def MSE(sampleSize):
totalSE = 0.0
for i in range(sampleSize):
in1 = random() * 6.0
in2 = random() * 6.0
error = targetFunction(in1, in2) - f(in1, in2)
totalSE = totalSE + error * error
def initialize(self):
self.topic_prob = np.zeros(
[self.no_of_docs, self.vocabulary_size, self.no_of_topics],
dtype=np.float)
self.document_topic_prob = random((self.no_of_docs, self.no_of_topics))
# self.document_topic_prob = normalize(self.document_topic_prob)
self.topic_word_prob = random(
(self.no_of_topics, self.vocabulary_size))
def MSE(sampleSize):
totalSE = 0.0
for i in range(sampleSize):
x = random() * 6.0
y = random() * 6.0
error = targetFunction(x, y) - f(x, y)
totalSE = totalSE + error * error
print 'The estimated MSE: ', (totalSE / sampleSize)
def MSE(sampleSize):
totalSE = 0.0
for i in range(sampleSize):
in1 = random() * 6.0
in2 = random() * 6.0
error = targetFunction(in1,in2) - f(in1,in2)
totalSE = totalSE + error * error
print('The estimated MSE: ', (totalSE / sampleSize))
def MSE(sampleSize):
totalSE = 0.0
for i in range(sampleSize):
x = random() * 6.0
y = random() * 6.0
error = targetFunction(x,y) - f(x,y)
totalSE = totalSE + error * error
print 'The estimated MSE: ', (totalSE / sampleSize)
def MSE(sampleSize):
totalSE = 0.0
for i in range(sampleSize):
in1 = random() * 6.0
in2 = random() * 6.0
error = targetFunction(in1, in2) - f(in1, in2)
totalSE = totalSE + error * error
print('The estimated MSE: ', (totalSE / sampleSize))
def __init__(self, corpus, stopWords):
self._corpus = corpus
self._stopWords = stopWords
self._K = 10 # number of topic
self._maxIteration = 20
self._threshold = 10.0
self._topicWordsNum = 10
self._doc_topic = '/Users/ruslantagirov/Desktop/Univer/3course/data-repo/LabWorks/labs/LW3/results/' \
'doc-topic.txt'
self._topic_word = '/Users/ruslantagirov/Desktop/Univer/3course/data-repo/LabWorks/labs/LW3/results' \
'/topic-word.txt'
self._dic = '/Users/ruslantagirov/Desktop/Univer/3course/data-repo/LabWorks/labs/LW3/results/dic.dic'
self._topics = '/Users/ruslantagirov/Desktop/Univer/3course/data-repo/LabWorks/labs/LW3/results/topics.txt'
self._N = len(corpus.getDocuments())
self._wordCounts = []
self._word2id = {}
self._id2word = {}
self._currentId = 0
for document in corpus.getDocuments():
normalized_list = Preprocessing.toNormalForm(Preprocessing
.documentToList(document))
self._segList = Preprocessing.removeStopWords(self._stopWords.getStopWords(),
normalized_list)
self._wordCount = {}
for word in self._segList:
word = word.lower().strip()
if len(word) > 1 and not re.search('[0-9]', word) and word not in self._stopWords.getStopWords():
if word not in self._word2id.keys():
self._word2id[word] = self._currentId
self._id2word[self._currentId] = word
self._currentId += 1
if word in self._wordCount:
self._wordCount[word] += 1
else:
self._wordCount[word] = 1
self._wordCounts.append(self._wordCount)
# length of dic
self._M = len(self._word2id)
# generate the document-word matrix
self._X = zeros([self._N, self._M], int8)
for word in self._word2id.keys():
j = self._word2id[word]
for i in range(0, self._N):
if word in self._wordCounts[i]:
self._X[i, j] = self._wordCounts[i][word]
# lambda: p(zj|di)
self._lambda = random([self._N, self._K])
# theta: p(wj|zi)
self._theta = random([self._K, self._M])
# p: p(zk|di,wj)
self._p = zeros([self._N, self._M, self._K])
def update():
global g
a = rd.choice(list(g.nodes()))
if g.node[a]['state'] == 0:
b = rd.choice(list(g.neighbors(a)))
if g.node[b]['state'] == 1:
g.node[a]['state'] = 1 if pylab.random() < p_i else 0
else:
g.node[a]['state'] = 0 if pylab.random() < p_r else 1
def random_rot_angles(x=True, y=True, z=True):
rotation = {}
if x:
rotation['x'] = pl.random() * 2 * pl.pi
if y:
rotation['y'] = pl.random() * 2 * pl.pi
if z:
rotation['z'] = pl.random() * 2 * pl.pi
return rotation
def test_com_jacobian(dq_norm=1e-3, q=None):
if q is None:
q = hrp.dof_llim + random(56) * (hrp.dof_ulim - hrp.dof_llim)
dq = random(56) * dq_norm
