def display(*args):
global x, y, move_x, move_y, NUMDOTS, NUMDOTS2, MAX_AGE, age
glClearColor(0.0, 0.0, 0.0, 0.0)
glClear(GL_COLOR_BUFFER_BIT)
glColor3f(1.0, 1.0, 0.0)
x = x + move_x
y = y + move_y
age = age + 1
which = greater(age, MAX_AGE)
x = choose(which, (x, random(NUMDOTS)))
y = choose(which, (y, random(NUMDOTS)))
age = choose(which, (age, 0))
x = choose(greater(x, 1.0), (x, x - 1.0)) # very cool - wraparound
y = choose(greater(y, 1.0), (y, y - 1.0))
x2 = random(NUMDOTS2)
y2 = random(NUMDOTS2)
v = concatenate(
(transpose(array([x, y])), transpose(array([x - .005, y + .005])),
transpose(array([x + .005, y - .005])), transpose(array([x2, y2]))))
glVertexPointerd(v)
glEnableClientState(GL_VERTEX_ARRAY)
glDrawArrays(GL_POINTS, 0, len(v))
glDisableClientState(GL_VERTEX_ARRAY)
glFlush()
glutSwapBuffers()
def _testSpeednD(self,nr_points, dim):
points = 100*numpy.random(dim, nr_points)
vals = 100*numpy.random(nr_points)
#build the model
lut_ss = LutStrategy()
lut_model = LutFactory().build(points, vals, lut_ss)
# test the model
target_points = points + 0.1
cnt=0
starttime=time.time()
while cnt < 2:
yhat = lut_model.simulate(target_points)
cnt=cnt+1
elapsed=time.time()-starttime
nb_lookups=nr_points * cnt
lookups_per_sec=nb_lookups / elapsed
print "%d simulations (%d-D) of %d points took %f seconds (%d lookups/sec)" % ( cnt, dim , nr_points, elapsed, lookups_per_sec)
def initNetwork():
global network, imW, imH, iWeights, netDepth, maskResH, maskResH
global layerLen, iBias, maxPixVal
for i in range(netDepth):
if i == 0:
iWeights.append([[
random() * 2 - 1
for x in range(round(1 / (maskResH * maskResW)))
] for y in range(layerLen[i])])
#iWeights.append([[((np.random.random_sample()*2)-1) for x in range(round(1/(maskResH*maskResW)))] for y in range(layerLen[i])])
#iWeights.append([[0 for x in range(round(1/(maskResH*maskResW)))] for y in range(layerLen[i])])
else:
iWeights.append(
[[random() * 2 - 1 for x in range(layerLen[i - 1])]
for y in range(layerLen[i])])
#iWeights.append([[((np.random.random_sample()*2)-1) for x in range(layerLen[i-1])] for y in range(layerLen[i])])
#iWeights.append([[0 for x in range(layerLen[i-1])] for y in range(layerLen[i])])
iBias.append([random() * 2 - 1 for x in range(layerLen[i])])
#iBias.append([(np.random.random_sample()*2-1) for x in range(layerLen[i])])
#iBias.append([0 for x in range(layerLen[i])])
#iErrors.append(0 for x in range(layerLen[i])])
tempLayer = {
'layer': None,
'weights': iWeights[i],
'bias': iBias[i],
'layerType': 'flat',
'error': [0 for x in range(layerLen[i])],
'prevLayer': None,
}
network.append(tempLayer)
def on_epoch_end(self):
'make X-train sample list'
"""
1. go over each class
2. select randomly #n_sample samples of each class
3. add selection list to dict with class as key
"""
self.class_selection_path = np.array([])
self.labels = np.array([])
for class_i in self.classes:
samples_class_i = randsomsample(
range(0, self.samples[class_i]),
self.number_samples_per_class_to_pick)
self.class_selection_path = np.append(self.class_selection_path, [
self.filename_dict[f"{self.class_indices[class_i]}_{i}"]
for i in samples_class_i
])
self.labels = np.append(
self.labels,
[self.class_indices[class_i] for i in samples_class_i])
self.list_IDs = self.class_selection_path
'Updates indexes after each epoch'
self.indexes = np.arange(len(self.list_IDs))
if self.shuffle == True:
if self.seed:
np.random(self.seed)
np.random.shuffle(self.indexes)
def init_args(args, **kwargs):
cfg = kwargs
params = Map({})
assert os.path.isdir(args.dump_dir), 'Dump dir must be a valid dir'
args.ckpt_save_dir = os.path.join(args.dump_dir, 'checkpoints')
args.log_dir = os.path.join(args.dump_dir, 'logs')
for dir in [args.ckpt_save_dir, args.log_dir]:
if not os.path.isdir(dir):
os.makedirs(dir, exist_ok=True)
args.is_cuda = torch.cuda.is_available()
args.device = torch.device('cuda' if args.is_cuda else 'cpu')
if args.is_cuda:
torch.cuda.empty_cache()
cudnn.deterministic = True
# os.environ["CUDA_VISIBLE_DEVICES"]
if args.seed is not None:
random.seed(args.seed)
np.random(args.seed)
torch.manual_seed(args.seed)
if args.is_cuda:
torch.cuda.manual_seed(args.seed)
# don't pass it as args since it can't be serialized
# https://discuss.pytorch.org/t/how-to-debug-saving-model-typeerror-cant-pickle-swigpyobject-objects/66304
params.tensorboard = SummaryWriter(log_dir=args.log_dir)
cfg.update(vars(args))
return Map(cfg), params
def __init__(self, center, radius, theshold, maxDepth):
