Example 1
def KMO(data):
cor_ = pd.DataFrame.corr(data)
invCor = np.linalg.inv(cor_)
rows = cor_.shape[0]
cols = cor_.shape[1]
A = np.ones((rows, cols))
for i in range(rows):
for j in range(i, cols):
A[i, j] = - (invCor[i, j]) / (np.sqrt(invCor[i, i] * invCor[j, j]))
A[j, i] = A[i, j]
num = np.sum(np.sum((cor_)**2)) - np.sum(np.sum(np.diag(cor_**2)))
den = num + (np.sum(np.sum(A**2)) - np.sum(np.sum(np.diag(A**2))))
kmo = num / den
return kmo Example 2
def load_ROI_mask(self):
proxy = nib.load(self.FLAIR_FILE)
image_array = np.asarray(proxy.dataobj)
mask = np.ones_like(image_array)
mask[np.where(image_array < 90)] = 0
# img = nib.Nifti1Image(mask, proxy.affine)
# nib.save(img, join(modalities_path,'mask.nii.gz'))
struct_element_size = (20, 20, 20)
mask_augmented = np.pad(mask, [(21, 21), (21, 21), (21, 21)], 'constant', constant_values=(0, 0))
mask_augmented = binary_closing(mask_augmented, structure=np.ones(struct_element_size, dtype=bool)).astype(
np.int)
return mask_augmented[21:-21, 21:-21, 21:-21].astype('bool') Example 3
def plot_region(self, region):
"""Shows the given region in the field plot.
Args:
region: Region to be plotted.
"""
if type(region) == reg.PointRegion:
self.axes.plot(np.ones(2) * region.point_coordinates / self._x_axis_factor,
np.array([-1, 1]) * self.scale, color='black')
elif type(region) == reg.LineRegion:
self.axes.plot(np.ones(2) * region.line_coordinates[0] / self._x_axis_factor,
np.array([-1, 1]) * self.scale, color='black')
self.axes.plot(np.ones(2) * region.line_coordinates[1] / self._x_axis_factor,
np.array([-1, 1]) * self.scale, color='black')
else:
raise TypeError('Unknown type in region list: {}'.format(type(region))) Example 4
def observed_perplexity(self, counts):
"""Compute perplexity = exp(entropy) of observed variables.
Perplexity is an information theoretic measure of the number of
clusters or latent classes. Perplexity is a real number in the range
[1, M], where M is model_num_clusters.
Args:
counts: A [V]-shaped array of multinomial counts.
Returns:
A [V]-shaped numpy array of perplexity.
"""
V, E, M, R = self._VEMR
if counts is not None:
counts = np.ones(V, dtype=np.int8)
assert counts.shape == (V, )
assert counts.dtype == np.int8
assert np.all(counts > 0)
observed_entropy = np.empty(V, dtype=np.float32)
for v in range(V):
beg, end = self._ragged_index[v:v + 2]
probs = np.dot(self._feat_cond[beg:end, :], self._vert_probs[v, :])
observed_entropy[v] = multinomial_entropy(probs, counts[v])
return np.exp(observed_entropy) Example 5
def sparse_to_dense(sp_indices, output_shape, values, default_value=0):
"""Build a dense matrix from sparse representations.
Args:
sp_indices: A [0-2]-D array that contains the index to place values.
shape: shape of the dense matrix.
values: A {0,1}-D array where values corresponds to the index in each row of
sp_indices.
default_value: values to set for indices not specified in sp_indices.
Return:
A dense numpy N-D array with shape output_shape.
