def __call__(self, t: np.float64, y: np.array) -> np.array:
# get interpolant data
v_gas = double(self._gas.Velocity(t))
T = double(self._gas.Temperature(
t)) # this cast is necessary, not sure why just yet
dT = double(self._gas.Temperature(t, derivative=1))
rho = self._gas.Density(t)
drho = self._gas.Density(t, derivative=1)
# call calculators
xpnd = drho / rho
vol = self._gas.mass_0 / rho
self._cbar[:] = self._gas.cbar(vol)
dydt = _f(self._dust_calc, self._dust_par, y, self._cbar, T, dT)
expand(xpnd, y[0:self._net.NG], dydt[0:self._net.NG])
dadt, d_conc = destroy(self._gas, self._net, vol, rho, y, T, v_gas)
conc_update(d_conc, dydt[0:self._net.NG], y[0:self._net.NG])
#erode(dadt, y[self._net.NG+self._net.ND*N_MOMENTS:], dydt[self._net.NG+self._net.ND*N_MOMENTS:], self._net.NG, self._dust_calc)
erode_grow(dadt, y, dydt, self._net.NG, self._dust_calc)
return dydt
def loglike_fct(new_theta, thetas, datapoint, rn, ATtcB, sampled_feature_index, mean_fixed_contrib, inv_covariance_fixed_contrib):
'''
Compute the loglikelihood of: theta_r | n_tc theta_r' tc
'''
# print 'what?', params, len(params)
# thetas = params[0]
# datapoint = params[1]
# # rn = params[2]
# # theta_mu = params[3]
# # theta_kappa = params[4]
# ATtcB = nub.double(params[5])
# sampled_feature_index = params[6]
# mean_fixed_contrib = params[7]
# inv_covariance_fixed_contrib = params[8]
# Put the new proposed point correctly
thetas[sampled_feature_index] = new_theta
# print nub.typeof(mean_fixed_contrib), nub.typeof(inv_covariance_fixed_contrib)
# print inv_covariance_fixed_contrib
# a = rn.get_network_response_numba(thetas)
like_mean = datapoint - mean_fixed_contrib - ATtcB*rn.get_network_response_numba(thetas)
# Using inverse covariance as param
# return theta_kappa*np.cos(thetas[sampled_feature_index] - theta_mu) - 0.5*np.dot(like_mean, np.dot(inv_covariance_fixed_contrib, like_mean))
return -0.5*nub.double(np.dot(like_mean, np.dot(inv_covariance_fixed_contrib, like_mean)))
def test_fromnumba():
import numba as nb
def fromstr(a):
return Type_fromstring(a)
def fromnumba(t):
return Type.fromnumba(t, target_info)
assert fromnumba(nb.void) == fromstr('void')
assert fromnumba(nb.boolean) == fromstr('bool')
assert fromnumba(nb.int8) == fromstr('int8')
assert fromnumba(nb.int16) == fromstr('int16')
assert fromnumba(nb.int32) == fromstr('int32')
assert fromnumba(nb.int64) == fromstr('int64')
assert fromnumba(nb.uint8) == fromstr('uint8')
assert fromnumba(nb.uint16) == fromstr('uint16')
assert fromnumba(nb.uint32) == fromstr('uint32')
assert fromnumba(nb.uint64) == fromstr('uint64')
assert fromnumba(nb.float_) == fromstr('float32')
assert fromnumba(nb.double) == fromstr('float64')
assert fromnumba(nb.complex64) == fromstr('complex64')
assert fromnumba(nb.complex128) == fromstr('complex128')
assert fromnumba(nb.types.CPointer(nb.float64)) == fromstr('double*')
assert fromnumba(nb.double(nb.int64, nb.float_)) == fromstr('d(i64, f)')
def __init__(self, w, h):
# All instance attributes must be defined in the initializer
self.width = w
self.height = h
# Types can be explicitly specified through casts
self.some_attr = double(1.0)
def __init__(self, w, h):
# All instance attributes must be defined in the initializer
self.width = w
self.height = h
# Types can be explicitly specified through casts
self.some_attr = double(1.0)
def __call__(self, t: np.float64, y: np.array) -> np.array:
# get interpolant data
T = double(self._gas.Temperature(
t)) # this cast is necessary, not sure why just yet
dT = double(self._gas.Temperature(t, derivative=1))
rho = self._gas.Density(t)
drho = self._gas.Density(t, derivative=1)
# call calculators
xpnd = drho / rho
vol = self._gas.mass_0 / rho
self._cbar[:] = self._gas.cbar(vol)
dydt = _f(self._dust_calc, self._dust_par, y, self._cbar, T, dT)
expand(xpnd, y[0:self._net.NG], dydt[0:self._net.NG])
return dydt
def SGD(R, P, Q, W, K=num_of_features, num_of_iterations=num_of_iterations):
steps = num_of_iterations * 10
weighted_errors = []
alpha = 0.002
beta = 0.01
QT = Q.T
n, m = R.shape
step = 0
err = 0.0
for step in xrange(steps):
for i in xrange(n):
for j in xrange(m):
if R[i,j] > 0:
temp = double(np.dot(P[i,:],QT[:,j]))
eij = R[i,j] - temp
for k in xrange(K):
P[i,k] += 2 * alpha * (eij * QT[k,j] - beta * P[i,k])
QT[k,j] += 2 * alpha * (eij * P[i,k] - beta * QT[k,j])
err = get_error(R, P, Q, W)
weighted_errors.append(err)
print_stamp("Step " + str(step) + " done.")
if err < 0.5:
break
return weighted_errors, P, QT.T, step + 1
def compile_rematch():
'''
Compile the rematch function with numba.