self.isLeaf = False
self.center = center
self.radius = radius
self.threshold = theshold
self.maxDepth = maxDepth
# self.color = (1., 0., 0.)
# self.color = (randint(0,255), randint(0, 255), randint(0, 255))
self.color = (random(), random(), random())
# print "self.color = ", self.color
self.children = [None, None, None, None, None, None, None, None]
# self.boundsOffsetTable = array([[-0.5, -0.5, -0.5],
# [+0.5, -0.5, -0.5],
# [-0.5, +0.5, -0.5],
# [+0.5, +0.5, -0.5],
# [-0.5, -0.5, +0.5],
# [+0.5, -0.5, +0.5],
# [-0.5, +0.5, +0.5],
# [+0.5, +0.5, +0.5]])
self.boundsOffsetTable = array(
[
[-0.5, -0.5, -0.5],
[+0.5, -0.5, -0.5],
[-0.5, -0.5, +0.5],
[+0.5, -0.5, +0.5],
[-0.5, +0.5, -0.5],
[+0.5, +0.5, -0.5],
[-0.5, +0.5, +0.5],
[+0.5, +0.5, +0.5],
]
)
def setdata(self, X, V):
A = self.bialtprodeye(2*self.F.J_coords)
"""Note: p, q <= min(n,m)"""
self.data.Brand = 2*(random((A.shape[0],self.data.p))-0.5)
self.data.Crand = 2*(random((A.shape[1],self.data.q))-0.5)
self.data.B = zeros((A.shape[0],self.data.p), float)
self.data.C = zeros((A.shape[1],self.data.q), float)
self.data.D = zeros((self.data.q,self.data.p), float)
U, S, Vh = linalg.svd(A)
self.data.b = U[:,-1:]
self.data.c = transpose(Vh)[:,-1:]
if self.update:
self.data.B[:,1] = self.data.b
self.data.C[:,1] = self.data.c
U2, S2, Vh2 = linalg.svd(c_[r_[A, transpose(self.data.C[:,1])], r_[self.data.B[:,1], [[0]]]])
self.data.B[:,2] = U2[0:A.shape[0],-1:]
self.data.C[:,2] = transpose(Vh2)[0:A.shape[1],-1:]
self.data.D[0,1] = U2[A.shape[0],-1]
self.data.D[1,0] = transpose(Vh2)[A.shape[1],-1]
else:
# self.data.B = eye(self.data.Brand.shape)
# self.data.C = eye(self.data.Crand.shape)
# USE OF RANDOM
self.data.B = self.data.Brand
self.data.C = self.data.Crand
def _init_(self, num_bias_weights, input_weights):
self.values = []
self.biases = []
for i in range(num_bias_weights):
self.biases.append(np.random(0, 1))
for i in range(num_bias_weights):
self.output_weights.append(np.random(0, 1))
self.input_weights = input_weights
def init_weights(self):
self.weights = {}
self.weights['W'] = np.random((self.n_visible, self.n_hidden), dtype=np.float64)
self.weights['A'] = np.random((self.n_condition, self.n_visible), dtype=np.float64)
self.weights['B'] = np.random((self.n_condition, self.n_hidden), dtype=np.float64)
self.weights['a_stat'] = np.zeros((self.n_visible), dtype=np.float64)
self.weights['b_stat'] = np.zeros((self.n_hidden), dtype=np.float64)
return
def default_weight_initializer(self):
"""initialize weight using a gaussianj distribution, mu=0, std=1.
The first layer is the iput later so we dont set any biases for those"""
self.biases = [np.random(y, 1) for y in self.sizes[1:]]
self.weights = [
np.random(y, x) / np.sqrt(x)
for x, y in zip(self.sizes[:-1], self.sizes[1:])
]
def randPointUnitBall(d):
if d == 1:
return 2 * random(size=(1, )) - 1
r = random()**(1 / d)
theta = 2 * pi * random()
p = randPointUnitBall(d - 1)
return r_[r * cos(theta), r * sin(theta) * p / numpy.linalg.norm(p)]
def __init__(self, number_of_classes):
self.input_images = tf.placeholder(
shape=[None, 227, 227, 3],
dtype=tf.float64,
name="input_images",
)
conv_1_kernel = tf.Variable(np.random.sample((11, 11, 3, 96)),
dtype=tf.float64,
name="conv_1_kernel")
conv_1 = tf.nn.conv2d(self.input_images,
conv_1_kernel,
strides=(4, 4, 4, 4),
dtype=tf.float64,
name="conv_1")
conv_1_activation = tf.nn.relu(conv_1, name="conv_1_activation")
conv_1_max_pool = tf.nn.max_pool(conv_1_activation,
ksize=(1, 3, 3, 1),
name="conv_1_max_pool")
conv_2_kernel = tf.Variable(np.random.sample((5, 5, 96, 256)),
name="conv_2_kernel")
conv_2 = tf.nn.conv2d(conv_1_max_pool, conv_2_kernel, name="conv_2")
conv_2_activation = tf.nn.relu(conv_2, name="conv_2_activation")
conv_2_max_pool = tf.nn.max_pool(conv_2_activation,
ksize=(1, 3, 3, 1),
name="conv_2_max_pool")
conv_3_kernel = tf.Variable(np.random((3, 3, 256, 384)),
name="conv_3_kernel")
conv_3 = tf.nn.conv2d(conv_2_max_pool,
conv_3_kernel,
strides=(1, 1, 1, 1),
name="conv_3")
conv_3_activation = tf.nn.relu(conv_3, name="conv_3_activation")
conv_4_kernel = tf.Variable(np.random((3, 3, 256, 384)),
name="conv_4_kernel")
conv_4 = tf.nn.conv2d(conv_3_activation,
conv_4_kernel,
strides=(1, 1, 1, 1),
name="conv_4")
conv_4_activation = tf.nn.relu(conv_4, name="conv_3_activation")
conv_5_kernel = tf.Variable(np.random((3, 3, 256, 384)),
name="conv_5_kernel")