com = hrp.compute_com(q)
J_com = hrp.compute_com_jacobian(q)
expected = com + dot(J_com, dq)
actual = hrp.compute_com(q + dq)
assert norm(actual - expected) < 2 * dq_norm ** 2
return J_com
def init():
global agents
agents = []
for i in range(n):
ag = agent()
ag.x = pylab.random()
ag.y = pylab.random()
ag.color = 1 if pylab.random() < 0.5 else 0
agents.append(ag)
print(len(agents))
def __init__(self, Fs=16000, TinSec=10):
'''
Fs: 取樣頻率，預設值為 16000，
TinSec: 保存語音長度，預設值為 10 sec
'''
print('RyAudio use %s' % pa.get_portaudio_version_text())
self.Fs = Fs
self.spBufferSize = 1024
self.fftWindowSize = self.spBufferSize
self.aP = pa.PyAudio()
self.iS = pa.Stream(PA_manager=self.aP,
input=True,
rate=self.Fs,
channels=1,
format=pa.paInt16)
self.oS = pa.Stream(PA_manager=self.aP,
output=True,
rate=self.Fs,
channels=1,
format=pa.paInt16)
self.iTh = None
self.oTh = None
#self.sound= None
#self.soundTime= 0
self.gettingSound = True
self.playingSound = True
self.t = 0
self.b = None # byte string
self.x = None # ndarray
self.fft = None
self.f0 = 0 #None
self.en = 0 #None
self.fm = 0 #None # frequency mean
self.fv = 0 #None # frequency var
self.fs = 0 #None # frequency std
self.enP = 0 #None # AllPass
self.enPL = 0 #None # LowPass
self.enPH = 0 #None # HighPass
self.entropy = 0 #None
self.frameI = 0
#self.frameN= self.spBufferSize/4 #1024/4 = 256
self.TinSec = TinSec #10 # sec
self.frameN = self.Fs * self.TinSec / self.spBufferSize #self.spBufferSize/4 #1024/4 = 256
self.frameN = int(self.frameN)
self.specgram = pl.random([self.frameN, self.spBufferSize / 2])
self.xBuf = pl.random([self.frameN, self.spBufferSize])
def main():
parser = ArgumentParser()
parser.add_argument('-e', help = " if specified, use the dictionary you made to classify the document", action="store_true", default = False)
parser.add_argument('-b', help = " best-result", action="store_true", default = False)
parser.add_argument('-d', help = " The doc.csv", type = str)
parser.add_argument('-g', help = " The group.csv", type = str)
parser.add_argument('-o', help = " output path : *.csv", type = str)
args = parser.parse_args()
global N, M, X, K, lamda, theta, maxIteration, p, WordsInGroup, Vocab_List, Save_dir, G
# Read_Doc(args.d)
N, M, X , Vocab_List= Read_Doc(args.d)
print('M = ',M)
K = 50 # number of topic
maxIteration = 100 # iter
threshold = 10
# lamda[i, j] : p(zj|di)
lamda = random([N, K])
# theta[i, j] : p(wj|zi)
theta = random([K, M])
# p[i, j, k] : p(zk|di,wj)
p = zeros([N, M, K])
lamda, theta = Initial(lamda, theta)
# EM algo
oldLoglikelihood = 1
newLoglikelihood = 1
print('===== EM Algorithm Start =====\n')
for i in range(0, maxIteration):
p = E_Step(theta, lamda, p)
theta, lamda = M_Step(theta, lamda, p, X)
newLoglikelihood = LogLikelihood(theta, lamda, X)
print("[", time.strftime('%Y-%m-%d %H:%M:%S',time.localtime(time.time())), "] ", i+1, " iteration ", str(newLoglikelihood))
# if(oldLoglikelihood != 1 and newLoglikelihood - oldLoglikelihood < threshold):
# break
oldLoglikelihood = newLoglikelihood
print('\n===== EM Algorithm end =====')
WordsInGroup ,G = Group(args.g, args.e)
Save_dir = 'K_'+str(K)+'Iter_'+str(maxIteration)+'Thre_'+str(threshold)
# OutPut() # save two matrix
# word_count_classifer(args.o)
plsa_classifer(args.o)
print("\n[", time.strftime('%Y-%m-%d %H:%M:%S',time.localtime(time.time())), "] OutPut Done!!! " )
def update():
global g
i = rd.choice(list(g.nodes()))
if g.node[i]['state'] == 0:
for j in list(g.neighbors(i)):
if g.node[j]['state'] == 1:
if pylab.random() < p_s:
g.remove_edge(i, j)
elif pylab.random() < p_i:
g.node[i]['state'] = 1
else:
if pylab.random() < p_r:
g.node[i]['state'] = 0
def check_on_random_instance():
"""
Check our criterion with an LP solver on a random instance of the problem.
Returns the random point, the criterion's outcome on this point (true or
false) and whether an LP solution was found (positive or negative). If the
criterion is correct, true == positive and false == negative.