:return: Compiled version of the rematch function.
'''
signatureRem = nb.double(nb.double[:, :], nb.double, nb.double)
nb_rematch = nb.jit(signatureRem, nopython=True, nogil=True,cache=True)(rematch)
return nb_rematch
def main(*args):
import numba as nb
test_ast = ast_module.parse('def test_fn(a, b):\n return a + b\n\n',
'<string>', 'exec')
exec(compile(test_ast, '<string>', 'exec'))
test_fn_ast = test_ast.body[-1]
test_fn_sig = nb.double(nb.double, nb.double)
test_fn_sig.name = test_fn.__name__
env = NumbaEnvironment.get_environment()
with TranslationContext(env, test_fn, test_fn_ast, test_fn_sig):
env.get_pipeline()(test_fn_ast, env)
assert env.pipeline_stages == pipeline
def main(*args):
import numba as nb
test_ast = ast_module.parse('def test_fn(a, b):\n return a + b\n\n',
'<string>', 'exec')
exec(compile(test_ast, '<string>', 'exec'))
test_fn_ast = test_ast.body[-1]
test_fn_sig = nb.double(nb.double, nb.double)
test_fn_sig.name = test_fn.__name__
env = NumbaEnvironment.get_environment()
with TranslationContext(env, test_fn, test_fn_ast, test_fn_sig):
env.get_pipeline()(test_fn_ast, env)
assert env.pipeline_stages == pipeline
def cross3(vec1, vec2, result):
""" Calculate the cross product of two 3d vectors. """
a1, a2, a3 = double(vec1[0]), double(vec1[1]), double(vec1[2])
b1, b2, b3 = double(vec2[0]), double(vec2[1]), double(vec2[2])
result[0] = a2 * b3 - a3 * b2
result[1] = a3 * b1 - a1 * b3
result[2] = a1 * b2 - a2 * b1
def numba_cross_(vec1, vec2, result):
"""calculates the cross product of two 3d vectors"""
a1, a2, a3 = double(vec1[0]), double(vec1[1]), double(vec1[2])
b1, b2, b3 = double(vec2[0]), double(vec2[1]), double(vec2[2])
result[0] = a2 * b3 - a3 * b2
result[1] = a3 * b1 - a1 * b3
result[2] = a1 * b2 - a2 * b1
return result
def rgbd_cal_dmask2cbox(depth_img, col_img_h, col_img_w, dcm, ccm, ext, depth_scl, depth_mask):
"""
Calibrating depth and color image for computing a bounding box
in color image space based on the input depth mask
"""
depth_height = depth_img.shape[0]
depth_width = depth_img.shape[1]
color_height = col_img_h
color_width = col_img_w
depth_mask_height = depth_mask.shape[0]
depth_mask_width = depth_mask.shape[1]
#assert depth_mask.shape == depth_img.shape, 'assertion failed -- rgbd_cal_dmask2cbox: depth_mask.shape == depth_img.shape'
aligned = np.zeros((depth_height, depth_width, 3), dtype=np.float_)
color_bbox = [color_width, color_height, 0, 0]
fx_d, fy_d, cx_d, cy_d = double(dcm[0][0]), double(dcm[1][1]), double(dcm[0][2]), double(dcm[1][2])
for v in range(depth_height):
for u in range(depth_width):
z = double(depth_img[v][u]) / double(depth_scl)
x = (u - cx_d) * z / fx_d
y = (v - cy_d) * z / fy_d
transformed = mul(ext, np.array([x, y, z, 1]))
aligned[v][u] = transformed[0:3]
fx_c, fy_c, cx_c, cy_c = double(ccm[0][0]), double(ccm[1][1]), double(ccm[0][2]), double(ccm[1][2])
validFlag = False
for v in range(depth_mask_height):
for u in range(depth_mask_width):
if depth_mask[v][u] == 0 or aligned[v][u][2] == 0:
continue
x = aligned[v][u][0] * fx_c / aligned[v][u][2] + cx_c
y = aligned[v][u][1] * fy_c / aligned[v][u][2] + cy_c
if x > color_width or y > color_height or x < 0 or y < 0:
continue
color_bbox[0] = min(int(round(x)), color_bbox[0])
color_bbox[1] = min(int(round(y)), color_bbox[1])
color_bbox[2] = max(int(round(x)), color_bbox[2])
color_bbox[3] = max(int(round(y)), color_bbox[3])
validFlag = True
if not validFlag:
color_bbox = [0, 0, color_width, color_height]
if color_bbox[2] - color_bbox[0] < 2:
color_bbox[2] = color_bbox[0] + 2
if color_bbox[3] - color_bbox[1] < 2:
color_bbox[3] = color_bbox[1] + 2
return (color_bbox)
def test_type_inference(self):
global vector_add
vector_add = vectorize([
bool_(double, int_),
double(double, double),
float_(double, float_),
])(add)
cfunc = jit(func)