conv_5 = tf.nn.conv2d(conv_4_activation,
conv_5_kernel,
strides=(1, 1, 1, 1),
name="conv_5")
conv_5_activation = tf.nn.relu(conv_5, name="conv_3_activation")
conv_5_max_pool = tf.nn.max_pool(conv_5_activation,
ksize=(1, 3, 3, 1),
name="conv_5_activation")
tf.nn.fla
def rand_unicirc():
t = 2 * pi * random()
u = random() + random()
if u > 1:
r = 2 - u
else:
r = u
return array([r * cos(t), r * sin(t)])
def update_state():
newly_infected.a = False
global has_infection
# visit the nodes in random order
vs = list(g.vertices())
shuffle(vs)
for v in vs:
if random() < x:
p[v] = 0.0
newly_infected[v] = True
elif has_infection[v] == True:
ns = list(v.out_neighbours())
if len(ns) > 0:
for w in ns:
if random() < p[w]: # chance de ser infectado
newly_infected[w] = True
p[w] = 0.0
if (p[v] < 1.0):
p[v] += recovery_rate
state[v] = [p[v], p[v], p[v], 1.0]
has_infection = cp.deepcopy(newly_infected)
#with open("plot.txt", "a") as myfile:
# myfile.write(str(counter["S"])+","+str(counter["I"])+","+str(counter["R"])+"\n")
#plot_values["S"].append(counter["S"])
#plot_values["I"].append(counter["I"])
#plot_values["R"].append(counter["R"])
# Filter out the recovered vertices
#g.set_vertex_filter(removed, inverted=True)
# The following will force the re-drawing of the graph, and issue a
# re-drawing of the GTK window.
win.graph.regenerate_surface()
win.graph.queue_draw()
#ax1.plot(range(len(plot_values["S"])), plot_values["S"],color='b')
#ax1.plot(range(len(plot_values["I"])), plot_values["I"],color='r')
#ax1.plot(range(len(plot_values["R"])), plot_values["R"],color='y')
#fig1.canvas.draw()
# if doing an offscreen animation, dump frame to disk
if offscreen:
global count
pixbuf = win.get_pixbuf()
pixbuf.savev(r'./frames/sirs%06d.png' % count, 'png', [], [])
if count > max_count:
sys.exit(0)
count += 1
# We need to return True so that the main loop will call this function more
# than once.
return True
def rpn_target(all_anchors, inside_inds,gt_labels, gt_boxes):
# keep inside anchors
anchors = all_anchors[inside_inds, :]
if Debug:
print('anchors.shape ' + anchors.shape)
labels = np.empty((len(inside_inds),) dtype=np.float32)
labels.fill(-1)
overlaps = bbox_overlaps(
np.ascontiguousarray(anchors, dtype=np.float32),
np.ascontiguousarray(gt_boxes, dtype=np.float32))
# indices of most possible labels for each anchors
argmax_overlaps = overlaps.argmax(overlaps, axis=1)
max_overlaps = overlaps[np.arange(len(inside_inds)), argmax_overlaps]
gt_argmax_overlaps = overlaps.argmax(overlaps, axis=0)
gt_max_overlaps = overlaps[gt_argmax_overlaps, np.arange(overlaps.shape[1])]
gt_argmax_overlaps = np.where(overlaps==gt_max_overlaps)[0]
# label 0 for background, 1 for object and -1 for nothing
labels[max_overlaps < cfg.TRAIN.RPN_NEGATIVE_OVERLAP] = 0
# for each gt, the anchor with highest overlap
labels[gt_argmax_overlaps] = 1
#
labels[max_overlaps > cfg.TRAIN.RPB_POSITIVE_OVERLAP] = 1
# subsample
num_pos = int(cfg.TRAIN.RPN_POS_FRACTION*cfg.TRAIN.RPN_BATCH_SIZES)
pos_inds = np.where(labels == 1)[0]
if (len(pos_inds) > num_pos):
disable_inds = random(
pos_inds, size=(len(pos_inds)-num_pos), replace=False)
labels[disable_inds] = -1
num_neg = cfg.TRAIN.RPN_BATCH_SIZES - np.sum(labels == 1)
neg_inds = np.where(labels == 1)[0]
if (len(neg_inds) > num_neg):
disable_inds = random(
neg_inds, size=(len(neg_inds)-neg_pos), replace=False)
labels[disable_inds] = -1
idx_label = np.where(labels != - 1)[0]
idx_pos = np.where(labels == 1)[0]
inds = inside_inds[idx_label]
labels = labels[idx_label]
pos_inds = inside_inds[idx_pos]
pos_anchors = anchors[idx_pos]
pos_gt_boxes = (gt_boxes[argmax_overlaps])[idx_pos]
targets = bbox(pos_gt_boxes, pos_anchors)
return inds, pos_inds, labels, targets
def update_state():
newly_infected.a = False
removed.a = False
# visit the nodes in random order
vs = list(g.vertices())
shuffle(vs)
for v in vs:
if state[v] == I:
if random() < r:
state[v] = R
elif state[v] == S:
if random() < x:
state[v] = I
else:
ns = list(v.out_neighbours())
if len(ns) > 0:
w = ns[randint(0, len(ns))] # choose a random neighbour
if state[w] == I:
state[v] = I
newly_infected[v] = True
elif random() < s:
state[v] = S
if state[v] == R:
removed[v] = True
if state[v] == S:
if I in [state[w] for w in v.out_neighbours()]:
vertex_sfcs[v] = Simg_fear
else:
vertex_sfcs[v] = Simg
else:
vertex_sfcs[v] = Iimg
# Filter out the recovered vertices
g.set_vertex_filter(removed, inverted=True)