"""
assert len(sp_indices) == len(values), \
'Length of sp_indices is not equal to length of values'
array = np.ones(output_shape) * default_value
for idx, value in zip(sp_indices, values):
array[tuple(idx)] = value
return array Example 6
def infExact_scipy_post(self, K, covars, y, sig2e, fixedEffects): n = y.shape[0] #mean vector m = covars.dot(fixedEffects) if (K.shape[1] < K.shape[0]): K_true = K.dot(K.T) else: K_true = K if sig2e<1e-6: L = la.cholesky(K_true + sig2e*np.eye(n), overwrite_a=True, check_finite=False) #Cholesky factor of covariance with noise sl = 1 pL = -self.solveChol(L, np.eye(n)) #L = -inv(K+inv(sW^2)) else: L = la.cholesky(K_true/sig2e + np.eye(n), overwrite_a=True, check_finite=False) #Cholesky factor of B sl = sig2e pL = L #L = chol(eye(n)+sW*sW'.*K) alpha = self.solveChol(L, y-m, overwrite_b=False) / sl post = dict([]) post['alpha'] = alpha #return the posterior parameters post['sW'] = np.ones(n) / np.sqrt(sig2e) #sqrt of noise precision vector post['L'] = pL return post
Example 7
def getTrainTestKernel(self, params, Xtest): self.checkParams(params) ell = np.exp(params[0]) p = np.exp(params[1]) Xtest_scaled = Xtest/np.sqrt(Xtest.shape[1]) d2 = sq_dist(self.X_scaled.T/ell, Xtest_scaled.T/ell) #precompute squared distances #compute dp dp = np.zeros(d2.shape) for d in xrange(self.X_scaled.shape[1]): dp += (np.outer(self.X_scaled[:,d], np.ones((1, Xtest_scaled.shape[0]))) - np.outer(np.ones((self.X_scaled.shape[0], 1)), Xtest_scaled[:,d])) dp /= p K = np.exp(-d2 / 2.0) return np.cos(2*np.pi*dp)*K
Example 8
def __init__(self, frameSize=1024, imageWidth=1024, imageHeight=1024, zmin=-1, zmax=1, defaultValue=0.0):
PlotBase.__init__(self)
self._frameSize = frameSize
self._sink = None
# Raster state
self._imageData = numpy.ones((imageHeight, imageWidth)) * defaultValue
self._image = self._plot.imshow(self._imageData, extent=(0, 1, 1, 0))
self._zmin = zmin
self._zmax = zmax
norm = self._getNorm(self._zmin, self._zmax)
self._image.set_norm(norm)
self._row = 0
self._xdelta = None
# Maintain aspect ratio of image
self._aspect = float(imageHeight)/imageWidth
self._plot.set_aspect(self._aspect)
# Add a colorbar
self._colorbar = self._figure.colorbar(self._image) Example 9
def test_with_fixed_inputs(self):
inputs = tf.random_normal(
[self.batch_size, self.sequence_length, self.input_depth])
seq_length = tf.ones(self.batch_size, dtype=tf.int32) * self.sequence_length
helper = decode_helper.TrainingHelper(
inputs=inputs, sequence_length=seq_length)
decoder_fn = self.create_decoder(
helper=helper, mode=tf.contrib.learn.ModeKeys.TRAIN)
initial_state = decoder_fn.cell.zero_state(
self.batch_size, dtype=tf.float32)
decoder_output, _ = decoder_fn(initial_state, helper)
#pylint: disable=E1101
with self.test_session() as sess:
sess.run(tf.global_variables_initializer())
decoder_output_ = sess.run(decoder_output)
np.testing.assert_array_equal(
decoder_output_.logits.shape,
[self.sequence_length, self.batch_size, self.vocab_size])
np.testing.assert_array_equal(decoder_output_.predicted_ids.shape,
[self.sequence_length, self.batch_size])
return decoder_output_ Example 10
def position_encoding(sentence_size, embedding_size):
"""
Position Encoding described in section 4.1 of
End-To-End Memory Networks (https://arxiv.org/abs/1503.08895).
Args:
sentence_size: length of the sentence
embedding_size: dimensionality of the embeddings
Returns:
A numpy array of shape [sentence_size, embedding_size] containing
the fixed position encodings for each sentence position.
"""
encoding = np.ones((sentence_size, embedding_size), dtype=np.float32)
ls = sentence_size + 1
le = embedding_size + 1
for k in range(1, le):
for j in range(1, ls):
encoding[j-1, k-1] = (1.0 - j/float(ls)) - (
k / float(le)) * (1. - 2. * j/float(ls))
return encoding Example 11
def create_test_panel_ohlc_source(sim_params, env):
start = sim_params.first_open \
if sim_params else pd.datetime(1990, 1, 3, 0, 0, 0, 0, pytz.utc)
end = sim_params.last_close \
if sim_params else pd.datetime(1990, 1, 8, 0, 0, 0, 0, pytz.utc)
index = env.days_in_range(start, end)
price = np.arange(0, len(index)) + 100
high = price * 1.05
low = price * 0.95
open_ = price + .1 * (price % 2 - .5)
volume = np.ones(len(index)) * 1000
arbitrary = np.ones(len(index))
df = pd.DataFrame({'price': price,
'high': high,
'low': low,
'open': open_,
'volume': volume,
'arbitrary': arbitrary},
index=index)
panel = pd.Panel.from_dict({0: df})
return DataPanelSource(panel), panel Example 12
def flow_orientation(orientation):
""" Currently not use anymore """
# Boolean map
_greater_pi = orientation > math.pi/2
_less_minuspi = orientation < -math.pi/2
_remaining_part = ~(_greater_pi & _less_minuspi)
# orientation map
greater_pi = orientation*_greater_pi
less_minuspi = orientation*_less_minuspi
remaining_part = orientation*_remaining_part
pi_map = math.pi * np.ones(orientation.shape)
# converted orientation map
convert_greater_pi = pi_map*_greater_pi - greater_pi
convert_less_minuspi = -pi_map*_less_minuspi - less_minuspi
new_orient = remaining_part + convert_greater_pi + convert_less_minuspi
return new_orient Example 13
def _normalise_data(self):
self.train_x_mean = np.zeros(self.input_dim)
self.train_x_std = np.ones(self.input_dim)
self.train_y_mean = np.zeros(self.output_dim)
self.train_y_std = np.ones(self.output_dim)
if self.normalise_data:
self.train_x_mean = np.mean(self.train_x, axis=0)
self.train_x_std = np.std(self.train_x, axis=0)
self.train_x_std[self.train_x_std == 0] = 1.