"""
K1, K2, K3, C1, C2 = 2 * pylab.random(5) - 1
px, py = X / (X + Y), Y / (X + Y)
D4max = .5 * min(2, 1 + C1, 1 + C2, 2 + C1 + C2)
D4min = .5 * max(-1 + C1, C1 + C2, -1 + C2, 0)
D4 = D4min + (D4max - D4min) * pylab.random()
D1, D2, D3 = .5 * (1 + C1) - D4, -.5 * (C1 + C2) + D4, .5 * (1 + C2) - D4
c = cvxopt.matrix(pylab.array([[1.]] * 8)) # score vector
G = cvxopt.matrix(pylab.array([
[+1, 0., 0., 0., 0., 0., 0., 0.],
[-1, 0., 0., 0., 0., 0., 0., 0.],
[0., +1, 0., 0., 0., 0., 0., 0.],
[0., -1, 0., 0., 0., 0., 0., 0.],
[0., 0., +1, 0., 0., 0., 0., 0.],
[0., 0., -1, 0., 0., 0., 0., 0.],
[0., 0., 0., +1, 0., 0., 0., 0.],
[0., 0., 0., -1, 0., 0., 0., 0.],
[0., 0., 0., 0., +1, 0., 0., 0.],
[0., 0., 0., 0., -1, 0., 0., 0.],
[0., 0., 0., 0., 0., +1, 0., 0.],
[0., 0., 0., 0., 0., -1, 0., 0.],
[0., 0., 0., 0., 0., 0., +1, 0.],
[0., 0., 0., 0., 0., 0., -1, 0.],
[0., 0., 0., 0., 0., 0., 0., +1],
[0., 0., 0., 0., 0., 0., 0., -1]]))
h = cvxopt.matrix(pylab.array([[1.]] * 16)) # h - G x >= 0
A = cvxopt.matrix(pylab.array([
[D1, D2, D3, D4, 0, 0, 0, 0],
[0, 0, 0, 0, D1, D2, D3, D4],
[-py * D1, +py * D2, +py * D3, -py * D4,
+px * D1, +px * D2, -px * D3, -px * D4]]))
b = cvxopt.matrix(pylab.array([K1, K2, K3]))
sol = cvxopt.solvers.lp(c, G, h, A, b)
K3min = -1 + py * abs(K1 - C1) + px * abs(K2 - C2)
K3max = 1 - py * abs(K1 + C1) - px * abs(K2 + C2)
is_true = K3min <= K3 <= K3max
is_positive = sol['x'] is not None
return is_true, is_positive, (K1, K2, K3, C1, C2)
def scatter_2():
count = 5
for x in range(count):
plb.cla()
array = plb.random((80, 120))
plb.imshow(array, cmap=plb.cm.gist_rainbow)
plb.pause(1)
def main(): shifts = [ [-1, 1], [0, 1], [1, 1], [-1, 0], [1, 0], [-1, -1], [0, -1], [1, -1] ] num_atoms = 100 num_dims = 2 # dimensions coords = pl.random((num_atoms, num_dims)) chosen = pl.random_integers(num_atoms) # from 1 to num_atoms chosen -= 1 # from 0 to num_atoms - 1 for i in range(len(shifts)): coords = pl.vstack((coords, coords[:num_atoms] + shifts[i])) num_atoms *= 9 # after 8 shifts added max_distance = 0.9 for i in range(num_atoms): if i != chosen: dx = coords[chosen, 0] - coords[i, 0] dy = coords[chosen, 1] - coords[i, 1] distance = pl.sqrt(dx*dx + dy*dy) if distance < max_distance: pl.plot([coords[i, 0]], [coords[i, 1]], "bo") else: pl.plot([coords[i, 0]], [coords[i, 1]], "ko") # plot last for visibility pl.plot([coords[chosen, 0]], [coords[chosen, 1]], "ro") pl.grid(True) pl.show()
def main():
num_atoms = 64
num_dims = 2 # dimensions
coords = pl.random((num_atoms, num_dims))
axis_limits = [0.0, 1.0]
points = plot_atoms(coords, num_atoms, axis_limits)
update_limit = 16
update_count = 0
while True:
chosen = pl.random_integers(num_atoms) - 1 # [0, num_atoms - 1]
new_x, new_y = new_xy(coords, chosen, axis_limits)
energy_old, energy_new = energies(coords, chosen, num_atoms, new_x,
new_y)
if energy_new < energy_old:
coords[chosen, 0] = new_x
coords[chosen, 1] = new_y
points[chosen].set_data([new_x, new_y])
update_count += 1
if not update_count < update_limit:
pl.draw()
update_count = 0
"""
def __init__(self, config=None):
super().__init__()
assert isinstance(config, Config)
"""
Parameters in config:
Name: Type: Default: Description: (Omitted when self-explanatory)
num_tilings int 32 Number of tilings
tiling_side_length int 8 The length of the tiling side
num_actions int 3 Number of actions
num_dims int 2 Number of dimensions
alpha float 0.1 Learning rate
state_space_range np.array [1,1] The range of the state space
"""
self.num_tilings = check_attribute_else_default(config, 'num_tilings', 32)
