# Python numpy.cos() Examples

The following are 30 code examples for showing how to use numpy.cos(). These examples are extracted from open source projects. You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example.

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Example 1
 Project: sklearn-audio-transfer-learning   Author: jordipons   File: mel_features.py    License: ISC License 8 votes
```def periodic_hann(window_length):
"""Calculate a "periodic" Hann window.

The classic Hann window is defined as a raised cosine that starts and
ends on zero, and where every value appears twice, except the middle
point for an odd-length window.  Matlab calls this a "symmetric" window
and np.hanning() returns it.  However, for Fourier analysis, this
actually represents just over one cycle of a period N-1 cosine, and
thus is not compactly expressed on a length-N Fourier basis.  Instead,
it's better to use a raised cosine that ends just before the final
zero value - i.e. a complete cycle of a period-N cosine.  Matlab
calls this a "periodic" window. This routine calculates it.

Args:
window_length: The number of points in the returned window.

Returns:
A 1D np.array containing the periodic hann window.
"""
return 0.5 - (0.5 * np.cos(2 * np.pi / window_length *
np.arange(window_length))) ```
Example 2
 Project: xrft   Author: xgcm   File: test_xrft.py    License: MIT License 6 votes
```def test_cross_phase_2d(self, dask):
Ny, Nx = (32, 16)
x = np.linspace(0, 1, num=Nx, endpoint=False)
y = np.ones(Ny)
f = 6
phase_offset = np.pi/2
signal1 = np.cos(2*np.pi*f*x)  # frequency = 1/(2*pi)
signal2 = np.cos(2*np.pi*f*x - phase_offset)
da1 = xr.DataArray(data=signal1*y[:,np.newaxis], name='a',
dims=['y','x'], coords={'y':y, 'x':x})
da2 = xr.DataArray(data=signal2*y[:,np.newaxis], name='b',
dims=['y','x'], coords={'y':y, 'x':x})
with pytest.raises(ValueError):
xrft.cross_phase(da1, da2, dim=['y','x'])

da1 = da1.chunk({'x': 16})
da2 = da2.chunk({'x': 16})
cp = xrft.cross_phase(da1, da2, dim=['x'])
actual_phase_offset = cp.sel(freq_x=f).values
npt.assert_almost_equal(actual_phase_offset, phase_offset) ```
Example 3
 Project: FRIDA   Author: LCAV   File: generators.py    License: MIT License 6 votes
```def unit_vec(doa):
"""
This function takes a 2D (phi) or 3D (phi,theta) polar coordinates
and returns a unit vector in cartesian coordinates.

:param doa: (ndarray) An (D-1)-by-N array where D is the dimension and
N the number of vectors.

:return: (ndarray) A D-by-N array of unit vectors (each column is a vector)
"""

if doa.ndim != 1 and doa.ndim != 2:
raise ValueError("DoA array should be 1D or 2D.")

doa = np.array(doa)

if doa.ndim == 0 or doa.ndim == 1:
return np.array([np.cos(doa), np.sin(doa)])

elif doa.ndim == 2 and doa.shape[0] == 1:
return np.array([np.cos(doa[0]), np.sin(doa[0])])

elif doa.ndim == 2 and doa.shape[0] == 2:
s = np.sin(doa[1])
return np.array([s * np.cos(doa[0]), s * np.sin(doa[0]), np.cos(doa[1])]) ```
Example 4
 Project: MPContribs   Author: materialsproject   File: pre_submission.py    License: MIT License 6 votes
```def load_RSM(filename):
om, tt, psd = xu.io.getxrdml_map(filename)
wavelength = 1.54056

q_y = (1 / wavelength) * (np.cos(tt) - np.cos(2 * om - tt))
q_x = (1 / wavelength) * (np.sin(tt) - np.sin(2 * om - tt))

xi = np.linspace(np.min(q_x), np.max(q_x), 100)
yi = np.linspace(np.min(q_y), np.max(q_y), 100)
psd[psd < 1] = 1
data_grid = griddata(
(q_x, q_y), psd, (xi[None, :], yi[:, None]), fill_value=1, method="cubic"
)
nx, ny = data_grid.shape