self.train_x = (self.train_x - np.full(self.train_x.shape, self.train_x_mean, dtype=np.float32)) / \
np.full(self.train_x.shape, self.train_x_std, dtype=np.float32)
self.test_x = (self.test_x - np.full(self.test_x.shape, self.train_x_mean, dtype=np.float32)) / \
np.full(self.test_x.shape, self.train_x_std, dtype=np.float32)
self.train_y_mean = np.mean(self.train_y, axis=0)
self.train_y_std = np.std(self.train_y, axis=0)
if self.train_y_std == 0:
self.train_y_std[self.train_y_std == 0] = 1.
self.train_y = (self.train_y - self.train_y_mean) / self.train_y_std Example 14
def main():
fish = loadmat('./data/fish.mat')
X1 = np.zeros((fish['X'].shape[0], fish['X'].shape[1] + 1))
X1[:,:-1] = fish['X']
X2 = np.ones((fish['X'].shape[0], fish['X'].shape[1] + 1))
X2[:,:-1] = fish['X']
X = np.vstack((X1, X2))
Y1 = np.zeros((fish['Y'].shape[0], fish['Y'].shape[1] + 1))
Y1[:,:-1] = fish['Y']
Y2 = np.ones((fish['Y'].shape[0], fish['Y'].shape[1] + 1))
Y2[:,:-1] = fish['Y']
Y = np.vstack((Y1, Y2))
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
callback = partial(visualize, ax=ax)
reg = affine_registration(X, Y)
reg.register(callback)
plt.show() Example 15
def test_bbs_in_bbs(self):
bbs_a = np.array([1, 1, 2.0, 3])
bbs_b = np.array([1, 0, 4, 5])
bbs_c = np.array([0, 0, 2, 2])
assert bbs_in_bbs(bbs_a, bbs_b).all()
assert bbs_in_bbs(bbs_b, bbs_c).any() is not True
assert bbs_in_bbs(bbs_a, bbs_c).any() is not True
bbs_d = np.array([
[0, 0, 5, 5],
[1, 2, 4, 4],
[2, 3, 4, 5]
])
assert (bbs_in_bbs(bbs_a, bbs_d) == np.array([1, 0, 0], dtype=np.bool)).all()
assert (bbs_in_bbs(bbs_d, bbs_d) == np.ones((3), dtype=np.bool)).all()
bbs_a *= 100
bbs_d *= 100
assert (bbs_in_bbs(bbs_a, bbs_d) == np.array([1, 0, 0], dtype=np.bool)).all() Example 16
def computeCost(X, y, theta):
'''YOUR CODE HERE'''
m = float(len(X))
d = 0
for i in range(len(X)):
h = np.dot(theta.transpose(), X[i])
c = (h - y[i])
c = (c **2)
d = (d + c)
j = (1.0 / (2 * m)) * d
return j
# Part 5: Prepare the data so that the input X has two columns: first a column of ones to accomodate theta0 and then a column of city population data Example 17
def test_write():
delete_layer()
cv, data = create_layer(size=(50,50,50,1), offset=(0,0,0))
replacement_data = np.zeros(shape=(50,50,50,1), dtype=np.uint8)
cv[0:50,0:50,0:50] = replacement_data
assert np.all(cv[0:50,0:50,0:50] == replacement_data)
replacement_data = np.random.randint(255, size=(50,50,50,1), dtype=np.uint8)
cv[0:50,0:50,0:50] = replacement_data
assert np.all(cv[0:50,0:50,0:50] == replacement_data)
# out of bounds
delete_layer()
cv, data = create_layer(size=(128,64,64,1), offset=(10,20,0))
with pytest.raises(ValueError):
cv[74:150,20:84,0:64] = np.ones(shape=(64,64,64,1), dtype=np.uint8)
# non-aligned writes
delete_layer()
cv, data = create_layer(size=(128,64,64,1), offset=(10,20,0))
with pytest.raises(ValueError):
cv[21:85,0:64,0:64] = np.ones(shape=(64,64,64,1), dtype=np.uint8) Example 18
def extract_and_save_bin_to(dir_to_bin, dir_to_source):
sets = [s for s in os.listdir(dir_to_source) if s in SETS]
for d in sets:
path = join(dir_to_source, d)
speakers = [s for s in os.listdir(path) if s in SPEAKERS]
for s in speakers:
path = join(dir_to_source, d, s)
output_dir = join(dir_to_bin, d, s)
if not tf.gfile.Exists(output_dir):
tf.gfile.MakeDirs(output_dir)
for f in os.listdir(path):
filename = join(path, f)
print(filename)
if not os.path.isdir(filename):
features = extract(filename)
labels = SPEAKERS.index(s) * np.ones(
[features.shape[0], 1],
np.float32,
)
b = os.path.splitext(f)[0]
features = np.concatenate([features, labels], 1)
with open(join(output_dir, '{}.bin'.format(b)), 'wb') as fp:
fp.write(features.tostring()) Example 19
def __mul__(self, other):
"""
Left-multiply RigidTransform with another rigid transform