# The following will force the re-drawing of the graph, and issue a
# re-drawing of the GTK window.
win.graph.regenerate_surface(lazy=False)
win.graph.queue_draw()
# if doing an offscreen animation, dump frame to disk
if offscreen:
global count
pixbuf = win.get_pixbuf()
pixbuf.savev(r'./frames/zombies%06d.png' % count, 'png', [], [])
if count > max_count:
sys.exit(0)
count += 1
# We need to return True so that the main loop will call this function more
# than once.
return True
def update_state():
newly_infected.a = False
removed.a = False
# visit the nodes in random order
vs = list(g.vertices())
shuffle(vs)
for v in vs:
if state[v] == I:
if random() < r:
state[v] = R
elif state[v] == S:
if random() < x:
state[v] = I
else:
ns = list(v.out_neighbours())
if len(ns) > 0:
w = ns[randint(0, len(ns))] # choose a random neighbour
if state[w] == I:
state[v] = I
newly_infected[v] = True
elif random() < s:
state[v] = S
if state[v] == R:
removed[v] = True
if state[v] == S:
if I in [state[w] for w in v.out_neighbours()]:
vertex_sfcs[v] = Simg_fear
else:
vertex_sfcs[v] = Simg
else:
vertex_sfcs[v] = Iimg
# Filter out the recovered vertices
g.set_vertex_filter(removed, inverted=True)
# The following will force the re-drawing of the graph, and issue a
# re-drawing of the GTK window.
win.graph.regenerate_surface()
win.graph.queue_draw()
# if doing an offscreen animation, dump frame to disk
if offscreen:
global count
pixbuf = win.get_pixbuf()
pixbuf.savev(r'./frames/zombies%06d.png' % count, 'png', [], [])
if count > max_count:
sys.exit(0)
count += 1
# We need to return True so that the main loop will call this function more
# than once.
return True
def mutate(p):
if random() < 0.5:
return random(), random()
else:
dx = normal(0, 0.0001)
dy = normal(0, 0.0001)
x = p[0] + dx
y = p[1] + dy
x = x - 1 if x > 1 else x + 1 if x < 0 else x
y = y - 1 if y > 1 else y + 1 if y < 0 else y
return x, y
def RandSelectFocalPoint(self):
objId = random.randint(0, self.GetObjectsCount()-1)
faceId = random.randint(0, self.GetObjectFacesCount(objId)-1)
pt1, pt2 ,pt3 = self.GetVertices(objId, faceId)
c1 = numpy.random()
c2 = numpy.random()
c3 = numpy.random()
c = c1 + c2 + c3
pt = (c1/c) * pt1 + (c2/c) * pt2 + (c3/c) * pt3
return pt
def setdata(self, A):
"""Note: p, q <= min(n,m)"""
self.data.Brand = 2*(random((A.shape[0],self.data.p))-0.5)
self.data.Crand = 2*(random((A.shape[1],self.data.q))-0.5)
self.data.D = zeros((self.data.q,self.data.p), float)
if self.update:
U, S, Vh = linalg.svd(A)
self.data.B = U[:,-1*self.data.p:]
self.data.C = transpose(Vh)[:,-1*self.data.q:]
else:
self.data.B = self.data.Brand
self.data.C = self.data.Crand
def FB_simulate(self):
seeds = list(range(1, 5))
self.set_seed(seeds)
count = {
'S': len(seeds),
'I': self.number_of_nodes() - len(seeds),
'R': 0
}
print(count)
print("=========================")
t_max = 1000
for time in range(t_max):
for i in self.nodes():
# while count['S'] > 0:
if self.node[i]['name'] != 'S':
continue
# active: Speader
for n in self.neighbors(i):
# passive: Ignorant
if self.node[n]['name'] != 'I':
continue
if random() < alpha:
# passive: I --> S or R
if random() < p:
# passive: I --> S
self.node[n]['name'] = 'S'
count['I'] -= 1
count['S'] += 1
print(count)
else:
# passive: I --> R
self.node[n]['name'] = 'R'
count['I'] -= 1
count['R'] += 1
print(count)
# passive: Spreader or Stifler
elif random() < lamda:
# active: S --> R
self.node[i]['name'] = 'R'
count['S'] -= 1
count['R'] += 1
print(count)
if count['S'] == 0:
spread_time = time
return (self, spread_time, count)
def subsample_imbalanced(X_enhancer, X_promoter, y, positive_subsample_frac):
n = np.shape(y_train)[0] # sample size (i.e., number of pairs)
# indices that are positive and selected to be retained or negative
to_keep = (np.random(n) < positive_subsample_frac) or (y == 1)
return X_enhancer[to_keep, :], X_promoter[to_keep, :], y[to_keep]
def buildArrays():
a = arange(0, n)
vertex = shuffle(cos(2 * pi * a / n), sin(2 * pi * a / n))
vertex.shape = (n, 2)
color = random(n * 3)
color.shape = (n, 3)
return vertex, color
def get_random_number():
m = random()
choice = [25, 75, 125, 175, 225, 275, 325, 375, 425, 525]
probabilities = [
0.24, 0.23, 0.18, 0.14, 0.11, 0.036, 0.02, 0.0103, 0.0103, 0.005155
]
return (float(choices(choice, probabilities)[0]) * m)
def step(self):