range_values = [np.min(q_x), np.max(q_x), np.min(q_y), np.max(q_y)]
output_data = (
Panel(np.log(data_grid).reshape(nx, ny, 1), minor_axis=["RSM"])
.transpose(2, 0, 1)
.to_frame()
)

return range_values, output_data ```
Example 5
 Project: neuropythy   Author: noahbenson   File: util.py    License: GNU Affero General Public License v3.0 6 votes
```def rotation_matrix_3D(u, th):
"""
rotation_matrix_3D(u, t) yields a 3D numpy matrix that rotates any vector about the axis u
"""
# normalize the axis:
u = normalize(u)
# We use the Euler-Rodrigues formula;
# see https://en.wikipedia.org/wiki/Euler-Rodrigues_formula
a = math.cos(0.5 * th)
s = math.sin(0.5 * th)
(b, c, d) = -s * u
(a2, b2, c2, d2) = (a*a, b*b, c*c, d*d)
(bc, ad, ac, ab, bd, cd) = (b*c, a*d, a*c, a*b, b*d, c*d)
return np.array([[a2 + b2 - c2 - d2, 2*(bc + ad),         2*(bd - ac)],
[2*(bc - ad),       a2 + c2 - b2 - d2,   2*(cd + ab)],
[2*(bd + ac),       2*(cd - ab),         a2 + d2 - b2 - c2]]) ```
Example 6
 Project: neuropythy   Author: noahbenson   File: __init__.py    License: GNU Affero General Public License v3.0 6 votes
```def test_cmag(self):
'''
test_cmag() ensures that the neuropythy.vision cortical magnification function is working.
'''
import neuropythy.vision as vis
logging.info('neuropythy: Testing areal cortical magnification...')
dset = ny.data['benson_winawer_2018']
sub = dset.subjects['S1202']
hem = [sub.lh, sub.rh][np.random.randint(2)]
cm = vis.areal_cmag(hem.midgray_surface, 'prf_',
weight='prf_variance_explained')
# cmag should get smaller in general
ths = np.arange(0, 2*np.pi, np.pi/3)
es = [0.5, 1, 2, 4]
x = np.diff([np.mean(cm(e*np.cos(ths), e*np.sin(ths))) for e in es])
self.assertTrue((x < 0).all()) ```
Example 7
 Project: fullrmc   Author: bachiraoun   File: Collection.py    License: GNU Affero General Public License v3.0 6 votes
```def get_rotation_matrix(rotationVector, angle):
"""
Calculate the rotation (3X3) matrix about an axis (rotationVector)
by a rotation angle.

:Parameters:
#. rotationVector (list, tuple, numpy.ndarray): Rotation axis
coordinates.
#. angle (float): Rotation angle in rad.

:Returns:
#. rotationMatrix (numpy.ndarray): Computed (3X3) rotation matrix
"""
angle = float(angle)
axis = rotationVector/np.sqrt(np.dot(rotationVector , rotationVector))
a = np.cos(angle/2)
b,c,d = -axis*np.sin(angle/2.)
return np.array( [ [a*a+b*b-c*c-d*d, 2*(b*c-a*d), 2*(b*d+a*c)],
[2*(b*c+a*d), a*a+c*c-b*b-d*d, 2*(c*d-a*b)],
[2*(b*d-a*c), 2*(c*d+a*b), a*a+d*d-b*b-c*c] ] , dtype = FLOAT_TYPE) ```
Example 8
 Project: DOTA_models   Author: ringringyi   File: nav_env.py    License: Apache License 2.0 6 votes
```def get_loc_axis(self, node, delta_theta, perturb=None):
"""Based on the node orientation returns X, and Y axis. Used to sample the
map in egocentric coordinate frame.
"""
if type(node) == tuple:
node = np.array([node])
if perturb is None:
perturb = np.zeros((node.shape[0], 4))
xyt = self.to_actual_xyt_vec(node)
x = xyt[:,[0]] + perturb[:,[0]]
y = xyt[:,[1]] + perturb[:,[1]]
t = xyt[:,[2]] + perturb[:,[2]]
theta = t*delta_theta
loc = np.concatenate((x,y), axis=1)
x_axis = np.concatenate((np.cos(theta), np.sin(theta)), axis=1)
y_axis = np.concatenate((np.cos(theta+np.pi/2.), np.sin(theta+np.pi/2.)),
axis=1)
# Flip the sampled map where need be.
y_axis[np.where(perturb[:,3] > 0)[0], :] *= -1.
return loc, x_axis, y_axis, theta ```
Example 9
 Project: soccer-matlab   Author: utra-robosoccer   File: minitaur_terrain_randomizer.py    License: BSD 2-Clause "Simplified" License 6 votes
```def sample(self):
"""Samples new points around some existing point.

Removes the sampling base point and also stores the new jksampled points if
they are far enough from all existing points.
"""
active_point = self._active_list.pop()
for _ in xrange(self._max_sample_size):
# Generate random points near the current active_point between the radius
random_angle = np.random.uniform(0, 2 * math.pi)

# The sampled 2D points near the active point
sample = random_radius * np.array(
[np.cos(random_angle), np.sin(random_angle)]) + active_point