Two variants:
RigidTransform: Identical to oplus operation
ndarray: transform [N x 3] point set (X_2 = p_21 * X_1)
"""
if isinstance(other, DualQuaternion):
return DualQuaternion.from_dq(other.real * self.real,
other.dual * self.real + other.real * self.dual)
elif isinstance(other, float):
return DualQuaternion.from_dq(self.real * other, self.dual * other)
# elif isinstance(other, nd.array):
# X = np.hstack([other, np.ones((len(other),1))]).T
# return (np.dot(self.matrix, X).T)[:,:3]
else:
raise TypeError('__mul__ typeerror {:}'.format(type(other))) Example 20
def effective_sample_size(x, mu, var, logger):
"""
Calculate the effective sample size of sequence generated by MCMC.
:param x:
:param mu: mean of the variable
:param var: variance of the variable
:param logger: logg
:return: effective sample size of the sequence
Make sure that `mu` and `var` are correct!
"""
# batch size, time, dimension
b, t, d = x.shape
ess_ = np.ones([d])
for s in range(1, t):
p = auto_correlation_time(x, s, mu, var)
if np.sum(p > 0.05) == 0:
break
else:
for j in range(0, d):
if p[j] > 0.05:
ess_[j] += 2.0 * p[j] * (1.0 - float(s) / t)
logger.info('ESS: max [%f] min [%f] / [%d]' % (t / np.min(ess_), t / np.max(ess_), t))
return t / ess_ Example 21
def train_linear_regression(X_train, y_train, max_iter, learning_rate, fit_intercept=False):
""" Train a linear regression model with gradient descent
Args:
X_train, y_train (numpy.ndarray, training data set)
max_iter (int, number of iterations)
learning_rate (float)
fit_intercept (bool, with an intercept w0 or not)
Returns:
numpy.ndarray, learned weights
"""
if fit_intercept:
intercept = np.ones((X_train.shape[0], 1))
X_train = np.hstack((intercept, X_train))
weights = np.zeros(X_train.shape[1])
for iteration in range(max_iter):
weights = update_weights_gd(X_train, y_train, weights, learning_rate)
# Check the cost for every 100 (for example) iterations
if iteration % 100 == 0:
print(compute_cost(X_train, y_train, weights))
return weights Example 22
def train_logistic_regression(X_train, y_train, max_iter, learning_rate, fit_intercept=False):
""" Train a logistic regression model
Args:
X_train, y_train (numpy.ndarray, training data set)
max_iter (int, number of iterations)
learning_rate (float)
fit_intercept (bool, with an intercept w0 or not)
Returns:
numpy.ndarray, learned weights
"""
if fit_intercept:
intercept = np.ones((X_train.shape[0], 1))
X_train = np.hstack((intercept, X_train))
weights = np.zeros(X_train.shape[1])
for iteration in range(max_iter):
weights = update_weights_gd(X_train, y_train, weights, learning_rate)
# Check the cost for every 100 (for example) iterations
if iteration % 1000 == 0:
print(compute_cost(X_train, y_train, weights))
return weights Example 23
def train_logistic_regression(X_train, y_train, max_iter, learning_rate, fit_intercept=False):
""" Train a logistic regression model
Args:
X_train, y_train (numpy.ndarray, training data set)
max_iter (int, number of iterations)
learning_rate (float)
fit_intercept (bool, with an intercept w0 or not)
Returns:
numpy.ndarray, learned weights
"""
if fit_intercept:
intercept = np.ones((X_train.shape[0], 1))
X_train = np.hstack((intercept, X_train))
weights = np.zeros(X_train.shape[1])
for iteration in range(max_iter):
weights = update_weights_sgd(X_train, y_train, weights, learning_rate)
# Check the cost for every 2 (for example) iterations
if iteration % 2 == 0:
print(compute_cost(X_train, y_train, weights))
return weights
# Train the SGD model based on 10000 samples Example 24
def norm(self, x):
"""compute the Mahalanobis norm that is induced by the
statistical model / sample distribution, specifically by
covariance matrix ``C``. The expected Mahalanobis norm is
about ``sqrt(dimension)``.