self.tiling_side_length = check_attribute_else_default(config, 'tiling_side_length', 8)
self.num_actions = check_attribute_else_default(config, 'num_actions', 3)
self.num_dims = check_attribute_else_default(config, 'num_dims', 2)
self.alpha = check_attribute_else_default(config, 'alpha', 0.1)
self.state_space_range = check_attribute_else_default(config, 'state_space_range', np.ones(self.num_dims))
self.scale_factor = self.tiling_side_length * (1 / self.state_space_range)
self.tiles_per_tiling = self.tiling_side_length ** self.num_dims
self.num_tiles = (self.num_tilings * self.tiles_per_tiling)
self.theta = 0.001 * random(self.num_tiles * self.num_actions)
self.iht = IHT(self.num_tiles)
def reset(self):
# random() returns a random float in the half open interval [0,1)
position = -0.6 + random() * 0.2
velocity = 0.0
self.current_state = np.array((position, velocity), dtype=np.float32)
self.step_count = 0
return self.current_state
def get_reading (self):
reading = []
t = self.target
for s in self.sensors:
r = sqrt ((t[0] - s[0])**2 + (t[1] - s[1])**2) + (random () - 0.5)
reading.append ([s[0], s[1], r])
return reading
def get_reading(self):
reading = []
t = self.target
for s in self.sensors:
r = sqrt((t[0] - s[0])**2 + (t[1] - s[1])**2) + (random() - 0.5)
reading.append([s[0], s[1], r])
return reading
def main(): num_atoms = 64 num_dims = 2 # dimensions coords = pl.random((num_atoms, num_dims)) axis_limits = [0.0, 1.0] points = plot_atoms(coords, num_atoms, axis_limits) update_limit = 16 update_count = 0 while True: chosen = pl.random_integers(num_atoms) - 1 # [0, num_atoms - 1] new_x, new_y = new_xy(coords, chosen, axis_limits) energy_old, energy_new = energies(coords, chosen, num_atoms, new_x, new_y) if energy_new < energy_old: coords[chosen, 0] = new_x coords[chosen, 1] = new_y points[chosen].set_data([new_x, new_y]) update_count += 1 if not update_count < update_limit: pl.draw() update_count = 0 """
def init_lamda(self):
lamda = random([self.N, self.K])
for i in range(0, self.N):
normalization = sum(lamda[i, :])
for j in range(0, self.K):
lamda[i, j] /= normalization
return lamda
def beeswarm(self, data, position, ratio=2.):
r"""Naive plotting of the data points
We assume gaussian distribution so we expect fewers dots
far from the mean/median. We'd like those dots to be close to the
axes. conversely, we expect lots of dots centered around the mean, in
which case, we'd like them to be spread in the box. We uniformly
distribute position using
.. math::
X = X + \dfrac{ U()-0.5 }{ratio} \times factor
but the factor is based on an arctan function:
.. math::
factor = 1 - \arctan( \dfrac{X - \mu }{\pi/2})
The farther the data is from the mean :math:`\mu`,
the closest it is to the axes that goes through the box.
"""
N = len(data)
m = np.median(data)
sd = np.std(data)
# arctan function to have a tapering window
factor = 1. - np.abs(np.arctan((data-m)/sd)/1.570796) # pi/2
newdata = position + (pylab.random(N) - 0.5)/float(ratio) * factor
return newdata
def beeswarm(self, data, position, ratio=2.):
r"""Naive plotting of the data points
We assume gaussian distribution so we expect fewers dots
far from the mean/median. We'd like those dots to be close to the
axes. conversely, we expect lots of dots centered around the mean, in
which case, we'd like them to be spread in the box. We uniformly
distribute position using
.. math::
X = X + \dfrac{ U()-0.5 }{ratio} \times factor
but the factor is based on an arctan function:
.. math::
factor = 1 - \arctan( \dfrac{X - \mu }{\pi/2})
The farther the data is from the mean :math:`\mu`,
the closest it is to the axes that goes through the box.