self.assertEqual(cfunc(np.dtype(np.float64), np.dtype('i')), int8[:])
self.assertEqual(cfunc(np.dtype(np.float64), np.dtype(np.float64)),
double[:])
self.assertEqual(cfunc(np.dtype(np.float64), np.dtype(np.float32)),
float_[:])
def test_tonumba():
def tonumba(a):
return Type_fromstring(a).tonumba()
assert tonumba('void') == nb.void
assert tonumba('bool') == nb.boolean
assert tonumba('int8') == nb.int8
assert tonumba('int16') == nb.int16
assert tonumba('int32') == nb.int32
assert tonumba('int64') == nb.int64
assert tonumba('uint8') == nb.uint8
assert tonumba('uint16') == nb.uint16
assert tonumba('uint32') == nb.uint32
assert tonumba('uint64') == nb.uint64
assert tonumba('float') == nb.float32
assert tonumba('double') == nb.float64
assert tonumba('complex') == nb.complex64
assert tonumba('complex128') == nb.complex128
assert tonumba('double*') == nb.types.CPointer(nb.float64)
assert tonumba('()') == nb.void()
assert tonumba('d(i64, f)') == nb.double(nb.int64, nb.float_)
def test_type_inference(self):
"""This is testing numpy ufunc dispatch machinery"""
global vector_add
vector_add = vectorize([
bool_(double, int_),
double(double, double),
float_(double, float_),
])(add)
cfunc = jit(func)
def numba_type_equal(a, b):
self.assertEqual(a.dtype, b.dtype)
self.assertEqual(a.ndim, b.ndim)
numba_type_equal(cfunc(np.dtype(np.float64), np.dtype("i")), bool_[:])
numba_type_equal(cfunc(np.dtype(np.float64), np.dtype(np.float64)),
double[:])
# This is because the double(double, double) matches first
numba_type_equal(cfunc(np.dtype(np.float64), np.dtype(np.float32)),
double[:])
def glm_one_group_numba(x, dispersion,
offset):
""" Returns the estimated betas using newton-raphson
Params
x : count matrix
dispersion : negative binomial dispersion value
"""
maxit = 50
ntags = x.shape[0]
nsamples = x.shape[1]
out = np.zeros(ntags)
low_level = 1e-10
for i in range(ntags):
beta = 0
nonzero = False
for j in range(nsamples):
cur_val = x[i, j]
if cur_val > low_level:
beta += cur_val/np.exp(offset[j])
nonzero = True
else: pass
if not nonzero:
beta = -np.inf
else:
beta = np.log(beta/double(nsamples))
for it in range(maxit):
dl = 0
info = 0
for k in range(nsamples):
mu = np.exp(beta + offset[k])
denominator = 1 + mu * dispersion[i]
dl += (x[i, k] - mu)/denominator
info += mu/denominator
step = dl/info
beta += step
if abs(step) < 1e-6:
break
out[i] = beta
return out
def glm_one_group_numba(x, dispersion, offset):
""" Returns the estimated betas using newton-raphson
Params
x : count matrix
dispersion : negative binomial dispersion value
"""
maxit = 50
ntags = x.shape[0]
nsamples = x.shape[1]
out = np.zeros(ntags)
low_level = 1e-10
for i in range(ntags):
beta = 0
nonzero = False
for j in range(nsamples):
cur_val = x[i, j]
if cur_val > low_level:
beta += cur_val / np.exp(offset[j])
nonzero = True
else:
pass
if not nonzero:
beta = -np.inf
else:
beta = np.log(beta / double(nsamples))
for it in range(maxit):
dl = 0
info = 0
for k in range(nsamples):
mu = np.exp(beta + offset[k])
denominator = 1 + mu * dispersion[i]
dl += (x[i, k] - mu) / denominator
info += mu / denominator
step = dl / info
beta += step
if abs(step) < 1e-6:
break
out[i] = beta
return out
def test_type_inference(self):
"""This is testing numpy ufunc dispatch machinery
"""
global vector_add
vector_add = vectorize([
bool_(double, int_),
double(double, double),
float_(double, float_),
])(add)
cfunc = jit(func)
def numba_type_equal(a, b):
self.assertEqual(a.dtype, b.dtype)
self.assertEqual(a.ndim, b.ndim)
numba_type_equal(cfunc(np.dtype(np.float64), np.dtype('i')), bool_[:])
numba_type_equal(cfunc(np.dtype(np.float64), np.dtype(np.float64)),
double[:])
# This is because the double(double, double) matches first
numba_type_equal(cfunc(np.dtype(np.float64), np.dtype(np.float32)),
double[:])
size_y : int
Size of cluster y
size_i : int
