def binomial(k1, k2):
## pr. honest finds less blocks
honest_pr = utils.binomial_cdf(k1 + k2, honest * s, e / s)
## attacker number of blocks at first round
malicious_1 = utils.binomial(k1, att * s, e / s)
## attacker number of blocks at second round
malicious_2 = utils.binomial(k2, att * s, e / s)
return honest_pr, malicious_1, malicious_2
def PhiCapHist(alpha, hAlpha, samples, freqDist, count):
phiCap = 0
for i in range(len(alpha)):
h = hAlpha[i]
b = 1
for j in range(config.num_samples):
if count in freqDist[j]:
b *= utils.binomial(alpha[j], len(samples[j]),
len(freqDist[j][count]))
else:
b *= utils.binomial(alpha[j], len(samples[j]), 0)
phiCap += h * b
return phiCap
def odf_marginal(self):
"""Computes the marginal ODF from the q-space signal attenuation
expressed in the SPF basis, following [cheng-ghosh-etal:10].
Returns
-------
spherical_harmonics : sh.SphericalHarmonics instance.
"""
dim_sh = sh.dimension(self.angular_rank)
sh_coefs = np.zeros(dim_sh)
sh_coefs[0] = 1 / np.sqrt(4 * np.pi)
for l in range(2, self.angular_rank + 1, 2):
for m in range(-l, l + 1):
j = sh.index_j(l, m)
for n in range(1, self.radial_order):
partial_sum = 0.0
for i in range(1, n + 1):
partial_sum += (-1)**i * \
utils.binomial(n + 0.5, n - i) * 2**i / i
sh_coefs[j] += partial_sum * kappa(self.zeta, n) * \
self.coefficients[n, j] * \
legendre(l)(0) * l * (l + 1) / (8 * np.pi)
return sh.SphericalHarmonics(sh_coefs)
def odf_marginal(self):
"""Computes the marginal ODF from the q-space signal attenuation
expressed in the SPF basis, following [cheng-ghosh-etal:10].
Returns
-------
spherical_harmonics : sh.SphericalHarmonics instance.
"""
dim_sh = sh.dimension(self.angular_rank)
sh_coefs = np.zeros(dim_sh)
sh_coefs[0] = 1 / np.sqrt(4 * np.pi)
for l in range(2, self.angular_rank + 1, 2):
for m in range(-l, l + 1):
j = sh.index_j(l, m)
for n in range(1, self.radial_order):
partial_sum = 0.0
for i in range(1, n + 1):
partial_sum += (-1)**i * \
utils.binomial(n + 0.5, n - i) * 2**i / i
sh_coefs[j] += partial_sum * kappa(self.zeta, n) * \
self.coefficients[n, j] * \
legendre(l)(0) * l * (l + 1) / (8 * np.pi)
return sh.SphericalHarmonics(sh_coefs)
def test_hamming_sphere(sk):
s, k = sk
result = list(hamming_sphere(s, k))
result_set = set(result)
assert len(result) == len(result_set)
assert len(result) == 3**k * binomial(len(s), k)
for t in result:
assert hamming_distance(s, t) == k
def test_binomial():
assert binomial(0, 0) == 1
assert binomial(0, 1) == 0
assert binomial(0, -1) == 0
assert binomial(1, 0) == 1
assert binomial(1, 1) == 1
assert binomial(1, 2) == 0
assert binomial(10, 5) == 10 * 9 * 8 * 7 * 6 // (2 * 3 * 4 * 5)
def radial_function(r, n, l, zeta):
result = 0.0
for i in range(n + 1):
result += \
(- 1)**i * utils.binomial(n + 0.5, n - i) / \
factorial(i) * 2**(0.5 * l + i - 0.5) * \
special.gamma(0.5 * l + i + 1.5) * \
hyp1f1((2 * i + l + 3) * 0.5, l + 1.5, - 2 * np.pi**2 * r**2 * zeta)