"""
N = len(data)
m = np.median(data)
sd = np.std(data)
# arctan function to have a tapering window
factor = 1. - np.abs(np.arctan((data - m) / sd) / 1.570796) # pi/2
newdata = position + (pylab.random(N) - 0.5) / float(ratio) * factor
return newdata
def update():
global agents
ag = agents[pylab.randint(n)]
neighbourhood = [
nb for nb in agents
if (nb.x - ag.x)**2 + (nb.y - ag.y)**2 < r**2 and nb != ag
]
num_similar = 0
for j in neighbourhood:
if j.color == ag.color:
num_similar += 1
if len(neighbourhood) > 0:
ratio = num_similar / float(len(neighbourhood))
if ratio < th:
ag.x = pylab.random()
ag.y = pylab.random()
def init():
global config, nextconfig
config = pylab.zeros([n, n])
for x in range(n):
for y in range(n):
config[x, y] = 1 if pylab.random() < p else 0
nextconfig = pylab.zeros([n, n])
def init():
global g, nextg
g = nx.karate_club_graph()
g.pos = nx.spring_layout(g)
for i in g.nodes():
g.node[i]['state'] = 1 if pylab.random() < 0.5 else 0
nextg = g.copy()
def init_theta(self):
theta = random([self.K, self.M])
for i in range(0, self.K):
normalization = sum(theta[i, :])
for j in range(0, self.M):
theta[i, j] /= normalization
return theta
def main():
shifts = [[-1, 1], [0, 1], [1, 1], [-1, 0], [1, 0], [-1, -1], [0, -1],
[1, -1]]
num_atoms = 100
num_dims = 2 # dimensions
coords = pl.random((num_atoms, num_dims))
chosen = pl.random_integers(num_atoms) # from 1 to num_atoms
chosen -= 1 # from 0 to num_atoms - 1
for i in range(len(shifts)):
coords = pl.vstack((coords, coords[:num_atoms] + shifts[i]))
num_atoms *= 9 # after 8 shifts added
max_distance = 0.9
for i in range(num_atoms):
if i != chosen:
dx = coords[chosen, 0] - coords[i, 0]
dy = coords[chosen, 1] - coords[i, 1]
distance = pl.sqrt(dx * dx + dy * dy)
if distance < max_distance:
pl.plot([coords[i, 0]], [coords[i, 1]], "bo")
else:
pl.plot([coords[i, 0]], [coords[i, 1]], "ko")
# plot last for visibility
pl.plot([coords[chosen, 0]], [coords[chosen, 1]], "ro")
pl.grid(True)
pl.show()
def __init__(self, Fs= 16000, TinSec= 10):
'''
Fs: 取樣頻率，預設值為 16000，
TinSec: 保存語音長度，預設值為 10 sec
'''
print('RyAudio use %s'%pa.get_portaudio_version_text())
self.Fs= Fs
self.spBufferSize= 1024
self.fftWindowSize= self.spBufferSize
self.aP= pa.PyAudio()
self.iS= pa.Stream(PA_manager= self.aP, input= True, rate= self.Fs, channels= 1, format= pa.paInt16)
self.oS= pa.Stream(PA_manager= self.aP, output= True, rate= self.Fs, channels= 1, format= pa.paInt16)
self.iTh= None
self.oTh= None
#self.sound= None
#self.soundTime= 0
self.gettingSound= True
self.playingSound= True
self.t= 0
self.b= None # byte string
self.x= None # ndarray
self.fft= None
self.f0= 0#None
self.en= 0#None
self.fm= 0#None # frequency mean
self.fv= 0#None # frequency var
self.fs= 0#None # frequency std
self.enP= 0#None # AllPass
self.enPL= 0#None # LowPass
self.enPH= 0#None # HighPass
self.entropy= 0#None
self.frameI= 0
#self.frameN= self.spBufferSize/4 #1024/4 = 256
self.TinSec= TinSec #10 # sec
self.frameN= self.Fs*self.TinSec/self.spBufferSize #self.spBufferSize/4 #1024/4 = 256
self.frameN= int(self.frameN)
self.specgram= pl.random([self.frameN, self.spBufferSize/2])
self.xBuf= pl.random([self.frameN, self.spBufferSize])
def initialize():
global config, nextconfig, density
density = []
config = pl.zeros([n, n])
for x in range(n):
for y in range(n):
config[x, y] = 1 if pl.random() < p else 0
nextconfig = pl.zeros([n, n])
def mc_counts2samples(self, counts):
values = []
bin = -180
for value in counts:
for i in arange(value):
values.append(bin + random() * self.step)
bin += self.step
return array(values)
def mc_counts2samples( self, counts ) :
values=[]
bin=-180
for value in counts:
for i in arange(value) :
values.append(bin+random()*self.step)
bin += self.step
return array(values)