Size of cluster i
Returns
-------
d_xyi : double
Distance from the new cluster xy to cluster i
"""
import math
import numba as nb
sig = nb.double(nb.double, nb.double, nb.double, nb.int64, nb.int64, nb.int64)
@nb.njit(sig)
def _single(d_xi, d_yi, d_xy, size_x, size_y, size_i):
return min(d_xi, d_yi)
@nb.njit(sig)
def _complete(d_xi, d_yi, d_xy, size_x, size_y, size_i):
return max(d_xi, d_yi)
@nb.njit(sig)
def _average(d_xi, d_yi, d_xy, size_x, size_y, size_i):
return (size_x * d_xi + size_y * d_yi) / (size_x + size_y)
import os
import cPickle as pickle
import csv
import data_analysis
from data_analysis import refdir,refdirahk114,caadir,vfile_store
#import calendar
import pandas as pd
from numba import jit,double
#plt.style.use('seaborn-darkgrid')
end_date=datetime(9999,1,1)
EXTMODE_INITIATE = ["SFGMJ059","SFGMJ064","SFGMSEXT","SFGMM002"]
EXTMODE_TERMINATE = ["SFGMJ065","SFGMJ050"]
EXTMODE_COMMANDS = EXTMODE_INITIATE+EXTMODE_TERMINATE
@jit(double(double[:]),nopython=True)
def numba_std(arr):
return np.std(arr)
@jit(double(double[:]),nopython=True)
def numba_mean(arr):
return np.mean(arr)
@jit(double(double[:]),nopython=True)
def numba_max(arr):
return np.max(arr)
@jit(double(double[:]),nopython=True)
def numba_min(arr):
return np.min(arr)
def getcommands(start_date,end_date):
extmode_commanding_list = []
for s in range(4):
elif xi >= x[Nx - 2]:
return Nx - 2
# b. binary search
half = Nx // 2
while half:
imid = imin + half
if x[imid] <= xi:
imin = imid
Nx -= half
half = Nx // 2
return imin
@njit(double(double[:], double[:], double))
def interp_linear_1d_scalar(grid, value, xi):
""" raw 1D interpolation """
# a. search
ix = binary_search(0, grid.size, grid, xi)
# b. relative positive
rel_x = (xi - grid[ix]) / (grid[ix + 1] - grid[ix])
# c. interpolate
return value[ix] + rel_x * (value[ix + 1] - value[ix])
@njit
def interp_linear_1d(grid, value, xi):
def test_blackscholes(self):
OPT_N = 400
iterations = 2
stockPrice = randfloat(np.random.random(OPT_N), 5.0, 30.0)
optionStrike = randfloat(np.random.random(OPT_N), 1.0, 100.0)
optionYears = randfloat(np.random.random(OPT_N), 0.25, 10.0)
callResultNumpy = np.zeros(OPT_N)
putResultNumpy = -np.ones(OPT_N)
callResultNumba = np.zeros(OPT_N)
putResultNumba = -np.ones(OPT_N)
# numpy
for i in range(iterations):
black_scholes(callResultNumpy, putResultNumpy, stockPrice,
optionStrike, optionYears, RISKFREE, VOLATILITY)
@cuda.jit(double(double), device=True, inline=True)
def cnd_cuda(d):
K = 1.0 / (1.0 + 0.2316419 * math.fabs(d))
ret_val = (RSQRT2PI * math.exp(-0.5 * d * d) *
(K * (A1 + K * (A2 + K * (A3 + K * (A4 + K * A5))))))
if d > 0:
ret_val = 1.0 - ret_val
return ret_val
@cuda.jit(
void(double[:], double[:], double[:], double[:], double[:], double,
double))
def black_scholes_cuda(callResult, putResult, S, X, T, R, V):
i = cuda.threadIdx.x + cuda.blockIdx.x * cuda.blockDim.x
if i >= S.shape[0]:
return
sqrtT = math.sqrt(T[i])
d1 = ((math.log(S[i] / X[i]) + (R + 0.5 * V * V) * T[i]) /
(V * sqrtT))
d2 = d1 - V * sqrtT
cndd1 = cnd_cuda(d1)
cndd2 = cnd_cuda(d2)
expRT = math.exp((-1. * R) * T[i])
callResult[i] = (S[i] * cndd1 - X[i] * expRT * cndd2)
putResult[i] = (X[i] * expRT * (1.0 - cndd2) - S[i] *
(1.0 - cndd1))
# numba
blockdim = 512, 1
griddim = int(math.ceil(float(OPT_N) / blockdim[0])), 1
stream = cuda.stream()
d_callResult = cuda.to_device(callResultNumba, stream)
d_putResult = cuda.to_device(putResultNumba, stream)
d_stockPrice = cuda.to_device(stockPrice, stream)
d_optionStrike = cuda.to_device(optionStrike, stream)
d_optionYears = cuda.to_device(optionYears, stream)
for i in range(iterations):
black_scholes_cuda[griddim, blockdim,
stream](d_callResult, d_putResult, d_stockPrice,
d_optionStrike, d_optionYears, RISKFREE,
VOLATILITY)
d_callResult.copy_to_host(callResultNumba, stream)
d_putResult.copy_to_host(putResultNumba, stream)