# logpability and loglike for stoch's current value:
logp = sum([stoch.logp for stoch in self.stochs]) + self.indicator.logp
loglike = self.loglike
# Sample a candidate value for the value and indicator of the stoch.
self.propose()
# logpability and loglike for stoch's proposed value:
logp_p = sum([stoch.logp
for stoch in self.stochs]) + self.indicator.logp
# Skip the rest if a bad value is proposed
if logp_p == -Inf:
for stoch in self.stochs:
stoch.revert()
return
loglike_p = self.loglike
# test:
test_val = logp_p + loglike_p - logp - loglike
test_val += self.inv_q(self.indicator)
test_val += self.q(self.indicator, self._u)
if self.Jacobian is not None:
test_val += self.Jacobian(self.indicator, self._u,
**self.stoch_dict)
if log(random()) > test_val:
for stoch in self.stochs:
stoch.revert
def allocate_data_to_agents(self, type='lin'):
'''
:param type: lin - linear space between attributes or
rnd - randomly distributed
'''
attr = self.p_feat
if type == 'lin':
means = np.linspace(np.min(self.data_train[[attr]].values),
np.max(self.data_train[[attr]].values),
self.n_agents + 2)[1:-1]
elif type == 'rnd':
means = np.random(np.min(self.data_train[[attr]].values),
np.max(self.data_train[[attr]].values),
self.n_agents)
agt_data_rows = {i: [] for i in range(self.n_agents)}
for index, row in self.data_train.iterrows():
Pr = to_probability(1 / (abs(row[attr] - means) + 0.000001))
i = np.random.choice(range(self.n_agents), p=Pr)
agt_data_rows[i].append(index)
self.agents_data = \
{i: self.data_train.iloc[agt_data_rows[i], :].reset_index(drop=True)
for i in range(self.n_agents)}
if _debug_:
print('allocated data to agents')
return self.agents_data
def generatePoint(self, i): """ Generates a new point through mutation and crossover. """ # Select 3 distinct indices different from i between 0 and np-1 indices=arange(self.Np) indices=concatenate((indices[:i], indices[i:]), axis=0) indices=permutation(indices) a, b, c = indices[0], indices[1], indices[2] # Get the point (x) x=self.population[i] # Generate mutant (y) y=self.population[a]+self.w*(self.population[b]-self.population[c]) # Place it inside the box self.bound(y) # Generate ndim random numbers from 0..1 uvec=random(self.ndim) # Crossover x and y, use components of y with probability self.pc yind=where(uvec<self.pc)[0] z=x.copy() z[yind]=y[yind] return z
def generate_harmonic_oscillators(self, number_ = None):
if number_ == None:
self.harmonic_oscillators = \
self.x_range*np.random.random(len(self.harmonic_oscillators)) \
- self.x_range/2.
else:
self.harmonic_oscillators = self.x_range*np.random(number_) - self.x_range/2.
def _init_state_value(self, s_name, randomized=True):
if not self._is_state_in_Q(s_name):
self.Q[s_name], self.E[s_name] = {}, {}
for action in range(self.action_space.n):
default_v = random() / 10 if randomized is True else 0.0
self.Q[s_name][action] = default_v
self.E[s_name][action] = 0.0
def next_slice(self):
"""Get a random slice of a file, together with its start position
and ID. Populates self.snd_slice, self.mel_slice, and self.mask"""
picks = np.random(0, self.n_total_samples, self.batch_size)
for vpos, b in enumerate(picks):
file_i = util.greatest_lower_bound(self.voffset, vpos)
last_in = self.n_snd_elem[file_i] - 1
last_out = self.n_samples[file_i] - 1
sam_i = vpos - self.voffset[file_i]
mel_in_b, mel_in_e = rf.get_rfield(self.mel_in, self.dec_out,
sam_i, sam_i, last_out)
dec_in_b, dec_in_e = rf.get_rfield(self.dec_in, self.dec_out,
sam_i, sam_i, last_out)
out_b, out_e = rf.get_ifield(self.ae_wav_in, self.dec_out,
snd_in_b, snd_in_e, last_in)
snd_off = self.snd_offset[file_i]
mel_off = self.mel_offset[file_i]
self.snd_slice[b] = self.snd_data[snd_off + dec_in_b:snd_off +
dec_in_e + 1]
self.mel_slice[b] = self.mel_data[mel_off + mel_in_b:mel_off +
mel_in_e + 1]
self.mask[b].zero_()
self.mask[b, sam_i - out_b] = 1
assert self.mask.size()[1] == out_e - out_b
def setdata(self, A):
"""Note: p, q <= min(n,m)"""
self.data.Brand = 2*(random((A.shape[0],self.data.p))-0.5)
self.data.Crand = 2*(random((A.shape[1],self.data.q))-0.5)
self.data.D = zeros((self.data.q,self.data.p), float)
if self.update:
U, S, Vh = linalg.svd(A)
self.data.B = U[:,-1*self.data.p:]
self.data.C = transpose(Vh)[:,-1*self.data.q:]
else:
# self.data.B = eye(self.data.Brand.shape)
# self.data.C = eye(self.data.Crand.shape)
# USE OF RANDOM
self.data.B = self.data.Brand
self.data.C = self.data.Crand
def isample_without_replacement(self, k):
""" Return a sample of size k, without replacement
k <= n
O(n)
Use a heap to keep track of selection.
"""
if k > len(self.weights):
raise ValueError("Sample size should be <= %d" % len(self.weights))
heap = []
random = self.random.random_sample
weights = random(len(self.weights)) ** (1.0/self.weights)
for ix, weight in enumerate(weights):
if ix < k:
heapq.heappush(heap, (weight, ix))
else:
if heap[0][0] < weight:
heapq.heapreplace(heap, (weight, ix))
# now sort the heap -- this is to make things repeatable
heap.sort()
# return permuted indices
return(self.random.permutation([x[1] for x in heap]))
def isample_without_replacement(self, k):
""" Return a sample of size k, without replacement
k <= n
O(n)
Use a heap to keep track of selection.
