime = t
if ctime < end_time:
ctime = end_time
# Otherwise end instantly
new_trace.append("%f end"%ctime)
return (ctime, new_trace)
def skip_test_bma(self):
storage = StorageFactory().get_storage('dict_storage')
storage.write_table(
table_name='dataset',
table_data={
"id":arange(100)+1,
"attr1":concatenate((random.randint(0,10, 50), random.randint(20,40, 50))),
"attr2":random.ranf(100),
"outcome": array(50*[0]+50*[1])
}
)
ds = Dataset(in_storage=storage, in_table_name='dataset', id_name="id")
specification = EquationSpecification(
variables=array(["constant", "attr2", "attr1"]),
coefficients=array(["constant", "ba2", "ba1"]))
filename = 'bma_output.pdf'
model = RegressionModel(estimate_config={'bma_imageplot_filename': filename})
model.estimate(specification, ds, "outcome", procedure="opus_core.bma_for_linear_regression_r")
def rpca_learn(datamat,dicts=500,learnstep=1000,iterperstep=50,stepdict=None,stepcode=None,l1_recon=1.0,l1_code=1.0,l2_dict=1.0,eps=1e-10):
"Robust PCA算法字典学习(离线)"
dictshape = (dicts,datamat.shape[1])
if stepdict==None:
stepdict = npr.ranf(dictshape)
codeshape = (datamat.shape[0],dicts)
CODELEN = np.prod(codeshape)
if stepcode==None:
stepcode = np.zeros(codeshape)
def fmin(code_dict):
code = code_dict[:CODELEN].reshape(codeshape)
idict = code_dict[CODELEN:].reshape(dictshape)
recons = dot(code,idict)
error = recons - datamat
loss_recon = np.sqrt(error * error + eps)
loss_code = np.sqrt(code * code + eps)
loss_dict = idict * idict
loss = l1_recon * loss_recon.sum() + l1_code * loss_code.sum() + l2_dict * loss_dict.sum()
grad_recon = l1_recon * error / loss_recon
grad_code = l1_code * code / loss_code
grad_dict = l2_dict * idict * 2
grad_code_2 = dot(grad_recon,idict.T)
grad_dict_2 = dot(code.T,grad_recon)
grad_code = grad_code + grad_code_2
grad_dict = grad_dict + grad_dict_2
print loss_recon.sum(), loss_code.sum(), loss_dict.sum(), loss
return loss, np.concatenate((grad_code.flatten(),grad_dict.flatten()))
for itx in range(learnstep):
print "ITERATION",itx
mres = minimize(fmin, np.concatenate((stepcode.flatten(),stepdict.flatten())), method='L-BFGS-B', jac=True, options={'maxiter':iterperstep, 'disp':False})
stepcode = mres.x[:CODELEN].reshape(codeshape)
stepdict = mres.x[CODELEN:].reshape(dictshape)
yield stepdict, stepcode
def shootPosAngle(self, n):
"""
cosine of positron angel generator
:param n: number of generated angles
:return: numpy.array of cos positron angels
"""
angleList = []
val = random.ranf(n)
for v in val: # цикл по множеству необходимых значений косинуса
for i in range(0, FirstOrder.cosTeta.size):
if self.p_probability[i] >= v:
deltaX = v - self.p_probability[i]
y = self.p_energyBin[i] - self.p_energyBin[i - 1]
x = self.p_probability[i] - self.p_probability[i - 1]
angleList.append(deltaX * y / x + self.p_energyBin[i])
if deltaX * y / x + self.p_energyBin[i] < -0.999995:
print('Yes, you got it!')
if deltaX * y / x + self.p_energyBin[i] > 0.999995:
print('Ups, you got it!')
break
return asarray(angleList)
def point_generator(n = 10, bound = 5.0):
plist = []
for i in range(n):
plist.append(point(rd.ranf() * bound, rd.ranf() * bound))
return plist
subterm = np.mean(arr4d,(2,3),keepdims = True)
divterm = 1.0/(arr4d.std(axis=(2,3),keepdims=True)+1e-10)
arr4d = (arr4d - subterm) * divterm
farr4d = fft.fft2(arr4d)
fftterm = 1.0/(np.sqrt(np.mean(np.abs(farr4d)**2,axis=0))+1e-10)
farr4d = farr4d * fftterm
arr4d = np.real(fft.ifft2(farr4d))
np.savez(cachename+'.npz',sub=subterm,div=divterm,fft=fftterm)
whiteconfs[cachename] = [subterm,divterm,fftterm]
return arr4d
def unwhite(arr4d, cachename):
assert cachename in whiteconfs
subterm, divterm, fftterm = whiteconfs[cachename]
farr4d = fft.fft2(arr4d)
farr4d = farr4d / fftterm
arr4d = np.real(fft.ifft2(farr4d))
return arr4d
if __name__=="__main__":
import numpy.random as npr
d = npr.ranf((10,1,20,20))
dw = white(d,'test')
d2 = unwhite(dw,'test')
os.unlink('test.npz')
print d
print dw
print np.sum(np.abs(d2-d))