stream.synchronize()
delta = np.abs(callResultNumpy - callResultNumba)
L1norm = delta.sum() / np.abs(callResultNumpy).sum()
max_abs_err = delta.max()
self.assertTrue(L1norm < 1e-13)
self.assertTrue(max_abs_err < 1e-13)
from ...containers import MuonEfficiencyContainer
from ...coordinates import CameraFrame, TelescopeFrame
from ...core import TelescopeComponent
from ...core.traits import FloatTelescopeParameter, IntTelescopeParameter
__all__ = ["MuonIntensityFitter"]
# ratio of the areas of the unit circle and a square of side lengths 2
CIRCLE_SQUARE_AREA_RATIO = np.pi / 4
# Sqrt of 2, as it is needed multiple times
SQRT2 = np.sqrt(2)
@vectorize([double(double, double, double)])
def chord_length(radius, rho, phi):
"""
Function for integrating the length of a chord across a circle
Parameters
----------
radius: float or ndarray
radius of circle
rho: float or ndarray
fractional distance of impact point from circle center
phi: float or ndarray in radians
rotation angles to calculate length
Returns
-------
"""
def fn( x ):
result = 0.0
for i in range( 100 ):
result += (1+i+x)/(1+x)
return result
"""
def fn( x ):
result = 0.0
for i in range( 10000 ):
result+=i*x
return result
nb_fn = jit( double(double, ), nopython=True )( fn )
class Test(unittest.TestCase):
def test_mvectorize(self):
x = np.linspace( 1, 1000, 10000 )
mf_fn = mvectorize( nb_fn, ( double[:], double[:] ), num_threads=8 )
result = mf_fn( x )
expected = np.vectorize( fn )( x )
np.testing.assert_array_equal( expected, result )
def test_mvectorize_performance(self):
#!/usr/bin/env python # coding: UTF-8 from __future__ import division import numpy as np import numba as nb from numba import double, jit def dot3_python(a,b): return a[0]*b[0] + a[1]*b[1] + a[2]*b[2] dot3_numba = jit(double(double[:],double[:]),nopython=True)(dot3_python) def _hamiltonian_jet_python(strengths, m,dH,ddH): """ Private function to Compute H and its gradient dH at the point m. This function is not meant to be used directly. """ n = len(strengths) H = 0.0 for i in range(n): for j in range(i): ## mi_dot_mj = m[3*i]*m[3*j] + m[3*i+1]*m[3*j+1] + m[3*i+2]*m[3*j+2] strength = strengths[i] * strengths[j] mi_dot_mj = dot3_numba(m[3*i:3*(i+1)],m[3*j:3*(j+1)]) lij = 1.0-mi_dot_mj lijsq = lij**2 H += strength*np.log(2.0*lij) for k in range(3): dH[3*i+k] -= strength*m[3*j+k]/lij dH[3*j+k] -= strength*m[3*i+k]/lij
$ cor_atm = CorsikaAtmosphere(new_location, new_season)
$ cor_atm.calc_thickl()
Replace _thickl values with printout.
"""
from scipy.integrate import quad
thickl = []
for h in self._atm_param[4]:
thickl.append('{0:4.6f}'.format(
quad(self.get_density, h, 112.8e5, epsrel=1e-4)[0]))
if dbg:
print '_thickl = np.array([' + ', '.join(thickl) + '])'
@jit(double(double, double, double[:, :]), target='cpu')
def planar_rho_inv_jit(X, cos_theta, param):
"""Optimized calculation of :math:`1/\\rho(X,\\theta)` in
planar approximation.
This function can be used for calculations where
:math:`\\theta < 70^\\circ`.
Args:
X (float): slant depth in g/cm**2
cos_theta (float): :math:`\\cos(\\theta)`
Returns:
float: :math:`1/\\rho(X,\\theta)` in cm**3/g
"""
a = param[0]
return 0.5 * np.floor( xi / 0.5 )
elif xi<=20.0:
return 1.0 * np.floor( xi / 1.0 )
elif xi<=30.0:
return 2.0 * np.floor( xi / 2.0 )
elif xi<=50.0:
return 2.0 * np.floor( xi / 2.0 )
elif xi<=100.0:
return 5.0 * np.floor( xi / 5.0 )
elif xi<=1000.0:
return 10.0 * np.floor( xi / 10.0 )
else:
return 1000.0
return 0.0
signature = double(double,)
print( 'Compiling jit function' )
nb_floor_closest_valid_odds = jit(signature, nopython=True)(floor_closest_valid_odds)
print( 'Compiling 4 thread')
mf4 = mvectorize( nb_floor_closest_valid_odds, ( double[:], double[:] ), num_threads=4 )
print( 'Compiling 6 thread')
mf6 = mvectorize( nb_floor_closest_valid_odds, ( double[:], double[:] ), num_threads=6 )