Example
-------
>>> import cma, numpy as np
>>> sm = cma.sampler.GaussFullSampler(np.ones(10))
>>> x = np.random.randn(10)
>>> d = sm.norm(x)
`d` is the norm "in" the true sample distribution,
sampled points have a typical distance of ``sqrt(2*sm.dim)``,
where ``sm.dim`` is the dimension, and an expected distance of
close to ``dim**0.5`` to the sample mean zero. In the example,
`d` is the Euclidean distance, because C = I.
"""
return sum((np.dot(self.B.T, x) / self.D)**2)**0.5 Example 25
def __init__(self, dimension,
constant_trace='None',
randn=np.random.randn,
quadratic=False,
**kwargs):
try:
self.dimension = len(dimension)
standard_deviations = np.asarray(dimension)
except TypeError:
self.dimension = dimension
standard_deviations = np.ones(dimension)
assert self.dimension == len(standard_deviations)
assert len(standard_deviations) == self.dimension
self.C = standard_deviations**2
"covariance matrix diagonal"
self.constant_trace = constant_trace
self.randn = randn
self.quadratic = quadratic
self.count_tell = 0 Example 26
def norm(self, x):
"""compute the Mahalanobis norm that is induced by the
statistical model / sample distribution, specifically by
covariance matrix ``C``. The expected Mahalanobis norm is
about ``sqrt(dimension)``.
Example
-------
>>> import cma, numpy as np
>>> sm = cma.sampler.GaussFullSampler(np.ones(10))
>>> x = np.random.randn(10)
>>> d = sm.norm(x)
`d` is the norm "in" the true sample distribution,
sampled points have a typical distance of ``sqrt(2*sm.dim)``,
where ``sm.dim`` is the dimension, and an expected distance of
close to ``dim**0.5`` to the sample mean zero. In the example,
`d` is the Euclidean distance, because C = I.
"""
return sum(np.asarray(x)**2 / self.C)**0.5 Example 27
def __init__(self, dimension, randn=np.random.randn, debug=False):
"""pass dimension of the underlying sample space
"""
try:
self.N = len(dimension)
std_vec = np.array(dimension, copy=True)
except TypeError:
self.N = dimension
std_vec = np.ones(self.N)
if self.N < 10:
print('Warning: Not advised to use VD-CMA for dimension < 10.')
self.randn = randn
self.dvec = std_vec
self.vvec = self.randn(self.N) / math.sqrt(self.N)
self.norm_v2 = np.dot(self.vvec, self.vvec)
self.norm_v = np.sqrt(self.norm_v2)
self.vn = self.vvec / self.norm_v
self.vnn = self.vn**2
self.pc = np.zeros(self.N)
self._debug = debug # plot covariance matrix Example 28
def covariance_matrix(self):
if self._debug:
# return None
ka = self.k_active
if ka > 0:
C = np.eye(self.N) + np.dot(self.V[:ka].T * self.S[:ka],
self.V[:ka])
C = (C * self.D).T * self.D
else:
C = np.diag(self.D**2)
C *= self.sigma**2
else:
# Fake Covariance Matrix for Speed
C = np.ones(1)
self.B = np.ones(1)
return C Example 29
def initwithsize(self, curshape, dim):
# DIM-dependent initialization
if self.dim != dim:
if self.zerox:
self.xopt = zeros(dim)
else:
self.xopt = compute_xopt(self.rseed, dim)
scale = max(1, dim ** .5 / 8.) # nota: different from scales in F8
self.linearTF = scale * compute_rotation(self.rseed, dim)
self.xopt = np.hstack(dot(.5 * np.ones((1, dim)), self.linearTF.T)) / scale ** 2
# DIM- and POPSI-dependent initialisations of DIM*POPSI matrices
if self.lastshape != curshape:
self.dim = dim
self.lastshape = curshape
self.arrxopt = resize(self.xopt, curshape) Example 30
def __imul__(self, factor):
"""define ``self *= factor``.