result = result * 4 * (-1)**(0.5 * l) * zeta**(0.5 * l + 1.5) * \
np.pi**(l + 1.5) * r**l / special.gamma(l + 1.5) * spf.kappa(zeta, n)
return result
def radial_function(r, n, l, zeta):
result = 0.0
for i in range(n + 1):
result += \
(- 1)**i * utils.binomial(n + 0.5, n - i) / \
factorial(i) * 2**(0.5 * l + i - 0.5) * \
special.gamma(0.5 * l + i + 1.5) * \
hyp1f1((2 * i + l + 3) * 0.5, l + 1.5, - 2 * np.pi**2 * r**2 * zeta)
result = result * 4 * (-1)**(0.5 * l) * zeta**(0.5 * l + 1.5) * \
np.pi**(l + 1.5) * r**l / special.gamma(l + 1.5) * spf.kappa(zeta, n)
return result
def R(self, j, mp, m):
"""compute transformation matrix element
j j 0 1 2 3
R (Q) = R (Q , Q , Q , Q )
m'm m'm
-j
in __
j \ j j
[R.u] = /__ u R (Q) ,
m m'=j m' m'm
according to the formula:
__ ___________________________
j \ /(j-m')(j+m' )(j-m )(j+m) j+m-k j-m'-k m'-m+k k
R = /__ \/ ( k )(m'-m+k)(m'-m+k)( k ) (a) (a*) (b) (-b*)
m'm k
0 3 2 1
where a := Q - i.Q ; b := -Q -i.Q .
first three arguments to be provided as multiplicities:
[J] = 2j+1, [M] = 2m+1, [MP] = 2m'+1, these are always integer
[-3/2] --> -2; [-1] --> -1; [-1/2] --> 0; [0] --> 1; [1/2] --> 2, etc.
"""
a = complex( self.q[0], -self.q[3] )
ac = complex( self.q[0], self.q[3] ) # complex conjugate of a
b = complex(-self.q[2], -self.q[1] )
mbc = complex( self.q[2], -self.q[1] ) # - complex conjugate of b
res = complex( 0.0 )
j_p_mp = ( j + mp - 2 ) // 2 # j+m'
j_m_mp = ( j - mp ) // 2 # j-m'
j_p_m = ( j + m - 2 ) // 2 # j+m
j_m_m = ( j - m ) // 2 # j-m
if j_p_mp < 0 or j_m_mp < 0 or j_p_m < 0 or j_m_m < 0:
return res
# prepare constant arrays
mp_m_m = j_p_mp - j_p_m
n = np.asarray([j_m_mp, j_p_mp, j_m_m, j_p_m])
kp = np.asarray([0, mp_m_m, mp_m_m, 0])
_a = np.asarray([a, ac, b, mbc])
aexp = np.asarray([j_p_m, j_m_mp, mp_m_m, 0])
# get range for loop
k_mx = int(j_p_m if (j_p_m < j_m_mp) else j_m_mp)
k_mn = int(-j_p_mp+j_p_m if (-j_p_mp+j_p_m > 0) else 0)
for k in range(k_mn, k_mx+1):
_k = kp + k
factor = np.sqrt(np.prod(utils.binomial(n, _k))*complex(1.))
_aexp = aexp + np.asarray([-k, -k, k, k])
prod = np.prod(np.power(_a, _aexp))
res += factor * prod
return res
def odf_tuch(self):
"""Computes the Tuch ODF from the q-space signal attenuation expressed
in the SPF basis, following [cheng-ghosh-etal:10].
Returns
-------
spherical_harmonics : sh.SphericalHarmonics instance.
"""
dim_sh = sh.dimension(self.angular_rank)
sh_coefs = np.zeros(dim_sh)
for j in range(dim_sh):
l = sh.index_l(j)
for n in range(self.radial_order):
partial_sum = 0.0
for i in range(n):
partial_sum += utils.binomial(i - 0.5, i) * (-1)**(n - i)
sh_coefs[j] += partial_sum * self.coefficients[n, j] \
* kappa(zeta, n)
sh_coefs[j] = sh_coefs[j] * legendre(l)(0)
return sh.SphericalHarmonics(sh_coefs)
def odf_tuch(self):
"""Computes the Tuch ODF from the q-space signal attenuation expressed
in the SPF basis, following [cheng-ghosh-etal:10].