print( 'Compiling 7 thread')
mf7 = mvectorize( nb_floor_closest_valid_odds, ( double[:], double[:] ), num_threads=7 )
print( 'Compiling 8 thread')
mf8 = mvectorize( nb_floor_closest_valid_odds, ( double[:], double[:] ), num_threads=8 )
signature = double[:](double[:],)
vf = vectorize(['float64(float64)'], nopython=True)(floor_closest_valid_odds)
ndi.correlate1d(output, [0.037659, 0.249153, 0.426375, 0.249153, 0.037659], ii, output, mode, cval, 0,) return return_value # Gaussian filter kernel # def getGaussian( xs, ys, zs ): """Return a gaussian filter kernel of the specified size """ tmp = np.zeros((xs,ys,zs)) tmp[xs//2, ys//2, zs//2] = 1.0 return ndi.gaussian_filter(tmp, (xs/6,ys/6,zs/6), mode='constant') # Convolution of 3D filter with 3D data - only calulates the output for the centre trace # Numba JIT used to accelerate the calculations # @jit(double(double[:,:,:], double[:,:,:])) def sconvolve(arr, filt): X,Y,Z = arr.shape Xf,Yf,Zf = filt.shape X2 = X//2 Y2 = Y//2 Xf2 = Xf//2 Yf2 = Yf//2 Zf2 = Zf//2 result = np.zeros(Z) for i in range(Zf2, Z-Zf2): num = 0.0 for ii in range(Xf): for jj in range(Yf): for kk in range(Zf): num += (filt[Xf-1-ii, Yf-1-jj, Zf-1-kk] * arr[X2-Xf2+ii, Y2-Yf2+jj, i-Zf2+kk])
np.sqrt((grid_im + m[im])**2 + (grid_jm + m[jm])**2 +
(grid_km + m[km])**2)), [res**3])
# add the energy for each |m|
e_k_per_cell = e_phys[im, jm, km] / (res**3)
for ii in range(res**3):
e_k_mag[int(
mgrid[ii])] = e_k_mag[int(mgrid[ii])] + e_k_per_cell
# compute the energy per physical wave number k (instead of m)
k_mag = 2 * np.pi / length * np.linspace(0, m_max, m_max + 1)
e_k_mag = e_k_mag * length / (2 * np.pi)
logging.info('FINISH CALCULATING SPECTRUM')
return k_mag, e_k_mag
@nb.jit(nb.double(nb.double, nb.double[:], nb.double[:]))
def energy_interp(k_mag, k_fit: np.ndarray, e_k_fit: np.ndarray):
i = 0
num = len(k_fit)
e_k = ((k_mag - k_fit[0]) / (k_fit[1] - k_fit[0]) *
(e_k_fit[1] - e_k_fit[0]) + e_k_fit[0])
while k_mag > k_fit[i]:
i += 1
if i == num - 1:
e_k = np.exp(
(np.log(k_mag) - np.log(k_fit[num - 2])) /
(np.log(k_fit[num - 1]) - np.log(k_fit[num - 2])) *
(np.log(e_k_fit[num - 1]) - np.log(e_k_fit[num - 2])) +
np.log(e_k_fit[num - 2]))
break
e_k = np.exp((np.log(k_mag) - np.log(k_fit[i - 1])) /
def mul(mat, vec):
m00, m01, m02, m03 = double(mat[0][0]), double(mat[0][1]), double(mat[0][2]), double(mat[0][3])
m10, m11, m12, m13 = double(mat[1][0]), double(mat[1][1]), double(mat[1][2]), double(mat[1][3])
m20, m21, m22, m23 = double(mat[2][0]), double(mat[2][1]), double(mat[2][2]), double(mat[2][3])
m30, m31, m32, m33 = double(mat[3][0]), double(mat[3][1]), double(mat[3][2]), double(mat[3][3])
v0, v1, v2, v3 = double(vec[0]), double(vec[1]), double(vec[2]), double(vec[3])
return np.array([m00 * v0 + m01 * v1 + m02 * v2 + m03 * v3,
m10 * v0 + m11 * v1 + m12 * v2 + m13 * v3,
m20 * v0 + m21 * v1 + m22 * v2 + m23 * v3,
m30 * v0 + m31 * v1 + m32 * v2 + m33 * v3])
import numpy as np
from numba import njit, boolean, int32, double, void
from .linear_interp import binary_search
@njit(double(double[:],double[:],double[:,:],double,double,int32,int32),fastmath=True)
def _interp_2d(grid1,grid2,value,xi1,xi2,j1,j2):
""" 2d interpolation for one point with known location
Args:
grid1 (numpy.ndarray): 1d grid
grid2 (numpy.ndarray): 1d grid
value (numpy.ndarray): value array (2d)
xi1 (double): input point
xi2 (double): input point
j1 (int): location in grid
j2 (int): location in grid
Returns:
yi (double): output
"""
# a. left/right
nom_1_left = grid1[j1+1]-xi1
nom_1_right = xi1-grid1[j1]
nom_2_left = grid2[j2+1]-xi2
nom_2_right = xi2-grid2[j2]
from math import pi
from numba import jit, double
is_windows = sys.platform.startswith('win32')
if is_windows:
raise OSError('Example does not work on Windows platforms yet.')