if not self._is_in_grid(sample):
continue

if self._is_close_to_existing_points(sample):
continue

self._active_list.append(sample)
self._grid[self._point_to_index_1d(sample)] = sample ```
Example 10
 Project: soccer-matlab   Author: utra-robosoccer   File: robot_locomotors.py    License: BSD 2-Clause "Simplified" License 6 votes
```def alive_bonus(self, z, pitch):
if self.frame%30==0 and self.frame>100 and self.on_ground_frame_counter==0:
target_xyz  = np.array(self.body_xyz)
robot_speed = np.array(self.robot_body.speed())
angle = self.np_random.uniform(low=-3.14, high=3.14)
from_dist   = 4.0
attack_speed   = self.np_random.uniform(low=20.0, high=30.0)  # speed 20..30 (* mass in cube.urdf = impulse)
time_to_travel = from_dist / attack_speed
target_xyz += robot_speed*time_to_travel  # predict future position at the moment the cube hits the robot
position = [target_xyz[0] + from_dist*np.cos(angle),
target_xyz[1] + from_dist*np.sin(angle),
target_xyz[2] + 1.0]
attack_speed_vector = target_xyz - np.array(position)
attack_speed_vector *= attack_speed / np.linalg.norm(attack_speed_vector)
attack_speed_vector += self.np_random.uniform(low=-1.0, high=+1.0, size=(3,))
self.aggressive_cube.reset_position(position)
self.aggressive_cube.reset_velocity(linearVelocity=attack_speed_vector)
if z < 0.8:
self.on_ground_frame_counter += 1
elif self.on_ground_frame_counter > 0:
self.on_ground_frame_counter -= 1
# End episode if the robot can't get up in 170 frames, to save computation and decorrelate observations.
self.frame += 1
return self.potential_leak() if self.on_ground_frame_counter<170 else -1 ```
Example 11
 Project: soccer-matlab   Author: utra-robosoccer   File: robot_manipulators.py    License: BSD 2-Clause "Simplified" License 6 votes
```def calc_state(self):
theta, self.theta_dot = self.central_joint.current_relative_position()
self.gamma, self.gamma_dot = self.elbow_joint.current_relative_position()
target_x, _ = self.jdict["target_x"].current_position()
target_y, _ = self.jdict["target_y"].current_position()
self.to_target_vec = np.array(self.fingertip.pose().xyz()) - np.array(self.target.pose().xyz())
return np.array([
target_x,
target_y,
self.to_target_vec[0],
self.to_target_vec[1],
np.cos(theta),
np.sin(theta),
self.theta_dot,
self.gamma,
self.gamma_dot,
]) ```
Example 12
 Project: robosuite   Author: StanfordVL   File: transform_utils.py    License: MIT License 6 votes
```def random_quat(rand=None):
"""Return uniform random unit quaternion.
rand: array like or None
Three independent random variables that are uniformly distributed
between 0 and 1.
>>> q = random_quat()
>>> np.allclose(1.0, vector_norm(q))
True
>>> q = random_quat(np.random.random(3))
>>> q.shape
(4,)
"""
if rand is None:
rand = np.random.rand(3)
else:
assert len(rand) == 3
r1 = np.sqrt(1.0 - rand[0])
r2 = np.sqrt(rand[0])
pi2 = math.pi * 2.0
t1 = pi2 * rand[1]
t2 = pi2 * rand[2]
return np.array(
(np.sin(t1) * r1, np.cos(t1) * r1, np.sin(t2) * r2, np.cos(t2) * r2),
dtype=np.float32,
) ```
Example 13
 Project: pywr   Author: pywr   File: test_parameters.py    License: GNU General Public License v3.0 6 votes
```def test_variable(self, model):
""" Test that variable updating works. """
p1 = AnnualHarmonicSeriesParameter(model, 0.5, [0.25], [np.pi/4], is_variable=True)

assert p1.double_size == 3
assert p1.integer_size == 0

new_var = np.array([0.6, 0.1, np.pi/2])
p1.set_double_variables(new_var)
np.testing.assert_allclose(p1.get_double_variables(), new_var)

with pytest.raises(NotImplementedError):
p1.set_integer_variables(np.arange(3, dtype=np.int32))

with pytest.raises(NotImplementedError):
p1.get_integer_variables()

si = ScenarioIndex(0, np.array([0], dtype=np.int32))

for ts in model.timestepper:
doy = (ts.datetime.dayofyear - 1)/365
np.testing.assert_allclose(p1.value(ts, si), 0.6 + 0.1*np.cos(doy*2*np.pi + np.pi/2)) ```
Example 14
 Project: EXOSIMS   Author: dsavransky   File: FakeCatalog.py    License: BSD 3-Clause "New" or "Revised" License 6 votes
```def inverse_method(self,N,d):