def __init__(self, numTilings=8, numActions=3):
self.actions = numActions
self.numTilings = numTilings
self.alpha_factor = 1 / self.numTilings
self.numTiles = (self.numTilings**3) * 4
self.iht = IHT(self.numTiles)
self.theta = 0.001 * random(self.numTiles * self.actions)
super().__init__()
def next(self):
Tnext = ((self.Konstant * self.t1) * 2) - self.t0
if len(self.values) % 100 > 70:
self.values.append(pylab.random() * 2 - 1)
else:
self.values.append(Tnext)
self.t0 = self.t1
self.t1 = Tnext
return self.values[-1]
def markov_trajectory(self,distribution,state=None):
if state == None :
state = self.start_point(distribution)
trj = []
for i in range(self.frames):
state = self.markov_step(state,distribution)
angle = self.mod2pi((state+random())*self.step-180)
trj.append(angle)
return array(trj)
def markov_trajectory(self, distribution, state=None):
if state == None:
state = self.start_point(distribution)
trj = []
for i in range(self.frames):
state = self.markov_step(state, distribution)
angle = self.mod2pi((state + random()) * self.step - 180)
trj.append(angle)
return array(trj)
def sqr_cplx(z):
"""
Fonction racine d'un complexe. Prend aléatoirement la racine
positive ou négative
"""
r, theta = cart2pol(z)
r = pl.sqrt(r)
theta = theta/2 + int(2*pl.random())*pl.pi
return pol2cart(r, theta)
def initialize(self, N, K, M, word2id, id2word, X):
self.word2id, self.id2word, self.X = word2id, id2word, X
self.N, self.K, self.M = N, K, M
# theta[i, j] : p(zj|di): 2-D matrix
self.theta = random([N, K])
# beta[i, j] : p(wj|zi): 2-D matrix
self.beta = random([K, M])
# p[i, j, k] : p(zk|di,wj): 3-D tensor
self.p = zeros([N, M, K])
for i in range(0, N):
normalization = sum(self.theta[i, :])
for j in range(0, K):
self.theta[i, j] /= normalization
for i in range(0, K):
normalization = sum(self.beta[i, :])
for j in range(0, M):
self.beta[i, j] /= normalization
def random_euler_angles():
r1,r2,r3 = pylab.random(3)
q1 = pylab.sqrt(1.0-r1)*pylab.sin(2.0*pylab.pi*r2)
q2 = pylab.sqrt(1.0-r1)*pylab.cos(2.0*pylab.pi*r2)
q3 = pylab.sqrt(r1)*pylab.sin(2.0*pylab.pi*r3)
q4 = pylab.sqrt(r1)*pylab.cos(2.0*pylab.pi*r3)
phi = math.atan2(2.0*(q1*q2+q3*q4), 1.0-2.0*(q2**2+q3**2))
theta = math.asin(2.0*(q1*q3-q4*q2))
psi = math.atan2(2.0*(q1*q4+q2*q3), 1.0-2.0*(q3**2+q4**2))
return [phi,theta,psi]
def update():
global g
chosenedge = rd.choice(list(g.edges()))
if (pylab.random() < 0.5):
listener = chosenedge[0]
speaker = chosenedge[1]
else:
listener = chosenedge[1]
speaker = chosenedge[0]
g.node[listener]['state'] = g.node[speaker]['state']
def initialize(self):
self.state = pylab.zeros([self.n, self.n])
for x in xrange(self.n):
for y in xrange(self.n):
self.state[x, y] = 1 if pylab.random() < self.init_p else 0
self.state[self.n/2, self.n/2] = 2
self.next_state = pylab.zeros([self.n, self.n])
for x in xrange(self.n):
for y in xrange(self.n):
if self.state[x, y] == 1 or self.state[x, y] == 2:
self.total_num_trees += 1
def GenerateRandomTrajectory(ncurve, ndof, bound):
def vector2string(v):
ndof = len(v)
s = str(ndof)
for a in v:
s += ' %f' % a
return s
p0a = vector2string(random(ndof) * 2 * bound - bound)
p0b = vector2string(random(ndof) * 2 * bound - bound)
p1a = vector2string(random(ndof) * 2 * bound - bound)
p1b = vector2string(random(ndof) * 2 * bound - bound)
s = '%d' % ncurve
s += '\n1.0 ' + p0a + ' ' + p0b
for k in range(ncurve - 1):
a = random(ndof) * 2 * bound - bound
b = random(ndof) * 2 * bound - bound
c = 2 * b - a
pa = vector2string(a)
pb = vector2string(b)
pc = vector2string(c)
s += ' ' + pa + ' ' + pb + '\n1.0 ' + pb + ' ' + pc
s += ' ' + p1a + ' ' + p1b
Tv, p0v, p1v, p2v, p3v = string2p(s)
return BezierToTrajectoryString(Tv, p0v, p1v, p2v, p3v)
def __init__(self,n=100,state=0.5,J=1.,T=2.,):
"""Constructor..."""