proc = CDLL(None)
c_sin = proc.sin
c_sin.argtypes = [c_double]
c_sin.restype = c_double
def use_c_sin(x):
return c_sin(x)
ctype_wrapping = CFUNCTYPE(c_double, c_double)(use_c_sin)
def use_ctype_wrapping(x):
return ctype_wrapping(x)
cfunc = jit(double(double))(use_c_sin)
print(cfunc(pi))
cfunc = jit(double(double))(use_ctype_wrapping)
print(cfunc(pi))
nomi = interp.nomi_last[i]*b
index = interp.index_last[i]+(pos_left+add)*facs
for k in range(interp.dimy):
nom[k] += nomi*interp.y[interp.yoffset[k] + index]
inv_denom = 1/denom
for k in range(interp.dimy):
yi[ixi*interp.dimy + k] = nom[k]*inv_denom
######
# 1D #
######
@njit(double(double[:],double[:],double))
def interp_1d(grid,value,xi):
""" raw 1D interpolation """
# a. search
ix = binary_search(0,grid.size,grid,xi)
# b. relative positive
rel_x = (xi - grid[ix])/(grid[ix+1]-grid[ix])
# c. interpolate
return value[ix] + rel_x * (value[ix+1]-value[ix])
@njit(void(double[:],double[:],double[:],double[:],boolean))
def _interp_1d_vec(grid,value,xi,yi,monotone):
""" raw 1D interpolation for a monotone vector """
# -*- coding: utf-8 -*-
from __future__ import print_function, division, absolute_import
from numba import double
from numba.decorators import jit as jit
def sum2d(arr):
M, N = arr.shape
result = 0.0
for i in range(M):
for j in range(N):
result += arr[i,j]
return result
jitsum2d = jit(sum2d)
csum2d = jitsum2d.compile(double(double[:,::1]))
from numpy import random
arr = random.randn(100, 100)
import time
start = time.time()
res = sum2d(arr)
duration = time.time() - start
print("Result from python is %s in %s (msec)" % (res, duration*1000))
csum2d(arr) # warm up
start = time.time()
res = csum2d(arr)
duration2 = time.time() - start
print("Result from compiled is %s in %s (msec)" % (res, duration2*1000))
import numpy as np
from numba import njit, boolean, int32, double, void
from .linear_interp import binary_search
@njit(double(double[:], double[:], double[:, :], double, double, int32, int32),
fastmath=True)
def _interp_2d(grid1, grid2, value, xi1, xi2, j1, j2):
""" 2d interpolation for one point with known location
Args:
grid1 (numpy.ndarray): 1d grid
grid2 (numpy.ndarray): 1d grid
value (numpy.ndarray): value array (2d)
xi1 (double): input point
xi2 (double): input point
j1 (int): location in grid
j2 (int): location in grid
Returns:
yi (double): output
"""
# a. left/right
nom_1_left = grid1[j1 + 1] - xi1
nom_1_right = xi1 - grid1[j1]
nom_2_left = grid2[j2 + 1] - xi2
from __future__ import print_function, division, absolute_import
from numba import double
from numba.decorators import jit as jit
def sum2d(arr):
M, N = arr.shape
result = 0.0
for i in range(M):
for j in range(N):
result += arr[i, j]
return result
jitsum2d = jit(sum2d)
csum2d = jitsum2d.compile(double(double[:, ::1]))
from numpy import random
arr = random.randn(100, 100)
import time
start = time.time()
res = sum2d(arr)
duration = time.time() - start
print("Result from python is %s in %s (msec)" % (res, duration * 1000))
csum2d(arr) # warm up
start = time.time()
res = csum2d(arr)
duration2 = time.time() - start
$ cor_atm = CorsikaAtmosphere(new_location, new_season)
$ cor_atm.calc_thickl()
Replace _thickl values with printout.
"""
from scipy.integrate import quad
thickl = []
for h in self._atm_param[4]:
thickl.append('{0:4.6f}'.format(quad(self.get_density, h,
112.8e5, epsrel=1e-4)[0]))
print '_thickl = np.array([' + ', '.join(thickl) + '])'
@jit(double(double, double, double[:, :]), target='cpu')
def planar_rho_inv_jit(X, cos_theta, param):
"""Optimized calculation of :math:`1/\\rho(X,\\theta)` in
planar approximation.
This function can be used for calculations where
:math:`\\theta < 70^\\circ`.
Args:
X (float): slant depth in g/cm**2
cos_theta (float): :math:`\\cos(\\theta)`
Returns:
float: :math:`1/\\rho(X,\\theta)` in cm**3/g
"""
a = param[0]
is_windows = sys.platform.startswith('win32')
if is_windows:
raise OSError('Example does not work on Windows platforms yet.')
proc = CDLL(None)
c_sin = proc.sin
c_sin.argtypes = [c_double]
c_sin.restype = c_double
def use_c_sin(x):
return c_sin(x)
ctype_wrapping = CFUNCTYPE(c_double, c_double)(use_c_sin)
def use_ctype_wrapping(x):
return ctype_wrapping(x)
cfunc = jit(double(double))(use_c_sin)
print(cfunc(pi))
cfunc = jit(double(double))(use_ctype_wrapping)
print(cfunc(pi))
V = tuple(V[:]) + (V[0], )
# loop through all edges of the polygon
for i in range(len(V) - 1): # edge from V[i] to V[i+1]
if V[i][1] <= P[1]: # start y <= P[1]
if V[i + 1][1] > P[1]: # an upward crossing
if is_left(V[i], V[i + 1], P) > 0: # P left of edge
wn += 1 # have a valid up intersect
else: # start y > P[1] (no test needed)
if V[i + 1][1] <= P[1]: # a downward crossing
if is_left(V[i], V[i + 1], P) < 0: # P right of edge
wn -= 1 # have a valid down intersect
return wn
@njit(nb.double(nb.double[:], nb.double[:], nb.double[:]))
def is_left(p0, p1, p2):
"""
is_left(): tests if a point is Left|On|Right of an infinite line.