As a shortcut for::
self = self.__imul__(factor)
"""
try:
if factor == 1:
return self
except: pass
try:
if (np.size(factor) == np.size(self.scaling) and
all(factor == 1)):
return self
except: pass
if self.is_identity and np.size(self.scaling) == 1:
self.scaling = np.ones(np.size(factor))
self.is_identity = False
self.scaling *= factor
self.dim = np.size(self.scaling)
return self Example 31
def check_string_input(self, input_name, input_value):
if type(input_value) is np.array:
if input_value.size == self.P:
setattr(self, input_name, input_value)
elif input_value.size == 1:
setattr(self, input_name, np.repeat(input_value, self.P))
else:
raise ValueError("length of %s is %d; should be %d" % (input_name, input_value.size, self.P))
elif type(input_value) is str:
setattr(self, input_name, float(input_value)*np.ones(self.P))
elif type(input_value) is list:
if len(input_value) == self.P:
setattr(self, input_name, np.array([str(x) for x in input_value]))
elif len(input_value) == 1:
setattr(self, input_name, np.repeat(input_value, self.P))
else:
raise ValueError("length of %s is %d; should be %d" % (input_name, len(input_value), self.P))
else:
raise ValueError("user provided %s with an unsupported type" % input_name) Example 32
def check_numeric_input(self, input_name, input_value):
if type(input_value) is np.ndarray:
if input_value.size == self.P:
setattr(self, input_name, input_value)
elif input_value.size == 1:
setattr(self, input_name, input_value*np.ones(self.P))
else:
raise ValueError("length of %s is %d; should be %d" % (input_name, input_value.size, self.P))
elif type(input_value) is float or type(input_value) is int:
setattr(self, input_name, float(input_value)*np.ones(self.P))
elif type(input_value) is list:
if len(input_value) == self.P:
setattr(self, input_name, np.array([float(x) for x in input_value]))
elif len(input_value) == 1:
setattr(self, input_name, np.array([float(x) for x in input_value]) * np.ones(self.P))
else:
raise ValueError("length of %s is %d; should be %d" % (input_name, len(input_value), self.P))
else:
raise ValueError("user provided %s with an unsupported type" % (input_name)) Example 33
def make_heatmaps_from_joints(input_size, heatmap_size, gaussian_variance, batch_joints):
# Generate ground-truth heatmaps from ground-truth 2d joints
scale_factor = input_size // heatmap_size
batch_gt_heatmap_np = []
for i in range(batch_joints.shape[0]):
gt_heatmap_np = []
invert_heatmap_np = np.ones(shape=(heatmap_size, heatmap_size))
for j in range(batch_joints.shape[1]):
cur_joint_heatmap = make_gaussian(heatmap_size,
gaussian_variance,
center=(batch_joints[i][j] // scale_factor))
gt_heatmap_np.append(cur_joint_heatmap)
invert_heatmap_np -= cur_joint_heatmap
gt_heatmap_np.append(invert_heatmap_np)
batch_gt_heatmap_np.append(gt_heatmap_np)
batch_gt_heatmap_np = np.asarray(batch_gt_heatmap_np)
batch_gt_heatmap_np = np.transpose(batch_gt_heatmap_np, (0, 2, 3, 1))
return batch_gt_heatmap_np Example 34
def primes_2_to_n(n):
"""
Efficient algorithm to find and list primes from
2 to `n'.
Args:
n (int): highest number from which to search for primes
Returns:
np array of all primes from 2 to n
References:
Robert William Hanks,
https://stackoverflow.com/questions/2068372/fastest-way-to-list-all-primes-below-n/
"""
sieve = np.ones(int(n / 3 + (n % 6 == 2)), dtype=np.bool)
for i in range(1, int((n ** 0.5) / 3 + 1)):
if sieve[i]:
k = 3 * i + 1 | 1
sieve[int(k * k / 3)::2 * k] = False
sieve[int(k * (k - 2 * (i & 1) + 4) / 3)::2 * k] = False
return np.r_[2, 3, ((3 * np.nonzero(sieve)[0][1:] + 1) | 1)] Example 35
def get_interv_table(model,intrv=True):
n_batches=25
table_outputs=[]
d_vals=np.linspace(TINY,0.6,n_batches)
for name in model.cc.node_names:
outputs=[]
for d_val in d_vals:
do_dict={model.cc.node_dict[name].label_logit : d_val*np.ones((model.batch_size,1))}
outputs.append(model.sess.run(model.fake_labels,do_dict))
out=np.vstack(outputs)
table_outputs.append(out)
table=np.stack(table_outputs,axis=2)
np.mean(np.round(table),axis=0)
return table
#dT=pd.DataFrame(index=p_names, data=T, columns=do_names)
#T=np.mean(np.round(table),axis=0)
#table=get_interv_table(model) Example 36
def __init__(self, pos, color, mode=None):
"""
=============== ==============================================================
**Arguments:**
pos Array of positions where each color is defined
color Array of RGBA colors.