self.n = n
self.spins = -1 * pl.ones((n,n))
self.J = J
self.T=T
self.init = state
self.config = "n=%d,init=%f,J=%f,T=%f" % (self.n,self.init,self.J,self.T)
for i in xrange(n):
for j in xrange(n):
if pl.random() < (1 + state) / 2.:
self.spins[i,j] = 1
def packing(dataset, radius=4, nifti=False, randoffset=False):
"""return a hexagonal close sphere packing grid for a PyMVPA fMRI dataset
Keyword arguments:
radius-- radius in voxels of the spheres to pack (default 4)
nifti-- write out a seed voxel mask as a nifti
randomoffset-- random jitter of the seed voxel grid
"""
from pylab import find, random
from numpy import ones, zeros, arange, sqrt, remainder
from mvpa2.suite import fmri_dataset, Dataset
import os
if randoffset:
ro = random(3)
else:
ro = zeros(3)
minco = dataset.fa.voxel_indices.min(0)
maxco = dataset.fa.voxel_indices.max(0)
rect = ones(dataset.a.voxel_dim)
fac = sqrt(6)*2*radius/3
for iz,z in enumerate(arange(minco[2], maxco[2], fac)):
for iy,y in enumerate(arange(minco[1], maxco[1], fac)):
for x in arange(minco[0], maxco[0], 2*radius):
hx = x + remainder(iy, 2)*radius + ro[0]*radius
hy = y + remainder(iz, 2)*fac + ro[1]*radius
hz = z + ro[2]*radius
if hz <= maxco[2]:
rect [hx, hy, hz] += 1
maskedrect = dataset.mapper.forward1(rect)
roiIndex = find((maskedrect == 2))
print 'number of seed voxel: '+str(len(roiIndex))
maskedrectds = Dataset([maskedrect])
maskedrectds.a = dataset.a.copy()
maskedrectds.fa = dataset.fa.copy()
if nifti:
from nibabel import Nifti1Image
Nifti1Image(maskedrectds.O.squeeze(),
dataset.a.imghdr.get_best_affine()
).to_filename(os.path.join('sparse'+str(int(radius))+'.nii.gz'))
return roiIndex, maskedrectds
def generate_waveforms(
N_harmonics=[8,16,32,64],
path='/home/ritz/mix/audio samples instruments/basic-waveforms/',
name='square_rnd_phase-%03dh-G2-(i).wav'):
'''Generate a series of basic additive waveforms with a varying number of harmonics.'''
f0 = 49.0
w0 = pl.round(sr / f0)
f0 = sr / w0
pl.clf()
for ii, N in enumerate(N_harmonics):
H = 1.0 + 2 * pl.arange(N)
waev = beep(pl.c_[f0 * H, pl.random(N) * tau, 1 / H], 8 * w0)
pl.subplot(3,4,ii+1)
pl.plot(waev)
write(waev, path + (name % N))
def markov_step(self,state,distribution):
state = int(state)
for i in range(self.keep_every) :
if state == len(distribution) :
state = 0
if state == 0 :
im = len(distribution)-1
else :
im = state-1
if state == len(distribution) - 1:
ip = 0
else :
ip = state+1
pi = distribution[state]
pim = distribution[im]
pip = distribution[ip]
attempt = randint(0,2)
if attempt == 0 :
if pim > pi :
state = im
else :
z = random()
if z < pim/pi :
state = im
else :
state = state
elif attempt == 1 :
if pip > pi:
state = ip
else :
z = random()
if z < pip/pi :
state = ip
else :
state = state
return state
def step(self):
"""Run one step of the Metropolis algorithm"""
site = self.getsite()
#Now need to work out the energy difference between the lattices.
#This is used to determine the probability that we'll keep the
#new configuration.
Ediff = -2 * self.Hij(site)
Sdiff = -2 * self.spins[site]
if self.probaccept(Ediff) > pl.random():
self.spinflip(site)
return (Ediff, Sdiff)
else:
return (0.,0.)
def SampleUnitTriangle(N, D):
"""Randomly sample from the unit triangle.
Args:
N: the number of points to sample.
D: the dimensionality.
Returns:
A matrix containing the sampled points.
Stolen from Elad's code. I'm a thief, I know.
"""
X = p.ones((N, D))
for i in xrange(N):
while (sum(X[i, :]) >= 1):
X[i, :] = p.random(D)
return X
def poisson_train(rate, duration):
"""Return time stamps from a simulated poisson process at given rate and over given duration. The granularity is 1ms.
We break up duration into N bins of 1ms size. The probability of there being an event (spike) in a given bin is the
same as the rate in kHz. We generate N uniformly distributed random numbers and use that to decide if a given bin has
a spike or not.
Inputs:
rate - In Hz
duration - in s
Output:
Array of time stamps in s
"""
p = rate/1000.0 #Probablity is rate (s-1) * bin size (s)
N = int(duration*1000) #One bin per ms
r = pylab.random(N)
idx = pylab.find(r < p)
return idx/1000.
def cstep(self):
"""Run one step of the Metropolis algorithm using weave"""
i,j = (pl.randint(0,self.n),pl.randint(0,self.n))
spins = self.spins
n = self.n
J = self.J
T = self.T
code = """
#include <math.h>
double neighbour_sum = 0;
neighbour_sum += spins(i%n,(j-1+n)%n);
neighbour_sum += spins(i%n,(j+1)%n);
neighbour_sum += spins((i-1+n)%n,j%n);
neighbour_sum += spins((i+1)%n,j%n);
double Ediff = 2 * J * spins(i,j) * neighbour_sum;
double Sdiff = -2 * spins(i,j);
double PA = 1.;
if(Ediff > 0) {
if(T == 0) {
PA = 0.;
}
else {
PA = exp(-1/T*Ediff);
}
}
py::tuple results(3);
results[0] = PA;
results[1] = Ediff;
results[2] = Sdiff;
return_val = results;
"""
PA,Ediff,Sdiff = weave.inline(code, ['spins','J','T','n','i','j'], type_converters=weave.converters.blitz)
if PA > pl.random():
self.spinflip((i,j))
return Ediff,Sdiff
else:
return 0.,0.