Returns
-------
spherical_harmonics : sh.SphericalHarmonics instance.
"""
dim_sh = sh.dimension(self.angular_rank)
sh_coefs = np.zeros(dim_sh)
for j in range(dim_sh):
l = sh.index_l(j)
for n in range(self.radial_order):
partial_sum = 0.0
for i in range(n):
partial_sum += utils.binomial(i - 0.5, i) * (-1)**(n - i)
sh_coefs[j] += partial_sum * self.coefficients[n, j] \
* kappa(zeta, n)
sh_coefs[j] = sh_coefs[j] * legendre(l)(0)
return sh.SphericalHarmonics(sh_coefs)
def basic(s, coeffs):
n = len(coeffs) - 1
r = 1.0 - s
if s >= 0.5:
sigma = r / s
multiplier = s
else:
sigma = s / r
multiplier = r
coeffs = coeffs[::-1]
result = coeffs[0]
for j in range(1, n + 1):
binom_val = utils.binomial(n, j)
modified_coeff = binom_val * coeffs[j]
result = result * sigma + modified_coeff
for _ in range(n):
result = multiplier * result
return result
def pr_a(info,target):
mean_prob = np.mean([info['prob'](info) for t in range(10)])
return u.binomial(target,info['honests'],mean_prob)
#!/usr/bin/env python3
import math
import numpy as np
import utils as u
# probability that if attacker chooses a time t \in T, it falls on 50% of the
# population node, or right before:
# Pr[node_i chooses t ] = d / T for a delay d
# Pr[attacker targets 50%] = binomial(h/2,h,d/T)
# Pr[ 50% < target < 60% ] = binomialCDF(60%) - binomialCDF(50%)
n = 100
att = n * (1.0 / 3.0)
hon = n - att
T = 80
delay = 10
pr_node = delay / T
target = int(0.5 * hon)
pr50 = u.binomial(target, hon, pr_node)
upto = int(0.60 * hon)
# Pr[ 50% < target < 60% ]
pr_to60 = u.binomial_cdf(upto, hon, pr_node) - u.binomial_cdf(
target, hon, pr_node)
print("pr50: {}".format(pr50))
print("pr[50->60]: {}".format(pr_to60))
def visible_to_hidden(self, v_sample):
wx_b = T.dot(v_sample, self.W) + self.hbias
return binomial(sigm(wx_b))
def save_metrics(self, figure_dir='', draw_mask=True):
if self.config.save_metrics:
print('-------- Save figures begin --------')
# print(history.history.keys())
if figure_dir == '':
figure_dir = os.path.join(
self.config.root_dir, 'figures', self.config.model_name,
self.config.run, '{}{:.4f}_{}{:.4f}'.format(
self.config.record_metrics[0],
self.results[self.config.record_metrics[0]],
self.config.record_metrics[1],
self.results[self.config.record_metrics[1]]))
else:
figure_dir = os.path.join(
figure_dir, '{}{:.4f}_{}{:.4f}'.format(
self.config.record_metrics[0],
self.results[self.config.record_metrics[0]],
self.config.record_metrics[1],
self.results[self.config.record_metrics[1]]))
if not os.path.exists(figure_dir):
os.makedirs(figure_dir)
epochs = self.history.epoch
metrics = self.history.history
with open(os.path.join(figure_dir, 'logs.txt'), 'w') as f:
f.write('epoch : ' + str(epochs) + '\n')
for key, value in metrics.items():
f.write(key + ' : ' + str(value) + '\n')
for key, value in self.results.items():
f.write(key + ' : ' + str(value) + '\n')
if self.config.run in ['prune', 'atuo']:
for key, value in self.prune_info.items():
f.write(key + ' : ' + str(value) + '\n')
pair_keys = [
'loss', 'ift_loss', 'rec_loss', 'PSNR', 'SSIM', 'ift_PSNR',
'ift_SSIM', 'rec_PSNR', 'rec_SSIM'