Integer data types are interpreted as 0-255; float data types
are interpreted as 0.0-1.0
mode Array of color modes (ColorMap.RGB, HSV_POS, or HSV_NEG)
indicating the color space that should be used when
interpolating between stops. Note that the last mode value is
ignored. By default, the mode is entirely RGB.
=============== ==============================================================
"""
self.pos = np.array(pos)
order = np.argsort(self.pos)
self.pos = self.pos[order]
self.color = np.array(color)[order]
if mode is None:
mode = np.ones(len(pos))
self.mode = mode
self.stopsCache = {} Example 37
def build_test_data(self, variable='v'):
metadata = {
'size': NCELLS,
'first_index': 0,
'first_id': 0,
'n': 505,
'variable': variable,
'last_id': NCELLS - 1,
'last_index': NCELLS - 1,
'dt': 0.1,
'label': "population0",
}
if variable == 'v':
metadata['units'] = 'mV'
elif variable == 'spikes':
metadata['units'] = 'ms'
data = np.empty((505, 2))
for i in range(NCELLS):
# signal
data[i*101:(i+1)*101, 0] = np.arange(i, i+101, dtype=float)
# index
data[i*101:(i+1)*101, 1] = i*np.ones((101,), dtype=float)
return data, metadata Example 38
def __init__(self, pos, color, mode=None):
"""
=============== ==============================================================
**Arguments:**
pos Array of positions where each color is defined
color Array of RGBA colors.
Integer data types are interpreted as 0-255; float data types
are interpreted as 0.0-1.0
mode Array of color modes (ColorMap.RGB, HSV_POS, or HSV_NEG)
indicating the color space that should be used when
interpolating between stops. Note that the last mode value is
ignored. By default, the mode is entirely RGB.
=============== ==============================================================
"""
self.pos = np.array(pos)
order = np.argsort(self.pos)
self.pos = self.pos[order]
self.color = np.array(color)[order]
if mode is None:
mode = np.ones(len(pos))
self.mode = mode
self.stopsCache = {} Example 39
def build_test_data(self, variable='v'):
metadata = {
'size': NCELLS,
'first_index': 0,
'first_id': 0,
'n': 505,
'variable': variable,
'last_id': NCELLS - 1,
'last_index': NCELLS - 1,
'dt': 0.1,
'label': "population0",
}
if variable == 'v':
metadata['units'] = 'mV'
elif variable == 'spikes':
metadata['units'] = 'ms'
data = np.empty((505, 2))
for i in range(NCELLS):
# signal
data[i*101:(i+1)*101, 0] = np.arange(i, i+101, dtype=float)
# index
data[i*101:(i+1)*101, 1] = i*np.ones((101,), dtype=float)
return data, metadata Example 40
def ONES(n):
return np.ones((n, n), np.uint8) Example 41
def gen_noisy_cube(cube,type='poisson',gauss_std=0.5,verbose=True):
"""
Generate noisy cube based on input cube.
--- INPUT ---
cube Data cube to be smoothed
type Type of noise to generate
poisson Generates poissonian (integer) noise
gauss Generates gaussian noise for a gaussian with standard deviation gauss_std=0.5
gauss_std Standard deviation of noise if type='gauss'
verbose Toggle verbosity
--- EXAMPLE OF USE ---
import tdose_utilities as tu
datacube = np.ones(([3,3,3])); datacube[0,1,1]=5; datacube[1,1,1]=6; datacube[2,1,1]=8
cube_with_noise = tu.gen_noisy_cube(datacube,type='gauss',gauss_std='0.5')
"""
if verbose: print ' - Generating "'+type+'" noise on data cube'
if type == 'poisson':
cube_with_noise = np.random.poisson(lam=cube, size=None)
elif type == 'gauss':
cube_with_noise = cube + np.random.normal(loc=np.zeros(cube.shape),scale=gauss_std, size=None)
else:
sys.exit(' ---> type="'+type+'" is not valid in call to mock_cube_sources.generate_cube_noise() ')
return cube_with_noise
# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = Example 42
def __init__(self, env, shape, clip=10.0, update_freq=100):
self.env = env
self.clip = clip
self.update_freq = update_freq
self.count = 0
self.sum = 0.0
self.sum_sqr = 0.0
self.mean = np.zeros(shape, dtype=np.double)
self.std = np.ones(shape, dtype=np.double) Example 43
def expectation(self, dataSplit, coefficients, variances):
assignment_weights = np.ones(
(len(dataSplit), self.num_components), dtype=float)
self.Q = len(self.endoVar)
for k in range(self.num_components):
coef_ = coefficients[k]
Beta = coef_.ix[self.endoVar][self.endoVar]
Gamma = coef_.ix[self.endoVar][self.exoVar]
a_ = (np.dot(Beta, self.fscores[
self.endoVar].T) + np.dot(Gamma, self.fscores[self.exoVar].T))
invert_ = np.linalg.inv(np.array(variances[k]))
exponential = np.exp(-0.5 * np.dot(np.dot(a_.T, invert_), a_))
den = (((2 * np.pi)**(self.Q / 2)) *
np.sqrt(np.linalg.det(variances[k])))
probabilities = exponential / den
probabilities = probabilities[0]
assignment_weights[:, k] = probabilities
assignment_weights /= assignment_weights.sum(axis=1)[:, np.newaxis]
# print(assignment_weights)
return assignment_weights Example 44
def create_matrices(self):
"""Creates the a_* matrices required for simulation."""