t = np.linspace(1e-3,0.999,N)
f = np.log( t / (1 - t) )
f = f/f[0]

psi= np.pi*f
cosPsi = np.cos(psi)
sinTheta = ( np.abs(cosPsi) + (1-np.abs(cosPsi))*np.random.rand(len(cosPsi)))

theta = np.arcsin(sinTheta)
theta = np.pi-theta + (2*theta - np.pi)*np.round(np.random.rand(len(t)))
cosPhi = cosPsi/sinTheta
phi = np.arccos(cosPhi)*(-1)**np.round(np.random.rand(len(t)))

return coords ```
Example 15
 Project: EXOSIMS   Author: dsavransky   File: GarrettCompleteness.py    License: BSD 3-Clause "New" or "Revised" License 6 votes
```def Jac(self, b):
"""Calculates determinant of the Jacobian transformation matrix to get
the joint probability density of dMag and s

Args:
b (ndarray):
Phase angles

Returns:
f (ndarray):
Determinant of Jacobian transformation matrix

"""

f = -2.5/(self.Phi(b)*np.log(10.0))*self.dPhi(b)*np.sin(b) - 5./np.log(10.0)*np.cos(b)

return f ```
Example 16
 Project: EXOSIMS   Author: dsavransky   File: keplerSTM.py    License: BSD 3-Clause "New" or "Revised" License 6 votes
```def psi2c2c3(self, psi0):

c2 = np.zeros(len(psi0))
c3 = np.zeros(len(psi0))

psi12 = np.sqrt(np.abs(psi0))
pos = psi0 >= 0
neg = psi0 < 0
if np.any(pos):
c2[pos] = (1 - np.cos(psi12[pos]))/psi0[pos]
c3[pos] = (psi12[pos] - np.sin(psi12[pos]))/psi12[pos]**3.
if any(neg):
c2[neg] = (1 - np.cosh(psi12[neg]))/psi0[neg]
c3[neg] = (np.sinh(psi12[neg]) - psi12[neg])/psi12[neg]**3.

tmp = c2+c3 == 0
if any(tmp):
c2[tmp] = 1./2.
c3[tmp] = 1./6.