"""
if k > len(self.weights):
raise ValueError("Sample size should be <= %d" % len(self.weights))
heap = []
random = self.random.random_sample
weights = random(len(self.weights))**(1.0 / self.weights)
for ix, weight in enumerate(weights):
if ix < k:
heapq.heappush(heap, (weight, ix))
else:
if heap[0][0] < weight:
heapq.heapreplace(heap, (weight, ix))
# now sort the heap -- this is to make things repeatable
heap.sort()
# return permuted indices
return (self.random.permutation([x[1] for x in heap]))
def step(self):
# logpability and loglike for stoch's current value:
logp = sum([stoch.logp for stoch in self.stochs]) + self.indicator.logp
loglike = self.loglike
# Sample a candidate value for the value and indicator of the stoch.
self.propose()
# logpability and loglike for stoch's proposed value:
logp_p = sum([stoch.logp for stoch in self.stochs]) + self.indicator.logp
# Skip the rest if a bad value is proposed
if logp_p == -Inf:
for stoch in self.stochs: stoch.revert()
return
loglike_p = self.loglike
# test:
test_val = logp_p + loglike_p - logp - loglike
test_val += self.inv_q(self.indicator)
test_val += self.q(self.indicator,self._u)
if self.Jacobian is not None:
test_val += self.Jacobian(self.indicator,self._u,**self.stoch_dict)
if log(random()) > test_val:
for stoch in self.stochs:
stoch.revert
def __init__(self, sizes):
self.sizes = sizes
self.n_layers = len(sizes)
self.learningRate = 2 # Note: typically needs to be lower when using 'sigm' activation function and non-normalized inputs.
self.momentum = 0.5
self.scaling_learningRate = 1 # Scaling factor for the learning rate (each epoch)
self.weightPenaltyL2 = 0 # L2 regularization
self.nonSparsityPenalty = 0 # Non sparsity penalty
self.sparsityTarget = 0.05 # Sparsity target
self.dropoutFraction = 0 # Dropout level
self.activation_function = 'tanh_opt' # Activation functions of hidden layers: 'sigm' (sigmoid) or 'tanh' (optimal tanh).
self.output = 'sigm' # output unit 'sigm' (=logistic), 'softmax' and 'linear'
self.testing = False
self.W = [None for _ in range(1, self.n_layers)]
self.vW = [None for _ in range(1, self.n_layers)]
self.p = [None for _ in range(1, self.n_layers)]
self.n_outputs = self.sizes[-1]
for i in range(1, self.n_layers):
# weights and weight momentum
# +1 in shape for bias
self.W[i - 1] = (np.random(self.sizes[i], self.sizes[i - 1]+1) - 0.5) * 2 * 4 * sqrt(6 / (self.sizes[i] + self.sizes[i - 1]))
self.vW[i - 1] = np.zeros_like(self.W[i - 1])
# average activations
self.p[i]= np.zeros(1, self.sizes[i])
def main():
f = Frame()
f.pack(side='top', expand=1)
quit = Button(f, text='Quit', command=sys.exit)
quit.pack(side='top')
o = Opengl(width=400, height=400, double=1)
a = arange(0, n)
vertex = shuffle(cos(2 * pi * a / n), sin(2 * pi * a / n))
vertex.shape = (n, 2)
# vertex1 = shuffle(0.5*cos(2*pi*a/n), 0.5*sin(2*pi*a/n))
# color=ones((n, 3), 'i')
# color[0]=[1,0,0]
# color[1]=[1,1,0]
# color[1]=[1,0,0]
color = random(n * 3)
color.shape = (n, 3)
glVertexPointerd(vertex)
glColorPointerd(color)
glEnableClientState(GL_VERTEX_ARRAY)
glEnableClientState(GL_COLOR_ARRAY)
o.redraw = redraw
o.pack(side='top', expand=1, fill='both')
o.mainloop()
def __init__(self, antenae1=None, antenae2=None):
if antenae1 is None or antenae2 is None:
self.theta1 = 2*pi*random()
self.theta2 = 2*pi*random()
self.l1 = randrange(Antennae._MIN_LENGTH, Antennae._MAX_LENGTH)
self.l2 = randrange(Antennae._MIN_LENGTH, Antennae._MAX_LENGTH)
else:
# TODO: make a little random
self.theta1 = (antenae1.theta1 + antenae2.theta1)/2
self.theta2 = (antenae1.theta2 + antenae2.theta2)/2
self.l1 = (antenae1.l1 + antenae2.l1)/2
self.l2 = (antenae1.l2 + antenae2.l2)/2
print 'Warning: antennae inheritance not implemented'
def hamil_i(numsites, site, J, V, m):
#Params
#numsites - positive integer for the number of sites in spin chain
#site - non-negative integer representing the site operated on
#J,V,h - arbitrary constants that define system potentials
#returns (qutip.Qobj) hamiltonian for fermions jumping from site
#to site oper_i means combined hilbert space operator acting at
#site i, with remaining sites untouched by the total operator
#build ith state operators
sigplus_i = operator_i('sigma plus', numsites, site)
sigminus_i = operator_i('sigma minus', numsites, site)
number_i = operator_i('number', numsites, site)
sigma_zi = operator_i('sigmaz', numsites, site)
sigplus_ip1 = operator_i('sigma plus', numsites, site+1)
sigminus_ip1 = operator_i('sigma minus', numsites, site+1)
number_ip1 = operator_i('number', numsites, site+1)
#crate parts of the hamiltonian
#i.e. H_i = J*(s+_i*s-_1+1 + s-_i*s+_i+1) + V*m_i*m_1+1 + m_i*h_i