def initLines(self, parameters):
p = parameters
p["imageObj"] = p["imageAx"].imshow(random([2, 2]), self.whiteCMap, interpolation="none", aspect="auto")
p["lineFitH"], = p["imageAx"].plot(
array([0, 1040]) * p["pixelSize"] * p["axScale"], [-1e5, -1e5], ":", lw=2, color="0.15"
)
p["lineFitV"], = p["imageAx"].plot(
[-1e5, -1e5], array([0, 1392]) * p["pixelSize"] * p["axScale"], ":", lw=2, color="0.15"
)
p["lineMarker1H"], = p["imageAx"].plot(
array([0, 1040]) * p["pixelSize"] * p["axScale"], [-1e5, -1e5], "k-", lw=1
)
p["lineMarker1V"], = p["imageAx"].plot(
[-1e5, -1e5], array([0, 1382]) * p["pixelSize"] * p["axScale"], "k-", lw=1
)
self.drawCrosshair(p["lineMarker1H"], p["lineMarker1V"], p["Marker1Pos"])
p["lineMarker2H"], = p["imageAx"].plot(
array([0, 1040]) * p["pixelSize"] * p["axScale"], [-1e5, -1e5], "r-", lw=1
)
p["lineMarker2V"], = p["imageAx"].plot(
[-1e5, -1e5], array([0, 1382]) * p["pixelSize"] * p["axScale"], "r-", lw=1
)
self.drawCrosshair(p["lineMarker2H"], p["lineMarker2V"], p["Marker2Pos"])
p["imageAx"].set_xlim(p["xylim"][0])
p["imageAx"].set_ylim(p["xylim"][1])
p["imageAx"].set_xlabel(u"\u00b5m")
p["imageAx"].set_ylabel(u"\u00b5m")
if not self.roiOnly_check_button.get_active():
lc = p["partLumCorr"] * p["pixelSize"] * p["axScale"]
ac = p["partAtomCount"] * p["pixelSize"] * p["axScale"]
rectLumCorr = plt.Rectangle((lc[2], lc[0]), lc[3] - lc[2], lc[1] - lc[0], ec="red", fc="none", ls="dotted")
rectAtomCount = plt.Rectangle(
(ac[2], ac[0]), ac[3] - ac[2], ac[1] - ac[0], ec="black", fc="none", ls="dashed"
)
p["imageAx"].add_patch(rectLumCorr)
p["imageAx"].add_patch(rectAtomCount)
def init():
position = -0.6 + random()*0.2
return position, 0.0
plt.show()
return ax
def clean(dir, var):
'''
Remove masked values in the two arrays, where if a direction data is masked,
the var data will also be removed in the cleaning process (and vice-versa)
'''
dirmask = dir.mask==False
varmask = var.mask==False
ind = dirmask*varmask
return dir[ind], var[ind]
if __name__=='__main__':
from pylab import figure, show, setp, random, grid, draw
vv=random(500)*6
dv=random(500)*360
fig = figure(figsize=(8, 8), dpi=80, facecolor='w', edgecolor='w')
rect = [0.1, 0.1, 0.8, 0.8]
ax = WindroseAxes(fig, rect, axisbg='w')
fig.add_axes(ax)
# ax.contourf(dv, vv, bins=np.arange(0,8,1), cmap=cm.hot)
# ax.contour(dv, vv, bins=np.arange(0,8,1), colors='k')
# ax.bar(dv, vv, normed=True, opening=0.8, edgecolor='white')
ax.box(dv, vv, normed=True)
l = ax.legend(axespad=-0.10)
setp(l.get_texts(), fontsize=8)
draw()
#print ax._info
show()
def train(numSteps):
for i in range(numSteps):
in1 = random() * 6.0
in2 = random() * 6.0
target = targetFunction(in1,in2)
learn(in1,in2,target)
def testAB():
A=20*P.random(50)
B=30+10*P.random(52)
plotAB(A,B)
datasetFilePath = sys.argv[1]
stopwordsFilePath = sys.argv[2]
K = int(sys.argv[3])
maxIteration = int(sys.argv[4])
threshold = float(sys.argv[5])
topicWordsNum = int(sys.argv[6])
docTopicDist = sys.argv[7]
topicWordDist = sys.argv[8]
dictionary = sys.argv[9]
topicWords = sys.argv[10]
# preprocessing
N, M, word2id, id2word, X = preprocessing(datasetFilePath, stopwordsFilePath)
# lamda[i, j] : p(zj|di)
lamda = random([N, K])
# theta[i, j] : p(wj|zi)
theta = random([K, M])
# p[i, j, k] : p(zk|di,wj)
p = zeros([N, M, K])
initializeParameters()
# EM algorithm
oldLoglikelihood = 1
newLoglikelihood = 1
for i in range(0, maxIteration):
EStep()
MStep()