return c2,c3 ```
Example 17
 Project: EXOSIMS   Author: dsavransky   File: PlanetPhysicalModel.py    License: BSD 3-Clause "New" or "Revised" License 6 votes
```def calc_Phi(self, beta):
"""Calculate the phase function. Prototype method uses the Lambert phase
function from Sobolev 1975.

Args:
beta (astropy Quantity array):
Planet phase angles at which the phase function is to be calculated,
in units of rad

Returns:
Phi (ndarray):
Planet phase function

"""

Phi = (np.sin(beta) + (np.pi - beta)*np.cos(beta))/np.pi

return Phi ```
Example 18
 Project: py360convert   Author: sunset1995   File: utils.py    License: MIT License 6 votes
```def equirect_facetype(h, w):
'''
0F 1R 2B 3L 4U 5D
'''
tp = np.roll(np.arange(4).repeat(w // 4)[None, :].repeat(h, 0), 3 * w // 8, 1)

# Prepare ceil mask
mask = np.zeros((h, w // 4), np.bool)
idx = np.linspace(-np.pi, np.pi, w // 4) / 4
idx = h // 2 - np.round(np.arctan(np.cos(idx)) * h / np.pi).astype(int)
for i, j in enumerate(idx):
mask[:j, i] = 1
mask = np.roll(np.concatenate([mask] * 4, 1), 3 * w // 8, 1)

tp[np.flip(mask, 0)] = 5

return tp.astype(np.int32) ```
Example 19
 Project: pointnet-registration-framework   Author: vinits5   File: helper.py    License: MIT License 6 votes
```def rotate_point_cloud_by_angle_y(batch_data, rotation_angle):
""" Rotate the point cloud along up direction with certain angle.
Input:
BxNx3 array, original batch of point clouds
Return:
BxNx3 array, rotated batch of point clouds
"""
rotated_data = np.zeros(batch_data.shape, dtype=np.float32)
for k in range(batch_data.shape[0]):
#rotation_angle = np.random.uniform() * 2 * np.pi
cosval = np.cos(rotation_angle)
sinval = np.sin(rotation_angle)
rotation_matrix = np.array([[cosval, 0, sinval],
[0, 1, 0],
[-sinval, 0, cosval]])
shape_pc = batch_data[k, ...]
# rotated_data[k, ...] = np.dot(shape_pc.reshape((-1, 3)), rotation_matrix)
rotated_data[k, ...] = np.dot(rotation_matrix, shape_pc.reshape((-1, 3)).T).T 		# Pre-Multiplication (changes done)
return rotated_data ```
Example 20
 Project: xrft   Author: xgcm   File: test_xrft.py    License: MIT License 5 votes
```def test_cross_phase_1d(self, dask):
N = 32
x = np.linspace(0, 1, num=N, endpoint=False)
f = 6
phase_offset = np.pi/2
signal1 = np.cos(2*np.pi*f*x)  # frequency = 1/(2*pi)
signal2 = np.cos(2*np.pi*f*x - phase_offset)
da1 = xr.DataArray(data=signal1, name='a', dims=['x'], coords={'x': x})
da2 = xr.DataArray(data=signal2, name='b', dims=['x'], coords={'x': x})

da1 = da1.chunk({'x': 32})
da2 = da2.chunk({'x': 32})
cp = xrft.cross_phase(da1, da2, dim=['x'])

actual_phase_offset = cp.sel(freq_x=f).values
npt.assert_almost_equal(actual_phase_offset, phase_offset)
assert cp.name == 'a_b_phase'

xrt.assert_equal(xrft.cross_phase(da1, da2), cp)

with pytest.raises(ValueError):
xrft.cross_phase(da1, da2.isel(x=0).drop('x'))