]
for key in pair_keys:
if key in metrics.keys() and 'val_' + key in metrics.keys():
plt.figure()
plt.plot(epochs, metrics[key])
plt.plot(epochs, metrics['val_' + key])
plt.grid(True)
plt.title(key + ' vs epoch')
plt.ylabel(key)
plt.xlabel('epoch')
plt.legend(['Train', 'Val'], loc='upper left')
plt.tight_layout()
plt.savefig(os.path.join(figure_dir,
key + '_vs_epoch.png'))
print('Saving figure at ' +
os.path.join(figure_dir, key + '_vs_epoch.png'))
plt.show(block=False)
plt.pause(0.01)
del metrics[key]
del metrics['val_' + key]
for key, value in metrics.items():
plt.figure()
plt.plot(epochs, value)
plt.grid(True)
plt.title(key + ' vs epoch')
plt.ylabel(key)
plt.xlabel('epoch')
plt.tight_layout()
plt.savefig(os.path.join(figure_dir, key + '_vs_epoch.png'))
print('Saving figure at ' +
os.path.join(figure_dir, key + '_vs_epoch.png'))
plt.show(block=False)
plt.pause(0.01)
if draw_mask:
pmask_layer_list = get_list(self.model, ['PMask2D'])
for i in range(len(pmask_layer_list)):
# prob, mask = pmask_layer_list[i].get_weights()[0], pmask_layer_list[i].mask
prob = np.squeeze(pmask_layer_list[i].get_weights()[0],
axis=(0, 3))
# mask = np.squeeze(pmask_layer_list[i].get_weights()[1], axis=(0, 3))
mask = binomial(prob)
plt.figure()
plt.title('Probability')
plt.subplot(2, 2, 1)
fig_obj = plt.imshow(prob, cmap=plt.get_cmap('jet'))
plt.colorbar(fig_obj)
plt.title('Probability (avg=%.4f)' % np.mean(prob))
plt.subplot(2, 2, 2)
fig_obj = plt.imshow(mask, cmap=plt.get_cmap('gray'))
plt.colorbar(fig_obj)
plt.title('Mask (%.2f%%)' %
(100.0 * np.sum(mask) / mask.size))
plt.subplot(2, 2, 3)
plt.plot(np.mean(prob, axis=0))
plt.plot(np.mean(prob, axis=1))
plt.legend(['Row', 'Col'])
plt.title('PDF')
plt.subplot(2, 2, 4)
plt.plot(np.mean(mask, axis=0))
plt.plot(np.mean(mask, axis=1))
plt.legend(['Row', 'Col'])
plt.title('PDF')
plt.tight_layout()
plt.savefig(os.path.join(figure_dir,
'Parametric_mask.png'))
print('Saving figure at ' +
os.path.join(figure_dir, 'Parametric_mask.png'))
plt.show(block=False)
plt.pause(0.01)
pmask_layer_list = get_list(self.model,
['PMask1DH', 'PMask1DV'])
for i in range(len(pmask_layer_list)):
# prob, mask = pmask_layer_list[i].get_weights()[0], pmask_layer_list[i].mask
prob = np.squeeze(pmask_layer_list[i].get_weights()[0],
axis=(0, 3))
mask = binomial(prob)
plt.figure()
plt.title('Probability')
plt.subplot(2, 2, 1)
fig_obj = plt.imshow(np.broadcast_to(prob, [256, 256]),
cmap=plt.get_cmap('jet'))
plt.colorbar(fig_obj)
plt.title('Probability (avg=%.4f)' % np.mean(prob))
plt.subplot(2, 2, 2)
fig_obj = plt.imshow(np.broadcast_to(mask, [256, 256]),
cmap=plt.get_cmap('gray'))
plt.colorbar(fig_obj)
plt.title('Mask (%.2f%%)' %
(100.0 * np.sum(mask) / mask.size))
plt.subplot(2, 2, 3)
plt.plot(prob)
plt.grid(True)
plt.title('PDF')
plt.tight_layout()
plt.savefig(os.path.join(figure_dir,
'Parametric_mask.png'))
print('Saving figure at ' +
os.path.join(figure_dir, 'Parametric_mask.png'))
plt.show(block=False)
plt.pause(0.01)
print('-------- Save figures end --------')