self.a_d_v = self.d_x(factors=(self.t.increment / self.x.increment *
np.ones(self.x.samples)))
self.a_v_p = self.d_x(factors=(self.t.increment / self.x.increment) *
np.ones(self.x.samples), variant='backward')
self.a_v_v = self.d_x2(factors=(self.t.increment / self.x.increment ** 2 *
self.material_vector('absorption_coef')))
self.a_v_v2 = self.d_x(factors=(self.t.increment / self.x.increment / 2) *
np.ones(self.x.samples), variant='central') Example 45
def test_field_component_boundary_2():
fc = fls.FieldComponent(100)
fc.values = np.ones(100)
fc.boundaries = [reg.Boundary(reg.LineRegion([5, 6, 7], [0, 0.2], 'test boundary'))]
fc.boundaries[0].value = [23, 42, 23]
fc.boundaries[0].additive = True
fc.apply_bounds(step=0)
assert np.allclose(fc.values[[5, 6, 7]], [24, 43, 24]) Example 46
def serve_files(model_path, config_path, num_samples):
"""INTERNAL Serve from pickled model, config."""
from treecat.serving import TreeCatServer
import numpy as np
model = pickle_load(model_path)
config = pickle_load(config_path)
model['config'] = config
server = TreeCatServer(model)
counts = np.ones(model['tree'].num_vertices, np.int8)
samples = server.sample(int(num_samples), counts)
server.logprob(samples)
server.median(counts, samples)
server.latent_correlation() Example 47
def validate_gof(N, V, C, M, server, conditional):
# Generate samples.
expected = C**V
num_samples = 1000 * expected
ones = np.ones(V, dtype=np.int8)
if conditional:
cond_data = server.sample(1, ones)[0, :]
else:
cond_data = server.make_zero_row()
samples = server.sample(num_samples, ones, cond_data)
logprobs = server.logprob(samples + cond_data[np.newaxis, :])
counts = {}
probs = {}
for sample, logprob in zip(samples, logprobs):
key = tuple(sample)
if key in counts:
counts[key] += 1
else:
counts[key] = 1
probs[key] = np.exp(logprob)
assert len(counts) == expected
# Check accuracy using Pearson's chi-squared test.
keys = sorted(counts.keys(), key=lambda key: -probs[key])
counts = np.array([counts[k] for k in keys], dtype=np.int32)
probs = np.array([probs[k] for k in keys])
probs /= probs.sum()
# Truncate to avoid low-precision.
truncated = False
valid = (probs * num_samples > 20)
if not valid.all():
T = valid.argmin()
T = max(8, T) # Avoid truncating too much
probs = probs[:T]
counts = counts[:T]
truncated = True
gof = multinomial_goodness_of_fit(
probs, counts, num_samples, plot=True, truncated=truncated)
assert 1e-2 < gof Example 48
def sample_tree(self, num_samples):
size = len(self._ensemble)
pvals = np.ones(size, dtype=np.float32) / size
sub_nums = np.random.multinomial(num_samples, pvals)
samples = []
for server, sub_num in zip(self._ensemble, sub_nums):
samples += server.sample_tree(sub_num)
np.random.shuffle(samples)
assert len(samples) == num_samples
return samples Example 49
def sample(self, N, counts, data=None):
size = len(self._ensemble)
pvals = np.ones(size, dtype=np.float32) / size
sub_Ns = np.random.multinomial(N, pvals)
samples = np.concatenate([
server.sample(sub_N, counts, data)
for server, sub_N in zip(self._ensemble, sub_Ns)
])
np.random.shuffle(samples)
assert samples.shape[0] == N
return samples Example 50
def arrangementToRasterMask( arrangement ):
rows = np.array(arrangement['rows'])
width = np.max(rows)
if arrangement['hex'] is True:
width+=1
height = len(rows)
mask = np.ones((height,width),dtype=int)
for row in range(len(rows)):
c = rows[row]
mask[row,(width-c)>>1:((width-c)>>1)+c] = 0
return {'width':width,'height':height,'mask':mask, 'count':np.sum(rows),'hex':arrangement['hex'],'type':arrangement['type']} 