with pytest.raises(ValueError):
xrft.cross_phase(da1, da2.rename({'x':'y'})) ```
Example 21
 Project: DDPAE-video-prediction   Author: jthsieh   File: moving_mnist.py    License: MIT License 5 votes
```def get_random_trajectory(self, seq_length):
''' Generate a random sequence of a MNIST digit '''
canvas_size = self.image_size_ - self.digit_size_
x = random.random()
y = random.random()
theta = random.random() * 2 * np.pi
v_y = np.sin(theta)
v_x = np.cos(theta)

start_y = np.zeros(seq_length)
start_x = np.zeros(seq_length)
for i in range(seq_length):
# Take a step along velocity.
y += v_y * self.step_length_
x += v_x * self.step_length_

# Bounce off edges.
if x <= 0:
x = 0
v_x = -v_x
if x >= 1.0:
x = 1.0
v_x = -v_x
if y <= 0:
y = 0
v_y = -v_y
if y >= 1.0:
y = 1.0
v_y = -v_y
start_y[i] = y
start_x[i] = x

# Scale to the size of the canvas.
start_y = (canvas_size * start_y).astype(np.int32)
start_x = (canvas_size * start_x).astype(np.int32)
return start_y, start_x ```
Example 22
 Project: FRIDA   Author: LCAV   File: point_cloud.py    License: MIT License 5 votes
```def align(self, marker, axis):
'''
Rotate the marker set around the given axis until it is aligned onto the given marker

Parameters
----------
marker : int or str
the index or label of the marker onto which to align the set
axis : int
the axis around which the rotation happens
'''

index = self.key2ind(marker)
axis = ['x','y','z'].index(axis) if isinstance(marker, (str, unicode)) else axis

# swap the axis around which to rotate to last position
Y = self.X
if self.dim == 3:
Y[axis,:], Y[2,:] = Y[2,:], Y[axis,:]

# Rotate around z to align x-axis to second point
theta = np.arctan2(Y[1,index],Y[0,index])
c = np.cos(theta)
s = np.sin(theta)
H = np.array([[c, s],[-s, c]])
Y[:2,:] = np.dot(H,Y[:2,:])

if self.dim == 3:
Y[axis,:], Y[2,:] = Y[2,:], Y[axis,:] ```
Example 23
 Project: FRIDA   Author: LCAV   File: utils.py    License: MIT License 5 votes
```def polar2cart(rho, phi):
"""
convert from polar to cartesian coordinates
:param phi: azimuth
:return:
"""
x = rho * np.cos(phi)
y = rho * np.sin(phi)
return x, y ```
Example 24
 Project: FRIDA   Author: LCAV   File: doa.py    License: MIT License 5 votes
```def polar_distance(x1, x2):
"""
Given two arrays of numbers x1 and x2, pairs the cells that are the
closest and provides the pairing matrix index: x1(index(1,:)) should be as
close as possible to x2(index(2,:)). The function outputs the average of
the absolute value of the differences abs(x1(index(1,:))-x2(index(2,:))).
:param x1: vector 1
:param x2: vector 2
:return: d: minimum distance between d
index: the permutation matrix
"""
x1 = np.reshape(x1, (1, -1), order='F')
x2 = np.reshape(x2, (1, -1), order='F')
N1 = x1.size
N2 = x2.size
diffmat = np.arccos(np.cos(x1 - np.reshape(x2, (-1, 1), order='F')))
min_N1_N2 = np.min([N1, N2])
index = np.zeros((min_N1_N2, 2), dtype=int)
if min_N1_N2 > 1:
for k in range(min_N1_N2):
d2 = np.min(diffmat, axis=0)
index2 = np.argmin(diffmat, axis=0)
index1 = np.argmin(d2)
index2 = index2[index1]
index[k, :] = [index1, index2]
diffmat[index2, :] = float('inf')
diffmat[:, index1] = float('inf')
d = np.mean(np.arccos(np.cos(x1[:, index[:, 0]] - x2[:, index[:, 1]])))
else:
d = np.min(diffmat)
index = np.argmin(diffmat)
if N1 == 1:
index = np.array([1, index])
else:
index = np.array([index, 1])
return d, index ```
Example 25
 Project: dustmaps   Author: gregreen   File: bh.py    License: GNU General Public License v2.0 5 votes
```def _lb2RN_northcap(self, l, b):
R = 100. + (90. - b) * np.sin(np.radians(l)) / 0.3
N = 100. + (90. - b) * np.cos(np.radians(l)) / 0.3
return np.round(R).astype('i4'), np.round(N).astype('i4') ```
Example 26
 Project: dustmaps   Author: gregreen   File: bh.py    License: GNU General Public License v2.0 5 votes
```def _lb2RN_southcap(self, l, b):
R = 100. + (90. + b) * np.sin(np.radians(l)) / 0.3
N = 100. + (90. + b) * np.cos(np.radians(l)) / 0.3
return np.round(R).astype('i4'), np.round(N).astype('i4') ```
Example 27
```def f(x):
return x * np.cos(np.pi * x) ```
Example 28
 Project: NiBetaSeries   Author: HBClab   File: conftest.py    License: MIT License 5 votes
```def preproc_file(deriv_dir, sub_metadata, deriv_bold_fname=deriv_bold_fname):
deriv_bold = deriv_dir.ensure(deriv_bold_fname)
with open(str(sub_metadata), 'r') as md:
# time_points
tp = 200
ix = np.arange(tp)
# create voxel timeseries
# add activations at every 40 time points
# waffles
# fries
# milkshakes
# csf
csf = np.cos(2*np.pi*ix*(50/tp)) * 0.1
# white matter
wm = np.sin(2*np.pi*ix*(22/tp)) * 0.1
# voxel time series (signal and noise)
voxel_ts = signal + csf + wm
# a 4d matrix with 2 identical timeseries
img_data = np.array([[[voxel_ts, voxel_ts]]])
# make a nifti image
img = nib.Nifti1Image(img_data, np.eye(4))
# save the nifti image
img.to_filename(str(deriv_bold))