# def prune(self, x_train, y_train, x_test, y_test):
#
# print('-------- Prune begin --------')
#
# batchnorm_layer_list = [layer for layer in self.model.layers if 'batch_normalization' in layer.name]
# mask_layer_list = [layer for layer in self.model.layers if 'mask' in layer.name]
# num_layers = len(mask_layer_list)
#
# for t in range(self.config.prune_steps):
# print('Before prune:')
# self.validate(x_test=x_test, y_test=y_test)
#
# print('-------- Prune step {}: {}% begin --------'.format(t, self.config.sparsity[t] * 100))
#
# prune_mask_vectors = prune_batchnorm(model=self.model, layer_list=batchnorm_layer_list,
# sparsity=self.config.sparsity[t])
#
# for i in range(num_layers):
# mask_layer_list[i].set_weights(
# [np.reshape(prune_mask_vectors[i], [1, 1, 1, len(prune_mask_vectors[i])])])
#
# print('After prune:')
# self.validate(x_test=x_test, y_test=y_test)
#
# print('Retrain:')
# ckpt_save_path = os.path.join(self.config.root_dir, 'checkpoints', self.config.model_name,
# 'prune_%.2f' % self.config.sparsity[t])
# log_dir = os.path.join(self.config.root_dir, 'logs', self.config.model_name,
# 'prune_%.2f' % self.config.sparsity[t])
# self.callbacks = self.instance.initialize_callbacks(ckpt_save_path=ckpt_save_path, log_dir=log_dir)
# self.train(x_train, y_train, x_test, y_test)
#
# print('After retrain:')
# self.validate(x_test=x_test, y_test=y_test)
#
# save_dir = os.path.join(self.config.root_dir, 'results', self.config.model_name,
# 'prune_%.2f' % self.config.sparsity[t])
# self.save_model(result_dir=save_dir)
#
# figure_dir = os.path.join(self.config.root_dir, 'figures', self.config.model_name,
# 'prune_%.2f' % self.config.sparsity[t])
# self.save_metrics(figure_dir=figure_dir)
#
# print('-------- Prune step {}: {}% end --------'.format(t, self.config.sparsity[t] * 100))
#
# print('-------- Prune end --------')
# def compress(self):
# print('-------- Compress begin --------')
#
# conv_layer_list = [layer for layer in self.model.layers if 'conv' in layer.name]
# batchnorm_layer_list = [layer for layer in self.model.layers if 'batch_normalization' in layer.name]
# mask_layer_list = [layer for layer in self.model.layers if 'mask' in layer.name]
# dense_layer_list = [layer for layer in self.model.layers if 'dense' in layer.name]
# num_layers = len(mask_layer_list)
#
# mask_vector = [None] * num_layers
# final_channel = [None] * num_layers
#
# # obtain mask and number of channels
# for i in range(num_layers):
# mask = mask_layer_list[i].get_weights()[0]
# mask_vector[i] = mask
# final_channel[i] = int(np.sum(mask))
# print('Final channel: ' + str([(i, mask_layer_list[i].name, final_channel[i]) for i in range(num_layers)]))
#
# self.config.final_channel = final_channel
# self.config.is_final = True
# self.config.restore_model = False
# self.config.bn_mask = False
# # create final model
# final_instance = interface.ModelAdapter(self.config)
# final_model = final_instance.create_model()
# final_instance.serialize_model()
#
# final_conv_layer_list = [layer for layer in final_model.layers if 'conv' in layer.name]
# final_batchnorm_layer_list = [layer for layer in final_model.layers if 