rand_dist = 2*m*(random()-0.5)
jump = J*(sigplus_i*sigminus_ip1 + sigminus_i*sigplus_ip1)
interaction_potential = V*(number_i*number_ip1)
site_potential = rand_dist*sigma_zi #write this into operator_i
#add pieces together
H_i = jump + interaction_potential + site_potential
return H_i
def buildArrays( ): a = arange(0,n) vertex = shuffle(cos(2*pi*a/n), sin(2*pi*a/n)) vertex.shape = (n, 2) color = random(n*3) color.shape = (n, 3) return vertex,color
def evaluate(self):
# load raw data
X_data_raw, Y_gender, Y_smile = self.read_data()
score = self.combined.evaluate(
[X_data_raw, np.random(0, 1,
(2723, 100, 1))], [X_data_raw, Y_gender])
print("score", score)
def leave_one_out(dataset, labels, dataset_name):
test_image_idx = np.random(0, 19)
test_indexes = None
if dataset_name == 'utrecht':
start = test_image_idx * constant.N_SLICE_UTRECHT
end = test_image_idx * constant.N_SLICE_UTRECHT + constant.N_SLICE_UTRECHT
test_image_idxes = np.arange(start, end)
elif dataset_name == 'singapore':
start = test_image_idx * constant.N_SLICE_SINGAPORE
end = test_image_idx * constant.N_SLICE_SINGAPORE + constant.N_SLICE_SINGAPORE
test_image_idxes = np.arange(start, end)
elif dataset_name == 'amsterdam':
start = test_image_idx * constant.N_SLICE_AMSTERDAM
end = test_image_idx * constant.N_SLICE_AMSTERDAM + constant.N_SLICE_AMSTERDAM
test_indexes = np.arange(start, end)
else:
print('Dataset name not found for LOO cross validation.')
return None
all_indexes = np.arange(0, len(dataset) - 1)
train_indexes = np.array(set(all_indexes).difference(set(test_indexes)))
train_data, test_data = dataset[train_indexes], dataset[test_indexes]
train_labels, test_labels = labels[train_indexes], labels[test_indexes]
return train_data, test_data, train_labels, test_labels
def sim_mh():
# MH
x0 = random(), random()
x = x0
z = []
M = 100000
c = 0
for i in range(0, M):
accept, x = mh_step(x)
if accept:
c += 1
z.append(x)
print("MH Acceptance rate:", 100 * c / M, "%")
plt.hexbin([x for x, y in z], [y for x, y in z])
def main(): f = Frame() f.pack(side = 'top', expand = 1) quit = Button(f, text = 'Quit', command = sys.exit) quit.pack(side = 'top') o = Opengl(width = 400, height = 400, double = 1) a = arange(0,n) vertex = shuffle(cos(2*pi*a/n), sin(2*pi*a/n)) vertex.shape = (n, 2) # vertex1 = shuffle(0.5*cos(2*pi*a/n), 0.5*sin(2*pi*a/n)) # color=ones((n, 3), 'i') # color[0]=[1,0,0] # color[1]=[1,1,0] # color[1]=[1,0,0] color = random(n*3) color.shape = (n, 3) glVertexPointerd(vertex) glColorPointerd(color) glEnableClientState(GL_VERTEX_ARRAY) glEnableClientState(GL_COLOR_ARRAY) o.redraw = redraw o.pack(side = 'top', expand = 1, fill = 'both') o.mainloop()
def find_in_list(distances, sizes, exposure, within_radius):
"""
Corresponds to the check_and_choose function.
Given a unit, ask which exposure might accept it as a target.
"""
for target_idx in within_radius:
for exp in exposure:
difference=abs(distances[target_idx]-
exp.exposure_distance)
if exp.target_idx is None:
exp.target_idx=target_idx
exp.target_distance=distances[target_idx]
exp.difference=difference
exp.cumulative_size+=sizes[target_idx]
elif abs(difference-exp.difference)<scenario.epsilon:
chance=np.random()< scenario.size[target_idx]/exp.cumulative_size
allowed=zoned[target_idx] is False and quarantined[target_idx] is False
if allowed and chance:
exp.target_idx=target_idx
exp.target_distance=distances[target_idx]
exp.difference=difference
exp.cumulative_size+=sizes[target_idx]
elif difference < exp.difference:
exp.target_idx=target_idx
exp.target_distance=distances[target_idx]
exp.difference=difference
exp.cumulative_size+=sizes[target_idx]
else:
pass
def layerModes():
N = mypaintlib.TILE_SIZE
dst = np.zeros((N, N, 4), 'uint16') # rgbu
dst_values = []
r1 = range(0, 20)
r2 = range((1 << 15)/2-10, (1 << 15)/2+10)
r3 = range((1 << 15)-19, (1 << 15)+1)
dst_values = r1 + r2 + r3
src = np.zeros((N, N, 4), 'int64')
alphas = np.hstack((
np.arange(N/4), # low alpha
(1 << 15)/2 - np.arange(N/4), # 50% alpha
(1 << 15) - np.arange(N/4), # high alpha
np.randint((1 << 15)+1, size=N/4), # random alpha
))
#plot(alphas); show()
src[:, :, 3] = alphas.reshape(N, 1) # alpha changes along y axis
src[:, :, 0] = alphas # red
src[:, N*0/4:N*1/4, 0] = np.arange(N/4) # dark colors
src[:, N*1/4:N*2/4, 0] = alphas[N*1/4:N*2/4]/2 + np.arange(N/4) - N/2 # 50% lightness
src[:, N*2/4:N*3/4, 0] = alphas[N*2/4:N*3/4] - np.arange(N/4) # bright colors
src[:, N*3/4:N*4/4, 0] = alphas[N*3/4:N*4/4] * np.random(N/4) # random colors
# clip away colors that are not possible due to low alpha
src[:, :, 0] = np.minimum(src[:, :, 0], src[:, :, 3]).clip(0, 1 << 15)
src = src.astype('uint16')