return deriv_bold ```
Example 29
 Project: NiBetaSeries   Author: HBClab   File: conftest.py    License: MIT License 5 votes
```def confounds_file(deriv_dir, preproc_file,
deriv_regressor_fname=deriv_regressor_fname):
confounds_file = deriv_dir.ensure(deriv_regressor_fname)
confound_dict = {}
ix = np.arange(tp)
# csf
confound_dict['csf'] = np.cos(2*np.pi*ix*(50/tp)) * 0.1
# white matter
confound_dict['white_matter'] = np.sin(2*np.pi*ix*(22/tp)) * 0.1
# framewise_displacement
confound_dict['framewise_displacement'] = np.random.random_sample(tp)
confound_dict['framewise_displacement'][0] = np.nan
# motion outliers
for motion_outlier in range(0, 5):
mo_name = 'motion_outlier0{}'.format(motion_outlier)
confound_dict[mo_name] = np.zeros(tp)
confound_dict[mo_name][motion_outlier] = 1
# derivatives
derive1 = [
'csf_derivative1',
'csf_derivative1_power2',
'global_signal_derivative1_power2',
'trans_x_derivative1',
'trans_y_derivative1',
'trans_z_derivative1',
'trans_x_derivative1_power2',
'trans_y_derivative1_power2',
'trans_z_derivative1_power2',
]
for d in derive1:
confound_dict[d] = np.random.random_sample(tp)
confound_dict[d][0] = np.nan

# transformations
for dir in ["trans_x", "trans_y", "trans_z"]:
confound_dict[dir] = np.random.random_sample(tp)

confounds_df = pd.DataFrame(confound_dict)
confounds_df.to_csv(str(confounds_file), index=False, sep='\t', na_rep='n/a')
return confounds_file ```
Example 30
 Project: neuropythy   Author: noahbenson   File: util.py    License: GNU Affero General Public License v3.0 5 votes
```def spherical_distance(pt0, pt1):
'''
spherical_distance(a, b) yields the angular distance between points a and b, both of which
should be expressed in spherical coordinates as (longitude, latitude).
If a and/or b are (2 x n) matrices, then the calculation is performed over all columns.
The spherical_distance function uses the Haversine formula; accordingly it may suffer from
rounding errors in the case of nearly antipodal points.
'''
dtheta = pt1[0] - pt0[0]
dphi   = pt1[1] - pt0[1]
a = np.sin(dphi/2)**2 + np.cos(pt0[1]) * np.cos(pt1[1]) * np.sin(dtheta/2)**2
return 2 * np.arcsin(np.sqrt(a)) ```