'batch_normalization' in layer.name]
# final_dense_layer_list = [layer for layer in final_model.layers if 'dense' in layer.name]
#
# # first conv-bn-mask-relu block
# print('Compress the first conv-bn-mask-relu block ' + conv_layer_list[0].name)
# conv_weights = conv_layer_list[0].get_weights()
# bn_weights = batchnorm_layer_list[0].get_weights()
# cur_mask = mask_vector[0]
# # kernel
# conv_weights[0] *= cur_mask
# conv_weights[0] = conv_weights[0][..., np.where(np.squeeze(cur_mask) == 1)[0]]
# # bias
# conv_weights[1] *= np.squeeze(cur_mask)
# conv_weights[1] = conv_weights[1][..., np.where(np.squeeze(cur_mask) == 1)[0]]
# # batchnorm: gamma, beta, mean, variance
# for j in range(len(bn_weights)):
# bn_weights[j] *= np.squeeze(cur_mask)
# bn_weights[j] = bn_weights[j][..., np.where(np.squeeze(cur_mask) == 1)[0]]
# # weights transfer
# final_conv_layer_list[0].set_weights(conv_weights)
# final_batchnorm_layer_list[0].set_weights(bn_weights)
#
# # reduce the in-channel of the convolution in the first Resblock
# conv_weights = conv_layer_list[1].get_weights()
# cur_mask = cur_mask.transpose(0, 1, 3, 2)
# # kernel
# conv_weights[0] *= cur_mask
# conv_weights[0] = conv_weights[0][..., np.where(np.squeeze(cur_mask) == 1)[0], :]
# # weight transfer
# final_conv_layer_list[1].set_weights(conv_weights)
#
# # depth-wise convlutional layers in skip connections
# dwc = [19, 36]
# for idx in dwc:
# print('Compress depth-wise ' + conv_layer_list[idx].name)
# final_conv_layer_list[idx].set_weights(conv_layer_list[idx].get_weights())
# # remove layer names in list
# conv_layer_list = np.delete(conv_layer_list, dwc)
# final_conv_layer_list = np.delete(final_conv_layer_list, dwc)
#
# # regular conv-bn-mask-relu block weights transfer
# for i in range(1, num_layers):
# print('Compress ' + str((i, conv_layer_list[i].name, batchnorm_layer_list[i].name)))
# conv_weights = conv_layer_list[i].get_weights()
# bn_weights = batchnorm_layer_list[i].get_weights()
# pre_mask = mask_vector[i - 1].transpose(0, 1, 3, 2)
# cur_mask = mask_vector[i]
# # kernel
# conv_weights[0] *= cur_mask
# if i % 2 == 1:
# conv_weights[0] = conv_weights[0][..., np.where(np.squeeze(cur_mask) == 1)[0]]
# if i % 2 == 0:
# conv_weights[0] *= pre_mask
# conv_weights[0] = conv_weights[0][..., np.where(np.squeeze(pre_mask) == 1)[0], :]
# # bias
# conv_weights[1] *= np.squeeze(cur_mask)
# if i % 2 == 1:
# conv_weights[1] = conv_weights[1][..., np.where(np.squeeze(cur_mask) == 1)[0]]
# # batchnorm: gamma, beta, mean, variance
# for j in range(len(bn_weights)):
# bn_weights[j] *= np.squeeze(cur_mask)
# if i % 2 == 1:
# bn_weights[j] = bn_weights[j][..., np.where(np.squeeze(cur_mask) == 1)[0]]
# # weight transfer
# final_conv_layer_list[i].set_weights(conv_weights)
# final_batchnorm_layer_list[i].set_weights(bn_weights)
#
# # dense layer weights transfer
# for i in range(len(dense_layer_list)):
# print('Compress ' + final_dense_layer_list[i].name)
# final_dense_layer_list[i].set_weights(dense_layer_list[i].get_weights())
#
# print('-------- Compress end --------')
return final_model