Input: three points P0, P1, and P2
Return: >0 for P2 left of the line through P0 and P1
=0 for P2 on the line
<0 for P2 right of the line
See: Algorithm 1 "Area of Triangles and Polygons"
http://geomalgorithms.com/a03-_inclusion.html
:param p0: point [x,y] array
:param p1: point [x,y] array
:param p2: point [x,y] array
:return:
xgk = np.array([ 0.995657163025808080735527280689003, 0.973906528517171720077964012084452, 0.930157491355708226001207180059508, 0.865063366688984510732096688423493, 0.780817726586416897063717578345042, 0.679409568299024406234327365114874, 0.562757134668604683339000099272694, 0.433395394129247190799265943165784, 0.294392862701460198131126603103866, 0.148874338981631210884826001129720, 0.000000000000000000000000000000000 ],dtype='double') # Bessels are from numerical recipies in C? @nb.jit(nb.double(nb.double),nopython=True) def bessel_i0(x): ax = fabs(x) if ax < 3.75: y = x/3.75 y *= y return 1.0+y*(3.5156229+y*(3.0899424+y*(1.2067492 +y*(0.2659732+y*(0.360768e-1+y*0.45813e-2))))) else: y = 3.75/ax ans = (exp(ax)/sqrt(ax)) * (0.39894228+y*(0.1328592e-1+y*(0.225319e-2+y*(-0.157565e-2+y*(0.916281e-2+y*(-0.2057706e-1+y*(0.2635537e-1+y*(-0.1647633e-1+y*0.392377e-2)))))))) return ans @nb.jit(nb.double(nb.double),nopython=True) def bessel_i1(x): ax = fabs(x)
@nb.jit(cache=True)
def drawDisIdx(idx, p, size=1):
# hight=max(idx)
# low=min(idx)
# while True:
# X = np.random.random_integers(low,hight)
# Y = np.random.uniform(0.0, 1)
# if Y < p[X]:
# return X
disc = stats.rv_discrete(name='disc', values=(idx, p))
return disc.rvs(size=size)
@nb.jit(nb.double(nb.double, nb.int32), cache=True)
def _drawTau(k, size=1):
# hight=k*1.5
# low=0
# while True:
# X = np.random.uniform(low,hight)
# Y = np.random.uniform(0.0, k)
# if Y < k*exp(-k*X):
# return X
sc = 1 / k
return stats.expon.rvs(scale=sc, size=size)
@nb.jit(nb.double(nb.int64, nb.double, nb.double), cache=True)
def _draw_P_B_Tr(pN, T, bg_rate):
while True:
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
from numba import jit, double, int64
@jit(double(double, double))
def cos2phi(qc, qt):
e1 = 3.94
e2 = 4.84
k1t = -0.105
k2t = 0.149
lamda = 0.262
Delta = 0.5 * (e2 + k2t * qt - e1 - k1t * qt)
return Delta / np.sqrt(Delta**2. + lamda**2. * qc**2.)
@jit(double(double, double))
def sin2phi(qc, qt):
e1 = 3.94
e2 = 4.84
k1t = -0.105
k2t = 0.149
lamda = 0.262
Delta = 0.5 * (e2 + k2t * qt - e1 - k1t * qt)
return lamda * qc / np.sqrt(Delta**2. + lamda**2. * qc**2.)
@jit()
def make_kmat(nc, nt, alpha1, alpha2, qc, qt, gam):
print(nc, nt)
# Gaussian filter kernel
#
def getGaussian(xs, ys, zs):
"""Return a gaussian filter kernel of the specified size
"""
tmp = np.zeros((xs, ys, zs))
tmp[xs // 2, ys // 2, zs // 2] = 1.0
return ndi.gaussian_filter(tmp, (xs / 6, ys / 6, zs / 6), mode='constant')
# Convolution of 3D filter with 3D data - only calulates the output for the centre trace
# Numba JIT used to accelerate the calculations
#
@jit(double(double[:, :, :], double[:, :, :]))
def sconvolve(arr, filt):
X, Y, Z = arr.shape
Xf, Yf, Zf = filt.shape
X2 = X // 2
Y2 = Y // 2
Xf2 = Xf // 2
Yf2 = Yf // 2
Zf2 = Zf // 2
result = np.zeros(Z)
for i in range(Zf2, Z - Zf2):
num = 0.0
for ii in range(Xf):
for jj in range(Yf):
for kk in range(Zf):
num += (filt[Xf - 1 - ii, Yf - 1 - jj, Zf - 1 - kk] *
size_y : int
Size of cluster y
size_i : int
Size of cluster i
Returns
-------
d_xyi : double
Distance from the new cluster xy to cluster i
"""
import math
import numba as nb
sig = nb.double(nb.double, nb.double, nb.double, nb.int64, nb.int64, nb.int64)
@nb.njit(sig)
def _single(d_xi, d_yi, d_xy, size_x, size_y, size_i):
return min(d_xi, d_yi)
@nb.njit(sig)
def _complete(d_xi, d_yi, d_xy, size_x, size_y, size_i):
return max(d_xi, d_yi)
@nb.njit(sig)
def _average(d_xi, d_yi, d_xy, size_x, size_y, size_i):
return (size_x * d_xi + size_y * d_yi) / (size_x + size_y)