#figure(1)
#imshow(src[:,:,3], interpolation='nearest')
#colorbar()
#figure(2)
#imshow(src[:,:,0], interpolation='nearest')
#colorbar()
#show()
src[:, :, 1] = src[:, :, 0] # green
src[:, :, 2] = src[:, :, 0] # blue
for name in dir(mypaintlib):
if not name.startswith('tile_composite_'):
continue
junk1, junk2, mode = name.split('_', 2)
print('testing', name, 'for invalid output')
f = getattr(mypaintlib, name)
for dst_value in dst_values:
for alpha in [1.0, 0.999, 0.99, 0.90, 0.51, 0.50, 0.49, 0.01, 0.001, 0.0]:
dst[:] = dst_value
dst_has_alpha = False
src_opacity = alpha
f(src, dst, dst_has_alpha, src_opacity)
#imshow(dst[:,:,0], interpolation='nearest')
#gray()
#colorbar()
#show()
errors = dst > (1 << 15)
assert not errors.any()
print('passed')
def mh_step(x, t=0):
y = mutate(x)
f1 = f(y, t)
f2 = f(x, t)
a = min(1, 0 if f1 == 0 else 1 if f2 == 0 else f1 / f2)
if random() < a:
return True, y
return False, x
def random_graph(self):
self.clear_graph()
for x in xrange(self.N):
v = self.graph.add_vertex()
for x in xrange(self.N):
for y in xrange(x):
if (random() < self.p and x is not y):
self.graph.add_edge(self.graph.vertex(x), self.graph.vertex(y))
def countsToSamples( counts ) :
values=[]
bin=-180
for value in counts:
for i in arange(value) :
values.append(bin+random()*step)
bin += step
return values
def solve(self):
new_X = np.random()
loss_history = []
loss_history.append(new_X)
for i in xrange(num_iterations):
x = new_X - 2 * self.t * np.dot(self.A.T, np.dot(self.A, new_X) - self.b)
new_X = LinearInverseSolver.t_operator(self.eta * self.t, x)
loss_history.append(new_X)
return loss_history
def _resample(self):
indices = []
C = [0.0] + [sum(self.w[: i + 1]) for i in range(self.num_particles)]
u0, j = random(), 0
for u in [(u0 + i) / self.num_particles for i in range(self.num_particles)]:
while u > C[j]:
j += 1
indices.append(j - 1)
self.particles = self.particles[indices, :]
def resample(self):
cumulative_sum = np.cumsum(self.weights)
cumulative_sum[-1] = 1. # avoid round-off error
indexes = np.searchsorted(cumulative_sum, random(self.N))
# resample according to indexes
self.particles = self.particles[indexes]
self.weights = self.weights[indexes]
self.weights /= np.sum(self.weights) # normalize
def run(filename=None, directory=None, revanConfigFile=None, seed=None):
if filename == None and directory == None:
print "*** No filename or directory provide ***"
print "Please provide a filename, a list of filenames, or a directory name"
return
# Check to see if the user supplied a directory. If so, get the list of source files
if directory != None:
sourcefiles = glob.glob(directory + '/*.source')
# Check if the user supplied a single file vs a list of files
if isinstance(filename, list) == False and filename != None:
sourcefiles = [filename]
# Get the revan config file if one was not provided
revanConfigFile = glob.glob(directory + '/*.cfg')[0]
# Generate a list of seeds
seeds = int(numpy.random(len(sourcefiles))*100)
# Loop through each of the source files and run them through cosima and revan, and analyze their output with EventAnalysis
for sourcefile, seed in zip(sourcefiles, seeds):
# Generate the cosima command
command_cosima = "cosima -s %s %s" % (seed, sourcefile)
# Issued the cosima command
print command_cosima
output = os.system(command_cosima)
# Generate the sim filename
simfile = sourcefile.replace('.source','.sim')
# Generate the revan command
command_revan = "revan -f %s -c %s" % (simfile, revanConfigFile)
# Issued the revan command
print command_revan
output = os.system(command_revan)
# Extract the number of triggered and simulated events
EventAnalysis.getTriggerEfficiency(filename=simfile)
# Generate the .tra filename
trafile = simfile.replace('.sim', '.tra')
# Analyze the results of the .tra file
# EventAnalysis.performCompleteAnalysis(filename=trafile)
return
def resample(weights):
n = len(weights)
indices = []
C = [0.] + [sum(weights[:i+1]) for i in range(n)]
u0, j = random(), 0
for u in [(u0+i)/n for i in range(n)]:
while u > C[j]:
j+=1
indices.append(j-1)
return indices
def r_smpl(w):
num = len(w)
index = []
count = [0.] + [sum(w[:i+1]) for i in range(num)]
e0, k = random(), 0
for e in [(e0+i)/num for i in range(num)]:
while e > count[k]:
k+=1
index.append(k-1)
return index
def resample(weights):
n = len(weights)
indices = []
P = [0.] + [sum(weights[:i+1]) for i in range(n)] # accumulerade summan equlient to discrete integration (really bad complexity, bootstrap please)
u0, j = random(), 0
for u in [(u0+i)/n for i in range(n)]:
while u > P[j]: #find index of first P[j] greater then u
j+=1
indices.append(j-1)
return indices
